Enhancer_id	Year	PMID	Title	Species	Genome_Build	Chromosome	Start	End	TF	Target_Gene	Type(Enhancer_or_SE)	Regulatory_State(Active/Silenced)	Condition(Disease/Normal)	Disease_Name	MONDO	DOID	Tissue	Tissue Ontology_ID	Cell_Source	CVCL_ID	Cell_Type	Cell Ontology_ID	Experiment_Type	High_Throughput_Method	Low_Throughput_Method
E_00001	2024	39688912	Regulation of sarcomere formation and function in the healthy heart requires a titin intronic enhancer	Homo sapiens	hg38	chr2	178806313	178806949	NKX2-5	TTN	Enhancer	Active	Disease	dilated cardiomyopathy	MONDO:0005021	DOID:12930	heart	UBERON:0000948	human induced pluripotent stem cell-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Endogenous enhancer perturbation assay; disease variant analysis	ATAC-seq; RNA-seq; single-nucleus RNA-seq; MPRA; whole-genome sequencing	Luciferase reporter assay; CRISPR/Cas9 deletion; TF motif mutation; transgenic mouse enhancer assay; qPCR; sarcomere analysis; cardiac contractility assay
E_00002	2024	39688912	Regulation of sarcomere formation and function in the healthy heart requires a titin intronic enhancer	Homo sapiens	hg38	chr2	178806313	178806949	NA	TTN	Enhancer	Active	Disease	dilated cardiomyopathy	MONDO:0005021	DOID:12930	heart	UBERON:0000948	human induced pluripotent stem cell-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Endogenous enhancer perturbation assay; disease variant analysis	ATAC-seq; RNA-seq; single-nucleus RNA-seq; MPRA; whole-genome sequencing	Luciferase reporter assay; CRISPR/Cas9 deletion; TF motif mutation; transgenic mouse enhancer assay; qPCR; sarcomere analysis; cardiac contractility assay
E_00003	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127082600	127082962	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	hPSC-derived microglia	NA	Brain microglia	NA	CRISPR-Cas9 loss-of-function deletion; PLAC-seq chromatin interaction; ChIP-qPCR	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; PLAC-seq; RNA-seq; LDSC GWAS heritability analysis	qRT-PCR, dual-luciferase reporter,; RNA FISH super-resolution imaging, subcellular fractionation, xenograft in vivo tumor assay; Flow cytometry
E_00004	2025	40854986	Characterization of cis-regulatory elements and functional variants in colorectal cancer using epigenomics and CRISPRi screenings	Homo sapiens	hg19	chr13	73958961	73960160	FOXP1	KLF5	Enhancer	Repressed	Disease	colorectal adenocarcinoma	MONDO:0005008	DOID:0050861	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	Dual-luciferase reporter assay; CRISPR-Cas9 base editing; CRISPRi silencing; 3C chromatin capture; ChIP-qPCR	ATAC-seq; H3K27ac ChIP-seq; Hi-C; RNA-seq; ABC model prediction; GWAS summary statistics	qRT-PCR; EMSA supershift assay; DNase I footprinting, cell proliferation assay, colony formation assay, mouse xenograft tumor assay; CRISPRi
E_00005	2025	40854986	Characterization of cis-regulatory elements and functional variants in colorectal cancer using epigenomics and CRISPRi screenings	Homo sapiens	hg19	chr13	73958961	73960160	FOXP1	PIBF1	Enhancer	Active	Disease	colorectal adenocarcinoma	MONDO:0005008	DOID:0050861	colon	UBERON:0001155	SW480	CVCL_0546	malignant cell	CL:0001064	Dual-luciferase reporter assay; CRISPR-Cas9 base editing; CRISPRi silencing; 3C chromatin capture; ChIP-qPCR	ATAC-seq; H3K27ac ChIP-seq; Hi-C; RNA-seq; ABC model prediction; GWAS summary statistics	qRT-PCR; EMSA supershift assay; DNase I footprinting, cell proliferation assay, colony formation assay, mouse xenograft tumor assay; CRISPRi
E_00006	2025	40854986	Characterization of cis-regulatory elements and functional variants in colorectal cancer using epigenomics and CRISPRi screenings	Homo sapiens	hg19	chr13	73958961	73960160	TCF7L2	KLF5	Enhancer	Active	Disease	colorectal adenocarcinoma	MONDO:0005008	DOID:0050861	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	Dual-luciferase reporter assay; CRISPR-Cas9 base editing; CRISPRi silencing; 3C chromatin capture; ChIP-qPCR	ATAC-seq; H3K27ac ChIP-seq; Hi-C; RNA-seq; ABC model prediction; GWAS summary statistics	qRT-PCR; EMSA supershift assay; DNase I footprinting, cell proliferation assay, colony formation assay, mouse xenograft tumor assay; CRISPRi
E_00007	2025	40854986	Characterization of cis-regulatory elements and functional variants in colorectal cancer using epigenomics and CRISPRi screenings	Homo sapiens	hg19	chr13	73958961	73960160	TCF7L2	PIBF1	Enhancer	Active	Disease	colorectal adenocarcinoma	MONDO:0005008	DOID:0050861	colon	UBERON:0001155	SW480	CVCL_0546	malignant cell	CL:0001064	Dual-luciferase reporter assay; CRISPR-Cas9 base editing; CRISPRi silencing; 3C chromatin capture; ChIP-qPCR	ATAC-seq; H3K27ac ChIP-seq; Hi-C; RNA-seq; ABC model prediction; GWAS summary statistics	qRT-PCR; EMSA supershift assay; DNase I footprinting, cell proliferation assay, colony formation assay, mouse xenograft tumor assay; CRISPRi
E_00008	2005	15677727	Elimination of a long-range cis-regulatory module causes complete loss of limb-specific Shh expression and truncation of the mouse limb	Mus musculus	mm10	chr5	28395077	28395877	NA	Shh	Enhancer	Active	Normal	NA	NA	NA	limb	UBERON:0002101	mouse embryonic limb bud	NA	NA	NA	Endogenous enhancer deletion; transgenic reporter; in vivo developmental phenotyping	NA	Targeted deletion in mouse; Transgenic reporter assay; Shh expression analysis; skeletal phenotyping
E_00009	2016	27774982	Genetic variation at the 8q24.21 renal cancer susceptibility locus affects HIF binding to a MYC enhancer	Homo sapiens	hg19	chr8	128889122	128889450	EPAS1	PVT1	Enhancer	Active	Disease	renal cell carcinoma	MONDO:0005086	DOID:4450	kidney	UBERON:0002113	786-O	CVCL_1051	renal cell carcinoma cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis; Endogenous enhancer perturbation	HIF ChIP-seq; H3K27ac/H3K4me1 ChIP-seq; DNase-seq; Capture-C; GWAS	CRISPR/Cas9 HRE disruption; HIF-2alpha/HIF-1beta ChIP-qPCR; RT-qPCR; FAIRE-qPCR; Luciferase reporter assay; CRISPR-Cas9 endogenous deletion/editing; ChIP
E_00010	2018	29358049	Ultraconserved Enhancers Are Required for Normal Development	Mus musculus	mm39	chrX	92344753	92346405	NA	Arx	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	mouse embryonic forebrain	NA	NA	NA	Endogenous enhancer knockout; single and combinatorial enhancer deletion; neurodevelopmental phenotyping	Single-cell transcriptomic profiling (Drop-seq) and expression profiling in selected enhancer-mutant tissues	CRISPR/genome-edited mouse enhancer deletion; histology; neuronal population analysis; structural brain phenotyping; developmental reporter evidence
E_00011	2023	36869052	An autoimmune pleiotropic SNP modulates IRF5 alternative promoter usage through ZBTB3-mediated chromatin looping	Homo sapiens	hg19	chr7	128573081	128573816	ZBTB3	IRF5	Enhancer	Active	Disease	autoimmune disease	MONDO:0007179	DOID:417	blood	UBERON:0000178	Primary CD14+ monocytes	NA	CD14-positive monocyte	CL:0001054	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis	RNA-seq; ChIP-seq; ATAC-seq; 3C-seq	Luciferase reporter assay, CRISPR knockout, CRISPRi, CRISPRa; ChIP-qPCR; 3C assay; 4C assay, EMSA; RT-qPCR; Western blot
E_00012	2023	36869052	An autoimmune pleiotropic SNP modulates IRF5 alternative promoter usage through ZBTB3-mediated chromatin looping	Homo sapiens	hg19	chr7	128573081	128574098	ZBTB3	IRF5	Enhancer	Active	Disease	autoimmune disease	MONDO:0007179	DOID:417	blood	UBERON:0000178	Primary CD14+ monocytes	NA	CD14-positive monocyte	CL:0001054	Allele-specific enhancer activity; TF binding; chromatin looping; causal-variant perturbation	GWAS fine-mapping; ATAC-seq; H3K27ac/H3K4me1 ChIP-seq; ZBTB3/CTCF/RAD21 ChIP-seq; RNA-seq; 4C-seq	Luciferase reporter assay; 3C; CRISPRa; CRISPRi; CRISPR-Cas9 deletion/knock-in; EMSA; ChIP-qPCR; RT-qPCR; macrophage-polarization assay
E_00013	2016	27774982	Genetic variation at the 8q24.21 renal cancer susceptibility locus affects HIF binding to a MYC enhancer	Homo sapiens	hg19	chr8	128889122	128889450	EPAS1	MYC	Enhancer	Active	Disease	clear cell renal cell carcinoma	MONDO:0005005	DOID:4467	kidney	UBERON:0002113	primary renal tumors and renal-cell validation	NA	clear cell renal cell carcinoma cell of renal tubular origin	NA	Causal renal-cancer risk enhancer; allele-specific HIF binding; Enhancer-promoter interaction; endogenous HRE editing	HIF ChIP-seq; H3K27ac ChIP-seq; RNA polymerase II ChIP-seq; Capture-C; TCGA RNA-seq/eQTL	Luciferase reporter; allele-specific ChIP-qPCR; FAIRE-qPCR; CRISPR-Cas9 HRE editing; RT-qPCR
E_00014	2016	27774982	Genetic variation at the 8q24.21 renal cancer susceptibility locus affects HIF binding to a MYC enhancer	Homo sapiens	hg19	chr8	128889122	128889450	ARNT	MYC	Enhancer	Active	Disease	clear cell renal cell carcinoma	MONDO:0005005	DOID:4467	kidney	UBERON:0002113	primary renal tumors and renal-cell validation	NA	clear cell renal cell carcinoma cell of renal tubular origin	NA	Causal renal-cancer risk enhancer; allele-specific HIF binding; Enhancer-promoter interaction; endogenous HRE editing	HIF ChIP-seq; H3K27ac ChIP-seq; RNA polymerase II ChIP-seq; Capture-C; TCGA RNA-seq/eQTL	Luciferase reporter; allele-specific ChIP-qPCR; FAIRE-qPCR; CRISPR-Cas9 HRE editing; RT-qPCR
E_00015	2023	36869052	An autoimmune pleiotropic SNP modulates IRF5 alternative promoter usage through ZBTB3-mediated chromatin looping	Homo sapiens	hg19	chr7	128573081	128573816	ZBTB3	IRF5	Enhancer	Active	Disease	autoimmune disease	MONDO:0007179	DOID:417	blood	UBERON:0000178	SC monocyte-derived cells	NA	monocyte	CL:0000576	Disease-variant functional analysis; Allele-specific enhancer activity; TF binding; chromatin looping; causal-variant perturbation	GWAS fine-mapping; ATAC-seq; H3K27ac/H3K4me1 ChIP-seq; ZBTB3/CTCF/RAD21 ChIP-seq; RNA-seq; 4C-seq	Luciferase reporter assay; 3C; CRISPRa; CRISPRi; CRISPR-Cas9 deletion/knock-in; EMSA; ChIP-qPCR; RT-qPCR; macrophage-polarization assay
E_00016	2023	36869052	An autoimmune pleiotropic SNP modulates IRF5 alternative promoter usage through ZBTB3-mediated chromatin looping	Homo sapiens	hg19	chr7	128573081	128574098	ZBTB3	IRF5	Enhancer	Active	Disease	autoimmune disease	MONDO:0007179	DOID:417	blood	UBERON:0000178	SC monocyte-derived cells	NA	monocyte	CL:0000576	Disease-variant functional analysis; Allele-specific enhancer activity; TF binding; chromatin looping; causal-variant perturbation	GWAS fine-mapping; ATAC-seq; H3K27ac/H3K4me1 ChIP-seq; ZBTB3/CTCF/RAD21 ChIP-seq; RNA-seq; 4C-seq	Luciferase reporter assay; 3C; CRISPRa; CRISPRi; CRISPR-Cas9 deletion/knock-in; EMSA; ChIP-qPCR; RT-qPCR; macrophage-polarization assay
E_00017	2023	36869052	An autoimmune pleiotropic SNP modulates IRF5 alternative promoter usage through ZBTB3-mediated chromatin looping	Homo sapiens	hg19	chr7	128573817	128574098	ZBTB3	IRF5	Enhancer	Active	Disease	autoimmune disease	MONDO:0007179	DOID:417	blood	UBERON:0000178	SC monocyte-derived cells	NA	monocyte	CL:0000576	Disease-variant functional analysis; Allele-specific enhancer activity; TF binding; chromatin looping; causal-variant perturbation	GWAS fine-mapping; ATAC-seq; H3K27ac/H3K4me1 ChIP-seq; ZBTB3/CTCF/RAD21 ChIP-seq; RNA-seq; 4C-seq	Luciferase reporter assay; 3C; CRISPRa; CRISPRi; CRISPR-Cas9 deletion/knock-in; EMSA; ChIP-qPCR; RT-qPCR; macrophage-polarization assay
E_00018	2023	36869052	An autoimmune pleiotropic SNP modulates IRF5 alternative promoter usage through ZBTB3-mediated chromatin looping	Homo sapiens	hg19	chr7	128573036	128573717	ZBTB3	IRF5	Enhancer	Active	Disease	autoimmune disease	MONDO:0007179	DOID:417	prostate gland	UBERON:0002367	Human prostate carcinoma cell	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis	ChIP-seq; RNA-seq; 3C-seq; ATAC-seq	Luciferase reporter assay; 3C assay; 4C assay, CRISPR knockout, CRISPRi, CRISPRa; RT-qPCR; Western blot, EMSA; ChIP-qPCR
E_00019	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23906940	23908253	GATA4	MYH7	Enhancer	Active	Disease	dilated cardiomyopathy	MONDO:0005021	DOID:12930	heart left ventricle	UBERON:0002084	GM03348-derived human iPSC cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Endogenous enhancer perturbation assay; Regulatory variant functional assay; genotype-phenotype association	promoter capture Hi-C; ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; GATA4 ChIP-seq; TBX5 ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis; biobank genotype-phenotype analysis	Dual-luciferase reporter assay of MYH7-C6 in iPSC-CMs and HL-1 cells; allele-specific reporter assay for rs875908; CRISPR/Cas9 dual-guide C6 deletion; Sanger genotyping; RT-qPCR; SDS-PAGE myosin isoform analysis; longitudinal echocardiographic association; rs875908 disrupts a TBX5 motif
E_00020	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23906940	23908253	GATA4	MYH7	Enhancer	Active	Disease	dilated cardiomyopathy	MONDO:0005021	DOID:12930	heart left ventricle	UBERON:0002084	HL-1	CVCL_0303	cardiac muscle cell	CL:0000746	Enhancer activity assay; Endogenous enhancer perturbation assay; Regulatory variant functional assay; genotype-phenotype association	promoter capture Hi-C; ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; GATA4 ChIP-seq; TBX5 ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis; biobank genotype-phenotype analysis	Dual-luciferase reporter assay of MYH7-C6 in iPSC-CMs and HL-1 cells; allele-specific reporter assay for rs875908; CRISPR/Cas9 dual-guide C6 deletion; Sanger genotyping; RT-qPCR; SDS-PAGE myosin isoform analysis; longitudinal echocardiographic association; rs875908 disrupts a TBX5 motif
E_00021	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23906940	23908253	TBX5	MYH7	Enhancer	Active	Disease	dilated cardiomyopathy	MONDO:0005021	DOID:12930	heart left ventricle	UBERON:0002084	GM03348-derived human iPSC cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Endogenous enhancer perturbation assay; Regulatory variant functional assay; genotype-phenotype association	promoter capture Hi-C; ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; GATA4 ChIP-seq; TBX5 ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis; biobank genotype-phenotype analysis	Dual-luciferase reporter assay of MYH7-C6 in iPSC-CMs and HL-1 cells; allele-specific reporter assay for rs875908; CRISPR/Cas9 dual-guide C6 deletion; Sanger genotyping; RT-qPCR; SDS-PAGE myosin isoform analysis; longitudinal echocardiographic association; rs875908 disrupts a TBX5 motif
E_00022	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23906940	23908253	TBX5	MYH7	Enhancer	Active	Disease	dilated cardiomyopathy	MONDO:0005021	DOID:12930	heart left ventricle	UBERON:0002084	HL-1	CVCL_0303	cardiac muscle cell	CL:0000746	Enhancer activity assay; Endogenous enhancer perturbation assay; Regulatory variant functional assay; genotype-phenotype association	promoter capture Hi-C; ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; GATA4 ChIP-seq; TBX5 ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis; biobank genotype-phenotype analysis	Dual-luciferase reporter assay of MYH7-C6 in iPSC-CMs and HL-1 cells; allele-specific reporter assay for rs875908; CRISPR/Cas9 dual-guide C6 deletion; Sanger genotyping; RT-qPCR; SDS-PAGE myosin isoform analysis; longitudinal echocardiographic association; rs875908 disrupts a TBX5 motif
E_00023	2026	42468524	Robust regulatory interplay of enhancers, facilitators, and promoters in a native chromatin context	Homo sapiens	hg38	chr4	55729891	55730343	GATA1	NMU	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	erythroleukemia cell	NA	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay; Functional cis-element perturbation assay; TF motif mutagenesis; Target-gene expression assay; Nascent transcription assay; Reporter assay	Barcoded recombinase-mediated enhancer mutagenesis with HCR-FlowFISH and amplicon sequencing; ATAC-seq; PRO-seq; p300 ChIP-seq; 4C-seq; ENCODE ChIP-seq reanalysis	Homozygous CRISPR deletion of e1; Bxb1-mediated single-copy enhancer rescue; GATA1 motif mutagenesis; GATA1 ChIP-qPCR; RT-qPCR; integrated and episomal NMU-promoter reporter assay; single-cell recombinant clone validation
E_00024	2026	42468524	Robust regulatory interplay of enhancers, facilitators, and promoters in a native chromatin context	Homo sapiens	hg38	chr4	55729891	55730343	RUNX1	NMU	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	erythroleukemia cell	NA	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay; Functional cis-element perturbation assay; TF motif mutagenesis; Target-gene expression assay; Nascent transcription assay; Reporter assay	Barcoded recombinase-mediated enhancer mutagenesis with HCR-FlowFISH and amplicon sequencing; ATAC-seq; PRO-seq; p300 ChIP-seq; 4C-seq; ENCODE ChIP-seq reanalysis	Homozygous CRISPR deletion of e1; Bxb1-mediated single-copy enhancer rescue; RUNX1 motif mutagenesis; RUNX1 ChIP-qPCR; RT-qPCR; integrated and episomal NMU-promoter reporter assay; single-cell recombinant clone validation
E_00025	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr4	56595855	56597095	NA	NMU	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	erythroleukemia cell	NA	Functional cis-element perturbation assay; Enhancer-target gene assignment assay; Target-gene expression assay	Multiplexed CRISPRi enhancer perturbation coupled with single-cell RNA-seq; singleton CRISPRi with bulk RNA-seq; bulk RNA-seq of monoclonal homozygous deletion clones; ENCODE epigenomic data integration; K562 Hi-C reanalysis	Monoclonal homozygous Cas9-mediated enhancer deletion; RNA flowFISH; scanning CRISPR/Cas9 deletion; deletion-genotyping PCR
E_00026	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr6	139766548	139767000	NA	CITED2	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	erythroleukemia cell	NA	Functional cis-element perturbation assay; Enhancer-target gene assignment assay; Target-gene expression assay	Multiplexed CRISPRi enhancer perturbation coupled with single-cell RNA-seq; singleton CRISPRi with bulk RNA-seq; bulk RNA-seq of monoclonal homozygous deletion clones; ENCODE epigenomic data integration; K562 Hi-C reanalysis	Monoclonal homozygous Cas9-mediated enhancer deletion; deletion-genotyping PCR
E_00027	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr1	182307087	182307634	NA	GLUL	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	erythroleukemia cell	NA	Functional cis-element perturbation assay; Enhancer-target gene assignment assay; Target-gene expression assay	Multiplexed CRISPRi enhancer perturbation coupled with single-cell RNA-seq; bulk RNA-seq of monoclonal homozygous deletion clones; ENCODE epigenomic data integration; K562 Hi-C reanalysis	Monoclonal homozygous Cas9-mediated enhancer deletion; deletion-genotyping PCR
E_00028	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg19	chrX	48641072	48641800	GATA1	GATA1	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	erythroleukemia cell	NA	Enhancer activity assay; TF binding assay; Functional cis-element perturbation assay; Target-gene expression assay; Reporter assay	Pooled CRISPRi tiling screen; ENCODE DHS-seq; H3K27ac ChIP-seq; GATA1 ChIP-seq; ChromHMM; K562 Hi-C reanalysis; RNA Pol II ChIA-PET reanalysis	Individual CRISPRi sgRNA validation; RT-qPCR; Luciferase reporter assay; competitive growth assay
E_00029	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg19	chrX	48641072	48641800	GATA1	HDAC6	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	erythroleukemia cell	NA	Enhancer activity assay; TF binding assay; Functional cis-element perturbation assay; Target-gene expression assay; Reporter assay	Pooled CRISPRi tiling screen; ENCODE DHS-seq; H3K27ac ChIP-seq; GATA1 ChIP-seq; ChromHMM; K562 Hi-C reanalysis; RNA Pol II ChIA-PET reanalysis	Individual CRISPRi sgRNA validation; RT-qPCR; Luciferase reporter assay; competitive growth assay
E_00030	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg19	chrX	48658825	48659664	GATA1	GATA1	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	erythroleukemia cell	NA	Enhancer activity assay; TF binding assay; Functional cis-element perturbation assay; Target-gene expression assay; Reporter assay	Pooled CRISPRi tiling screen; ENCODE DHS-seq; H3K27ac ChIP-seq; GATA1 ChIP-seq; ChromHMM; K562 Hi-C reanalysis; RNA Pol II ChIA-PET reanalysis	Individual CRISPRi sgRNA validation; RT-qPCR; Luciferase reporter assay; competitive growth assay
E_00031	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg19	chrX	48658825	48659664	GATA1	HDAC6	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	erythroleukemia cell	NA	Enhancer activity assay; TF binding assay; Functional cis-element perturbation assay; Target-gene expression assay; Reporter assay	Pooled CRISPRi tiling screen; ENCODE DHS-seq; H3K27ac ChIP-seq; GATA1 ChIP-seq; ChromHMM; K562 Hi-C reanalysis; RNA Pol II ChIA-PET reanalysis	Individual CRISPRi sgRNA validation; RT-qPCR; Luciferase reporter assay; competitive growth assay
E_00032	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg19	chr8	128910608	128912213	NA	MYC	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	erythroleukemia cell	NA	Enhancer activity assay; Chromatin interaction assay; Functional cis-element perturbation assay; Target-gene expression assay; Reporter assay	Pooled CRISPRi tiling screen; ENCODE DHS-seq; H3K27ac ChIP-seq; TF ChIP-seq integration; K562 Hi-C; RNA Pol II ChIA-PET	Individual CRISPRi sgRNA validation; RT-qPCR; Luciferase reporter assay; competitive growth assay
E_00033	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg19	chr8	128972255	128973230	NA	MYC	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	erythroleukemia cell	NA	Enhancer activity assay; Chromatin interaction assay; Functional cis-element perturbation assay; Target-gene expression assay; Reporter assay	Pooled CRISPRi tiling screen; ENCODE DHS-seq; H3K27ac ChIP-seq; TF ChIP-seq integration; K562 Hi-C; RNA Pol II ChIA-PET	Individual CRISPRi sgRNA validation; RT-qPCR; Luciferase reporter assay; allele-specific CRISPR/Cas9 enhancer deletion; competitive growth assay
E_00034	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg19	chr8	129056967	129058438	NA	MYC	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	erythroleukemia cell	NA	Enhancer activity assay; Chromatin interaction assay; Functional cis-element perturbation assay; Target-gene expression assay; Reporter assay	Pooled CRISPRi tiling screen; ENCODE DHS-seq; H3K27ac ChIP-seq; TF ChIP-seq integration; K562 Hi-C; RNA Pol II ChIA-PET	Individual CRISPRi sgRNA validation; RT-qPCR; Luciferase reporter assay; allele-specific CRISPR/Cas9 enhancer deletion; competitive growth assay
E_00035	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg19	chr8	129060477	129062593	NA	MYC	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	erythroleukemia cell	NA	Enhancer activity assay; Chromatin interaction assay; Functional cis-element perturbation assay; Target-gene expression assay; Reporter assay	Pooled CRISPRi tiling screen; ENCODE DHS-seq; H3K27ac ChIP-seq; TF ChIP-seq integration; K562 Hi-C; RNA Pol II ChIA-PET	Individual CRISPRi sgRNA validation; RT-qPCR; Luciferase reporter assay; allele-specific CRISPR/Cas9 enhancer deletion; competitive growth assay
E_00036	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg19	chr8	130594100	130596043	NA	MYC	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	erythroleukemia cell	NA	Enhancer activity assay; Chromatin interaction assay; Functional cis-element perturbation assay; Target-gene expression assay; Reporter assay	Pooled CRISPRi tiling screen; ENCODE DHS-seq; H3K27ac ChIP-seq; TF ChIP-seq integration; K562 Hi-C; RNA Pol II ChIA-PET	Individual CRISPRi sgRNA validation; RT-qPCR; Luciferase reporter assay; competitive growth assay
E_00037	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg19	chr8	130700606	130702818	NA	MYC	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	erythroleukemia cell	NA	Enhancer activity assay; Chromatin interaction assay; Functional cis-element perturbation assay; Target-gene expression assay; Reporter assay	Pooled CRISPRi tiling screen; ENCODE DHS-seq; H3K27ac ChIP-seq; TF ChIP-seq integration; K562 Hi-C; RNA Pol II ChIA-PET	Individual CRISPRi sgRNA validation; RT-qPCR; Luciferase reporter assay; competitive growth assay
E_00038	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg19	chr8	130703671	130705886	NA	MYC	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	erythroleukemia cell	NA	Enhancer activity assay; Chromatin interaction assay; Functional cis-element perturbation assay; Target-gene expression assay; Reporter assay	Pooled CRISPRi tiling screen; ENCODE DHS-seq; H3K27ac ChIP-seq; TF ChIP-seq integration; K562 Hi-C; RNA Pol II ChIA-PET	Individual CRISPRi sgRNA validation; RT-qPCR; Luciferase reporter assay; competitive growth assay
E_00039	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr15	74724384	74724924	NA	SIN3A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11 i3N iPSC-derived excitatory neurons	CVCL_C7XJ	glutamatergic neuron	CL:0000679	Chromatin accessibility assay; Functional cis-element perturbation assay; Enhancer-target gene assay; Target-gene expression assay; Allele-specific cis-regulation assay	CREST-seq paired-sgRNA tiling deletion screen; FACS-based reporter selection; paired-end deep sequencing; RELICS functional-sequence analysis; ATAC-seq reanalysis	Independent paired-sgRNA CRISPR deletion; Flow cytometry; allele-specific reporter analysis
E_00040	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr15	74751789	74752496	NA	SIN3A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11 i3N iPSC-derived excitatory neurons	CVCL_C7XJ	glutamatergic neuron	CL:0000679	Functional cis-element perturbation assay; Enhancer-target gene assay; Target-gene expression assay; Allele-specific cis-regulation assay	CREST-seq paired-sgRNA tiling deletion screen; FACS-based reporter selection; paired-end deep sequencing; RELICS functional-sequence analysis	Independent paired-sgRNA CRISPR deletion; Flow cytometry; allele-specific reporter analysis
E_00041	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr15	74768848	74769811	CTCF	SIN3A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11 i3N iPSC-derived excitatory neurons	CVCL_C7XJ	glutamatergic neuron	CL:0000679	TF binding assay; Chromatin accessibility assay; Functional cis-element perturbation assay; Enhancer-target gene assay; Target-gene expression assay; Histone modification assay; TF motif perturbation assay; Allele-specific cis-regulation assay	CREST-seq paired-sgRNA tiling deletion screen; FACS-based reporter selection; paired-end deep sequencing; RELICS functional-sequence analysis; H3K4me1 ChIP-seq reanalysis; ATAC-seq reanalysis; CTCF ChIP-seq reanalysis	Independent paired-sgRNA CRISPR deletion; CTCF-motif CRISPR editing; Flow cytometry; targeted amplicon sequencing; FACS single-cell cloning; allele-specific SNP analysis; RT-qPCR; Sanger sequencing
E_00042	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr15	74776955	74778648	NA	SIN3A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11 i3N iPSC-derived excitatory neurons	CVCL_C7XJ	glutamatergic neuron	CL:0000679	Functional cis-element perturbation assay; Enhancer-target gene assay; Target-gene expression assay; Histone modification assay; Allele-specific cis-regulation assay	CREST-seq paired-sgRNA tiling deletion screen; FACS-based reporter selection; paired-end deep sequencing; RELICS functional-sequence analysis; H3K4me1 ChIP-seq reanalysis	Independent paired-sgRNA CRISPR deletion; Flow cytometry; allele-specific reporter analysis
E_00043	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chrX	147913308	147914958	NA	FMR1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11 i3N iPSC-derived excitatory neurons	CVCL_C7XJ	glutamatergic neuron	CL:0000679	Chromatin interaction assay; Functional cis-element perturbation assay; Enhancer-target gene assay; Target-gene expression assay; Histone modification assay	CREST-seq paired-sgRNA tiling deletion screen; FACS-based reporter selection; paired-end deep sequencing; RELICS functional-sequence analysis; H3K4me1/H3K4me3/H3K27ac ChIP-seq reanalysis; H3K4me3 PLAC-seq reanalysis	Independent paired-sgRNA CRISPR deletion; Flow cytometry; genotyping PCR
E_00044	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chrX	154024507	154026006	NA	MECP2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11 i3N iPSC-derived excitatory neurons	CVCL_C7XJ	glutamatergic neuron	CL:0000679	Chromatin interaction assay; Chromatin accessibility assay; Functional cis-element perturbation assay; Enhancer-target gene assay; Target-gene expression assay; Histone modification assay	CREST-seq paired-sgRNA tiling deletion screen; FACS-based reporter selection; paired-end deep sequencing; RELICS functional-sequence analysis; H3K4me1/H3K27ac ChIP-seq reanalysis; ATAC-seq reanalysis; H3K4me3 PLAC-seq reanalysis	Independent paired-sgRNA CRISPR deletion; FACS single-cell cloning; Flow cytometry; RT-qPCR; genotyping PCR
E_00045	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chrX	154040709	154041748	NA	MECP2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11 i3N iPSC-derived excitatory neurons	CVCL_C7XJ	glutamatergic neuron	CL:0000679	Functional cis-element perturbation assay; Enhancer-target gene assay; Target-gene expression assay; Histone modification assay	CREST-seq paired-sgRNA tiling deletion screen; FACS-based reporter selection; paired-end deep sequencing; RELICS functional-sequence analysis; H3K4me1 ChIP-seq reanalysis	Independent paired-sgRNA CRISPR deletion; Flow cytometry; genotyping PCR
E_00046	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chrX	154049781	154050862	NA	MECP2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11 i3N iPSC-derived excitatory neurons	CVCL_C7XJ	glutamatergic neuron	CL:0000679	Functional cis-element perturbation assay; Enhancer-target gene assay; Target-gene expression assay	CREST-seq paired-sgRNA tiling deletion screen; FACS-based reporter selection; paired-end deep sequencing; RELICS functional-sequence analysis	Independent paired-sgRNA CRISPR deletion; FACS single-cell cloning; Flow cytometry; RT-qPCR; genotyping PCR
E_00047	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chrX	154060475	154061957	NA	MECP2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11 i3N iPSC-derived excitatory neurons	CVCL_C7XJ	glutamatergic neuron	CL:0000679	Chromatin accessibility assay; Functional cis-element perturbation assay; Enhancer-target gene assay; Target-gene expression assay; Histone modification assay	CREST-seq paired-sgRNA tiling deletion screen; FACS-based reporter selection; paired-end deep sequencing; RELICS functional-sequence analysis; H3K4me1/H3K27ac ChIP-seq reanalysis; ATAC-seq reanalysis	Independent paired-sgRNA CRISPR deletion; FACS single-cell cloning; Flow cytometry; RT-qPCR; genotyping PCR
E_00048	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60725424	60725688	GATA1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary human CD34+ hematopoietic progenitor cells	NA	erythroid progenitor cell	CL:0000038	Endogenous enhancer requirement; enhancer fine-mapping; lineage-specific target-gene regulation; fetal hemoglobin regulation	CRISPR-Cas9 pooled saturating mutagenesis; chromatin profiling	Primary-cell genome editing; BCL11A expression analysis; HbF/HbF-positive-cell analysis; mouse transgenesis
E_00049	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60722238	60722466	GATA1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary human CD34+ hematopoietic progenitor cells	NA	erythroid progenitor cell	CL:0000038	Endogenous enhancer requirement; enhancer fine-mapping; lineage-specific target-gene regulation; fetal hemoglobin regulation	CRISPR-Cas9 pooled saturating mutagenesis; chromatin profiling	Primary-cell genome editing; BCL11A expression analysis; HbF/HbF-positive-cell analysis; mouse transgenesis
E_00050	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60718042	60718186	GATA1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary human CD34+ hematopoietic progenitor cells	NA	erythroid progenitor cell	CL:0000038	Endogenous enhancer requirement; enhancer fine-mapping; lineage-specific target-gene regulation; fetal hemoglobin regulation	CRISPR-Cas9 pooled saturating mutagenesis; chromatin profiling	Primary-cell genome editing; BCL11A expression analysis; HbF/HbF-positive-cell analysis; mouse transgenesis
E_00051	2020	32169219	Comprehensive In Vivo Interrogation Reveals Phenotypic Impact of Human Enhancer Variants	Homo sapiens	hg19	chr7	156583402	156585773	NA	SHH	Enhancer	Active	Disease	ZRS-associated preaxial polydactyly	NA	NA	limb bud	NA	embryonic limb bud	NA	limb bud mesenchymal cell	NA	Enhancer variant functional assay; In vivo enhancer activity assay; endogenous variant knock-in; developmental phenotype assay	High-throughput in vivo mouse enhancer reporter assay; systematic single-nucleotide and combinatorial mutagenesis	CRISPR-Cas9 knock-in; transgenic mouse reporter assay; lacZ reporter assay; embryonic limb phenotyping
E_00052	2025	39957428	Functional characterization of OXTR-associated enhancers	Homo sapiens	hg38	chr3	8757366	8759184	NA	OXTR	Enhancer	Active	Normal	NA	NA	NA	olfactory bulb	UBERON:0002264	mHypoA-Pomc cells; transgenic mouse olfactory bulb	NA	hypothalamic neuronal cell; olfactory bulb neuron	NA	Enhancer activity assay; candidate cis-regulatory element validation; in vivo tissue-specific enhancer assay	Single-cell RNA/ATAC-seq-based candidate enhancer discovery	Luciferase reporter assay; Site-directed mutagenesis; transgenic mouse Hsp68-mCherry enhancer assay; Sanger sequencing
E_00053	2025	41057395	Evidence for enhancer activity in intron 1 of TNFRSF1A using CRISPR/Cas9 in human induced pluripotent stem cell-derived macrophages	Homo sapiens	hg19	chr12	6444399	6447744	NA	TNFRSF1A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	human iPSC-derived macrophages	NA	macrophage	CL:0000235	Endogenous enhancer deletion; enhancer chromatin-state validation; target-gene regulation	ATAC-seq; H3K27ac ChIP-seq; RNA-seq	CRISPR-Cas9 genomic deletion; PCR; Sanger sequencing; droplet digital PCR; macrophage differentiation
E_00054	2026	41191525	Silencing of BCL11A by disrupting enhancer-dependent epigenetic insulation	Homo sapiens	hg19	chr2	60725424	60725688	GATA1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	adult erythroid cells	NA	erythroid lineage cell	CL:0000764	Enhancer-dependent chromatin insulation; enhancer RNA function; target-gene regulation; fetal hemoglobin regulation	Chromatin conformation profiling; chromatin architecture analysis; transcriptomic analysis	CRISPR enhancer disruption; enhancer RNA depletion by antisense oligonucleotides; BCL11A expression assay; HbF reactivation assay
E_00055	2026	41191525	Silencing of BCL11A by disrupting enhancer-dependent epigenetic insulation	Homo sapiens	hg19	chr2	60722238	60722466	GATA1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	adult erythroid cells	NA	erythroid lineage cell	CL:0000764	Enhancer-dependent chromatin insulation; enhancer RNA function; target-gene regulation; fetal hemoglobin regulation	Chromatin conformation profiling; chromatin architecture analysis; transcriptomic analysis	CRISPR enhancer disruption; enhancer RNA depletion by antisense oligonucleotides; BCL11A expression assay; HbF reactivation assay
E_00056	2026	41191525	Silencing of BCL11A by disrupting enhancer-dependent epigenetic insulation	Homo sapiens	hg19	chr2	60718042	60718186	GATA1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	adult erythroid cells	NA	erythroid lineage cell	CL:0000764	Enhancer-dependent chromatin insulation; enhancer RNA function; target-gene regulation; fetal hemoglobin regulation	Chromatin conformation profiling; chromatin architecture analysis; transcriptomic analysis	CRISPR enhancer disruption; enhancer RNA depletion by antisense oligonucleotides; BCL11A expression assay; HbF reactivation assay
E_00057	2020	32095812	Looping of upstream cis-regulatory elements is required for CFTR expression in human airway epithelial cells	Homo sapiens	hg19	chr7	117075400	117076000	BACH1	CFTR	Enhancer	Active	Normal	NA	NA	NA	bronchus	UBERON:0002185	16HBE14o-	CVCL_0112	bronchial epithelial cell	CL:0002328	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis; Endogenous enhancer perturbation	ChIP-seq; H3K27ac ChIP-seq; 4C-seq	CRISPR/Cas9 deletion; Luciferase reporter assay; RT-qPCR; ChIP-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_00058	2020	32095812	Looping of upstream cis-regulatory elements is required for CFTR expression in human airway epithelial cells	Homo sapiens	hg19	chr7	117075400	117076000	BACH1	CFTR	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	Calu-3	CVCL_0609	epithelial cell	CL:0000066	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis; Endogenous enhancer perturbation	ChIP-seq; H3K27ac ChIP-seq; 4C-seq	CRISPR/Cas9 deletion; Luciferase reporter assay; RT-qPCR; ChIP-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_00059	2020	32095812	Looping of upstream cis-regulatory elements is required for CFTR expression in human airway epithelial cells	Homo sapiens	hg19	chr7	117075400	117076000	MAFK	CFTR	Enhancer	Active	Normal	NA	NA	NA	bronchus	UBERON:0002185	16HBE14o-	CVCL_0112	bronchial epithelial cell	CL:0002328	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis; Endogenous enhancer perturbation	ChIP-seq; H3K27ac ChIP-seq; 4C-seq	CRISPR/Cas9 deletion; Luciferase reporter assay; RT-qPCR; ChIP-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_00060	2020	32095812	Looping of upstream cis-regulatory elements is required for CFTR expression in human airway epithelial cells	Homo sapiens	hg19	chr7	117075400	117076000	MAFK	CFTR	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	Calu-3	CVCL_0609	epithelial cell	CL:0000066	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis; Endogenous enhancer perturbation	ChIP-seq; H3K27ac ChIP-seq; 4C-seq	CRISPR/Cas9 deletion; Luciferase reporter assay; RT-qPCR; ChIP-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_00061	2020	32095812	Looping of upstream cis-regulatory elements is required for CFTR expression in human airway epithelial cells	Homo sapiens	hg19	chr7	117075400	117076000	NFE2L2	CFTR	Enhancer	Active	Normal	NA	NA	NA	bronchus	UBERON:0002185	16HBE14o-	CVCL_0112	bronchial epithelial cell	CL:0002328	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis; Endogenous enhancer perturbation	ChIP-seq; H3K27ac ChIP-seq; 4C-seq	CRISPR/Cas9 deletion; Luciferase reporter assay; RT-qPCR; ChIP-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_00062	2020	32095812	Looping of upstream cis-regulatory elements is required for CFTR expression in human airway epithelial cells	Homo sapiens	hg19	chr7	117075400	117076000	NFE2L2	CFTR	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	Calu-3	CVCL_0609	epithelial cell	CL:0000066	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis; Endogenous enhancer perturbation	ChIP-seq; H3K27ac ChIP-seq; 4C-seq	CRISPR/Cas9 deletion; Luciferase reporter assay; RT-qPCR; ChIP-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_00063	2020	32095812	Looping of upstream cis-regulatory elements is required for CFTR expression in human airway epithelial cells	Homo sapiens	hg19	chr7	117084000	117086500	CEBPB	CFTR	Enhancer	Active	Normal	NA	NA	NA	bronchus	UBERON:0002185	16HBE14o-	CVCL_0112	bronchial epithelial cell	CL:0002328	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis; Endogenous enhancer perturbation	ChIP-seq; H3K27ac ChIP-seq; RNAPII ChIP-seq; 4C-seq	CRISPR/Cas9 deletion; Luciferase reporter assay; RT-qPCR; ChIP-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_00064	2025	41057395	Evidence for enhancer activity in intron 1 of TNFRSF1A using CRISPR/Cas9 in human induced pluripotent stem cell-derived macrophages	Homo sapiens	hg19	chr12	6444399	6447744	NA	TNFRSF1A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	human induced pluripotent stem cell-derived macrophages	NA	macrophage	CL:0000235	Endogenous enhancer deletion; chromatin accessibility validation; enhancer chromatin-state validation; target-gene regulation	ATAC-seq; H3K27ac ChIP-seq; RNA-seq	CRISPR-Cas9 genomic deletion; PCR; Sanger sequencing; droplet digital PCR; iPSC-to-macrophage differentiation; TNFRSF1A expression analysis
E_00065	2017	28260788	APOBEC signature mutation generates an oncogenic enhancer that drives LMO1 expression in T-ALL	Homo sapiens	hg19	chr11	8289240	8289522	GATA3	LMO1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Jurkat	CVCL_0065	T cell	CL:0000084	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Endogenous enhancer perturbation	H3K27ac ChIP-seq; GATA3 ChIP-seq; polyA RNA-seq; ChIA-PET	Luciferase reporter assay using 585-bp wild-type and mutant enhancer fragments; Sanger sequencing; qRT-PCR; Site-directed/motif mutagenesis
E_00066	2017	28260788	APOBEC signature mutation generates an oncogenic enhancer that drives LMO1 expression in T-ALL	Homo sapiens	hg19	chr11	8289240	8289522	RUNX1	LMO1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Jurkat	CVCL_0065	T cell	CL:0000084	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Endogenous enhancer perturbation	H3K27ac ChIP-seq; RUNX1 ChIP-seq; polyA RNA-seq; ChIA-PET	Luciferase reporter assay using 585-bp wild-type and mutant enhancer fragments; Sanger sequencing; qRT-PCR; Site-directed/motif mutagenesis
E_00067	2017	28260788	APOBEC signature mutation generates an oncogenic enhancer that drives LMO1 expression in T-ALL	Homo sapiens	hg19	chr11	8289240	8289522	TAL1	LMO1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Jurkat	CVCL_0065	T cell	CL:0000084	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Endogenous enhancer perturbation	H3K27ac ChIP-seq; TAL1 ChIP-seq; polyA RNA-seq; ChIA-PET	Luciferase reporter assay using 585-bp wild-type and mutant enhancer fragments; Sanger sequencing; qRT-PCR; Site-directed/motif mutagenesis
E_00068	2015	26287746	FTO Obesity Variant Circuitry and Adipocyte Browning in Humans	Homo sapiens	hg19	chr16	53800454	53801454	ARID5B	IRX3	Enhancer	Active	Disease	obesity	MONDO:0011122	DOID:9970	subcutaneous adipose tissue	UBERON:0002190	SGBS	CVCL_GS28	preadipocyte	CL:0002334	Enhancer activity assay; Disease-variant functional analysis; Endogenous enhancer perturbation; endogenous allele editing; TF binding assay; target-gene perturbation	Roadmap epigenomic chromatin-state analysis; long-range chromatin interaction analysis; eQTL/trans-eQTL analysis; gene-expression profiling	Luciferase reporter assay; CRISPR-Cas9 single-nucleotide editing; EMSA; ARID5B knockdown/overexpression; IRX3 knockdown/overexpression; RT-qPCR; oxygen-consumption and thermogenesis assays; CRISPR-Cas9 endogenous deletion/editing; Allele-specific reporter assay
E_00069	2015	26287746	FTO Obesity Variant Circuitry and Adipocyte Browning in Humans	Homo sapiens	hg19	chr16	53800454	53801454	ARID5B	IRX5	Enhancer	Active	Disease	obesity	MONDO:0011122	DOID:9970	subcutaneous adipose tissue	UBERON:0002190	SGBS	CVCL_GS28	preadipocyte	CL:0002334	Enhancer activity assay; Disease-variant functional analysis; Endogenous enhancer perturbation; endogenous allele editing; TF binding assay; target-gene perturbation	Roadmap epigenomic chromatin-state analysis; long-range chromatin interaction analysis; eQTL/trans-eQTL analysis; gene-expression profiling	Luciferase reporter assay; CRISPR-Cas9 single-nucleotide editing; EMSA; ARID5B knockdown/overexpression; IRX5 knockdown/overexpression; RT-qPCR; oxygen-consumption and thermogenesis assays; CRISPR-Cas9 endogenous deletion/editing; Allele-specific reporter assay
E_00070	2016	27774982	Genetic variation at the 8q24.21 renal cancer susceptibility locus affects HIF binding to a MYC enhancer	Homo sapiens	hg19	chr8	128889122	128889450	EPAS1	MYC	Enhancer	Active	Disease	clear cell renal cell carcinoma	MONDO:0005005	DOID:4467	kidney	UBERON:0002113	786-O	CVCL_1051	clear cell renal cell carcinoma cell of renal tubular origin	NA	Causal renal-cancer risk enhancer; allele-specific HIF binding; Enhancer-promoter interaction; endogenous HRE editing	HIF ChIP-seq; H3K27ac ChIP-seq; RNA polymerase II ChIP-seq; Capture-C; TCGA RNA-seq/eQTL	Luciferase reporter; allele-specific ChIP-qPCR; FAIRE-qPCR; CRISPR-Cas9 HRE editing; RT-qPCR
E_00071	2016	27774982	Genetic variation at the 8q24.21 renal cancer susceptibility locus affects HIF binding to a MYC enhancer	Homo sapiens	hg19	chr8	128889122	128889450	ARNT	MYC	Enhancer	Active	Disease	clear cell renal cell carcinoma	MONDO:0005005	DOID:4467	kidney	UBERON:0002113	786-O	CVCL_1051	clear cell renal cell carcinoma cell of renal tubular origin	NA	Causal renal-cancer risk enhancer; allele-specific HIF binding; Enhancer-promoter interaction; endogenous HRE editing	HIF ChIP-seq; H3K27ac ChIP-seq; RNA polymerase II ChIP-seq; Capture-C; TCGA RNA-seq/eQTL	Luciferase reporter; allele-specific ChIP-qPCR; FAIRE-qPCR; CRISPR-Cas9 HRE editing; RT-qPCR
E_00072	2024	39688912	Regulation of sarcomere formation and function in the healthy heart requires a titin intronic enhancer	Homo sapiens	hg38	chr2	178806313	178806949	NKX2-5	TTN	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	Cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Functional perturbation assay; TF binding assay; Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation	ATAC-seq, Hi-C; ChIP-seq	Luciferase reporter assay, Transgenic reporter assay, CRISPR knockout, CRISPRi, qRT-PCR; Site-directed/motif mutagenesis; Allele-specific reporter assay; Mouse genetic deletion/knock-in; In vivo phenotyping
E_00073	2025	41129262	The hematopoietic stem cell MYB enhancer is essential for and recurrently amplified during T cell leukemogenesis	Mus musculus	mm10	chr10	21054606	21054974	Ets1	Myb	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary mouse hematopoietic stem cells	NA	hematopoietic stem cell	CL:0000037	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Endogenous enhancer perturbation	ChIP-seq; ATAC-seq, Hi-C; RNA-seq; pooled CRISPRi screen	Luciferase reporter assay, CRISPR knockout, CRISPRi; ChIP-qPCR, qRT-PCR; Western blot; CRISPRi; conditional enhancer knockout in mice; RT-qPCR; Flow cytometry; serial bone-marrow transplantation
E_00074	2018	29731168	Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element	Homo sapiens	hg19	chr8	128821774	128822358	NA	MYC	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	MDA-MB-231	CVCL_0062	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation; Promoter-enhancer competition assay	H3K27ac HiChIP	CRISPRi; UMI-4C; Luciferase reporter assay; qRT-PCR; ChIP-qPCR; CRISPR-Cas9 endogenous deletion/editing; In vivo phenotyping
E_00075	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85463935	85468299	Mef2a	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Primary mouse cortical neurons	NA	neuron	CL:0000540	Endogenous enhancer perturbation; Stimulus-responsive enhancer assay; Enhancer-promoter interaction	RNA-seq; ChIP-seq and chromatin-state integration	Luciferase reporter assay; enhancer RNA RT-qPCR; 3C; CRISPRi; MEF2A ChIP; transcription-factor perturbation
E_00076	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85463935	85468299	Srf	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Primary mouse cortical neurons	NA	neuron	CL:0000540	Endogenous enhancer perturbation; Stimulus-responsive enhancer assay; Enhancer-promoter interaction	RNA-seq; ChIP-seq and chromatin-state integration	Luciferase reporter assay; enhancer RNA RT-qPCR; 3C; CRISPRi; SRF binding and transcription-factor perturbation
E_00077	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85490344	85493924	Creb1	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Primary mouse cortical neurons	NA	neuron	CL:0000540	Endogenous enhancer perturbation; Stimulus-responsive enhancer assay; Enhancer-promoter interaction	RNA-seq; ChIP-seq and chromatin-state integration	Luciferase reporter assay; enhancer RNA RT-qPCR; 3C; CRISPRi; CREB binding and transcription-factor perturbation
E_00078	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85490344	85493924	Mef2a	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Primary mouse cortical neurons	NA	neuron	CL:0000540	Endogenous enhancer perturbation; Stimulus-responsive enhancer assay; Enhancer-promoter interaction	RNA-seq; ChIP-seq and chromatin-state integration	Luciferase reporter assay; enhancer RNA RT-qPCR; 3C; CRISPRi; MEF2A ChIP; transcription-factor perturbation
E_00079	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	Gata1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay; In vivo functional validation; Endogenous enhancer deletion assay	DNase-seq; GATA1/TAL1/KLF1/NFE2/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted enhancer deletion mouse model; NanoString expression analysis; stable transgenic LacZ reporter assay; chick embryo enhancer reporter assay; Southern blot; Sequencing; hematologic phenotyping; In vivo phenotyping
E_00080	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	Gata1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay; In vivo functional validation; Endogenous enhancer deletion assay	DNase-seq; GATA1/TAL1/KLF1/NFE2/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted enhancer deletion mouse model; NanoString expression analysis; stable transgenic LacZ reporter assay; chick embryo enhancer reporter assay; Southern blot; Sequencing; hematologic phenotyping; In vivo phenotyping
E_00081	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	Klf1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay; In vivo functional validation; Endogenous enhancer deletion assay	DNase-seq; GATA1/TAL1/KLF1/NFE2/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted enhancer deletion mouse model; NanoString expression analysis; stable transgenic LacZ reporter assay; chick embryo enhancer reporter assay; Southern blot; Sequencing; hematologic phenotyping; In vivo phenotyping
E_00082	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	Klf1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay; In vivo functional validation; Endogenous enhancer deletion assay	DNase-seq; GATA1/TAL1/KLF1/NFE2/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted enhancer deletion mouse model; NanoString expression analysis; stable transgenic LacZ reporter assay; chick embryo enhancer reporter assay; Southern blot; Sequencing; hematologic phenotyping; In vivo phenotyping
E_00083	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	Nfe2	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay; In vivo functional validation; Endogenous enhancer deletion assay	DNase-seq; GATA1/TAL1/KLF1/NFE2/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted enhancer deletion mouse model; NanoString expression analysis; stable transgenic LacZ reporter assay; chick embryo enhancer reporter assay; Southern blot; Sequencing; hematologic phenotyping; In vivo phenotyping
E_00084	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	Nfe2	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay; In vivo functional validation; Endogenous enhancer deletion assay	DNase-seq; GATA1/TAL1/KLF1/NFE2/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted enhancer deletion mouse model; NanoString expression analysis; stable transgenic LacZ reporter assay; chick embryo enhancer reporter assay; Southern blot; Sequencing; hematologic phenotyping; In vivo phenotyping
E_00085	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	Tal1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay; In vivo functional validation; Endogenous enhancer deletion assay	DNase-seq; GATA1/TAL1/KLF1/NFE2/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted enhancer deletion mouse model; NanoString expression analysis; stable transgenic LacZ reporter assay; chick embryo enhancer reporter assay; Southern blot; Sequencing; hematologic phenotyping; In vivo phenotyping
E_00086	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	Tal1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay; In vivo functional validation; Endogenous enhancer deletion assay	DNase-seq; GATA1/TAL1/KLF1/NFE2/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted enhancer deletion mouse model; NanoString expression analysis; stable transgenic LacZ reporter assay; chick embryo enhancer reporter assay; Southern blot; Sequencing; hematologic phenotyping; In vivo phenotyping
E_00087	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	Gata1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay; In vivo functional validation; Endogenous enhancer deletion assay	DNase-seq; GATA1/TAL1/KLF1/NFE2/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted enhancer deletion mouse model; NanoString expression analysis; stable transgenic LacZ reporter assay; chick embryo enhancer reporter assay; Southern blot; Sequencing; hematologic phenotyping; In vivo phenotyping
E_00088	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	Gata1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay; In vivo functional validation; Endogenous enhancer deletion assay	DNase-seq; GATA1/TAL1/KLF1/NFE2/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted enhancer deletion mouse model; NanoString expression analysis; stable transgenic LacZ reporter assay; chick embryo enhancer reporter assay; Southern blot; Sequencing; hematologic phenotyping; In vivo phenotyping
E_00089	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	Klf1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay; In vivo functional validation; Endogenous enhancer deletion assay	DNase-seq; GATA1/TAL1/KLF1/NFE2/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted enhancer deletion mouse model; NanoString expression analysis; stable transgenic LacZ reporter assay; chick embryo enhancer reporter assay; Southern blot; Sequencing; hematologic phenotyping; In vivo phenotyping
E_00090	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	Klf1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay; In vivo functional validation; Endogenous enhancer deletion assay	DNase-seq; GATA1/TAL1/KLF1/NFE2/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted enhancer deletion mouse model; NanoString expression analysis; stable transgenic LacZ reporter assay; chick embryo enhancer reporter assay; Southern blot; Sequencing; hematologic phenotyping; In vivo phenotyping
E_00091	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	Nfe2	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay; In vivo functional validation; Endogenous enhancer deletion assay	DNase-seq; GATA1/TAL1/KLF1/NFE2/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted enhancer deletion mouse model; NanoString expression analysis; stable transgenic LacZ reporter assay; chick embryo enhancer reporter assay; Southern blot; Sequencing; hematologic phenotyping; In vivo phenotyping
E_00092	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	Nfe2	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay; In vivo functional validation; Endogenous enhancer deletion assay	DNase-seq; GATA1/TAL1/KLF1/NFE2/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted enhancer deletion mouse model; NanoString expression analysis; stable transgenic LacZ reporter assay; chick embryo enhancer reporter assay; Southern blot; Sequencing; hematologic phenotyping; In vivo phenotyping
E_00093	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	Tal1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay; In vivo functional validation; Endogenous enhancer deletion assay	DNase-seq; GATA1/TAL1/KLF1/NFE2/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted enhancer deletion mouse model; NanoString expression analysis; stable transgenic LacZ reporter assay; chick embryo enhancer reporter assay; Southern blot; Sequencing; hematologic phenotyping; In vivo phenotyping
E_00094	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	Tal1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay; In vivo functional validation; Endogenous enhancer deletion assay	DNase-seq; GATA1/TAL1/KLF1/NFE2/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted enhancer deletion mouse model; NanoString expression analysis; stable transgenic LacZ reporter assay; chick embryo enhancer reporter assay; Southern blot; Sequencing; hematologic phenotyping; In vivo phenotyping
E_00095	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	Gata1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00096	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	Gata1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00097	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	Klf1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00098	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	Klf1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00099	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	Nfe2	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00100	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	Nfe2	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00101	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	Tal1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00102	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	Tal1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00103	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	Gata1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00104	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	Gata1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00105	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	Klf1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00106	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	Klf1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00107	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	Nfe2	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00108	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	Nfe2	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00109	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	Tal1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00110	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	Tal1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00111	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32156048	32157191	Gata1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00112	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32156048	32157191	Gata1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00113	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32156048	32157191	Gata1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Super-enhancer constituent functional assay; Endogenous cis-element deletion assay	DNase-seq; GATA1/TAL1/KLF1/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted R3 deletion mouse model; NanoString; chick embryo reporter assay; stable transgenic LacZ reporter assay; In vivo phenotyping
E_00114	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32156048	32157191	Gata1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Super-enhancer constituent functional assay; Endogenous cis-element deletion assay	DNase-seq; GATA1/TAL1/KLF1/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted R3 deletion mouse model; NanoString; chick embryo reporter assay; stable transgenic LacZ reporter assay; In vivo phenotyping
E_00115	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32156048	32157191	Klf1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00116	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32156048	32157191	Klf1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00117	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32156048	32157191	Klf1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Super-enhancer constituent functional assay; Endogenous cis-element deletion assay	DNase-seq; GATA1/TAL1/KLF1/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted R3 deletion mouse model; NanoString; chick embryo reporter assay; stable transgenic LacZ reporter assay; In vivo phenotyping
E_00118	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32156048	32157191	Klf1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Super-enhancer constituent functional assay; Endogenous cis-element deletion assay	DNase-seq; GATA1/TAL1/KLF1/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted R3 deletion mouse model; NanoString; chick embryo reporter assay; stable transgenic LacZ reporter assay; In vivo phenotyping
E_00119	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32156048	32157191	Tal1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00120	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32156048	32157191	Tal1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00121	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32156048	32157191	Tal1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Super-enhancer constituent functional assay; Endogenous cis-element deletion assay	DNase-seq; GATA1/TAL1/KLF1/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted R3 deletion mouse model; NanoString; chick embryo reporter assay; stable transgenic LacZ reporter assay; In vivo phenotyping
E_00122	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32156048	32157191	Tal1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Super-enhancer constituent functional assay; Endogenous cis-element deletion assay	DNase-seq; GATA1/TAL1/KLF1/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted R3 deletion mouse model; NanoString; chick embryo reporter assay; stable transgenic LacZ reporter assay; In vivo phenotyping
E_00123	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32165011	32165922	Gata1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00124	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32165011	32165922	Gata1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00125	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32165011	32165922	Gata1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Super-enhancer constituent functional assay; Endogenous cis-element deletion assay	DNase-seq; GATA1/NFE2/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted Rm deletion mouse model; NanoString; chick embryo reporter assay; stable transgenic LacZ reporter assay; In vivo phenotyping
E_00126	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32165011	32165922	Gata1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Super-enhancer constituent functional assay; Endogenous cis-element deletion assay	DNase-seq; GATA1/NFE2/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted Rm deletion mouse model; NanoString; chick embryo reporter assay; stable transgenic LacZ reporter assay; In vivo phenotyping
E_00127	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32165011	32165922	Nfe2	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00128	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32165011	32165922	Nfe2	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00129	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32165011	32165922	Nfe2	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Super-enhancer constituent functional assay; Endogenous cis-element deletion assay	DNase-seq; GATA1/NFE2/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted Rm deletion mouse model; NanoString; chick embryo reporter assay; stable transgenic LacZ reporter assay; In vivo phenotyping
E_00130	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32165011	32165922	Nfe2	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Super-enhancer constituent functional assay; Endogenous cis-element deletion assay	DNase-seq; GATA1/NFE2/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted Rm deletion mouse model; NanoString; chick embryo reporter assay; stable transgenic LacZ reporter assay; In vivo phenotyping
E_00131	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32168783	32169689	Gata1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00132	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32168783	32169689	Gata1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00133	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32168783	32169689	Gata1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Super-enhancer constituent functional assay; Endogenous cis-element deletion assay	DNase-seq; GATA1/TAL1/KLF1/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted R4 deletion mouse model; NanoString; chick embryo reporter assay; stable transgenic LacZ reporter assay; hematologic phenotyping; In vivo phenotyping
E_00134	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32168783	32169689	Gata1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Super-enhancer constituent functional assay; Endogenous cis-element deletion assay	DNase-seq; GATA1/TAL1/KLF1/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted R4 deletion mouse model; NanoString; chick embryo reporter assay; stable transgenic LacZ reporter assay; hematologic phenotyping; In vivo phenotyping
E_00135	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32168783	32169689	Klf1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00136	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32168783	32169689	Klf1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00137	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32168783	32169689	Klf1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Super-enhancer constituent functional assay; Endogenous cis-element deletion assay	DNase-seq; GATA1/TAL1/KLF1/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted R4 deletion mouse model; NanoString; chick embryo reporter assay; stable transgenic LacZ reporter assay; hematologic phenotyping; In vivo phenotyping
E_00138	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32168783	32169689	Klf1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Super-enhancer constituent functional assay; Endogenous cis-element deletion assay	DNase-seq; GATA1/TAL1/KLF1/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted R4 deletion mouse model; NanoString; chick embryo reporter assay; stable transgenic LacZ reporter assay; hematologic phenotyping; In vivo phenotyping
E_00139	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32168783	32169689	Tal1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00140	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32168783	32169689	Tal1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; In vivo functional validation; Super-enhancer constituent functional dissection	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; transgenic/Citrine enhancer reporter assay; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00141	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32168783	32169689	Tal1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Super-enhancer constituent functional assay; Endogenous cis-element deletion assay	DNase-seq; GATA1/TAL1/KLF1/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted R4 deletion mouse model; NanoString; chick embryo reporter assay; stable transgenic LacZ reporter assay; hematologic phenotyping; In vivo phenotyping
E_00142	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32168783	32169689	Tal1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary E12.5 fetal-liver erythroid cells	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Super-enhancer constituent functional assay; Endogenous cis-element deletion assay	DNase-seq; GATA1/TAL1/KLF1/MED1 ChIP-seq; ATAC-seq; nascent RNA-seq; NG Capture-C	Targeted R4 deletion mouse model; NanoString; chick embryo reporter assay; stable transgenic LacZ reporter assay; hematologic phenotyping; In vivo phenotyping
E_00143	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis; In vivo functional validation	GWAS fine-mapping; DNase-seq; ChIP-seq; GWAS	ChIP-qPCR; 3C; allele-specific TF-binding analysis; Transgenic reporter assay; TALEN-mediated orthologous enhancer deletion; RT-qPCR; Western blot; In vivo phenotyping
E_00144	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis; In vivo functional validation	GWAS fine-mapping; DNase-seq; ChIP-seq; GWAS	ChIP-qPCR; 3C; allele-specific TF-binding analysis; Transgenic reporter assay; TALEN-mediated orthologous enhancer deletion; RT-qPCR; Western blot; In vivo phenotyping
E_00145	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis; In vivo functional validation	ChIP-seq; DNase-seq; GWAS	ChIP-qPCR; 3C; Transgenic reporter assay; TALEN-mediated enhancer deletion; RT-qPCR; In vivo phenotyping
E_00146	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis; In vivo functional validation	GWAS fine-mapping; DNase-seq; ChIP-seq; GWAS	ChIP-qPCR; 3C; Transgenic reporter assay; TALEN-mediated orthologous enhancer deletion; RT-qPCR; Western blot; In vivo phenotyping
E_00147	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis; In vivo functional validation; Functional variant assay; Genetic association analysis	ChIP-seq; DNase-seq; GWAS	Allele-specific ChIP-pyrosequencing; ChIP-qPCR; 3C; Transgenic reporter assay; RT-qPCR; In vivo phenotyping
E_00148	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis; In vivo functional validation; Genetic association analysis	ChIP-seq; DNase-seq; GWAS	ChIP-qPCR; 3C; Transgenic reporter assay; RT-qPCR; In vivo phenotyping
E_00149	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	GATA1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human CD34-positive erythroid progenitors	NA	erythroid progenitor cell	CL:0000038	Lineage-specific enhancer characterization; endogenous functional validation	GWAS fine-mapping; DNase-seq; H3K4me1/H3K27ac ChIP-seq; GATA1/TAL1 ChIP-seq; CRISPR-Cas9 saturating mutagenesis in follow-up PMID 26375006	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; Transgenic enhancer reporter assay; genome engineering; RT-qPCR
E_00150	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	GATA1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human erythroblasts	NA	erythroblast	CL:0000765	Lineage-specific enhancer characterization; endogenous functional validation	GWAS fine-mapping; DNase-seq; H3K4me1/H3K27ac ChIP-seq; GATA1/TAL1 ChIP-seq; CRISPR-Cas9 saturating mutagenesis in follow-up PMID 26375006	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; Transgenic enhancer reporter assay; genome engineering; RT-qPCR
E_00151	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human CD34-positive erythroid progenitors	NA	erythroid progenitor cell	CL:0000038	Lineage-specific enhancer characterization; endogenous functional validation	GWAS fine-mapping; DNase-seq; H3K4me1/H3K27ac ChIP-seq; GATA1/TAL1 ChIP-seq; CRISPR-Cas9 saturating mutagenesis in follow-up PMID 26375006	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; Transgenic enhancer reporter assay; genome engineering; RT-qPCR
E_00152	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human erythroblasts	NA	erythroblast	CL:0000765	Lineage-specific enhancer characterization; endogenous functional validation	GWAS fine-mapping; DNase-seq; H3K4me1/H3K27ac ChIP-seq; GATA1/TAL1 ChIP-seq; CRISPR-Cas9 saturating mutagenesis in follow-up PMID 26375006	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; Transgenic enhancer reporter assay; genome engineering; RT-qPCR
E_00153	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	GATA1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human CD34-positive erythroid progenitors	NA	erythroid progenitor cell	CL:0000038	Lineage-specific enhancer characterization; endogenous functional validation	GWAS fine-mapping; DNase-seq; H3K4me1/H3K27ac ChIP-seq; GATA1/TAL1 ChIP-seq; CRISPR-Cas9 saturating mutagenesis in follow-up PMID 26375006	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; Transgenic enhancer reporter assay; genome engineering; RT-qPCR
E_00154	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	GATA1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human erythroblasts	NA	erythroblast	CL:0000765	Lineage-specific enhancer characterization; endogenous functional validation	GWAS fine-mapping; DNase-seq; H3K4me1/H3K27ac ChIP-seq; GATA1/TAL1 ChIP-seq; CRISPR-Cas9 saturating mutagenesis in follow-up PMID 26375006	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; Transgenic enhancer reporter assay; genome engineering; RT-qPCR
E_00155	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human CD34-positive erythroid progenitors	NA	erythroid progenitor cell	CL:0000038	Lineage-specific enhancer characterization; endogenous functional validation	GWAS fine-mapping; DNase-seq; H3K4me1/H3K27ac ChIP-seq; GATA1/TAL1 ChIP-seq; CRISPR-Cas9 saturating mutagenesis in follow-up PMID 26375006	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; Transgenic enhancer reporter assay; genome engineering; RT-qPCR
E_00156	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human erythroblasts	NA	erythroblast	CL:0000765	Lineage-specific enhancer characterization; endogenous functional validation	GWAS fine-mapping; DNase-seq; H3K4me1/H3K27ac ChIP-seq; GATA1/TAL1 ChIP-seq; CRISPR-Cas9 saturating mutagenesis in follow-up PMID 26375006	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; Transgenic enhancer reporter assay; genome engineering; RT-qPCR
E_00157	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	GATA1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human CD34-positive erythroid progenitors	NA	erythroid progenitor cell	CL:0000038	Lineage-specific enhancer characterization; endogenous functional validation	GWAS fine-mapping; DNase-seq; H3K4me1/H3K27ac ChIP-seq; GATA1/TAL1 ChIP-seq; CRISPR-Cas9 saturating mutagenesis in follow-up PMID 26375006	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; Transgenic enhancer reporter assay; genome engineering; RT-qPCR
E_00158	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	GATA1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human erythroblasts	NA	erythroblast	CL:0000765	Lineage-specific enhancer characterization; endogenous functional validation	GWAS fine-mapping; DNase-seq; H3K4me1/H3K27ac ChIP-seq; GATA1/TAL1 ChIP-seq; CRISPR-Cas9 saturating mutagenesis in follow-up PMID 26375006	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; Transgenic enhancer reporter assay; genome engineering; RT-qPCR
E_00159	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human CD34-positive erythroid progenitors	NA	erythroid progenitor cell	CL:0000038	Lineage-specific enhancer characterization; endogenous functional validation	GWAS fine-mapping; DNase-seq; H3K4me1/H3K27ac ChIP-seq; GATA1/TAL1 ChIP-seq; CRISPR-Cas9 saturating mutagenesis in follow-up PMID 26375006	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; Transgenic enhancer reporter assay; genome engineering; RT-qPCR
E_00160	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human erythroblasts	NA	erythroblast	CL:0000765	Lineage-specific enhancer characterization; endogenous functional validation	GWAS fine-mapping; DNase-seq; H3K4me1/H3K27ac ChIP-seq; GATA1/TAL1 ChIP-seq; CRISPR-Cas9 saturating mutagenesis in follow-up PMID 26375006	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; Transgenic enhancer reporter assay; genome engineering; RT-qPCR
E_00161	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr12	25538591	25539583	NA	KRAS	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Disease-variant functional analysis	targeted CRE resequencing; pooled enCRISPRi/enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq; chromatin interaction profiling	individual enCRISPRi/enCRISPRa; CRISPR-Cas9 enhancer deletion; enhancer luciferase reporter assay; variant knock-in; ChIP-qPCR; RT-qPCR; EMSA
E_00162	2015	25381333	Functional characterization of CYP2D6 enhancer polymorphisms	Homo sapiens	hg19	chr22	42411693	42414130	NA	CYP2D6	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	epithelial cell	CL:0000066	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Chromatin accessibility assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Functional variant assay	4C-seq; Capture-C	P300 ChIP-qPCR; DNase I accessibility assay; Luciferase reporter assay; CRISPR-Cas9 enhancer deletion; Site-directed mutagenesis; qRT-PCR; CRISPR-Cas9 endogenous deletion/editing; ChIP; 4C
E_00163	2015	25381333	Functional characterization of CYP2D6 enhancer polymorphisms	Homo sapiens	hg19	chr22	42411693	42414130	NA	CYP2D6	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	NA	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Chromatin accessibility assay; Gene expression assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Cofactor occupancy assay	Capture-C	Luciferase reporter assay; P300 ChIP-qPCR; DNase I accessibility assay (CHART-PCR); CRISPR-Cas9 enhancer deletion; RT-qPCR; Site-directed mutagenesis; PCR deletion genotyping; CRISPR-Cas9 endogenous deletion/editing; ChIP; 4C
E_00164	2024	39688912	Regulation of sarcomere formation and function in the healthy heart requires a titin intronic enhancer	Homo sapiens	hg38	chr2	178806313	178806949	NKX2-5	TTN	Enhancer	Active	Disease	dilated cardiomyopathy	MONDO:0005021	DOID:12930	heart	UBERON:0000948	human induced pluripotent stem cell-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; TF binding assay; Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation; Endogenous enhancer perturbation assay; disease variant analysis	ATAC-seq; RNA-seq; single-nucleus RNA-seq; MPRA; whole-genome sequencing	Luciferase reporter assay; CRISPR/Cas9 deletion; TF motif mutation; transgenic mouse enhancer assay; qPCR; sarcomere analysis; cardiac contractility assay; Site-directed/motif mutagenesis; Allele-specific reporter assay; Mouse genetic deletion/knock-in; In vivo phenotyping
E_00165	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23912000	23912961	NKX2-5	MYH7	Enhancer	Active	Normal	NA	NA	NA	heart left ventricle	UBERON:0002084	GM03348-derived human iPSC cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Endogenous enhancer perturbation assay; engineered heart tissue functional assay	promoter capture Hi-C; ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Dual-luciferase reporter assay of the exact 961-bp MYH7-C3 construct in iPSC-CMs and HL-1 cells; CRISPR/Cas9 dual-guide enhancer deletion in GM03348-derived iPSCs; Sanger genotyping; RT-qPCR; SDS-PAGE myosin isoform analysis; cardiac troponin T flow cytometry; engineered heart tissue contractility assay
E_00166	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23912000	23912961	NKX2-5	MYH7	Enhancer	Active	Normal	NA	NA	NA	heart left ventricle	UBERON:0002084	HL-1	CVCL_0303	cardiac muscle cell	CL:0000746	Enhancer activity assay; Endogenous enhancer perturbation assay; engineered heart tissue functional assay	promoter capture Hi-C; ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Dual-luciferase reporter assay of the exact 961-bp MYH7-C3 construct in iPSC-CMs and HL-1 cells; CRISPR/Cas9 dual-guide enhancer deletion in GM03348-derived iPSCs; Sanger genotyping; RT-qPCR; SDS-PAGE myosin isoform analysis; cardiac troponin T flow cytometry; engineered heart tissue contractility assay
E_00167	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23912000	23912961	TCF21	MYH7	Enhancer	Active	Normal	NA	NA	NA	heart left ventricle	UBERON:0002084	GM03348-derived human iPSC cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Endogenous enhancer perturbation assay; engineered heart tissue functional assay	promoter capture Hi-C; ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Dual-luciferase reporter assay of the exact 961-bp MYH7-C3 construct in iPSC-CMs and HL-1 cells; CRISPR/Cas9 dual-guide enhancer deletion in GM03348-derived iPSCs; Sanger genotyping; RT-qPCR; SDS-PAGE myosin isoform analysis; cardiac troponin T flow cytometry; engineered heart tissue contractility assay
E_00168	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23912000	23912961	TCF21	MYH7	Enhancer	Active	Normal	NA	NA	NA	heart left ventricle	UBERON:0002084	HL-1	CVCL_0303	cardiac muscle cell	CL:0000746	Enhancer activity assay; Endogenous enhancer perturbation assay; engineered heart tissue functional assay	promoter capture Hi-C; ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Dual-luciferase reporter assay of the exact 961-bp MYH7-C3 construct in iPSC-CMs and HL-1 cells; CRISPR/Cas9 dual-guide enhancer deletion in GM03348-derived iPSCs; Sanger genotyping; RT-qPCR; SDS-PAGE myosin isoform analysis; cardiac troponin T flow cytometry; engineered heart tissue contractility assay
E_00169	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23913940	23915344	TBX5	MYH7	Enhancer	Active	Normal	NA	NA	NA	heart left ventricle	UBERON:0002084	GM03348-derived human iPSC cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Regulatory variant functional assay; endogenous perturbation control	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Dual-luciferase reporter assay of MYH7-C4-1; allele-specific luciferase assay; CRISPR/Cas9 C4-region deletion with no significant MYH6 or MYH7 expression effect; RT-qPCR; SDS-PAGE; reporter activity is positive but endogenous deletion did not support a required MYH7 enhancer role
E_00170	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23913940	23915344	TBX5	MYH7	Enhancer	Active	Normal	NA	NA	NA	heart left ventricle	UBERON:0002084	HL-1	CVCL_0303	cardiac muscle cell	CL:0000746	Enhancer activity assay; Regulatory variant functional assay; endogenous perturbation control	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Dual-luciferase reporter assay of MYH7-C4-1; allele-specific luciferase assay; CRISPR/Cas9 C4-region deletion with no significant MYH6 or MYH7 expression effect; RT-qPCR; SDS-PAGE; reporter activity is positive but endogenous deletion did not support a required MYH7 enhancer role
E_00171	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	126521490	126522490	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	H1-derived microglia	NA	microglial cell	CL:0000129	Disease-variant functional analysis; Regulatory element functional validation; 3D chromatin interaction mapping	ChIP-seq; ATAC-seq; PLAC-seq; RNA-seq	CRISPR-Cas9 deletion; RT-qPCR; Western blot; Flow cytometry
E_00172	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892600	127892962	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	primary human microglia	NA	microglial cell	CL:0000129	Disease-risk enhancer annotation; enhancer-promoter interaction mapping	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; PLAC-seq; GWAS fine-mapping; LDSC	Independent functional support by CRISPR-Cas9 deletion in hPSC-derived microglia; Flow cytometry
E_00173	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127082600	127082962	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	human brain microglia / iPSC-derived brain-cell models	NA	microglial cell	CL:0000129	Disease-variant functional analysis; Cell-type-specific enhancer-promoter mapping; disease-risk integration; Endogenous enhancer deletion	ATAC-seq; H3K27ac ChIP-seq; PLAC-seq / promoter interactome profiling	CRISPR-Cas9 enhancer deletion; RT-qPCR; Western blot; Flow cytometry
E_00174	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892629	127892991	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	cerebral cortex	UBERON:0000956	human cortical PU.1-positive microglial nuclei	NA	microglial cell	CL:0000129	cell-type-specific enhancer-promoter mapping plus endogenous causal enhancer deletion	H3K27ac ChIP-seq; H3K4me3 ChIP-seq; ATAC-seq; H3K4me3 PLAC-seq; RNA-seq; GWAS fine-mapping/integration	CRISPR-Cas9 363-bp enhancer deletion in two PSC lines; differentiation to microglia, neurons and astrocytes; Western blot; immunohistochemistry
E_00175	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892629	127892991	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	cerebral cortex	UBERON:0000956	EC11 iPSC-	NA	microglial cell	CL:0000129	cell-type-specific enhancer-promoter mapping plus endogenous causal enhancer deletion	H3K27ac ChIP-seq; H3K4me3 ChIP-seq; ATAC-seq; H3K4me3 PLAC-seq; RNA-seq; GWAS fine-mapping/integration	CRISPR-Cas9 363-bp enhancer deletion in two PSC lines; differentiation to microglia, neurons and astrocytes; Western blot; immunohistochemistry
E_00176	2025	41129262	The hematopoietic stem cell MYB enhancer is essential for and recurrently amplified during T cell leukemogenesis	Homo sapiens	hg38	chr6	135323327	135323580	ETS1	MYB	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	THP-6 T-ALL cells	NA	T-ALL lymphoblast	NA	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation	ATAC-seq; ChIP-seq; RNA-seq; pooled CRISPRi screen; genome-wide CRISPRi screen; ATAC-seq; H3K27ac ChIP-seq; WGS	Luciferase reporter assay, CRISPRi; RT-qPCR; CRISPRi; targeted CRISPRi; ETS motif mutagenesis; reverse ChIP; RT-qPCR; Luciferase reporter assay; xenotransplant
E_00177	2024	39688912	Regulation of sarcomere formation and function in the healthy heart requires a titin intronic enhancer	Homo sapiens	hg38	chr2	178806313	178806949	NA	TTN	Enhancer	Active	Disease	dilated cardiomyopathy	MONDO:0005021	DOID:12930	heart	UBERON:0000948	human induced pluripotent stem cell-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; TF binding assay; Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation; TF motif functional assay; Target-gene expression assay; phenotypic assay	ATAC-seq; MPRA; single-nucleus RNA-seq	CRISPR/Cas9 E0/E1 deletion; GFP reporter assay; MEF2-site mutagenesis; transgenic mouse reporter assay; RT-qPCR; Western blot; sarcomere analysis; engineered cardiac microtissue contractility assay; Site-directed/motif mutagenesis; Allele-specific reporter assay; Mouse genetic deletion/knock-in; In vivo phenotyping
E_00178	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85490344	85493924	Creb1	Fos	Enhancer	Active	Normal	NA	NA	NA	cerebral cortex	UBERON:0000956	Primary mouse cortical neurons	NA	neuron	CL:0000540	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Enhancer RNA assay	Published activity-regulated TF ChIP-seq; H3K4me1/H3K27ac ChIP-seq data integration; RNA-seq	Luciferase reporter assay; eRNA RT-qPCR; CREB knockdown; CRISPRi; 3C; ChIP-qPCR; Fos pre-mRNA RT-qPCR
E_00179	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85509692	85513444	Creb1	Fos	Enhancer	Active	Normal	NA	NA	NA	cerebral cortex	UBERON:0000956	Primary mouse cortical neurons	NA	neuron	CL:0000540	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Enhancer RNA assay	Published CREB ChIP-seq; H3K4me1/H3K27ac ChIP-seq data integration; RNA-seq	Luciferase reporter assay; eRNA RT-qPCR; CREB knockdown; CRISPRi; 3C; ChIP-qPCR; Fos pre-mRNA RT-qPCR
E_00180	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85509692	85513444	Creb1	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Primary mouse cortical neurons	NA	neuron	CL:0000540	Stimulus-responsive enhancer activity; Enhancer-promoter interaction; endogenous CRISPRi test	RNA-seq; ChIP-seq and chromatin-state integration	Luciferase reporter assay; enhancer RNA RT-qPCR; 3C; CRISPRi; CREB binding and transcription-factor perturbation
E_00181	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85509692	85513444	Mef2a	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Primary mouse cortical neurons	NA	neuron	CL:0000540	Stimulus-responsive enhancer activity; Enhancer-promoter interaction; endogenous CRISPRi test	RNA-seq; ChIP-seq and chromatin-state integration	Luciferase reporter assay; enhancer RNA RT-qPCR; 3C; CRISPRi; MEF2A ChIP; transcription-factor perturbation
E_00182	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	Gata1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; In vivo functional validation	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00183	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	Gata1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; In vivo functional validation	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00184	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	Klf1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; In vivo functional validation	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00185	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	Klf1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; In vivo functional validation	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00186	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	Nfe2	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; In vivo functional validation	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00187	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	Nfe2	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; In vivo functional validation	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00188	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	Tal1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; In vivo functional validation	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00189	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	Tal1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; In vivo functional validation	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00190	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	Gata1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; In vivo functional validation	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00191	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	Gata1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; In vivo functional validation	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00192	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	Klf1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; In vivo functional validation	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00193	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	Klf1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; In vivo functional validation	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00194	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	Nfe2	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; In vivo functional validation	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00195	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	Nfe2	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; In vivo functional validation	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00196	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	Tal1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; In vivo functional validation	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00197	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	Tal1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; In vivo functional validation	DNase-seq; ChIP-seq; ATAC-seq; NG Capture-C; RNA-seq	Targeted in vivo enhancer deletion; Southern blot; Sequencing; RT-qPCR; hematologic phenotyping; In vivo phenotyping
E_00198	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	GATA1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-GATA1 occupancy; corrected from non-minimal composite interval	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00199	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	GATA1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-GATA1 occupancy; corrected from non-minimal composite interval	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00200	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-TF occupancy and genetic-variant evidence	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00201	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-TF occupancy and genetic-variant evidence	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00202	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-TF occupancy and enhancer-promoter looping evidence	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00203	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-TF occupancy and enhancer-promoter looping evidence	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00204	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-GWAS fine-mapping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00205	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-GWAS fine-mapping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00206	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-developmental transgenic-reporter evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00207	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-developmental transgenic-reporter evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00208	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Constituent +62 enhancer-TF occupancy and genetic-variant evidence	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00209	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Constituent +62 enhancer-TF occupancy and genetic-variant evidence	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00210	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Constituent +62 enhancer-GWAS fine-mapping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00211	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Constituent +62 enhancer-GWAS fine-mapping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00212	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Constituent +62 enhancer-3C looping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00213	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Constituent +62 enhancer-3C looping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00214	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Constituent +62 enhancer-developmental transgenic-reporter evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00215	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Constituent +62 enhancer-developmental transgenic-reporter evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00216	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Constituent +55 enhancer-TF occupancy and chromatin-state evidence	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00217	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Constituent +55 enhancer-TF occupancy and chromatin-state evidence	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00218	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Constituent +55 enhancer-GWAS fine-mapping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00219	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Constituent +55 enhancer-GWAS fine-mapping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00220	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Constituent +55 enhancer-3C looping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00221	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Constituent +55 enhancer-3C looping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00222	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Constituent +55 enhancer-developmental transgenic-reporter evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00223	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Constituent +55 enhancer-developmental transgenic-reporter evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00224	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892710	127893072	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	Resected cerebral cortex NEUN+ nuclei	NA	neuron	CL:0000540	Enhancer activity assay; Chromatin interaction assay; Functional perturbation negative-control assay	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; H3K4me3 PLAC-seq; RNA-seq	CRISPR-Cas9 363-bp enhancer deletion; genomic PCR; amplicon cloning and sequencing; immunohistochemistry; Western blot; Flow cytometry
E_00225	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892710	127893072	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	H1-hESC	CVCL_9771	neuron	CL:0000540	Enhancer activity assay; Chromatin interaction assay; Functional perturbation negative-control assay	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; H3K4me3 PLAC-seq; RNA-seq	CRISPR-Cas9 363-bp enhancer deletion; genomic PCR; amplicon cloning and sequencing; immunohistochemistry; Western blot; Flow cytometry
E_00226	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892710	127893072	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	EC11 iPSC-derived neurons	NA	neuron	CL:0000540	Enhancer activity assay; Chromatin interaction assay; Functional perturbation negative-control assay	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; H3K4me3 PLAC-seq; RNA-seq	CRISPR-Cas9 363-bp enhancer deletion; genomic PCR; amplicon cloning and sequencing; immunohistochemistry; Western blot; Flow cytometry
E_00227	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892710	127893072	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	Resected cerebral cortex PU.1+ nuclei	NA	microglial cell	CL:0000129	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; H3K4me3 PLAC-seq; RNA-seq; PU.1 ChIP-seq (supporting PMID 28546318)	CRISPR-Cas9 363-bp enhancer deletion; genomic PCR; amplicon cloning and sequencing; immunohistochemistry; Western blot; Flow cytometry
E_00228	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892710	127893072	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	H1-hESC	CVCL_9771	microglial cell	CL:0000129	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; H3K4me3 PLAC-seq; RNA-seq; PU.1 ChIP-seq (supporting PMID 28546318)	CRISPR-Cas9 363-bp enhancer deletion; genomic PCR; amplicon cloning and sequencing; immunohistochemistry; Western blot; Flow cytometry
E_00229	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892710	127893072	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	EC11 iPSC-derived microglia	NA	microglial cell	CL:0000129	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; H3K4me3 PLAC-seq; RNA-seq; PU.1 ChIP-seq (supporting PMID 28546318)	CRISPR-Cas9 363-bp enhancer deletion; genomic PCR; amplicon cloning and sequencing; immunohistochemistry; Western blot; Flow cytometry
E_00230	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892710	127893072	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	Human cerebral cortex NEUN+ nuclei	NA	neuron	CL:0000540	Cell-type specificity negative-control validation of the same enhancer; Endogenous enhancer deletion	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; H3K4me3 PLAC-seq; RNA-seq; supporting SPI1/PU.1 ChIP-seq in human microglia from PMID 28546318	Paired-sgRNA CRISPR-Cas9 363-bp endogenous enhancer deletion; genomic PCR; TOPO-TA cloning and sequencing; lineage-marker immunocytochemistry; Western blot; Flow cytometry
E_00231	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892710	127893072	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	H1-hESC	CVCL_9771	neuron	CL:0000540	Cell-type specificity negative-control validation of the same enhancer; Endogenous enhancer deletion	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; H3K4me3 PLAC-seq; RNA-seq; supporting SPI1/PU.1 ChIP-seq in human microglia from PMID 28546318	Paired-sgRNA CRISPR-Cas9 363-bp endogenous enhancer deletion; genomic PCR; TOPO-TA cloning and sequencing; lineage-marker immunocytochemistry; Western blot; Flow cytometry
E_00232	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892710	127893072	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	EC11 iPSC-derived neurons	NA	neuron	CL:0000540	Cell-type specificity negative-control validation of the same enhancer; Endogenous enhancer deletion	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; H3K4me3 PLAC-seq; RNA-seq; supporting SPI1/PU.1 ChIP-seq in human microglia from PMID 28546318	Paired-sgRNA CRISPR-Cas9 363-bp endogenous enhancer deletion; genomic PCR; TOPO-TA cloning and sequencing; lineage-marker immunocytochemistry; Western blot; Flow cytometry
E_00233	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892710	127893072	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	Human cerebral cortex PU.1+ nuclei	NA	microglial cell	CL:0000129	Epigenomic enhancer mapping; enhancer-promoter interaction mapping; TF binding support; Endogenous enhancer deletion; cell-type-specific functional validation	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; H3K4me3 PLAC-seq; RNA-seq; supporting SPI1/PU.1 ChIP-seq from PMID 28546318	Paired-sgRNA CRISPR-Cas9 363-bp endogenous enhancer deletion; genomic PCR; TOPO-TA cloning and sequencing; lineage-marker immunocytochemistry; Western blot; Flow cytometry
E_00234	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892710	127893072	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	H1-hESC	CVCL_9771	microglial cell	CL:0000129	Epigenomic enhancer mapping; enhancer-promoter interaction mapping; TF binding support; Endogenous enhancer deletion; cell-type-specific functional validation	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; H3K4me3 PLAC-seq; RNA-seq; supporting SPI1/PU.1 ChIP-seq from PMID 28546318	Paired-sgRNA CRISPR-Cas9 363-bp endogenous enhancer deletion; genomic PCR; TOPO-TA cloning and sequencing; lineage-marker immunocytochemistry; Western blot; Flow cytometry
E_00235	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892710	127893072	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	EC11 iPSC-derived microglia	NA	microglial cell	CL:0000129	Epigenomic enhancer mapping; enhancer-promoter interaction mapping; TF binding support; Endogenous enhancer deletion; cell-type-specific functional validation	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; H3K4me3 PLAC-seq; RNA-seq; supporting SPI1/PU.1 ChIP-seq from PMID 28546318	Paired-sgRNA CRISPR-Cas9 363-bp endogenous enhancer deletion; genomic PCR; TOPO-TA cloning and sequencing; lineage-marker immunocytochemistry; Western blot; Flow cytometry
E_00236	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892710	127893072	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	Human cerebral cortex NEUN+ nuclei	NA	neuron	CL:0000540	Cell-type specificity negative-control validation of the same enhancer; Endogenous enhancer deletion	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; H3K4me3 PLAC-seq; RNA-seq	Paired-sgRNA CRISPR-Cas9 363-bp enhancer deletion; genomic PCR and amplicon sequencing; immunocytochemistry; Western blot; Flow cytometry
E_00237	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892710	127893072	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	H1-hESC	CVCL_9771	neuron	CL:0000540	Cell-type specificity negative-control validation of the same enhancer; Endogenous enhancer deletion	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; H3K4me3 PLAC-seq; RNA-seq	Paired-sgRNA CRISPR-Cas9 363-bp enhancer deletion; genomic PCR and amplicon sequencing; immunocytochemistry; Western blot; Flow cytometry
E_00238	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892710	127893072	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	EC11 iPSC-derived neurons	NA	neuron	CL:0000540	Cell-type specificity negative-control validation of the same enhancer; Endogenous enhancer deletion	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; H3K4me3 PLAC-seq; RNA-seq	Paired-sgRNA CRISPR-Cas9 363-bp enhancer deletion; genomic PCR and amplicon sequencing; immunocytochemistry; Western blot; Flow cytometry
E_00239	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892710	127893072	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	Human cerebral cortex PU.1+ nuclei	NA	microglial cell	CL:0000129	Epigenomic enhancer mapping; Enhancer-promoter interaction; TF-binding support; Endogenous enhancer deletion; cell-type-specific functional validation	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; H3K4me3 PLAC-seq; RNA-seq; supporting SPI1/PU.1 ChIP-seq from PMID 28546318	Paired-sgRNA CRISPR-Cas9 363-bp enhancer deletion; genomic PCR and amplicon sequencing; immunocytochemistry; Western blot; Flow cytometry
E_00240	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892710	127893072	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	H1-hESC	CVCL_9771	microglial cell	CL:0000129	Epigenomic enhancer mapping; Enhancer-promoter interaction; TF-binding support; Endogenous enhancer deletion; cell-type-specific functional validation	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; H3K4me3 PLAC-seq; RNA-seq; supporting SPI1/PU.1 ChIP-seq from PMID 28546318	Paired-sgRNA CRISPR-Cas9 363-bp enhancer deletion; genomic PCR and amplicon sequencing; immunocytochemistry; Western blot; Flow cytometry
E_00241	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892710	127893072	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	EC11 iPSC-derived microglia	NA	microglial cell	CL:0000129	Epigenomic enhancer mapping; Enhancer-promoter interaction; TF-binding support; Endogenous enhancer deletion; cell-type-specific functional validation	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; H3K4me3 PLAC-seq; RNA-seq; supporting SPI1/PU.1 ChIP-seq from PMID 28546318	Paired-sgRNA CRISPR-Cas9 363-bp enhancer deletion; genomic PCR and amplicon sequencing; immunocytochemistry; Western blot; Flow cytometry
E_00242	2016	27774982	Genetic variation at the 8q24.21 renal cancer susceptibility locus affects HIF binding to a MYC enhancer	Homo sapiens	hg19	chr8	128889122	128889450	HIF1A	MYC	Enhancer	Active	Disease	renal cell carcinoma	MONDO:0005086	DOID:4450	kidney	UBERON:0002113	renal cell carcinoma model (paper-derived RCC cells)	NA	renal cell carcinoma cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis; Endogenous enhancer perturbation	ChIP-seq, Hi-C; GWAS	Luciferase reporter assay, CRISPR knockout; CRISPR-Cas9 endogenous deletion/editing; ChIP
E_00243	2015	25381333	Functional characterization of CYP2D6 enhancer polymorphisms	Homo sapiens	hg19	chr22	42411693	42414130	NA	CYP2D6	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	primary human hepatocytes	NA	hepatocyte	CL:0000182	Chromatin interaction assay; Chromatin accessibility assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Enhancer-associated cofactor binding assay	4C-seq; Capture-C	P300 ChIP-qPCR; DNase I accessibility assay; qRT-PCR; CRISPR-Cas9 endogenous deletion/editing; ChIP; 4C
E_00244	2015	25381333	Functional characterization of CYP2D6 enhancer polymorphisms	Homo sapiens	hg19	chr22	42411333	42413643	NA	CYP2D6	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Human Primary Hepatocytes	NA	hepatocyte	CL:0000182	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 4C; RT-qPCR/qPCR
E_00245	2024	39196225	A transcriptional enhancer regulates cardiac maturation	Homo sapiens	hg38	chr1	236660389	236660646	MEF2C	ACTN2	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	H9 human pluripotent stem cells differentiated into hPSC-CMs	NA	cardiac muscle cell	CL:0000746	causal enhancer deletion/CRISPRi/enCRISPRa plus direct TF-binding validation	scRNA-seq; bulk RNA-seq; cardiomyocyte ATAC-seq; H3K27ac/H3K4me1/p300 ChIP-seq reanalysis; differentiation-stage Hi-C	heterozygous enhancer deletion; CRISPRi at rs535411; enCRISPRa; Luciferase reporter; MEF2C ChIP-qPCR; modified-MEF2C mRNA overexpression; cardiomyocyte differentiation; contractility; mitochondrial respiration; RT-qPCR; immunoblot
E_00246	2024	39196225	A transcriptional enhancer regulates cardiac maturation	Homo sapiens	hg38	chr1	236660389	236660646	MEF2C	ACTN2	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	mouse cardiomyocyte and in-vivo heart validation	NA	cardiac muscle cell	CL:0000746	causal enhancer deletion/CRISPRi/enCRISPRa plus direct TF-binding validation	scRNA-seq; bulk RNA-seq; cardiomyocyte ATAC-seq; H3K27ac/H3K4me1/p300 ChIP-seq reanalysis; differentiation-stage Hi-C	heterozygous enhancer deletion; CRISPRi at rs535411; enCRISPRa; Luciferase reporter; MEF2C ChIP-qPCR; modified-MEF2C mRNA overexpression; cardiomyocyte differentiation; contractility; mitochondrial respiration; RT-qPCR; immunoblot
E_00247	2024	39196225	A transcriptional enhancer regulates cardiac maturation	Homo sapiens	hg38	chr1	236660389	236660646	GATA4	ACTN2	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	H9 human pluripotent stem cells differentiated into hPSC-CMs	NA	cardiac muscle cell	CL:0000746	causal enhancer validation plus direct TF-binding validation	scRNA-seq; bulk RNA-seq; cardiomyocyte ATAC-seq; H3K27ac/H3K4me1/p300 ChIP-seq reanalysis; differentiation-stage Hi-C	heterozygous enhancer deletion; CRISPRi at rs535411; enCRISPRa; Luciferase reporter; GATA4 ChIP-qPCR; cardiomyocyte differentiation; contractility; mitochondrial respiration; RT-qPCR; immunoblot
E_00248	2024	39196225	A transcriptional enhancer regulates cardiac maturation	Homo sapiens	hg38	chr1	236660389	236660646	GATA4	ACTN2	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	mouse cardiomyocyte and in-vivo heart validation	NA	cardiac muscle cell	CL:0000746	causal enhancer validation plus direct TF-binding validation	scRNA-seq; bulk RNA-seq; cardiomyocyte ATAC-seq; H3K27ac/H3K4me1/p300 ChIP-seq reanalysis; differentiation-stage Hi-C	heterozygous enhancer deletion; CRISPRi at rs535411; enCRISPRa; Luciferase reporter; GATA4 ChIP-qPCR; cardiomyocyte differentiation; contractility; mitochondrial respiration; RT-qPCR; immunoblot
E_00249	2024	39196225	A transcriptional enhancer regulates cardiac maturation	Homo sapiens	hg38	chr1	236660389	236660646	MEF2A	ACTN2	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	H9 human pluripotent stem cells differentiated into hPSC-CMs	NA	cardiac muscle cell	CL:0000746	causal enhancer validation plus TF-responsive reporter/in-vivo temporal occupancy support	scRNA-seq; bulk RNA-seq; cardiomyocyte ATAC-seq; H3K27ac/H3K4me1/p300 ChIP-seq reanalysis; differentiation-stage Hi-C	heterozygous enhancer deletion; CRISPRi at rs535411; enCRISPRa; Luciferase reporter; modified-MEF2A mRNA overexpression; adult-mouse Mef2a ChIP-seq/ChIP-qPCR context; cardiomyocyte maturation assays
E_00250	2024	39196225	A transcriptional enhancer regulates cardiac maturation	Homo sapiens	hg38	chr1	236660389	236660646	MEF2A	ACTN2	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	mouse cardiomyocyte and in-vivo heart validation	NA	cardiac muscle cell	CL:0000746	causal enhancer validation plus TF-responsive reporter/in-vivo temporal occupancy support	scRNA-seq; bulk RNA-seq; cardiomyocyte ATAC-seq; H3K27ac/H3K4me1/p300 ChIP-seq reanalysis; differentiation-stage Hi-C	heterozygous enhancer deletion; CRISPRi at rs535411; enCRISPRa; Luciferase reporter; modified-MEF2A mRNA overexpression; adult-mouse Mef2a ChIP-seq/ChIP-qPCR context; cardiomyocyte maturation assays
E_00251	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892600	127892962	SPI1	BIN1	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	hPSC-derived microglia	NA	microglial cell	CL:0000129	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; PLAC-seq; RNA-seq	CRISPR-Cas9 363-bp enhancer deletion; Western blot; Flow cytometry
E_00252	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Disease-variant functional analysis; In vivo functional validation; Erythroid enhancer mapping; TF occupancy; enhancer-promoter looping; genetic and genome-editing validation	DNase-seq; GATA1/TAL1 ChIP-seq; genetic fine-mapping; GWAS	ChIP-qPCR; 3C; allele-specific analysis; enhancer reporter; endogenous genome-editing validation; In vivo phenotyping
E_00253	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Disease-variant functional analysis; In vivo functional validation; Genetic fine-mapping; erythroid enhancer mapping; TF occupancy; chromatin interaction	DNase-seq; GATA1/TAL1 ChIP-seq; genetic fine-mapping; GWAS	3C; enhancer reporter; allele-specific functional analysis; subsequent endogenous genome-editing validation; In vivo phenotyping
E_00254	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Disease-variant functional analysis; In vivo functional validation; Erythroid enhancer mapping; TF occupancy; enhancer-promoter looping; genetic and genome-editing validation	DNase-seq; GATA1/TAL1 ChIP-seq; genetic fine-mapping; GWAS	ChIP-qPCR; 3C; allele-specific analysis; enhancer reporter; endogenous genome-editing validation; In vivo phenotyping
E_00255	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Disease-variant functional analysis; In vivo functional validation; Genetic fine-mapping; erythroid enhancer mapping; TF occupancy; chromatin interaction	DNase-seq; GATA1/TAL1 ChIP-seq; genetic fine-mapping; GWAS	3C; enhancer reporter; allele-specific functional analysis; subsequent endogenous genome-editing validation; In vivo phenotyping
E_00256	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	GATA1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	MEL and pre-B cells for orthologous enhancer deletion	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-GATA1 occupancy; corrected from non-minimal composite interval	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00257	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	GATA1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	transgenic mice	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-GATA1 occupancy; corrected from non-minimal composite interval	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00258	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	GATA1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	MEL and pre-B cells for orthologous enhancer deletion	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-GATA1 occupancy; corrected from non-minimal composite interval	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00259	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	GATA1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	transgenic mice	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-GATA1 occupancy; corrected from non-minimal composite interval	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00260	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	MEL and pre-B cells for orthologous enhancer deletion	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-TF occupancy and genetic-variant evidence	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00261	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	transgenic mice	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-TF occupancy and genetic-variant evidence	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00262	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	MEL and pre-B cells for orthologous enhancer deletion	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-TF occupancy and genetic-variant evidence	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00263	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	transgenic mice	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-TF occupancy and genetic-variant evidence	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00264	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	MEL and pre-B cells for orthologous enhancer deletion	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-TF occupancy and enhancer-promoter looping evidence	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00265	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	transgenic mice	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-TF occupancy and enhancer-promoter looping evidence	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00266	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	MEL and pre-B cells for orthologous enhancer deletion	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-TF occupancy and enhancer-promoter looping evidence	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00267	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	transgenic mice	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-TF occupancy and enhancer-promoter looping evidence	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00268	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	MEL and pre-B cells for orthologous enhancer deletion	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-GWAS fine-mapping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00269	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	transgenic mice	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-GWAS fine-mapping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00270	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	MEL and pre-B cells for orthologous enhancer deletion	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-GWAS fine-mapping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00271	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	transgenic mice	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-GWAS fine-mapping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00272	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	MEL and pre-B cells for orthologous enhancer deletion	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-developmental transgenic-reporter evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00273	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	transgenic mice	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-developmental transgenic-reporter evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00274	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	MEL and pre-B cells for orthologous enhancer deletion	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-developmental transgenic-reporter evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00275	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	transgenic mice	NA	erythroid progenitor cell	CL:0000038	Constituent +58 enhancer-developmental transgenic-reporter evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00276	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	MEL and pre-B cells for orthologous enhancer deletion	NA	erythroid progenitor cell	CL:0000038	Constituent +62 enhancer-TF occupancy and genetic-variant evidence	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00277	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	transgenic mice	NA	erythroid progenitor cell	CL:0000038	Constituent +62 enhancer-TF occupancy and genetic-variant evidence	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00278	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	MEL and pre-B cells for orthologous enhancer deletion	NA	erythroid progenitor cell	CL:0000038	Constituent +62 enhancer-TF occupancy and genetic-variant evidence	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00279	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	transgenic mice	NA	erythroid progenitor cell	CL:0000038	Constituent +62 enhancer-TF occupancy and genetic-variant evidence	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00280	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	MEL and pre-B cells for orthologous enhancer deletion	NA	erythroid progenitor cell	CL:0000038	Constituent +62 enhancer-GWAS fine-mapping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00281	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	transgenic mice	NA	erythroid progenitor cell	CL:0000038	Constituent +62 enhancer-GWAS fine-mapping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00282	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	MEL and pre-B cells for orthologous enhancer deletion	NA	erythroid progenitor cell	CL:0000038	Constituent +62 enhancer-GWAS fine-mapping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00283	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	transgenic mice	NA	erythroid progenitor cell	CL:0000038	Constituent +62 enhancer-GWAS fine-mapping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00284	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	MEL and pre-B cells for orthologous enhancer deletion	NA	erythroid progenitor cell	CL:0000038	Constituent +62 enhancer-3C looping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00285	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	transgenic mice	NA	erythroid progenitor cell	CL:0000038	Constituent +62 enhancer-3C looping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00286	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	MEL and pre-B cells for orthologous enhancer deletion	NA	erythroid progenitor cell	CL:0000038	Constituent +62 enhancer-3C looping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00287	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	transgenic mice	NA	erythroid progenitor cell	CL:0000038	Constituent +62 enhancer-3C looping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00288	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	MEL and pre-B cells for orthologous enhancer deletion	NA	erythroid progenitor cell	CL:0000038	Constituent +62 enhancer-developmental transgenic-reporter evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00289	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	transgenic mice	NA	erythroid progenitor cell	CL:0000038	Constituent +62 enhancer-developmental transgenic-reporter evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00290	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	MEL and pre-B cells for orthologous enhancer deletion	NA	erythroid progenitor cell	CL:0000038	Constituent +62 enhancer-developmental transgenic-reporter evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00291	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	transgenic mice	NA	erythroid progenitor cell	CL:0000038	Constituent +62 enhancer-developmental transgenic-reporter evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00292	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	MEL and pre-B cells for orthologous enhancer deletion	NA	erythroid progenitor cell	CL:0000038	Constituent +55 enhancer-TF occupancy and chromatin-state evidence	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00293	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	transgenic mice	NA	erythroid progenitor cell	CL:0000038	Constituent +55 enhancer-TF occupancy and chromatin-state evidence	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00294	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	MEL and pre-B cells for orthologous enhancer deletion	NA	erythroid progenitor cell	CL:0000038	Constituent +55 enhancer-TF occupancy and chromatin-state evidence	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00295	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	transgenic mice	NA	erythroid progenitor cell	CL:0000038	Constituent +55 enhancer-TF occupancy and chromatin-state evidence	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00296	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	MEL and pre-B cells for orthologous enhancer deletion	NA	erythroid progenitor cell	CL:0000038	Constituent +55 enhancer-GWAS fine-mapping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00297	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	transgenic mice	NA	erythroid progenitor cell	CL:0000038	Constituent +55 enhancer-GWAS fine-mapping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00298	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	MEL and pre-B cells for orthologous enhancer deletion	NA	erythroid progenitor cell	CL:0000038	Constituent +55 enhancer-GWAS fine-mapping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00299	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	transgenic mice	NA	erythroid progenitor cell	CL:0000038	Constituent +55 enhancer-GWAS fine-mapping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00300	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	MEL and pre-B cells for orthologous enhancer deletion	NA	erythroid progenitor cell	CL:0000038	Constituent +55 enhancer-3C looping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00301	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	transgenic mice	NA	erythroid progenitor cell	CL:0000038	Constituent +55 enhancer-3C looping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00302	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	MEL and pre-B cells for orthologous enhancer deletion	NA	erythroid progenitor cell	CL:0000038	Constituent +55 enhancer-3C looping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00303	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	transgenic mice	NA	erythroid progenitor cell	CL:0000038	Constituent +55 enhancer-3C looping evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00304	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	MEL and pre-B cells for orthologous enhancer deletion	NA	erythroid progenitor cell	CL:0000038	Constituent +55 enhancer-developmental transgenic-reporter evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00305	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	transgenic mice	NA	erythroid progenitor cell	CL:0000038	Constituent +55 enhancer-developmental transgenic-reporter evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00306	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	MEL and pre-B cells for orthologous enhancer deletion	NA	erythroid progenitor cell	CL:0000038	Constituent +55 enhancer-developmental transgenic-reporter evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00307	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	transgenic mice	NA	erythroid progenitor cell	CL:0000038	Constituent +55 enhancer-developmental transgenic-reporter evidence record	GWAS fine-mapping; DNase-seq; GATA1/TAL1 ChIP-seq; erythroid chromatin-state profiling	ChIP-qPCR; allele-specific ChIP/pyrosequencing; 3C; transgenic lacZ enhancer reporter; orthologous endogenous enhancer deletion; RT-qPCR; immunoblot
E_00308	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85475057	85477322	Mef2a	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Primary mouse cortical neurons	NA	neuron	CL:0000540	Endogenous enhancer perturbation; Stimulus-responsive enhancer assay	RNA-seq; ChIP-seq and chromatin-state integration	Luciferase reporter assay; enhancer RNA RT-qPCR; CRISPRi; MEF2A ChIP; transcription-factor perturbation
E_00309	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85475057	85477322	Npas4	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Primary mouse cortical neurons	NA	neuron	CL:0000540	Endogenous enhancer perturbation; Stimulus-responsive enhancer assay	RNA-seq; ChIP-seq and chromatin-state integration	Luciferase reporter assay; enhancer RNA RT-qPCR; CRISPRi; NPAS4 binding and transcription-factor perturbation
E_00310	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85433906	85439068	Creb1	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00311	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85433906	85439068	Mef2a	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00312	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85433906	85439068	Mef2c	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00313	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85433906	85439068	Mef2d	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00314	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85433906	85439068	Npas4	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00315	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85433906	85439068	Srf	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00316	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85452549	85458571	Creb1	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00317	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85452549	85458571	Mef2a	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00318	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85452549	85458571	Mef2c	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00319	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85452549	85458571	Mef2d	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00320	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85452549	85458571	Npas4	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00321	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85452549	85458571	Srf	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00322	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85466416	85469570	Creb1	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00323	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85466416	85469570	Mef2a	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00324	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85466416	85469570	Mef2c	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00325	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85466416	85469570	Mef2d	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00326	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85466416	85469570	Npas4	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00327	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85466416	85469570	Srf	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00328	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85470646	85474086	Creb1	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00329	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85470646	85474086	Mef2a	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00330	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85470646	85474086	Mef2c	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00331	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85470646	85474086	Mef2d	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00332	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85470646	85474086	Npas4	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00333	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85470646	85474086	Srf	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00334	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85482048	85490068	Creb1	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00335	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85482048	85490068	Mef2a	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00336	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85482048	85490068	Mef2c	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00337	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85482048	85490068	Mef2d	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00338	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85482048	85490068	Npas4	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00339	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85482048	85490068	Srf	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Cortical Neurons	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00340	2016	27774982	Genetic variation at the 8q24.21 renal cancer susceptibility locus affects HIF binding to a MYC enhancer	Homo sapiens	hg19	chr8	128889122	128889450	HIF1A	PVT1	Enhancer	Active	Disease	renal cell carcinoma	MONDO:0005086	DOID:4450	kidney	UBERON:0002113	RCC4	CVCL_0498	renal cell carcinoma cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Disease-variant functional analysis; Endogenous enhancer perturbation	HIF ChIP-seq; H3K27ac/H3K4me1 ChIP-seq; DNase-seq; GWAS	HIF-alpha siRNA; allele-specific HIF ChIP-qPCR; ChIP-PCR amplicon sequencing; FAIRE-qPCR; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; ChIP
E_00341	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85463935	85468299	Npas4	Fos	Enhancer	Active	Normal	NA	NA	NA	cerebral cortex	UBERON:0000956	Primary mouse cortical neurons	NA	neuron	CL:0000540	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Enhancer RNA assay	NPAS4 ChIP-seq; activity-regulated TF ChIP-seq; RNA-seq	Luciferase reporter assay; eRNA RT-qPCR; NPAS4 knockdown; CRISPRi; 3C; Fos pre-mRNA RT-qPCR
E_00342	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85490344	85493924	Npas4	Fos	Enhancer	Active	Normal	NA	NA	NA	cerebral cortex	UBERON:0000956	Primary mouse cortical neurons	NA	neuron	CL:0000540	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Enhancer RNA assay	NPAS4 ChIP-seq; activity-regulated TF ChIP-seq; RNA-seq	Luciferase reporter assay; eRNA RT-qPCR; NPAS4 knockdown; CRISPRi; 3C; Fos pre-mRNA RT-qPCR
E_00343	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85509692	85513444	Npas4	Fos	Enhancer	Active	Normal	NA	NA	NA	cerebral cortex	UBERON:0000956	Primary mouse cortical neurons	NA	neuron	CL:0000540	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Enhancer RNA assay	NPAS4 ChIP-seq; activity-regulated TF ChIP-seq; RNA-seq	Luciferase reporter assay; eRNA RT-qPCR; NPAS4 knockdown; CRISPRi; 3C; Fos pre-mRNA RT-qPCR
E_00344	2015	25381333	Functional characterization of CYP2D6 enhancer polymorphisms	Homo sapiens	hg19	chr22	42411693	42414130	NA	CYP2D6	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary human hepatocytes (Hep4)	NA	hepatocyte	CL:0000182	Chromatin interaction assay; Chromatin accessibility assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Cofactor occupancy assay; Epigenomic enhancer characterization	4C-seq; Capture-C	P300 ChIP-qPCR; DNase I accessibility assay (CHART-PCR); CRISPR-Cas9 endogenous deletion/editing; ChIP; 4C
E_00345	2024	39688912	Regulation of sarcomere formation and function in the healthy heart requires a titin intronic enhancer	Homo sapiens	hg38	chr2	178806313	178806949	NA	TTN	Enhancer	Active	Disease	dilated cardiomyopathy	MONDO:0005021	DOID:12930	heart	UBERON:0000948	human induced pluripotent stem cell-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation; Endogenous enhancer perturbation assay; disease variant analysis	ATAC-seq; RNA-seq; single-nucleus RNA-seq; MPRA; whole-genome sequencing	Luciferase reporter assay; CRISPR/Cas9 deletion; TF motif mutation; transgenic mouse enhancer assay; qPCR; sarcomere analysis; cardiac contractility assay; Site-directed/motif mutagenesis; Allele-specific reporter assay; Mouse genetic deletion/knock-in; In vivo phenotyping
E_00346	2025	41129262	The hematopoietic stem cell MYB enhancer is essential for and recurrently amplified during T cell leukemogenesis	Homo sapiens	hg19	chr14	98664280	98665247	ETS1	NKX2-5	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	THP-6	CVCL_4686	T cell	CL:0000084	TF binding assay; Endogenous enhancer perturbation; Enhancer essentiality screen; Enhancer hijacking analysis	Genome-wide CRISPRi screen; ETS1 ChIP-seq; H3K27ac ChIP-seq; ATAC-seq; WGS; RNA-seq; pooled CRISPRi screen	CRISPRi
E_00347	2024	39196225	A transcriptional enhancer regulates cardiac maturation	Homo sapiens	hg38	chr1	154150000	154150500	MEF2C	ACTN2	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	hPSC-CMs	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; TF binding assay; Endogenous enhancer perturbation; In vivo functional validation	ChIP-seq; ATAC-seq; RNA-seq	Luciferase reporter assay; ChIP-qPCR, CRISPR knockout; RT-qPCR; CRISPRa; Mouse genetic deletion/knock-in; In vivo phenotyping
E_00348	2024	39196225	A transcriptional enhancer regulates cardiac maturation	Homo sapiens	hg38	chr1	154151000	154151500	GATA4	ACTN2	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	hPSC-CMs	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; TF binding assay; Endogenous enhancer perturbation; In vivo functional validation	ChIP-seq; ATAC-seq; RNA-seq	Luciferase reporter assay; ChIP-qPCR, CRISPR knockout; RT-qPCR; CRISPRa; Mouse genetic deletion/knock-in; In vivo phenotyping
E_00349	2023	36869052	An autoimmune pleiotropic SNP modulates IRF5 alternative promoter usage through ZBTB3-mediated chromatin looping	Homo sapiens	hg19	chr7	128573817	128574098	ZBTB3	IRF5	Enhancer	Active	Disease	autoimmune disease	MONDO:0007179	DOID:417	blood	UBERON:0000178	Primary CD14+ monocytes	NA	CD14-positive monocyte	CL:0001054	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis	ChIP-seq; ATAC-seq	Luciferase reporter assay, EMSA; ChIP-qPCR; 3C assay; 4C assay; RT-qPCR
E_00350	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg38	chr14	23437399	23439399	TBX5	MYH7	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart	UBERON:0000948	human induced pluripotent stem cell-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Chromatin interaction assay; Disease-variant functional analysis; Enhancer variant functional assay; Endogenous enhancer deletion; target-gene expression; cardiac phenotype	ATAC-seq; H3K27ac profiling; promoter-capture chromatin conformation analysis; Capture-C	CRISPR-Cas9 enhancer deletion; TBX5 motif analysis; gene-expression assay; engineered heart tissue contractility assay
E_00351	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr12	14409708	14410606	NA	NA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	individual enCRISPRi/enCRISPRa; CRISPR-Cas9 enhancer deletion; enhancer luciferase reporter assay; variant knock-in; ChIP-qPCR; RT-qPCR; EMSA
E_00352	2016	27774982	Genetic variation at the 8q24.21 renal cancer susceptibility locus affects HIF binding to a MYC enhancer	Homo sapiens	hg19	chr8	128889122	128889450	ARNT	PVT1	Enhancer	Active	Disease	clear cell renal cell carcinoma	MONDO:0005005	DOID:4467	kidney	UBERON:0002113	renal tubular cells	NA	renal epithelial cell	NA	Disease-risk enhancer; Enhancer-promoter interaction; allele-specific TF binding; endogenous genome editing	HIF ChIP-seq; DNase/chromatin profiling; cancer genetic association	Capture-C/chromatin-conformation assay; allele-specific ChIP; luciferase; CRISPR HRE editing; RT-qPCR
E_00353	2016	27774982	Genetic variation at the 8q24.21 renal cancer susceptibility locus affects HIF binding to a MYC enhancer	Homo sapiens	hg19	chr8	128889122	128889450	ARNT	PVT1	Enhancer	Active	Disease	clear cell renal cell carcinoma	MONDO:0005005	DOID:4467	kidney	UBERON:0002113	RCC4	CVCL_0498	renal epithelial cell	NA	Disease-risk enhancer; Enhancer-promoter interaction; allele-specific TF binding; endogenous genome editing	HIF ChIP-seq; DNase/chromatin profiling; cancer genetic association	Capture-C/chromatin-conformation assay; allele-specific ChIP; luciferase; CRISPR HRE editing; RT-qPCR
E_00354	2016	27774982	Genetic variation at the 8q24.21 renal cancer susceptibility locus affects HIF binding to a MYC enhancer	Homo sapiens	hg19	chr8	128889122	128889450	ARNT	PVT1	Enhancer	Active	Disease	clear cell renal cell carcinoma	MONDO:0005005	DOID:4467	kidney	UBERON:0002113	786-O	CVCL_1051	renal epithelial cell	NA	Disease-risk enhancer; Enhancer-promoter interaction; allele-specific TF binding; endogenous genome editing	HIF ChIP-seq; DNase/chromatin profiling; cancer genetic association	Capture-C/chromatin-conformation assay; allele-specific ChIP; luciferase; CRISPR HRE editing; RT-qPCR
E_00355	2016	27774982	Genetic variation at the 8q24.21 renal cancer susceptibility locus affects HIF binding to a MYC enhancer	Homo sapiens	hg19	chr8	128889122	128889450	ARNT	PVT1	Enhancer	Active	Disease	clear cell renal cell carcinoma	MONDO:0005005	DOID:4467	kidney	UBERON:0002113	renal tubular cells	NA	renal epithelial cell	NA	Disease-risk enhancer; allele-specific HIF binding; chromatin interaction; endogenous HRE editing	HIF ChIP-seq; chromatin-accessibility profiling; genetic association	Capture-C/chromatin conformation; allele-specific ChIP; luciferase; CRISPR HRE editing; RT-qPCR
E_00356	2016	27774982	Genetic variation at the 8q24.21 renal cancer susceptibility locus affects HIF binding to a MYC enhancer	Homo sapiens	hg19	chr8	128889122	128889450	ARNT	PVT1	Enhancer	Active	Disease	clear cell renal cell carcinoma	MONDO:0005005	DOID:4467	kidney	UBERON:0002113	RCC4	CVCL_0498	renal epithelial cell	NA	Disease-risk enhancer; allele-specific HIF binding; chromatin interaction; endogenous HRE editing	HIF ChIP-seq; chromatin-accessibility profiling; genetic association	Capture-C/chromatin conformation; allele-specific ChIP; luciferase; CRISPR HRE editing; RT-qPCR
E_00357	2016	27774982	Genetic variation at the 8q24.21 renal cancer susceptibility locus affects HIF binding to a MYC enhancer	Homo sapiens	hg19	chr8	128889122	128889450	ARNT	PVT1	Enhancer	Active	Disease	clear cell renal cell carcinoma	MONDO:0005005	DOID:4467	kidney	UBERON:0002113	786-O	CVCL_1051	renal epithelial cell	NA	Disease-risk enhancer; allele-specific HIF binding; chromatin interaction; endogenous HRE editing	HIF ChIP-seq; chromatin-accessibility profiling; genetic association	Capture-C/chromatin conformation; allele-specific ChIP; luciferase; CRISPR HRE editing; RT-qPCR
E_00358	2016	27774982	Genetic variation at the 8q24.21 renal cancer susceptibility locus affects HIF binding to a MYC enhancer	Homo sapiens	hg19	chr8	128889122	128889450	EPAS1	PVT1	Enhancer	Active	Disease	clear cell renal cell carcinoma	MONDO:0005005	DOID:4467	kidney	UBERON:0002113	renal tubular cells	NA	renal epithelial cell	NA	Disease-risk enhancer; allele-specific HIF binding; chromatin interaction; endogenous HRE editing	HIF ChIP-seq; chromatin-accessibility profiling; genetic association	Capture-C/chromatin conformation; allele-specific ChIP; luciferase; CRISPR HRE editing; RT-qPCR
E_00359	2016	27774982	Genetic variation at the 8q24.21 renal cancer susceptibility locus affects HIF binding to a MYC enhancer	Homo sapiens	hg19	chr8	128889122	128889450	EPAS1	PVT1	Enhancer	Active	Disease	clear cell renal cell carcinoma	MONDO:0005005	DOID:4467	kidney	UBERON:0002113	RCC4	CVCL_0498	renal epithelial cell	NA	Disease-risk enhancer; allele-specific HIF binding; chromatin interaction; endogenous HRE editing	HIF ChIP-seq; chromatin-accessibility profiling; genetic association	Capture-C/chromatin conformation; allele-specific ChIP; luciferase; CRISPR HRE editing; RT-qPCR
E_00360	2016	27774982	Genetic variation at the 8q24.21 renal cancer susceptibility locus affects HIF binding to a MYC enhancer	Homo sapiens	hg19	chr8	128889122	128889450	EPAS1	PVT1	Enhancer	Active	Disease	clear cell renal cell carcinoma	MONDO:0005005	DOID:4467	kidney	UBERON:0002113	786-O	CVCL_1051	renal epithelial cell	NA	Disease-risk enhancer; allele-specific HIF binding; chromatin interaction; endogenous HRE editing	HIF ChIP-seq; chromatin-accessibility profiling; genetic association	Capture-C/chromatin conformation; allele-specific ChIP; luciferase; CRISPR HRE editing; RT-qPCR
E_00361	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23912000	23912961	NKX2-5	MYH7	Enhancer	Active	Normal	NA	NA	NA	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Functional perturbation assay; Regulatory variant functional assay; Engineered heart tissue functional assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq	qRT-PCR
E_00362	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23912000	23912961	TCF21	MYH7	Enhancer	Active	Normal	NA	NA	NA	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Functional perturbation assay; Regulatory variant functional assay; Engineered heart tissue functional assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq	qRT-PCR
E_00363	2015	25381333	Functional characterization of CYP2D6 enhancer polymorphisms	Homo sapiens	hg19	chr22	42411693	42414130	NA	CYP2D6	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep8	NA	hepatocyte	CL:0000182	Chromatin interaction assay; Chromatin accessibility assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Cofactor occupancy assay; Epigenomic enhancer characterization	4C-seq; Capture-C	P300 ChIP-qPCR; DNase I accessibility assay (CHART-PCR); CRISPR-Cas9 endogenous deletion/editing; ChIP; 4C
E_00364	2015	25381333	Functional characterization of CYP2D6 enhancer polymorphisms	Homo sapiens	hg19	chr22	42411693	42414130	NA	CYP2D6	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep10	NA	hepatocyte	CL:0000182	Chromatin interaction assay; Chromatin accessibility assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Cofactor occupancy assay; Epigenomic enhancer characterization	4C-seq; Capture-C	P300 ChIP-qPCR; DNase I accessibility assay (CHART-PCR); CRISPR-Cas9 endogenous deletion/editing; ChIP; 4C
E_00365	2015	25381333	Functional characterization of CYP2D6 enhancer polymorphisms	Homo sapiens	hg19	chr22	42411693	42414130	NA	CYP2D6	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary human hepatocytes (Hep11)	NA	hepatocyte	CL:0000182	Chromatin interaction assay; Chromatin accessibility assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Cofactor occupancy assay; Epigenomic enhancer characterization	4C-seq; Capture-C	P300 ChIP-qPCR; DNase I accessibility assay (CHART-PCR); CRISPR-Cas9 endogenous deletion/editing; ChIP; 4C
E_00366	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85428000	85428500	Mef2a	Fos	Enhancer	Active	Normal	NA	NA	NA	cerebral cortex	UBERON:0000956	Cortical neurons	NA	cortical neuron	NA	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq	Luciferase reporter assay, 3C; ChIP-qPCR; CRISPRi
E_00367	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85429000	85429500	Srf	Fos	Enhancer	Active	Normal	NA	NA	NA	cerebral cortex	UBERON:0000956	Cortical neurons	NA	cortical neuron	NA	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq	Luciferase reporter assay, 3C; ChIP-qPCR; CRISPRi
E_00368	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718043	60725451	GATA1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary human erythroid precursors/erythroblasts	NA	erythroid progenitor cell	CL:0000038	Enhancer activity assay; Functional perturbation assay; TF binding assay; Disease-variant functional analysis; In vivo functional validation	ChIP-seq; RNA-seq; GWAS	Luciferase reporter assay, CRISPR knockout; ChIP-qPCR; In vivo phenotyping
E_00369	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr12	25538591	25539583	NA	KRAS	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Disease-variant functional analysis	targeted CRE resequencing; pooled enCRISPRi/enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq; chromatin interaction profiling	Individual CRISPRi; CRISPR-Cas55 TF-binding-site deletion
E_00370	2015	26287746	FTO Obesity Variant Circuitry and Adipocyte Browning in Humans	Homo sapiens	hg19	chr16	53800454	53801454	ARID5B	IRX3	Enhancer	Active	Disease	obesity	MONDO:0011122	DOID:9970	subcutaneous adipose tissue	UBERON:0002190	primary human subcutaneous adipose progenitors	NA	subcutaneous preadipocyte	CL:0002583	Enhancer activity assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous enhancer-variant validation; target-gene perturbation; cellular phenotype assay	eQTL/trans-eQTL analysis; gene-expression profiling	CRISPR-Cas9 bidirectional single-nucleotide editing; IRX3 knockdown/overexpression; RT-qPCR; oxygen-consumption and thermogenesis assays; CRISPR-Cas9 endogenous deletion/editing; Allele-specific reporter assay
E_00371	2015	26287746	FTO Obesity Variant Circuitry and Adipocyte Browning in Humans	Homo sapiens	hg19	chr16	53800454	53801454	ARID5B	IRX5	Enhancer	Active	Disease	obesity	MONDO:0011122	DOID:9970	subcutaneous adipose tissue	UBERON:0002190	primary human subcutaneous adipose progenitors	NA	subcutaneous preadipocyte	CL:0002583	Enhancer activity assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous enhancer-variant validation; target-gene perturbation; cellular phenotype assay	eQTL/trans-eQTL analysis; gene-expression profiling	CRISPR-Cas9 bidirectional single-nucleotide editing; IRX5 knockdown/overexpression; RT-qPCR; oxygen-consumption and thermogenesis assays; CRISPR-Cas9 endogenous deletion/editing; Allele-specific reporter assay
E_00372	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892710	127893072	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	Human cerebral cortex NEUN-negative/LHX2+ nuclei	NA	astrocyte	CL:0000127	Cell-type specificity negative-control validation of the same enhancer; Endogenous enhancer deletion	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; RNA-seq; supporting SPI1/PU.1 ChIP-seq in human microglia from PMID 28546318	Paired-sgRNA CRISPR-Cas9 363-bp endogenous enhancer deletion; genomic PCR; TOPO-TA cloning and sequencing; lineage-marker immunocytochemistry; Western blot; Flow cytometry
E_00373	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892710	127893072	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	H1-hESC	CVCL_9771	astrocyte	CL:0000127	Cell-type specificity negative-control validation of the same enhancer; Endogenous enhancer deletion	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; RNA-seq; supporting SPI1/PU.1 ChIP-seq in human microglia from PMID 28546318	Paired-sgRNA CRISPR-Cas9 363-bp endogenous enhancer deletion; genomic PCR; TOPO-TA cloning and sequencing; lineage-marker immunocytochemistry; Western blot; Flow cytometry
E_00374	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892710	127893072	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	EC11 iPSC-derived astrocytes	NA	astrocyte	CL:0000127	Cell-type specificity negative-control validation of the same enhancer; Endogenous enhancer deletion	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; RNA-seq; supporting SPI1/PU.1 ChIP-seq in human microglia from PMID 28546318	Paired-sgRNA CRISPR-Cas9 363-bp endogenous enhancer deletion; genomic PCR; TOPO-TA cloning and sequencing; lineage-marker immunocytochemistry; Western blot; Flow cytometry
E_00375	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892710	127893072	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	Human cerebral cortex NEUN-negative/LHX2+ nuclei	NA	astrocyte	CL:0000127	Cell-type specificity negative-control validation of the same enhancer; Endogenous enhancer deletion	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; RNA-seq	Paired-sgRNA CRISPR-Cas9 363-bp enhancer deletion; genomic PCR and amplicon sequencing; immunocytochemistry; Western blot; Flow cytometry
E_00376	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892710	127893072	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	H1-hESC	CVCL_9771	astrocyte	CL:0000127	Cell-type specificity negative-control validation of the same enhancer; Endogenous enhancer deletion	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; RNA-seq	Paired-sgRNA CRISPR-Cas9 363-bp enhancer deletion; genomic PCR and amplicon sequencing; immunocytochemistry; Western blot; Flow cytometry
E_00377	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892710	127893072	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	EC11 iPSC-derived astrocytes	NA	astrocyte	CL:0000127	Cell-type specificity negative-control validation of the same enhancer; Endogenous enhancer deletion	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; RNA-seq	Paired-sgRNA CRISPR-Cas9 363-bp enhancer deletion; genomic PCR and amplicon sequencing; immunocytochemistry; Western blot; Flow cytometry
E_00378	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892710	127893072	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	Resected cerebral cortex NEUN-negative/LHX2+ nuclei	NA	astrocyte	CL:0000127	Enhancer activity assay; Functional perturbation negative-control assay	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; RNA-seq	CRISPR-Cas9 363-bp enhancer deletion; genomic PCR; amplicon cloning and sequencing; immunohistochemistry; Western blot; Flow cytometry
E_00379	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892710	127893072	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	H1-hESC	CVCL_9771	astrocyte	CL:0000127	Enhancer activity assay; Functional perturbation negative-control assay	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; RNA-seq	CRISPR-Cas9 363-bp enhancer deletion; genomic PCR; amplicon cloning and sequencing; immunohistochemistry; Western blot; Flow cytometry
E_00380	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892710	127893072	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	EC11 iPSC-derived astrocytes	NA	astrocyte	CL:0000127	Enhancer activity assay; Functional perturbation negative-control assay	ATAC-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; RNA-seq	CRISPR-Cas9 363-bp enhancer deletion; genomic PCR; amplicon cloning and sequencing; immunohistochemistry; Western blot; Flow cytometry
E_00381	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	Gata1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary mouse erythroid cells / enhancer-deletion mice	NA	erythroid lineage cell	CL:0000764	Endogenous constituent-enhancer knockout; chromatin and 3D-conformation dissection	ChIP-seq; chromatin profiling; Capture-C/3C-based interaction mapping	Targeted enhancer deletion mouse; RT-qPCR; chromatin assays
E_00382	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	Gata1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary mouse erythroid cells / enhancer-deletion mice	NA	erythroid lineage cell	CL:0000764	Endogenous constituent-enhancer knockout; chromatin and 3D-conformation dissection	ChIP-seq; chromatin profiling; Capture-C/3C-based interaction mapping	Targeted enhancer deletion mouse; RT-qPCR; chromatin assays
E_00383	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	Tal1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary mouse erythroid cells / enhancer-deletion mice	NA	erythroid lineage cell	CL:0000764	Endogenous constituent-enhancer knockout; chromatin and 3D-conformation dissection	ChIP-seq; chromatin profiling; Capture-C/3C-based interaction mapping	Targeted enhancer deletion mouse; RT-qPCR; chromatin assays
E_00384	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	Tal1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary mouse erythroid cells / enhancer-deletion mice	NA	erythroid lineage cell	CL:0000764	Endogenous constituent-enhancer knockout; chromatin and 3D-conformation dissection	ChIP-seq; chromatin profiling; Capture-C/3C-based interaction mapping	Targeted enhancer deletion mouse; RT-qPCR; chromatin assays
E_00385	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	Gata1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary mouse erythroid cells / enhancer-deletion mice	NA	erythroid lineage cell	CL:0000764	Endogenous constituent-enhancer knockout; chromatin and 3D-conformation dissection	ChIP-seq; chromatin profiling; Capture-C/3C-based interaction mapping	Targeted enhancer deletion mouse; RT-qPCR; chromatin assays
E_00386	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	Gata1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary mouse erythroid cells / enhancer-deletion mice	NA	erythroid lineage cell	CL:0000764	Endogenous constituent-enhancer knockout; chromatin and 3D-conformation dissection	ChIP-seq; chromatin profiling; Capture-C/3C-based interaction mapping	Targeted enhancer deletion mouse; RT-qPCR; chromatin assays
E_00387	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	Tal1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary mouse erythroid cells / enhancer-deletion mice	NA	erythroid lineage cell	CL:0000764	Endogenous constituent-enhancer knockout; chromatin and 3D-conformation dissection	ChIP-seq; chromatin profiling; Capture-C/3C-based interaction mapping	Targeted enhancer deletion mouse; RT-qPCR; chromatin assays
E_00388	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	Tal1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary mouse erythroid cells / enhancer-deletion mice	NA	erythroid lineage cell	CL:0000764	Endogenous constituent-enhancer knockout; chromatin and 3D-conformation dissection	ChIP-seq; chromatin profiling; Capture-C/3C-based interaction mapping	Targeted enhancer deletion mouse; RT-qPCR; chromatin assays
E_00389	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr1	16160379	16162282	NA	SPEN-AS1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis	enCRISPRi screen; enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas9 mediated enhancer perturbation
E_00390	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr1	16160379	16162282	NA	SPEN-AS1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas9 TF-binding-site deletion
E_00391	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr1	24717819	24718917	NA	STPG1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas9 TF-binding-site deletion
E_00392	2025	41129262	The hematopoietic stem cell MYB enhancer is essential for and recurrently amplified during T cell leukemogenesis	Homo sapiens	hg19	chr8	130180012	130180748	ETS1	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	THP-6	CVCL_4686	T cell	CL:0000084	Functional perturbation assay; TF binding assay; Endogenous enhancer perturbation; Enhancer essentiality screen	Genome-wide CRISPRi screen; ETS1 ChIP-seq; H3K27ac ChIP-seq; ATAC-seq; pooled CRISPRi screen	CRISPRi
E_00393	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85475057	85477322	Npas4	Fos	Enhancer	Active	Normal	NA	NA	NA	cerebral cortex	UBERON:0000956	Primary mouse cortical neurons	NA	neuron	CL:0000540	Enhancer activity assay; Functional perturbation assay; TF binding assay; Enhancer RNA assay	NPAS4 ChIP-seq; activity-regulated TF ChIP-seq; RNA-seq	Luciferase reporter assay; eRNA RT-qPCR; NPAS4 perturbation; CRISPRi; Fos pre-mRNA RT-qPCR
E_00394	2025	41129262	The hematopoietic stem cell MYB enhancer is essential for and recurrently amplified during T cell leukemogenesis	Homo sapiens	hg19	chr11	128345996	128346496	ETS1	NA	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	THP-6	CVCL_4686	T cell	CL:0000084	TF binding assay; Endogenous enhancer perturbation; Enhancer essentiality screen	Genome-wide CRISPRi screen; ETS1 ChIP-seq; H3K27ac ChIP-seq; ATAC-seq; pooled CRISPRi screen	CRISPRi
E_00395	2025	41129262	The hematopoietic stem cell MYB enhancer is essential for and recurrently amplified during T cell leukemogenesis	Homo sapiens	hg19	chr11	128346532	128347032	ETS1	NA	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	THP-6	CVCL_4686	T cell	CL:0000084	TF binding assay; Endogenous enhancer perturbation; Enhancer essentiality screen	Genome-wide CRISPRi screen; ETS1 ChIP-seq; H3K27ac ChIP-seq; ATAC-seq; pooled CRISPRi screen	CRISPRi
E_00396	2025	41129262	The hematopoietic stem cell MYB enhancer is essential for and recurrently amplified during T cell leukemogenesis	Homo sapiens	hg19	chr17	8867991	8869544	ETS1	NA	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	THP-6	CVCL_4686	T cell	CL:0000084	TF binding assay; Endogenous enhancer perturbation; Enhancer essentiality screen	Genome-wide CRISPRi screen; ETS1 ChIP-seq; H3K27ac ChIP-seq; ATAC-seq; pooled CRISPRi screen	CRISPRi
E_00397	2025	41129262	The hematopoietic stem cell MYB enhancer is essential for and recurrently amplified during T cell leukemogenesis	Homo sapiens	hg19	chr17	56409696	56410196	ETS1	NA	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	THP-6	CVCL_4686	T cell	CL:0000084	TF binding assay; Endogenous enhancer perturbation; Enhancer essentiality screen	Genome-wide CRISPRi screen; ETS1 ChIP-seq; H3K27ac ChIP-seq; ATAC-seq; pooled CRISPRi screen	CRISPRi
E_00398	2025	41129262	The hematopoietic stem cell MYB enhancer is essential for and recurrently amplified during T cell leukemogenesis	Homo sapiens	hg19	chr3	127316882	127317656	ETS1	NA	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	THP-6	CVCL_4686	T cell	CL:0000084	TF binding assay; Endogenous enhancer perturbation; Enhancer essentiality screen	Genome-wide CRISPRi screen; ETS1 ChIP-seq; H3K27ac ChIP-seq; ATAC-seq; pooled CRISPRi screen	CRISPRi
E_00399	2025	41129262	The hematopoietic stem cell MYB enhancer is essential for and recurrently amplified during T cell leukemogenesis	Homo sapiens	hg19	chr5	169063976	169065285	ETS1	NA	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	THP-6	CVCL_4686	T cell	CL:0000084	TF binding assay; Endogenous enhancer perturbation; Enhancer essentiality screen	Genome-wide CRISPRi screen; ETS1 ChIP-seq; H3K27ac ChIP-seq; ATAC-seq; pooled CRISPRi screen	CRISPRi
E_00400	2023	36869052	An autoimmune pleiotropic SNP modulates IRF5 alternative promoter usage through ZBTB3-mediated chromatin looping	Homo sapiens	hg19	chr7	128573817	128574098	ZBTB3	IRF5	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	HEK293	CVCL_0045	embryonic kidney cell	NA	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ChIP-seq; ATAC-seq	Luciferase reporter assay; EMSA; ChIP-qPCR; 3C assay; 4C assay; RT-qPCR
E_00401	2024	39196225	A transcriptional enhancer regulates cardiac maturation	Mus musculus	mm10	chr1	154149500	154150000	Mef2a	Actn2	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	Mouse embryonic/Adult cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Functional perturbation assay; TF binding assay; Endogenous enhancer perturbation; In vivo functional validation	ChIP-seq; RNA-seq	ChIP-qPCR; RT-qPCR; Western blot; CRISPRa; Mouse genetic deletion/knock-in; In vivo phenotyping
E_00402	2024	39196225	A transcriptional enhancer regulates cardiac maturation	Mus musculus	mm10	chr1	154150000	154150500	Mef2c	Actn2	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	Mouse embryonic/Adult cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Functional perturbation assay; TF binding assay; Endogenous enhancer perturbation; In vivo functional validation	ChIP-seq; RNA-seq	ChIP-qPCR; RT-qPCR; Western blot; CRISPRa; Mouse genetic deletion/knock-in; In vivo phenotyping
E_00403	2024	39196225	A transcriptional enhancer regulates cardiac maturation	Mus musculus	mm10	chr1	154151000	154151500	Gata4	Actn2	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	Mouse embryonic/Adult cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Functional perturbation assay; TF binding assay; Endogenous enhancer perturbation; In vivo functional validation	ChIP-seq; RNA-seq	ChIP-qPCR; RT-qPCR; Western blot; CRISPRa; Mouse genetic deletion/knock-in; In vivo phenotyping
E_00404	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr1	16160379	16162282	NA	SPEN-AS1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas11 TF-binding-site deletion
E_00405	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr1	24717819	24718917	NA	STPG1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas12 TF-binding-site deletion
E_00406	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr1	26827000	26828194	NA	HMGN2	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas10 TF-binding-site deletion
E_00407	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr1	26827000	26828194	NA	HMGN2	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas13 TF-binding-site deletion
E_00408	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr1	90223243	90223945	NA	LRRC8C	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas14 TF-binding-site deletion
E_00409	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr1	90223243	90223945	NA	LRRC8C	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas11 TF-binding-site deletion
E_00410	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr1	92269671	92270441	NA	TGFBR3	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas15 TF-binding-site deletion
E_00411	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr1	92269671	92270441	NA	TGFBR3	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas12 TF-binding-site deletion
E_00412	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr1	92970067	92970871	NA	EVI5	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas16 TF-binding-site deletion
E_00413	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr1	92970067	92970871	NA	EVI5	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas13 TF-binding-site deletion
E_00414	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr1	152432052	152433139	NA	CRNN	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas17 TF-binding-site deletion
E_00415	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr1	152432052	152433139	NA	CRNN	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas14 TF-binding-site deletion
E_00416	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr10	8287120	8287832	NA	LINC00708	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas44 TF-binding-site deletion
E_00417	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr10	8287120	8287832	NA	LINC00708	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas41 TF-binding-site deletion
E_00418	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr10	12490188	12491664	NA	CAMK1D	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis	enCRISPRi screen; enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; target gene expression analysis
E_00419	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr10	12490188	12491664	NA	CAMK1D	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas45 TF-binding-site deletion
E_00420	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr10	12490188	12491664	NA	CAMK1D	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas42 TF-binding-site deletion
E_00421	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr10	73648369	73649316	NA	PSAP	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas46 TF-binding-site deletion
E_00422	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr10	73648369	73649316	NA	PSAP	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas43 TF-binding-site deletion
E_00423	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr10	74090966	74091882	NA	DNAJB12	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas47 TF-binding-site deletion
E_00424	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr10	74090966	74091882	NA	DNAJB12	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas44 TF-binding-site deletion
E_00425	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr10	75625477	75626252	NA	CAMK2G	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas48 TF-binding-site deletion
E_00426	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr10	75625477	75626252	NA	CAMK2G	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas45 TF-binding-site deletion
E_00427	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr10	98459973	98460780	NA	PIK3AP1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis	enCRISPRi screen; enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; target gene expression analysis
E_00428	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr10	98459973	98460780	NA	PIK3AP1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas49 TF-binding-site deletion
E_00429	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr10	98459973	98460780	NA	PIK3AP1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas46 TF-binding-site deletion
E_00430	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr10	134401705	134403146	NA	INPP5A	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas50 TF-binding-site deletion
E_00431	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr10	134401705	134403146	NA	INPP5A	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas47 TF-binding-site deletion
E_00432	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr11	122614110	122615622	NA	UBASH3B	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas52 TF-binding-site deletion
E_00433	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr11	122614110	122615622	NA	UBASH3B	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas49 TF-binding-site deletion
E_00434	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr12	1905658	1906492	NA	CACNA2D4	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas53 TF-binding-site deletion
E_00435	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr12	1905658	1906492	NA	CACNA2D4	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas50 TF-binding-site deletion
E_00436	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr12	24967199	24968349	NA	BCAT1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas53 TF-binding-site deletion
E_00437	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr12	24967199	24968349	NA	BCAT1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas52 TF-binding-site deletion
E_00438	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr12	25429052	25430002	NA	KRAS	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas54 TF-binding-site deletion
E_00439	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr12	25429052	25430002	NA	KRAS	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas53 TF-binding-site deletion
E_00440	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr12	27702331	27703065	NA	PPFIBP1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas56 TF-binding-site deletion
E_00441	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr12	27702331	27703065	NA	PPFIBP1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas53 TF-binding-site deletion
E_00442	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr12	120729447	120730585	NA	SIRT4	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas57 TF-binding-site deletion
E_00443	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr12	120729447	120730585	NA	SIRT4	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas54 TF-binding-site deletion
E_00444	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr14	52487681	52488440	NA	NID2	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas58 TF-binding-site deletion
E_00445	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr14	52487681	52488440	NA	NID2	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas55 TF-binding-site deletion
E_00446	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr14	91254408	91255183	NA	TTC7B	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas59 TF-binding-site deletion
E_00447	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr14	91254408	91255183	NA	TTC7B	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas56 TF-binding-site deletion
E_00448	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr15	33493747	33494735	NA	FMN1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas63 TF-binding-site deletion
E_00449	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr15	33493747	33494735	NA	FMN1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas60 TF-binding-site deletion
E_00450	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr15	77196826	77197790	NA	SCAPER	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas61 TF-binding-site deletion
E_00451	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr15	77196826	77197790	NA	SCAPER	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas58 TF-binding-site deletion
E_00452	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr15	83517842	83518593	NA	HOMER2	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas62 TF-binding-site deletion
E_00453	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr15	83517842	83518593	NA	HOMER2	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas59 TF-binding-site deletion
E_00454	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr16	3208813	3209656	NA	ZNF213	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas64 TF-binding-site deletion
E_00455	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr16	3208813	3209656	NA	ZNF213	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas61 TF-binding-site deletion
E_00456	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr16	83972527	83973363	NA	OSGIN1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas65 TF-binding-site deletion
E_00457	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr16	83972527	83973363	NA	OSGIN1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas62 TF-binding-site deletion
E_00458	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr17	6656019	6656759	NA	XAF1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas66 TF-binding-site deletion
E_00459	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr17	6656019	6656759	NA	XAF1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas63 TF-binding-site deletion
E_00460	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr17	35447019	35447926	NA	ACACA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas67 TF-binding-site deletion
E_00461	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr17	35447019	35447926	NA	ACACA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas64 TF-binding-site deletion
E_00462	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr19	3434613	3435744	NA	NFIC	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas68 TF-binding-site deletion
E_00463	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr19	3434613	3435744	NA	NFIC	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas65 TF-binding-site deletion
E_00464	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr19	13278523	13279241	NA	IER2	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas69 TF-binding-site deletion
E_00465	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr19	13278523	13279241	NA	IER2	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas66 TF-binding-site deletion
E_00466	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr19	49389348	49390121	NA	TULP2	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas70 TF-binding-site deletion
E_00467	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr19	49389348	49390121	NA	TULP2	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas67 TF-binding-site deletion
E_00468	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr19	50860281	50861408	NA	NAPSA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas71 TF-binding-site deletion
E_00469	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr19	50860281	50861408	NA	NAPSA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas68 TF-binding-site deletion
E_00470	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr2	86262562	86264318	NA	POLR1A	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas19 TF-binding-site deletion
E_00471	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr2	86262562	86264318	NA	POLR1A	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas16 TF-binding-site deletion
E_00472	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr2	225795025	225795782	NA	DOCK10	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas20 TF-binding-site deletion
E_00473	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr2	225795025	225795782	NA	DOCK10	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas17 TF-binding-site deletion
E_00474	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr3	42705321	42706477	NA	ZBTB47	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas21 TF-binding-site deletion
E_00475	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr3	42705321	42706477	NA	ZBTB47	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas18 TF-binding-site deletion
E_00476	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr3	193859290	193860013	NA	HES1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas22 TF-binding-site deletion
E_00477	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr3	193859290	193860013	NA	HES1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas19 TF-binding-site deletion
E_00478	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr4	8169111	8170256	NA	ABLIM2	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas23 TF-binding-site deletion
E_00479	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr4	8169111	8170256	NA	ABLIM2	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas20 TF-binding-site deletion
E_00480	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr4	40552794	40553798	NA	RBM47	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas24 TF-binding-site deletion
E_00481	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr4	40552794	40553798	NA	RBM47	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas21 TF-binding-site deletion
E_00482	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr4	176867777	176868491	NA	GPM6A	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas27 TF-binding-site deletion
E_00483	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr4	176867777	176868491	NA	GPM6A	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas24 TF-binding-site deletion
E_00484	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr6	27470012	27470721	NA	ZNF184	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas28 TF-binding-site deletion
E_00485	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr6	27470012	27470721	NA	ZNF184	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas25 TF-binding-site deletion
E_00486	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr6	41673311	41674775	NA	TFEB	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas29 TF-binding-site deletion
E_00487	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr6	41673311	41674775	NA	TFEB	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas26 TF-binding-site deletion
E_00488	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr6	100795540	100797229	NA	SIM1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas30 TF-binding-site deletion
E_00489	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr6	100795540	100797229	NA	SIM1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas27 TF-binding-site deletion
E_00490	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr6	135504517	135505261	NA	MYB	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas31 TF-binding-site deletion
E_00491	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr6	135504517	135505261	NA	MYB	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas28 TF-binding-site deletion
E_00492	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr7	2933701	2934454	NA	CARD11	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas32 TF-binding-site deletion
E_00493	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr7	2933701	2934454	NA	CARD11	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas29 TF-binding-site deletion
E_00494	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr7	4764779	4765676	NA	FOXK1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas33 TF-binding-site deletion
E_00495	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr7	4764779	4765676	NA	FOXK1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas30 TF-binding-site deletion
E_00496	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr7	8215498	8216965	NA	ICA1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas34 TF-binding-site deletion
E_00497	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr7	8215498	8216965	NA	ICA1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas31 TF-binding-site deletion
E_00498	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr7	65958067	65959039	NA	RABGEF1P1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas35 TF-binding-site deletion
E_00499	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr7	65958067	65959039	NA	RABGEF1P1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas32 TF-binding-site deletion
E_00500	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr7	129649912	129650743	NA	ZC3HC1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas36 TF-binding-site deletion
E_00501	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr7	129649912	129650743	NA	ZC3HC1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas33 TF-binding-site deletion
E_00502	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr8	102120481	102121738	NA	SLEAR	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas37 TF-binding-site deletion
E_00503	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr8	102120481	102121738	NA	SLEAR	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas34 TF-binding-site deletion
E_00504	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr8	116660008	116661198	NA	TRPS1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas38 TF-binding-site deletion
E_00505	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr8	116660008	116661198	NA	TRPS1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas35 TF-binding-site deletion
E_00506	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr9	96928325	96929213	NA	MIRLET7A1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas40 TF-binding-site deletion
E_00507	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr9	96928325	96929213	NA	MIRLET7A1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas37 TF-binding-site deletion
E_00508	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr9	115625021	115625725	NA	SNX30	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas42 TF-binding-site deletion
E_00509	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr9	115625021	115625725	NA	SNX30	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas39 TF-binding-site deletion
E_00510	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr9	127882943	127884195	NA	SCAI	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas43 TF-binding-site deletion
E_00511	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr9	127882943	127884195	NA	SCAI	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas40 TF-binding-site deletion
E_00512	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23876121	23878188	NKX2-5	MYH7	Enhancer	Active	Normal	NA	NA	NA	heart left ventricle	UBERON:0002084	GM03348-derived human iPSC cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Regulatory variant functional assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Dual-luciferase reporter assay of MYH7-C2; allele-specific luciferase assay
E_00513	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23876121	23878188	NKX2-5	MYH7	Enhancer	Active	Normal	NA	NA	NA	heart left ventricle	UBERON:0002084	HL-1	CVCL_0303	cardiac muscle cell	CL:0000746	Enhancer activity assay; Regulatory variant functional assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Dual-luciferase reporter assay of MYH7-C2; allele-specific luciferase assay
E_00514	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr1	155937201	155938359	NA	LMNA	Enhancer	Active	Normal	NA	NA	NA	heart left ventricle	UBERON:0002084	GM03348-derived human iPSC cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; p300 ChIP-seq; cardiac TF ChIP-seq	Dual-luciferase reporter assay of LMNA-C1-1 in iPSC-CMs and HL-1 cells
E_00515	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr1	155937201	155938359	NA	LMNA	Enhancer	Active	Normal	NA	NA	NA	heart left ventricle	UBERON:0002084	HL-1	CVCL_0303	cardiac muscle cell	CL:0000746	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; p300 ChIP-seq; cardiac TF ChIP-seq	Dual-luciferase reporter assay of LMNA-C1-1 in iPSC-CMs and HL-1 cells
E_00516	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr1	156074366	156075480	NA	LMNA	Enhancer	Active	Normal	NA	NA	NA	heart left ventricle	UBERON:0002084	GM03348-derived human iPSC cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; p300 ChIP-seq; cardiac TF ChIP-seq	Dual-luciferase reporter assay of LMNA-C3-1 in iPSC-CMs and HL-1 cells
E_00517	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr1	156074366	156075480	NA	LMNA	Enhancer	Active	Normal	NA	NA	NA	heart left ventricle	UBERON:0002084	HL-1	CVCL_0303	cardiac muscle cell	CL:0000746	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; p300 ChIP-seq; cardiac TF ChIP-seq	Dual-luciferase reporter assay of LMNA-C3-1 in iPSC-CMs and HL-1 cells
E_00518	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr1	156093103	156094494	NA	LMNA	Enhancer	Active	Normal	NA	NA	NA	heart left ventricle	UBERON:0002084	GM03348-derived human iPSC cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; p300 ChIP-seq; cardiac TF ChIP-seq	Dual-luciferase reporter assay of LMNA-C4-2 in iPSC-CMs and HL-1 cells
E_00519	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr1	156093103	156094494	NA	LMNA	Enhancer	Active	Normal	NA	NA	NA	heart left ventricle	UBERON:0002084	HL-1	CVCL_0303	cardiac muscle cell	CL:0000746	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; p300 ChIP-seq; cardiac TF ChIP-seq	Dual-luciferase reporter assay of LMNA-C4-2 in iPSC-CMs and HL-1 cells
E_00520	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr1	156095724	156096574	NA	LMNA	Enhancer	Active	Normal	NA	NA	NA	heart left ventricle	UBERON:0002084	GM03348-derived human iPSC cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; p300 ChIP-seq; cardiac TF ChIP-seq	Dual-luciferase reporter assay of LMNA-C5 in iPSC-CMs and HL-1 cells
E_00521	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr1	156095724	156096574	NA	LMNA	Enhancer	Active	Normal	NA	NA	NA	heart left ventricle	UBERON:0002084	HL-1	CVCL_0303	cardiac muscle cell	CL:0000746	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; p300 ChIP-seq; cardiac TF ChIP-seq	Dual-luciferase reporter assay of LMNA-C5 in iPSC-CMs and HL-1 cells
E_00522	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr1	156099538	156100640	NA	LMNA	Enhancer	Active	Normal	NA	NA	NA	heart left ventricle	UBERON:0002084	GM03348-derived human iPSC cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; p300 ChIP-seq; cardiac TF ChIP-seq	Dual-luciferase reporter assay of LMNA-C6 in iPSC-CMs and HL-1 cells
E_00523	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr1	156099538	156100640	NA	LMNA	Enhancer	Active	Normal	NA	NA	NA	heart left ventricle	UBERON:0002084	HL-1	CVCL_0303	cardiac muscle cell	CL:0000746	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; p300 ChIP-seq; cardiac TF ChIP-seq	Dual-luciferase reporter assay of LMNA-C6 in iPSC-CMs and HL-1 cells
E_00524	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23871436	23872136	NA	MYH7	Enhancer	Active	Normal	NA	NA	NA	heart left ventricle	UBERON:0002084	GM03348-derived human iPSC cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; p300 ChIP-seq; cardiac TF ChIP-seq	Dual-luciferase reporter assay of MYH7-C1-4 in iPSC-CMs and HL-1 cells
E_00525	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23871436	23872136	NA	MYH7	Enhancer	Active	Normal	NA	NA	NA	heart left ventricle	UBERON:0002084	HL-1	CVCL_0303	cardiac muscle cell	CL:0000746	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; p300 ChIP-seq; cardiac TF ChIP-seq	Dual-luciferase reporter assay of MYH7-C1-4 in iPSC-CMs and HL-1 cells
E_00526	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr12	25398284	25400000	NA	KRAS	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay	enCRISPRi screen; enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq; targeted resequencing	Individual CRISPRi; CRISPR activation; expression analysis
E_00527	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr11	39392559	39393437	NA	NA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas51 TF-binding-site deletion
E_00528	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr11	39392559	39393437	NA	NA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas48 TF-binding-site deletion
E_00529	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr12	14409708	14410606	NA	NA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas51 TF-binding-site deletion
E_00530	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr15	70820443	70821348	NA	NA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas60 TF-binding-site deletion
E_00531	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr15	70820443	70821348	NA	NA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas57 TF-binding-site deletion
E_00532	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr2	61990869	61991991	NA	NA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas18 TF-binding-site deletion
E_00533	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr2	61990869	61991991	NA	NA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas15 TF-binding-site deletion
E_00534	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr4	107629151	107629921	NA	NA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas25 TF-binding-site deletion
E_00535	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr4	107629151	107629921	NA	NA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas22 TF-binding-site deletion
E_00536	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr4	139409505	139410233	NA	NA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas26 TF-binding-site deletion
E_00537	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr4	139409505	139410233	NA	NA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas23 TF-binding-site deletion
E_00538	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr8	126517993	126518698	NA	NA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas39 TF-binding-site deletion
E_00539	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr8	126517993	126518698	NA	NA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas36 TF-binding-site deletion
E_00540	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr9	107877035	107877852	NA	NA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas41 TF-binding-site deletion
E_00541	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr9	107877035	107877852	NA	NA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	bone marrow	UBERON:0002371	MKPL-1	CVCL_2116	malignant cell	CL:0001064	Disease-variant functional analysis; High-throughput functional CRE perturbation screen; candidate enhancer annotation	pooled enCRISPRi screen; pooled enCRISPRa screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; CRISPR-Cas38 TF-binding-site deletion
E_00542	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85479010	85480701	Npas4	Fos	Enhancer	Active	Normal	NA	NA	NA	cerebral cortex	UBERON:0000956	Primary mouse cortical neurons	NA	neuron	CL:0000540	TF binding assay; Enhancer chromatin-state assay; Enhancer RNA assay	NPAS4/CBP ChIP-seq; H3K4me1/H3K27ac ChIP-seq data integration; RNA-seq	Luciferase reporter assay; eRNA RT-qPCR
E_00543	2016	26595656	Stimulus-specific combinatorial functionality of neuronal c-fos enhancers	Mus musculus	mm10	chr12	85479010	85480701	Npas4	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Primary mouse cortical neurons	NA	neuron	CL:0000540	Stimulus-responsive enhancer characterization	RNA-seq; ChIP-seq and chromatin-state integration	Luciferase reporter assay; enhancer RNA RT-qPCR; no strong endogenous perturbation evidence
E_00544	2015	25381333	Functional characterization of CYP2D6 enhancer polymorphisms	Homo sapiens	hg19	chr22	42411544	42415106	NA	CYP2D6	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Human Primary Hepatocytes	NA	hepatocyte	CL:0000182	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 4C
E_00545	2015	25381333	Functional characterization of CYP2D6 enhancer polymorphisms	Homo sapiens	hg19	chr22	42411769	42414470	NA	CYP2D6	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Human Primary Hepatocytes	NA	hepatocyte	CL:0000182	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 4C
E_00546	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892600	127892962	SPI1	BIN1	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	hPSC-derived astrocyte	NA	astrocyte	CL:0000127	Negative cell-type-specificity control	RNA-seq	CRISPR-Cas9 enhancer deletion; Western blot; Flow cytometry
E_00547	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892600	127892962	SPI1	BIN1	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	hPSC-derived neuron	NA	neuron	CL:0000540	Negative cell-type-specificity control	RNA-seq	CRISPR-Cas9 enhancer deletion; Western blot; Flow cytometry
E_00548	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr11	122614110	122615622	NA	UBASH3B	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	3C
E_00549	2017	28260788	APOBEC signature mutation generates an oncogenic enhancer that drives LMO1 expression in T-ALL	Homo sapiens	hg19	chr11	8289240	8289522	MYB	LMO1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	breast	UBERON:0000310	MCF-10A	CVCL_0598	breast epithelial cell	NA	Enhancer activity assay	ChIP-seq	Luciferase reporter assay
E_00550	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr1	16160379	16162282	NA	SPEN-AS1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00551	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr1	24717819	24718917	NA	STPG1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00552	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr1	26827000	26828194	NA	HMGN2	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00553	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr1	90223243	90223945	NA	LRRC8C	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00554	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr1	92269671	92270441	NA	TGFBR3	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00555	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr1	92970067	92970871	NA	EVI5	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00556	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr1	152432052	152433139	NA	CRNN	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00557	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr10	8287120	8287832	NA	LINC00708	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00558	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr10	12490188	12491664	NA	CAMK1D	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00559	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr10	73648369	73649316	NA	PSAP	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00560	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr10	74090966	74091882	NA	DNAJB12	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00561	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr10	75625477	75626252	NA	CAMK2G	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00562	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr10	98459973	98460780	NA	PIK3AP1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00563	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr10	134401705	134403146	NA	INPP5A	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00564	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr12	1905658	1906492	NA	CACNA2D4	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00565	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr12	24967199	24968349	NA	BCAT1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00566	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr12	25429052	25430002	NA	KRAS	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00567	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr12	27702331	27703065	NA	PPFIBP1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00568	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr12	120729447	120730585	NA	SIRT4	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00569	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr14	52487681	52488440	NA	NID2	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00570	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr14	91254408	91255183	NA	TTC7B	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00571	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr15	33493747	33494735	NA	FMN1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00572	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr15	77196826	77197790	NA	SCAPER	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00573	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr15	83517842	83518593	NA	HOMER2	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00574	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr16	3208813	3209656	NA	ZNF213	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00575	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr16	83972527	83973363	NA	OSGIN1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00576	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr17	6656019	6656759	NA	XAF1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00577	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr17	35447019	35447926	NA	ACACA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00578	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr19	3434613	3435744	NA	NFIC	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00579	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr19	13278523	13279241	NA	IER2	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00580	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr19	49389348	49390121	NA	TULP2	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00581	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr19	50860281	50861408	NA	NAPSA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00582	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr2	86262562	86264318	NA	POLR1A	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00583	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr2	225795025	225795782	NA	DOCK10	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00584	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr3	42705321	42706477	NA	ZBTB47	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00585	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr3	193859290	193860013	NA	HES1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00586	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr4	8169111	8170256	NA	ABLIM2	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00587	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr4	40552794	40553798	NA	RBM47	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISCRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00588	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr4	176867777	176868491	NA	GPM6A	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00589	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr6	27470012	27470721	NA	ZNF184	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00590	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr6	41673311	41674775	NA	TFEB	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00591	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr6	100795540	100797229	NA	SIM1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00592	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr6	135504517	135505261	NA	MYB	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00593	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr7	2933701	2934454	NA	CARD11	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00594	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr7	4764779	4765676	NA	FOXK1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00595	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr7	8215498	8216965	NA	ICA1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00596	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr7	65958067	65959039	NA	RABGEF1P1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00597	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr7	129649912	129650743	NA	ZC3HC1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00598	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr8	102120481	102121738	NA	SLEAR	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00599	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr8	116660008	116661198	NA	TRPS1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00600	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr9	96928325	96929213	NA	MIRLET7A1	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00601	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr9	115625021	115625725	NA	SNX30	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00602	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr9	127882943	127884195	NA	SCAI	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00603	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr11	39392559	39393437	NA	NA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00604	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr12	14409708	14410606	NA	NA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00605	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr12	25538591	25539583	NA	NA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00606	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr15	70820443	70821348	NA	NA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00607	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr2	61990869	61991991	NA	NA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00608	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr4	107629151	107629921	NA	NA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00609	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr4	139409505	139410233	NA	NA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00610	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr8	126517993	126518698	NA	NA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00611	2020	32188707	Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies	Homo sapiens	hg19	chr9	107877035	107877852	NA	NA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Functional perturbation assay	enCRISPRa screen; enCRISPRi screen; targeted resequencing	CRISPR activation; CRISPR interference
E_00612	2026	41861825	Species-specific chromatin architecture and neurogenesis mediated by a human enhancer	Homo sapiens	hg38	chr3	186239308	186239606	ETV5	ETV5	Enhancer	Active	Normal	NA	NA	NA	cerebral cortex	UBERON:0000956	WA09-derived cortical organoid	NA	neural progenitor cell	CL:0011020	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis	scRNA-seq; RNA-seq; Hi-C; H3K27ac ChIP-seq; DNase-seq	CRISPR-Cas9 reciprocal HAR1984 replacement; dCas9-KRAB CRISPRi; RT-qPCR; Immunofluorescence; NanoLuc/Firefly luciferase reporter assay; ETV5 ChIP-qPCR; DNA-FISH
E_00613	2026	41861825	Species-specific chromatin architecture and neurogenesis mediated by a human enhancer	Homo sapiens	hg38	chr3	186239308	186239606	ETV5	TRA2B	Enhancer	Active	Normal	NA	NA	NA	cerebral cortex	UBERON:0000956	WA09-derived cortical organoid	NA	neural progenitor cell	CL:0011020	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis	scRNA-seq; RNA-seq; Hi-C; H3K27ac ChIP-seq; DNase-seq	CRISPR-Cas9 reciprocal HAR1984 replacement; dCas9-KRAB CRISPRi; RT-qPCR; Immunofluorescence; NanoLuc/Firefly luciferase reporter assay; ETV5 ChIP-qPCR; DNA-FISH
E_00614	2025	39704037	RUNX2 Phase Separation Mediates Long-Range Regulation Between Osteoporosis-Susceptibility Variant and XCR1 to Promote Osteoblast Differentiation	Homo sapiens	hg38	chr3	46186503	46187707	RUNX2	XCR1	Enhancer	Active	Disease	osteoporosis	MONDO:0005298	DOID:11476	bone element	UBERON:0001474	Primary human osteoblast	NA	osteoblast	CL:0000062	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis	GWAS; GTEx eQTL analysis; transcription-factor motif analysis	Dual-luciferase reporter assay; CRISPR-Cas9 enhancer deletion; 3C-qPCR; ChIP-qPCR; RT-qPCR; Western blot
E_00615	2025	39704037	RUNX2 Phase Separation Mediates Long-Range Regulation Between Osteoporosis-Susceptibility Variant and XCR1 to Promote Osteoblast Differentiation	Homo sapiens	hg38	chr3	46186503	46187707	RUNX2	XCR1	Enhancer	Active	Disease	osteoporosis	MONDO:0005298	DOID:11476	bone element	UBERON:0001474	MG-63	CVCL_0426	osteoblast	CL:0000062	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis	GWAS; GTEx eQTL analysis; transcription-factor motif analysis	Dual-luciferase reporter assay; CRISPR-Cas9 enhancer deletion; 3C-qPCR; ChIP-qPCR; RT-qPCR; Western blot; DNA FISH
E_00616	2014	25394790	Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element	Homo sapiens	hg19	chr1	47704954	47704983	MYB	TAL1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Jurkat	CVCL_0065	T cell	CL:0000084	Mutation-created oncogenic enhancer; TF recruitment; endogenous allele dependency	H3K27ac ChIP-seq; MYB/RUNX1/GATA3/TAL1/TCF12 ChIP-seq; RNA polymerase II and MED1 profiling; mutation sequencing	Luciferase reporter assay using 400-bp enhancer fragments; MYB siRNA; co-immunoprecipitation; allele-specific CRISPR-Cas9 deletion; qRT-PCR; immunoblotting
E_00617	2014	25394790	Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element	Homo sapiens	hg19	chr1	47704954	47704983	MYB	TAL1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	MOLT-3	CVCL_0624	T cell	CL:0000084	Mutation-created oncogenic enhancer; TF recruitment; endogenous allele dependency	H3K27ac ChIP-seq; MYB/RUNX1/GATA3/TAL1/TCF12 ChIP-seq; RNA polymerase II and MED1 profiling; mutation sequencing	Luciferase reporter assay using 400-bp enhancer fragments; MYB siRNA; co-immunoprecipitation; allele-specific CRISPR-Cas9 deletion; qRT-PCR; immunoblotting
E_00618	2014	25394790	Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element	Homo sapiens	hg19	chr1	47704954	47704983	RUNX1	TAL1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Jurkat	CVCL_0065	T cell	CL:0000084	Mutation-created oncogenic enhancer; TF recruitment; endogenous allele dependency	H3K27ac ChIP-seq; MYB/RUNX1/GATA3/TAL1/TCF12 ChIP-seq; RNA polymerase II and MED1 profiling; mutation sequencing	Luciferase reporter assay using 400-bp enhancer fragments; co-immunoprecipitation; allele-specific CRISPR-Cas9 deletion; qRT-PCR; immunoblotting
E_00619	2014	25394790	Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element	Homo sapiens	hg19	chr1	47704954	47704983	RUNX1	TAL1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	MOLT-3	CVCL_0624	T cell	CL:0000084	Mutation-created oncogenic enhancer; TF recruitment; endogenous allele dependency	H3K27ac ChIP-seq; MYB/RUNX1/GATA3/TAL1/TCF12 ChIP-seq; RNA polymerase II and MED1 profiling; mutation sequencing	Luciferase reporter assay using 400-bp enhancer fragments; co-immunoprecipitation; allele-specific CRISPR-Cas9 deletion; qRT-PCR; immunoblotting
E_00620	2014	25394790	Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element	Homo sapiens	hg19	chr1	47704954	47704983	GATA3	TAL1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Jurkat	CVCL_0065	T cell	CL:0000084	Mutation-created oncogenic enhancer; TF recruitment; endogenous allele dependency	H3K27ac ChIP-seq; MYB/RUNX1/GATA3/TAL1/TCF12 ChIP-seq; RNA polymerase II and MED1 profiling; mutation sequencing	Luciferase reporter assay using 400-bp enhancer fragments; co-immunoprecipitation; allele-specific CRISPR-Cas9 deletion; qRT-PCR; immunoblotting
E_00621	2014	25394790	Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element	Homo sapiens	hg19	chr1	47704954	47704983	GATA3	TAL1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	MOLT-3	CVCL_0624	T cell	CL:0000084	Mutation-created oncogenic enhancer; TF recruitment; endogenous allele dependency	H3K27ac ChIP-seq; MYB/RUNX1/GATA3/TAL1/TCF12 ChIP-seq; RNA polymerase II and MED1 profiling; mutation sequencing	Luciferase reporter assay using 400-bp enhancer fragments; co-immunoprecipitation; allele-specific CRISPR-Cas9 deletion; qRT-PCR; immunoblotting
E_00622	2014	25394790	Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element	Homo sapiens	hg19	chr1	47704954	47704983	TAL1	TAL1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Jurkat	CVCL_0065	T cell	CL:0000084	Mutation-created oncogenic enhancer; TF recruitment; endogenous allele dependency	H3K27ac ChIP-seq; MYB/RUNX1/GATA3/TAL1/TCF12 ChIP-seq; RNA polymerase II and MED1 profiling; mutation sequencing	Luciferase reporter assay using 400-bp enhancer fragments; co-immunoprecipitation; allele-specific CRISPR-Cas9 deletion; qRT-PCR; immunoblotting
E_00623	2014	25394790	Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element	Homo sapiens	hg19	chr1	47704954	47704983	TAL1	TAL1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	MOLT-3	CVCL_0624	T cell	CL:0000084	Mutation-created oncogenic enhancer; TF recruitment; endogenous allele dependency	H3K27ac ChIP-seq; MYB/RUNX1/GATA3/TAL1/TCF12 ChIP-seq; RNA polymerase II and MED1 profiling; mutation sequencing	Luciferase reporter assay using 400-bp enhancer fragments; co-immunoprecipitation; allele-specific CRISPR-Cas9 deletion; qRT-PCR; immunoblotting
E_00624	2014	25394790	Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element	Homo sapiens	hg19	chr1	47704954	47704983	TCF12	TAL1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Jurkat	CVCL_0065	T cell	CL:0000084	Mutation-created oncogenic enhancer; TF recruitment; endogenous allele dependency	H3K27ac ChIP-seq; MYB/RUNX1/GATA3/TAL1/TCF12 ChIP-seq; RNA polymerase II and MED1 profiling; mutation sequencing	Luciferase reporter assay using 400-bp enhancer fragments; co-immunoprecipitation; allele-specific CRISPR-Cas9 deletion; qRT-PCR; immunoblotting
E_00625	2014	25394790	Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element	Homo sapiens	hg19	chr1	47704954	47704983	TCF12	TAL1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	MOLT-3	CVCL_0624	T cell	CL:0000084	Mutation-created oncogenic enhancer; TF recruitment; endogenous allele dependency	H3K27ac ChIP-seq; MYB/RUNX1/GATA3/TAL1/TCF12 ChIP-seq; RNA polymerase II and MED1 profiling; mutation sequencing	Luciferase reporter assay using 400-bp enhancer fragments; co-immunoprecipitation; allele-specific CRISPR-Cas9 deletion; qRT-PCR; immunoblotting
E_00626	2026	41861825	Species-specific chromatin architecture and neurogenesis mediated by a human enhancer	Homo sapiens	hg38	chr3	186239308	186239606	ETV5	ETV5	Enhancer	Active	Normal	NA	NA	NA	cerebral cortex	UBERON:0000956	8799-derived neural progenitor cells	NA	neural progenitor cell	CL:0011020	Enhancer activity assay; Chromatin interaction assay; Disease-variant functional analysis; TF regulatory assay	Hi-C; H3K27ac ChIP-seq; DNase-seq	NanoLuc/Firefly luciferase reporter assay; ETV5 overexpression transactivation assay; DNA-FISH; ETV5 ChIP-qPCR
E_00627	2026	41861825	Species-specific chromatin architecture and neurogenesis mediated by a human enhancer	Homo sapiens	hg38	chr3	186239308	186239606	ETV5	TRA2B	Enhancer	Active	Normal	NA	NA	NA	cerebral cortex	UBERON:0000956	8799-derived neural progenitor cells	NA	neural progenitor cell	CL:0011020	Enhancer activity assay; Chromatin interaction assay; Disease-variant functional analysis; TF regulatory assay	Hi-C; H3K27ac ChIP-seq; DNase-seq	NanoLuc/Firefly luciferase reporter assay; ETV5 overexpression transactivation assay; DNA-FISH; ETV5 ChIP-qPCR
E_00628	2025	39704037	RUNX2 Phase Separation Mediates Long-Range Regulation Between Osteoporosis-Susceptibility Variant and XCR1 to Promote Osteoblast Differentiation	Homo sapiens	hg38	chr3	46186503	46187707	RUNX2	XCR1	Enhancer	Active	Disease	osteoporosis	MONDO:0005298	DOID:11476	bone element	UBERON:0001474	hFOB1.19	NA	osteoblast	CL:0000062	Enhancer activity assay; TF binding assay; Disease-variant functional analysis	GWAS; GTEx eQTL analysis; transcription-factor motif analysis	Dual-luciferase reporter assay; ChIP-qPCR; RT-qPCR
E_00629	2017	29078395	STAT5-mediated chromatin interactions in superenhancers activate IL-2 highly inducible genes: Functional dissection of the Il2ra gene locus	Mus musculus	mm39	chr2	11661224	11661284	Stat5b	Il2ra	Super-enhancer	Active	Normal	NA	NA	NA	blood/lymphoid tissue	NA	primary mouse activated CD4+ T cells	NA	T cell	CL:0000084	TF binding assay; Chromatin interaction assay; Endogenous functional perturbation assay	STAT5/STAT3/CTCF/H3K27ac/H3K4me3 ChIP-seq; RNA polymerase II ChIA-PET; ChIA-PET	CRISPR/Cas9 deletion of IN1a GAS element in mice; targeted sequencing/genotyping; Luciferase reporter assay; RT-qPCR; Flow cytometry; CRISPR-Cas9
E_00630	2017	29078395	STAT5-mediated chromatin interactions in superenhancers activate IL-2 highly inducible genes: Functional dissection of the Il2ra gene locus	Mus musculus	mm39	chr2	11664841	11664854	Stat5b	Il2ra	Enhancer	Active	Normal	NA	NA	NA	blood/lymphoid tissue	NA	primary mouse activated CD4+ T cells	NA	T cell	CL:0000084	TF binding assay; Chromatin interaction assay; Endogenous functional perturbation assay	STAT5/STAT3/CTCF/H3K27ac/H3K4me3 ChIP-seq; RNA polymerase II ChIA-PET; ChIA-PET	CRISPR/Cas9 deletion of IN1b GAS element in mice; targeted sequencing/genotyping; Luciferase reporter assay; RT-qPCR; Flow cytometry; CRISPR-Cas9
E_00631	2017	29078395	STAT5-mediated chromatin interactions in superenhancers activate IL-2 highly inducible genes: Functional dissection of the Il2ra gene locus	Mus musculus	mm39	chr2	11661224	11661284	Stat5b	Il2ra	Super-enhancer	Active	Normal	NA	NA	NA	blood/lymphoid tissue	NA	mutant mouse T cells	NA	T cell	CL:0000084	TF binding assay; Chromatin interaction assay; Endogenous functional perturbation assay	STAT5/STAT3/CTCF/H3K27ac/H3K4me3 ChIP-seq; RNA polymerase II ChIA-PET; ChIA-PET	CRISPR/Cas9 deletion of IN1a GAS element in mice; targeted sequencing/genotyping; Luciferase reporter assay; RT-qPCR; Flow cytometry; CRISPR-Cas9
E_00632	2017	29078395	STAT5-mediated chromatin interactions in superenhancers activate IL-2 highly inducible genes: Functional dissection of the Il2ra gene locus	Mus musculus	mm39	chr2	11664841	11664854	Stat5b	Il2ra	Enhancer	Active	Normal	NA	NA	NA	blood/lymphoid tissue	NA	mutant mouse T cells	NA	T cell	CL:0000084	TF binding assay; Chromatin interaction assay; Endogenous functional perturbation assay	STAT5/STAT3/CTCF/H3K27ac/H3K4me3 ChIP-seq; RNA polymerase II ChIA-PET; ChIA-PET	CRISPR/Cas9 deletion of IN1b GAS element in mice; targeted sequencing/genotyping; Luciferase reporter assay; RT-qPCR; Flow cytometry; CRISPR-Cas9
E_00633	2017	29078395	STAT5-mediated chromatin interactions in superenhancers activate IL-2 highly inducible genes: Functional dissection of the Il2ra gene locus	Mus musculus	mm10	chr8	11564419	11614821	Stat3	Il2ra	Super-enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	T Cell	NA	T cell	CL:0000084	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; RNA-seq; ChIA-PET	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_00634	2017	29078395	STAT5-mediated chromatin interactions in superenhancers activate IL-2 highly inducible genes: Functional dissection of the Il2ra gene locus	Mus musculus	mm10	chr8	11564419	11614821	Stat5a	Il2ra	Super-enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	T Cell	NA	T cell	CL:0000084	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; RNA-seq; ChIA-PET	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_00635	2026	42366973	Engineered Heart Tissues Facilitate Noncoding Variant Studies in Cardiomyopathy	Homo sapiens	hg38	chr10	112731665	112732664	NA	TCF7L2	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart	UBERON:0000948	engineered heart tissue cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Enhancer reporter assay; noncoding variant functional assay	single-cell RNA-seq; cell-type-resolved ATAC-seq; cardiomyopathy GWAS fine-mapping; Hi-C/chromatin-contact integration; RNA-seq; GWAS	Dual-luciferase reporter assay of the article-described 1-kb genomic fragment centered on rs10885378; rs10885378-T showed enhancer activity whereas the C allele was not significantly different from the gene-desert control; Start/End denote the reporter fragment rather than an endogenous enhancer boundary; CRISPR-Cas9 endogenous deletion/editing; Allele-specific reporter assay; Reporter assay
E_00636	2026	42366973	Engineered Heart Tissues Facilitate Noncoding Variant Studies in Cardiomyopathy	Homo sapiens	hg38	chr8	11941645	11942644	NA	GATA4	Enhancer	Active	Disease	dilated cardiomyopathy	MONDO:0005021	DOID:12930	heart	UBERON:0000948	engineered heart tissue cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Enhancer reporter assay; noncoding variant functional assay	single-cell RNA-seq; cell-type-resolved ATAC-seq; cardiomyopathy GWAS fine-mapping; Hi-C/chromatin-contact integration; RNA-seq; GWAS	Dual-luciferase reporter assay of the article-described 1-kb genomic fragment centered on rs13260325; Start/End denote the experimentally assayed 1000-bp reporter fragment rather than an endogenous chromatin enhancer boundary; CRISPR-Cas9 endogenous deletion/editing; Allele-specific reporter assay; Reporter assay
E_00637	2026	42366973	Engineered Heart Tissues Facilitate Noncoding Variant Studies in Cardiomyopathy	Homo sapiens	hg38	chr3	14229951	14235950	NA	GRIP2	Enhancer	Active	Disease	dilated cardiomyopathy	MONDO:0005021	DOID:12930	heart	UBERON:0000948	human iPSC-derived cardiomyocytes in engineered heart tissues	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Haplotype-resolved enhancer reporter assay; endogenous CRISPR deletion assay; target-gene expression profiling; engineered heart tissue functional assay	single-cell RNA-seq; cell-type-resolved ATAC-seq; cardiomyopathy GWAS fine-mapping; Hi-C/chromatin-contact integration; bulk RNA-seq; RNA-seq; GWAS	Haplotype-resolved dual-luciferase reporter assay; synthetic haplotype mutagenesis; CRISPR/Cas9 approximately 6-kb endogenous enhancer deletion; PCR; Sanger sequencing; engineered heart tissue contractility assay; Start/End are a standardized 6000-bp interval centered on rs6807275 at hg38 chr3:14232951 and are not exact CRISPR guide breakpoints; CRISPR-Cas9 endogenous deletion/editing; Allele-specific reporter assay; Reporter assay
E_00638	2026	42366973	Engineered Heart Tissues Facilitate Noncoding Variant Studies in Cardiomyopathy	Homo sapiens	hg38	chr3	14229951	14235950	NA	GRIP2	Enhancer	Active	Disease	dilated cardiomyopathy	MONDO:0005021	DOID:12930	heart	UBERON:0000948	primary human cardiac fibroblasts present in EHTs	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Haplotype-resolved enhancer reporter assay; endogenous CRISPR deletion assay; target-gene expression profiling; engineered heart tissue functional assay	single-cell RNA-seq; cell-type-resolved ATAC-seq; cardiomyopathy GWAS fine-mapping; Hi-C/chromatin-contact integration; bulk RNA-seq; RNA-seq; GWAS	Haplotype-resolved dual-luciferase reporter assay; synthetic haplotype mutagenesis; CRISPR/Cas9 approximately 6-kb endogenous enhancer deletion; PCR; Sanger sequencing; engineered heart tissue contractility assay; Start/End are a standardized 6000-bp interval centered on rs6807275 at hg38 chr3:14232951 and are not exact CRISPR guide breakpoints; CRISPR-Cas9 endogenous deletion/editing; Allele-specific reporter assay; Reporter assay
E_00639	2026	42366973	Engineered Heart Tissues Facilitate Noncoding Variant Studies in Cardiomyopathy	Homo sapiens	hg38	chr3	14229951	14235950	NA	SLC6A6	Enhancer	Active	Disease	dilated cardiomyopathy	MONDO:0005021	DOID:12930	heart	UBERON:0000948	human iPSC-derived cardiomyocytes in engineered heart tissues	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Haplotype-resolved enhancer reporter assay; endogenous CRISPR deletion assay; target-gene expression profiling; engineered heart tissue functional assay	single-cell RNA-seq; cell-type-resolved ATAC-seq; cardiomyopathy GWAS fine-mapping; Hi-C/chromatin-contact integration; bulk RNA-seq; RNA-seq; GWAS	Haplotype-resolved dual-luciferase reporter assay; synthetic haplotype mutagenesis; CRISPR/Cas9 approximately 6-kb endogenous enhancer deletion; PCR; Sanger sequencing; engineered heart tissue contractility assay; Start/End are a standardized 6000-bp interval centered on rs6807275 at hg38 chr3:14232951 and are not exact CRISPR guide breakpoints; CRISPR-Cas9 endogenous deletion/editing; Allele-specific reporter assay; Reporter assay
E_00640	2026	42366973	Engineered Heart Tissues Facilitate Noncoding Variant Studies in Cardiomyopathy	Homo sapiens	hg38	chr3	14229951	14235950	NA	SLC6A6	Enhancer	Active	Disease	dilated cardiomyopathy	MONDO:0005021	DOID:12930	heart	UBERON:0000948	primary human cardiac fibroblasts present in EHTs	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Haplotype-resolved enhancer reporter assay; endogenous CRISPR deletion assay; target-gene expression profiling; engineered heart tissue functional assay	single-cell RNA-seq; cell-type-resolved ATAC-seq; cardiomyopathy GWAS fine-mapping; Hi-C/chromatin-contact integration; bulk RNA-seq; RNA-seq; GWAS	Haplotype-resolved dual-luciferase reporter assay; synthetic haplotype mutagenesis; CRISPR/Cas9 approximately 6-kb endogenous enhancer deletion; PCR; Sanger sequencing; engineered heart tissue contractility assay; Start/End are a standardized 6000-bp interval centered on rs6807275 at hg38 chr3:14232951 and are not exact CRISPR guide breakpoints; CRISPR-Cas9 endogenous deletion/editing; Allele-specific reporter assay; Reporter assay
E_00641	2016	26809507	Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model	Mus musculus	mm10	chr7	35156536	35156974	Tal1	Cebpa	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	HPC-7	CVCL_RB19	hematopoietic multipotent progenitor cell	CL:0000837	Enhancer activity assay; Chromatin interaction assay	17-factor ChIP-seq; histone-modification ChIP-seq; DNase-seq; RNA-seq; Hi-C; promoter capture Hi-C	F0 transgenic mouse LacZ reporter assay; X-gal staining; histological analysis
E_00642	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg38	chrX	48782664	48783392	GATA1	GATA1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Endogenous enhancer perturbation	CRISPRi tiling screen; DNase-seq data integration; H3K27ac ChIP-seq data integration; GATA1 ChIP-seq data integration; in situ Hi-C data integration	Individual dCas9-KRAB CRISPRi; RT-qPCR; plasmid-based reporter assay; competitive growth assay; CRISPRi
E_00643	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg38	chrX	48782664	48783392	GATA1	HDAC6	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Endogenous enhancer perturbation	CRISPRi tiling screen; DNase-seq data integration; H3K27ac ChIP-seq data integration; GATA1 ChIP-seq data integration; in situ Hi-C data integration	Individual dCas9-KRAB CRISPRi; RT-qPCR; plasmid-based reporter assay; competitive growth assay; CRISPRi
E_00644	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg38	chr8	127898362	127899967	NA	MYC	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Endogenous enhancer perturbation	CRISPRi tiling screen; DNase-seq data integration; H3K27ac ChIP-seq data integration; in situ Hi-C data integration; ChIA-PET data integration	Individual dCas9-KRAB CRISPRi; RT-qPCR; plasmid-based reporter assay; competitive growth assay; CRISPRi
E_00645	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg38	chr8	127960009	127960984	NA	MYC	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Endogenous enhancer perturbation	CRISPRi tiling screen; DNase-seq data integration; H3K27ac ChIP-seq data integration; in situ Hi-C data integration; ChIA-PET data integration	Individual dCas9-KRAB CRISPRi; RT-qPCR; plasmid-based reporter assay; CRISPR-Cas9 genomic deletion; allele-specific expression assay; competitive growth assay; CRISPRi
E_00646	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg38	chr8	128044721	128046192	NA	MYC	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Endogenous enhancer perturbation	CRISPRi tiling screen; DNase-seq data integration; H3K27ac ChIP-seq data integration; in situ Hi-C data integration; ChIA-PET data integration	Individual dCas9-KRAB CRISPRi; RT-qPCR; plasmid-based reporter assay; CRISPR-Cas9 genomic deletion; allele-specific expression assay; competitive growth assay; CRISPRi
E_00647	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg38	chr8	128048231	128050347	NA	MYC	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Endogenous enhancer perturbation	CRISPRi tiling screen; DNase-seq data integration; H3K27ac ChIP-seq data integration; in situ Hi-C data integration; ChIA-PET data integration	Individual dCas9-KRAB CRISPRi; RT-qPCR; plasmid-based reporter assay; CRISPR-Cas9 genomic deletion; allele-specific expression assay; competitive growth assay; CRISPRi
E_00648	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg38	chr8	129581780	129583797	NA	MYC	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Endogenous enhancer perturbation	CRISPRi tiling screen; DNase-seq data integration; H3K27ac ChIP-seq data integration; in situ Hi-C data integration; ChIA-PET data integration	Individual dCas9-KRAB CRISPRi; RT-qPCR; plasmid-based reporter assay; competitive growth assay; CRISPRi
E_00649	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg38	chr8	129688360	129690572	NA	MYC	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Endogenous enhancer perturbation	CRISPRi tiling screen; DNase-seq data integration; H3K27ac ChIP-seq data integration; in situ Hi-C data integration; ChIA-PET data integration	Individual dCas9-KRAB CRISPRi; RT-qPCR; plasmid-based reporter assay; competitive growth assay; CRISPRi
E_00650	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg38	chr8	129691425	129693640	NA	MYC	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Endogenous enhancer perturbation	CRISPRi tiling screen; DNase-seq data integration; H3K27ac ChIP-seq data integration; in situ Hi-C data integration; ChIA-PET data integration	Individual dCas9-KRAB CRISPRi; RT-qPCR; plasmid-based reporter assay; competitive growth assay; CRISPRi
E_00651	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg38	chrX	48800418	48801257	NA	GATA1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Endogenous enhancer perturbation	CRISPRi tiling screen; DNase-seq data integration; H3K27ac ChIP-seq data integration; in situ Hi-C data integration	Individual dCas9-KRAB CRISPRi; RT-qPCR; plasmid-based reporter assay; competitive growth assay; CRISPRi
E_00652	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg38	chrX	48800418	48801257	NA	HDAC6	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Endogenous enhancer perturbation	CRISPRi tiling screen; DNase-seq data integration; H3K27ac ChIP-seq data integration; in situ Hi-C data integration	Individual dCas9-KRAB CRISPRi; RT-qPCR; plasmid-based reporter assay; competitive growth assay; CRISPRi
E_00653	2026	42366973	Engineered Heart Tissues Facilitate Noncoding Variant Studies in Cardiomyopathy	Homo sapiens	hg38	chr10	112731665	112732664	NA	TCF7L2	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart	UBERON:0000948	human iPSC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Enhancer reporter assay; noncoding variant functional assay	single-cell RNA-seq; cell-type-resolved ATAC-seq; cardiomyopathy GWAS fine-mapping; Hi-C/chromatin-contact integration; RNA-seq; GWAS	Dual-luciferase reporter assay of the article-described 1-kb genomic fragment centered on rs10885378; rs10885378-T showed enhancer activity whereas the C allele was not significantly different from the gene-desert control; Start/End denote the reporter fragment rather than an endogenous enhancer boundary; CRISPR-Cas9 endogenous deletion/editing; Allele-specific reporter assay; Reporter assay
E_00654	2026	42366973	Engineered Heart Tissues Facilitate Noncoding Variant Studies in Cardiomyopathy	Homo sapiens	hg38	chr8	11941645	11942644	NA	GATA4	Enhancer	Active	Disease	dilated cardiomyopathy	MONDO:0005021	DOID:12930	heart	UBERON:0000948	human iPSC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Enhancer reporter assay; noncoding variant functional assay	single-cell RNA-seq; cell-type-resolved ATAC-seq; cardiomyopathy GWAS fine-mapping; Hi-C/chromatin-contact integration; RNA-seq; GWAS	Dual-luciferase reporter assay of the article-described 1-kb genomic fragment centered on rs13260325; Start/End denote the experimentally assayed 1000-bp reporter fragment rather than an endogenous chromatin enhancer boundary; CRISPR-Cas9 endogenous deletion/editing; Allele-specific reporter assay; Reporter assay
E_00655	2026	42366973	Engineered Heart Tissues Facilitate Noncoding Variant Studies in Cardiomyopathy	Homo sapiens	hg38	chr17	66306034	66307033	NA	PRKCA	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart	UBERON:0000948	engineered heart tissue cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Allele-specific enhancer reporter assay; noncoding variant functional assay	single-cell RNA-seq; cell-type-resolved ATAC-seq; cardiomyopathy GWAS fine-mapping; GTEx left-ventricle cis-eQTL analysis; RNA-seq; GWAS	Dual-luciferase reporter assay of the article-described 1-kb genomic fragment centered on rs12601850; Allele-specific reporter assay; Start/End denote the experimentally assayed 1000-bp reporter fragment rather than an endogenous chromatin enhancer boundary; CRISPR-Cas9 endogenous deletion/editing; Reporter assay
E_00656	2026	42366973	Engineered Heart Tissues Facilitate Noncoding Variant Studies in Cardiomyopathy	Homo sapiens	hg38	chr17	66307175	66308174	NA	PRKCA	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart	UBERON:0000948	engineered heart tissue cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Allele-specific enhancer reporter assay; noncoding variant functional assay	single-cell RNA-seq; cell-type-resolved ATAC-seq; cardiomyopathy GWAS fine-mapping; GTEx left-ventricle cis-eQTL analysis; RNA-seq; GWAS	Dual-luciferase reporter assay of the article-described 1-kb genomic fragment centered on rs9892651; Allele-specific reporter assay; the variant did not overlap an OCR in the study datasets; Start/End denote the reporter fragment rather than an endogenous enhancer boundary; CRISPR-Cas9 endogenous deletion/editing; Reporter assay
E_00657	2026	42366973	Engineered Heart Tissues Facilitate Noncoding Variant Studies in Cardiomyopathy	Homo sapiens	hg38	chr17	66306034	66307033	NA	PRKCA	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart	UBERON:0000948	human iPSC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Allele-specific enhancer reporter assay; noncoding variant functional assay	single-cell RNA-seq; cell-type-resolved ATAC-seq; cardiomyopathy GWAS fine-mapping; GTEx left-ventricle cis-eQTL analysis; RNA-seq; GWAS	Dual-luciferase reporter assay of the article-described 1-kb genomic fragment centered on rs12601850; Allele-specific reporter assay; Start/End denote the experimentally assayed 1000-bp reporter fragment rather than an endogenous chromatin enhancer boundary; CRISPR-Cas9 endogenous deletion/editing; Reporter assay
E_00658	2026	42366973	Engineered Heart Tissues Facilitate Noncoding Variant Studies in Cardiomyopathy	Homo sapiens	hg38	chr17	66307175	66308174	NA	PRKCA	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart	UBERON:0000948	human iPSC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Allele-specific enhancer reporter assay; noncoding variant functional assay	single-cell RNA-seq; cell-type-resolved ATAC-seq; cardiomyopathy GWAS fine-mapping; GTEx left-ventricle cis-eQTL analysis; RNA-seq; GWAS	Dual-luciferase reporter assay of the article-described 1-kb genomic fragment centered on rs9892651; Allele-specific reporter assay; the variant did not overlap an OCR in the study datasets; Start/End denote the reporter fragment rather than an endogenous enhancer boundary; CRISPR-Cas9 endogenous deletion/editing; Reporter assay
E_00659	2016	26809507	Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model	Mus musculus	mm10	chr4	115040426	115042426	Cbfa2t3	Tal1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HPC-7	CVCL_RB19	NA	NA	Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; Hi-C	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_00660	2016	26809507	Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model	Mus musculus	mm10	chr4	115040426	115042426	Cebpa	Tal1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HPC-7	CVCL_RB19	NA	NA	Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; Hi-C	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_00661	2016	26809507	Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model	Mus musculus	mm10	chr4	115040426	115042426	Cebpb	Tal1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HPC-7	CVCL_RB19	NA	NA	Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; Hi-C	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_00662	2016	26809507	Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model	Mus musculus	mm10	chr4	115040426	115042426	E2f4	Tal1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HPC-7	CVCL_RB19	NA	NA	Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; Hi-C	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_00663	2016	26809507	Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model	Mus musculus	mm10	chr4	115040426	115042426	Egr1	Tal1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HPC-7	CVCL_RB19	NA	NA	Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; Hi-C	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_00664	2016	26809507	Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model	Mus musculus	mm10	chr4	115040426	115042426	Elf1	Tal1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HPC-7	CVCL_RB19	NA	NA	Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; Hi-C	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_00665	2016	26809507	Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model	Mus musculus	mm10	chr4	115040426	115042426	Fos	Tal1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HPC-7	CVCL_RB19	NA	NA	Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; Hi-C	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_00666	2016	26809507	Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model	Mus musculus	mm10	chr4	115040426	115042426	Jun	Tal1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HPC-7	CVCL_RB19	NA	NA	Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; Hi-C	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_00667	2016	26809507	Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model	Mus musculus	mm10	chr4	115040426	115042426	Ldb1	Tal1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HPC-7	CVCL_RB19	NA	NA	Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; Hi-C	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_00668	2016	26809507	Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model	Mus musculus	mm10	chr4	115040426	115042426	Max	Tal1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HPC-7	CVCL_RB19	NA	NA	Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; Hi-C	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_00669	2016	26809507	Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model	Mus musculus	mm10	chr4	115040426	115042426	Myb	Tal1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HPC-7	CVCL_RB19	NA	NA	Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; Hi-C	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_00670	2016	26809507	Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model	Mus musculus	mm10	chr4	115040426	115042426	Myc	Tal1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HPC-7	CVCL_RB19	NA	NA	Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; Hi-C	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_00671	2016	26809507	Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model	Mus musculus	mm10	chr4	115040426	115042426	Nfe2	Tal1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HPC-7	CVCL_RB19	NA	NA	Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; Hi-C	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_00672	2016	26809507	Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model	Mus musculus	mm10	chr4	115040426	115042426	Rad21	Tal1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HPC-7	CVCL_RB19	NA	NA	Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; Hi-C	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_00673	2016	26809507	Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model	Mus musculus	mm10	chr4	115040426	115042426	Stat3	Tal1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HPC-7	CVCL_RB19	NA	NA	Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; Hi-C	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_00674	2016	26809507	Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model	Mus musculus	mm10	chr4	115040426	115042426	Trp53	Tal1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HPC-7	CVCL_RB19	NA	NA	Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; Hi-C	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_00675	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg38	chr8	127898362	127899967	NA	MYC	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Endogenous enhancer perturbation; Genome-scale enhancer-target functional perturbation assay	pooled dCas9-KRAB CRISPRi tiling screen; chromatin-accessibility and TF-occupancy integration	single-guide CRISPRi validation; Luciferase reporter; qRT-PCR; genomic enhancer perturbation; CRISPRi
E_00676	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg38	chr8	127960009	127960984	NA	MYC	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Endogenous enhancer perturbation; Genome-scale enhancer-target functional perturbation assay	pooled dCas9-KRAB CRISPRi tiling screen; chromatin-accessibility and TF-occupancy integration	single-guide CRISPRi; Luciferase reporter; genomic enhancer deletion; qRT-PCR; allele-specific expression validation; CRISPRi
E_00677	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg38	chr8	128044721	128046192	NA	MYC	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Endogenous enhancer perturbation; Genome-scale enhancer-target functional perturbation assay	pooled dCas9-KRAB CRISPRi tiling screen; chromatin-accessibility and TF-occupancy integration	single-guide CRISPRi; Luciferase reporter; genomic enhancer deletion; qRT-PCR; allele-specific expression validation; CRISPRi
E_00678	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg38	chr8	128048231	128050347	NA	MYC	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Endogenous enhancer perturbation; Genome-scale enhancer-target functional perturbation assay	pooled dCas9-KRAB CRISPRi tiling screen; chromatin-accessibility and TF-occupancy integration	single-guide CRISPRi; Luciferase reporter; genomic enhancer deletion; qRT-PCR; allele-specific expression validation; CRISPRi
E_00679	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg38	chr8	129581780	129583797	NA	MYC	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Endogenous enhancer perturbation; Genome-scale enhancer-target functional perturbation assay	pooled dCas9-KRAB CRISPRi tiling screen; chromatin-accessibility and TF-occupancy integration	single-guide CRISPRi validation; Luciferase reporter; qRT-PCR; CRISPRi
E_00680	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg38	chr8	129688360	129690572	NA	MYC	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Endogenous enhancer perturbation; Genome-scale enhancer-target functional perturbation assay	pooled dCas9-KRAB CRISPRi tiling screen; chromatin-accessibility and TF-occupancy integration	single-guide CRISPRi validation; Luciferase reporter; qRT-PCR; CRISPRi
E_00681	2016	27708057	Systematic mapping of functional enhancer-promoter connections with CRISPR interference	Homo sapiens	hg38	chr8	129691425	129693640	NA	MYC	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Endogenous enhancer perturbation; Genome-scale enhancer-target functional perturbation assay	pooled dCas9-KRAB CRISPRi tiling screen; chromatin-accessibility and TF-occupancy integration	single-guide CRISPRi validation; Luciferase reporter; qRT-PCR; CRISPRi
E_00682	2016	26809507	Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model	Mus musculus	mm10	chr19	45050000	45051000	Tal1	Hhex	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	HPC-7	CVCL_RB19	hematopoietic progenitor cell	NA	Enhancer activity assay	ChIP-seq	Transgenic reporter assay
E_00683	2024	39312195	Selective Enhancer Gain-of-Function Deregulates MYC Expression in Multiple Myeloma	Homo sapiens	hg38	chr8	128264000	128277000	IRF4	MYC	Enhancer	Active	Disease	plasma cell myeloma	MONDO:0009693	DOID:9538	blood	UBERON:0000178	ANBL-6	CVCL_5425	plasma cell	CL:0000786	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	Pooled CRISPRi tiling screen; H3K27ac ChIP-seq; IRF4 ChIP-seq; Micro-C	Individual CRISPRi; CRISPR-Cas9 IRF4-binding-site mutagenesis; Dual-luciferase reporter assay; qRT-PCR
E_00684	2024	39312195	Selective Enhancer Gain-of-Function Deregulates MYC Expression in Multiple Myeloma	Homo sapiens	hg38	chr8	128264000	128277000	MAF	MYC	Enhancer	Active	Disease	plasma cell myeloma	MONDO:0009693	DOID:9538	blood	UBERON:0000178	ANBL-6	CVCL_5425	plasma cell	CL:0000786	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	Pooled CRISPRi tiling screen; H3K27ac ChIP-seq; MAF ChIP-seq; Micro-C	Individual CRISPRi; CRISPR-Cas9 MAF-binding-site mutagenesis; Dual-luciferase reporter assay; qRT-PCR
E_00685	2023	36803948	eRNA profiling uncovers the enhancer landscape of oesophageal adenocarcinoma and reveals new deregulated pathways	Homo sapiens	hg38	chr17	41792666	41793322	KLF5	GRB7	Enhancer	Active	Disease	esophageal adenocarcinoma	MONDO:0005028	DOID:4914	esophagus	UBERON:0001043	OE19	CVCL_1622	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ATAC-seq; RNA-seq; ChIP-seq, Hi-C; RNA-seq	Luciferase reporter assay, CRISPR knockout/CRISPRi; RT-qPCR; Western blot
E_00686	2023	36803948	eRNA profiling uncovers the enhancer landscape of oesophageal adenocarcinoma and reveals new deregulated pathways	Homo sapiens	hg38	chr17	41792666	41793322	KLF5	JUP	Enhancer	Active	Disease	esophageal adenocarcinoma	MONDO:0005028	DOID:4914	esophagus	UBERON:0001043	OE19	CVCL_1622	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ATAC-seq; RNA-seq; ChIP-seq, Hi-C; RNA-seq	Luciferase reporter assay, CRISPR knockout/CRISPRi; RT-qPCR; Western blot
E_00687	2019	31431624	PAX8 activates metabolic genes via enhancer elements in Renal Cell Carcinoma	Homo sapiens	hg19	chr3	148898000	148901500	PAX8	CP	Enhancer	Active	Disease	clear cell renal cell carcinoma	MONDO:0005005	DOID:4467	kidney	UBERON:0002113	Caki-1	CVCL_0234	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; ATAC-seq; 3C-seq	ChIP-qPCR; CRISPR knockout; CRISPRi; Luciferase reporter assay, qRT-PCR; Western blot
E_00688	2019	31431624	PAX8 activates metabolic genes via enhancer elements in Renal Cell Carcinoma	Homo sapiens	hg19	chr3	148898000	148901500	PAX8	CP	Enhancer	Active	Disease	clear cell renal cell carcinoma	MONDO:0005005	DOID:4467	kidney	UBERON:0002113	VMRC-RCW	CVCL_1790	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; ATAC-seq; 3C-seq	ChIP-qPCR; CRISPR knockout; CRISPRi; Luciferase reporter assay, qRT-PCR; Western blot
E_00689	2022	36159594	A novel oncogenic enhancer of estrogen receptor-positive breast cancer	Homo sapiens	hg38	chr8	127668529	127669329	ESR1	MYC	Enhancer	Active	Disease	estrogen receptor-positive breast cancer	MONDO:0006512	DOID:0060075	breast	UBERON:0000310	MCF-7	CVCL_0031	breast adenocarcinoma epithelial cell	NA	Oncogenic MYC enhancer (αEmyc) activity; ER-associated chromatin; endogenous enhancer deletion/CRISPRi; cancer phenotype	H3K27ac ChIP-seq; H3K4me1 ChIP-seq; public RNA polymerase II/ER-alpha ChIA-PET	Dual-luciferase reporter; CRISPR-Cas9 enhancer deletion; dCas9-KRAB blockade; ChIP-qPCR; RT-qPCR; Western blot; cell-cycle, apoptosis and proliferation assays
E_00690	2023	37370109	Epigenetic reprogramming-induced guanidinoacetic acid synthesis promotes pancreatic cancer metastasis and transcription-activating histone modifications	Homo sapiens	hg19	chr15	45731612	45732080	NA	GATM	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	Capan-1	CVCL_0237	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; Enhancer functional validation	In situ Hi-C; H3K27ac ChIP-seq; RNA-seq; CUT&RUN	CRISPRi (dCas9-KRAB); H3K27ac ChIP-qPCR; 3C-qPCR; RT-qPCR; CRISPRi; Luciferase reporter assay; ChIP; 3C; Western blot; In vivo phenotyping; Xenograft/xenotransplant
E_00691	2023	37370109	Epigenetic reprogramming-induced guanidinoacetic acid synthesis promotes pancreatic cancer metastasis and transcription-activating histone modifications	Homo sapiens	hg19	chr15	45731612	45732080	NA	GATM	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	PANC-1-IN (PANC-1-derived highly invasive cells)	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; Enhancer functional validation; metastatic phenotype validation	In situ Hi-C; H3K27ac ChIP-seq; RNA-seq; CUT&RUN	CRISPRi (dCas9-KRAB); H3K27ac ChIP-qPCR; 3C-qPCR; RT-qPCR; Western blot; transwell migration; in vivo tumor/metastasis assay; CRISPRi; Luciferase reporter assay; ChIP; 3C; In vivo phenotyping; Xenograft/xenotransplant
E_00692	2023	37370109	Epigenetic reprogramming-induced guanidinoacetic acid synthesis promotes pancreatic cancer metastasis and transcription-activating histone modifications	Homo sapiens	hg19	chr15	45737631	45738460	NA	GATM	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	Capan-1	CVCL_0237	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; Enhancer functional validation	In situ Hi-C; H3K27ac ChIP-seq; RNA-seq; CUT&RUN	CRISPRi (dCas9-KRAB); H3K27ac ChIP-qPCR; 3C-qPCR; RT-qPCR; CRISPRi; Luciferase reporter assay; ChIP; 3C; Western blot; In vivo phenotyping; Xenograft/xenotransplant
E_00693	2023	37370109	Epigenetic reprogramming-induced guanidinoacetic acid synthesis promotes pancreatic cancer metastasis and transcription-activating histone modifications	Homo sapiens	hg19	chr15	45737631	45738460	NA	GATM	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	PANC-1-IN (PANC-1-derived highly invasive cells)	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; Enhancer functional validation; metastatic phenotype validation	In situ Hi-C; H3K27ac ChIP-seq; RNA-seq; CUT&RUN	CRISPRi (dCas9-KRAB); H3K27ac ChIP-qPCR; 3C-qPCR; RT-qPCR; Western blot; transwell migration; in vivo tumor/metastasis assay; CRISPRi; Luciferase reporter assay; ChIP; 3C; In vivo phenotyping; Xenograft/xenotransplant
E_00694	2023	37370109	Epigenetic reprogramming-induced guanidinoacetic acid synthesis promotes pancreatic cancer metastasis and transcription-activating histone modifications	Homo sapiens	hg19	chr15	45742113	45742770	NA	GATM	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	Capan-1	CVCL_0237	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; Enhancer functional validation	In situ Hi-C; H3K27ac ChIP-seq; RNA-seq; CUT&RUN	CRISPRi (dCas9-KRAB); H3K27ac ChIP-qPCR; 3C-qPCR; RT-qPCR; CRISPRi; Luciferase reporter assay; ChIP; 3C; Western blot; In vivo phenotyping; Xenograft/xenotransplant
E_00695	2023	37370109	Epigenetic reprogramming-induced guanidinoacetic acid synthesis promotes pancreatic cancer metastasis and transcription-activating histone modifications	Homo sapiens	hg19	chr15	45742113	45742770	NA	GATM	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	PANC-1-IN (PANC-1-derived highly invasive cells)	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; Enhancer functional validation; metastatic phenotype validation	In situ Hi-C; H3K27ac ChIP-seq; RNA-seq; CUT&RUN	CRISPRi (dCas9-KRAB); H3K27ac ChIP-qPCR; 3C-qPCR; RT-qPCR; Western blot; transwell migration; in vivo tumor/metastasis assay; CRISPRi; Luciferase reporter assay; ChIP; 3C; In vivo phenotyping; Xenograft/xenotransplant
E_00696	2023	37370109	Epigenetic reprogramming-induced guanidinoacetic acid synthesis promotes pancreatic cancer metastasis and transcription-activating histone modifications	Homo sapiens	hg19	chr15	45731612	45732080	NA	GATM	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	CFPAC-1	CVCL_1119	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; Candidate enhancer state annotation within PDAC cell-line panel	H3K27ac ChIP-seq/RNA-seq integration; RNA-seq; CUT&RUN	H3K27ac ChIP-qPCR; RT-qPCR; CRISPRi; Luciferase reporter assay; ChIP; 3C; Western blot; In vivo phenotyping; Xenograft/xenotransplant
E_00697	2023	37370109	Epigenetic reprogramming-induced guanidinoacetic acid synthesis promotes pancreatic cancer metastasis and transcription-activating histone modifications	Homo sapiens	hg19	chr15	45737631	45738460	NA	GATM	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	CFPAC-1	CVCL_1119	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; Candidate enhancer state annotation within PDAC cell-line panel	H3K27ac ChIP-seq/RNA-seq integration; RNA-seq; CUT&RUN	H3K27ac ChIP-qPCR; RT-qPCR; CRISPRi; Luciferase reporter assay; ChIP; 3C; Western blot; In vivo phenotyping; Xenograft/xenotransplant
E_00698	2023	37370109	Epigenetic reprogramming-induced guanidinoacetic acid synthesis promotes pancreatic cancer metastasis and transcription-activating histone modifications	Homo sapiens	hg19	chr15	45742113	45742770	NA	GATM	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	CFPAC-1	CVCL_1119	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; Candidate enhancer state annotation within PDAC cell-line panel	H3K27ac ChIP-seq/RNA-seq integration; RNA-seq; CUT&RUN	H3K27ac ChIP-qPCR; RT-qPCR; CRISPRi; Luciferase reporter assay; ChIP; 3C; Western blot; In vivo phenotyping; Xenograft/xenotransplant
E_00699	2018	29528523	Multiple Functional Variants at 13q14 Risk Locus for Osteoporosis Regulate RANKL Expression Through Long-Range Super-Enhancer	Homo sapiens	hg19	chr13	42940000	42940969	NFIC	TNFSF11	Enhancer	Active	Disease	osteoporosis	MONDO:0005298	DOID:11476	blood	UBERON:0000178	GM12878	CVCL_7526	B lymphoblastoid cell	NA	GWAS/eQTL integration; Enhancer activity; chromatin interaction; endogenous perturbation	GWAS/eQTL; Hi-C; epigenomic annotation; RNA-seq/ChIP-seq integration; eQTL analysis	Dual-luciferase reporter assay; CRISPR-Cas9 deletion of rs9533090 region; ChIP-qPCR; qRT-PCR; protein analysis; CRISPR-Cas9; Luciferase reporter assay
E_00700	2017	28973302	Pseudoexfoliation and Alzheimer's associated CLU risk variant, rs2279590, lies within an enhancer element and regulates CLU, EPHX2 and PTK2B gene expression	Homo sapiens	hg19	chr8	27456153	27456353	HSF1	CLU	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	lens of camera-type eye	UBERON:0000965	HEK293	CVCL_0045	HEK293 transformed human cell; lens-capsule tissue sample	NA	causal risk-enhancer validation with allele-specific TF mechanism	ENCODE H3K27ac/DNase regulatory annotation; GTEx eQTL analysis	Luciferase reporter; CRISPR-Cas9 115-bp deletion; EMSA; HSF1 supershift; HSF1 ChIP-qPCR; HSF1 siRNA; RT-qPCR; Western blot
E_00701	2017	28973302	Pseudoexfoliation and Alzheimer's associated CLU risk variant, rs2279590, lies within an enhancer element and regulates CLU, EPHX2 and PTK2B gene expression	Homo sapiens	hg19	chr8	27456153	27456353	HSF1	CLU	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	lens of camera-type eye	UBERON:0000965	human lens-capsule disease samples	NA	HEK293 transformed human cell; lens-capsule tissue sample	NA	causal risk-enhancer validation with allele-specific TF mechanism	ENCODE H3K27ac/DNase regulatory annotation; GTEx eQTL analysis	Luciferase reporter; CRISPR-Cas9 115-bp deletion; EMSA; HSF1 supershift; HSF1 ChIP-qPCR; HSF1 siRNA; RT-qPCR; Western blot
E_00702	2017	28973302	Pseudoexfoliation and Alzheimer's associated CLU risk variant, rs2279590, lies within an enhancer element and regulates CLU, EPHX2 and PTK2B gene expression	Homo sapiens	hg19	chr8	27456153	27456353	HSF1	CLU	Enhancer	Active	Disease	exfoliation syndrome	MONDO:0008327	DOID:13641	lens of camera-type eye	UBERON:0000965	HEK293	CVCL_0045	HEK293 transformed human cell; lens-capsule tissue sample	NA	causal risk-enhancer validation with allele-specific TF mechanism	ENCODE H3K27ac/DNase regulatory annotation; GTEx eQTL analysis	Luciferase reporter; CRISPR-Cas9 115-bp deletion; EMSA; HSF1 supershift; HSF1 ChIP-qPCR; HSF1 siRNA; RT-qPCR; Western blot
E_00703	2017	28973302	Pseudoexfoliation and Alzheimer's associated CLU risk variant, rs2279590, lies within an enhancer element and regulates CLU, EPHX2 and PTK2B gene expression	Homo sapiens	hg19	chr8	27456153	27456353	HSF1	CLU	Enhancer	Active	Disease	exfoliation syndrome	MONDO:0008327	DOID:13641	lens of camera-type eye	UBERON:0000965	human lens-capsule disease samples	NA	HEK293 transformed human cell; lens-capsule tissue sample	NA	causal risk-enhancer validation with allele-specific TF mechanism	ENCODE H3K27ac/DNase regulatory annotation; GTEx eQTL analysis	Luciferase reporter; CRISPR-Cas9 115-bp deletion; EMSA; HSF1 supershift; HSF1 ChIP-qPCR; HSF1 siRNA; RT-qPCR; Western blot
E_00704	2018	29528523	Multiple Functional Variants at 13q14 Risk Locus for Osteoporosis Regulate RANKL Expression Through Long-Range Super-Enhancer	Homo sapiens	hg19	chr13	42940000	42940969	NFIC	TNFSF11	Enhancer	Active	Disease	osteoporosis	MONDO:0005298	DOID:11476	bone	NA	U-2 OS	CVCL_0042	osteosarcoma-derived osteoblast-like cell	NA	GWAS/eQTL integration; Enhancer activity; chromatin interaction; endogenous perturbation	GWAS/eQTL; Hi-C; epigenomic annotation; RNA-seq/ChIP-seq integration; eQTL analysis	Dual-luciferase reporter assay; CRISPR-Cas9 deletion of rs9533090 region; ChIP-qPCR; qRT-PCR; protein analysis; CRISPR-Cas9; Luciferase reporter assay
E_00705	2018	29528523	Multiple Functional Variants at 13q14 Risk Locus for Osteoporosis Regulate RANKL Expression Through Long-Range Super-Enhancer	Homo sapiens	hg19	chr13	42955000	42955967	NA	TNFSF11	Super-enhancer	Active	Disease	osteoporosis	MONDO:0005298	DOID:11476	bone marrow	UBERON:0002371	CD34+ hematopoietic stem/progenitor cells	NA	hematopoietic stem/progenitor cell	NA	Risk-variant regulatory analysis; super-enhancer annotation; enhancer-gene interaction	GWAS/eQTL; Hi-C; ChIP-seq/RNA-seq integration; eQTL analysis	Reporter/qRT-PCR/ChIP-qPCR validation for selected functional variants/constituents; CRISPR-Cas9; Luciferase reporter assay
E_00706	2018	29528523	Multiple Functional Variants at 13q14 Risk Locus for Osteoporosis Regulate RANKL Expression Through Long-Range Super-Enhancer	Homo sapiens	hg19	chr13	42955000	42955967	NA	TNFSF11	Super-enhancer	Active	Disease	osteoporosis	MONDO:0005298	DOID:11476	blood	UBERON:0000178	GM12878	CVCL_7526	B lymphoblastoid cell	NA	Risk-variant regulatory analysis; super-enhancer annotation; enhancer-gene interaction	GWAS/eQTL; Hi-C; ChIP-seq/RNA-seq integration; eQTL analysis	Reporter/qRT-PCR/ChIP-qPCR validation for selected functional variants/constituents; CRISPR-Cas9; Luciferase reporter assay
E_00707	2018	29528523	Multiple Functional Variants at 13q14 Risk Locus for Osteoporosis Regulate RANKL Expression Through Long-Range Super-Enhancer	Homo sapiens	hg19	chr13	42956000	42956832	NA	TNFSF11	Super-enhancer	Active	Disease	osteoporosis	MONDO:0005298	DOID:11476	bone marrow	UBERON:0002371	CD34+ hematopoietic stem/progenitor cells	NA	hematopoietic stem/progenitor cell	NA	Risk-variant regulatory analysis; super-enhancer annotation; enhancer-gene interaction	GWAS/eQTL; Hi-C; ChIP-seq/RNA-seq integration; eQTL analysis	Reporter/qRT-PCR/ChIP-qPCR validation for selected functional variants/constituents; CRISPR-Cas9; Luciferase reporter assay
E_00708	2018	29528523	Multiple Functional Variants at 13q14 Risk Locus for Osteoporosis Regulate RANKL Expression Through Long-Range Super-Enhancer	Homo sapiens	hg19	chr13	42956000	42956832	NA	TNFSF11	Super-enhancer	Active	Disease	osteoporosis	MONDO:0005298	DOID:11476	blood	UBERON:0000178	GM12878	CVCL_7526	B lymphoblastoid cell	NA	Risk-variant regulatory analysis; super-enhancer annotation; enhancer-gene interaction	GWAS/eQTL; Hi-C; ChIP-seq/RNA-seq integration; eQTL analysis	Reporter/qRT-PCR/ChIP-qPCR validation for selected functional variants/constituents; CRISPR-Cas9; Luciferase reporter assay
E_00709	2018	29528523	Multiple Functional Variants at 13q14 Risk Locus for Osteoporosis Regulate RANKL Expression Through Long-Range Super-Enhancer	Homo sapiens	hg19	chr13	42965000	42965891	NA	TNFSF11	Super-enhancer	Active	Disease	osteoporosis	MONDO:0005298	DOID:11476	bone marrow	UBERON:0002371	CD34+ hematopoietic stem/progenitor cells	NA	hematopoietic stem/progenitor cell	NA	Risk-variant regulatory analysis; super-enhancer annotation; enhancer-gene interaction	GWAS/eQTL; Hi-C; ChIP-seq/RNA-seq integration; eQTL analysis	Reporter/qRT-PCR/ChIP-qPCR validation for selected functional variants/constituents; CRISPR-Cas9; Luciferase reporter assay
E_00710	2018	29528523	Multiple Functional Variants at 13q14 Risk Locus for Osteoporosis Regulate RANKL Expression Through Long-Range Super-Enhancer	Homo sapiens	hg19	chr13	42965000	42965891	NA	TNFSF11	Super-enhancer	Active	Disease	osteoporosis	MONDO:0005298	DOID:11476	blood	UBERON:0000178	GM12878	CVCL_7526	B lymphoblastoid cell	NA	Risk-variant regulatory analysis; super-enhancer annotation; enhancer-gene interaction	GWAS/eQTL; Hi-C; ChIP-seq/RNA-seq integration; eQTL analysis	Reporter/qRT-PCR/ChIP-qPCR validation for selected functional variants/constituents; CRISPR-Cas9; Luciferase reporter assay
E_00711	2018	29528523	Multiple Functional Variants at 13q14 Risk Locus for Osteoporosis Regulate RANKL Expression Through Long-Range Super-Enhancer	Homo sapiens	hg19	chr13	42955000	42955967	NA	TNFSF11	Super-enhancer	Active	Disease	osteoporosis	MONDO:0005298	DOID:11476	bone	NA	U-2 OS	CVCL_0042	osteosarcoma-derived osteoblast-like cell	NA	Risk-variant regulatory analysis; super-enhancer annotation; enhancer-gene interaction	GWAS/eQTL; Hi-C; ChIP-seq/RNA-seq integration; eQTL analysis	Reporter/qRT-PCR/ChIP-qPCR validation for selected functional variants/constituents; CRISPR-Cas9; Luciferase reporter assay
E_00712	2018	29528523	Multiple Functional Variants at 13q14 Risk Locus for Osteoporosis Regulate RANKL Expression Through Long-Range Super-Enhancer	Homo sapiens	hg19	chr13	42956000	42956832	NA	TNFSF11	Super-enhancer	Active	Disease	osteoporosis	MONDO:0005298	DOID:11476	bone	NA	U-2 OS	CVCL_0042	osteosarcoma-derived osteoblast-like cell	NA	Risk-variant regulatory analysis; super-enhancer annotation; enhancer-gene interaction	GWAS/eQTL; Hi-C; ChIP-seq/RNA-seq integration; eQTL analysis	Reporter/qRT-PCR/ChIP-qPCR validation for selected functional variants/constituents; CRISPR-Cas9; Luciferase reporter assay
E_00713	2018	29528523	Multiple Functional Variants at 13q14 Risk Locus for Osteoporosis Regulate RANKL Expression Through Long-Range Super-Enhancer	Homo sapiens	hg19	chr13	42965000	42965891	NA	TNFSF11	Super-enhancer	Active	Disease	osteoporosis	MONDO:0005298	DOID:11476	bone	NA	U-2 OS	CVCL_0042	osteosarcoma-derived osteoblast-like cell	NA	Risk-variant regulatory analysis; super-enhancer annotation; enhancer-gene interaction	GWAS/eQTL; Hi-C; ChIP-seq/RNA-seq integration; eQTL analysis	Reporter/qRT-PCR/ChIP-qPCR validation for selected functional variants/constituents; CRISPR-Cas9; Luciferase reporter assay
E_00714	2019	31431624	PAX8 activates metabolic genes via enhancer elements in Renal Cell Carcinoma	Homo sapiens	hg19	chr3	148898000	148901500	PAX8	CP	Enhancer	Active	Disease	clear cell renal cell carcinoma	MONDO:0005005	DOID:4467	kidney	UBERON:0002113	769-P	CVCL_1050	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; ATAC-seq; 4C-seq	ChIP-qPCR; CRISPR perturbation; Luciferase reporter assay; qRT-PCR; Western blot
E_00715	2019	31431624	PAX8 activates metabolic genes via enhancer elements in Renal Cell Carcinoma	Homo sapiens	hg19	chr3	148898000	148901500	PAX8	CP	Enhancer	Active	Disease	clear cell renal cell carcinoma	MONDO:0005005	DOID:4467	kidney	UBERON:0002113	786-O	CVCL_1051	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; ATAC-seq; 4C-seq	ChIP-qPCR; CRISPR perturbation; Luciferase reporter assay; qRT-PCR; Western blot
E_00716	2024	39312195	Selective Enhancer Gain-of-Function Deregulates MYC Expression in Multiple Myeloma	Homo sapiens	hg38	chr8	12891950	12892610	SPIB	MYC	Enhancer	Active	Disease	plasma cell myeloma	MONDO:0009693	DOID:9538	bone marrow	UBERON:0002371	ANBL-6	CVCL_5425	multiple myeloma cell line	NA	dCas9-KRAB CRISPRi; CRISPR-Cas9 binding site knockout; dual-luciferase reporter assay; Micro-C chromatin contact validation	H3K27ac ChIP-seq; ATAC-seq; WGS; RNA-seq, pooled CRISPRi tiling screen	qRT-PCR, sgRNA lentiviral quantification
E_00717	2018	29528523	Multiple Functional Variants at 13q14 Risk Locus for Osteoporosis Regulate RANKL Expression Through Long-Range Super-Enhancer	Homo sapiens	hg19	chr13	42939000	42967000	NA	TNFSF11	Super-enhancer	Active	Disease	osteoporosis	MONDO:0005298	DOID:11476	bone marrow	UBERON:0002371	CD34+ hematopoietic stem/progenitor cells	NA	hematopoietic stem/progenitor cell	NA	GWAS/eQTL integration; Enhancer activity; chromatin interaction; endogenous perturbation	GWAS/eQTL; Hi-C; epigenomic annotation; RNA-seq/ChIP-seq integration; eQTL analysis	Dual-luciferase reporter assay; CRISPR-Cas9 deletion of rs9533090 region; ChIP-qPCR; qRT-PCR; protein analysis; CRISPR-Cas9; Luciferase reporter assay
E_00718	2018	29528523	Multiple Functional Variants at 13q14 Risk Locus for Osteoporosis Regulate RANKL Expression Through Long-Range Super-Enhancer	Homo sapiens	hg19	chr13	42939000	42967000	NA	TNFSF11	Super-enhancer	Active	Disease	osteoporosis	MONDO:0005298	DOID:11476	blood	UBERON:0000178	GM12878	CVCL_7526	B lymphoblastoid cell	NA	GWAS/eQTL integration; Enhancer activity; chromatin interaction; endogenous perturbation	GWAS/eQTL; Hi-C; epigenomic annotation; RNA-seq/ChIP-seq integration; eQTL analysis	Dual-luciferase reporter assay; CRISPR-Cas9 deletion of rs9533090 region; ChIP-qPCR; qRT-PCR; protein analysis; CRISPR-Cas9; Luciferase reporter assay
E_00719	2018	29528523	Multiple Functional Variants at 13q14 Risk Locus for Osteoporosis Regulate RANKL Expression Through Long-Range Super-Enhancer	Homo sapiens	hg19	chr13	42939000	42967000	NA	TNFSF11	Super-enhancer	Active	Disease	osteoporosis	MONDO:0005298	DOID:11476	bone	NA	U-2 OS	CVCL_0042	osteosarcoma-derived osteoblast-like cell	NA	GWAS/eQTL integration; Enhancer activity; chromatin interaction; endogenous perturbation	GWAS/eQTL; Hi-C; epigenomic annotation; RNA-seq/ChIP-seq integration; eQTL analysis	Dual-luciferase reporter assay; CRISPR-Cas9 deletion of rs9533090 region; ChIP-qPCR; qRT-PCR; protein analysis; CRISPR-Cas9; Luciferase reporter assay
E_00720	2023	36803948	eRNA profiling uncovers the enhancer landscape of oesophageal adenocarcinoma and reveals new deregulated pathways	Homo sapiens	hg38	chr19	29844909	29845562	KLF5	CCNE1	Enhancer	Active	Disease	esophageal adenocarcinoma	MONDO:0005028	DOID:4914	esophagus	UBERON:0001043	OE19	CVCL_1622	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	ATAC-seq; RNA-seq; ChIP-seq; RNA-seq	Luciferase reporter assay, CRISPR knockout/CRISPRi; RT-qPCR; Western blot
E_00721	2017	28973302	Pseudoexfoliation and Alzheimer's associated CLU risk variant, rs2279590, lies within an enhancer element and regulates CLU, EPHX2 and PTK2B gene expression	Homo sapiens	hg19	chr8	27455903	27456103	HSF1	CLU	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	NA	NA	HEK293	CVCL_0045	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_00722	2017	28973302	Pseudoexfoliation and Alzheimer's associated CLU risk variant, rs2279590, lies within an enhancer element and regulates CLU, EPHX2 and PTK2B gene expression	Homo sapiens	hg19	chr8	27455903	27456103	HSF1	EPHX2	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	NA	NA	HEK293	CVCL_0045	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_00723	2017	28973302	Pseudoexfoliation and Alzheimer's associated CLU risk variant, rs2279590, lies within an enhancer element and regulates CLU, EPHX2 and PTK2B gene expression	Homo sapiens	hg19	chr8	27455903	27456103	HSF1	PTK2B	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	NA	NA	HEK293	CVCL_0045	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_00724	2023	36803948	eRNA profiling uncovers the enhancer landscape of oesophageal adenocarcinoma and reveals new deregulated pathways	Homo sapiens	hg38	chr19	29844909	29845562	KLF5	CCNE1	Enhancer	Active	Normal	NA	NA	NA	esophagus	UBERON:0001043	CP-A	CVCL_C451	esophageal epithelial cell	NA	Enhancer activity; KLF5 binding; functional CRISPRi perturbation	Patient RNA-seq; ATAC-seq; KAS-seq; H3K27ac ChIP-seq; KLF5 ChIP-seq; RNA-seq	Luciferase reporter assay; dCas9-KRAB CRISPRi; siKLF5; RT-qPCR; Western blot; cell-fitness assay
E_00725	2017	28973302	Pseudoexfoliation and Alzheimer's associated CLU risk variant, rs2279590, lies within an enhancer element and regulates CLU, EPHX2 and PTK2B gene expression	Homo sapiens	hg19	chr8	27456150	27456350	HSF1	CLU	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	HEK293	CVCL_0045	embryonic kidney cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	eQTL analysis	Luciferase reporter assay; CRISPR knockout; ChIP-qPCR; EMSA; RT-qPCR; Western blot; CRISPR-Cas9; Reporter assay
E_00726	2017	28973302	Pseudoexfoliation and Alzheimer's associated CLU risk variant, rs2279590, lies within an enhancer element and regulates CLU, EPHX2 and PTK2B gene expression	Homo sapiens	hg19	chr8	27456150	27456350	HSF1	EPHX2	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	HEK293	CVCL_0045	embryonic kidney cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	eQTL analysis	Luciferase reporter assay; CRISPR knockout; ChIP-qPCR; EMSA; RT-qPCR; Western blot; CRISPR-Cas9; Reporter assay
E_00727	2017	28973302	Pseudoexfoliation and Alzheimer's associated CLU risk variant, rs2279590, lies within an enhancer element and regulates CLU, EPHX2 and PTK2B gene expression	Homo sapiens	hg19	chr8	27456150	27456350	HSF1	PTK2B	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	HEK293	CVCL_0045	embryonic kidney cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	eQTL analysis	Luciferase reporter assay; CRISPR knockout; ChIP-qPCR; EMSA; RT-qPCR; Western blot; CRISPR-Cas9; Reporter assay
E_00728	2023	36803948	eRNA profiling uncovers the enhancer landscape of oesophageal adenocarcinoma and reveals new deregulated pathways	Homo sapiens	hg38	chr20	43657287	43657942	NA	MYBL2	Enhancer	Active	Disease	esophageal adenocarcinoma	MONDO:0005028	DOID:4914	esophagus	UBERON:0001043	OE19	CVCL_1622	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay	ATAC-seq; RNA-seq; RNA-seq	Luciferase reporter assay, CRISPR knockout/CRISPRi; RT-qPCR; Western blot
E_00729	2017	28973302	Pseudoexfoliation and Alzheimer's associated CLU risk variant, rs2279590, lies within an enhancer element and regulates CLU, EPHX2 and PTK2B gene expression	Homo sapiens	hg19	chr8	27456153	27456353	NA	PTK2B	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	lens of camera-type eye	UBERON:0000965	HEK293	CVCL_0045	HEK293 transformed human cell; lens-capsule tissue sample	NA	distal enhancer-target validation; no target-specific TF mechanism separately demonstrated	ENCODE regulatory annotation; GTEx eQTL context; later chromatin-interaction support	Luciferase reporter; CRISPR-Cas9 115-bp enhancer deletion; RT-qPCR; follow-up chromatin-interaction validation for enhancer-PTK2B linkage
E_00730	2017	28973302	Pseudoexfoliation and Alzheimer's associated CLU risk variant, rs2279590, lies within an enhancer element and regulates CLU, EPHX2 and PTK2B gene expression	Homo sapiens	hg19	chr8	27456153	27456353	NA	PTK2B	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	lens of camera-type eye	UBERON:0000965	human lens-capsule disease samples	NA	HEK293 transformed human cell; lens-capsule tissue sample	NA	distal enhancer-target validation; no target-specific TF mechanism separately demonstrated	ENCODE regulatory annotation; GTEx eQTL context; later chromatin-interaction support	Luciferase reporter; CRISPR-Cas9 115-bp enhancer deletion; RT-qPCR; follow-up chromatin-interaction validation for enhancer-PTK2B linkage
E_00731	2017	28973302	Pseudoexfoliation and Alzheimer's associated CLU risk variant, rs2279590, lies within an enhancer element and regulates CLU, EPHX2 and PTK2B gene expression	Homo sapiens	hg19	chr8	27456153	27456353	NA	PTK2B	Enhancer	Active	Disease	exfoliation syndrome	MONDO:0008327	DOID:13641	lens of camera-type eye	UBERON:0000965	HEK293	CVCL_0045	HEK293 transformed human cell; lens-capsule tissue sample	NA	distal enhancer-target validation; no target-specific TF mechanism separately demonstrated	ENCODE regulatory annotation; GTEx eQTL context; later chromatin-interaction support	Luciferase reporter; CRISPR-Cas9 115-bp enhancer deletion; RT-qPCR; follow-up chromatin-interaction validation for enhancer-PTK2B linkage
E_00732	2017	28973302	Pseudoexfoliation and Alzheimer's associated CLU risk variant, rs2279590, lies within an enhancer element and regulates CLU, EPHX2 and PTK2B gene expression	Homo sapiens	hg19	chr8	27456153	27456353	NA	PTK2B	Enhancer	Active	Disease	exfoliation syndrome	MONDO:0008327	DOID:13641	lens of camera-type eye	UBERON:0000965	human lens-capsule disease samples	NA	HEK293 transformed human cell; lens-capsule tissue sample	NA	distal enhancer-target validation; no target-specific TF mechanism separately demonstrated	ENCODE regulatory annotation; GTEx eQTL context; later chromatin-interaction support	Luciferase reporter; CRISPR-Cas9 115-bp enhancer deletion; RT-qPCR; follow-up chromatin-interaction validation for enhancer-PTK2B linkage
E_00733	2017	28973302	Pseudoexfoliation and Alzheimer's associated CLU risk variant, rs2279590, lies within an enhancer element and regulates CLU, EPHX2 and PTK2B gene expression	Homo sapiens	hg19	chr8	27456153	27456353	NA	EPHX2	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	lens of camera-type eye	UBERON:0000965	HEK293	CVCL_0045	HEK293 transformed human cell; lens-capsule tissue sample	NA	distal enhancer-target validation; no target-specific TF mechanism separately demonstrated	ENCODE regulatory annotation; GTEx eQTL context; later chromatin-interaction support	Luciferase reporter; CRISPR-Cas9 115-bp enhancer deletion; RT-qPCR; follow-up chromatin-interaction validation for enhancer-EPHX2 linkage
E_00734	2017	28973302	Pseudoexfoliation and Alzheimer's associated CLU risk variant, rs2279590, lies within an enhancer element and regulates CLU, EPHX2 and PTK2B gene expression	Homo sapiens	hg19	chr8	27456153	27456353	NA	EPHX2	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	lens of camera-type eye	UBERON:0000965	human lens-capsule disease samples	NA	HEK293 transformed human cell; lens-capsule tissue sample	NA	distal enhancer-target validation; no target-specific TF mechanism separately demonstrated	ENCODE regulatory annotation; GTEx eQTL context; later chromatin-interaction support	Luciferase reporter; CRISPR-Cas9 115-bp enhancer deletion; RT-qPCR; follow-up chromatin-interaction validation for enhancer-EPHX2 linkage
E_00735	2017	28973302	Pseudoexfoliation and Alzheimer's associated CLU risk variant, rs2279590, lies within an enhancer element and regulates CLU, EPHX2 and PTK2B gene expression	Homo sapiens	hg19	chr8	27456153	27456353	NA	EPHX2	Enhancer	Active	Disease	exfoliation syndrome	MONDO:0008327	DOID:13641	lens of camera-type eye	UBERON:0000965	HEK293	CVCL_0045	HEK293 transformed human cell; lens-capsule tissue sample	NA	distal enhancer-target validation; no target-specific TF mechanism separately demonstrated	ENCODE regulatory annotation; GTEx eQTL context; later chromatin-interaction support	Luciferase reporter; CRISPR-Cas9 115-bp enhancer deletion; RT-qPCR; follow-up chromatin-interaction validation for enhancer-EPHX2 linkage
E_00736	2017	28973302	Pseudoexfoliation and Alzheimer's associated CLU risk variant, rs2279590, lies within an enhancer element and regulates CLU, EPHX2 and PTK2B gene expression	Homo sapiens	hg19	chr8	27456153	27456353	NA	EPHX2	Enhancer	Active	Disease	exfoliation syndrome	MONDO:0008327	DOID:13641	lens of camera-type eye	UBERON:0000965	human lens-capsule disease samples	NA	HEK293 transformed human cell; lens-capsule tissue sample	NA	distal enhancer-target validation; no target-specific TF mechanism separately demonstrated	ENCODE regulatory annotation; GTEx eQTL context; later chromatin-interaction support	Luciferase reporter; CRISPR-Cas9 115-bp enhancer deletion; RT-qPCR; follow-up chromatin-interaction validation for enhancer-EPHX2 linkage
E_00737	2023	36924774	Enhancer variants on chromosome 2p14 regulating SPRED2 and ACTR2 act as a signal amplifier to protect against rheumatoid arthritis	Homo sapiens	hg19	chr2	65608668	65609150	CEBPB	SPRED2	Enhancer	Active	Disease	rheumatoid arthritis	MONDO:0008383	DOID:7148	pericardium	UBERON:0002407	MH7A	CVCL_0427	synovial fibroblast	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	Hi-C; ATAC-seq; ChIP-seq	CRISPR knockout; Luciferase reporter assay; RT-qPCR; Western blot
E_00738	2023	37591943	TAL1 hijacks MYCN enhancer that induces MYCN expression and dependence on mevalonate pathway in T-cell acute lymphoblastic leukemia	Homo sapiens	hg19	chr2	16619625	16621501	TAL1	MYCN	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	primary TAL1-positive T-ALL cells	NA	T cell	CL:0000084	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; In vivo functional validation	TAL1/H3K27ac ChIP-seq; ATAC-seq; 3D-chromatin profiling; RNA-seq	ChIP-qPCR; RT-qPCR; MYCN functional-dependency assays; Xenograft/xenotransplant
E_00739	2023	36924774	Enhancer variants on chromosome 2p14 regulating SPRED2 and ACTR2 act as a signal amplifier to protect against rheumatoid arthritis	Homo sapiens	hg19	chr2	65609946	65610996	NA	ACTR2	Enhancer	Active	Disease	rheumatoid arthritis	MONDO:0008383	DOID:7148	pericardium	UBERON:0002407	MH7A	CVCL_0427	synovial fibroblast	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	Hi-C; ATAC-seq; ChIP-seq	CRISPR knockout; Luciferase reporter assay; RT-qPCR; Western blot
E_00740	2023	36924774	Enhancer variants on chromosome 2p14 regulating SPRED2 and ACTR2 act as a signal amplifier to protect against rheumatoid arthritis	Homo sapiens	hg19	chr2	65609946	65610996	NA	SPRED2	Enhancer	Active	Disease	rheumatoid arthritis	MONDO:0008383	DOID:7148	pericardium	UBERON:0002407	MH7A	CVCL_0427	synovial fibroblast	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	Hi-C; ATAC-seq; ChIP-seq	CRISPR knockout; Luciferase reporter assay; RT-qPCR; Western blot
E_00741	2023	36924774	Enhancer variants on chromosome 2p14 regulating SPRED2 and ACTR2 act as a signal amplifier to protect against rheumatoid arthritis	Homo sapiens	hg19	chr2	65633710	65634058	NA	SPRED2	Enhancer	Active	Disease	rheumatoid arthritis	MONDO:0008383	DOID:7148	pericardium	UBERON:0002407	MH7A	CVCL_0427	synovial fibroblast	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	Hi-C; ATAC-seq; ChIP-seq	CRISPR knockout; Luciferase reporter assay; RT-qPCR; Western blot
E_00742	2023	37591943	TAL1 hijacks MYCN enhancer that induces MYCN expression and dependence on mevalonate pathway in T-cell acute lymphoblastic leukemia	Homo sapiens	hg19	chr2	16619625	16621501	TAL1	MYCN	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	primary/PDX T-ALL cells	NA	T cell	CL:0000084	Functional perturbation assay; In vivo functional validation; Enhancer-associated oncogene dependency assay	RNA-seq; primary T-ALL chromatin-data integration	MYCN perturbation; cell-growth assays; xenograft/dependency assays; Western blot; Xenograft/xenotransplant
E_00743	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Foxc2	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	primary mouse lymphatic endothelial cells	NA	endothelial cell of lymphatic vessel	CL:0002138	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; Endogenous enhancer perturbation assay; developmental phenotype assay	ChIP-seq; RNA-seq	Transgenic lacZ reporter assay; transgenic zebrafish GFP reporter assay; CRISPR-Cas9 1068-bp enhancer deletion; CRISPR-Cas9 5-bp GATA2-site deletion; ChIP-qPCR; 3C; RT-qPCR; Immunofluorescence; Flow cytometry; colony-forming assay; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_00744	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Gata2	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	primary mouse lymphatic endothelial cells	NA	endothelial cell of lymphatic vessel	CL:0002138	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; Endogenous enhancer perturbation assay; developmental phenotype assay	ChIP-seq; RNA-seq	Transgenic lacZ reporter assay; transgenic zebrafish GFP reporter assay; CRISPR-Cas9 1068-bp enhancer deletion; CRISPR-Cas9 5-bp GATA2-site deletion; ChIP-qPCR; 3C; RT-qPCR; Immunofluorescence; Flow cytometry; colony-forming assay; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_00745	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Nfatc1	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	primary mouse lymphatic endothelial cells	NA	endothelial cell of lymphatic vessel	CL:0002138	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; Endogenous enhancer perturbation assay; developmental phenotype assay	ChIP-seq; RNA-seq	Transgenic lacZ reporter assay; transgenic zebrafish GFP reporter assay; CRISPR-Cas9 1068-bp enhancer deletion; CRISPR-Cas9 5-bp GATA2-site deletion; ChIP-qPCR; 3C; RT-qPCR; Immunofluorescence; Flow cytometry; colony-forming assay; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_00746	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Prox1	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	primary mouse lymphatic endothelial cells	NA	endothelial cell of lymphatic vessel	CL:0002138	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; Endogenous enhancer perturbation assay; developmental phenotype assay	ChIP-seq; RNA-seq	Transgenic lacZ reporter assay; transgenic zebrafish GFP reporter assay; CRISPR-Cas9 1068-bp enhancer deletion; CRISPR-Cas9 5-bp GATA2-site deletion; ChIP-qPCR; 3C; RT-qPCR; Immunofluorescence; Flow cytometry; colony-forming assay; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_00747	2023	37066790	SOX17 Enhancer Variants Disrupt Transcription Factor Binding And Enhancer Inactivity Drives Pulmonary Hypertension	Homo sapiens	hg19	chr8	55251754	55251853	RORA	SOX17	Enhancer	Active	Disease	pulmonary arterial hypertension	MONDO:0015924	NA	pulmonary artery endothelium	UBERON:0005317	primary human pulmonary artery endothelial cells (hPAECs)	NA	pulmonary artery endothelial cell	CL:1001568	Enhancer activity assay; Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation	ChIP-seq; RNA-seq; GWAS	Luciferase reporter assay; ChIP-qPCR; siRNA knockdown; Mouse genetic deletion/knock-in; In vivo phenotyping
E_00748	2023	37066790	SOX17 Enhancer Variants Disrupt Transcription Factor Binding And Enhancer Inactivity Drives Pulmonary Hypertension	Homo sapiens	hg19	chr8	55269891	55269990	HOXA5	SOX17	Enhancer	Active	Disease	pulmonary arterial hypertension	MONDO:0015924	NA	pulmonary artery endothelium	UBERON:0005317	primary human pulmonary artery endothelial cells (hPAECs)	NA	pulmonary artery endothelial cell	CL:1001568	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation	ChIP-seq; RNA-seq; GWAS	Luciferase reporter assay, CRISPRi, CRISPR knockout, EMSA; ChIP-qPCR; siRNA knockdown; Mouse genetic deletion/knock-in; In vivo phenotyping
E_00749	2023	37066790	SOX17 Enhancer Variants Disrupt Transcription Factor Binding And Enhancer Inactivity Drives Pulmonary Hypertension	Homo sapiens	hg19	chr8	55251754	55251853	RORA	SOX17	Enhancer	Active	Disease	pulmonary arterial hypertension	MONDO:0015924	NA	pulmonary artery endothelium	UBERON:0005317	primary human pulmonary artery endothelial cells (hPAECs)	NA	pulmonary artery endothelial cell	CL:1001568	Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation; Allele-specific enhancer activity; TF binding assay; disease-mechanism validation	RNA-seq; PAH GWAS/WGS fine-mapping and endothelial epigenomic integration from discovery study; GWAS	100-bp allele-specific luciferase reporter; CRISPRi; EMSA/antibody supershift; SOX17 expression assays; endothelial functional assays; enhancer-knockout mouse PH phenotyping; siRNA knockdown; Mouse genetic deletion/knock-in; In vivo phenotyping
E_00750	2023	37066790	SOX17 Enhancer Variants Disrupt Transcription Factor Binding And Enhancer Inactivity Drives Pulmonary Hypertension	Homo sapiens	hg19	chr8	55251754	55251853	RORA	SOX17	Enhancer	Active	Disease	pulmonary arterial hypertension	MONDO:0015924	NA	pulmonary artery endothelium	UBERON:0005317	primary human pulmonary artery endothelial cells (hPAECs)	NA	pulmonary artery endothelial cell	CL:1001568	TF binding assay; Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation; Regulatory variant enhancer assay; Endogenous enhancer perturbation assay; endothelial functional assay	GWAS fine-mapping; RNA-seq; transcriptomic analysis; epigenomic integration; GWAS	CRISPR/Cas9 deletion of the SOX17 signal-1 enhancer; Allele-specific reporter assay; EMSA; antibody supershift EMSA; HOXA5 ChIP-qPCR; RT-qPCR; endothelial apoptosis assay; proliferation assay; barrier-function assay; orthologous enhancer-knockout mouse hypoxia and SU5416/hypoxia challenge; siRNA knockdown; Mouse genetic deletion/knock-in; In vivo phenotyping
E_00751	2023	37066790	SOX17 Enhancer Variants Disrupt Transcription Factor Binding And Enhancer Inactivity Drives Pulmonary Hypertension	Homo sapiens	hg19	chr8	55251754	55251853	RORA	SOX17	Enhancer	Active	Disease	pulmonary arterial hypertension	MONDO:0015924	NA	pulmonary artery endothelium	UBERON:0005317	primary human pulmonary artery endothelial cells (hPAECs)	NA	pulmonary artery endothelial cell	CL:1001568	TF binding assay; Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation; Regulatory variant enhancer assay; CRISPR interference assay; endothelial functional assay	GWAS fine-mapping; RNA-seq; transcriptomic analysis; epigenomic integration; GWAS	CRISPRi targeting the rs765727 signal-2 enhancer; 100-bp allele-specific dual-luciferase reporter assay; EMSA; antibody supershift EMSA; RT-qPCR; endothelial apoptosis assay; proliferation assay; barrier-function assay; Start/End are a standardized 100-bp interval centered on rs765727 at hg19 chr8:55251803 because exact cloning endpoints were not explicitly stated; siRNA knockdown; Mouse genetic deletion/knock-in; In vivo phenotyping
E_00752	2023	37066790	SOX17 Enhancer Variants Disrupt Transcription Factor Binding And Enhancer Inactivity Drives Pulmonary Hypertension	Homo sapiens	hg19	chr8	55269891	55269990	HOXA5	SOX17	Enhancer	Active	Disease	pulmonary arterial hypertension	MONDO:0015924	NA	pulmonary artery endothelium	UBERON:0005317	primary human pulmonary artery endothelial cells (hPAECs)	NA	pulmonary artery endothelial cell	CL:1001568	Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation; Allele-specific enhancer activity; TF binding assay; disease-mechanism validation	RNA-seq; PAH GWAS/WGS fine-mapping and endothelial epigenomic integration from discovery study; GWAS	100-bp allele-specific luciferase reporter; CRISPR deletion/CRISPRi; EMSA/supershift; HOXA5 ChIP-qPCR; SOX17 expression assays; endothelial functional assays; enhancer-knockout mouse PH phenotyping; siRNA knockdown; Mouse genetic deletion/knock-in; In vivo phenotyping
E_00753	2023	37066790	SOX17 Enhancer Variants Disrupt Transcription Factor Binding And Enhancer Inactivity Drives Pulmonary Hypertension	Homo sapiens	hg19	chr8	55269891	55269990	HOXA5	SOX17	Enhancer	Active	Disease	pulmonary arterial hypertension	MONDO:0015924	NA	pulmonary artery endothelium	UBERON:0005317	primary human pulmonary artery endothelial cells (hPAECs)	NA	pulmonary artery endothelial cell	CL:1001568	TF binding assay; Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation; Regulatory variant enhancer assay; Endogenous enhancer perturbation assay; endothelial functional assay	GWAS fine-mapping; RNA-seq; transcriptomic analysis; epigenomic integration; GWAS	CRISPR/Cas9 deletion of the SOX17 signal-1 enhancer; Allele-specific reporter assay; EMSA; antibody supershift EMSA; HOXA5 ChIP-qPCR; RT-qPCR; endothelial apoptosis assay; proliferation assay; barrier-function assay; orthologous enhancer-knockout mouse hypoxia and SU5416/hypoxia challenge; siRNA knockdown; Mouse genetic deletion/knock-in; In vivo phenotyping
E_00754	2023	37066790	SOX17 Enhancer Variants Disrupt Transcription Factor Binding And Enhancer Inactivity Drives Pulmonary Hypertension	Homo sapiens	hg19	chr8	55269891	55269990	HOXA5	SOX17	Enhancer	Active	Disease	pulmonary arterial hypertension	MONDO:0015924	NA	pulmonary artery endothelium	UBERON:0005317	primary human pulmonary artery endothelial cells (hPAECs)	NA	pulmonary artery endothelial cell	CL:1001568	TF binding assay; Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation; Regulatory variant enhancer assay; CRISPR interference assay; endothelial functional assay	GWAS fine-mapping; RNA-seq; transcriptomic analysis; epigenomic integration; GWAS	CRISPRi targeting the rs765727 signal-2 enhancer; 100-bp allele-specific dual-luciferase reporter assay; EMSA; antibody supershift EMSA; RT-qPCR; endothelial apoptosis assay; proliferation assay; barrier-function assay; Start/End are a standardized 100-bp interval centered on rs765727 at hg19 chr8:55251803 because exact cloning endpoints were not explicitly stated; siRNA knockdown; Mouse genetic deletion/knock-in; In vivo phenotyping
E_00755	2023	37702072	Temporal analyses reveal a pivotal role for sense and antisense enhancer RNAs in coordinate immunoglobulin lambda locus activation	Mus musculus	mm10	chr16	19007329	19008187	Irf4	Iglv1	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary pro-/pre-B cells	NA	pro-B cell	CL:0000826	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Endogenous functional perturbation assay	Pro-/pre-B ATAC-seq; GRO-seq; MED1 chromatin-data integration	CRISPR/Cas9 deletion spanning PU.1/IRF4 sites; temporal ChIP-qPCR; 3C-qPCR; eRNA perturbation; RT-qPCR
E_00756	2023	37702072	Temporal analyses reveal a pivotal role for sense and antisense enhancer RNAs in coordinate immunoglobulin lambda locus activation	Mus musculus	mm10	chr16	19007329	19008187	Spi1	Iglv1	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary pro-/pre-B cells	NA	pro-B cell	CL:0000826	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Endogenous functional perturbation assay	Pro-/pre-B ATAC-seq; GRO-seq; MED1 chromatin-data integration	CRISPR/Cas9 deletion spanning PU.1/IRF4 sites; temporal ChIP-qPCR; 3C-qPCR; eRNA perturbation; RT-qPCR
E_00757	2023	37702072	Temporal analyses reveal a pivotal role for sense and antisense enhancer RNAs in coordinate immunoglobulin lambda locus activation	Mus musculus	mm10	chr16	19026931	19027772	Irf4	Iglj1	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary pro-/pre-B cells	NA	pro-B cell	CL:0000826	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Endogenous functional perturbation assay	Pro-/pre-B ATAC-seq; GRO-seq; MED1 chromatin-data integration	CRISPR/Cas9 deletion spanning PU.1/IRF4 sites; temporal ChIP-qPCR; 3C-qPCR; eRNA shRNA perturbation; RT-qPCR; Sanger sequencing
E_00758	2023	37702072	Temporal analyses reveal a pivotal role for sense and antisense enhancer RNAs in coordinate immunoglobulin lambda locus activation	Mus musculus	mm10	chr16	19026931	19027772	Spi1	Iglj1	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary pro-/pre-B cells	NA	pro-B cell	CL:0000826	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Endogenous functional perturbation assay	Pro-/pre-B ATAC-seq; GRO-seq; MED1 chromatin-data integration	CRISPR/Cas9 deletion spanning PU.1/IRF4 sites; temporal ChIP-qPCR; 3C-qPCR; eRNA shRNA perturbation; RT-qPCR
E_00759	2023	37922339	Distinct use of super-enhancer elements controls cell type-specific CD25 transcription and function	Mus musculus	mm10	chr2	11656369	11660078	Stat5b	Il2ra	Super-enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	primary CD8-positive T cells	NA	CD8-positive, alpha-beta T cell	CL:0000625	Regulatory element functional validation; 3D chromatin interaction mapping	ChIP-seq; HiChIP; RNA-seq	CRISPR-Cas9 deletion, flow cytometry, reporter assay
E_00760	2023	37922339	Distinct use of super-enhancer elements controls cell type-specific CD25 transcription and function	Mus musculus	mm39	chr2	11661180	11664889	Stat5b	Il2ra	Super-enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	primary splenic CD8-positive T cells	NA	CD8-positive, alpha-beta T cell	CL:0000625	TF binding assay; Chromatin interaction assay; Super-enhancer functional dissection; Endogenous functional perturbation assay	STAT5B ChIP-seq; ATAC-seq; RNA-seq; H3K27ac HiChIP	CRISPR/Cas9 endogenous intronic-region deletion mouse models; anti-CD3/CD28 and IL-2 stimulation; Flow cytometry; RT-qPCR/RT-PCR; CD25 protein-expression analysis
E_00761	2023	37922339	Distinct use of super-enhancer elements controls cell type-specific CD25 transcription and function	Mus musculus	mm39	chr2	11661180	11664889	Stat5b	Il2ra	Super-enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	primary splenic natural killer cells	NA	natural killer cell	CL:0000623	TF binding assay; Super-enhancer functional dissection; Endogenous functional perturbation assay	STAT5B ChIP-seq; ATAC-seq; RNA-seq; H3K27ac HiChIP	CRISPR/Cas9 endogenous intronic-region deletion mouse models; IL-15 and IL-12 cytokine stimulation; Flow cytometry; RT-qPCR/RT-PCR; CD25 protein-expression analysis
E_00762	2023	37922339	Distinct use of super-enhancer elements controls cell type-specific CD25 transcription and function	Mus musculus	mm39	chr2	11661224	11661284	Stat5b	Il2ra	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	primary peripheral CD8-positive T cells	NA	CD8-positive, alpha-beta T cell	CL:0000625	TF binding assay; Super-enhancer constituent validation; STAT5-binding-site functional perturbation assay	STAT5B ChIP-seq; ATAC-seq; RNA-seq; H3K27ac HiChIP	CRISPR/Cas9 endogenous IN1a/IN1b deletion mouse model; cytokine stimulation; Flow cytometry; RT-qPCR/RT-PCR; CD25 protein-expression analysis
E_00763	2023	37922339	Distinct use of super-enhancer elements controls cell type-specific CD25 transcription and function	Mus musculus	mm39	chr2	11663068	11663249	Stat5b	Il2ra	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	primary peripheral CD8-positive T cells	NA	CD8-positive, alpha-beta T cell	CL:0000625	TF binding assay; Super-enhancer constituent validation; STAT5-binding-site functional perturbation assay	STAT5B ChIP-seq; ATAC-seq; RNA-seq; H3K27ac HiChIP	CRISPR/Cas9 endogenous IN1m deletion mouse model; cytokine stimulation; Flow cytometry; RT-qPCR/RT-PCR; CD25 protein-expression analysis
E_00764	2021	35122059	TNF-α-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer	Homo sapiens	hg38	chr17	34255285	34257203	JUN	CCL2	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	FACS-sorted PDAC patient epithelial cells	NA	malignant cell	CL:0001064	Functional perturbation assay; TF binding/epigenomic regulatory assay	JUN/JUNB and H3K27ac ChIP-seq; ATAC-seq; RNA-seq; chromatin-conformation/i4C-associated profiling; patient/PDX transcriptomic integration	JUN ChIP-qPCR; JUN siRNA/overexpression; BET/JQ1 inhibition; CCL2 qRT-PCR; Western blot; CCL2 ELISA; macrophage recruitment/feedback assays
E_00765	2021	35122059	TNF-α-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer	Homo sapiens	hg38	chr17	34255285	34257203	JUN	CCL2	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	primary PDAC epithelial cells	NA	malignant cell	CL:0001064	Functional perturbation assay; TF binding/epigenomic regulatory assay	JUN/JUNB and H3K27ac ChIP-seq; ATAC-seq; RNA-seq; chromatin-conformation/i4C-associated profiling; patient/PDX transcriptomic integration	JUN ChIP-qPCR; JUN siRNA/overexpression; BET/JQ1 inhibition; CCL2 qRT-PCR; Western blot; CCL2 ELISA; macrophage recruitment/feedback assays
E_00766	2016	26656844	Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers	Homo sapiens	hg19	chr8	129543949	129554294	NA	MYC	Super-enhancer	Active	Disease	endometrial carcinoma	MONDO:0002447	DOID:2871	uterus	UBERON:0000995	Endometrial Carcinoma Cell Lines Ishikawa	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR; RNAi/siRNA/shRNA
E_00767	2018	29236325	AML1/ETO trans-activates c-KIT expression through the long range interaction between promoter and intronic enhancer	Homo sapiens	hg19	chr4	55859107	55860311	RUNX1	KIT	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Kasumi-1,U937-AE	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR; RNAi/siRNA/shRNA
E_00768	2016	26656844	Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers	Homo sapiens	hg19	chr13	73880413	74042621	CEBPB	KLF5	Super-enhancer	Active	Disease	lung adenocarcinoma	MONDO:0005061	DOID:3910	lung	UBERON:0002048	Esophageal Carcinoma	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR; RNAi/siRNA/shRNA
E_00769	2016	26656844	Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers	Homo sapiens	hg19	chr13	73880413	74042621	NFE2L2	KLF5	Super-enhancer	Active	Disease	lung adenocarcinoma	MONDO:0005061	DOID:3910	lung	UBERON:0002048	Esophageal Carcinoma	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR; RNAi/siRNA/shRNA
E_00770	2023	37922339	Distinct use of super-enhancer elements controls cell type-specific CD25 transcription and function	Mus musculus	mm39	chr2	11664841	11664854	Stat5b	Il2ra	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	primary peripheral CD8-positive T cells	NA	CD8-positive, alpha-beta T cell	CL:0000625	TF binding assay; Super-enhancer constituent minimal functional core; STAT5-binding-site functional perturbation assay	STAT5B ChIP-seq; ATAC-seq; RNA-seq; H3K27ac HiChIP	CRISPR/Cas9 endogenous IN1a/IN1b deletion mouse model; cytokine stimulation; Flow cytometry; RT-qPCR/RT-PCR; CD25 protein-expression analysis
E_00771	2021	35122059	TNF-α-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer	Homo sapiens	hg38	chr10	17228241	17237593	JUN	VIM	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	Capan-2	CVCL_0026	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	JUN/JUNB and H3K27ac ChIP-seq; ATAC-seq; RNA-seq; chromatin-conformation/i4C-associated profiling; patient/PDX transcriptomic integration	VIM promoter+En2 luciferase reporter; JUN overexpression; ChIP-qPCR; RT-qPCR; Western blot
E_00772	2021	35122059	TNF-α-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer	Homo sapiens	hg38	chr10	17228241	17237593	JUN	VIM	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	PANC-1	CVCL_0480	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	JUN/JUNB and H3K27ac ChIP-seq; ATAC-seq; RNA-seq; chromatin-conformation/i4C-associated profiling; patient/PDX transcriptomic integration	VIM promoter+En2 luciferase reporter; JUN overexpression; ChIP-qPCR; RT-qPCR; Western blot
E_00773	2016	26656844	Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers	Homo sapiens	hg19	chr8	129188417	129189959	CEBPB	MYC	Enhancer	Active	Disease	lung adenocarcinoma	MONDO:0005061	DOID:3910	lung	UBERON:0002048	A-549	CVCL_0023	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Endogenous enhancer perturbation; TF motif functional assay	H3K27ac ChIP-seq; p300 ChIP-seq; DNase-seq; CEBPB ChIP-seq	Luciferase reporter assay; mini-e3 reporter dissection; site-directed CEBPB motif deletion; CEBPB siRNA knockdown; RT-qPCR; Western blot; CRISPR-Cas9 endogenous deletion/editing
E_00774	2016	26656844	Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers	Homo sapiens	hg19	chr8	129188417	129189959	NFE2L2	MYC	Enhancer	Active	Disease	lung adenocarcinoma	MONDO:0005061	DOID:3910	lung	UBERON:0002048	A-549	CVCL_0023	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Endogenous enhancer perturbation; TF motif functional assay	H3K27ac ChIP-seq; p300 ChIP-seq; DNase-seq; NFE2L2 ChIP-seq	Luciferase reporter assay; mini-e3 reporter dissection; site-directed NFE2L2 motif deletion; NFE2L2 siRNA knockdown; RT-qPCR; Western blot; CRISPR-Cas9 endogenous deletion/editing
E_00775	2016	26656844	Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers	Homo sapiens	hg19	chr20	48997377	49019434	NA	PARD6B	Super-enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Hep-G2	CVCL_0027	hepatocyte	CL:0000182	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR; RNAi/siRNA/shRNA
E_00776	2023	37702072	Temporal analyses reveal a pivotal role for sense and antisense enhancer RNAs in coordinate immunoglobulin lambda locus activation	Mus musculus	mm10	chr16	19007329	19008187	Irf4	Iglv1	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	PIPER-15 inducible pro-B-cell model	NA	pro-B cell	CL:0000826	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Endogenous functional perturbation assay	Pro-/pre-B ATAC-seq; GRO-seq; MED1 chromatin-data integration	CRISPR/Cas9 deletion spanning PU.1/IRF4 sites; temporal ChIP-qPCR; 3C-qPCR; eRNA perturbation; RT-qPCR
E_00777	2023	37702072	Temporal analyses reveal a pivotal role for sense and antisense enhancer RNAs in coordinate immunoglobulin lambda locus activation	Mus musculus	mm10	chr16	19007329	19008187	Spi1	Iglv1	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	PIPER-15 inducible pro-B-cell model	NA	pro-B cell	CL:0000826	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Endogenous functional perturbation assay	Pro-/pre-B ATAC-seq; GRO-seq; MED1 chromatin-data integration	CRISPR/Cas9 deletion spanning PU.1/IRF4 sites; temporal ChIP-qPCR; 3C-qPCR; eRNA perturbation; RT-qPCR
E_00778	2023	37702072	Temporal analyses reveal a pivotal role for sense and antisense enhancer RNAs in coordinate immunoglobulin lambda locus activation	Mus musculus	mm10	chr16	19026931	19027772	Irf4	Iglj1	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	PIPER-15 inducible pro-B-cell model	NA	pro-B cell	CL:0000826	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Endogenous functional perturbation assay	Pro-/pre-B ATAC-seq; GRO-seq; MED1 chromatin-data integration	CRISPR/Cas9 deletion spanning PU.1/IRF4 sites; temporal ChIP-qPCR; 3C-qPCR; eRNA shRNA perturbation; RT-qPCR; Sanger sequencing
E_00779	2023	37702072	Temporal analyses reveal a pivotal role for sense and antisense enhancer RNAs in coordinate immunoglobulin lambda locus activation	Mus musculus	mm10	chr16	19026931	19027772	Spi1	Iglj1	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	PIPER-15 inducible pro-B-cell model	NA	pro-B cell	CL:0000826	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Endogenous functional perturbation assay	Pro-/pre-B ATAC-seq; GRO-seq; MED1 chromatin-data integration	CRISPR/Cas9 deletion spanning PU.1/IRF4 sites; temporal ChIP-qPCR; 3C-qPCR; eRNA shRNA perturbation; RT-qPCR
E_00780	2023	37922339	Distinct use of super-enhancer elements controls cell type-specific CD25 transcription and function	Mus musculus	mm10	chr2	11621753	11635500	Rbpj	Il2ra	Super-enhancer	Active	Normal	NA	NA	NA	thymus	UBERON:0002370	DN thymocytes	NA	double negative thymocyte	CL:0002489	Endogenous enhancer perturbation; In vivo functional validation; Regulatory element functional validation; 3D chromatin interaction mapping	ChIP-seq, HiChIP; RNA-seq	CRISPR-Cas9 deletion, flow cytometry, reporter assay; Mouse genetic deletion/knock-in
E_00781	2023	37922339	Distinct use of super-enhancer elements controls cell type-specific CD25 transcription and function	Mus musculus	mm10	chr2	11621753	11635500	Stat5b	Il2ra	Super-enhancer	Active	Normal	NA	NA	NA	thymus	UBERON:0002370	DN thymocytes	NA	double negative thymocyte	CL:0002489	Endogenous enhancer perturbation; In vivo functional validation; Regulatory element functional validation; 3D chromatin interaction mapping	ChIP-seq, HiChIP; RNA-seq	CRISPR-Cas9 deletion, flow cytometry, reporter assay; Mouse genetic deletion/knock-in
E_00782	2021	35122059	TNF-α-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer	Homo sapiens	hg38	chr17	34255285	34257203	JUN	CCL2	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	AsPC-1	CVCL_0152	malignant cell	CL:0001064	Functional perturbation assay; TF binding/epigenomic regulatory assay	JUN/JUNB and H3K27ac ChIP-seq; ATAC-seq; RNA-seq; chromatin-conformation/i4C-associated profiling; patient/PDX transcriptomic integration	JUN ChIP-qPCR; JUN siRNA/overexpression; BET/JQ1 inhibition; CCL2 qRT-PCR; Western blot; CCL2 ELISA; macrophage recruitment/feedback assays
E_00783	2021	35122059	TNF-α-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer	Homo sapiens	hg38	chr17	34255285	34257203	JUN	CCL2	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	Capan-1	CVCL_0237	malignant cell	CL:0001064	Functional perturbation assay; TF binding/epigenomic regulatory assay	JUN/JUNB and H3K27ac ChIP-seq; ATAC-seq; RNA-seq; chromatin-conformation/i4C-associated profiling; patient/PDX transcriptomic integration	JUN ChIP-qPCR; JUN siRNA/overexpression; BET/JQ1 inhibition; CCL2 qRT-PCR; Western blot; CCL2 ELISA; macrophage recruitment/feedback assays
E_00784	2021	35122059	TNF-α-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer	Homo sapiens	hg38	chr17	34255285	34257203	JUN	CCL2	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	MIA PaCa-2	CVCL_0428	malignant cell	CL:0001064	Functional perturbation assay; TF binding/epigenomic regulatory assay	JUN/JUNB and H3K27ac ChIP-seq; ATAC-seq; RNA-seq; chromatin-conformation/i4C-associated profiling; patient/PDX transcriptomic integration	JUN ChIP-qPCR; JUN siRNA/overexpression; BET/JQ1 inhibition; CCL2 qRT-PCR; Western blot; CCL2 ELISA; macrophage recruitment/feedback assays
E_00785	2021	35122059	TNF-α-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer	Homo sapiens	hg38	chr17	34255285	34257203	JUN	CCL2	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	PANC-1	CVCL_0480	malignant cell	CL:0001064	Functional perturbation assay; TF binding/epigenomic regulatory assay	JUN/JUNB and H3K27ac ChIP-seq; ATAC-seq; RNA-seq; chromatin-conformation/i4C-associated profiling; patient/PDX transcriptomic integration	JUN ChIP-qPCR; JUN siRNA/overexpression; BET/JQ1 inhibition; CCL2 qRT-PCR; Western blot; CCL2 ELISA; macrophage recruitment/feedback assays
E_00786	2021	35122059	TNF-α-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer	Homo sapiens	hg38	chr17	34255285	34257203	JUN	CCL2	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	PDX-derived basal-like PDAC cells	NA	malignant cell	CL:0001064	Functional perturbation assay; TF binding/epigenomic regulatory assay	JUN/JUNB and H3K27ac ChIP-seq; ATAC-seq; RNA-seq; chromatin-conformation/i4C-associated profiling; patient/PDX transcriptomic integration	JUN ChIP-qPCR; JUN siRNA/overexpression; BET/JQ1 inhibition; CCL2 qRT-PCR; Western blot; CCL2 ELISA; macrophage recruitment/feedback assays
E_00787	2018	29236325	AML1/ETO trans-activates c-KIT expression through the long range interaction between promoter and intronic enhancer	Homo sapiens	hg19	chr4	55572140	55572780	RUNX1::RUNX1T1	KIT	Enhancer	Active	Disease	acute myeloid leukemia with t(8; 21)(q22; q22.1)	MONDO:0850492	DOID:0081093	blood	UBERON:0000178	Kasumi-1	CVCL_0589	myeloblast	CL:0000835	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq data analysis; patient expression-cohort analysis; ChIP-seq; 3C	Luciferase reporter assay; ChIP-qPCR; ChIP-3CqPCR; siRNA knockdown; RT-qPCR; Reporter assay; qPCR
E_00788	2018	29236325	AML1/ETO trans-activates c-KIT expression through the long range interaction between promoter and intronic enhancer	Homo sapiens	hg19	chr4	55575000	55577000	RUNX1::RUNX1T1	KIT	Enhancer	Active	Disease	acute myeloid leukemia with t(8; 21)(q22; q22.1)	MONDO:0850492	DOID:0081093	blood	UBERON:0000178	Kasumi-1	CVCL_0589	myeloblast	CL:0000835	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	AML1/ETO and cofactor ChIP-seq data analysis; AML patient expression-cohort analysis; ChIP-seq; 3C	Luciferase reporter assay; ChIP-qPCR; ChIP-3C-qPCR; AML1/ETO siRNA knockdown; RT-qPCR; Reporter assay; qPCR
E_00789	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181703	190182534	Gata2	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	Lymphatic endothelial cells (LECs)	NA	endothelial cell of lymphatic vessel	CL:0002138	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; 3C-seq	Transgenic reporter assay; CRISPR knockout; ChIP-qPCR, qRT-PCR; Immunostaining
E_00790	2021	35122059	TNF-α-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer	Homo sapiens	hg38	chr1	58751000	58752500	JUN	JUN	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	primary/PDX PDAC epithelial cells	NA	malignant cell	CL:0001064	Functional perturbation assay; Enhancer-reprogramming/TF occupancy assay	JUN/JUNB and H3K27ac ChIP-seq; ATAC-seq; RNA-seq; chromatin-conformation/i4C-associated profiling; patient/PDX transcriptomic integration	JUN ChIP-qPCR; JUN knockdown/overexpression; BET/JQ1 perturbation; TNF--- stimulation; RT-qPCR; Western blot
E_00791	2021	35122059	TNF-α-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer	Homo sapiens	hg38	chr1	58765000	58766500	JUN	JUN	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	primary/PDX PDAC epithelial cells	NA	malignant cell	CL:0001064	Functional perturbation assay; Enhancer-reprogramming/TF occupancy assay	JUN/JUNB and H3K27ac ChIP-seq; ATAC-seq; RNA-seq; chromatin-conformation/i4C-associated profiling; patient/PDX transcriptomic integration	JUN ChIP-qPCR; JUN knockdown/overexpression; BET/JQ1 perturbation; TNF--- stimulation; RT-qPCR; Western blot
E_00792	2021	35122059	TNF-α-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer	Homo sapiens	hg38	chr1	58770000	58771500	JUN	JUN	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	primary/PDX PDAC epithelial cells	NA	malignant cell	CL:0001064	Functional perturbation assay; Enhancer-reprogramming/TF occupancy assay	JUN/JUNB and H3K27ac ChIP-seq; ATAC-seq; RNA-seq; chromatin-conformation/i4C-associated profiling; patient/PDX transcriptomic integration	JUN ChIP-qPCR; JUN knockdown/overexpression; BET/JQ1 perturbation; TNF--- stimulation; RT-qPCR; Western blot
E_00793	2021	35122059	TNF-α-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer	Homo sapiens	hg38	chr17	34255285	34257203	JUN	CCL2	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	HEK293	CVCL_0045	assay cell	NA	Functional perturbation assay; TF binding/epigenomic regulatory assay	JUN/JUNB and H3K27ac ChIP-seq; ATAC-seq; RNA-seq; chromatin-conformation/i4C-associated profiling; patient/PDX transcriptomic integration	JUN ChIP-qPCR; JUN siRNA/overexpression; BET/JQ1 inhibition; CCL2 qRT-PCR; Western blot; CCL2 ELISA; macrophage recruitment/feedback assays
E_00794	2016	26656844	Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers	Homo sapiens	hg19	chr8	129166547	129190290	CEBPB	MYC	Super-enhancer	Active	Disease	lung adenocarcinoma	MONDO:0005061	DOID:3910	lung	UBERON:0002048	Human non-small cell lung carcinoma cell	NA	malignant cell	CL:0001064	Endogenous enhancer perturbation; Epigenomic mapping; Enhancer functional validation; Genome editing	GISTIC copy number analysis, H3K27ac ChIP-seq, p300 ChIP-seq; DNase-seq; RNA-seq, NFE2L2 ChIP-seq, CEBPB ChIP-seq, Gene set enrichment analysis	Luciferase reporter assay, CRISPR-Cas9 enhancer deletion, CRISPR dCas9 KRAB repression, Chromosome conformation capture RT-qPCR, siRNA knockdown, Clonogenic growth assay, Anchorage independent growth assay, TaqMan RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_00795	2016	26656844	Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers	Homo sapiens	hg19	chr8	129166547	129190290	NFE2L2	MYC	Super-enhancer	Active	Disease	lung adenocarcinoma	MONDO:0005061	DOID:3910	lung	UBERON:0002048	Human non-small cell lung carcinoma cell	NA	malignant cell	CL:0001064	Endogenous enhancer perturbation; Epigenomic mapping; Enhancer functional validation; Genome editing	GISTIC copy number analysis, H3K27ac ChIP-seq, p300 ChIP-seq; DNase-seq; RNA-seq, NFE2L2 ChIP-seq, CEBPB ChIP-seq, Gene set enrichment analysis	Luciferase reporter assay, CRISPR-Cas9 enhancer deletion, CRISPR dCas9 KRAB repression, Chromosome conformation capture RT-qPCR, siRNA knockdown, Clonogenic growth assay, Anchorage independent growth assay, TaqMan RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_00796	2016	26656844	Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers	Homo sapiens	hg19	chr8	129543949	129554294	NA	MYC	Super-enhancer	Active	Disease	endometrial carcinoma	MONDO:0002447	DOID:2871	endometrium	UBERON:0001295	Ishikawa	CVCL_2529	malignant cell	CL:0001064	Chromatin interaction assay; Endogenous enhancer perturbation; Super-enhancer profiling; Copy-number-expression association analysis	H3K27ac ChIP-seq; p300 ChIP-seq; DNase-seq; TCGA copy-number analysis; RNA-seq; ROSE super-enhancer calling	3C-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_00797	2016	26656844	Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers	Homo sapiens	hg19	chr8	129543949	129554294	NA	MYC	Super-enhancer	Active	Disease	endometrial carcinoma	MONDO:0002447	DOID:2871	endometrium	UBERON:0001295	Ishikawa	CVCL_2529	epithelial cell	CL:0000066	Chromatin interaction assay; Endogenous enhancer perturbation; Super-enhancer profiling; Copy-number amplification analysis	H3K27ac ChIP-seq; p300 ChIP-seq; copy-number analysis	3C-qPCR; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_00798	2016	26656844	Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers	Homo sapiens	hg19	chr13	73880690	73990596	NA	KLF5	Super-enhancer	Active	Disease	Esophageal Carcinoma	NA	DOID:1107	NA	NA	BICR-31	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR; RNAi/siRNA/shRNA
E_00799	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Foxc2	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	Primary embryonic mouse lymphatic endothelium	NA	endothelial cell of lymphatic vessel	CL:0002138	Enhancer activity assay; Endogenous enhancer perturbation; In vivo functional validation; TF binding assay; Chromatin interaction assay; endogenous functional perturbation	ChIP-seq; RNA-seq; transcriptome profiling	CRISPR-Cas9 GATA2-site deletion; transgenic lacZ reporter; ChIP-qPCR/ChIP; 3C; Immunofluorescence; Flow cytometry; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_00800	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Foxc2	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	orthogonal TF occupancy in primary human dermal lymphatic endothelial cells	NA	endothelial cell of lymphatic vessel	CL:0002138	Enhancer activity assay; Endogenous enhancer perturbation; In vivo functional validation; TF binding assay; Chromatin interaction assay; endogenous functional perturbation	ChIP-seq; RNA-seq; transcriptome profiling	CRISPR-Cas9 GATA2-site deletion; transgenic lacZ reporter; ChIP-qPCR/ChIP; 3C; Immunofluorescence; Flow cytometry; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_00801	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Gata2	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	Primary embryonic mouse lymphatic endothelium	NA	endothelial cell of lymphatic vessel	CL:0002138	Enhancer activity assay; Endogenous enhancer perturbation; In vivo functional validation; TF binding assay; Chromatin interaction assay; endogenous functional perturbation	ChIP-seq; RNA-seq; transcriptome profiling	CRISPR-Cas9 5-bp GATA2-site deletion; transgenic lacZ reporter; ChIP-qPCR/ChIP; 3C; Immunofluorescence; Flow cytometry; OP9 differentiation; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_00802	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Gata2	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	orthogonal TF occupancy in primary human dermal lymphatic endothelial cells	NA	endothelial cell of lymphatic vessel	CL:0002138	Enhancer activity assay; Endogenous enhancer perturbation; In vivo functional validation; TF binding assay; Chromatin interaction assay; endogenous functional perturbation	ChIP-seq; RNA-seq; transcriptome profiling	CRISPR-Cas9 5-bp GATA2-site deletion; transgenic lacZ reporter; ChIP-qPCR/ChIP; 3C; Immunofluorescence; Flow cytometry; OP9 differentiation; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_00803	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Nfatc1	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	Primary embryonic mouse lymphatic endothelium	NA	endothelial cell of lymphatic vessel	CL:0002138	Enhancer activity assay; Endogenous enhancer perturbation; In vivo functional validation; TF binding assay; Chromatin interaction assay; endogenous functional perturbation	ChIP-seq; RNA-seq; transcriptome profiling	CRISPR-Cas9 GATA2-site deletion; transgenic lacZ reporter; ChIP-qPCR/ChIP; 3C; Immunofluorescence; Flow cytometry; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_00804	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Nfatc1	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	orthogonal TF occupancy in primary human dermal lymphatic endothelial cells	NA	endothelial cell of lymphatic vessel	CL:0002138	Enhancer activity assay; Endogenous enhancer perturbation; In vivo functional validation; TF binding assay; Chromatin interaction assay; endogenous functional perturbation	ChIP-seq; RNA-seq; transcriptome profiling	CRISPR-Cas9 GATA2-site deletion; transgenic lacZ reporter; ChIP-qPCR/ChIP; 3C; Immunofluorescence; Flow cytometry; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_00805	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Prox1	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	Primary embryonic mouse lymphatic endothelium	NA	endothelial cell of lymphatic vessel	CL:0002138	Enhancer activity assay; Endogenous enhancer perturbation; In vivo functional validation; TF binding assay; Chromatin interaction assay; endogenous functional perturbation	ChIP-seq; RNA-seq; transcriptome profiling	CRISPR-Cas9 GATA2-site deletion; transgenic lacZ reporter; ChIP-qPCR/ChIP; 3C; Immunofluorescence; Flow cytometry; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_00806	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Prox1	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	orthogonal TF occupancy in primary human dermal lymphatic endothelial cells	NA	endothelial cell of lymphatic vessel	CL:0002138	Enhancer activity assay; Endogenous enhancer perturbation; In vivo functional validation; TF binding assay; Chromatin interaction assay; endogenous functional perturbation	ChIP-seq; RNA-seq; transcriptome profiling	CRISPR-Cas9 GATA2-site deletion; transgenic lacZ reporter; ChIP-qPCR/ChIP; 3C; Immunofluorescence; Flow cytometry; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_00807	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Gata2	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	Primary embryonic mouse lymphatic endothelial cells	NA	endothelial cell of lymphatic vessel	CL:0002138	Developmental enhancer activity; TF binding; Enhancer-promoter interaction; endogenous motif/enhancer perturbation; in vivo lineage phenotyping	ChIP-seq; RNA-seq/transcriptome profiling	CRISPR-Cas9 GATA2-site/enhancer editing; transgenic lacZ reporter; ChIP-qPCR; 3C; Immunofluorescence; Flow cytometry; OP9 differentiation; mouse genetic phenotyping
E_00808	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Gata2	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	primary human dermal lymphatic endothelial cells for orthogonal occupancy validation	NA	endothelial cell of lymphatic vessel	CL:0002138	Developmental enhancer activity; TF binding; Enhancer-promoter interaction; endogenous motif/enhancer perturbation; in vivo lineage phenotyping	ChIP-seq; RNA-seq/transcriptome profiling	CRISPR-Cas9 GATA2-site/enhancer editing; transgenic lacZ reporter; ChIP-qPCR; 3C; Immunofluorescence; Flow cytometry; OP9 differentiation; mouse genetic phenotyping
E_00809	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Foxc2	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	Primary embryonic mouse lymphatic endothelial cells	NA	endothelial cell of lymphatic vessel	CL:0002138	Developmental enhancer activity; TF binding; Enhancer-promoter interaction; endogenous motif/enhancer perturbation; in vivo lineage phenotyping	ChIP-seq; RNA-seq/transcriptome profiling	CRISPR-Cas9 GATA2-site/enhancer editing; transgenic lacZ reporter; ChIP-qPCR; 3C; Immunofluorescence; Flow cytometry; OP9 differentiation; mouse genetic phenotyping
E_00810	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Foxc2	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	primary human dermal lymphatic endothelial cells for orthogonal occupancy validation	NA	endothelial cell of lymphatic vessel	CL:0002138	Developmental enhancer activity; TF binding; Enhancer-promoter interaction; endogenous motif/enhancer perturbation; in vivo lineage phenotyping	ChIP-seq; RNA-seq/transcriptome profiling	CRISPR-Cas9 GATA2-site/enhancer editing; transgenic lacZ reporter; ChIP-qPCR; 3C; Immunofluorescence; Flow cytometry; OP9 differentiation; mouse genetic phenotyping
E_00811	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Nfatc1	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	Primary embryonic mouse lymphatic endothelial cells	NA	endothelial cell of lymphatic vessel	CL:0002138	Developmental enhancer activity; TF binding; Enhancer-promoter interaction; endogenous motif/enhancer perturbation; in vivo lineage phenotyping	ChIP-seq; RNA-seq/transcriptome profiling	CRISPR-Cas9 GATA2-site/enhancer editing; transgenic lacZ reporter; ChIP-qPCR; 3C; Immunofluorescence; Flow cytometry; OP9 differentiation; mouse genetic phenotyping
E_00812	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Nfatc1	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	primary human dermal lymphatic endothelial cells for orthogonal occupancy validation	NA	endothelial cell of lymphatic vessel	CL:0002138	Developmental enhancer activity; TF binding; Enhancer-promoter interaction; endogenous motif/enhancer perturbation; in vivo lineage phenotyping	ChIP-seq; RNA-seq/transcriptome profiling	CRISPR-Cas9 GATA2-site/enhancer editing; transgenic lacZ reporter; ChIP-qPCR; 3C; Immunofluorescence; Flow cytometry; OP9 differentiation; mouse genetic phenotyping
E_00813	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Prox1	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	Primary embryonic mouse lymphatic endothelial cells	NA	endothelial cell of lymphatic vessel	CL:0002138	Developmental enhancer activity; TF binding; Enhancer-promoter interaction; endogenous motif/enhancer perturbation; in vivo lineage phenotyping	ChIP-seq; RNA-seq/transcriptome profiling	CRISPR-Cas9 GATA2-site/enhancer editing; transgenic lacZ reporter; ChIP-qPCR; 3C; Immunofluorescence; Flow cytometry; OP9 differentiation; mouse genetic phenotyping
E_00814	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Prox1	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	primary human dermal lymphatic endothelial cells for orthogonal occupancy validation	NA	endothelial cell of lymphatic vessel	CL:0002138	Developmental enhancer activity; TF binding; Enhancer-promoter interaction; endogenous motif/enhancer perturbation; in vivo lineage phenotyping	ChIP-seq; RNA-seq/transcriptome profiling	CRISPR-Cas9 GATA2-site/enhancer editing; transgenic lacZ reporter; ChIP-qPCR; 3C; Immunofluorescence; Flow cytometry; OP9 differentiation; mouse genetic phenotyping
E_00815	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Gata2	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	Primary embryonic mouse lymphatic endothelial cells	NA	endothelial cell of lymphatic vessel	CL:0002138	Prox1 ?11-kb developmental enhancer; direct TF occupancy; GATA2-site endogenous editing; Enhancer-promoter interaction; in vivo lymphatic-endothelial identity validation	ChIP-seq; RNA-seq/transcriptome profiling	CRISPR-Cas9 5-bp GATA2-site editing; transgenic lacZ reporter; ChIP-qPCR/ChIP; 3C; Immunofluorescence; Flow cytometry; OP9 differentiation; mouse genetic phenotyping
E_00816	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Gata2	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	primary human dermal lymphatic endothelial cells for orthogonal occupancy validation	NA	endothelial cell of lymphatic vessel	CL:0002138	Prox1 ?11-kb developmental enhancer; direct TF occupancy; GATA2-site endogenous editing; Enhancer-promoter interaction; in vivo lymphatic-endothelial identity validation	ChIP-seq; RNA-seq/transcriptome profiling	CRISPR-Cas9 5-bp GATA2-site editing; transgenic lacZ reporter; ChIP-qPCR/ChIP; 3C; Immunofluorescence; Flow cytometry; OP9 differentiation; mouse genetic phenotyping
E_00817	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Foxc2	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	Primary embryonic mouse lymphatic endothelial cells	NA	endothelial cell of lymphatic vessel	CL:0002138	Prox1 ?11-kb developmental enhancer; FOXC2 occupancy; Enhancer-promoter interaction; endogenous enhancer/motif perturbation and in vivo lymphatic-lineage validation	ChIP-seq; RNA-seq/transcriptome profiling	CRISPR-Cas9 GATA2-site/enhancer editing; transgenic lacZ reporter; ChIP-qPCR/ChIP; 3C; Immunofluorescence; Flow cytometry; OP9 differentiation; mouse genetic phenotyping
E_00818	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Foxc2	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	primary human dermal lymphatic endothelial cells for orthogonal occupancy validation	NA	endothelial cell of lymphatic vessel	CL:0002138	Prox1 ?11-kb developmental enhancer; FOXC2 occupancy; Enhancer-promoter interaction; endogenous enhancer/motif perturbation and in vivo lymphatic-lineage validation	ChIP-seq; RNA-seq/transcriptome profiling	CRISPR-Cas9 GATA2-site/enhancer editing; transgenic lacZ reporter; ChIP-qPCR/ChIP; 3C; Immunofluorescence; Flow cytometry; OP9 differentiation; mouse genetic phenotyping
E_00819	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Nfatc1	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	Primary embryonic mouse lymphatic endothelial cells	NA	endothelial cell of lymphatic vessel	CL:0002138	Prox1 ?11-kb developmental enhancer; NFATC1 occupancy; Enhancer-promoter interaction; endogenous enhancer/motif perturbation and in vivo lymphatic-lineage validation	ChIP-seq; RNA-seq/transcriptome profiling	CRISPR-Cas9 GATA2-site/enhancer editing; transgenic lacZ reporter; ChIP-qPCR/ChIP; 3C; Immunofluorescence; Flow cytometry; OP9 differentiation; mouse genetic phenotyping
E_00820	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Nfatc1	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	primary human dermal lymphatic endothelial cells for orthogonal occupancy validation	NA	endothelial cell of lymphatic vessel	CL:0002138	Prox1 ?11-kb developmental enhancer; NFATC1 occupancy; Enhancer-promoter interaction; endogenous enhancer/motif perturbation and in vivo lymphatic-lineage validation	ChIP-seq; RNA-seq/transcriptome profiling	CRISPR-Cas9 GATA2-site/enhancer editing; transgenic lacZ reporter; ChIP-qPCR/ChIP; 3C; Immunofluorescence; Flow cytometry; OP9 differentiation; mouse genetic phenotyping
E_00821	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Prox1	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	Primary embryonic mouse lymphatic endothelial cells	NA	endothelial cell of lymphatic vessel	CL:0002138	Prox1 ?11-kb developmental enhancer; PROX1 occupancy/autoregulatory association; Enhancer-promoter interaction; endogenous enhancer perturbation and in vivo lymphatic-lineage validation	ChIP-seq; RNA-seq/transcriptome profiling	CRISPR-Cas9 GATA2-site/enhancer editing; transgenic lacZ reporter; ChIP-qPCR/ChIP; 3C; Immunofluorescence; Flow cytometry; OP9 differentiation; mouse genetic phenotyping
E_00822	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Prox1	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	primary human dermal lymphatic endothelial cells for orthogonal occupancy validation	NA	endothelial cell of lymphatic vessel	CL:0002138	Prox1 ?11-kb developmental enhancer; PROX1 occupancy/autoregulatory association; Enhancer-promoter interaction; endogenous enhancer perturbation and in vivo lymphatic-lineage validation	ChIP-seq; RNA-seq/transcriptome profiling	CRISPR-Cas9 GATA2-site/enhancer editing; transgenic lacZ reporter; ChIP-qPCR/ChIP; 3C; Immunofluorescence; Flow cytometry; OP9 differentiation; mouse genetic phenotyping
E_00823	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Gata2	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	Primary embryonic mouse lymphatic endothelial cells	NA	endothelial cell of lymphatic vessel	CL:0002138	Prox1 ?11-kb enhancer; direct TF occupancy; Enhancer-promoter interaction; endogenous GATA2-motif editing; in vivo lineage phenotyping	ChIP-seq; RNA-seq	CRISPR-Cas9 5-bp GATA2-site editing; transgenic lacZ reporter; ChIP-qPCR; 3C; Immunofluorescence; Flow cytometry; OP9 differentiation; mouse genetic phenotyping
E_00824	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Gata2	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	primary human dermal lymphatic endothelial cells for orthogonal occupancy validation	NA	endothelial cell of lymphatic vessel	CL:0002138	Prox1 ?11-kb enhancer; direct TF occupancy; Enhancer-promoter interaction; endogenous GATA2-motif editing; in vivo lineage phenotyping	ChIP-seq; RNA-seq	CRISPR-Cas9 5-bp GATA2-site editing; transgenic lacZ reporter; ChIP-qPCR; 3C; Immunofluorescence; Flow cytometry; OP9 differentiation; mouse genetic phenotyping
E_00825	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Foxc2	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	Primary embryonic mouse lymphatic endothelial cells	NA	endothelial cell of lymphatic vessel	CL:0002138	Endogenous enhancer perturbation; Prox1 ?11-kb enhancer; FOXC2 occupancy; Enhancer-promoter interaction; in vivo lineage validation	ChIP-seq; RNA-seq	CRISPR-Cas9 GATA2-site editing; transgenic lacZ reporter; ChIP-qPCR; 3C; Immunofluorescence; Flow cytometry; mouse genetic phenotyping
E_00826	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Nfatc1	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	Primary embryonic mouse lymphatic endothelial cells	NA	endothelial cell of lymphatic vessel	CL:0002138	Endogenous enhancer perturbation; Prox1 ?11-kb enhancer; NFATC1 occupancy; Enhancer-promoter interaction; in vivo lineage validation	ChIP-seq; RNA-seq	CRISPR-Cas9 GATA2-site editing; transgenic lacZ reporter; ChIP-qPCR; 3C; Immunofluorescence; Flow cytometry; mouse genetic phenotyping
E_00827	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Prox1	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	Primary embryonic mouse lymphatic endothelial cells	NA	endothelial cell of lymphatic vessel	CL:0002138	Endogenous enhancer perturbation; Prox1 ?11-kb enhancer; PROX1 occupancy/autoregulatory association; Enhancer-promoter interaction; in vivo lineage validation	ChIP-seq; RNA-seq	CRISPR-Cas9 GATA2-site editing; transgenic lacZ reporter; ChIP-qPCR; 3C; Immunofluorescence; Flow cytometry; mouse genetic phenotyping
E_00828	2021	35122059	TNF-α-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer	Homo sapiens	hg38	chr1	58751000	58752500	JUN	JUN	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	MIA PaCa-2	CVCL_0428	malignant cell	CL:0001064	Functional perturbation assay; Enhancer-reprogramming/TF occupancy assay	JUN/JUNB and H3K27ac ChIP-seq; ATAC-seq; RNA-seq; chromatin-conformation/i4C-associated profiling; patient/PDX transcriptomic integration	JUN ChIP-qPCR; JUN knockdown/overexpression; BET/JQ1 perturbation; TNF--- stimulation; RT-qPCR; Western blot
E_00829	2021	35122059	TNF-α-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer	Homo sapiens	hg38	chr1	58751000	58752500	JUN	JUN	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	PANC-1	CVCL_0480	malignant cell	CL:0001064	Functional perturbation assay; Enhancer-reprogramming/TF occupancy assay	JUN/JUNB and H3K27ac ChIP-seq; ATAC-seq; RNA-seq; chromatin-conformation/i4C-associated profiling; patient/PDX transcriptomic integration	JUN ChIP-qPCR; JUN knockdown/overexpression; BET/JQ1 perturbation; TNF--- stimulation; RT-qPCR; Western blot
E_00830	2021	35122059	TNF-α-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer	Homo sapiens	hg38	chr1	58765000	58766500	JUN	JUN	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	MIA PaCa-2	CVCL_0428	malignant cell	CL:0001064	Functional perturbation assay; Enhancer-reprogramming/TF occupancy assay	JUN/JUNB and H3K27ac ChIP-seq; ATAC-seq; RNA-seq; chromatin-conformation/i4C-associated profiling; patient/PDX transcriptomic integration	JUN ChIP-qPCR; JUN knockdown/overexpression; BET/JQ1 perturbation; TNF--- stimulation; RT-qPCR; Western blot
E_00831	2021	35122059	TNF-α-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer	Homo sapiens	hg38	chr1	58765000	58766500	JUN	JUN	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	PANC-1	CVCL_0480	malignant cell	CL:0001064	Functional perturbation assay; Enhancer-reprogramming/TF occupancy assay	JUN/JUNB and H3K27ac ChIP-seq; ATAC-seq; RNA-seq; chromatin-conformation/i4C-associated profiling; patient/PDX transcriptomic integration	JUN ChIP-qPCR; JUN knockdown/overexpression; BET/JQ1 perturbation; TNF--- stimulation; RT-qPCR; Western blot
E_00832	2021	35122059	TNF-α-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer	Homo sapiens	hg38	chr1	58770000	58771500	JUN	JUN	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	MIA PaCa-2	CVCL_0428	malignant cell	CL:0001064	Functional perturbation assay; Enhancer-reprogramming/TF occupancy assay	JUN/JUNB and H3K27ac ChIP-seq; ATAC-seq; RNA-seq; chromatin-conformation/i4C-associated profiling; patient/PDX transcriptomic integration	JUN ChIP-qPCR; JUN knockdown/overexpression; BET/JQ1 perturbation; TNF--- stimulation; RT-qPCR; Western blot
E_00833	2021	35122059	TNF-α-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer	Homo sapiens	hg38	chr1	58770000	58771500	JUN	JUN	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	PANC-1	CVCL_0480	malignant cell	CL:0001064	Functional perturbation assay; Enhancer-reprogramming/TF occupancy assay	JUN/JUNB and H3K27ac ChIP-seq; ATAC-seq; RNA-seq; chromatin-conformation/i4C-associated profiling; patient/PDX transcriptomic integration	JUN ChIP-qPCR; JUN knockdown/overexpression; BET/JQ1 perturbation; TNF--- stimulation; RT-qPCR; Western blot
E_00834	2016	26656844	Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers	Homo sapiens	hg19	chr8	129188417	129189959	NA	MYC	Enhancer	Active	Disease	lung adenocarcinoma	MONDO:0005061	DOID:3910	lymph node	UBERON:0000029	NCI-H2009	CVCL_1514	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation; Chromatin profiling	H3K27ac ChIP-seq; p300 ChIP-seq; DNase-seq; RNA-seq; copy-number analysis	Luciferase reporter assay; KRAB-dCas9 CRISPRi; CRISPR-Cas9 enhancer deletion; RT-qPCR; deletion PCR and Sanger sequencing; anchorage-independent growth assay; clonogenic assay; CRISPR-Cas9 endogenous deletion/editing
E_00835	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Foxc2	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	human dermal lymphatic endothelial cells	NA	endothelial cell of lymphatic vessel	CL:0002138	Endogenous enhancer perturbation; Prox1 ?11-kb enhancer; FOXC2 occupancy; Enhancer-promoter interaction; in vivo lineage validation	ChIP-seq; RNA-seq	CRISPR-Cas9 GATA2-site editing; transgenic lacZ reporter; ChIP-qPCR; 3C; Immunofluorescence; Flow cytometry; mouse genetic phenotyping
E_00836	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Nfatc1	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	human dermal lymphatic endothelial cells	NA	endothelial cell of lymphatic vessel	CL:0002138	Endogenous enhancer perturbation; Prox1 ?11-kb enhancer; NFATC1 occupancy; Enhancer-promoter interaction; in vivo lineage validation	ChIP-seq; RNA-seq	CRISPR-Cas9 GATA2-site editing; transgenic lacZ reporter; ChIP-qPCR; 3C; Immunofluorescence; Flow cytometry; mouse genetic phenotyping
E_00837	2023	36697821	A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature	Mus musculus	mm10	chr1	190181400	190182400	Prox1	Prox1	Enhancer	Active	Normal	NA	NA	NA	lymphatic vessel	UBERON:0001473	human dermal lymphatic endothelial cells	NA	endothelial cell of lymphatic vessel	CL:0002138	Endogenous enhancer perturbation; Prox1 ?11-kb enhancer; PROX1 occupancy/autoregulatory association; Enhancer-promoter interaction; in vivo lineage validation	ChIP-seq; RNA-seq	CRISPR-Cas9 GATA2-site editing; transgenic lacZ reporter; ChIP-qPCR; 3C; Immunofluorescence; Flow cytometry; mouse genetic phenotyping
E_00838	2016	26656844	Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers	Homo sapiens	hg19	chr8	129188417	129189959	NA	MYC	Enhancer	Active	Disease	lung adenocarcinoma	MONDO:0005061	DOID:3910	lung	UBERON:0002048	NCI-H358	CVCL_1559	club cell	CL:0000158	Enhancer activity assay; Endogenous enhancer perturbation; Chromatin profiling	H3K27ac ChIP-seq; p300 ChIP-seq; DNase-seq	Luciferase reporter assay of constituent enhancers e1-e5; CRISPR-Cas9 endogenous deletion/editing
E_00839	2014	24413736	Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants	Homo sapiens	hg18	chr6	37883250	37883831	FOXA2	ZFAND3	Enhancer	Active	Disease	type 2 diabetes mellitus	MONDO:0005148	DOID:9352	islet of Langerhans	UBERON:0000006	primary human pancreatic islets	NA	NA	NA	Enhancer activity assay; TF binding assay; Disease-variant functional analysis; Allele-specific functional assay; Genetic risk-variant analysis	PDX1 ChIP-seq; FOXA2 ChIP-seq; NKX2-2 ChIP-seq; NKX6-1 ChIP-seq; H3K4me1 ChIP-seq; H3K27ac ChIP-seq; FAIRE-seq; RNA-seq	allele-specific luciferase reporter assay in MIN6 beta cells; EMSA; NEUROD1 supershift
E_00840	2014	24413736	Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants	Homo sapiens	hg18	chr6	37883250	37883831	NEUROD1	ZFAND3	Enhancer	Active	Disease	type 2 diabetes mellitus	MONDO:0005148	DOID:9352	islet of Langerhans	UBERON:0000006	primary human pancreatic islets	NA	NA	NA	Enhancer activity assay; TF binding assay; Disease-variant functional analysis; Allele-specific functional assay; Genetic risk-variant analysis	FOXA2 ChIP-seq; PDX1 ChIP-seq; NKX2-2 ChIP-seq; NKX6-1 ChIP-seq; MAFB ChIP-seq; H3K4me1 ChIP-seq; H3K27ac ChIP-seq; FAIRE-seq; RNA-seq	EMSA; NEUROD1 antibody supershift; allele-specific luciferase reporter assay in MIN6 beta cells
E_00841	2014	24413736	Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants	Homo sapiens	hg18	chr6	37883250	37883831	NKX2-2	ZFAND3	Enhancer	Active	Disease	type 2 diabetes mellitus	MONDO:0005148	DOID:9352	islet of Langerhans	UBERON:0000006	primary human pancreatic islets	NA	NA	NA	Enhancer activity assay; TF binding assay; Disease-variant functional analysis; Allele-specific functional assay; Genetic risk-variant analysis	PDX1 ChIP-seq; FOXA2 ChIP-seq; NKX2-2 ChIP-seq; NKX6-1 ChIP-seq; H3K4me1 ChIP-seq; H3K27ac ChIP-seq; FAIRE-seq; RNA-seq	allele-specific luciferase reporter assay in MIN6 beta cells; EMSA; NEUROD1 supershift
E_00842	2014	24413736	Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants	Homo sapiens	hg18	chr6	37883250	37883831	NKX6-1	ZFAND3	Enhancer	Active	Disease	type 2 diabetes mellitus	MONDO:0005148	DOID:9352	islet of Langerhans	UBERON:0000006	primary human pancreatic islets	NA	NA	NA	Enhancer activity assay; TF binding assay; Disease-variant functional analysis; Allele-specific functional assay; Genetic risk-variant analysis	PDX1 ChIP-seq; FOXA2 ChIP-seq; NKX2-2 ChIP-seq; NKX6-1 ChIP-seq; H3K4me1 ChIP-seq; H3K27ac ChIP-seq; FAIRE-seq; RNA-seq	allele-specific luciferase reporter assay in MIN6 beta cells; EMSA; NEUROD1 supershift
E_00843	2014	24413736	Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants	Homo sapiens	hg18	chr6	37883250	37883831	PDX1	ZFAND3	Enhancer	Active	Disease	type 2 diabetes mellitus	MONDO:0005148	DOID:9352	islet of Langerhans	UBERON:0000006	primary human pancreatic islets	NA	NA	NA	Enhancer activity assay; TF binding assay; Disease-variant functional analysis; Allele-specific functional assay; Genetic risk-variant analysis	PDX1 ChIP-seq; FOXA2 ChIP-seq; NKX2-2 ChIP-seq; NKX6-1 ChIP-seq; H3K4me1 ChIP-seq; H3K27ac ChIP-seq; FAIRE-seq; RNA-seq	allele-specific luciferase reporter assay in MIN6 beta cells; EMSA; NEUROD1 supershift
E_00844	2025	40604280	Range extender mediates long-distance enhancer activity	Homo sapiens	hg38	chr16	51623658	51623900	NA	SHH	Enhancer	Active	Normal	NA	NA	NA	forelimb bud	UBERON:0005417	Limb bud mesenchymal cells	NA	mesenchymal cell	CL:0008019	Enhancer activity assay; Functional perturbation assay	NA	Transgenic reporter assay; CRISPR Knock-in; PCR Genotyping; Skeletal staining; RT-qPCR; Knock-in mouse
E_00845	2014	24413736	Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants	Homo sapiens	hg19	chr10	114758249	114758449	FOXA2	TCF7L2	Enhancer	Active	Disease	type 2 diabetes mellitus	MONDO:0005148	DOID:9352	pancreas	UBERON:0001264	primary human pancreatic islets	NA	pancreatic endocrine cell	CL:0008024	Disease-risk enhancer mapping; TF binding; allele-specific enhancer activity	H3K27ac/H3K4me1 ChIP-seq; islet TF ChIP-seq; RNA-seq; chromatin-domain mapping	allele-specific DNA-binding and enhancer-reporter assays
E_00846	2014	24413736	Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants	Homo sapiens	hg19	chr10	114758249	114758449	MAFB	TCF7L2	Enhancer	Active	Disease	type 2 diabetes mellitus	MONDO:0005148	DOID:9352	pancreas	UBERON:0001264	primary human pancreatic islets	NA	pancreatic endocrine cell	CL:0008024	Disease-risk enhancer mapping; TF binding; allele-specific enhancer activity	H3K27ac/H3K4me1 ChIP-seq; islet TF ChIP-seq; RNA-seq; chromatin-domain mapping	allele-specific DNA-binding and enhancer-reporter assays
E_00847	2014	24413736	Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants	Homo sapiens	hg19	chr10	114758249	114758449	NKX2-2	TCF7L2	Enhancer	Active	Disease	type 2 diabetes mellitus	MONDO:0005148	DOID:9352	pancreas	UBERON:0001264	primary human pancreatic islets	NA	pancreatic endocrine cell	CL:0008024	Disease-risk enhancer mapping; TF binding; allele-specific enhancer activity	H3K27ac/H3K4me1 ChIP-seq; islet TF ChIP-seq; RNA-seq; chromatin-domain mapping	allele-specific DNA-binding and enhancer-reporter assays
E_00848	2014	24413736	Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants	Homo sapiens	hg19	chr5	50400000	50401200	FOXA2	ISL1	Enhancer	Active	Normal	NA	NA	NA	islet of Langerhans	UBERON:0000006	Human pancreatic islet	NA	pancreatic islet cell	NA	Enhancer activity assay	ChIP-seq	Luciferase reporter assay
E_00849	2025	40382324	Auricular malformations are driven by copy number variations in a hierarchical enhancer cluster and a dominant enhancer recapitulates human pathogenesis	Homo sapiens	hg19	chr4	8698911	8707711	MEIS1	HMX1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	SC monocyte-derived cells	NA	monocyte-derived cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; ATAC-seq; Hi-C; RNA-seq	Luciferase reporter assay; Transgenic reporter assay; CRISPR knockout; EMSA; ChIP-qPCR; RT-qPCR
E_00850	2022	34605909	Functional annotation and investigation of the 10q24.33 melanoma risk locus identifies a common variant that influences transcriptional regulation of OBFC1	Homo sapiens	hg19	chr10	105668100	105669000	MEOX2	STN1	Enhancer	Active	Disease	cutaneous melanoma	MONDO:0005012	DOID:8923	NA	NA	human neural crest cells	NA	neural crest cell	CL:0011012	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Regulatory variant functional assay	Hi-C; epigenomic annotation; tumor expression/eQTL analysis	Luciferase reporter assay; 3C; CRISPR-Cas9 enhancer deletion; MEOX2 binding analysis; RT-qPCR
E_00851	2022	35715427	Context-dependent enhancer function revealed by targeted inter-TAD relocation	Mus musculus	mm10	chr2	74075311	74075843	Hoxa13	Hoxd11	Enhancer	Active	Normal	NA	NA	NA	limb	UBERON:0002101	E12.5 distal forelimb cells	NA	limb bud mesenchymal cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay	ATAC-seq; CUT&RUN; Capture Hi-C	Transgenic LacZ reporter assay; pronuclear injection; HOX13-binding-site mutagenesis; CRISPR-Cas9 deletion; targeted enhancer relocation; whole-mount in situ hybridization; RT-qPCR
E_00852	2022	35715427	Context-dependent enhancer function revealed by targeted inter-TAD relocation	Mus musculus	mm10	chr2	74075311	74075843	Hoxa13	Hoxd12	Enhancer	Active	Normal	NA	NA	NA	limb	UBERON:0002101	E12.5 distal forelimb cells	NA	limb bud mesenchymal cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay	ATAC-seq; CUT&RUN; Capture Hi-C	Transgenic LacZ reporter assay; pronuclear injection; HOX13-binding-site mutagenesis; CRISPR-Cas9 deletion; targeted enhancer relocation; whole-mount in situ hybridization; RT-qPCR
E_00853	2022	35715427	Context-dependent enhancer function revealed by targeted inter-TAD relocation	Mus musculus	mm10	chr2	74075311	74075843	Hoxa13	Hoxd13	Enhancer	Active	Normal	NA	NA	NA	limb	UBERON:0002101	E12.5 distal forelimb cells	NA	limb bud mesenchymal cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay	ATAC-seq; CUT&RUN; Capture Hi-C	Transgenic LacZ reporter assay; pronuclear injection; HOX13-binding-site mutagenesis; CRISPR-Cas9 deletion; targeted enhancer relocation; whole-mount in situ hybridization; RT-qPCR
E_00854	2022	35715427	Context-dependent enhancer function revealed by targeted inter-TAD relocation	Mus musculus	mm10	chr2	74075311	74075843	Hoxd13	Hoxd11	Enhancer	Active	Normal	NA	NA	NA	limb	UBERON:0002101	E12.5 distal forelimb cells	NA	limb bud mesenchymal cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay	ATAC-seq; CUT&RUN; Capture Hi-C	Transgenic LacZ reporter assay; pronuclear injection; HOX13-binding-site mutagenesis; CRISPR-Cas9 deletion; targeted enhancer relocation; whole-mount in situ hybridization; RT-qPCR
E_00855	2022	35715427	Context-dependent enhancer function revealed by targeted inter-TAD relocation	Mus musculus	mm10	chr2	74075311	74075843	Hoxd13	Hoxd12	Enhancer	Active	Normal	NA	NA	NA	limb	UBERON:0002101	E12.5 distal forelimb cells	NA	limb bud mesenchymal cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay	ATAC-seq; CUT&RUN; Capture Hi-C	Transgenic LacZ reporter assay; pronuclear injection; HOX13-binding-site mutagenesis; CRISPR-Cas9 deletion; targeted enhancer relocation; whole-mount in situ hybridization; RT-qPCR
E_00856	2022	35715427	Context-dependent enhancer function revealed by targeted inter-TAD relocation	Mus musculus	mm10	chr2	74075311	74075843	Hoxd13	Hoxd13	Enhancer	Active	Normal	NA	NA	NA	limb	UBERON:0002101	E12.5 distal forelimb cells	NA	limb bud mesenchymal cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay	ATAC-seq; CUT&RUN; Capture Hi-C	Transgenic LacZ reporter assay; pronuclear injection; HOX13-binding-site mutagenesis; CRISPR-Cas9 deletion; targeted enhancer relocation; whole-mount in situ hybridization; RT-qPCR
E_00857	2022	35982471	Super-enhancer hijacking LINC01977 promotes malignancy of early-stage lung adenocarcinoma addicted to the canonical TGF-β/SMAD3 pathway	Homo sapiens	hg38	chr17	79459000	79507000	SMAD3	LINC01977	Super-enhancer	Active	Disease	lung adenocarcinoma	MONDO:0005061	DOID:3910	lung	UBERON:0002048	A-549	CVCL_0023	epithelial cell of lung	CL:0000082	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin-state profiling; In vivo functional validation	H3K27ac ChIP-seq (ENCODE reanalysis); H3K4me1 ChIP-seq (ENCODE reanalysis); Hi-C (ENCODE reanalysis); RNA-seq; ChIP-seq; Hi-C	Dual-luciferase reporter assay; ChIP-qPCR; qRT-PCR; JQ1 Treatment; TGF-β/SIS3/SB431542 Perturbation; LINC01977 ASO Knockdown; CRISPR-Cas9 Knockout of SMAD3/CREBBP/EP300; Western blot; EdU Assay; Transwell Migration and Invasion Assay; Colony Formation Assay; Tumor Spheroid Assay; In Vivo Xenograft Assay; Lung Metastasis Assay; Luciferase reporter assay; ChIP; In vivo phenotyping; Reporter assay
E_00858	2022	35982471	Super-enhancer hijacking LINC01977 promotes malignancy of early-stage lung adenocarcinoma addicted to the canonical TGF-β/SMAD3 pathway	Homo sapiens	hg19	chr17	79780000	79828000	CREBBP	LINC01977	Enhancer	Active	Disease	lung adenocarcinoma	MONDO:0005061	DOID:3910	lung	UBERON:0002048	PC-9	CVCL_B260	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin-state profiling; In vivo functional validation	ChIP-seq, Hi-C; RNA-seq; ChIP-seq; Hi-C	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot; Luciferase reporter assay; ChIP; In vivo phenotyping; Reporter assay
E_00859	2022	35982471	Super-enhancer hijacking LINC01977 promotes malignancy of early-stage lung adenocarcinoma addicted to the canonical TGF-β/SMAD3 pathway	Homo sapiens	hg19	chr17	79780000	79828000	SMAD3	LINC01977	Enhancer	Active	Disease	lung adenocarcinoma	MONDO:0005061	DOID:3910	lung	UBERON:0002048	PC-9	CVCL_B260	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin-state profiling; In vivo functional validation	ChIP-seq, Hi-C; RNA-seq; ChIP-seq; Hi-C	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot; Luciferase reporter assay; ChIP; In vivo phenotyping; Reporter assay
E_00860	2016	27693352	Enhancer Variants Synergistically Drive Dysfunction of a Gene Regulatory Network In Hirschsprung Disease	Homo sapiens	hg19	chr10	43581812	43582711	SOX10	RET	Enhancer	Active	Disease	Hirschsprung disease	MONDO:0018309	DOID:10487	intestine	UBERON:0000160	SK-N-SH	CVCL_0531	neuroblastoma cell line	NA	Enhancer activity assay; Allele-specific TF binding assay; Regulatory variant functional assay; In vivo developmental enhancer assay; Genetic association assay	Human fetal-intestine H3K4me1/H3K27ac epigenomic data; DNase-seq and ENCODE TF-binding data integration	Allele-specific luciferase reporter assay; EMSA; SOX10 ChIP-qPCR; SOX10 siRNA knockdown; RT-qPCR; transgenic mouse LacZ enhancer assay; genotyping and haplotype analysis
E_00861	2022	34605909	Functional annotation and investigation of the 10q24.33 melanoma risk locus identifies a common variant that influences transcriptional regulation of OBFC1	Homo sapiens	hg19	chr10	105668100	105669000	MEOX2	STN1	Enhancer	Active	Disease	cutaneous melanoma	MONDO:0005012	DOID:8923	zone of skin	UBERON:0000014	A-375	CVCL_0132	melanoma cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; Hi-C; 3C	Luciferase reporter assay, 3C; CRISPR knockout; RT-qPCR; Western blot; ChIP-qPCR; CRISPR-Cas9
E_00862	2022	34605909	Functional annotation and investigation of the 10q24.33 melanoma risk locus identifies a common variant that influences transcriptional regulation of OBFC1	Homo sapiens	hg19	chr10	105668100	105669000	MEOX2	STN1	Enhancer	Active	Disease	cutaneous melanoma	MONDO:0005012	DOID:8923	zone of skin	UBERON:0000014	CJM [Human OCSCC]	CVCL_8663	melanoma cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; Hi-C; 3C	Luciferase reporter assay, 3C; CRISPR knockout; RT-qPCR; Western blot; ChIP-qPCR; CRISPR-Cas9
E_00863	2022	34605909	Functional annotation and investigation of the 10q24.33 melanoma risk locus identifies a common variant that influences transcriptional regulation of OBFC1	Homo sapiens	hg19	chr10	105668100	105669000	MEOX2	STN1	Enhancer	Active	Disease	cutaneous melanoma	MONDO:0005012	DOID:8923	zone of skin	UBERON:0000014	UACC1816	NA	melanoma cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; Hi-C; 3C	Luciferase reporter assay, 3C; CRISPR knockout; RT-qPCR; Western blot; ChIP-qPCR; CRISPR-Cas9
E_00864	2022	34605909	Functional annotation and investigation of the 10q24.33 melanoma risk locus identifies a common variant that influences transcriptional regulation of OBFC1	Homo sapiens	hg19	chr10	105668100	105669000	MEOX2	STN1	Enhancer	Active	Normal	NA	NA	NA	neural crest	UBERON:0002342	human neural crest cells	NA	neural crest cell	CL:0011012	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; Hi-C; 3C	Luciferase reporter assay, 3C; CRISPR knockout; RT-qPCR; Western blot; ChIP-qPCR; CRISPR-Cas9
E_00865	2025	40382324	Auricular malformations are driven by copy number variations in a hierarchical enhancer cluster and a dominant enhancer recapitulates human pathogenesis	Homo sapiens	hg38	chr4	8691119	8700974	NA	HMX1	Enhancer	Active	Normal	NA	NA	NA	pulmonary lobule	UBERON:0010368	hCNCC	NA	cranial neural crest cell	NA	Enhancer activity assay; Functional perturbation assay	ATAC-seq; ChIP-seq	Luciferase reporter assay; CRISPR knockout; RT-qPCR
E_00866	2025	40382324	Auricular malformations are driven by copy number variations in a hierarchical enhancer cluster and a dominant enhancer recapitulates human pathogenesis	Homo sapiens	hg19	chr4	8712912	8728565	NA	HMX1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay	ChIP-seq; ATAC-seq, Hi-C	Transgenic reporter assay
E_00867	2016	27693352	Enhancer Variants Synergistically Drive Dysfunction of a Gene Regulatory Network In Hirschsprung Disease	Homo sapiens	hg19	chr10	43581812	43582888	SOX10	RET	Enhancer	Active	Disease	Hirschsprung disease	MONDO:0018309	DOID:10487	digestive tract	UBERON:0001555	human fetal gut	NA	enteric neural crest cell	NA	Enhancer-variant association; TF binding; functional enhancer assay	human fetal gut epigenomic profiling; chromatin-state and accessibility data integration	allele-specific luciferase; EMSA; transgenic enhancer assay; RET expression analysis
E_00868	2016	27693352	Enhancer Variants Synergistically Drive Dysfunction of a Gene Regulatory Network In Hirschsprung Disease	Homo sapiens	hg19	chr10	43581812	43582888	SOX10	RET	Enhancer	Active	Disease	Hirschsprung disease	MONDO:0018309	DOID:10487	digestive tract	UBERON:0001555	enteric neural crest reporter models	NA	enteric neural crest cell	NA	Enhancer-variant association; TF binding; functional enhancer assay	human fetal gut epigenomic profiling; chromatin-state and accessibility data integration	allele-specific luciferase; EMSA; transgenic enhancer assay; RET expression analysis
E_00869	2016	27693352	Enhancer Variants Synergistically Drive Dysfunction of a Gene Regulatory Network In Hirschsprung Disease	Homo sapiens	hg19	chr10	43447346	43448347	RARB	RET	Enhancer	Active	Disease	neuroblastoma	MONDO:0005072	DOID:769	adult organism	UBERON:0007023	Neuroblastoma cell	NA	neuroblastoma cell	NA	Enhancer activity assay; TF binding assay	ChIP-seq; DNase-seq	Luciferase reporter assay; EMSA
E_00870	2016	27693352	Enhancer Variants Synergistically Drive Dysfunction of a Gene Regulatory Network In Hirschsprung Disease	Homo sapiens	hg19	chr10	43552395	43553394	GATA2	RET	Enhancer	Active	Disease	neuroblastoma	MONDO:0005072	DOID:769	adrenal gland	UBERON:0002369	Neuroblastoma cell	NA	neuroblastoma cell	NA	Enhancer activity assay; TF binding assay	ChIP-seq; DNase-seq	Luciferase reporter assay; EMSA
E_00871	2023	37904237	Landscape of enhancer disruption and functional screen in melanoma cells	Homo sapiens	hg19	chr10	89986509	89987396	NA	PTEN	Enhancer	Active	Disease	cutaneous melanoma	MONDO:0005012	DOID:8923	zone of skin	UBERON:0000014	Melanoma cell line	NA	melanoma cell	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	HiChIP; ATAC-seq; ChIP-seq; RNA-seq; whole-genome sequencing	Luciferase reporter assay; CRISPR knockout; CRISPRi; 3C-seq; 4C-seq; RT-qPCR; Western blot; CRISPRi
E_00872	2023	37904237	Landscape of enhancer disruption and functional screen in melanoma cells	Homo sapiens	hg19	chr15	99982353	99983277	NA	MEF2A	Enhancer	Active	Disease	cutaneous melanoma	MONDO:0005012	DOID:8923	zone of skin	UBERON:0000014	Melanoma cell line	NA	melanoma cell	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	HiChIP; ATAC-seq; ChIP-seq; RNA-seq; whole-genome sequencing	Luciferase reporter assay; CRISPR knockout; CRISPRi; 3C-seq; 4C-seq; RT-qPCR; Western blot; CRISPRi
E_00873	2021	34040254	Enhancer release and retargeting activates disease-susceptibility genes	Homo sapiens	hg19	chr5	1320064	1320208	NA	TERT	Enhancer	Active	Disease	cancer	MONDO:0004992	DOID:0050686	NA	NA	HEK293T	CVCL_0063	transformed cell line	NA	Chromatin interaction assay; Enhancer retargeting assay; Functional promoter-tether perturbation assay; Cancer mutation analysis	Hi-C; ChIA-PET; GRO-seq; WGS	CRISPR/Cas9 promoter deletion; CRISPR knock-in; 4C-seq; qRT-PCR; ChIP-qPCR; Sanger sequencing; CRISPRi
E_00874	2021	34040254	Enhancer release and retargeting activates disease-susceptibility genes	Homo sapiens	hg19	chr9	37104181	37105469	NA	PAX5	Enhancer	Active	Disease	cancer	MONDO:0004992	DOID:0050686	NA	NA	HEK293T	CVCL_0063	transformed cell line	NA	Chromatin interaction assay; Enhancer retargeting assay; Functional promoter-tether perturbation assay; Cancer mutation analysis	Hi-C; ChIA-PET; GRO-seq; WGS	CRISPRi; CRISPR/Cas9 promoter deletion; 4C-seq; qRT-PCR; Sanger sequencing
E_00875	2025	38760566	Bidirectional epigenetic editing reveals hierarchies in gene regulation	Homo sapiens	hg38	chr4	122542425	122542887	FOS	IL2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Activated primary human CD4+ T cells	NA	CD4-positive, alpha-beta T cell	CL:0000624	Enhancer activity assay; Functional perturbation assay; TF binding assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Enhancer-promoter regulatory interaction analysis	Pooled CRISPRi/CRISPRai gRNA enrichment sequencing; public FOS ChIP-seq; public histone ChIP-seq; published ATAC-seq; ABC-model enhancer-promoter contact analysis using public Hi-C; single-cell RNA-seq; RNA-seq	Individual CRISPRi; intracellular IL2 flow cytometry; CRISPRi; CRISPRa
E_00876	2025	38760566	Bidirectional epigenetic editing reveals hierarchies in gene regulation	Homo sapiens	hg38	chr4	122542425	122542887	JUNB	IL2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Activated primary human CD4+ T cells	NA	CD4-positive, alpha-beta T cell	CL:0000624	Enhancer activity assay; Functional perturbation assay; TF binding assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Enhancer-promoter regulatory interaction analysis	Pooled CRISPRi/CRISPRai gRNA enrichment sequencing; public JUNB ChIP-seq; public histone ChIP-seq; published ATAC-seq; ABC-model enhancer-promoter contact analysis using public Hi-C; single-cell RNA-seq; RNA-seq	Individual CRISPRi; intracellular IL2 flow cytometry; CRISPRi; CRISPRa
E_00877	2020	32500120	CRISPRi-mediated functional analysis of lung disease-associated loci at non-coding regions	Homo sapiens	hg19	chr17	38081807	38083807	NA	GSDMB	Enhancer	Active	Disease	asthma	MONDO:0004979	DOID:2841	lung	UBERON:0002048	A-549	CVCL_0023	epithelial cell of lung	CL:0000082	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Gene expression assay; Chromatin-state profiling; Disease-variant functional analysis; Endogenous enhancer perturbation	Hi-C; ChIP-seq; eQTL analysis; GWAS	CRISPRi; RT-qPCR; ChIP
E_00878	2019	31666509	An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo	Mus musculus	mm10	chr9	119377827	119389749	NA	Scn5a	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	mouse heart/cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation; Canonical RE6-9 cluster; deletion reduces Scn5a and alters topology	RNA-seq; H3K27ac ChIP-seq; 4C-seq	Genome editing/deletion mouse; transgenic reporter; luciferase assay; RT-qPCR; ECG/conduction phenotyping; CRISPR-Cas9 endogenous deletion/editing; In vivo phenotyping
E_00879	2019	31666509	An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo	Mus musculus	mm10	chr9	119377827	119389749	NA	Scn5a	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	mouse heart/cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation; Independent in vivo/topology evidence context for same canonical cluster	RNA-seq; H3K27ac ChIP-seq; 4C-seq	Genome editing/deletion mouse; transgenic reporter; luciferase assay; RT-qPCR; ECG/conduction phenotyping; CRISPR-Cas9 endogenous deletion/editing; In vivo phenotyping
E_00880	2025	38760566	Bidirectional epigenetic editing reveals hierarchies in gene regulation	Homo sapiens	hg38	chr4	122458532	122459022	NA	IL2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human CD4+ memory T cells from healthy donors	NA	CD4-positive, alpha-beta memory T cell	CL:0000897	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Enhancer-promoter regulatory interaction analysis	Pooled CRISPRi gRNA enrichment sequencing; published ATAC-seq; public histone ChIP-seq; ABC-model enhancer-promoter contact analysis using public Hi-C; single-cell RNA-seq; RNA-seq	Individual CRISPRi; intracellular IL2 flow cytometry; CRISPRi; CRISPRa
E_00881	2019	30659195	Aberrant enhancer hypomethylation contributes to hepatic carcinogenesis through global transcriptional reprogramming	Homo sapiens	hg19	chr20	48900221	48901229	CEBPB	CEBPB	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Hep-G2	CVCL_0027	hepatoblast	CL:0005026	Enhancer activity assay; Functional perturbation assay; TF binding assay; Endogenous enhancer perturbation	MBDCap-seq; WGBS; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; H3K4me3 ChIP-seq; H3K27me3 ChIP-seq; CEBPB ChIP-seq; BRD4 ChIP-seq; RNA-seq; whole-genome sequencing	Luciferase reporter assay; CEBPB motif mutagenesis; CRISPR-Cas9 enhancer deletion; dCas9-TET1 targeted enhancer demethylation; ChIP-qPCR; bisulfite pyrosequencing; Northern blot; eRNA RT-qPCR; CEBPB knockdown; JQ1 treatment; Western blot; xenograft assay; CRISPR-Cas9 endogenous deletion/editing
E_00882	2019	30659195	Aberrant enhancer hypomethylation contributes to hepatic carcinogenesis through global transcriptional reprogramming	Homo sapiens	hg19	chr20	48900221	48901229	CEBPB	CEBPB	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Hep-G2	CVCL_0027	NA	NA	Endogenous enhancer perturbation; Enhancer methylation mapping; Endogenous enhancer deletion; enhancer-target and tumorigenic validation	MBDCap-seq; WGBS; ChIP-seq; RNA-seq; Hi-C; whole-genome sequencing	CRISPR-Cas9 enhancer deletion; Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot; bisulfite pyrosequencing; CRISPR-Cas9 endogenous deletion/editing
E_00883	2019	30659195	Aberrant enhancer hypomethylation contributes to hepatic carcinogenesis through global transcriptional reprogramming	Homo sapiens	hg19	chr20	48900221	48901229	CEBPB	CEBPB	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Hep-G2	CVCL_0027	NA	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Endogenous enhancer perturbation; DNA methylation assay; eRNA/gene expression assay	CEBPB ChIP-seq; BRD4 ChIP-seq; H3K27ac ChIP-seq; RNA-seq; whole-genome sequencing	CRISPR-Cas9 enhancer deletion; Luciferase reporter assay; CEBPB-motif mutagenesis; ChIP-qPCR; eRNA siRNA knockdown; RT-qPCR; Western blot; Colony formation assay; Invasion assay; Xenograft assay; CRISPR-Cas9 endogenous deletion/editing
E_00884	2019	30659195	Aberrant enhancer hypomethylation contributes to hepatic carcinogenesis through global transcriptional reprogramming	Homo sapiens	hg19	chr20	48900221	48901229	NA	CEBPB	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Human hepatocellular carcinoma cell	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Endogenous enhancer perturbation	MBDCap-seq, WGBS; ChIP-seq; RNA-seq, Hi-C; whole-genome sequencing	Luciferase reporter assay, CRISPR knockout; ChIP-qPCR; RT-qPCR; Western blot, Bisulfite pyrosequencing; CRISPR-Cas9 endogenous deletion/editing
E_00885	2019	30659195	Aberrant enhancer hypomethylation contributes to hepatic carcinogenesis through global transcriptional reprogramming	Homo sapiens	hg19	chr20	48900221	48901229	NA	CEBPB	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Human normal liver cell	NA	hepatocyte	CL:0000182	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Endogenous enhancer perturbation	MBDCap-seq, WGBS; ChIP-seq; RNA-seq, Hi-C; whole-genome sequencing	Luciferase reporter assay, CRISPR knockout; ChIP-qPCR; RT-qPCR; Western blot, Bisulfite pyrosequencing; CRISPR-Cas9 endogenous deletion/editing
E_00886	2019	30659195	Aberrant enhancer hypomethylation contributes to hepatic carcinogenesis through global transcriptional reprogramming	Homo sapiens	hg19	chr20	48900221	48901229	NA	CEBPB	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Hep-G2	CVCL_0027	NA	NA	Endogenous enhancer perturbation; Enhancer methylation mapping; Endogenous enhancer deletion; enhancer-target and tumorigenic validation	MBDCap-seq; WGBS; ChIP-seq; RNA-seq; Hi-C; whole-genome sequencing	CRISPR-Cas9 enhancer deletion; Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot; bisulfite pyrosequencing; CRISPR-Cas9 endogenous deletion/editing
E_00887	2019	30659195	Aberrant enhancer hypomethylation contributes to hepatic carcinogenesis through global transcriptional reprogramming	Homo sapiens	hg19	chr20	48900221	48901229	NA	CEBPB	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Huh-7	CVCL_0336	NA	NA	Endogenous enhancer perturbation; Enhancer methylation mapping; Endogenous enhancer deletion; enhancer-target and tumorigenic validation	MBDCap-seq; WGBS; ChIP-seq; RNA-seq; Hi-C; whole-genome sequencing	CRISPR-Cas9 enhancer deletion; Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot; bisulfite pyrosequencing; CRISPR-Cas9 endogenous deletion/editing
E_00888	2025	38760566	Bidirectional epigenetic editing reveals hierarchies in gene regulation	Homo sapiens	hg38	chr4	122458532	122459022	NA	IL2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Jurkat E6.1	CVCL_0367	T cell	CL:0000084	Enhancer activity assay; Functional perturbation assay; Chromatin accessibility assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Enhancer-promoter regulatory interaction analysis	Pooled bidirectional CRISPRai gRNA enrichment sequencing; ATAC-seq; public histone ChIP-seq; ABC-model enhancer-promoter contact analysis using public Hi-C; published enhancer-interaction data; single-cell RNA-seq; RNA-seq	CRISPRa; CRISPRi; intracellular IL2 flow cytometry; ATAC-qPCR
E_00889	2022	35915089	A Ctnnb1 enhancer regulates neocortical neurogenesis by controlling the abundance of intermediate progenitors	Mus musculus	mm10	chr9	120869524	120870219	NA	Ctnnb1	Enhancer	Active	Normal	NA	NA	NA	brown adipose tissue	UBERON:0001348	Brown adipocytes (SVF)	NA	brown adipocyte	CL:0000449	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq	Transgenic reporter assay, CRISPR knockout, CRISPRi, CRISPRa, 3C; ChIP-qPCR, Luciferase reporter assay
E_00890	2020	32500120	CRISPRi-mediated functional analysis of lung disease-associated loci at non-coding regions	Homo sapiens	hg19	chr19	41868242	41871230	NA	B9D2	Enhancer	Active	Disease	asthma	MONDO:0004979	DOID:2841	lung	UBERON:0002048	A-549	CVCL_0023	epithelial cell of lung	CL:0000082	Enhancer activity assay; Functional perturbation assay; Gene expression assay	Hi-C; H3K27ac ChIP-seq; ChIP-seq; eQTL analysis	CRISPRi; RT-qPCR
E_00891	2020	32500120	CRISPRi-mediated functional analysis of lung disease-associated loci at non-coding regions	Homo sapiens	hg19	chr19	41868242	41871230	NA	B9D2	Enhancer	Active	Disease	chronic obstructive pulmonary disease	MONDO:0005002	DOID:3083	lung	UBERON:0002048	A-549	CVCL_0023	epithelial cell of lung	CL:0000082	Enhancer activity assay; Functional perturbation assay; Gene expression assay	Hi-C; H3K27ac ChIP-seq; ChIP-seq; eQTL analysis	CRISPRi; RT-qPCR
E_00892	2020	32500120	CRISPRi-mediated functional analysis of lung disease-associated loci at non-coding regions	Homo sapiens	hg19	chr19	41868242	41871230	NA	TGFB1	Enhancer	Active	Disease	asthma	MONDO:0004979	DOID:2841	lung	UBERON:0002048	A-549	CVCL_0023	epithelial cell of lung	CL:0000082	Enhancer activity assay; Functional perturbation assay; Gene expression assay	Hi-C; H3K27ac ChIP-seq; ChIP-seq; eQTL analysis	CRISPRi; RT-qPCR
E_00893	2020	32500120	CRISPRi-mediated functional analysis of lung disease-associated loci at non-coding regions	Homo sapiens	hg19	chr19	41868242	41871230	NA	TGFB1	Enhancer	Active	Disease	chronic obstructive pulmonary disease	MONDO:0005002	DOID:3083	lung	UBERON:0002048	A-549	CVCL_0023	epithelial cell of lung	CL:0000082	Enhancer activity assay; Functional perturbation assay; Gene expression assay	Hi-C; H3K27ac ChIP-seq; ChIP-seq; eQTL analysis	CRISPRi; RT-qPCR
E_00894	2020	32500120	CRISPRi-mediated functional analysis of lung disease-associated loci at non-coding regions	Homo sapiens	hg19	chr19	41868242	41871230	NA	TMEM91	Enhancer	Active	Disease	asthma	MONDO:0004979	DOID:2841	lung	UBERON:0002048	A-549	CVCL_0023	epithelial cell of lung	CL:0000082	Enhancer activity assay; Functional perturbation assay; Gene expression assay	Hi-C; H3K27ac ChIP-seq; ChIP-seq; eQTL analysis	CRISPRi; RT-qPCR
E_00895	2020	32500120	CRISPRi-mediated functional analysis of lung disease-associated loci at non-coding regions	Homo sapiens	hg19	chr19	41868242	41871230	NA	TMEM91	Enhancer	Active	Disease	chronic obstructive pulmonary disease	MONDO:0005002	DOID:3083	lung	UBERON:0002048	A-549	CVCL_0023	epithelial cell of lung	CL:0000082	Enhancer activity assay; Functional perturbation assay; Gene expression assay	Hi-C; H3K27ac ChIP-seq; ChIP-seq; eQTL analysis	CRISPRi; RT-qPCR
E_00896	2019	31666509	An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo	Mus musculus	mm10	chr9	119377827	119379749	Tbx5	Scn5a	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	Mouse cardiomyocyte cell	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Functional perturbation assay; TF binding assay; Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation	ChIP-seq; RNA-seq; ATAC-seq	CRISPR knockout; RT-qPCR, Luciferase reporter assay; Western blot; CRISPR-Cas9 endogenous deletion/editing; In vivo phenotyping
E_00897	2025	38760566	Bidirectional epigenetic editing reveals hierarchies in gene regulation	Homo sapiens	hg38	chr4	122578161	122579217	NA	IL2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Jurkat E6.1	CVCL_0367	T cell	CL:0000084	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Enhancer-enhancer regulatory interaction analysis; Enhancer-promoter regulatory interaction analysis	Pooled bidirectional CRISPRai gRNA enrichment sequencing; public histone ChIP-seq; ABC-model enhancer-promoter contact analysis using public Hi-C; published enhancer-interaction data; single-cell RNA-seq; RNA-seq	CRISPRa; CRISPRi; intracellular IL2 flow cytometry
E_00898	2022	35915089	A Ctnnb1 enhancer regulates neocortical neurogenesis by controlling the abundance of intermediate progenitors	Homo sapiens	hg38	chr3	41119924	41122071	NA	CTNNB1	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	Hi-C; ATAC-seq; ChIP-seq; RNA-seq	ChIP-qPCR, qRT-PCR; Western blot
E_00899	2019	31666509	An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo	Mus musculus	mm10	chr9	119378700	119379271	Tbx5	Scn5a	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	Mouse cardiomyocyte cell	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation	ChIP-seq; RNA-seq	Luciferase reporter assay, CRISPR knockout; RT-qPCR; Western blot; CRISPR-Cas9 endogenous deletion/editing; In vivo phenotyping
E_00900	2019	30659195	Aberrant enhancer hypomethylation contributes to hepatic carcinogenesis through global transcriptional reprogramming	Homo sapiens	hg19	chr20	48900221	48901229	CEBPB	CEBPB	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	uterine cervix	UBERON:0000002	L-02	CVCL_6926	NA	NA	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation; DNA methylation assay; eRNA/gene expression assay	whole-genome sequencing	CRISPR-Cas9 enhancer deletion; Luciferase reporter assay; CEBPB-motif mutagenesis; eRNA siRNA knockdown; qRT-PCR; Colony formation assay; Invasion assay; CRISPR-Cas9 endogenous deletion/editing
E_00901	2019	30659195	Aberrant enhancer hypomethylation contributes to hepatic carcinogenesis through global transcriptional reprogramming	Homo sapiens	hg19	chr20	48900221	48901229	CEBPB	CEBPB	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Primary HCC tumor tissue	NA	NA	NA	Endogenous enhancer perturbation; DNA methylation profiling; Clinical epigenomic validation; Enhancer-target association	MBDCap-seq; WGBS; Nanoscale chromatin profiling; RNA-seq; whole-genome sequencing	Bisulfite pyrosequencing; qRT-PCR; CRISPR-Cas9 endogenous deletion/editing
E_00902	2025	40164603	Enhancer RNA transcription pinpoints functional genetic variants linked to asthma	Homo sapiens	hg38	chr12	56075734	56076734	NR3C1	GCNT1	Enhancer	Active	Disease	asthma	MONDO:0004979	DOID:2841	lung	UBERON:0002048	BEAS-2B	CVCL_0168	bronchial epithelial cell	CL:0002328	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis	GRO-seq, Micro-C; ChIP-seq	Luciferase reporter assay, CRISPR knockout, CRISPRi; RT-qPCR
E_00903	2025	41419462	A novel super-enhancer-driven lncRNA LINC00973 governs head and neck squamous cell carcinoma progression through EN2	Homo sapiens	hg19	chr3	98678906	98697335	FOSL1	LINC00973	Super-enhancer	Active	Disease	head and neck squamous cell carcinoma	MONDO:0010150	DOID:5520	liver	UBERON:0002107	Hep-G2	CVCL_0027	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation	ChIP-seq; RNA-seq, Hi-C; ATAC-seq; H3K27ac HiChIP; HiChIP	ChIP-qPCR, CRISPRi, Luciferase reporter assay, qRT-PCR; Western blot, co-IP; CRISPRi; In vivo phenotyping
E_00904	2024	37994973	rs10924104 in the expression enhancer motif of CD58 confers susceptibility to human autoimmune diseases	Homo sapiens	hg38	chr1	116506181	116506381	ZNF35	CD58	Enhancer	Active	Disease	autoimmune disease	MONDO:0007179	DOID:417	blood	UBERON:0000178	THP-1	CVCL_0006	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis	Hi-C; GWAS	Luciferase reporter assay, CRISPR knockout; ChIP-qPCR, EMSA; RT-qPCR
E_00905	2024	38417378	Identification of a distal enhancer regulating hedgehog interacting protein gene in human lung epithelial cells	Homo sapiens	hg38	chr4	145218235	145219235	SMAD3	HHIP	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	Human bronchial epithelial cells	NA	bronchial epithelial cell	CL:0002328	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin-state profiling; Disease-variant functional analysis; Endogenous enhancer perturbation	RNA-seq; ATAC-seq; ChIP-seq, Hi-C; ATAC-seq; Hi-C; GWAS	CRISPR knockout, Luciferase reporter assay; ChIP-qPCR; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; ChIP; RT-qPCR; Western blot; Reporter assay
E_00906	2024	38417378	Identification of a distal enhancer regulating hedgehog interacting protein gene in human lung epithelial cells	Homo sapiens	hg38	chr4	144579000	144586000	SMAD3	HHIP	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Kasumi-1	CVCL_0589	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin-state profiling; Disease-variant functional analysis; Endogenous enhancer perturbation	snATAC-seq, Hi-C; ChIP-seq; ATAC-seq; Hi-C; GWAS	Luciferase reporter assay; ChIP-qPCR, CRISPR knockout/CRISPRi; RT-qPCR; Western blot; 3C-RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; ChIP; RT-qPCR; Western blot; Reporter assay
E_00907	2024	38720882	Integrated enhancer regulatory network by enhancer-promoter looping in gastric cancer	Homo sapiens	hg38	chr6	135266000	135268000	TCF7	MYB	Enhancer	Active	Disease	gastric cancer	MONDO:0001056	DOID:10534	stomach	UBERON:0000945	SNU-719	CVCL_5086	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Endogenous enhancer perturbation	H3K4me1 ChIP-seq; H3K4me3 ChIP-seq; H3K27ac ChIP-seq; TCF7 ChIP-seq; H3K27ac HiChIP; ATAC-seq; RNA-seq; H3K27ac CUT&Tag; single-cell RNA-seq	CRISPRi (dCas9-KRAB) targeting MYB E3; H3K9me3 ChIP-qPCR; H3K27ac ChIP-qPCR; 4C-seq; TCF7 siRNA knockdown; MYB siRNA knockdown; RT-qPCR; Western blot; CCK-8 assay; competitive FACS growth assay; colony formation assay; CRISPRi
E_00908	2024	38720882	Integrated enhancer regulatory network by enhancer-promoter looping in gastric cancer	Homo sapiens	hg38	chr6	135266000	135268000	TCF7	MYB	Enhancer	Active	Disease	gastric cancer	MONDO:0001056	DOID:10534	stomach	UBERON:0000945	YCCEL1	CVCL_9647	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Endogenous enhancer perturbation	H3K4me1 ChIP-seq; H3K4me3 ChIP-seq; H3K27ac ChIP-seq; TCF7 ChIP-seq; H3K27ac HiChIP; ATAC-seq; RNA-seq; H3K27ac CUT&Tag; single-cell RNA-seq	CRISPRi (dCas9-KRAB) targeting MYB E3; TCF7 siRNA knockdown; MYB siRNA knockdown; RT-qPCR; Western blot; CCK-8 assay; competitive growth assay; CRISPRi
E_00909	2019	31126313	The inherited variations of a p53-responsive enhancer in 13q12.12 confer lung cancer risk by attenuating TNFRSF19 expression	Homo sapiens	hg19	chr13	24149800	24150800	TP53	TNFRSF19	Enhancer	Active	Disease	non-small cell lung carcinoma	MONDO:0005233	DOID:3908	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Disease-variant functional analysis; In vivo functional validation	eQTL analysis; GWAS	Luciferase reporter assay, CRISPR knockout, 3C; RT-qPCR, EMSA; In vivo phenotyping
E_00910	2014	25248036	Evidence that breast cancer risk at the 2q35 locus is mediated through IGFBP5 regulation	Homo sapiens	hg19	chr2	217918268	217921910	FOXA1	IGFBP5	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	Breast Cancer Cell	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_00911	2010	20236932	A downstream intergenic cluster of regulatory enhancers contributes to the induction of CYP24A1 expression by 1alpha,25-dihydroxyvitamin D3	Homo sapiens	hg38	chr20	52173000	52174500	VDR	CYP24A1	Enhancer	Active	Normal	NA	NA	NA	colon	UBERON:0001155	LS180	CVCL_0397	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation	ChIP-seq, ChIP-chip; RNA-seq; ChIP-seq	Luciferase reporter assay; ChIP-qPCR; RT-qPCR, 3C; Luciferase reporter assay; ChIP; Mouse genetic deletion/knock-in
E_00912	2019	31406378	Cryptic activation of an Irf8 enhancer governs cDC1 fate specification	Mus musculus	mm39	chr8	121495079	121495626	Batf3	Irf8	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	primary CD24+ cDC1	NA	classical dendritic cell type 1	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin accessibility assay; In vivo enhancer deletion assay	ATAC-seq; BATF3 ChIP-seq; IRF8 ChIP-seq; p300 ChIP-seq; chromatin profiling	Retroviral enhancer reporter assay; AICE site-directed mutagenesis; CRISPR-Cas9 enhancer deletion; RT-qPCR; Flow cytometry; Flt3L bone-marrow differentiation assay; CRISPR-Cas9
E_00913	2019	31406378	Cryptic activation of an Irf8 enhancer governs cDC1 fate specification	Mus musculus	mm39	chr8	121495079	121495626	Irf8	Irf8	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	primary CD24+ cDC1	NA	classical dendritic cell type 1	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin accessibility assay; In vivo enhancer deletion assay	ATAC-seq; BATF3 ChIP-seq; IRF8 ChIP-seq; p300 ChIP-seq; chromatin profiling	Retroviral enhancer reporter assay; AICE site-directed mutagenesis; CRISPR-Cas9 enhancer deletion; RT-qPCR; Flow cytometry; Flt3L bone-marrow differentiation assay; CRISPR-Cas9
E_00914	2011	21551367	An evolutionarily conserved TNF-alpha-responsive enhancer in the far upstream region of human CCL2 locus influences its gene expression	Homo sapiens	hg19	chr17	32565596	32566796	NFKB1	CCL2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	U-87MG ATCC	CVCL_0022	misidentified glioblastoma-like cell line	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay	NA	Luciferase reporter assay; in vivo genomic footprinting; EMSA/supershift; ChIP-PCR; NF-kB-site mutagenesis; RELA/p65 siRNA; nuclease-sensitivity assay; 3C; RT-qPCR
E_00915	2011	21551367	An evolutionarily conserved TNF-alpha-responsive enhancer in the far upstream region of human CCL2 locus influences its gene expression	Homo sapiens	hg19	chr17	32565596	32566796	RELA	CCL2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	U-87MG ATCC	CVCL_0022	misidentified glioblastoma-like cell line	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay	NA	Luciferase reporter assay; in vivo genomic footprinting; EMSA/supershift; ChIP-PCR; NF-kB-site mutagenesis; RELA/p65 siRNA; nuclease-sensitivity assay; 3C; RT-qPCR
E_00916	2011	21551367	An evolutionarily conserved TNF-alpha-responsive enhancer in the far upstream region of human CCL2 locus influences its gene expression	Homo sapiens	hg19	chr17	32565596	32566796	CEBPB	CCL2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	U-87MG	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay; 3C; RT-qPCR/qPCR
E_00917	2011	21551367	An evolutionarily conserved TNF-alpha-responsive enhancer in the far upstream region of human CCL2 locus influences its gene expression	Homo sapiens	hg19	chr17	32565596	32566796	NFKB1	CCL2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	U-87MG	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay; 3C; RT-qPCR/qPCR
E_00918	2011	21551367	An evolutionarily conserved TNF-alpha-responsive enhancer in the far upstream region of human CCL2 locus influences its gene expression	Homo sapiens	hg19	chr17	32565596	32566796	SP1	CCL2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	U-87MG	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay; 3C; RT-qPCR/qPCR
E_00919	2019	31406378	Cryptic activation of an Irf8 enhancer governs cDC1 fate specification	Mus musculus	mm10	chr8	120777048	120777744	Tcf3	Irf8	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary mouse bone-marrow MDP/CDP/pre-cDC1 populations	NA	common dendritic progenitor	CL:0001029	Endogenous enhancer perturbation; Chromatin-state mapping; TF-binding analysis; Endogenous enhancer deletion; lineage differentiation assay	ATAC-seq; H3K27ac/H3K4me1 ChIP-seq; E2A/TCF3 ChIP-seq integration; transcriptome profiling	CRISPR-Cas9 enhancer deletion in mice; Flt3L bone-marrow culture; Flow cytometry; bone-marrow chimera; enhancer reporter assay; CRISPR-Cas9 endogenous deletion/editing
E_00920	2019	31406378	Cryptic activation of an Irf8 enhancer governs cDC1 fate specification	Mus musculus	mm39	chr8	121503787	121504483	NA	Irf8	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	common dendritic cell progenitors and pre-cDC1	NA	dendritic cell progenitor	NA	Functional perturbation assay; Chromatin accessibility assay; In vivo enhancer deletion assay	ATAC-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; chromatin profiling	CRISPR-Cas9 enhancer deletion; E-box deletion analysis; RT-qPCR; Flow cytometry; Flt3L bone-marrow differentiation assay; CRISPR-Cas9
E_00921	2010	20236932	A downstream intergenic cluster of regulatory enhancers contributes to the induction of CYP24A1 expression by 1alpha,25-dihydroxyvitamin D3	Homo sapiens	hg38	chr20	52157000	52158500	VDR	CYP24A1	Enhancer	Active	Disease	Kaposi's sarcoma	MONDO:0005055	DOID:8632	zone of skin	UBERON:0000014	JOV675	CVCL_8250	Kaposi sarcoma cell	NA	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ChIP-seq; ChIP-chip; RNA-seq	Luciferase reporter assay; ChIP-qPCR; RT-qPCR, 3C
E_00922	2025	40164603	Enhancer RNA transcription pinpoints functional genetic variants linked to asthma	Homo sapiens	hg38	chr5	143200112	143200889	NA	NR3C1	Enhancer	Repressed	Disease	asthma	MONDO:0004979	DOID:2841	liver	UBERON:0002107	CHME-5	CVCL_5J53	malignant cell	CL:0001064	Enhancer activity assay; Disease-variant functional analysis	PRO-seq	Luciferase reporter assay
E_00923	2014	25248036	Evidence that breast cancer risk at the 2q35 locus is mediated through IGFBP5 regulation	Homo sapiens	hg19	chr2	217920100	217921400	NA	IGFBP5	Enhancer	Active	Disease	cutaneous melanoma	MONDO:0005012	DOID:8923	zone of skin	UBERON:0000014	GA-10 clone 4	CVCL_1224	melanoma cell	NA	Enhancer activity assay	NA	Luciferase reporter assay
E_00924	2022	35264579	An enhancer variant at 16q22.1 predisposes to hepatocellular carcinoma via regulating PRMT7 expression	Homo sapiens	hg19	chr16	68362000	68362400	HNF4A	PRMT7	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	hepatocellular carcinoma cell model	NA	hepatocellular carcinoma cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis; In vivo functional validation	ChIP-seq; RNA-seq, Hi-C	Luciferase reporter assay; ChIP-qPCR, CRISPR knockout, CRISPRi, CRISPRa, qRT-PCR; Western blot, EMSA; Luciferase reporter assay; Allele-specific reporter assay; In vivo phenotyping
E_00925	2020	32238901	Accelerated evolution of an Lhx2 enhancer shapes mammalian social hierarchies	Homo sapiens	hg19	chr9	126770367	126771183	CTCF	LHX2	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	NA	NA	NA	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; Hi-C; ATAC-seq	Luciferase reporter assay; Transgenic reporter assay; CRISPR knockout; CRISPRi, qRT-PCR; Knock-in mouse
E_00926	2020	32991838	Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder	Homo sapiens	hg19	chr17	68663972	68675613	TWIST1	SOX9	Enhancer	Active	Normal	NA	NA	NA	cranial neural crest	UBERON:0003099	hCNCC	NA	cranial neural crest cell	NA	Enhancer activity assay; Functional perturbation assay	ChIP-seq; ATAC-seq; RNA-seq; 3C-seq	Luciferase reporter assay; CRISPR knockout; RT-qPCR
E_00927	2020	32991838	Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder	Mus musculus	mm39	chr11	111456657	111460228	Twist1	Sox9	Enhancer	Active	Disease	isolated Pierre Robin sequence	MONDO:0009869	NA	developing mandible / craniofacial mesenchyme	NA	Human cranial neural crest cells plus endogenous orthologous mouse EC1.45 deletion models	NA	cranial neural crest cell	NA	EC1.45/Rr80 extreme long-range enhancer cluster; TWIST1 occupancy; Capture-C target assignment; endogenous orthologous enhancer deletion; craniofacial phenotyping	p300/H3K27ac ChIP-seq; ATAC-seq; Capture-C	Luciferase reporter; CRISPR-Cas9 EC1.45 deletion; allele-specific RT-ddPCR; mouse lacZ reporter; in situ hybridization; Coordinator-motif deletion
E_00928	2024	39333082	A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders	Homo sapiens	hg38	chr22	27493955	27497536	NA	MN1	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	BxPC-3	CVCL_0186	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; Disease-variant functional analysis; In vivo functional validation	scATAC-seq, scRNA-seq, scCUT&Tag	Transgenic reporter assay; In vivo phenotyping
E_00929	2017	28753427	A Genetic Variant Associated with Five Vascular Diseases Is a Distal Regulator of Endothelin-1 Gene Expression	Homo sapiens	hg19	chr6	12902957	12904957	NA	EDN1	Enhancer	Active	Disease	vascular disease susceptibility	NA	NA	aorta	UBERON:0000947	pluripotent stem cell-derived endothelial cells	NA	endothelial cell	CL:0000115	Chromatin interaction assay; Disease-associated enhancer variant functional perturbation	Genetic fine-mapping; H3K27ac ChIP-seq; epigenomic profiling; 4C-seq	CRISPR/Cas9 allele editing and regulatory-element deletion; RT-qPCR; endothelin-1 quantification
E_00930	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr1	226215164	226215656	EOMES	MIXL1	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00931	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr1	226215164	226215656	GATA6	MIXL1	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00932	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr1	226215164	226215656	MIXL1	MIXL1	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00933	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr1	226215164	226215656	SOX17	MIXL1	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00934	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr18	21933810	21935298	EOMES	GATA6	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00935	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr18	21933810	21935298	GATA6	GATA6	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00936	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr18	21933810	21935298	GATA6	GATA6	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES 8	CVCL_B207	endodermal cell	CL:0000223	Chromatin interaction assay; Endogenous enhancer perturbation; Pooled CRISPRi enhancer screening; individual enhancer validation; TF binding; chromatin-state/3D integration	Pooled CRISPRi screen; RNA-seq; scRNA-seq; ATAC-seq; H3K27ac/EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; CRISPR genetic screen	Individual CRISPRi; RT-qPCR; flow cytometry/FACS; CRISPRi
E_00937	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr18	21933810	21935298	MIXL1	GATA6	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00938	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr18	21933810	21935298	SOX17	GATA6	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00939	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr18	22194123	22194455	EOMES	GATA6	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00940	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr18	22194123	22194455	GATA6	GATA6	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00941	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr18	22194123	22194455	GATA6	GATA6	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES 8	CVCL_B207	endodermal cell	CL:0000223	Chromatin interaction assay; Endogenous enhancer perturbation; Pooled CRISPRi enhancer screening; individual enhancer validation; TF binding; chromatin-state/3D integration	Pooled CRISPRi screen; RNA-seq; scRNA-seq; ATAC-seq; H3K27ac/EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; CRISPR genetic screen	Individual CRISPRi; RT-qPCR; flow cytometry/FACS; CRISPRi
E_00942	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr18	22194123	22194455	MIXL1	GATA6	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00943	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr18	22194123	22194455	SOX17	GATA6	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00944	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr3	27712007	27712923	EOMES	EOMES	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00945	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr3	27712007	27712923	EOMES	EOMES	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES 8	CVCL_B207	endodermal cell	CL:0000223	Chromatin interaction assay; Endogenous enhancer perturbation; Pooled CRISPRi enhancer screening; individual enhancer validation; TF binding; chromatin-state/3D integration	Pooled CRISPRi screen; RNA-seq; scRNA-seq; ATAC-seq; H3K27ac/EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; CRISPR genetic screen	Individual CRISPRi; RT-qPCR; flow cytometry/FACS; CRISPRi
E_00946	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr3	27712007	27712923	GATA6	EOMES	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00947	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr3	27712007	27712923	MIXL1	EOMES	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00948	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr3	27712007	27712923	SOX17	EOMES	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00949	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr3	27728339	27729090	EOMES	EOMES	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00950	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr3	27728339	27729090	EOMES	EOMES	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES 8	CVCL_B207	endodermal cell	CL:0000223	Chromatin interaction assay; Endogenous enhancer perturbation; Pooled CRISPRi enhancer screening; individual enhancer validation; TF binding; chromatin-state/3D integration	Pooled CRISPRi screen; RNA-seq; scRNA-seq; ATAC-seq; H3K27ac/EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; CRISPR genetic screen	Individual CRISPRi; RT-qPCR; flow cytometry/FACS; CRISPRi
E_00951	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr3	27728339	27729090	GATA6	EOMES	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00952	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr3	27728339	27729090	MIXL1	EOMES	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00953	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr3	27728339	27729090	SOX17	EOMES	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00954	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr3	27730029	27730667	EOMES	EOMES	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00955	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr3	27730029	27730667	EOMES	EOMES	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES 8	CVCL_B207	endodermal cell	CL:0000223	Chromatin interaction assay; Endogenous enhancer perturbation; Pooled CRISPRi enhancer screening; individual enhancer validation; TF binding; chromatin-state/3D integration	Pooled CRISPRi screen; RNA-seq; scRNA-seq; ATAC-seq; H3K27ac/EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; CRISPR genetic screen	Individual CRISPRi; RT-qPCR; flow cytometry/FACS; CRISPRi
E_00956	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr3	27730029	27730667	GATA6	EOMES	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00957	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr3	27730029	27730667	MIXL1	EOMES	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00958	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr3	27730029	27730667	SOX17	EOMES	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00959	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54224560	54225711	EOMES	SOX17	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00960	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54224560	54225711	GATA6	SOX17	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00961	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54224560	54225711	MIXL1	SOX17	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00962	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54224560	54225711	SOX17	SOX17	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00963	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54224560	54225711	SOX17	SOX17	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES 8	CVCL_B207	endodermal cell	CL:0000223	Chromatin interaction assay; Endogenous enhancer perturbation; Pooled CRISPRi enhancer screening; individual enhancer validation; TF binding; chromatin-state/3D integration	Pooled CRISPRi screen; RNA-seq; scRNA-seq; ATAC-seq; H3K27ac/EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; CRISPR genetic screen	Individual CRISPRi; RT-qPCR; flow cytometry/FACS; CRISPRi
E_00964	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54259816	54260322	EOMES	SOX17	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00965	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54259816	54260322	GATA6	SOX17	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00966	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54259816	54260322	MIXL1	SOX17	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00967	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54259816	54260322	SOX17	SOX17	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00968	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54259816	54260322	SOX17	SOX17	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES 8	CVCL_B207	endodermal cell	CL:0000223	Chromatin interaction assay; Endogenous enhancer perturbation; Pooled CRISPRi enhancer screening; individual enhancer validation; TF binding; chromatin-state/3D integration	Pooled CRISPRi screen; RNA-seq; scRNA-seq; ATAC-seq; H3K27ac/EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; CRISPR genetic screen	Individual CRISPRi; RT-qPCR; flow cytometry/FACS; CRISPRi
E_00969	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54300591	54300987	EOMES	SOX17	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00970	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54300591	54300987	GATA6	SOX17	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00971	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54300591	54300987	MIXL1	SOX17	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00972	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54300591	54300987	SOX17	SOX17	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00973	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54300591	54300987	SOX17	SOX17	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES 8	CVCL_B207	endodermal cell	CL:0000223	Chromatin interaction assay; Endogenous enhancer perturbation; Pooled CRISPRi enhancer screening; individual enhancer validation; TF binding; chromatin-state/3D integration	Pooled CRISPRi screen; RNA-seq; scRNA-seq; ATAC-seq; H3K27ac/EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; CRISPR genetic screen	Individual CRISPRi; RT-qPCR; flow cytometry/FACS; CRISPRi
E_00974	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54301978	54302426	EOMES	SOX17	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00975	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54301978	54302426	GATA6	SOX17	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00976	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54301978	54302426	MIXL1	SOX17	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00977	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54301978	54302426	SOX17	SOX17	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00978	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54301978	54302426	SOX17	SOX17	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES 8	CVCL_B207	endodermal cell	CL:0000223	Chromatin interaction assay; Endogenous enhancer perturbation; Pooled CRISPRi enhancer screening; individual enhancer validation; TF binding; chromatin-state/3D integration	Pooled CRISPRi screen; RNA-seq; scRNA-seq; ATAC-seq; H3K27ac/EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; CRISPR genetic screen	Individual CRISPRi; RT-qPCR; flow cytometry/FACS; CRISPRi
E_00979	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54454106	54455036	EOMES	SOX17	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00980	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54454106	54455036	GATA6	SOX17	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00981	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54454106	54455036	MIXL1	SOX17	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00982	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54454106	54455036	SOX17	SOX17	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	HCC827	CVCL_2063	embryonic stem cell	CL:0002322	Chromatin interaction assay; Endogenous enhancer perturbation; CRISPR interference-based functional screen	CRISPRi screen; RNA-seq; ATAC-seq; ChIP-seq, Hi-C; Hi-C; CRISPR genetic screen	RT-qPCR, flow cytometry, FACS; CRISPRi
E_00983	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54454106	54455036	SOX17	SOX17	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES 8	CVCL_B207	endodermal cell	CL:0000223	Chromatin interaction assay; Endogenous enhancer perturbation; Pooled CRISPRi enhancer screening; individual enhancer validation; TF binding; chromatin-state/3D integration	Pooled CRISPRi screen; RNA-seq; scRNA-seq; ATAC-seq; H3K27ac/EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; CRISPR genetic screen	Individual CRISPRi; RT-qPCR; flow cytometry/FACS; CRISPRi
E_00984	2023	37832549	Genome-wide CRISPR activation screening in senescent cells reveals SOX5 as a driver and therapeutic target of rejuvenation	Homo sapiens	hg19	chr4	174249537	174250490	SOX5	HMGB2	Enhancer	Active	Normal	NA	NA	NA	connective tissue	UBERON:0002384	WT hMPC	NA	mesenchymal stem cell	CL:0000134	Endogenous enhancer perturbation; In vivo functional validation; Baseline HMGB2 enhancer / SOX5 comparison	ATAC-seq; ChIP-seq; RNA-seq; Hi-C; pooled CRISPRa screen; CRISPR genetic screen	ChIP-qPCR; RT-qPCR; Western blot; CRISPRa; In vivo phenotyping
E_00985	2017	28511927	Coordinated regulation of IFITM1, 2 and 3 genes by an IFN-responsive enhancer through long-range chromatin interactions	Homo sapiens	hg19	chr11	354514	356503	STAT1	IFITM1	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	A-549	CVCL_0023	epithelial cell	CL:0000066	Enhancer activity assay; TF binding assay; Endogenous enhancer perturbation; In vivo functional validation; Enhancer activity; endogenous perturbation; chromatin interaction; TF binding	STAT1/chromatin ChIP-seq and public epigenomic integration	CRISPR-Cas9 enhancer deletion; Luciferase reporter; STAT1 ChIP-qPCR; EMSA; 3C; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; Luciferase reporter assay; ChIP; In vivo phenotyping; Reporter assay
E_00986	2017	28511927	Coordinated regulation of IFITM1, 2 and 3 genes by an IFN-responsive enhancer through long-range chromatin interactions	Homo sapiens	hg19	chr11	354514	356503	STAT1	IFITM2	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	HEK293	CVCL_0045	epithelial cell	CL:0000066	Enhancer activity assay; TF binding assay; Endogenous enhancer perturbation; In vivo functional validation; Enhancer activity; endogenous perturbation; chromatin interaction; TF binding	STAT1/chromatin ChIP-seq and public epigenomic integration	CRISPR-Cas9 enhancer deletion; Luciferase reporter; STAT1 ChIP-qPCR; EMSA; 3C; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; Luciferase reporter assay; ChIP; In vivo phenotyping; Reporter assay
E_00987	2017	28511927	Coordinated regulation of IFITM1, 2 and 3 genes by an IFN-responsive enhancer through long-range chromatin interactions	Homo sapiens	hg19	chr11	354514	356503	STAT1	IFITM3	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	A-549	CVCL_0023	epithelial cell	CL:0000066	Enhancer activity assay; TF binding assay; Endogenous enhancer perturbation; In vivo functional validation; Enhancer activity; endogenous perturbation; chromatin interaction; TF binding	STAT1/chromatin ChIP-seq and public epigenomic integration	CRISPR-Cas9 enhancer deletion; Luciferase reporter; STAT1 ChIP-qPCR; 3C; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; Luciferase reporter assay; EMSA; ChIP; In vivo phenotyping; Reporter assay
E_00988	2017	28511927	Coordinated regulation of IFITM1, 2 and 3 genes by an IFN-responsive enhancer through long-range chromatin interactions	Homo sapiens	hg19	chr11	355447	358949	STAT1	IFITM1	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	A-549	CVCL_0023	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation	ENCODE ChIP-seq; RNA Pol II ChIA-PET data mining	Luciferase reporter assay; 3C; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; EMSA; ChIP; In vivo phenotyping; Reporter assay
E_00989	2017	28511927	Coordinated regulation of IFITM1, 2 and 3 genes by an IFN-responsive enhancer through long-range chromatin interactions	Homo sapiens	hg19	chr11	355447	358949	STAT1	IFITM2	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	A-549	CVCL_0023	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation	ENCODE ChIP-seq; RNA Pol II ChIA-PET data mining	Luciferase reporter assay; 3C; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; EMSA; ChIP; In vivo phenotyping; Reporter assay
E_00990	2017	28511927	Coordinated regulation of IFITM1, 2 and 3 genes by an IFN-responsive enhancer through long-range chromatin interactions	Homo sapiens	hg19	chr11	355447	358949	STAT1	IFITM3	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	A-549	CVCL_0023	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation	ENCODE ChIP-seq; RNA Pol II ChIA-PET data mining	Luciferase reporter assay; 3C; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; EMSA; ChIP; In vivo phenotyping; Reporter assay
E_00991	2017	28511927	Coordinated regulation of IFITM1, 2 and 3 genes by an IFN-responsive enhancer through long-range chromatin interactions	Homo sapiens	hg19	chr11	355447	358949	STAT1	IFITM1	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	A-549	CVCL_0023	malignant cell	CL:0001064	Interferon-responsive enhancer activity; STAT1 binding; long-range chromatin interaction; endogenous enhancer editing	ENCODE STAT1/chromatin ChIP-seq data mining; RNA polymerase II ChIA-PET data mining	Luciferase reporter; 3C; CRISPR-Cas9 endogenous enhancer editing; EMSA; ChIP/ChIP-qPCR; RT-qPCR
E_00992	2017	28511927	Coordinated regulation of IFITM1, 2 and 3 genes by an IFN-responsive enhancer through long-range chromatin interactions	Homo sapiens	hg19	chr11	355447	358949	STAT1	IFITM1	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	HEK293	CVCL_0045	epithelial cell	CL:0000066	Interferon-responsive enhancer activity; STAT1 binding; long-range chromatin interaction; endogenous enhancer editing	ENCODE STAT1/chromatin ChIP-seq data mining; RNA polymerase II ChIA-PET data mining	Luciferase reporter; 3C; CRISPR-Cas9 endogenous enhancer editing; EMSA; ChIP/ChIP-qPCR; RT-qPCR
E_00993	2017	28511927	Coordinated regulation of IFITM1, 2 and 3 genes by an IFN-responsive enhancer through long-range chromatin interactions	Homo sapiens	hg19	chr11	355447	358949	STAT1	IFITM2	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	A-549	CVCL_0023	malignant cell	CL:0001064	Interferon-responsive enhancer activity; STAT1 binding; long-range chromatin interaction; endogenous enhancer editing	ENCODE STAT1/chromatin ChIP-seq data mining; RNA polymerase II ChIA-PET data mining	Luciferase reporter; 3C; CRISPR-Cas9 endogenous enhancer editing; EMSA; ChIP/ChIP-qPCR; RT-qPCR
E_00994	2017	28511927	Coordinated regulation of IFITM1, 2 and 3 genes by an IFN-responsive enhancer through long-range chromatin interactions	Homo sapiens	hg19	chr11	355447	358949	STAT1	IFITM2	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	HEK293	CVCL_0045	epithelial cell	CL:0000066	Interferon-responsive enhancer activity; STAT1 binding; long-range chromatin interaction; endogenous enhancer editing	ENCODE STAT1/chromatin ChIP-seq data mining; RNA polymerase II ChIA-PET data mining	Luciferase reporter; 3C; CRISPR-Cas9 endogenous enhancer editing; EMSA; ChIP/ChIP-qPCR; RT-qPCR
E_00995	2017	28511927	Coordinated regulation of IFITM1, 2 and 3 genes by an IFN-responsive enhancer through long-range chromatin interactions	Homo sapiens	hg19	chr11	355447	358949	STAT1	IFITM3	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	A-549	CVCL_0023	malignant cell	CL:0001064	Interferon-responsive enhancer activity; STAT1 binding; long-range chromatin interaction; endogenous enhancer editing	ENCODE STAT1/chromatin ChIP-seq data mining; RNA polymerase II ChIA-PET data mining	Luciferase reporter; 3C; CRISPR-Cas9 endogenous enhancer editing; EMSA; ChIP/ChIP-qPCR; RT-qPCR
E_00996	2017	28511927	Coordinated regulation of IFITM1, 2 and 3 genes by an IFN-responsive enhancer through long-range chromatin interactions	Homo sapiens	hg19	chr11	355447	358949	STAT1	IFITM3	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	HEK293	CVCL_0045	epithelial cell	CL:0000066	Interferon-responsive enhancer activity; STAT1 binding; long-range chromatin interaction; endogenous enhancer editing	ENCODE STAT1/chromatin ChIP-seq data mining; RNA polymerase II ChIA-PET data mining	Luciferase reporter; 3C; CRISPR-Cas9 endogenous enhancer editing; EMSA; ChIP/ChIP-qPCR; RT-qPCR
E_00997	2015	25605944	Enhancer-bound LDB1 regulates a corticotrope promoter-pausing repression program	Mus musculus	mm8	chr12	3946672	3948652	Ascl1	Pomc	Enhancer	Active	Normal	NA	NA	NA	pituitary gland	UBERON:0000007	AtT-20	CVCL_2300	corticotroph	CL:0002309	Enhancer activity assay; Functional perturbation assay; TF binding assay; Enhancer-promoter looping assay; Nascent transcription assay	ASCL1 ChIP-seq; LDB1 ChIP-seq; TBX19 ChIP-seq; EP300 ChIP-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; GRO-seq	ASCL1 knockdown; LDB1 knockdown; transient reporter assay; PE3C-DSL; 3C-qPCR; ChIP-qPCR; RT-qPCR; Western blot; co-immunoprecipitation
E_00998	2015	25605944	Enhancer-bound LDB1 regulates a corticotrope promoter-pausing repression program	Mus musculus	mm8	chr12	3946672	3948652	Ascl1	Pomc	Enhancer	Active	Normal	NA	NA	NA	pituitary gland	UBERON:0000007	AtT-20	CVCL_2300	corticotroph	CL:0002309	Enhancer activity assay; Functional perturbation assay; Enhancer-promoter looping assay; Transcriptional regulation assay	ASCL1 ChIP-seq; LDB1 ChIP-seq; TBX19 ChIP-seq; EP300 ChIP-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; GRO-seq	ASCL1 knockdown; LDB1 knockdown; transient reporter assay; 3C-qPCR; PE3C-DSL; ChIP-qPCR; co-immunoprecipitation; mass spectrometry; RT-qPCR; Western blot
E_00999	2015	25605944	Enhancer-bound LDB1 regulates a corticotrope promoter-pausing repression program	Mus musculus	mm8	chr12	3946672	3948652	Ascl1	Pomc	Enhancer	Active	Normal	NA	NA	NA	pituitary gland	UBERON:0000007	AtT-20	CVCL_2300	corticotroph	CL:0002309	Enhancer activity assay; Functional perturbation assay; TF binding assay; Enhancer-promoter looping assay; Nascent transcription assay	ASCL1 ChIP-seq; LDB1 ChIP-seq; TBX19 ChIP-seq; EP300 ChIP-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; GRO-seq	ASCL1 knockdown; LDB1 knockdown; transient reporter assay; PE3C-DSL; 3C-qPCR; ChIP-qPCR; co-immunoprecipitation; mass spectrometry; RT-qPCR; Western blot
E_01000	2015	25605944	Enhancer-bound LDB1 regulates a corticotrope promoter-pausing repression program	Mus musculus	mm8	chr12	3946672	3948652	Tbx19	Pomc	Enhancer	Active	Normal	NA	NA	NA	pituitary gland	UBERON:0000007	AtT-20	CVCL_2300	corticotroph	CL:0002309	Enhancer activity assay; Functional perturbation assay; TF binding assay; Enhancer-promoter looping assay; Nascent transcription assay	ASCL1 ChIP-seq; LDB1 ChIP-seq; TBX19 ChIP-seq; EP300 ChIP-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; GRO-seq	TBX19 knockdown; LDB1 knockdown; transient reporter assay; PE3C-DSL; 3C-qPCR; ChIP-qPCR; RT-qPCR; Western blot
E_01001	2015	25605944	Enhancer-bound LDB1 regulates a corticotrope promoter-pausing repression program	Mus musculus	mm8	chr12	3946672	3948652	Tbx19	Pomc	Enhancer	Active	Normal	NA	NA	NA	pituitary gland	UBERON:0000007	AtT-20	CVCL_2300	corticotroph	CL:0002309	Functional perturbation assay; Enhancer occupancy assay; Enhancer-promoter looping assay; Transcriptional regulation assay	ASCL1 ChIP-seq; LDB1 ChIP-seq; TBX19 ChIP-seq; EP300 ChIP-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; GRO-seq	TBX19 knockdown; LDB1 knockdown; transient reporter assay; 3C-qPCR; PE3C-DSL; ChIP-qPCR; RT-qPCR; Western blot
E_01002	2014	25486255	CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells	Mus musculus	mm9	chr3	34652359	34665321	Nanog	Sox2	Super-enhancer	Active	Normal	NA	NA	NA	blastocyst	UBERON:0000358	F123	CVCL_VC43	embryonic stem cell	CL:0002322	Functional perturbation assay; TF binding assay; Gene expression assay; Super-enhancer functional validation; Chromatin interaction analysis; Epigenomic profiling	H3K27ac ChIP-seq; H3K4me3 ChIP-seq; Nanog ChIP-seq reanalysis; RNA-seq; Hi-C reanalysis	CRISPR/Cas9 double-sgRNA super-enhancer deletion; PCR genotyping; qPCR copy-number genotyping; Sanger sequencing; allele-specific RT-qPCR; Western blot; alkaline phosphatase staining; cell proliferation assay
E_01003	2014	25486255	CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells	Mus musculus	mm9	chr3	34652359	34665321	Pou5f1	Sox2	Super-enhancer	Active	Normal	NA	NA	NA	blastocyst	UBERON:0000358	F123	CVCL_VC43	embryonic stem cell	CL:0002322	Functional perturbation assay; TF binding assay; Gene expression assay; Super-enhancer functional validation; Chromatin interaction analysis; Epigenomic profiling	H3K27ac ChIP-seq; H3K4me3 ChIP-seq; Pou5f1 ChIP-seq reanalysis; RNA-seq; Hi-C reanalysis	CRISPR/Cas9 double-sgRNA super-enhancer deletion; PCR genotyping; qPCR copy-number genotyping; Sanger sequencing; allele-specific RT-qPCR; Western blot; alkaline phosphatase staining; cell proliferation assay
E_01004	2014	25486255	CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells	Mus musculus	mm9	chr3	34652359	34665321	Sox2	Sox2	Super-enhancer	Active	Normal	NA	NA	NA	blastocyst	UBERON:0000358	F123	CVCL_VC43	embryonic stem cell	CL:0002322	Functional perturbation assay; TF binding assay; Gene expression assay; Super-enhancer functional validation; Chromatin interaction analysis; Epigenomic profiling	H3K27ac ChIP-seq; H3K4me3 ChIP-seq; Sox2 ChIP-seq reanalysis; RNA-seq; Hi-C reanalysis	CRISPR/Cas9 double-sgRNA super-enhancer deletion; PCR genotyping; qPCR copy-number genotyping; Sanger sequencing; allele-specific RT-qPCR; Western blot; alkaline phosphatase staining; cell proliferation assay
E_01005	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr18	22026135	22027396	GATA6	GATA6	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES 8	CVCL_B207	human embryonic stem cell	NA	dCas9-KRAB CRISPRi loss-of-function; CRISPR-Cas9 clonal deletion; Hi-C chromatin contact validation	ATAC-seq; H3K27ac ChIP-seq; RNA-seq, scRNA-seq, pooled CRISPRi screening; Hi-C	RT-qPCR; FACS flow cytometry, lentiviral transduction, dual clonal enhancer knockout generation; CRISPRi
E_01006	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr18	22061243	22062444	GATA6	GATA6	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES 8	CVCL_B207	human embryonic stem cell	NA	dCas9-KRAB CRISPRi loss-of-function; CRISPR-Cas9 clonal deletion; Hi-C chromatin contact validation	ATAC-seq; H3K27ac ChIP-seq; RNA-seq, scRNA-seq, pooled CRISPRi screening; Hi-C	RT-qPCR; FACS flow cytometry, lentiviral transduction, dual clonal enhancer knockout generation; CRISPRi
E_01007	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr3	27713393	27715978	EOMES	EOMES	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES 8	CVCL_B207	human embryonic stem cell	NA	dCas9-KRAB CRISPRi loss-of-function; Hi-C chromatin contact validation	ATAC-seq; H3K27ac ChIP-seq; RNA-seq, scRNA-seq, pooled CRISPRi screening; Hi-C	RT-qPCR; FACS flow cytometry, lentiviral transduction, single enhancer clonal CRISPR-Cas9 deletion; CRISPRi
E_01008	2020	32238901	Accelerated evolution of an Lhx2 enhancer shapes mammalian social hierarchies	Mus musculus	mm9	chr2	38203254	38204076	NA	Lhx2	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Neuro-2a	CVCL_0470	neuroblastoma cell	NA	Enhancer activity assay; In vivo functional perturbation assay; Evolutionary cis-regulatory analysis	CAGE; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; DNase-seq; Hi-C	Luciferase reporter assay; PAS1 knockout mouse; PAS1 knock-in mouse; embryonic reporter assay
E_01009	2019	30990414	Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from na?ve pluripotency	Mus musculus	mm10	chr1	63189000	63192000	Pou5f1	Zdbf2	Enhancer	Active	Normal	NA	NA	NA	embryonic stem/epiblast cell state	NA	J1	CVCL_6412	embryonic stem cell	CL:0002322	Dynamic enhancer partitioning; chromatin interaction; genetic perturbation	4C-seq; ATAC-seq; ChIP-seq; RNA-seq; WGBS; DNA methylation profiling	CRISPR/Cas9 perturbation; ChIP-qPCR; RT-qPCR; bisulfite pyrosequencing
E_01010	2019	30990414	Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from na?ve pluripotency	Mus musculus	mm10	chr1	63193000	63196000	Pou5f1	Zdbf2	Enhancer	Active	Normal	NA	NA	NA	embryonic stem/epiblast cell state	NA	J1	CVCL_6412	embryonic stem cell	CL:0002322	Dynamic enhancer partitioning; chromatin interaction; genetic perturbation	4C-seq; ATAC-seq; ChIP-seq; RNA-seq; WGBS; DNA methylation profiling	CRISPR/Cas9 perturbation; ChIP-qPCR; RT-qPCR; bisulfite pyrosequencing
E_01011	2017	28511927	Coordinated regulation of IFITM1, 2 and 3 genes by an IFN-responsive enhancer through long-range chromatin interactions	Homo sapiens	hg19	chr11	355447	358949	STAT1	IFITM1	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	HEK293	CVCL_0045	adenovirus-transformed embryonic kidney cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ENCODE ChIP-seq; RNA Pol II ChIA-PET data mining	Luciferase reporter assay; CRISPR/Cas9 enhancer truncation; ChIP; EMSA; 3C; RT-qPCR; Western blot; IAV infection assay; CRISPR-Cas9; Reporter assay; In vivo CRISPR perturbation
E_01012	2017	28511927	Coordinated regulation of IFITM1, 2 and 3 genes by an IFN-responsive enhancer through long-range chromatin interactions	Homo sapiens	hg19	chr11	355447	358949	STAT1	IFITM2	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	HEK293	CVCL_0045	adenovirus-transformed embryonic kidney cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ENCODE ChIP-seq; RNA Pol II ChIA-PET data mining	Luciferase reporter assay; CRISPR/Cas9 enhancer truncation; ChIP; EMSA; 3C; RT-qPCR; Western blot; IAV infection assay; CRISPR-Cas9; Reporter assay; In vivo CRISPR perturbation
E_01013	2017	28511927	Coordinated regulation of IFITM1, 2 and 3 genes by an IFN-responsive enhancer through long-range chromatin interactions	Homo sapiens	hg19	chr11	355447	358949	STAT1	IFITM3	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	HEK293	CVCL_0045	adenovirus-transformed embryonic kidney cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ENCODE ChIP-seq; RNA Pol II ChIA-PET data mining	Luciferase reporter assay; CRISPR/Cas9 enhancer truncation; ChIP; EMSA; 3C; RT-qPCR; Western blot; IAV infection assay; CRISPR-Cas9; Reporter assay; In vivo CRISPR perturbation
E_01014	2017	28753427	A Genetic Variant Associated with Five Vascular Diseases Is a Distal Regulator of Endothelin-1 Gene Expression	Homo sapiens	hg19	chr6	12852000	12853000	NA	EDN1	Enhancer	Active	Disease	coronary artery disease	NA	NA	lung	UBERON:0002048	BEAS-2B	CVCL_0168	bronchial epithelial cell	CL:0002328	Disease-variant functional analysis; Enhancer perturbation assay	ChIP-seq; 4C-seq; GWAS	CRISPR knockout, Luciferase reporter assay
E_01015	2024	39333082	A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders	Homo sapiens	hg38	chr11	72308500	72309000	NA	PHOX2A	Enhancer	Active	Normal	NA	NA	NA	brainstem	UBERON:0002298	Cranial motor neurons	NA	motor neuron	CL:0000100	Enhancer activity assay; Chromatin interaction assay; Disease-variant functional analysis; In vivo functional validation	scATAC-seq, scRNA-seq, scCUT&Tag	Transgenic reporter assay; In vivo phenotyping
E_01016	2017	28511927	Coordinated regulation of IFITM1, 2 and 3 genes by an IFN-responsive enhancer through long-range chromatin interactions	Homo sapiens	hg19	chr11	355447	358949	STAT1	IFITM1	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	A-549	CVCL_0023	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; EMSA/gel-shift assay; 3C; Western blot
E_01017	2017	28511927	Coordinated regulation of IFITM1, 2 and 3 genes by an IFN-responsive enhancer through long-range chromatin interactions	Homo sapiens	hg19	chr11	355447	358949	STAT1	IFITM2	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	A-549	CVCL_0023	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; EMSA/gel-shift assay; 3C; Western blot
E_01018	2017	28511927	Coordinated regulation of IFITM1, 2 and 3 genes by an IFN-responsive enhancer through long-range chromatin interactions	Homo sapiens	hg19	chr11	355447	358949	STAT1	IFITM3	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	A-549	CVCL_0023	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; EMSA/gel-shift assay; 3C; Western blot
E_01019	2017	28511927	Coordinated regulation of IFITM1, 2 and 3 genes by an IFN-responsive enhancer through long-range chromatin interactions	Homo sapiens	hg19	chr11	355447	358949	STAT1	IFITM1	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	HEK293	CVCL_0045	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; EMSA/gel-shift assay; 3C; Western blot
E_01020	2017	28511927	Coordinated regulation of IFITM1, 2 and 3 genes by an IFN-responsive enhancer through long-range chromatin interactions	Homo sapiens	hg19	chr11	355447	358949	STAT1	IFITM2	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	HEK293	CVCL_0045	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; EMSA/gel-shift assay; 3C; Western blot
E_01021	2017	28511927	Coordinated regulation of IFITM1, 2 and 3 genes by an IFN-responsive enhancer through long-range chromatin interactions	Homo sapiens	hg19	chr11	355447	358949	STAT1	IFITM3	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	HEK293	CVCL_0045	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; EMSA/gel-shift assay; 3C; Western blot
E_01022	2017	28753427	A Genetic Variant Associated with Five Vascular Diseases Is a Distal Regulator of Endothelin-1 Gene Expression	Homo sapiens	hg19	chr6	12902957	12904957	NA	EDN1	Enhancer	Active	Disease	vascular disease susceptibility	NA	NA	blood vessel	UBERON:0001981	iPSC-derived endothelial cells	NA	endothelial cell	CL:0000115	Chromatin interaction assay; Functional enhancer variant assay; Genome editing	Genetic fine-mapping; H3K27ac epigenomic profiling; 4C-seq	CRISPR/Cas9 allele editing; CRISPR regulatory-region deletion; RT-qPCR; endothelin-1 quantification
E_01023	2023	37832549	Genome-wide CRISPR activation screening in senescent cells reveals SOX5 as a driver and therapeutic target of rejuvenation	Homo sapiens	hg19	chr4	174249537	174250490	SOX5	HMGB2	Enhancer	Active	Disease	Werner syndrome	MONDO:0010196	DOID:5688	connective tissue	UBERON:0002384	WS hMPC	NA	mesenchymal stem cell	CL:0000134	Endogenous enhancer perturbation; In vivo functional validation; HMGB2 enhancer activation and rejuvenation response	ATAC-seq; RNA-seq; Hi-C; single-cell multiome; pooled CRISPRa screen; CRISPR genetic screen	HMGB2 overexpression; RT-qPCR; Western blot; SA-β-gal assay; CRISPRa; In vivo phenotyping
E_01024	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr1	226210519	226211619	MIXL1	MIXL1	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES 8	CVCL_B207	human embryonic stem cell	NA	dCas9-KRAB CRISPRi loss-of-function; Hi-C chromatin contact validation	ATAC-seq; H3K27ac ChIP-seq; RNA-seq, scRNA-seq, pooled CRISPRi screening; Hi-C	RT-qPCR; FACS flow cytometry, lentiviral transduction; CRISPRi
E_01025	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54268120	54269407	SOX17	SOX17	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES 8	CVCL_B207	human embryonic stem cell	NA	dCas9-KRAB CRISPRi loss-of-function; Hi-C chromatin contact validation	ATAC-seq; H3K27ac ChIP-seq; RNA-seq, scRNA-seq, pooled CRISPRi screening; Hi-C	RT-qPCR; FACS flow cytometry, lentiviral transduction; CRISPRi
E_01026	2023	37832549	Genome-wide CRISPR activation screening in senescent cells reveals SOX5 as a driver and therapeutic target of rejuvenation	Homo sapiens	hg19	chr4	174249537	174250490	SOX5	HMGB2	Enhancer	Active	Normal	NA	NA	NA	connective tissue	UBERON:0002384	Primary human mesenchymal progenitor cells	NA	mesenchymal stem cell	CL:0000134	Endogenous enhancer perturbation; In vivo functional validation; Functional perturbation and enhancer activity validation	genome-wide CRISPRa screen; ATAC-seq; ChIP-seq; RNA-seq; pooled CRISPRa screen; CRISPR genetic screen	CRISPRa; SOX5/HMGB2 overexpression; ChIP-qPCR; RT-qPCR; In vivo phenotyping
E_01027	2023	37832549	Genome-wide CRISPR activation screening in senescent cells reveals SOX5 as a driver and therapeutic target of rejuvenation	Homo sapiens	hg19	chr4	174249537	174250490	SOX5	HMGB2	Enhancer	Active	Disease	osteoarthritis	MONDO:0005178	DOID:8398	connective tissue	UBERON:0002384	WS hMPC	NA	mesenchymal stem cell	CL:0000134	Endogenous enhancer perturbation; In vivo functional validation; SOX5 binding / HMGB2 enhancer activation	SOX5 ChIP-seq; H3K27ac/H3K4me1 ChIP-seq; ATAC-seq; RNA-seq; pooled CRISPRa screen; CRISPR genetic screen	SOX5 overexpression; ChIP-qPCR; RT-qPCR; Western blot; CRISPRa; In vivo phenotyping
E_01028	2023	37832549	Genome-wide CRISPR activation screening in senescent cells reveals SOX5 as a driver and therapeutic target of rejuvenation	Homo sapiens	hg19	chr4	174249537	174250490	SOX5	HMGB2	Enhancer	Active	Disease	Werner syndrome	MONDO:0010196	DOID:5688	connective tissue	UBERON:0002384	WS hMPC	NA	mesenchymal stem cell	CL:0000134	Endogenous enhancer perturbation; In vivo functional validation; Senescence-associated enhancer remodeling	SOX5 ChIP-seq; H3K27ac/H3K4me1 ChIP-seq; ATAC-seq; RNA-seq; pooled CRISPRa screen; CRISPR genetic screen	SOX5 overexpression; ChIP-qPCR; RT-qPCR; senescence phenotyping; CRISPRa; In vivo phenotyping
E_01029	2015	25605944	Enhancer-bound LDB1 regulates a corticotrope promoter-pausing repression program	Mus musculus	mm10	chr12	3944001	3947078	NA	Pomc	Enhancer	Repressed	Normal	NA	NA	NA	NA	NA	AtT-20,Pituitary Corticotrope Cell	NA	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; GRO-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_01030	2015	25605944	Enhancer-bound LDB1 regulates a corticotrope promoter-pausing repression program	Mus musculus	mm10	chr12	3956137	3961266	NA	Pomc	Enhancer	Repressed	Normal	NA	NA	NA	NA	NA	AtT-20,Pituitary Corticotrope Cell	NA	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; GRO-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_01031	2015	25605944	Enhancer-bound LDB1 regulates a corticotrope promoter-pausing repression program	Mus musculus	mm10	chr12	3938522	3942093	NA	Pomc	Enhancer	Repressed	Normal	NA	NA	NA	NA	NA	Pituitary Corticotrope Cell	NA	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; GRO-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_01032	2023	37832549	Genome-wide CRISPR activation screening in senescent cells reveals SOX5 as a driver and therapeutic target of rejuvenation	Homo sapiens	hg19	chr4	174249537	174250490	SOX5	HMGB2	Enhancer	Active	Normal	NA	NA	NA	connective tissue	UBERON:0002384	WT hMPC	NA	mesenchymal stem cell	CL:0000134	Endogenous enhancer perturbation; In vivo functional validation; SOX5-responsive HMGB2 enhancer in senescent hMPCs	SOX5 ChIP-seq; H3K27ac/H3K4me1 ChIP-seq; RNA-seq; pooled CRISPRa screen; CRISPR genetic screen	SOX5 overexpression; ChIP-qPCR; RT-qPCR; Western blot; CRISPRa; In vivo phenotyping
E_01033	2023	37832549	Genome-wide CRISPR activation screening in senescent cells reveals SOX5 as a driver and therapeutic target of rejuvenation	Homo sapiens	hg19	chr4	174249537	174250490	SOX5	HMGB2	Enhancer	Active	Normal	NA	NA	NA	connective tissue	UBERON:0002384	WT hMPC	NA	mesenchymal stem cell	CL:0000134	Endogenous enhancer perturbation; In vivo functional validation; Mechanistic validation linked to cartilage rejuvenation	RNA-seq; ChIP-seq; ATAC-seq; pooled CRISPRa screen; CRISPR genetic screen	SOX5/HMGB2 overexpression; RT-qPCR; Western blot; lentiviral in vivo gene therapy in aged mouse cartilage; CRISPRa; In vivo phenotyping
E_01034	2017	28753427	A Genetic Variant Associated with Five Vascular Diseases Is a Distal Regulator of Endothelin-1 Gene Expression	Homo sapiens	hg19	chr6	12903457	12904457	NA	EDN1	Enhancer	Active	Disease	pleiotropic vascular-disease susceptibility locus	NA	NA	red nucleus	UBERON:0001947	HUVEC and CRISPR-edited endothelial models	NA	endothelial cell	CL:0000115	Allele-specific distal regulatory-variant perturbation and target analysis	vascular epigenomic/transcriptomic integration	CRISPR-Cas9 allelic editing; 4C; RT-qPCR; EDN1 protein assay; endothelial functional assays
E_01035	2023	37832549	Genome-wide CRISPR activation screening in senescent cells reveals SOX5 as a driver and therapeutic target of rejuvenation	Homo sapiens	hg19	chr4	174249537	174250490	SOX5	HMGB2	Enhancer	Active	Disease	osteoarthritis	MONDO:0005178	DOID:8398	connective tissue	UBERON:0002384	WS hMPC	NA	mesenchymal stem cell	CL:0000134	Endogenous enhancer perturbation; In vivo functional validation; Genome-wide CRISPRa rejuvenation screen with HMGB2 mechanistic validation	genome-wide CRISPRa screen; RNA-seq; Hi-C; single-cell multiome; pooled CRISPRa screen; CRISPR genetic screen	CRISPRa; SOX5/HMGB2 overexpression; RT-qPCR; Western blot; In vivo phenotyping
E_01036	2024	39443808	Chromatin remodelling drives immune cell-fibroblast communication in heart failure	Mus musculus	mm10	chr2	129323600	129328600	NA	Il1b	Enhancer	Active	Disease	atherosclerosis	MONDO:0005311	DOID:1936	heart	UBERON:0000948	Macrophage	NA	macrophage	CL:0000235	Enhancer activity assay; Endogenous enhancer perturbation; In vivo functional validation	scATAC-seq	Luciferase reporter assay, CRISPR knockout; RT-qPCR; Mouse genetic deletion/knock-in; In vivo phenotyping
E_01037	2024	39333082	A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders	Mus musculus	mm10	chr13	115686619	115688040	NA	Isl1	Enhancer	Active	Normal	NA	NA	NA	brainstem	UBERON:0002298	Embryonic cranial motor neurons	NA	motor neuron	CL:0000100	Enhancer activity assay; Disease-variant functional analysis; In vivo functional validation; Single-cell chromatin accessibility profiling; Peak-to-gene linking; Histone modification profiling	scATAC-seq; scRNA-seq; scMultiome ATAC + Gene Expression; H3K27ac scCUT&Tag	In vivo transgenic lacZ reporter assay; In vivo phenotyping
E_01038	2024	39333082	A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders	Mus musculus	mm10	chr13	116087428	116088064	NA	Isl1	Enhancer	Active	Normal	NA	NA	NA	brainstem	UBERON:0002298	Embryonic cranial motor neurons (cMN3/4, cMN6 and cMN7)	NA	motor neuron	CL:0000100	Enhancer activity assay; Disease-variant functional analysis; In vivo functional validation; Single-cell chromatin accessibility profiling; Peak-to-gene linking; Histone modification profiling	scATAC-seq; scRNA-seq; scMultiome ATAC + Gene Expression; H3K27ac scCUT&Tag	In vivo transgenic lacZ reporter assay; In vivo phenotyping
E_01039	2024	39333082	A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders	Mus musculus	mm10	chr13	116514002	116515994	NA	Isl1	Enhancer	Active	Normal	NA	NA	NA	brainstem	UBERON:0002298	Embryonic cranial motor neurons	NA	motor neuron	CL:0000100	Enhancer activity assay; Disease-variant functional analysis; In vivo functional validation; Single-cell chromatin accessibility profiling; Peak-to-gene linking; Histone modification profiling	scATAC-seq; scRNA-seq; scMultiome ATAC + Gene Expression; H3K27ac scCUT&Tag	In vivo transgenic lacZ reporter assay; In vivo phenotyping
E_01040	2024	39333082	A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders	Mus musculus	mm10	chr13	116632748	116634332	NA	Isl1	Enhancer	Active	Normal	NA	NA	NA	brainstem	UBERON:0002298	Embryonic cranial motor neuron atlas	NA	motor neuron	CL:0000100	Enhancer activity assay; Disease-variant functional analysis; In vivo functional validation; Single-cell chromatin accessibility profiling; Peak-to-gene linking; Histone modification profiling	scATAC-seq; scRNA-seq; scMultiome ATAC + Gene Expression; H3K27ac scCUT&Tag	In vivo transgenic lacZ reporter assay; In vivo phenotyping
E_01041	2014	25486255	CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells	Mus musculus	mm10	chr3	34743178	34776096	Nanog	Sox2	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01042	2014	25486255	CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells	Mus musculus	mm10	chr3	34743178	34776096	Pou5f1	Sox2	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01043	2014	25486255	CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells	Mus musculus	mm10	chr3	34743178	34776096	Sox2	Sox2	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01044	2025	40133308	Identification of a SNAI1 enhancer RNA that drives cancer cell plasticity	Homo sapiens	hg38	chr20	50027744	50030383	SMAD3	SNAI1	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	lung	UBERON:0002048	A-549	CVCL_0023	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; In vivo functional validation	RNA-seq; 4C-seq; ChIP-seq; 3C-seq	Luciferase reporter assay, CRISPR knockout, CRISPRa, CRISPRi; ChIP-qPCR; RT-qPCR; Western blot; In vivo phenotyping
E_01045	2025	40133308	Identification of a SNAI1 enhancer RNA that drives cancer cell plasticity	Homo sapiens	hg38	chr20	50027744	50030383	SMAD3	SNAI1	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	MDA-MB-231	CVCL_0062	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; In vivo functional validation	RNA-seq; 4C-seq; ChIP-seq; 3C-seq	Luciferase reporter assay, CRISPR knockout, CRISPRa, CRISPRi; ChIP-qPCR; RT-qPCR; Western blot; In vivo phenotyping
E_01046	2024	38661000	Multiple genetic variants at the SLC30A8 locus affect local super-enhancer activity and influence pancreatic β-cell survival and function	Homo sapiens	hg19	chr8	118183060	118260108	NA	EXT1	Super-enhancer	Active	Disease	type 2 diabetes mellitus	MONDO:0005148	DOID:9352	islet of Langerhans	UBERON:0000006	EndoC-betaH3	CVCL_IS72	pancreatic beta cell	CL:0000169	Functional perturbation assay; Chromatin interaction assay; Super-enhancer characterization	ATAC-seq; H3K27ac ChIP-seq; RNA-seq; Hi-C; promoter capture Hi-C; ChIA-PET; eQTL analysis	CRISPR-Cas9 regional deletion; RT-qPCR; Sanger sequencing; glucose-stimulated insulin secretion assay; CRISPR-Cas9
E_01047	2024	38661000	Multiple genetic variants at the SLC30A8 locus affect local super-enhancer activity and influence pancreatic β-cell survival and function	Homo sapiens	hg19	chr8	118183060	118260108	NA	MED30	Super-enhancer	Active	Disease	type 2 diabetes mellitus	MONDO:0005148	DOID:9352	islet of Langerhans	UBERON:0000006	EndoC-betaH3	CVCL_IS72	pancreatic beta cell	CL:0000169	Functional perturbation assay; Chromatin interaction assay; Super-enhancer characterization	ATAC-seq; H3K27ac ChIP-seq; RNA-seq; Hi-C; promoter capture Hi-C; ChIA-PET; eQTL analysis	CRISPR-Cas9 regional deletion; RT-qPCR; Sanger sequencing; glucose-stimulated insulin secretion assay; CRISPR-Cas9
E_01048	2024	38661000	Multiple genetic variants at the SLC30A8 locus affect local super-enhancer activity and influence pancreatic β-cell survival and function	Homo sapiens	hg19	chr8	118183060	118260108	NA	RAD21	Super-enhancer	Active	Disease	type 2 diabetes mellitus	MONDO:0005148	DOID:9352	islet of Langerhans	UBERON:0000006	EndoC-betaH3	CVCL_IS72	pancreatic beta cell	CL:0000169	Functional perturbation assay; Chromatin interaction assay; Super-enhancer characterization	ATAC-seq; H3K27ac ChIP-seq; RNA-seq; Hi-C; promoter capture Hi-C; ChIA-PET; eQTL analysis	CRISPR-Cas9 regional deletion; RT-qPCR; Sanger sequencing; glucose-stimulated insulin secretion assay; CRISPR-Cas9
E_01049	2023	36990511	Cis interactions in the Irf8 locus regulate stage-dependent enhancer activation	Mus musculus	mm10	chr8	121495097	121496097	NA	Irf8	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary dendritic-cell lineage populations	NA	classical dendritic cell	CL:0000451	Functional perturbation assay; Chromatin interaction assay; Enhancer essentiality assay	RNA-seq; ATAC-seq; ChIP-seq; 4C-seq	CRISPR-Cas9 enhancer deletion; compound-heterozygous enhancer genetics; Flow cytometry; RT-qPCR
E_01050	2023	36990511	Cis interactions in the Irf8 locus regulate stage-dependent enhancer activation	Mus musculus	mm10	chr8	121504097	121505097	NA	Irf8	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary dendritic-cell lineage populations	NA	classical dendritic cell	CL:0000451	Functional perturbation assay; Chromatin interaction assay; Enhancer essentiality assay	RNA-seq; ATAC-seq; ChIP-seq; 4C-seq	CRISPR-Cas9 enhancer deletion; compound-heterozygous enhancer genetics; Flow cytometry; RT-qPCR
E_01051	2022	35908104	Requirement for TP73 and genetic alterations originating from its intragenic super-enhancer in adult T-cell leukemia	Homo sapiens	hg19	chr1	3593076	3594185	IRF4	TP73	Enhancer	Active	Disease	adult T-cell leukemia/lymphoma	MONDO:0019471	DOID:0050523	blood	UBERON:0000178	TL-Om1	CVCL_B473	T cell	CL:0000084	TF binding assay; In vivo functional validation; Super-enhancer constituent activity assay; Enhancer-promoter interaction assay; Functional enhancer perturbation assay	H3K27ac ChIP-seq; IRF4 ChIP-seq; RELA ChIP-seq; H3K27ac HiChIP; RNA-seq	CRISPR/Cas9 enhancer excision; dCas9-KRAB CRISPRi; RT-qPCR; Western blot; In vivo phenotyping
E_01052	2022	35908104	Requirement for TP73 and genetic alterations originating from its intragenic super-enhancer in adult T-cell leukemia	Homo sapiens	hg19	chr1	3593076	3594185	RELA	TP73	Enhancer	Active	Disease	adult T-cell leukemia/lymphoma	MONDO:0019471	DOID:0050523	blood	UBERON:0000178	TL-Om1	CVCL_B473	T cell	CL:0000084	TF binding assay; In vivo functional validation; Super-enhancer constituent activity assay; Enhancer-promoter interaction assay; Functional enhancer perturbation assay	H3K27ac ChIP-seq; IRF4 ChIP-seq; RELA ChIP-seq; H3K27ac HiChIP; RNA-seq	CRISPR/Cas9 enhancer excision; dCas9-KRAB CRISPRi; RT-qPCR; Western blot; In vivo phenotyping
E_01053	2024	38661000	Multiple genetic variants at the SLC30A8 locus affect local super-enhancer activity and influence pancreatic β-cell survival and function	Homo sapiens	hg38	chr8	118183060	118185060	FOXA2	SLC30A8	Enhancer	Active	Normal	NA	NA	NA	islet of Langerhans	UBERON:0000006	BRE	CVCL_A5NF	pancreatic beta cell	CL:0000169	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; Hi-C; eQTL analysis	CRISPR knockout; Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot; CRISPR-Cas9
E_01054	2024	38661000	Multiple genetic variants at the SLC30A8 locus affect local super-enhancer activity and influence pancreatic β-cell survival and function	Homo sapiens	hg38	chr8	118250000	118252000	PDX1	SLC30A8	Enhancer	Active	Normal	NA	NA	NA	islet of Langerhans	UBERON:0000006	BRE	CVCL_A5NF	pancreatic beta cell	CL:0000169	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; Hi-C; eQTL analysis	CRISPR knockout; Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot; CRISPR-Cas9
E_01055	2024	38661000	Multiple genetic variants at the SLC30A8 locus affect local super-enhancer activity and influence pancreatic β-cell survival and function	Homo sapiens	hg38	chr8	118183060	118185060	FOXA2	UTP23	Enhancer	Active	Normal	NA	NA	NA	islet of Langerhans	UBERON:0000006	Human Pancreatic Islets	NA	pancreatic islet cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; Hi-C; eQTL analysis	CRISPR knockout; Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot; CRISPR-Cas9
E_01056	2023	36990511	Cis interactions in the Irf8 locus regulate stage-dependent enhancer activation	Mus musculus	mm39	chr8	121495079	121495626	Batf3	Irf8	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	maturing cDC1 cells	NA	dendritic cell lineage	NA	TF binding assay; Chromatin interaction assay; Endogenous enhancer perturbation assay	RNA-seq; ATAC-seq; ChIP-seq; 4C-seq	CRISPR-Cas9 enhancer deletion; compound enhancer genetics; BATF3 occupancy analysis; Flow cytometry; RT-qPCR; CRISPR-Cas9
E_01057	2023	36990511	Cis interactions in the Irf8 locus regulate stage-dependent enhancer activation	Mus musculus	mm39	chr8	121495079	121495626	Irf8	Irf8	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	maturing cDC1 cells	NA	dendritic cell lineage	NA	Chromatin interaction assay; Enhancer activity/occupancy assay; Endogenous enhancer perturbation assay	RNA-seq; ATAC-seq; ChIP-seq; 4C-seq	CRISPR-Cas9 enhancer deletion; compound-heterozygous mouse genetics; Flow cytometry; RT-qPCR; chromatin-accessibility/occupancy validation; CRISPR-Cas9
E_01058	2023	36990511	Cis interactions in the Irf8 locus regulate stage-dependent enhancer activation	Mus musculus	mm39	chr8	121503787	121504483	Tcf3	Irf8	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	pre-cDC1 / dendritic progenitors	NA	dendritic cell lineage	NA	Chromatin interaction assay; Enhancer activity/occupancy assay; Endogenous enhancer perturbation assay	RNA-seq; ATAC-seq; ChIP-seq; 4C-seq	CRISPR-Cas9 enhancer deletion; mouse genetics; Flow cytometry; RT-qPCR; E-box functional analysis; CRISPR-Cas9
E_01059	2023	36990511	Cis interactions in the Irf8 locus regulate stage-dependent enhancer activation	Mus musculus	mm39	chr8	121503787	121504483	Tcf4	Irf8	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	pre-cDC1 / dendritic progenitors	NA	dendritic cell lineage	NA	Chromatin interaction assay; Enhancer activity/occupancy assay; Endogenous enhancer perturbation assay	RNA-seq; ATAC-seq; ChIP-seq; 4C-seq	CRISPR-Cas9 enhancer deletion; mouse genetics; Flow cytometry; RT-qPCR; E-box functional analysis; CRISPR-Cas9
E_01060	2022	35732734	Ablation of cDC2 development by triple mutations within the Zeb2 enhancer	Mus musculus	mm10	chr2	45279107	45280206	Cebpa	Zeb2	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary mouse bone-marrow dendritic progenitors	NA	common dendritic progenitor	CL:0001029	TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation; endogenous enhancer mutagenesis; lineage differentiation assay	CUT&RUN; ChIP-seq; RNA-seq	EMSA; enhancer reporter assay; CRISPR-Cas9 triple motif editing in mice; Flow cytometry; progenitor differentiation; CRISPR-Cas9 endogenous deletion/editing; ChIP; In vivo phenotyping
E_01061	2022	35732734	Ablation of cDC2 development by triple mutations within the Zeb2 enhancer	Mus musculus	mm10	chr2	45279107	45280206	Cebpb	Zeb2	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary mouse bone-marrow dendritic progenitors	NA	common dendritic progenitor	CL:0001029	TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation; endogenous enhancer mutagenesis; lineage differentiation assay	CUT&RUN; ChIP-seq; RNA-seq	EMSA; enhancer reporter assay; CRISPR-Cas9 triple motif editing in mice; Flow cytometry; progenitor differentiation; CRISPR-Cas9 endogenous deletion/editing; ChIP; In vivo phenotyping
E_01062	2022	35732734	Ablation of cDC2 development by triple mutations within the Zeb2 enhancer	Mus musculus	mm10	chr2	45279107	45280206	Nfil3	Zeb2	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary mouse bone-marrow dendritic progenitors	NA	common dendritic progenitor	CL:0001029	TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation; endogenous enhancer mutagenesis; lineage differentiation assay	CUT&RUN; ChIP-seq; RNA-seq	EMSA; enhancer reporter assay; CRISPR-Cas9 triple motif editing in mice; Flow cytometry; progenitor differentiation; helminth challenge; CRISPR-Cas9 endogenous deletion/editing; ChIP; In vivo phenotyping
E_01063	2017	28575289	MyoD- and FoxO3-mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation	Mus musculus	mm10	chr1	136170800	136171203	Myog	Myog	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast/myotube	NA	Enhancer activity assay; Functional perturbation assay	ChIP-seq; RNA-seq; 3C-seq	Luciferase reporter assay; ChIP-qPCR; CRISPR knockout; RT-qPCR, 3C-PCR
E_01064	2017	28575289	MyoD- and FoxO3-mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation	Mus musculus	mm10	chr1	136171700	136172103	Foxo3	Myog	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast/myotube	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; 3C-seq	Luciferase reporter assay; ChIP-qPCR; CRISPR knockout; RT-qPCR, 3C-PCR
E_01065	2017	28575289	MyoD- and FoxO3-mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation	Mus musculus	mm10	chr1	136177900	136178345	Myod1	Myog	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast/myotube	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; 3C-seq	Luciferase reporter assay; ChIP-qPCR; CRISPR knockout; RT-qPCR, 3C-PCR; DNA Pulldown Assay; Immunoprecipitation
E_01066	2017	28575289	MyoD- and FoxO3-mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation	Mus musculus	mm10	chr1	136180500	136180903	Myod1	Myog	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast/myotube	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; 3C-seq	Luciferase reporter assay; ChIP-qPCR; CRISPR knockout; RT-qPCR, 3C-PCR
E_01067	2017	28575289	MyoD- and FoxO3-mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation	Mus musculus	mm10	chr1	136184128	136184880	Myod1	Myog	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast/myotube	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; 3C-seq	Luciferase reporter assay; ChIP-qPCR; CRISPR knockout; RT-qPCR, 3C-PCR
E_01068	2014	25369933	Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia	Homo sapiens	hg19	chr8	130180217	130180629	NOTCH1	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Primary ATL cells	NA	T cell	CL:0000084	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq	Luciferase reporter assay, 3C; ChIP-qPCR; RT-qPCR
E_01069	2014	25369933	Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia	Homo sapiens	hg19	chr8	130180217	130180629	RBPJ	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Primary ATL cells	NA	T cell	CL:0000084	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq	Luciferase reporter assay, 3C; ChIP-qPCR; RT-qPCR
E_01070	2014	25369933	Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia	Mus musculus	mm9	chr15	63087071	63087595	Notch1	Myc	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	NA	NA	T6E murine T-ALL cells	NA	T cell	CL:0000084	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	Notch1 ChIP-seq; Rbpj ChIP-seq; Histone modification ChIP-seq	Luciferase reporter assay; EMSA; 3C-qPCR; ChIP-qPCR; Site-directed mutagenesis; Gamma-secretase inhibition; qRT-PCR
E_01071	2014	25369933	Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia	Mus musculus	mm9	chr15	63087071	63087595	Rbpj	Myc	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	NA	NA	T6E murine T-ALL cells	NA	T cell	CL:0000084	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	Notch1 ChIP-seq; Rbpj ChIP-seq; Histone modification ChIP-seq	Luciferase reporter assay; EMSA; 3C-qPCR; ChIP-qPCR; Rbpj-site mutagenesis; Gamma-secretase inhibition; qRT-PCR
E_01072	2017	28575289	MyoD- and FoxO3-mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation	Mus musculus	mm10	chr1	136170803	136192554	Myod1	Myog	Super-enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast/myotube	NA	Enhancer activity assay	ChIP-seq; RNA-seq; 3C-seq	Luciferase reporter assay; ChIP-qPCR; CRISPR knockout; RT-qPCR; Western blot; Immunofluorescence Staining
E_01073	2022	35732734	Ablation of cDC2 development by triple mutations within the Zeb2 enhancer	Mus musculus	mm10	chr2	45279107	45280206	Cebpa	Zeb2	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Hoxb8-immortalized DC precursor system used for mechanistic assays	NA	common dendritic progenitor	CL:0001029	TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation; endogenous enhancer mutagenesis; lineage differentiation assay	CUT&RUN; ChIP-seq; RNA-seq	EMSA; enhancer reporter assay; CRISPR-Cas9 triple motif editing in mice; Flow cytometry; progenitor differentiation; CRISPR-Cas9 endogenous deletion/editing; ChIP; In vivo phenotyping
E_01074	2022	35732734	Ablation of cDC2 development by triple mutations within the Zeb2 enhancer	Mus musculus	mm10	chr2	45279107	45280206	Cebpb	Zeb2	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Hoxb8-immortalized DC precursor system used for mechanistic assays	NA	common dendritic progenitor	CL:0001029	TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation; endogenous enhancer mutagenesis; lineage differentiation assay	CUT&RUN; ChIP-seq; RNA-seq	EMSA; enhancer reporter assay; CRISPR-Cas9 triple motif editing in mice; Flow cytometry; progenitor differentiation; CRISPR-Cas9 endogenous deletion/editing; ChIP; In vivo phenotyping
E_01075	2022	35732734	Ablation of cDC2 development by triple mutations within the Zeb2 enhancer	Mus musculus	mm10	chr2	45279107	45280206	Nfil3	Zeb2	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Hoxb8-immortalized DC precursor system used for mechanistic assays	NA	common dendritic progenitor	CL:0001029	TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation; endogenous enhancer mutagenesis; lineage differentiation assay	CUT&RUN; ChIP-seq; RNA-seq	EMSA; enhancer reporter assay; CRISPR-Cas9 triple motif editing in mice; Flow cytometry; progenitor differentiation; helminth challenge; CRISPR-Cas9 endogenous deletion/editing; ChIP; In vivo phenotyping
E_01076	2022	35908104	Requirement for TP73 and genetic alterations originating from its intragenic super-enhancer in adult T-cell leukemia	Homo sapiens	hg19	chr1	3572730	3574116	IRF4	TP73	Enhancer	Active	Disease	adult T-cell leukemia/lymphoma	MONDO:0019471	DOID:0050523	blood	UBERON:0000178	T cell leukemia cell	NA	T cell	CL:0000084	Enhancer activity assay; Functional perturbation assay; TF binding assay; In vivo functional validation	ChIP-seq; RNA-seq, Hi-ChIP	CRISPR knockout, CRISPRi; RT-qPCR; Western blot; In vivo phenotyping
E_01077	2017	28575289	MyoD- and FoxO3-mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation	Mus musculus	mm10	chr1	136179654	136180057	Foxo3	Myog	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin-state profiling	ChIP-seq	Luciferase reporter assay, CRISPR knockout, CRISPRi; ChIP-qPCR; ChIP
E_01078	2017	28575289	MyoD- and FoxO3-mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation	Mus musculus	mm10	chr1	136185854	136186299	Myod1	Myog	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin-state profiling	ChIP-seq	Luciferase reporter assay, CRISPR knockout, CRISPRi; ChIP-qPCR; ChIP
E_01079	2017	28575289	MyoD- and FoxO3-mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation	Mus musculus	mm10	chr1	136188454	136188857	Myod1	Myog	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin-state profiling	ChIP-seq	Luciferase reporter assay, CRISPR knockout, CRISPRi; ChIP-qPCR; ChIP
E_01080	2022	35732734	Ablation of cDC2 development by triple mutations within the Zeb2 enhancer	Mus musculus	mm10	chr2	45279107	45280206	Nfil3	Zeb2	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary mouse bone-marrow dendritic progenitors	NA	common dendritic progenitor	CL:0001029	TF competition at Zeb2 ?165-kb enhancer; endogenous triple-motif mutagenesis; lineage differentiation and in vivo functional validation	CUT&RUN; ChIP-seq; RNA-seq	EMSA; enhancer reporter; CRISPR-Cas9 triple-motif editing in mice; Flow cytometry; progenitor differentiation; ChIP; helminth-challenge phenotyping
E_01081	2022	35732734	Ablation of cDC2 development by triple mutations within the Zeb2 enhancer	Mus musculus	mm10	chr2	45279107	45280206	Cebpa	Zeb2	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary mouse bone-marrow dendritic progenitors	NA	common dendritic progenitor	CL:0001029	TF competition at Zeb2 ?165-kb enhancer; endogenous triple-motif mutagenesis; lineage differentiation and in vivo functional validation	CUT&RUN; ChIP-seq; RNA-seq	EMSA; enhancer reporter; CRISPR-Cas9 triple-motif editing in mice; Flow cytometry; progenitor differentiation; ChIP; helminth-challenge phenotyping
E_01082	2022	35732734	Ablation of cDC2 development by triple mutations within the Zeb2 enhancer	Mus musculus	mm10	chr2	45279107	45280206	Cebpb	Zeb2	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary mouse bone-marrow dendritic progenitors	NA	common dendritic progenitor	CL:0001029	TF competition at Zeb2 ?165-kb enhancer; endogenous triple-motif mutagenesis; lineage differentiation and in vivo functional validation	CUT&RUN; ChIP-seq; RNA-seq	EMSA; enhancer reporter; CRISPR-Cas9 triple-motif editing in mice; Flow cytometry; progenitor differentiation; ChIP; helminth-challenge phenotyping
E_01083	2017	28575289	MyoD- and FoxO3-mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation	Mus musculus	mm10	chr1	136179600	136180045	Foxo3	Myog	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Enhancer activity assay; TF binding assay; Chromatin-state profiling	ChIP-seq	Luciferase reporter assay, CRISPR knockout; ChIP
E_01084	2017	28575289	MyoD- and FoxO3-mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation	Mus musculus	mm10	chr1	136170878	136192613	Foxo3	Myog	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	C2C12	CVCL_0188	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR; Western blot
E_01085	2017	28575289	MyoD- and FoxO3-mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation	Mus musculus	mm10	chr1	136170878	136192613	Myod1	Myog	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	C2C12	CVCL_0188	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR; Western blot
E_01086	2017	28575289	MyoD- and FoxO3-mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation	Mus musculus	mm10	chr1	136188400	136188845	Myod1	Myog	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Functional perturbation assay; TF binding assay; Chromatin-state profiling	ChIP-seq	CRISPR knockout; RT-qPCR; ChIP
E_01087	2022	35732734	Ablation of cDC2 development by triple mutations within the Zeb2 enhancer	Mus musculus	mm10	chr2	45279107	45280206	Nfil3	Zeb2	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Hoxb8-immortalized dendritic-cell precursor system	NA	common dendritic progenitor	CL:0001029	TF competition at Zeb2 ?165-kb enhancer; endogenous triple-motif mutagenesis; lineage differentiation and in vivo functional validation	CUT&RUN; ChIP-seq; RNA-seq	EMSA; enhancer reporter; CRISPR-Cas9 triple-motif editing in mice; Flow cytometry; progenitor differentiation; ChIP; helminth-challenge phenotyping
E_01088	2022	35732734	Ablation of cDC2 development by triple mutations within the Zeb2 enhancer	Mus musculus	mm10	chr2	45279107	45280206	Cebpa	Zeb2	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Hoxb8-immortalized dendritic-cell precursor system	NA	common dendritic progenitor	CL:0001029	TF competition at Zeb2 ?165-kb enhancer; endogenous triple-motif mutagenesis; lineage differentiation and in vivo functional validation	CUT&RUN; ChIP-seq; RNA-seq	EMSA; enhancer reporter; CRISPR-Cas9 triple-motif editing in mice; Flow cytometry; progenitor differentiation; ChIP; helminth-challenge phenotyping
E_01089	2022	35732734	Ablation of cDC2 development by triple mutations within the Zeb2 enhancer	Mus musculus	mm10	chr2	45279107	45280206	Cebpb	Zeb2	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Hoxb8-immortalized dendritic-cell precursor system	NA	common dendritic progenitor	CL:0001029	TF competition at Zeb2 ?165-kb enhancer; endogenous triple-motif mutagenesis; lineage differentiation and in vivo functional validation	CUT&RUN; ChIP-seq; RNA-seq	EMSA; enhancer reporter; CRISPR-Cas9 triple-motif editing in mice; Flow cytometry; progenitor differentiation; ChIP; helminth-challenge phenotyping
E_01090	2014	25369933	Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia	Homo sapiens	hg19	chr8	130180217	130180629	NOTCH1	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	NA	NA	HPB-ALL	CVCL_1820	T cell	CL:0000084	Long-range enhancer-target validation; TF-dependent enhancer activity; signaling-dependent enhancer regulation	NOTCH1 ChIP-seq; RBPJ ChIP-seq; H3K27ac chromatin profiling	Luciferase reporter assay; 3C; NOTCH inhibition; enhancer-promoter interaction assay
E_01091	2014	25369933	Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia	Homo sapiens	hg19	chr8	130180217	130180629	NOTCH1	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	NA	NA	CUTLL1	CVCL_4966	T cell	CL:0000084	Long-range enhancer-target validation; TF-dependent enhancer activity; signaling-dependent enhancer regulation	NOTCH1 ChIP-seq; RBPJ ChIP-seq; H3K27ac chromatin profiling	Luciferase reporter assay; 3C; NOTCH inhibition; enhancer-promoter interaction assay
E_01092	2014	25369933	Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia	Homo sapiens	hg19	chr8	130180217	130180629	RBPJ	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	NA	NA	HPB-ALL	CVCL_1820	T cell	CL:0000084	Long-range enhancer-target validation; TF-site-dependent enhancer activity	NOTCH1 ChIP-seq; RBPJ ChIP-seq; H3K27ac chromatin profiling	Luciferase reporter assay; EMSA; conserved NOTCH-complex-site analysis; 3C; NOTCH inhibition
E_01093	2014	25369933	Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia	Homo sapiens	hg19	chr8	130180217	130180629	RBPJ	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	NA	NA	CUTLL1	CVCL_4966	T cell	CL:0000084	Long-range enhancer-target validation; TF-site-dependent enhancer activity	NOTCH1 ChIP-seq; RBPJ ChIP-seq; H3K27ac chromatin profiling	Luciferase reporter assay; EMSA; conserved NOTCH-complex-site analysis; 3C; NOTCH inhibition
E_01094	2014	25369933	Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia	Homo sapiens	hg19	chr8	130180065	130180972	NOTCH1	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	NA	NA	HPB-ALL	CVCL_1820	T cell	CL:0000084	Enhancer-promoter interaction; TF-dependent enhancer activity	NOTCH1 ChIP-seq; RBPJ ChIP-seq; chromatin profiling	3C; Luciferase reporter assay; NOTCH inhibition; binding-site functional analysis
E_01095	2014	25369933	Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia	Homo sapiens	hg19	chr8	130180065	130180972	NOTCH1	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	NA	NA	CUTLL1	CVCL_4966	T cell	CL:0000084	Enhancer-promoter interaction; TF-dependent enhancer activity	NOTCH1 ChIP-seq; RBPJ ChIP-seq; chromatin profiling	3C; Luciferase reporter assay; NOTCH inhibition; binding-site functional analysis
E_01096	2014	25369933	Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia	Homo sapiens	hg19	chr8	130180065	130180972	RBPJ	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	NA	NA	HPB-ALL	CVCL_1820	T cell	CL:0000084	Enhancer-promoter interaction; TF-site-dependent enhancer activity	NOTCH1 ChIP-seq; RBPJ ChIP-seq; chromatin profiling	3C; Luciferase reporter assay; RBPJ/NOTCH-complex binding-site analysis; NOTCH inhibition
E_01097	2014	25369933	Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia	Homo sapiens	hg19	chr8	130180065	130180972	RBPJ	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	NA	NA	CUTLL1	CVCL_4966	T cell	CL:0000084	Enhancer-promoter interaction; TF-site-dependent enhancer activity	NOTCH1 ChIP-seq; RBPJ ChIP-seq; chromatin profiling	3C; Luciferase reporter assay; RBPJ/NOTCH-complex binding-site analysis; NOTCH inhibition
E_01098	2014	25369933	Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia	Homo sapiens	hg19	chr8	130180065	130180972	NOTCH1	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	additional T-ALL models	NA	T-lineage lymphoblast/leukemia cell	NA	Enhancer-promoter interaction; TF-dependent enhancer activity	NOTCH1 ChIP-seq; RBPJ ChIP-seq; chromatin profiling	3C; Luciferase reporter assay; NOTCH inhibition; binding-site functional analysis
E_01099	2014	25369933	Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia	Homo sapiens	hg19	chr8	130180065	130180972	NOTCH1	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	additional T-ALL models	NA	T-lineage lymphoblast/leukemia cell	NA	Enhancer-promoter interaction; TF-dependent enhancer activity	NOTCH1 ChIP-seq; RBPJ ChIP-seq; chromatin profiling	3C; Luciferase reporter assay; NOTCH inhibition; binding-site functional analysis
E_01100	2014	25369933	Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia	Homo sapiens	hg19	chr8	130180065	130180972	RBPJ	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	additional T-ALL models	NA	T-lineage lymphoblast/leukemia cell	NA	Enhancer-promoter interaction; TF-site-dependent enhancer activity	NOTCH1 ChIP-seq; RBPJ ChIP-seq; chromatin profiling	3C; Luciferase reporter assay; RBPJ/NOTCH-complex binding-site analysis; NOTCH inhibition
E_01101	2014	25369933	Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia	Homo sapiens	hg19	chr8	130180065	130180972	RBPJ	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	additional T-ALL models	NA	T-lineage lymphoblast/leukemia cell	NA	Enhancer-promoter interaction; TF-site-dependent enhancer activity	NOTCH1 ChIP-seq; RBPJ ChIP-seq; chromatin profiling	3C; Luciferase reporter assay; RBPJ/NOTCH-complex binding-site analysis; NOTCH inhibition
E_01102	2024	39163202	CRISPR screening uncovers a long-range enhancer for ONECUT1 in pancreatic differentiation and links a diabetes risk variant	Homo sapiens	hg38	chr15	53455006	53455051	GATA4	ONECUT1	Enhancer	Active	Disease	type 2 diabetes mellitus	MONDO:0005148	DOID:9352	pancreas	UBERON:0001264	Progenitor cells	NA	progenitor cell	CL:0011026	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis; Endogenous enhancer perturbation	ChIP-seq, Hi-C; RNA-seq; CRISPR genetic screen	CRISPR knockout, Luciferase reporter assay; CRISPRi
E_01103	2022	35769482	Regulatory Architecture of the RCA Gene Cluster Captures an Intragenic TAD Boundary, CTCF-Mediated Chromatin Looping and a Long-Range Intergenic Enhancer	Homo sapiens	hg19	chr1	207584741	207589069	NA	CD55	Enhancer	Active	Normal	NA	NA	NA	maxilla	UBERON:0002397	Raji	CVCL_0511	B cell	CL:0000236	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Disease-variant functional analysis	NA	Luciferase reporter assay; H3K27ac ChIP-qPCR; ChART-PCR; MNase nucleosome occupancy assay; CRISPR-Cas9 enhancer deletion; PCR; Sanger sequencing; RT-qPCR; Flow cytometry; 4C
E_01104	2020	32416589	Miswired Enhancer Logic Drives a Cancer of the Muscle Lineage	Homo sapiens	hg19	chr13	40800476	40817024	MYCN	PAX3::FOXO1	Enhancer	Active	Disease	alveolar rhabdomyosarcoma	MONDO:0009994	DOID:4051	NA	NA	Rh4	CVCL_5916	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin-state profiling	ChIP-seq; ChIP-Rx; RNA-seq; 4C-seq; H3K27ac HiChIP; pooled CRISPR screen; HiChIP	Individual CRISPR-Cas9 enhancer perturbation; 3C PCR; RT-qPCR; Western blot; Sanger sequencing; ChIP
E_01105	2020	32416589	Miswired Enhancer Logic Drives a Cancer of the Muscle Lineage	Homo sapiens	hg19	chr13	40800476	40817024	MYOD1	PAX3::FOXO1	Enhancer	Active	Disease	alveolar rhabdomyosarcoma	MONDO:0009994	DOID:4051	NA	NA	Rh4	CVCL_5916	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin-state profiling	ChIP-seq; ChIP-Rx; RNA-seq; 4C-seq; H3K27ac HiChIP; pooled CRISPR screen; HiChIP	Individual CRISPR-Cas9 enhancer perturbation; 3C PCR; RT-qPCR; Western blot; Sanger sequencing; ChIP
E_01106	2020	32416589	Miswired Enhancer Logic Drives a Cancer of the Muscle Lineage	Homo sapiens	hg19	chr13	40800476	40817024	MYOG	PAX3::FOXO1	Enhancer	Active	Disease	alveolar rhabdomyosarcoma	MONDO:0009994	DOID:4051	NA	NA	Rh4	CVCL_5916	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin-state profiling	ChIP-seq; ChIP-Rx; RNA-seq; 4C-seq; H3K27ac HiChIP; pooled CRISPR screen; HiChIP	Individual CRISPR-Cas9 enhancer perturbation; 3C PCR; RT-qPCR; Western blot; Sanger sequencing; ChIP
E_01107	2020	33196849	Generation of onco-enhancer enhances chromosomal remodeling and accelerates tumorigenesis	Homo sapiens	hg19	chr12	86257615	86258800	CTCF	NTS	Enhancer	Active	Disease	uveal melanoma	MONDO:0006486	DOID:6039	eye	UBERON:0000970	OCM-8	CVCL_6938	uveal melanoma metastatic cell	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	RNA-seq; CTCF ChIP-seq; FAIRE; TCGA transcriptomic analysis; ChIP-seq	CRISPR-Cas9 enhancer deletion; 3C assay; Luciferase reporter assay; ChIP-qPCR; qRT-PCR; Western blot; Colony formation assay; Xenograft tumor assay; CRISPR-Cas9
E_01108	2020	33196849	Generation of onco-enhancer enhances chromosomal remodeling and accelerates tumorigenesis	Homo sapiens	hg19	chr12	86257615	86258800	CTCF	NTS	Enhancer	Active	Disease	uveal melanoma	MONDO:0006486	DOID:6039	eye	UBERON:0000970	OM431	CVCL_J308	uveal melanoma cell	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	RNA-seq; CTCF ChIP-seq; FAIRE; TCGA transcriptomic analysis; ChIP-seq	CRISPR-Cas9 enhancer deletion; 3C assay; Luciferase reporter assay; ChIP-qPCR; qRT-PCR; Western blot; Colony formation assay; Xenograft tumor assay; CRISPR-Cas9
E_01109	2020	33196849	Generation of onco-enhancer enhances chromosomal remodeling and accelerates tumorigenesis	Homo sapiens	hg19	chr12	86257615	86258800	CTCF	NTS	Enhancer	Active	Disease	uveal melanoma	MONDO:0006486	DOID:6039	eye	UBERON:0000970	OMM-1	CVCL_6939	uveal melanoma cell	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	RNA-seq; CTCF ChIP-seq; FAIRE; TCGA transcriptomic analysis; ChIP-seq	CRISPR-Cas9 enhancer deletion; 3C assay; Luciferase reporter assay; ChIP-qPCR; qRT-PCR; Western blot; Colony formation assay; Xenograft tumor assay; CRISPR-Cas9
E_01110	2018	29898989	Disruption of a -35 kb Enhancer Impairs CTCF Binding and MLH1 Expression in Colorectal Cells	Homo sapiens	hg19	chr3	36999364	37001216	CTCF	MLH1	Enhancer	Active	Disease	Lynch Syndrome	NA	DOID:3883	colon	UBERON:0001155	SW620,RKO	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_01111	2015	25775043	Functional annotation of native enhancers with a Cas9-histone demethylase fusion	Mus musculus	mm10	chr17	35499359	35507923	Tbx3	NA	Enhancer	Repressed	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; TF-binding/chromatin assay	ATAC-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C
E_01112	2015	25775043	Functional annotation of native enhancers with a Cas9-histone demethylase fusion	Mus musculus	mm10	chr5	119654061	119663588	Tbx3	Tbx3	Enhancer	Repressed	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ATAC-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C
E_01113	2018	29903884	Sex reversal following deletion of a single distal enhancer of Sox9	Mus musculus	mm10	chr11	112217398	112217642	Sox9	Sox9	Enhancer	Active	Normal	NA	NA	NA	testis	UBERON:0000473	primary embryonic mouse XY gonadal somatic cells	NA	Sertoli cell / supporting-cell lineage	NA	In vivo developmental enhancer validation; TF binding assay; Endogenous enhancer deletion	ATAC-seq/chromatin-accessibility profiling; ChIP-seq data integration	CRISPR-Cas9 Enh13 deletion mouse model; transgenic enhancer reporter; ChIP-qPCR; qRT-PCR; histology
E_01114	2018	29903884	Sex reversal following deletion of a single distal enhancer of Sox9	Mus musculus	mm10	chr11	112217398	112217642	Sry	Sox9	Enhancer	Active	Normal	NA	NA	NA	testis	UBERON:0000473	primary embryonic mouse XY gonadal somatic cells	NA	Sertoli cell / supporting-cell lineage	NA	In vivo developmental enhancer validation; TF binding assay; Endogenous enhancer deletion	ATAC-seq/chromatin-accessibility profiling; ChIP-seq data integration	CRISPR-Cas9 Enh13 deletion mouse model; transgenic enhancer reporter; ChIP-qPCR; qRT-PCR; histology
E_01115	2018	29903884	Sex reversal following deletion of a single distal enhancer of Sox9	Mus musculus	mm10	chr11	10941473	10942029	Nr5a1	Sox9	Enhancer	Active	Disease	sex reversal	MONDO:0008637	DOID:14450	gonadal ridge	UBERON:0005294	Bipotential gonadal somatic cells	NA	gonadal somatic cell	NA	Developmental biology assay; Functional genomics assay; Epigenomic profiling assay; Genome editing assay; Transcriptional regulation assay; In vivo transgenic reporter assay; In vivo functional assay	ATAC-seq; ChIP-seq; DNase-seq	CRISPR-Cas9 enhancer deletion; RT-qPCR; ChIP-qPCR; LacZ Transgenic reporter assay; Immunofluorescence; H&E staining; FACS; Genotyping PCR; Sanger sequencing
E_01116	2018	29903884	Sex reversal following deletion of a single distal enhancer of Sox9	Mus musculus	mm10	chr11	10941473	10942029	Sox9	Sox9	Enhancer	Active	Disease	sex reversal	MONDO:0008637	DOID:14450	gonadal ridge	UBERON:0005294	Bipotential gonadal somatic cells	NA	gonadal somatic cell	NA	Developmental biology assay; Functional genomics assay; Epigenomic profiling assay; Genome editing assay; Transcriptional regulation assay; In vivo transgenic reporter assay; In vivo functional assay	ATAC-seq; ChIP-seq; DNase-seq	CRISPR-Cas9 enhancer deletion; RT-qPCR; ChIP-qPCR; LacZ Transgenic reporter assay; Immunofluorescence; H&E staining; FACS; Genotyping PCR; Sanger sequencing
E_01117	2018	29903884	Sex reversal following deletion of a single distal enhancer of Sox9	Mus musculus	mm10	chr11	10941473	10942029	Sry	Sox9	Enhancer	Active	Disease	sex reversal	MONDO:0008637	DOID:14450	gonadal ridge	UBERON:0005294	Bipotential gonadal somatic cells	NA	gonadal somatic cell	NA	Developmental biology assay; Functional genomics assay; Epigenomic profiling assay; Genome editing assay; Transcriptional regulation assay; In vivo transgenic reporter assay; In vivo functional assay	ATAC-seq; ChIP-seq; DNase-seq	CRISPR-Cas9 enhancer deletion; RT-qPCR; ChIP-qPCR; LacZ Transgenic reporter assay; Immunofluorescence; H&E staining; FACS; Genotyping PCR; Sanger sequencing
E_01118	2023	36632736	TAL1 activation in T-cell acute lymphoblastic leukemia: a novel oncogenic 3' neo-enhancer	Homo sapiens	hg19	chr1	47677544	47677944	MYB	TAL1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	engineered Jurkat models	NA	T cell	CL:0000084	Somatic neo-enhancer discovery and functional engineering	WGS; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; RNA-seq	CRISPR engineering; Reporter assay; Sanger sequencing; allele-specific expression analysis
E_01119	2018	29903884	Sex reversal following deletion of a single distal enhancer of Sox9	Mus musculus	mm10	chr11	10954273	10955559	NA	Sox9	Enhancer	Active	Disease	sex reversal	MONDO:0008637	DOID:14450	testis	UBERON:0000473	Sertoli cells	NA	Sertoli cell	CL:0000216	Developmental biology assay; Functional genomics assay; Epigenomic profiling assay; Genome editing assay; Transcriptional regulation assay; In vivo transgenic reporter assay	ATAC-seq; ChIP-seq [targets: H3K27ac]; DNase-seq	CRISPR-Cas9 Mediated Enhancer Deletion, qRT-PCR; LacZ Transgenic reporter assay; Immunofluorescence Microscopy; Pronuclear Microinjection; Genotyping PCR; Sanger sequencing
E_01120	2016	26673704	Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus	Homo sapiens	hg19	chr7	117099048	117099450	CDX2	CFTR	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Caco-2	CVCL_0025	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	NA	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 4C; RT-qPCR/qPCR
E_01121	2016	26673704	Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus	Homo sapiens	hg19	chr7	117099048	117099450	FOXA1	CFTR	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Caco-2	CVCL_0025	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	NA	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 4C; RT-qPCR/qPCR
E_01122	2016	26673704	Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus	Homo sapiens	hg19	chr7	117099048	117099450	FOXA2	CFTR	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Caco-2	CVCL_0025	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	NA	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 4C; RT-qPCR/qPCR
E_01123	2016	26673704	Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus	Homo sapiens	hg19	chr7	117099048	117099450	HNF1A	CFTR	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Caco-2	CVCL_0025	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	NA	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 4C; RT-qPCR/qPCR
E_01124	2016	26673704	Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus	Homo sapiens	hg19	chr7	117228051	117229440	CDX2	CFTR	Enhancer	Repressed	Normal	NA	NA	NA	NA	NA	Caco-2	CVCL_0025	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	NA	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 4C; RT-qPCR/qPCR
E_01125	2016	26673704	Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus	Homo sapiens	hg19	chr7	117228051	117229440	FOXA1	CFTR	Enhancer	Repressed	Normal	NA	NA	NA	NA	NA	Caco-2	CVCL_0025	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	NA	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 4C; RT-qPCR/qPCR
E_01126	2016	26673704	Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus	Homo sapiens	hg19	chr7	117228051	117229440	FOXA2	CFTR	Enhancer	Repressed	Normal	NA	NA	NA	NA	NA	Caco-2	CVCL_0025	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	NA	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 4C; RT-qPCR/qPCR
E_01127	2016	26673704	Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus	Homo sapiens	hg19	chr7	117228051	117229440	HNF1A	CFTR	Enhancer	Repressed	Normal	NA	NA	NA	NA	NA	Caco-2	CVCL_0025	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	NA	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 4C; RT-qPCR/qPCR
E_01128	2016	26673704	Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus	Homo sapiens	hg19	chr7	117038917	117040917	CDX2	CFTR	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Caco-2	CVCL_0025	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	NA	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 4C; RT-qPCR/qPCR
E_01129	2016	26673704	Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus	Homo sapiens	hg19	chr7	117038917	117040917	FOXA1	CFTR	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Caco-2	CVCL_0025	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	NA	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 4C; RT-qPCR/qPCR
E_01130	2016	26673704	Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus	Homo sapiens	hg19	chr7	117038917	117040917	FOXA2	CFTR	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Caco-2	CVCL_0025	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	NA	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 4C; RT-qPCR/qPCR
E_01131	2016	26673704	Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus	Homo sapiens	hg19	chr7	117038917	117040917	HNF1A	CFTR	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Caco-2	CVCL_0025	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	NA	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 4C; RT-qPCR/qPCR
E_01132	2018	29903884	Sex reversal following deletion of a single distal enhancer of Sox9	Mus musculus	mm10	chr11	10996600	10999794	Nr5a1	Sox9	Enhancer	Active	Disease	sex reversal	MONDO:0008637	DOID:14450	testis	UBERON:0000473	Sertoli cell precursors	NA	Sertoli cell precursor	NA	Developmental biology assay; Functional genomics assay; Epigenomic profiling assay; Genome editing assay; Transcriptional regulation assay; In vivo functional assay	ChIP-seq; DNase-seq; ATAC-seq	CRISPR-Cas9 enhancer deletion; RT-qPCR; ChIP-qPCR; Immunofluorescence; Genotyping PCR; Sanger sequencing
E_01133	2018	29903884	Sex reversal following deletion of a single distal enhancer of Sox9	Mus musculus	mm10	chr11	10996600	10999794	Sox9	Sox9	Enhancer	Active	Disease	sex reversal	MONDO:0008637	DOID:14450	testis	UBERON:0000473	Sertoli cell precursors	NA	Sertoli cell precursor	NA	Developmental biology assay; Functional genomics assay; Epigenomic profiling assay; Genome editing assay; Transcriptional regulation assay; In vivo functional assay	ChIP-seq; DNase-seq; ATAC-seq	CRISPR-Cas9 enhancer deletion; RT-qPCR; ChIP-qPCR; Immunofluorescence; Genotyping PCR; Sanger sequencing
E_01134	2018	29903884	Sex reversal following deletion of a single distal enhancer of Sox9	Mus musculus	mm10	chr11	10996600	10999794	Sry	Sox9	Enhancer	Active	Disease	sex reversal	MONDO:0008637	DOID:14450	testis	UBERON:0000473	Sertoli cell precursors	NA	Sertoli cell precursor	NA	Developmental biology assay; Functional genomics assay; Epigenomic profiling assay; Genome editing assay; Transcriptional regulation assay; In vivo functional assay	ChIP-seq; DNase-seq; ATAC-seq	CRISPR-Cas9 enhancer deletion; RT-qPCR; ChIP-qPCR; Immunofluorescence; Genotyping PCR; Sanger sequencing
E_01135	2016	26673704	Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus	Homo sapiens	hg19	chr7	117125000	117126200	FOXA1	CFTR	Enhancer	Active	Normal	NA	NA	NA	colon	UBERON:0001155	Human normal colon epithelial cell	NA	colon epithelial cell	CL:0011108	Enhancer activity assay; TF binding assay; Endogenous enhancer perturbation	NA	ChIP-qPCR; CRISPR-Cas9 endogenous deletion/editing; siRNA knockdown
E_01136	2018	29035388	A novel HER2 gene body enhancer contributes to HER2 expression	Homo sapiens	hg19	chr17	37900000	37900500	TFAP2C	ERBB2	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	SK-BR-3	CVCL_0033	malignant cell	CL:0001064	TF binding assay; Enhancer functional assay	ChIP-seq	Luciferase reporter assay, CRISPR knockout
E_01137	2018	29903884	Sex reversal following deletion of a single distal enhancer of Sox9	Mus musculus	mm9	chr11	112078592	112079149	Sry	Sox9	Enhancer	Active	Normal	NA	NA	NA	testis	UBERON:0000473	embryonic gonad	NA	Sertoli cell lineage	NA	557-bp Sox9 Enh13 (original paper coordinate); essential endogenous sex-determining enhancer	ATAC-seq/DNase-seq; comparative epigenomics	Transgenic enhancer reporter assay; CRISPR/Cas9 Enh13 deletion mouse; RT-qPCR
E_01138	2018	29035388	A novel HER2 gene body enhancer contributes to HER2 expression	Homo sapiens	hg19	chr17	37879571	37880263	TFAP2C	ERBB2	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_01139	2022	35769482	Regulatory Architecture of the RCA Gene Cluster Captures an Intragenic TAD Boundary, CTCF-Mediated Chromatin Looping and a Long-Range Intergenic Enhancer	Homo sapiens	hg19	chr1	207411000	207424000	NA	CR2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Reh	CVCL_1650	B-lymphoblast	CL:0017006	Functional perturbation assay; Chromatin interaction assay; Disease-variant functional analysis	Hi-C; 3C-seq	CRISPR knockout; RT-qPCR, Flow Cytometry; 4C
E_01140	2018	29903884	Sex reversal following deletion of a single distal enhancer of Sox9	Mus musculus	mm10	chr11	10999900	11000869	Nr5a1	Sox9	Enhancer	Active	Disease	sex reversal	MONDO:0008637	DOID:14450	testis	UBERON:0000473	Sertoli cells	NA	Sertoli cell	CL:0000216	Developmental biology assay; Functional genomics assay; Epigenomic profiling assay; Transcriptional regulation assay; In vivo transgenic reporter assay	ATAC-seq; ChIP-seq; DNase-seq	RT-qPCR; LacZ Transgenic reporter assay; Immunofluorescence; Pronuclear Microinjection; Genotyping PCR; Sanger sequencing
E_01141	2018	29903884	Sex reversal following deletion of a single distal enhancer of Sox9	Mus musculus	mm10	chr11	10999900	11000869	Sox9	Sox9	Enhancer	Active	Disease	sex reversal	MONDO:0008637	DOID:14450	testis	UBERON:0000473	Sertoli cells	NA	Sertoli cell	CL:0000216	Developmental biology assay; Functional genomics assay; Epigenomic profiling assay; Transcriptional regulation assay; In vivo transgenic reporter assay	ATAC-seq; ChIP-seq; DNase-seq	RT-qPCR; LacZ Transgenic reporter assay; Immunofluorescence; Pronuclear Microinjection; Genotyping PCR; Sanger sequencing
E_01142	2018	29903884	Sex reversal following deletion of a single distal enhancer of Sox9	Mus musculus	mm10	chr11	10997900	10999300	Nr5a1	Sox9	Enhancer	Active	Disease	sex reversal	MONDO:0008637	DOID:14450	testis	UBERON:0000473	Sertoli cell precursors	NA	Sertoli cell precursor	NA	Developmental biology assay; Functional genomics assay; Transcriptional regulation assay	ChIP-seq; DNase-seq	ChIP-qPCR; Dual-luciferase reporter assay; EMSA
E_01143	2018	29903884	Sex reversal following deletion of a single distal enhancer of Sox9	Mus musculus	mm10	chr11	10997900	10999300	Sox9	Sox9	Enhancer	Active	Disease	sex reversal	MONDO:0008637	DOID:14450	testis	UBERON:0000473	Sertoli cell precursors	NA	Sertoli cell precursor	NA	Developmental biology assay; Functional genomics assay; Transcriptional regulation assay	ChIP-seq; DNase-seq	ChIP-qPCR; Dual-luciferase reporter assay; EMSA
E_01144	2018	29903884	Sex reversal following deletion of a single distal enhancer of Sox9	Mus musculus	mm10	chr11	10997900	10999300	Sry	Sox9	Enhancer	Active	Disease	sex reversal	MONDO:0008637	DOID:14450	testis	UBERON:0000473	Sertoli cell precursors	NA	Sertoli cell precursor	NA	Developmental biology assay; Functional genomics assay; Transcriptional regulation assay	ChIP-seq; DNase-seq	ChIP-qPCR; Dual-luciferase reporter assay; EMSA
E_01145	2022	35977485	Transcriptomics, regulatory syntax, and enhancer identification in mesoderm-induced ESCs at single-cell resolution	Mus musculus	mm10	chr4	139771035	139771985	NA	Pax7	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Mouse hematopoietic stem cells (HSCs)	NA	mouse hematopoietic stem cell	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	Hi-C; ATAC-seq; RNA-seq; ChIP-seq	Luciferase reporter assay; CRISPR knockout; CRISPRi, qRT-PCR; Western blot
E_01146	2021	34260936	Neuronal activity-induced BRG1 phosphorylation regulates enhancer activation	Mus musculus	mm10	chr12	8570500	8571000	Smarca4	Fos	Enhancer	Active	Normal	NA	NA	NA	cerebral cortex	UBERON:0000956	Primary mouse cortical neurons	NA	cortical neuron	NA	Activity-induced enhancer assay; Chromatin remodeling/looping assay; In vivo phosphosite knock-in functional assay	BRG1/H3K27ac/cohesin ChIP-seq; ATAC-seq; RNA-seq	ChIP-qPCR; 3C; enhancer RNA/gene RT-qPCR; Western blot; SMARCA4 phosphosite knock-in mouse phenotyping
E_01147	2020	32701507	ERG orchestrates chromatin interactions to drive prostate cell fate reprogramming	Mus musculus	mm10	chr16	25574210	25575090	Erg	Trp63	Enhancer	Active	Normal	NA	NA	NA	prostate gland	UBERON:0002367	LCD prostate organoids	NA	prostate epithelial cell	NA	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ERG ChIP-seq; H3K27ac ChIP-seq; BL-Hi-C	CRISPR-Cas9 enhancer deletion; qRT-PCR
E_01148	2019	30952671	Identification of a novel enhancer of CEBPE essential for granulocytic differentiation	Mus musculus	mm10	chr14	54705845	54707084	Cebpa	Cebpe	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary Mouse Bone Marrow Cells	NA	mouse bone marrow cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	4C-seq; RNA-seq; ChIP-seq; 4C	Luciferase reporter assay; CRISPR knockout; CRISPRi; ChIP-qPCR; RT-qPCR; CRISPR-Cas9
E_01149	2024	38341433	Matrin3 mediates differentiation through stabilizing chromatin loop-domain interactions and YY1 mediated enhancer-promoter interactions	Mus musculus	mm10	chr14	57395000	57400000	Myod1	Mphosph8	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay	Hi-C; ATAC-seq; MyoD CUT&RUN; YY1 CUT&RUN; H3K27ac profiling; RNA-seq; SLAM-seq	CRISPR-Cas9 Matr3 knockout; dTAG47-mediated acute Matr3 degradation; Yy1 knockout; Western blot; Immunofluorescence; C2C12 myogenic differentiation assay
E_01150	2024	38341433	Matrin3 mediates differentiation through stabilizing chromatin loop-domain interactions and YY1 mediated enhancer-promoter interactions	Mus musculus	mm10	chr14	57395000	57400000	Yy1	Mphosph8	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay	Hi-C; ATAC-seq; CUT&RUN; ChIP-seq; RNA-seq; SLAM-seq	CRISPR-Cas9 Matr3 knockout; dTAG47-mediated acute Matr3 degradation; Yy1 knockout; Western blot; Immunofluorescence; C2C12 myogenic differentiation assay
E_01151	2024	38341433	Matrin3 mediates differentiation through stabilizing chromatin loop-domain interactions and YY1 mediated enhancer-promoter interactions	Mus musculus	mm10	chr14	57520000	57525000	Myod1	Mphosph8	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay	Hi-C; ATAC-seq; MyoD CUT&RUN; YY1 CUT&RUN; H3K27ac profiling; RNA-seq; SLAM-seq	CRISPR-Cas9 Matr3 knockout; dTAG47-mediated acute Matr3 degradation; Yy1 knockout; Western blot; Immunofluorescence; C2C12 myogenic differentiation assay
E_01152	2024	38341433	Matrin3 mediates differentiation through stabilizing chromatin loop-domain interactions and YY1 mediated enhancer-promoter interactions	Mus musculus	mm10	chr14	57520000	57525000	Yy1	Mphosph8	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay	Hi-C; ATAC-seq; CUT&RUN; ChIP-seq; RNA-seq; SLAM-seq	CRISPR-Cas9 Matr3 knockout; dTAG47-mediated acute Matr3 degradation; Yy1 knockout; Western blot; Immunofluorescence; C2C12 myogenic differentiation assay
E_01153	2024	38341433	Matrin3 mediates differentiation through stabilizing chromatin loop-domain interactions and YY1 mediated enhancer-promoter interactions	Mus musculus	mm10	chr14	57665000	57670000	Myod1	Mphosph8	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay	Hi-C; ATAC-seq; MyoD CUT&RUN; YY1 CUT&RUN; H3K27ac profiling; RNA-seq; SLAM-seq	CRISPR-Cas9 Matr3 knockout; dTAG47-mediated acute Matr3 degradation; Yy1 knockout; Western blot; Immunofluorescence; C2C12 myogenic differentiation assay
E_01154	2024	38341433	Matrin3 mediates differentiation through stabilizing chromatin loop-domain interactions and YY1 mediated enhancer-promoter interactions	Mus musculus	mm10	chr14	57665000	57670000	Yy1	Mphosph8	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin accessibility assay	Hi-C; ATAC-seq; CUT&RUN; ChIP-seq; RNA-seq; SLAM-seq	CRISPR-Cas9 Matr3 knockout; dTAG47-mediated acute Matr3 degradation; Yy1 knockout; Western blot; Immunofluorescence; C2C12 myogenic differentiation assay
E_01155	2020	32817427	Enhancer dependence of cell-type-specific gene expression increases with developmental age	Mus musculus	mm10	chr4	46410632	46411247	Gata1	Hemgn	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Erythroblasts	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; Chromatin interaction assay; Endogenous enhancer perturbation	HiChIP; ChIP-seq; RNA-seq; ATAC-seq; HiChIP	CRISPR knockout; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_01156	2020	32817427	Enhancer dependence of cell-type-specific gene expression increases with developmental age	Mus musculus	mm10	chr4	46410632	46411247	Gata1	Trmo	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	MB-1 [Human thyroid carcinoma]	CVCL_2109	erythroid progenitor cell	CL:0000038	Functional perturbation assay; TF binding assay; Chromatin interaction assay	HiChIP; ChIP-seq; RNA-seq; ATAC-seq	CRISPR knockout; RT-qPCR
E_01157	2017	28028313	Aberrant activation of the GIMAP enhancer by oncogenic transcription factors in T-cell acute lymphoblastic leukemia	Homo sapiens	hg19	chr7	150360481	150366493	TAL1	GIMAP5	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Jurkat and primary T-ALL models	NA	T-lymphoblast/T-ALL cell	NA	Oncogenic TF occupancy; Enhancer activity; Endogenous enhancer deletion	TAL1/RUNX1/GATA3/H3K27ac ChIP-seq; transcriptomic analysis	CRISPR-Cas9 enhancer deletion; Luciferase reporter; ChIP-qPCR; qRT-PCR; in-vivo reporter assays
E_01158	2020	32817427	Enhancer dependence of cell-type-specific gene expression increases with developmental age	Mus musculus	mm10	chr12	111517811	111518523	Myb	Tnfaip2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	E13.5 fetal liver derived erythroblasts	NA	definitive erythroblast	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	ATAC-seq; H3K27ac ChIP-seq; Myb ChIP-seq; Gata1 HiChIP; RNA-seq	v4C; CRISPR/Cas9 deletion; qRT-PCR
E_01159	2020	32817427	Enhancer dependence of cell-type-specific gene expression increases with developmental age	Mus musculus	mm10	chr12	111517811	111518523	Myb	Tnfaip2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	MEL cells	NA	definitive erythroblast	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	ATAC-seq; H3K27ac ChIP-seq; Myb ChIP-seq; Gata1 HiChIP; RNA-seq	v4C; CRISPR/Cas9 deletion; qRT-PCR
E_01160	2015	25938608	The +37 kb Cebpa Enhancer Is Critical for Cebpa Myeloid Gene Expression and Contains Functional Sites that Bind SCL, GATA2, C/EBPα, PU.1, and Additional Ets Factors	Mus musculus	mm10	chr7	35156536	35156974	Spi1	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary mouse hematopoietic stem/progenitor-cell context	NA	common myeloid progenitor / myeloid progenitor cell	NA	Cebpa +37-kb enhancer TF-site dissection; endogenous Ets-site replacement; target-gene expression validation	H3K4me1 ChIP-seq; H3K27ac ChIP-seq; TF ChIP-seq/occupancy integration	Enhancer-promoter reporter; site-directed TF-motif mutagenesis; EMSA; CRISPR-Cas9 endogenous seven-Ets-site replacement; RT-qPCR
E_01161	2015	25938608	The +37 kb Cebpa Enhancer Is Critical for Cebpa Myeloid Gene Expression and Contains Functional Sites that Bind SCL, GATA2, C/EBPα, PU.1, and Additional Ets Factors	Mus musculus	mm10	chr7	35156536	35156974	Cebpa	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary mouse hematopoietic stem/progenitor-cell context	NA	common myeloid progenitor / myeloid progenitor cell	NA	Cebpa +37-kb enhancer TF-site dissection; endogenous Ets-site replacement; target-gene expression validation	H3K4me1 ChIP-seq; H3K27ac ChIP-seq; TF ChIP-seq/occupancy integration	Enhancer-promoter reporter; site-directed TF-motif mutagenesis; EMSA; CRISPR-Cas9 endogenous seven-Ets-site replacement; RT-qPCR
E_01162	2015	25938608	The +37 kb Cebpa Enhancer Is Critical for Cebpa Myeloid Gene Expression and Contains Functional Sites that Bind SCL, GATA2, C/EBPα, PU.1, and Additional Ets Factors	Mus musculus	mm10	chr7	35156536	35156974	Gata2	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary mouse hematopoietic stem/progenitor-cell context	NA	common myeloid progenitor / myeloid progenitor cell	NA	Cebpa +37-kb enhancer TF-site dissection; endogenous Ets-site replacement; target-gene expression validation	H3K4me1 ChIP-seq; H3K27ac ChIP-seq; TF ChIP-seq/occupancy integration	Enhancer-promoter reporter; site-directed TF-motif mutagenesis; EMSA; CRISPR-Cas9 endogenous seven-Ets-site replacement; RT-qPCR
E_01163	2015	25938608	The +37 kb Cebpa Enhancer Is Critical for Cebpa Myeloid Gene Expression and Contains Functional Sites that Bind SCL, GATA2, C/EBPα, PU.1, and Additional Ets Factors	Mus musculus	mm10	chr7	35156536	35156974	Tal1	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary mouse hematopoietic stem/progenitor-cell context	NA	common myeloid progenitor / myeloid progenitor cell	NA	Cebpa +37-kb enhancer TF-site dissection; endogenous Ets-site replacement; target-gene expression validation	H3K4me1 ChIP-seq; H3K27ac ChIP-seq; TF ChIP-seq/occupancy integration	Enhancer-promoter reporter; site-directed TF-motif mutagenesis; EMSA; CRISPR-Cas9 endogenous seven-Ets-site replacement; RT-qPCR
E_01164	2015	25938608	The +37 kb Cebpa Enhancer Is Critical for Cebpa Myeloid Gene Expression and Contains Functional Sites that Bind SCL, GATA2, C/EBPα, PU.1, and Additional Ets Factors	Mus musculus	mm10	chr7	35156536	35156974	Fli1	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary mouse hematopoietic stem/progenitor-cell context	NA	common myeloid progenitor / myeloid progenitor cell	NA	Cebpa +37-kb enhancer TF-site dissection; endogenous Ets-site replacement; target-gene expression validation	H3K4me1 ChIP-seq; H3K27ac ChIP-seq; TF ChIP-seq/occupancy integration	Enhancer-promoter reporter; site-directed TF-motif mutagenesis; EMSA; CRISPR-Cas9 endogenous seven-Ets-site replacement; RT-qPCR
E_01165	2015	25938608	The +37 kb Cebpa Enhancer Is Critical for Cebpa Myeloid Gene Expression and Contains Functional Sites that Bind SCL, GATA2, C/EBPα, PU.1, and Additional Ets Factors	Mus musculus	mm10	chr7	35156536	35156974	Erg	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary mouse hematopoietic stem/progenitor-cell context	NA	common myeloid progenitor / myeloid progenitor cell	NA	Cebpa +37-kb enhancer TF-site dissection; endogenous Ets-site replacement; target-gene expression validation	H3K4me1 ChIP-seq; H3K27ac ChIP-seq; TF ChIP-seq/occupancy integration	Enhancer-promoter reporter; site-directed TF-motif mutagenesis; EMSA; CRISPR-Cas9 endogenous seven-Ets-site replacement; RT-qPCR
E_01166	2015	25938608	The +37 kb Cebpa Enhancer Is Critical for Cebpa Myeloid Gene Expression and Contains Functional Sites that Bind SCL, GATA2, C/EBPα, PU.1, and Additional Ets Factors	Mus musculus	mm10	chr7	35156536	35156974	Runx1	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary mouse hematopoietic stem/progenitor-cell context	NA	common myeloid progenitor / myeloid progenitor cell	NA	Cebpa +37-kb enhancer TF-site dissection; endogenous Ets-site replacement; target-gene expression validation	H3K4me1 ChIP-seq; H3K27ac ChIP-seq; TF ChIP-seq/occupancy integration	Enhancer-promoter reporter; site-directed TF-motif mutagenesis; EMSA; CRISPR-Cas9 endogenous seven-Ets-site replacement; RT-qPCR
E_01167	2015	25938608	The +37 kb Cebpa Enhancer Is Critical for Cebpa Myeloid Gene Expression and Contains Functional Sites that Bind SCL, GATA2, C/EBPα, PU.1, and Additional Ets Factors	Mus musculus	mm10	chr7	35156536	35156974	Ets1	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary mouse hematopoietic stem/progenitor-cell context	NA	common myeloid progenitor / myeloid progenitor cell	NA	Cebpa +37-kb enhancer TF-site dissection; endogenous Ets-site replacement; target-gene expression validation	H3K4me1 ChIP-seq; H3K27ac ChIP-seq; TF ChIP-seq/occupancy integration	Enhancer-promoter reporter; site-directed TF-motif mutagenesis; EMSA; CRISPR-Cas9 endogenous seven-Ets-site replacement; RT-qPCR
E_01168	2015	25938608	The +37 kb Cebpa Enhancer Is Critical for Cebpa Myeloid Gene Expression and Contains Functional Sites that Bind SCL, GATA2, C/EBPα, PU.1, and Additional Ets Factors	Mus musculus	mm10	chr7	35156536	35156974	Myb	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary mouse hematopoietic stem/progenitor-cell context	NA	common myeloid progenitor / myeloid progenitor cell	NA	Cebpa +37-kb enhancer TF-site dissection; endogenous Ets-site replacement; target-gene expression validation	H3K4me1 ChIP-seq; H3K27ac ChIP-seq; TF ChIP-seq/occupancy integration	Enhancer-promoter reporter; site-directed TF-motif mutagenesis; EMSA; CRISPR-Cas9 endogenous seven-Ets-site replacement; RT-qPCR
E_01169	2014	25081415	Up-regulation of type II collagen gene by 17β-estradiol in articular chondrocytes involves Sp1/3, Sox-9, and estrogen receptor α	Homo sapiens	hg19	chr12	48368875	48369590	ESR1	COL2A1	Enhancer	Active	Normal	NA	NA	NA	cartilage tissue	UBERON:0002418	primary differentiated human articular chondrocytes	NA	chondrocyte	CL:0000138	TF binding assay; In vivo functional validation; Hormone-responsive enhancer/TF-complex activity assay	NA	17β-estradiol stimulation; ChIP/Re-ChIP; TF siRNA; DNA-binding assay; Reporter assay; RT-qPCR; Western blot; ChIP; siRNA knockdown; In vivo phenotyping
E_01170	2014	25081415	Up-regulation of type II collagen gene by 17β-estradiol in articular chondrocytes involves Sp1/3, Sox-9, and estrogen receptor α	Homo sapiens	hg19	chr12	48368875	48369590	SOX9	COL2A1	Enhancer	Active	Normal	NA	NA	NA	cartilage tissue	UBERON:0002418	primary differentiated human articular chondrocytes	NA	chondrocyte	CL:0000138	TF binding assay; In vivo functional validation; Hormone-responsive enhancer/TF-complex activity assay	NA	17β-estradiol stimulation; ChIP/Re-ChIP; TF siRNA; DNA-binding assay; Reporter assay; RT-qPCR; Western blot; ChIP; siRNA knockdown; In vivo phenotyping
E_01171	2014	25081415	Up-regulation of type II collagen gene by 17β-estradiol in articular chondrocytes involves Sp1/3, Sox-9, and estrogen receptor α	Homo sapiens	hg19	chr12	48368875	48369590	SP1	COL2A1	Enhancer	Active	Normal	NA	NA	NA	cartilage tissue	UBERON:0002418	primary differentiated human articular chondrocytes	NA	chondrocyte	CL:0000138	TF binding assay; In vivo functional validation; Hormone-responsive enhancer/TF-complex activity assay	NA	17β-estradiol stimulation; ChIP/Re-ChIP; TF siRNA; DNA-binding assay; Reporter assay; RT-qPCR; Western blot; ChIP; siRNA knockdown; In vivo phenotyping
E_01172	2014	25081415	Up-regulation of type II collagen gene by 17β-estradiol in articular chondrocytes involves Sp1/3, Sox-9, and estrogen receptor α	Homo sapiens	hg19	chr12	48368875	48369590	SP3	COL2A1	Enhancer	Active	Normal	NA	NA	NA	cartilage tissue	UBERON:0002418	primary differentiated human articular chondrocytes	NA	chondrocyte	CL:0000138	TF binding assay; In vivo functional validation; Hormone-responsive enhancer/TF-complex activity assay	NA	17β-estradiol stimulation; ChIP/Re-ChIP; TF siRNA; DNA-binding assay; Reporter assay; RT-qPCR; Western blot; ChIP; siRNA knockdown; In vivo phenotyping
E_01173	2014	25081415	Up-regulation of type II collagen gene by 17β-estradiol in articular chondrocytes involves Sp1/3, Sox-9, and estrogen receptor α	Homo sapiens	hg19	chr12	48368875	48369590	ESR1	COL2A1	Enhancer	Active	Disease	osteoarthritis	MONDO:0005178	DOID:8398	cartilage tissue	UBERON:0002418	dedifferentiated OA-phenotype human articular chondrocytes	NA	chondrocyte	CL:0000138	TF binding assay; In vivo functional validation; Hormone-responsive enhancer/TF-complex activity assay	NA	17β-estradiol stimulation; ChIP/Re-ChIP; TF siRNA; DNA-binding assay; Reporter assay; RT-qPCR; Western blot; ChIP; siRNA knockdown; In vivo phenotyping
E_01174	2014	25081415	Up-regulation of type II collagen gene by 17β-estradiol in articular chondrocytes involves Sp1/3, Sox-9, and estrogen receptor α	Homo sapiens	hg19	chr12	48368875	48369590	SOX9	COL2A1	Enhancer	Active	Disease	osteoarthritis	MONDO:0005178	DOID:8398	cartilage tissue	UBERON:0002418	dedifferentiated OA-phenotype human articular chondrocytes	NA	chondrocyte	CL:0000138	TF binding assay; In vivo functional validation; Hormone-responsive enhancer/TF-complex activity assay	NA	17β-estradiol stimulation; ChIP/Re-ChIP; TF siRNA; DNA-binding assay; Reporter assay; RT-qPCR; Western blot; ChIP; siRNA knockdown; In vivo phenotyping
E_01175	2014	25081415	Up-regulation of type II collagen gene by 17β-estradiol in articular chondrocytes involves Sp1/3, Sox-9, and estrogen receptor α	Homo sapiens	hg19	chr12	48368875	48369590	SP1	COL2A1	Enhancer	Active	Disease	osteoarthritis	MONDO:0005178	DOID:8398	cartilage tissue	UBERON:0002418	dedifferentiated OA-phenotype human articular chondrocytes	NA	chondrocyte	CL:0000138	TF binding assay; In vivo functional validation; Hormone-responsive enhancer/TF-complex activity assay	NA	17β-estradiol stimulation; ChIP/Re-ChIP; TF siRNA; DNA-binding assay; Reporter assay; RT-qPCR; Western blot; ChIP; siRNA knockdown; In vivo phenotyping
E_01176	2014	25081415	Up-regulation of type II collagen gene by 17β-estradiol in articular chondrocytes involves Sp1/3, Sox-9, and estrogen receptor α	Homo sapiens	hg19	chr12	48368875	48369590	SP3	COL2A1	Enhancer	Active	Disease	osteoarthritis	MONDO:0005178	DOID:8398	cartilage tissue	UBERON:0002418	dedifferentiated OA-phenotype human articular chondrocytes	NA	chondrocyte	CL:0000138	TF binding assay; In vivo functional validation; Hormone-responsive enhancer/TF-complex activity assay	NA	17β-estradiol stimulation; ChIP/Re-ChIP; TF siRNA; DNA-binding assay; Reporter assay; RT-qPCR; Western blot; ChIP; siRNA knockdown; In vivo phenotyping
E_01177	2021	34260936	Neuronal activity-induced BRG1 phosphorylation regulates enhancer activation	Mus musculus	mm10	chr15	8079500	8080000	NA	Arc	Enhancer	Active	Normal	NA	NA	NA	cerebral cortex	UBERON:0000956	Primary mouse cortical neurons	NA	mouse cortical neuron	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	ChIP-seq; RNA-seq; ATAC-seq	ChIP-qPCR, 3C, qRT-PCR; Western blot; CRISPR Knockin
E_01178	2020	32817427	Enhancer dependence of cell-type-specific gene expression increases with developmental age	Mus musculus	mm10	chr12	111517811	111518523	Gata1	Tnfaip2	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Erythroblasts	NA	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay; Chromatin interaction assay	HiChIP; ChIP-seq; RNA-seq; ATAC-seq	qRT-PCR
E_01179	2015	25938608	The +37 kb Cebpa Enhancer Is Critical for Cebpa Myeloid Gene Expression and Contains Functional Sites that Bind SCL, GATA2, C/EBPα, PU.1, and Additional Ets Factors	Mus musculus	mm10	chr7	35156536	35156974	Spi1	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	32Dcl3 myeloid progenitor cells	NA	common myeloid progenitor / myeloid progenitor cell	NA	Cebpa +37-kb enhancer TF-site dissection; endogenous Ets-site replacement; target-gene expression validation	H3K4me1 ChIP-seq; H3K27ac ChIP-seq; TF ChIP-seq/occupancy integration	Enhancer-promoter reporter; site-directed TF-motif mutagenesis; EMSA; CRISPR-Cas9 endogenous seven-Ets-site replacement; RT-qPCR
E_01180	2015	25938608	The +37 kb Cebpa Enhancer Is Critical for Cebpa Myeloid Gene Expression and Contains Functional Sites that Bind SCL, GATA2, C/EBPα, PU.1, and Additional Ets Factors	Mus musculus	mm10	chr7	35156536	35156974	Cebpa	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	32Dcl3 myeloid progenitor cells	NA	common myeloid progenitor / myeloid progenitor cell	NA	Cebpa +37-kb enhancer TF-site dissection; endogenous Ets-site replacement; target-gene expression validation	H3K4me1 ChIP-seq; H3K27ac ChIP-seq; TF ChIP-seq/occupancy integration	Enhancer-promoter reporter; site-directed TF-motif mutagenesis; EMSA; CRISPR-Cas9 endogenous seven-Ets-site replacement; RT-qPCR
E_01181	2015	25938608	The +37 kb Cebpa Enhancer Is Critical for Cebpa Myeloid Gene Expression and Contains Functional Sites that Bind SCL, GATA2, C/EBPα, PU.1, and Additional Ets Factors	Mus musculus	mm10	chr7	35156536	35156974	Gata2	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	32Dcl3 myeloid progenitor cells	NA	common myeloid progenitor / myeloid progenitor cell	NA	Cebpa +37-kb enhancer TF-site dissection; endogenous Ets-site replacement; target-gene expression validation	H3K4me1 ChIP-seq; H3K27ac ChIP-seq; TF ChIP-seq/occupancy integration	Enhancer-promoter reporter; site-directed TF-motif mutagenesis; EMSA; CRISPR-Cas9 endogenous seven-Ets-site replacement; RT-qPCR
E_01182	2015	25938608	The +37 kb Cebpa Enhancer Is Critical for Cebpa Myeloid Gene Expression and Contains Functional Sites that Bind SCL, GATA2, C/EBPα, PU.1, and Additional Ets Factors	Mus musculus	mm10	chr7	35156536	35156974	Tal1	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	32Dcl3 myeloid progenitor cells	NA	common myeloid progenitor / myeloid progenitor cell	NA	Cebpa +37-kb enhancer TF-site dissection; endogenous Ets-site replacement; target-gene expression validation	H3K4me1 ChIP-seq; H3K27ac ChIP-seq; TF ChIP-seq/occupancy integration	Enhancer-promoter reporter; site-directed TF-motif mutagenesis; EMSA; CRISPR-Cas9 endogenous seven-Ets-site replacement; RT-qPCR
E_01183	2015	25938608	The +37 kb Cebpa Enhancer Is Critical for Cebpa Myeloid Gene Expression and Contains Functional Sites that Bind SCL, GATA2, C/EBPα, PU.1, and Additional Ets Factors	Mus musculus	mm10	chr7	35156536	35156974	Fli1	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	32Dcl3 myeloid progenitor cells	NA	common myeloid progenitor / myeloid progenitor cell	NA	Cebpa +37-kb enhancer TF-site dissection; endogenous Ets-site replacement; target-gene expression validation	H3K4me1 ChIP-seq; H3K27ac ChIP-seq; TF ChIP-seq/occupancy integration	Enhancer-promoter reporter; site-directed TF-motif mutagenesis; EMSA; CRISPR-Cas9 endogenous seven-Ets-site replacement; RT-qPCR
E_01184	2015	25938608	The +37 kb Cebpa Enhancer Is Critical for Cebpa Myeloid Gene Expression and Contains Functional Sites that Bind SCL, GATA2, C/EBPα, PU.1, and Additional Ets Factors	Mus musculus	mm10	chr7	35156536	35156974	Erg	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	32Dcl3 myeloid progenitor cells	NA	common myeloid progenitor / myeloid progenitor cell	NA	Cebpa +37-kb enhancer TF-site dissection; endogenous Ets-site replacement; target-gene expression validation	H3K4me1 ChIP-seq; H3K27ac ChIP-seq; TF ChIP-seq/occupancy integration	Enhancer-promoter reporter; site-directed TF-motif mutagenesis; EMSA; CRISPR-Cas9 endogenous seven-Ets-site replacement; RT-qPCR
E_01185	2015	25938608	The +37 kb Cebpa Enhancer Is Critical for Cebpa Myeloid Gene Expression and Contains Functional Sites that Bind SCL, GATA2, C/EBPα, PU.1, and Additional Ets Factors	Mus musculus	mm10	chr7	35156536	35156974	Runx1	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	32Dcl3 myeloid progenitor cells	NA	common myeloid progenitor / myeloid progenitor cell	NA	Cebpa +37-kb enhancer TF-site dissection; endogenous Ets-site replacement; target-gene expression validation	H3K4me1 ChIP-seq; H3K27ac ChIP-seq; TF ChIP-seq/occupancy integration	Enhancer-promoter reporter; site-directed TF-motif mutagenesis; EMSA; CRISPR-Cas9 endogenous seven-Ets-site replacement; RT-qPCR
E_01186	2015	25938608	The +37 kb Cebpa Enhancer Is Critical for Cebpa Myeloid Gene Expression and Contains Functional Sites that Bind SCL, GATA2, C/EBPα, PU.1, and Additional Ets Factors	Mus musculus	mm10	chr7	35156536	35156974	Ets1	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	32Dcl3 myeloid progenitor cells	NA	common myeloid progenitor / myeloid progenitor cell	NA	Cebpa +37-kb enhancer TF-site dissection; endogenous Ets-site replacement; target-gene expression validation	H3K4me1 ChIP-seq; H3K27ac ChIP-seq; TF ChIP-seq/occupancy integration	Enhancer-promoter reporter; site-directed TF-motif mutagenesis; EMSA; CRISPR-Cas9 endogenous seven-Ets-site replacement; RT-qPCR
E_01187	2015	25938608	The +37 kb Cebpa Enhancer Is Critical for Cebpa Myeloid Gene Expression and Contains Functional Sites that Bind SCL, GATA2, C/EBPα, PU.1, and Additional Ets Factors	Mus musculus	mm10	chr7	35156536	35156974	Myb	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	32Dcl3 myeloid progenitor cells	NA	common myeloid progenitor / myeloid progenitor cell	NA	Cebpa +37-kb enhancer TF-site dissection; endogenous Ets-site replacement; target-gene expression validation	H3K4me1 ChIP-seq; H3K27ac ChIP-seq; TF ChIP-seq/occupancy integration	Enhancer-promoter reporter; site-directed TF-motif mutagenesis; EMSA; CRISPR-Cas9 endogenous seven-Ets-site replacement; RT-qPCR
E_01188	2014	25081415	Up-regulation of type II collagen gene by 17β-estradiol in articular chondrocytes involves Sp1/3, Sox-9, and estrogen receptor α	Homo sapiens	hg19	chr12	48395262	48395977	SOX9	COL2A1	Enhancer	Active	Normal	NA	NA	NA	articular cartilage	NA	Primary articular chondrocytes	NA	chondrocyte	CL:0000138	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Luciferase reporter assay; ChIP; Re-ChIP; EMSA; siRNA knockdown; RT-qPCR
E_01189	2014	25081415	Up-regulation of type II collagen gene by 17β-estradiol in articular chondrocytes involves Sp1/3, Sox-9, and estrogen receptor α	Homo sapiens	hg19	chr12	48395262	48395977	SP1	COL2A1	Enhancer	Active	Normal	NA	NA	NA	articular cartilage	NA	Primary articular chondrocytes	NA	chondrocyte	CL:0000138	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Luciferase reporter assay; ChIP; Re-ChIP; EMSA; siRNA knockdown; RT-qPCR
E_01190	2014	25081415	Up-regulation of type II collagen gene by 17β-estradiol in articular chondrocytes involves Sp1/3, Sox-9, and estrogen receptor α	Homo sapiens	hg19	chr12	48395262	48395977	SP3	COL2A1	Enhancer	Active	Normal	NA	NA	NA	articular cartilage	NA	Primary articular chondrocytes	NA	chondrocyte	CL:0000138	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Luciferase reporter assay; ChIP; Re-ChIP; EMSA; siRNA knockdown; RT-qPCR
E_01191	2017	28028313	Aberrant activation of the GIMAP enhancer by oncogenic transcription factors in T-cell acute lymphoblastic leukemia	Homo sapiens	hg19	chr7	150360500	150366500	TAL1	GIMAP4	Super-enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	T-acute lymphoblastic leukemia (T-ALL)	NA	malignant cell	CL:0001064	Endogenous enhancer perturbation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_01192	2017	28028313	Aberrant activation of the GIMAP enhancer by oncogenic transcription factors in T-cell acute lymphoblastic leukemia	Homo sapiens	hg19	chr7	150360500	150366500	TAL1	GIMAP7	Super-enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	T-acute lymphoblastic leukemia (T-ALL)	NA	malignant cell	CL:0001064	Endogenous enhancer perturbation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_01193	2017	28854172	Discovery of stimulation-responsive immune enhancers with CRISPR activation	Homo sapiens	hg19	chr10	6094588	6094934	NA	IL2RA	Enhancer	Active	Disease	autoimmune disease	MONDO:0007179	DOID:417	blood	UBERON:0000178	Jurkat E6.1	CVCL_0367	T cell	CL:0000084	Enhancer activity assay; Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation; Functional enhancer discovery; disease-variant perturbation	Tiled CRISPRa screen; RNA-seq; H3K27ac HiChIP; ATAC-seq; GWAS fine-mapping; response-eQTL analysis	Individual-gRNA CRISPRa; stimulation-dependent luciferase reporter assay; rs61839660 allele reporter assay; Flow cytometry; CRISPRa; Mouse genetic deletion/knock-in
E_01194	2017	28854172	Discovery of stimulation-responsive immune enhancers with CRISPR activation	Homo sapiens	hg19	chr10	6094588	6094934	NA	IL2RA	Enhancer	Active	Disease	autoimmune disease	MONDO:0007179	DOID:417	blood	UBERON:0000178	primary human CD4-positive T cells	NA	CD4-positive, alpha-beta T cell	CL:0000624	Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation; Disease-variant functional validation; endogenous response-eQTL assay	RNA-seq; H3K27ac HiChIP; ATAC-seq; GWAS fine-mapping; response-eQTL analysis	Anti-CD3/CD28 stimulation; rs61839660 genotype-expression analysis; Flow cytometry; CRISPRa; Mouse genetic deletion/knock-in
E_01195	2025	39799319	Mir-483-5p-mediated activating of IGF2/H19 enhancer up-regulates IGF2/H19 expression via chromatin loops to promote the malignant progression of hepatocellular carcinoma	Homo sapiens	hg38	chr11	1986889	1991809	NA	IGF2	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	HCCLM3	CVCL_6832	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; In vivo functional validation; epigenetic activation assay; disease phenotype assay	TCGA transcriptomic correlation analysis	Wild-type/mutant dual-luciferase reporter assay; miR-483-5p mimic/inhibitor perturbation; ChIP-qPCR; IGF2/H19 eRNA qRT-PCR; 3C-PCR; RIP-qPCR; co-immunoprecipitation; MED1 rescue; qRT-PCR; Western blot; CCK-8 assay; Transwell assay; In vivo phenotyping
E_01196	2025	39799319	Mir-483-5p-mediated activating of IGF2/H19 enhancer up-regulates IGF2/H19 expression via chromatin loops to promote the malignant progression of hepatocellular carcinoma	Homo sapiens	hg38	chr11	1986889	1991809	NA	H19	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	HCCLM3	CVCL_6832	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; In vivo functional validation; epigenetic activation assay; disease phenotype assay	TCGA transcriptomic correlation analysis	Wild-type/mutant dual-luciferase reporter assay; miR-483-5p mimic/inhibitor perturbation; ChIP-qPCR; IGF2/H19 eRNA qRT-PCR; 3C-PCR; RIP-qPCR; co-immunoprecipitation; MED1 rescue; qRT-PCR; Western blot; CCK-8 assay; Transwell assay; In vivo phenotyping
E_01197	2025	39799319	Mir-483-5p-mediated activating of IGF2/H19 enhancer up-regulates IGF2/H19 expression via chromatin loops to promote the malignant progression of hepatocellular carcinoma	Homo sapiens	hg38	chr11	1986889	1991809	NA	IGF2	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Huh-7	CVCL_0336	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; In vivo functional validation; epigenetic activation assay; disease phenotype assay	TCGA transcriptomic correlation analysis	Wild-type/mutant dual-luciferase reporter assay; miR-483-5p mimic/inhibitor perturbation; ChIP-qPCR; IGF2/H19 eRNA qRT-PCR; 3C-PCR; RIP-qPCR; co-immunoprecipitation; MED1 rescue; qRT-PCR; Western blot; CCK-8 assay; Transwell assay; lentiviral MED1/miR-483-5p perturbation; nude-mouse xenograft assay; In vivo phenotyping
E_01198	2025	39799319	Mir-483-5p-mediated activating of IGF2/H19 enhancer up-regulates IGF2/H19 expression via chromatin loops to promote the malignant progression of hepatocellular carcinoma	Homo sapiens	hg38	chr11	1986889	1991809	NA	H19	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Huh-7	CVCL_0336	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; In vivo functional validation; epigenetic activation assay; disease phenotype assay	TCGA transcriptomic correlation analysis	Wild-type/mutant dual-luciferase reporter assay; miR-483-5p mimic/inhibitor perturbation; ChIP-qPCR; IGF2/H19 eRNA qRT-PCR; 3C-PCR; RIP-qPCR; co-immunoprecipitation; MED1 rescue; qRT-PCR; Western blot; CCK-8 assay; Transwell assay; lentiviral MED1/miR-483-5p perturbation; nude-mouse xenograft assay; In vivo phenotyping
E_01199	2025	41080543	Essential roles of CTCF binding sites at TAD boundaries in modulating chromatin interactions and transcriptional regulation at the Ifng locus	Mus musculus	mm10	chr10	118242449	118243449	Tbx21	Ifng	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	CD4+ Th1 cells	NA	CD4+ T helper 1 cell	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	CTCF ChIP-seq; RNA-seq; Hi-C; Region Capture Micro-C; 3C	Luciferase reporter assay; 3C-qPCR; ChIP-qPCR; CRISPR-Cas9 perturbation; CRISPR-Cas9
E_01200	2025	41080543	Essential roles of CTCF binding sites at TAD boundaries in modulating chromatin interactions and transcriptional regulation at the Ifng locus	Mus musculus	mm10	chr10	118254449	118255449	Tbx21	Ifng	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	CD4+ Th1 cells	NA	CD4+ T helper 1 cell	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	CTCF ChIP-seq; RNA-seq; Hi-C; Region Capture Micro-C; 3C	Luciferase reporter assay; 3C-qPCR; ChIP-qPCR; CRISPR-Cas9 perturbation; CRISPR-Cas9
E_01201	2025	41080543	Essential roles of CTCF binding sites at TAD boundaries in modulating chromatin interactions and transcriptional regulation at the Ifng locus	Mus musculus	mm10	chr10	118295449	118296449	Tbx21	Ifng	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	CD4+ Th1 cells	NA	CD4+ T helper 1 cell	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	CTCF ChIP-seq; RNA-seq; Hi-C; Region Capture Micro-C; 3C	Luciferase reporter assay; 3C-qPCR; ChIP-qPCR; CRISPR-Cas9 perturbation; CRISPR-Cas9
E_01202	2025	41080543	Essential roles of CTCF binding sites at TAD boundaries in modulating chromatin interactions and transcriptional regulation at the Ifng locus	Mus musculus	mm10	chr10	118305449	118306449	Tbx21	Ifng	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	CD4+ Th1 cells	NA	CD4+ T helper 1 cell	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	CTCF ChIP-seq; RNA-seq; Hi-C; Region Capture Micro-C; 3C	Luciferase reporter assay; 3C-qPCR; ChIP-qPCR; CRISPR-Cas9 perturbation; CRISPR-Cas9
E_01203	2024	38855864	Chromatin profiling identifies chondrocyte-specific Sox9 enhancers important for skeletal development	Mus musculus	mm9	chr11	112334364	112335294	Pitx1	Sox9	Enhancer	Active	Normal	NA	NA	NA	cartilage tissue	UBERON:0002418	Primary rib chondrocytes from newborn mice	NA	chondrocyte	CL:0000138	Enhancer activity assay; Functional perturbation assay; TF binding assay; Endogenous enhancer perturbation; In vivo functional validation	ATAC-seq; H3K27ac ChIP-seq; H3K4me2 ChIP-seq; RNA-seq	Luciferase reporter assay; Pitx1 ChIP-qPCR; RT-qPCR; Western blot; Biotinylated DNA Pull-Down Assay; CRISPR-Cas9 enhancer deletion; genomic PCR; RNA in situ hybridization; Alcian blue/alizarin red S skeletal staining; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_01204	2024	38855864	Chromatin profiling identifies chondrocyte-specific Sox9 enhancers important for skeletal development	Mus musculus	mm9	chr11	112482190	112483273	Pitx1	Sox9	Enhancer	Active	Normal	NA	NA	NA	cartilage tissue	UBERON:0002418	Primary rib chondrocytes from newborn mice	NA	chondrocyte	CL:0000138	Enhancer activity assay; Functional perturbation assay; TF binding assay; Endogenous enhancer perturbation; In vivo functional validation	ATAC-seq; H3K27ac ChIP-seq; H3K4me2 ChIP-seq; RNA-seq	Luciferase reporter assay; Pitx1 ChIP-qPCR; RT-qPCR; Western blot; Biotinylated DNA Pull-Down Assay; CRISPR-Cas9 enhancer deletion; genomic PCR; RNA in situ hybridization; Alcian blue/alizarin red S skeletal staining; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_01205	2024	39186674	CRISPR Screening of Transcribed Super-Enhancers Identifies Drivers of Triple-Negative Breast Cancer Progression	Homo sapiens	hg19	chr2	106412871	106423516	NA	CMPK2	Super-enhancer	Active	Disease	triple-negative breast carcinoma	MONDO:0005494	DOID:0060081	mammary gland	UBERON:0001911	MDA-MB-436	CVCL_0623	malignant cell	CL:0001064	CRISPR-Cas9 knockout loss-of-function; dCas9-KRAB CRISPRi repression; Hi-C chromatin looping validation; CasRx eRNA knockdown	ChIP-seq(H3K27ac); GRO-seq; ATAC-seq; RNA-seq; Hi-C; single-cell RNA-seq	qRT-PCR, colony formation assay, cell proliferation assay
E_01206	2024	39186674	CRISPR Screening of Transcribed Super-Enhancers Identifies Drivers of Triple-Negative Breast Cancer Progression	Homo sapiens	hg19	chr2	106412871	106423516	NA	RSAD2	Super-enhancer	Active	Disease	triple-negative breast carcinoma	MONDO:0005494	DOID:0060081	mammary gland	UBERON:0001911	MDA-MB-436	CVCL_0623	malignant cell	CL:0001064	CRISPR-Cas9 knockout loss-of-function; dCas9-KRAB CRISPRi repression; Hi-C chromatin looping validation; CasRx eRNA knockdown	ChIP-seq(H3K27ac); GRO-seq; ATAC-seq; RNA-seq; Hi-C; single-cell RNA-seq	qRT-PCR, colony formation assay, cell proliferation assay
E_01207	2024	39186674	CRISPR Screening of Transcribed Super-Enhancers Identifies Drivers of Triple-Negative Breast Cancer Progression	Homo sapiens	hg19	chr7	131323622	131334609	NA	PODXL	Super-enhancer	Active	Disease	triple-negative breast carcinoma	MONDO:0005494	DOID:0060081	mammary gland	UBERON:0001911	MDA-MB-231	CVCL_0062	malignant cell	CL:0001064	CRISPR-Cas9 knockout loss-of-function; dCas9-KRAB CRISPRi repression; Hi-C chromatin looping validation; CasRx eRNA knockdown	ChIP-seq(H3K27ac); GRO-seq; ATAC-seq; RNA-seq; Hi-C, scATAC-seq, scRNA-seq; TCGA bulk omics; single-cell RNA-seq; Hi-C	qRT-PCR, transwell migration assay, crystal violet proliferation assay, mouse mammary fat pad xenograft, tail vein metastasis model; IHC staining
E_01208	2024	39186674	CRISPR Screening of Transcribed Super-Enhancers Identifies Drivers of Triple-Negative Breast Cancer Progression	Homo sapiens	hg19	chr7	131323622	131334609	NA	PODXL	Super-enhancer	Active	Disease	triple-negative breast carcinoma	MONDO:0005494	DOID:0060081	mammary gland	UBERON:0001911	MDA-MB-436	CVCL_0623	malignant cell	CL:0001064	CRISPR-Cas9 knockout loss-of-function; dCas9-KRAB CRISPRi repression; Hi-C chromatin looping validation; CasRx eRNA knockdown	ChIP-seq(H3K27ac); GRO-seq; ATAC-seq; RNA-seq; Hi-C, scATAC-seq, scRNA-seq; TCGA bulk omics; single-cell RNA-seq; Hi-C	qRT-PCR, transwell migration assay, crystal violet proliferation assay, mouse mammary fat pad xenograft, tail vein metastasis model; IHC staining
E_01209	2024	39186674	CRISPR Screening of Transcribed Super-Enhancers Identifies Drivers of Triple-Negative Breast Cancer Progression	Homo sapiens	hg19	chr7	131323622	131334609	NA	PODXL	Super-enhancer	Active	Disease	triple-negative breast carcinoma	MONDO:0005494	DOID:0060081	mammary gland	UBERON:0001911	MDA-MB-468	CVCL_0419	malignant cell	CL:0001064	CRISPR-Cas9 knockout loss-of-function; dCas9-KRAB CRISPRi repression; Hi-C chromatin looping validation; CasRx eRNA knockdown	ChIP-seq(H3K27ac); GRO-seq; ATAC-seq; RNA-seq; Hi-C, scATAC-seq, scRNA-seq; TCGA bulk omics; single-cell RNA-seq; Hi-C	qRT-PCR, transwell migration assay, crystal violet proliferation assay, mouse mammary fat pad xenograft, tail vein metastasis model; IHC staining
E_01210	2023	37165057	Identification of a genomic DNA sequence that quantitatively modulates KLF1 transcription factor expression in differentiating human hematopoietic cells	Homo sapiens	hg19	chr19	12995236	12998015	ETV6	KLF1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human CD34+-derived erythroid cells	NA	erythroid progenitor cell	CL:0000038	TF binding assay; In vivo functional validation; Enhancer chromatin-accessibility assay; Endogenous enhancer editing assay	ATAC-seq; GATA1/SMAD1/TAL1/ETV6 ChIP-seq integration; edited-locus deep sequencing	TALEN/Cpf1 editing; Luciferase reporter; ChIP-qPCR; qRT-PCR; erythroid differentiation analysis; In vivo phenotyping
E_01211	2023	37165057	Identification of a genomic DNA sequence that quantitatively modulates KLF1 transcription factor expression in differentiating human hematopoietic cells	Homo sapiens	hg19	chr19	12995236	12998015	GATA1	KLF1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human CD34+-derived erythroid cells	NA	erythroid progenitor cell	CL:0000038	TF binding assay; In vivo functional validation; Enhancer chromatin-accessibility assay; Endogenous enhancer editing assay	ATAC-seq; GATA1/SMAD1/TAL1/ETV6 ChIP-seq integration; edited-locus deep sequencing	TALEN/Cpf1 editing; Luciferase reporter; ChIP-qPCR; qRT-PCR; erythroid differentiation analysis; In vivo phenotyping
E_01212	2022	36224171	Lineage-selective super enhancers mediate core regulatory circuitry during adipogenic and osteogenic differentiation of human mesenchymal stem cells	Homo sapiens	hg19	chr15	99948331	99948831	ETS1	MEF2A	Enhancer	Active	Disease	obesity	MONDO:0011122	DOID:9970	mesenchyme of umbilical cord	UBERON:0003422	Primary human umbilical cord-derived hMSCs after osteogenic differentiation	NA	osteoblast	CL:0000062	TF binding assay; Disease-variant functional analysis; Super-enhancer constituent activity assay; Functional enhancer perturbation assay; Lineage-specific differentiation assay	H3K27ac ChIP-seq; DNase-seq; RNA-seq; GWAS	CRISPR-Cas9 deletion of MEF2A-SE functional region FR2; ETS1 ChIP-qPCR; RT-qPCR; ALP staining; dCas9-KRAB CRISPRi
E_01213	2022	36224171	Lineage-selective super enhancers mediate core regulatory circuitry during adipogenic and osteogenic differentiation of human mesenchymal stem cells	Homo sapiens	hg19	chr15	99948331	99948831	MEF2A	MEF2A	Enhancer	Active	Disease	obesity	MONDO:0011122	DOID:9970	mesenchyme of umbilical cord	UBERON:0003422	Primary human umbilical cord-derived hMSCs after osteogenic differentiation	NA	osteoblast	CL:0000062	TF binding assay; Disease-variant functional analysis; Super-enhancer constituent activity assay; Functional enhancer perturbation assay; Lineage-specific differentiation assay	H3K27ac ChIP-seq; DNase-seq; RNA-seq; GWAS	CRISPR-Cas9 deletion of MEF2A-SE functional region FR2; MEF2A ChIP-qPCR; RT-qPCR; ALP staining; dCas9-KRAB CRISPRi
E_01214	2024	38509385	Increased enhancer-promoter interactions during developmental enhancer activation in mammals	Mus musculus	mm10	chr5	115553982	115555842	NA	Zic1	Enhancer	Active	Normal	NA	NA	NA	heart primordium	UBERON:0003084	E11.5 mouse embryo	NA	embryonic neural cells	NA	Enhancer capture Hi-C assay; In vivo enhancer validation	Capture Hi-C; ChIP-seq; RNA-seq; Bisulfite-seq	CRISPR-Cas9 enhancer deletion; RT-qPCR; Transgenic reporter assay
E_01215	2024	38509385	Increased enhancer-promoter interactions during developmental enhancer activation in mammals	Mus musculus	mm10	chr5	115553982	115555842	NA	Zic4	Enhancer	Active	Normal	NA	NA	NA	heart primordium	UBERON:0003084	E11.5 mouse embryo	NA	embryonic neural cells	NA	Enhancer capture Hi-C assay; In vivo enhancer validation	Capture Hi-C; ChIP-seq; RNA-seq; Bisulfite-seq	CRISPR-Cas9 enhancer deletion; RT-qPCR; Transgenic reporter assay
E_01216	2023	37756562	Super Enhancer-Regulated LncRNA LINC01089 Induces Alternative Splicing of DIAPH3 to Drive Hepatocellular Carcinoma Metastasis	Homo sapiens	hg38	chr12	121799763	121803094	E2F1	LINC01089	Super-enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Hep-G2	CVCL_0027	hepatocyte	CL:0000182	In vivo functional validation; SE activity / TF-binding validation	H3K27ac ChIP-seq; ATAC-seq; E2F1 ChIP-seq; RNA-seq	Dual-luciferase reporter assay; CRISPRi; ChIP-qPCR; RT-qPCR; E2F1 knockdown/overexpression; In vivo phenotyping
E_01217	2023	37756562	Super Enhancer-Regulated LncRNA LINC01089 Induces Alternative Splicing of DIAPH3 to Drive Hepatocellular Carcinoma Metastasis	Homo sapiens	hg38	chr12	121799763	121803094	E2F1	LINC01089	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	SK-HEP-1	CVCL_0525	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; In vivo functional validation	ChIP-seq; ATAC-seq; RNA-seq	Luciferase reporter assay, CRISPR knockout, CRISPRi; ChIP-qPCR; RT-qPCR; In vivo phenotyping
E_01218	2022	34059508	Chromatin state dynamics confers specific therapeutic strategies in enhancer subtypes of colorectal cancer	Homo sapiens	hg19	chr11	2233643	2234213	NA	ASCL2	Enhancer	Active	Disease	colorectal adenocarcinoma	MONDO:0005008	DOID:0050861	colon	UBERON:0001155	colorectal adenocarcinoma/adenoma/normal colon tissues	NA	epithelial cell	CL:0000066	Chromatin interaction assay; Tumor-specific enhancer mapping; CRISPR epigenomic perturbation	H3K27ac/H3K4me1/H3K4me3/H3K79me2/H3K27me3/H3K9me3 ChIP-seq; RNA-seq; H3K27ac HiChIP	dCas9-KRAB enhancer repression; H3K27ac ChIP-qPCR; 3C; RT-qPCR; proliferation assay
E_01219	2022	34059508	Chromatin state dynamics confers specific therapeutic strategies in enhancer subtypes of colorectal cancer	Homo sapiens	hg19	chr12	130610556	130610854	NA	FZD10	Enhancer	Active	Disease	colorectal adenocarcinoma	MONDO:0005008	DOID:0050861	colon	UBERON:0001155	colorectal adenocarcinoma/adenoma/normal colon tissues	NA	epithelial cell	CL:0000066	Chromatin interaction assay; Tumor-specific enhancer mapping; CRISPR epigenomic perturbation	H3K27ac/H3K4me1/H3K4me3/H3K79me2/H3K27me3/H3K9me3 ChIP-seq; RNA-seq; H3K27ac HiChIP	dCas9-KRAB enhancer repression; H3K27ac ChIP-qPCR; 3C; RT-qPCR; proliferation assay
E_01220	2022	35994645	Stroke-associated intergenic variants modulate a human FOXF2 transcriptional enhancer	Homo sapiens	hg19	chr6	1335829	1335870	ETS1	FOXF2	Enhancer	Active	Disease	stroke susceptibility	MONDO:0005098	DOID:0051061	cerebral microvasculature / vascular wall	NA	HEK293	CVCL_0045	pericyte / vascular mural cell	NA	Experimentally defined ETS1/SNP functional core within the 750-bp FOXF2 construct-E enhancer; endogenous enhancer perturbation and disease-variant analysis	GWAS; ENCODE chromatin/TF integration; human-brain single-cell RNA-seq integration	Luciferase reporter; iCRISPRi; CRISPR enhancer excision; ChIP-qPCR; 42-bp deletion; allele/site-directed mutagenesis; qPCR; zebrafish reporter and vascular phenotyping
E_01221	2022	35994645	Stroke-associated intergenic variants modulate a human FOXF2 transcriptional enhancer	Homo sapiens	hg19	chr6	1335829	1335870	ETS1	FOXF2	Enhancer	Active	Disease	stroke susceptibility	MONDO:0005098	DOID:0051061	cerebral microvasculature / vascular wall	NA	zebrafish vascular mural-cell models	NA	pericyte / vascular mural cell	NA	Experimentally defined ETS1/SNP functional core within the 750-bp FOXF2 construct-E enhancer; endogenous enhancer perturbation and disease-variant analysis	GWAS; ENCODE chromatin/TF integration; human-brain single-cell RNA-seq integration	Luciferase reporter; iCRISPRi; CRISPR enhancer excision; ChIP-qPCR; 42-bp deletion; allele/site-directed mutagenesis; qPCR; zebrafish reporter and vascular phenotyping
E_01222	2022	35994645	Stroke-associated intergenic variants modulate a human FOXF2 transcriptional enhancer	Homo sapiens	hg19	chr6	1335829	1335870	ETS1	FOXF2	Enhancer	Active	Disease	stroke susceptibility	MONDO:0005098	DOID:0051061	cerebral microvasculature / vascular wall	NA	human GWAS cohorts	NA	pericyte / vascular mural cell	NA	Experimentally defined ETS1/SNP functional core within the 750-bp FOXF2 construct-E enhancer; endogenous enhancer perturbation and disease-variant analysis	GWAS; ENCODE chromatin/TF integration; human-brain single-cell RNA-seq integration	Luciferase reporter; iCRISPRi; CRISPR enhancer excision; ChIP-qPCR; 42-bp deletion; allele/site-directed mutagenesis; qPCR; zebrafish reporter and vascular phenotyping
E_01223	2022	35994645	Stroke-associated intergenic variants modulate a human FOXF2 transcriptional enhancer	Homo sapiens	hg19	chr6	1335829	1335870	RBPJ	FOXF2	Enhancer	Active	Disease	stroke susceptibility	MONDO:0005098	DOID:0051061	cerebral microvasculature / vascular wall	NA	HEK293	CVCL_0045	pericyte / vascular mural cell	NA	Functional core within the 750-bp construct-E enhancer; RBPJ occupancy/site mutagenesis; endogenous enhancer perturbation and FOXF2 target validation	GWAS; ENCODE chromatin/TF integration; human-brain single-cell RNA-seq integration	Luciferase reporter; iCRISPRi; CRISPR enhancer excision; ChIP-qPCR; RBPJ motif mutagenesis; qPCR; zebrafish enhancer reporter
E_01224	2022	35994645	Stroke-associated intergenic variants modulate a human FOXF2 transcriptional enhancer	Homo sapiens	hg19	chr6	1335829	1335870	RBPJ	FOXF2	Enhancer	Active	Disease	stroke susceptibility	MONDO:0005098	DOID:0051061	cerebral microvasculature / vascular wall	NA	zebrafish vascular mural-cell models	NA	pericyte / vascular mural cell	NA	Functional core within the 750-bp construct-E enhancer; RBPJ occupancy/site mutagenesis; endogenous enhancer perturbation and FOXF2 target validation	GWAS; ENCODE chromatin/TF integration; human-brain single-cell RNA-seq integration	Luciferase reporter; iCRISPRi; CRISPR enhancer excision; ChIP-qPCR; RBPJ motif mutagenesis; qPCR; zebrafish enhancer reporter
E_01225	2022	35994645	Stroke-associated intergenic variants modulate a human FOXF2 transcriptional enhancer	Homo sapiens	hg19	chr6	1335829	1335870	RBPJ	FOXF2	Enhancer	Active	Disease	stroke susceptibility	MONDO:0005098	DOID:0051061	cerebral microvasculature / vascular wall	NA	human GWAS cohorts	NA	pericyte / vascular mural cell	NA	Functional core within the 750-bp construct-E enhancer; RBPJ occupancy/site mutagenesis; endogenous enhancer perturbation and FOXF2 target validation	GWAS; ENCODE chromatin/TF integration; human-brain single-cell RNA-seq integration	Luciferase reporter; iCRISPRi; CRISPR enhancer excision; ChIP-qPCR; RBPJ motif mutagenesis; qPCR; zebrafish enhancer reporter
E_01226	2022	36224171	Lineage-selective super enhancers mediate core regulatory circuitry during adipogenic and osteogenic differentiation of human mesenchymal stem cells	Homo sapiens	hg19	chr9	94190762	94191795	NA	NFIL3	Enhancer	Active	Disease	obesity	MONDO:0011122	DOID:9970	mesenchyme of umbilical cord	UBERON:0003422	Primary human umbilical cord-derived hMSCs after adipogenic differentiation	NA	adipocyte	CL:0000136	Disease-variant functional analysis; Super-enhancer constituent activity assay; Functional enhancer perturbation assay; Lineage-specific differentiation assay	H3K27ac ChIP-seq; DNase-seq; RNA-seq; GWAS	CRISPR-Cas9 deletion of NFIL3-SE functional region FR3; RT-qPCR; Nile red staining
E_01227	2018	29277702	The transcription factors GATA2 and microphthalmia-associated transcription factor regulate Hdc gene expression in mast cells and are required for IgE/mast cell-mediated anaphylaxis	Mus musculus	mm10	chr2	24942670	24943220	Gata2	Hdc	Enhancer	Active	Disease	anaphylaxis	MONDO:0100053	NA	bone marrow	UBERON:0002371	bone marrow-derived mast cells	NA	mast cell	CL:0000097	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation	H3K4me1 ChIP-seq; H3K27ac ChIP-seq; ChIP-seq	Luciferase reporter assay; MITF-binding-site mutagenesis; ChIP-qPCR; shRNA knockdown; RT-qPCR; passive systemic anaphylaxis assay; ChIP; Mouse genetic deletion/knock-in; In vivo phenotyping
E_01228	2018	29277702	The transcription factors GATA2 and microphthalmia-associated transcription factor regulate Hdc gene expression in mast cells and are required for IgE/mast cell-mediated anaphylaxis	Mus musculus	mm10	chr2	24942670	24943220	Mitf	Hdc	Enhancer	Active	Disease	anaphylaxis	MONDO:0100053	NA	bone marrow	UBERON:0002371	bone marrow-derived mast cells	NA	mast cell	CL:0000097	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation	H3K4me1 ChIP-seq; H3K27ac ChIP-seq; ChIP-seq	Luciferase reporter assay; MITF-binding-site mutagenesis; ChIP-qPCR; shRNA knockdown; RT-qPCR; passive systemic anaphylaxis assay; ChIP; Mouse genetic deletion/knock-in; In vivo phenotyping
E_01229	2018	29277702	The transcription factors GATA2 and microphthalmia-associated transcription factor regulate Hdc gene expression in mast cells and are required for IgE/mast cell-mediated anaphylaxis	Mus musculus	mm10	chr2	126627537	126628771	Mitf	Hdc	Enhancer	Active	Disease	anaphylaxis	MONDO:0100053	NA	bone marrow	UBERON:0002371	bone marrow-derived mast cells	NA	mast cell	CL:0000097	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation	H3K4me1 ChIP-seq; H3K27ac ChIP-seq; ChIP-seq	Luciferase reporter assay; MITF-binding-site mutagenesis; ChIP-qPCR; shRNA knockdown; RT-qPCR; passive systemic anaphylaxis assay; ChIP; Mouse genetic deletion/knock-in; In vivo phenotyping
E_01230	2018	29277702	The transcription factors GATA2 and microphthalmia-associated transcription factor regulate Hdc gene expression in mast cells and are required for IgE/mast cell-mediated anaphylaxis	Mus musculus	mm10	chr2	126631900	126633000	Mitf	Hdc	Enhancer	Active	Disease	anaphylaxis	MONDO:0100053	NA	bone marrow	UBERON:0002371	bone marrow-derived mast cells	NA	mast cell	CL:0000097	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation	H3K4me1 ChIP-seq; H3K27ac ChIP-seq; published MITF ChIP-seq integration; ChIP-seq	Luciferase reporter assay; MITF-binding-site mutagenesis; MITF ChIP-qPCR; Mitf shRNA knockdown; RT-qPCR; histamine ELISA; passive systemic anaphylaxis assay; ChIP; Mouse genetic deletion/knock-in; In vivo phenotyping
E_01231	2023	37165057	Identification of a genomic DNA sequence that quantitatively modulates KLF1 transcription factor expression in differentiating human hematopoietic cells	Homo sapiens	hg19	chr19	12995236	12998015	ETV6	KLF1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	KU812/JK1 assay models	NA	erythroid progenitor cell	CL:0000038	TF binding assay; In vivo functional validation; Enhancer chromatin-accessibility assay; Endogenous enhancer editing assay	ATAC-seq; GATA1/SMAD1/TAL1/ETV6 ChIP-seq integration; edited-locus deep sequencing	TALEN/Cpf1 editing; Luciferase reporter; ChIP-qPCR; qRT-PCR; erythroid differentiation analysis; In vivo phenotyping
E_01232	2023	37165057	Identification of a genomic DNA sequence that quantitatively modulates KLF1 transcription factor expression in differentiating human hematopoietic cells	Homo sapiens	hg19	chr19	12995236	12998015	GATA1	KLF1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	KU812/JK1 assay models	NA	erythroid progenitor cell	CL:0000038	TF binding assay; In vivo functional validation; Enhancer chromatin-accessibility assay; Endogenous enhancer editing assay	ATAC-seq; GATA1/SMAD1/TAL1/ETV6 ChIP-seq integration; edited-locus deep sequencing	TALEN/Cpf1 editing; Luciferase reporter; ChIP-qPCR; qRT-PCR; erythroid differentiation analysis; In vivo phenotyping
E_01233	2023	37756562	Super Enhancer-Regulated LncRNA LINC01089 Induces Alternative Splicing of DIAPH3 to Drive Hepatocellular Carcinoma Metastasis	Homo sapiens	hg38	chr12	121799763	121803094	NA	LINC01089	Super-enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Huh-7	CVCL_0336	malignant cell	CL:0001064	In vivo functional validation; SE activity / TF-binding validation	H3K27ac ChIP-seq; RNA-seq	Dual-luciferase reporter assay; CRISPRi; ChIP-qPCR; RT-qPCR; E2F1 knockdown/overexpression; In vivo phenotyping
E_01234	2023	37756562	Super Enhancer-Regulated LncRNA LINC01089 Induces Alternative Splicing of DIAPH3 to Drive Hepatocellular Carcinoma Metastasis	Homo sapiens	hg38	chr12	121799763	121803094	NA	LINC01089	Super-enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	SNU-387	CVCL_0250	malignant cell	CL:0001064	In vivo functional validation; SE activity / TF-binding validation	H3K27ac ChIP-seq; RNA-seq	Dual-luciferase reporter assay; CRISPRi; ChIP-qPCR; RT-qPCR; In vivo phenotyping
E_01235	2023	37756562	Super Enhancer-Regulated LncRNA LINC01089 Induces Alternative Splicing of DIAPH3 to Drive Hepatocellular Carcinoma Metastasis	Homo sapiens	hg38	chr12	121803095	121805690	NA	LINC01089	Super-enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Hep-G2	CVCL_0027	hepatocyte	CL:0000182	In vivo functional validation; SE activity validation	H3K27ac ChIP-seq; ATAC-seq; RNA-seq	Dual-luciferase reporter assay; CRISPRi; RT-qPCR; In vivo phenotyping
E_01236	2023	37756562	Super Enhancer-Regulated LncRNA LINC01089 Induces Alternative Splicing of DIAPH3 to Drive Hepatocellular Carcinoma Metastasis	Homo sapiens	hg38	chr12	121803095	121805690	NA	LINC01089	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	SK-HEP-1	CVCL_0525	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; In vivo functional validation	ChIP-seq; ATAC-seq; RNA-seq	Luciferase reporter assay, CRISPR knockout, CRISPRi; RT-qPCR; In vivo phenotyping
E_01237	2023	37756562	Super Enhancer-Regulated LncRNA LINC01089 Induces Alternative Splicing of DIAPH3 to Drive Hepatocellular Carcinoma Metastasis	Homo sapiens	hg38	chr12	121803095	121805690	NA	LINC01089	Super-enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Huh-7	CVCL_0336	malignant cell	CL:0001064	In vivo functional validation; SE activity validation	H3K27ac ChIP-seq; RNA-seq	Dual-luciferase reporter assay; CRISPRi; RT-qPCR; In vivo phenotyping
E_01238	2023	37756562	Super Enhancer-Regulated LncRNA LINC01089 Induces Alternative Splicing of DIAPH3 to Drive Hepatocellular Carcinoma Metastasis	Homo sapiens	hg38	chr12	121803095	121805690	NA	LINC01089	Super-enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	SNU-387	CVCL_0250	malignant cell	CL:0001064	In vivo functional validation; SE activity validation	H3K27ac ChIP-seq; RNA-seq	Dual-luciferase reporter assay; CRISPRi; RT-qPCR; In vivo phenotyping
E_01239	2022	34059508	Chromatin state dynamics confers specific therapeutic strategies in enhancer subtypes of colorectal cancer	Homo sapiens	hg19	chr11	2233643	2234213	NA	ASCL2	Enhancer	Active	Disease	colorectal adenocarcinoma	MONDO:0005008	DOID:0050861	colon	UBERON:0001155	SW480	CVCL_0546	malignant cell	CL:0001064	Chromatin interaction assay; Tumor-specific enhancer mapping; CRISPR epigenomic perturbation	H3K27ac/H3K4me1/H3K4me3/H3K79me2/H3K27me3/H3K9me3 ChIP-seq; RNA-seq; H3K27ac HiChIP	dCas9-KRAB enhancer repression; H3K27ac ChIP-qPCR; 3C; RT-qPCR; proliferation assay
E_01240	2022	34059508	Chromatin state dynamics confers specific therapeutic strategies in enhancer subtypes of colorectal cancer	Homo sapiens	hg19	chr12	130610556	130610854	NA	FZD10	Enhancer	Active	Disease	colorectal adenocarcinoma	MONDO:0005008	DOID:0050861	colon	UBERON:0001155	SW480	CVCL_0546	malignant cell	CL:0001064	Chromatin interaction assay; Tumor-specific enhancer mapping; CRISPR epigenomic perturbation	H3K27ac/H3K4me1/H3K4me3/H3K79me2/H3K27me3/H3K9me3 ChIP-seq; RNA-seq; H3K27ac HiChIP	dCas9-KRAB enhancer repression; H3K27ac ChIP-qPCR; 3C; RT-qPCR; proliferation assay
E_01241	2022	34059508	Chromatin state dynamics confers specific therapeutic strategies in enhancer subtypes of colorectal cancer	Homo sapiens	hg19	chr11	2223156	2236495	NA	ASCL2	Enhancer	Active	Disease	colorectal adenocarcinoma	MONDO:0005008	DOID:0050861	colon	UBERON:0001155	SW480	CVCL_0546	malignant cell	CL:0001064	Functional perturbation assay; Chromatin interaction assay; Enhancer functional validation	H3K27ac ChIP-seq; H3K27ac HiChIP; RNA-seq	CRISPRi (dCas9-KRAB); ChIP-qPCR; 3C; ASCL2 mRNA quantification; cell proliferation assay
E_01242	2022	34059508	Chromatin state dynamics confers specific therapeutic strategies in enhancer subtypes of colorectal cancer	Homo sapiens	hg38	chr11	2201926	2215265	NA	ASCL2	Enhancer	Active	Disease	colorectal adenocarcinoma	MONDO:0005008	DOID:0050861	colon	UBERON:0001155	SW480	CVCL_0546	malignant cell	CL:0001064	Functional perturbation assay; Chromatin interaction assay; Enhancer functional validation	H3K27ac ChIP-seq; H3K27ac HiChIP; RNA-seq	CRISPRi (dCas9-KRAB); ChIP-qPCR; 3C; ASCL2 mRNA quantification; cell proliferation assay
E_01243	2022	35994645	Stroke-associated intergenic variants modulate a human FOXF2 transcriptional enhancer	Homo sapiens	hg19	chr6	1335829	1335870	CTCF	FOXF2	Enhancer	Active	Disease	stroke susceptibility	MONDO:0005098	DOID:0051061	cerebral microvasculature / vascular wall	NA	HEK293	CVCL_0045	pericyte / vascular mural cell	NA	Functional FOXF2 enhancer core with CTCF occupancy; endogenous enhancer perturbation and target-gene validation	GWAS; ENCODE chromatin/TF integration; human-brain single-cell RNA-seq integration	Luciferase reporter; iCRISPRi; CRISPR enhancer excision; ChIP-qPCR; qPCR; zebrafish enhancer reporter
E_01244	2022	35994645	Stroke-associated intergenic variants modulate a human FOXF2 transcriptional enhancer	Homo sapiens	hg19	chr6	1335829	1335870	CTCF	FOXF2	Enhancer	Active	Disease	stroke susceptibility	MONDO:0005098	DOID:0051061	cerebral microvasculature / vascular wall	NA	zebrafish vascular mural-cell models	NA	pericyte / vascular mural cell	NA	Functional FOXF2 enhancer core with CTCF occupancy; endogenous enhancer perturbation and target-gene validation	GWAS; ENCODE chromatin/TF integration; human-brain single-cell RNA-seq integration	Luciferase reporter; iCRISPRi; CRISPR enhancer excision; ChIP-qPCR; qPCR; zebrafish enhancer reporter
E_01245	2022	35994645	Stroke-associated intergenic variants modulate a human FOXF2 transcriptional enhancer	Homo sapiens	hg19	chr6	1335829	1335870	CTCF	FOXF2	Enhancer	Active	Disease	stroke susceptibility	MONDO:0005098	DOID:0051061	cerebral microvasculature / vascular wall	NA	human GWAS cohorts	NA	pericyte / vascular mural cell	NA	Functional FOXF2 enhancer core with CTCF occupancy; endogenous enhancer perturbation and target-gene validation	GWAS; ENCODE chromatin/TF integration; human-brain single-cell RNA-seq integration	Luciferase reporter; iCRISPRi; CRISPR enhancer excision; ChIP-qPCR; qPCR; zebrafish enhancer reporter
E_01246	2024	38509385	Increased enhancer-promoter interactions during developmental enhancer activation in mammals	Mus musculus	mm10	chr13	73425662	73427510	NA	Mir9-2	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	E11.5 mouse embryo	NA	embryonic forebrain neural cells	NA	Enhancer capture Hi-C assay; In vivo enhancer validation	Capture Hi-C; ChIP-seq; RNA-seq; Bisulfite-seq	CRISPR-Cas9 enhancer knockout; RT-qPCR
E_01247	2024	38509385	Increased enhancer-promoter interactions during developmental enhancer activation in mammals	Mus musculus	mm10	chr13	73511172	73512191	NA	Mir9-2	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	E11.5 mouse embryo	NA	embryonic forebrain neural cells	NA	Enhancer capture Hi-C assay; In vivo enhancer validation	Capture Hi-C; ChIP-seq; RNA-seq; Bisulfite-seq	CRISPR-Cas9 enhancer knockout; RT-qPCR
E_01248	2024	38509385	Increased enhancer-promoter interactions during developmental enhancer activation in mammals	Mus musculus	mm10	chr13	73578542	73580243	NA	Mir9-2	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	E11.5 mouse embryo	NA	embryonic forebrain neural cells	NA	Enhancer capture Hi-C assay; In vivo enhancer validation	Capture Hi-C; ChIP-seq; RNA-seq; Bisulfite-seq	CRISPR-Cas9 enhancer knockout; RT-qPCR
E_01249	2024	38509385	Increased enhancer-promoter interactions during developmental enhancer activation in mammals	Mus musculus	mm10	chr2	166631000	166633000	NA	Zic1	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	E11.5 mouse embryo	NA	embryonic forebrain tissue	NA	Enhancer capture Hi-C assay; In vivo enhancer validation	Capture Hi-C; ChIP-seq; RNA-seq	CRISPR-Cas9 enhancer deletion; RT-qPCR
E_01250	2024	38509385	Increased enhancer-promoter interactions during developmental enhancer activation in mammals	Mus musculus	mm10	chr2	166634000	166636000	NA	Zic4	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	E11.5 mouse embryo	NA	embryonic forebrain tissue	NA	Enhancer capture Hi-C assay; In vivo enhancer validation	Capture Hi-C; ChIP-seq; RNA-seq	CRISPR-Cas9 enhancer deletion; RT-qPCR
E_01251	2024	38509385	Increased enhancer-promoter interactions during developmental enhancer activation in mammals	Mus musculus	mm10	chr5	87787087	87788935	NA	Mir9-2	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	E11.5 mouse embryo	NA	embryonic forebrain tissue	NA	Enhancer capture Hi-C assay; In vivo enhancer validation	Capture Hi-C; ChIP-seq; RNA-seq; Bisulfite-seq	CRISPR-Cas9 enhancer deletion; RT-qPCR
E_01252	2024	38509385	Increased enhancer-promoter interactions during developmental enhancer activation in mammals	Mus musculus	mm10	chr5	87872597	87873616	NA	Mir9-2	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	E11.5 mouse embryo	NA	embryonic forebrain tissue	NA	Enhancer capture Hi-C assay; In vivo enhancer validation	Capture Hi-C; ChIP-seq; RNA-seq; Bisulfite-seq	CRISPR-Cas9 enhancer deletion; RT-qPCR
E_01253	2024	38509385	Increased enhancer-promoter interactions during developmental enhancer activation in mammals	Mus musculus	mm10	chr5	87944125	87945828	NA	Mir9-2	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	E11.5 mouse embryo	NA	embryonic forebrain tissue	NA	Enhancer capture Hi-C assay; In vivo enhancer validation	Capture Hi-C; ChIP-seq; RNA-seq; Bisulfite-seq	CRISPR-Cas9 enhancer deletion; RT-qPCR
E_01254	2024	38509385	Increased enhancer-promoter interactions during developmental enhancer activation in mammals	Mus musculus	mm10	chr5	87787087	87788935	NA	Mir9-2	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	E11.5 mouse embryo	NA	embryonic forebrain tissue	NA	Enhancer-promoter interaction assay; In vivo enhancer validation	Capture Hi-C; ChIP-seq; RNA-seq; Bisulfite-seq	CRISPR-Cas9 enhancer deletion; RT-qPCR
E_01255	2024	38509385	Increased enhancer-promoter interactions during developmental enhancer activation in mammals	Mus musculus	mm10	chr5	87872597	87873616	NA	Mir9-2	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	E11.5 mouse embryo	NA	embryonic forebrain tissue	NA	Enhancer-promoter interaction assay; In vivo enhancer validation	Capture Hi-C; ChIP-seq; RNA-seq; Bisulfite-seq	CRISPR-Cas9 enhancer deletion; RT-qPCR
E_01256	2024	38509385	Increased enhancer-promoter interactions during developmental enhancer activation in mammals	Mus musculus	mm10	chr5	87944125	87945828	NA	Mir9-2	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	E11.5 mouse embryo	NA	embryonic forebrain tissue	NA	Enhancer-promoter interaction assay; In vivo enhancer validation	Capture Hi-C; ChIP-seq; RNA-seq; Bisulfite-seq	CRISPR-Cas9 enhancer deletion; RT-qPCR
E_01257	2023	37756562	Super Enhancer-Regulated LncRNA LINC01089 Induces Alternative Splicing of DIAPH3 to Drive Hepatocellular Carcinoma Metastasis	Homo sapiens	hg38	chr12	121799763	121803094	E2F1	LINC01089	Super-enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Hep-G2	CVCL_0027	hepatocyte	CL:0000182	In vivo functional validation; SE functional perturbation; EMT / metastasis validation	H3K27ac ChIP-seq; RNA-seq	CRISPRi; RT-qPCR; LINC01089 knockdown; migration/invasion assay; in vivo metastasis assay; In vivo phenotyping
E_01258	2023	37756562	Super Enhancer-Regulated LncRNA LINC01089 Induces Alternative Splicing of DIAPH3 to Drive Hepatocellular Carcinoma Metastasis	Homo sapiens	hg38	chr12	121799763	121803094	NA	LINC01089	Super-enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Huh-7	CVCL_0336	malignant cell	CL:0001064	In vivo functional validation; SE functional perturbation; EMT / metastasis validation	H3K27ac ChIP-seq; RNA-seq	CRISPRi; RT-qPCR; LINC01089 knockdown; migration/invasion assay; in vivo metastasis assay; In vivo phenotyping
E_01259	2023	37756562	Super Enhancer-Regulated LncRNA LINC01089 Induces Alternative Splicing of DIAPH3 to Drive Hepatocellular Carcinoma Metastasis	Homo sapiens	hg38	chr12	121799763	121803094	NA	LINC01089	Super-enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	SNU-387	CVCL_0250	malignant cell	CL:0001064	In vivo functional validation; SE functional perturbation; EMT / metastasis validation	H3K27ac ChIP-seq; RNA-seq	CRISPRi; RT-qPCR; LINC01089 knockdown; migration/invasion assay; in vivo metastasis assay; In vivo phenotyping
E_01260	2023	37756562	Super Enhancer-Regulated LncRNA LINC01089 Induces Alternative Splicing of DIAPH3 to Drive Hepatocellular Carcinoma Metastasis	Homo sapiens	hg38	chr12	121803095	121805690	NA	LINC01089	Super-enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Hep-G2	CVCL_0027	hepatocyte	CL:0000182	In vivo functional validation; SE functional perturbation; LINC01089-dependent metastatic phenotype	H3K27ac ChIP-seq; RNA-seq	CRISPRi; RT-qPCR; migration/invasion assay; in vivo metastasis assay; In vivo phenotyping
E_01261	2023	37756562	Super Enhancer-Regulated LncRNA LINC01089 Induces Alternative Splicing of DIAPH3 to Drive Hepatocellular Carcinoma Metastasis	Homo sapiens	hg38	chr12	121803095	121805690	NA	LINC01089	Super-enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Huh-7	CVCL_0336	malignant cell	CL:0001064	In vivo functional validation; SE functional perturbation; LINC01089-dependent metastatic phenotype	H3K27ac ChIP-seq; RNA-seq	CRISPRi; RT-qPCR; migration/invasion assay; in vivo metastasis assay; In vivo phenotyping
E_01262	2023	37756562	Super Enhancer-Regulated LncRNA LINC01089 Induces Alternative Splicing of DIAPH3 to Drive Hepatocellular Carcinoma Metastasis	Homo sapiens	hg38	chr12	121803095	121805690	NA	LINC01089	Super-enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	SNU-387	CVCL_0250	malignant cell	CL:0001064	In vivo functional validation; SE functional perturbation; LINC01089-dependent metastatic phenotype	H3K27ac ChIP-seq; RNA-seq	CRISPRi; RT-qPCR; migration/invasion assay; in vivo metastasis assay; In vivo phenotyping
E_01263	2022	34059508	Chromatin state dynamics confers specific therapeutic strategies in enhancer subtypes of colorectal cancer	Homo sapiens	hg38	chr11	62864230	62864780	NA	FZD10	Enhancer	Active	Disease	colorectal adenocarcinoma	MONDO:0005008	DOID:0050861	colon	UBERON:0001155	colorectal cancer tissues and cell lines	NA	malignant cell	CL:0001064	Tumor-specific enhancer functional perturbation	H3K27ac ChIP-seq; H3K4me1 ChIP-seq; H3K4me3 ChIP-seq; H3K79me2 ChIP-seq; H3K27me3 ChIP-seq; H3K9me3 ChIP-seq; RNA-seq	CRISPR/dCas9 epigenomic enhancer repression; proliferation assay
E_01264	2022	34059508	Chromatin state dynamics confers specific therapeutic strategies in enhancer subtypes of colorectal cancer	Homo sapiens	hg38	chr12	97432140	97432710	NA	ASCL2	Enhancer	Active	Disease	colorectal adenocarcinoma	MONDO:0005008	DOID:0050861	colon	UBERON:0001155	colorectal cancer tissues and cell lines	NA	malignant cell	CL:0001064	Tumor-specific enhancer functional perturbation	H3K27ac ChIP-seq; H3K4me1 ChIP-seq; H3K4me3 ChIP-seq; H3K79me2 ChIP-seq; H3K27me3 ChIP-seq; H3K9me3 ChIP-seq; RNA-seq	CRISPR/dCas9 epigenomic enhancer repression; proliferation assay
E_01265	2024	38509385	Increased enhancer-promoter interactions during developmental enhancer activation in mammals	Mus musculus	mm10	chr9	90690384	90694866	NA	Zic1	Enhancer	Active	Normal	NA	NA	NA	midbrain	UBERON:0001891	transgenic mouse embryo	NA	mouse embryo	NA	CRISPR deletion; Transgenic reporter assay	Capture Hi-C	RT-qPCR, lacZ whole-mount staining
E_01266	2018	29277702	The transcription factors GATA2 and microphthalmia-associated transcription factor regulate Hdc gene expression in mast cells and are required for IgE/mast cell-mediated anaphylaxis	Mus musculus	mm10	chr2	126593905	126595430	Gata2	Hdc	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Connective Tissue Mast Cell	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR; RNAi/siRNA/shRNA
E_01267	2018	29277702	The transcription factors GATA2 and microphthalmia-associated transcription factor regulate Hdc gene expression in mast cells and are required for IgE/mast cell-mediated anaphylaxis	Mus musculus	mm10	chr2	126593905	126595430	Mitf	Hdc	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Connective Tissue Mast Cell	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR; RNAi/siRNA/shRNA
E_01268	2018	29277702	The transcription factors GATA2 and microphthalmia-associated transcription factor regulate Hdc gene expression in mast cells and are required for IgE/mast cell-mediated anaphylaxis	Mus musculus	mm10	chr2	126601468	126603468	Gata2	Hdc	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Connective Tissue Mast Cell	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR; RNAi/siRNA/shRNA
E_01269	2018	29277702	The transcription factors GATA2 and microphthalmia-associated transcription factor regulate Hdc gene expression in mast cells and are required for IgE/mast cell-mediated anaphylaxis	Mus musculus	mm10	chr2	126601468	126603468	Mitf	Hdc	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Connective Tissue Mast Cell	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR; RNAi/siRNA/shRNA
E_01270	2024	38855864	Chromatin profiling identifies chondrocyte-specific Sox9 enhancers important for skeletal development	Mus musculus	mm9	chr11	112334364	112335294	Pitx1	Sox9	Enhancer	Active	Normal	NA	NA	NA	NA	NA	ATDC-5	CVCL_3894	chondrogenic cell	NA	Enhancer activity assay; Differentiation-associated enhancer activity assay	NA	Luciferase reporter assay; H3K27ac ChIP-qPCR; RT-qPCR; Western blot; Alcian Blue Staining
E_01271	2024	38855864	Chromatin profiling identifies chondrocyte-specific Sox9 enhancers important for skeletal development	Mus musculus	mm9	chr11	112482190	112483273	Pitx1	Sox9	Enhancer	Active	Normal	NA	NA	NA	NA	NA	ATDC-5	CVCL_3894	chondrogenic cell	NA	Enhancer activity assay; Differentiation-associated enhancer activity assay	NA	Luciferase reporter assay; H3K27ac ChIP-qPCR; RT-qPCR; Western blot; Alcian Blue Staining
E_01272	2026	41328346	Enhancer-mediated NR2F2 recruitment activates BGN to promote tumor growth and shape tumor microenvironment in papillary thyroid cancer	Homo sapiens	hg38	chrX	153492724	153500546	NR2F2	BGN	Enhancer	Active	Disease	thyroid gland carcinoma	MONDO:0015075	DOID:3963	thyroid gland	UBERON:0002046	Thyroid carcinoma cell	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Endogenous enhancer perturbation	ChIP-seq; RNA-seq; single-cell RNA-seq; RNA-seq	Luciferase reporter assay; ChIP-qPCR, CRISPRi; 3C assay; RT-qPCR; Western blot; CRISPRi; Luciferase reporter assay; Flow cytometry
E_01273	2025	39964764	Super-enhancer-driven EFNA1 fuels tumor progression in cervical cancer via the FOSL2-Src/AKT/STAT3 axis	Homo sapiens	hg38	chr1	155100545	155103815	FOSL2	EFNA1	Enhancer	Active	Disease	cervical cancer	MONDO:0002974	DOID:4362	thyroid gland	UBERON:0002046	TPC-1	CVCL_6298	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; In vivo functional validation	ChIP-seq	Luciferase reporter assay, CRISPR knockout, CRISPRi; ChIP-qPCR; In vivo phenotyping
E_01274	2025	40321134	Enhancer-Associated LncRNA-ITGA2 Promotes Vascular Remodeling Through ITGA2	Homo sapiens	hg38	chr5	53031762	53032075	NA	ITGA2	Enhancer	Active	Disease	coronary artery disease	NA	NA	vasculature	UBERON:0002049	Primary human vascular smooth muscle cells	NA	vascular associated smooth muscle cell	CL:0000359	Enhancer activity assay; Chromatin interaction assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation; Enhancer-associated lncRNA functional perturbation assay; RNA-chromatin interaction assay; RNA-protein interaction assay	H3K4me1/H3K27ac CUT&Tag; promoter capture Hi-C; lncRNA microarray; RNA-seq; H3K27ac ChIP-seq; ChIRP-MS; ChIP-seq	ChIRP-qPCR; RIP-qPCR; NONO ChIP-qPCR; CRISPR-Cas9 gene editing; LncRNA-ITGA2 gain- and loss-of-function; RT-qPCR; Western blot; VSMC proliferation assay; VSMC migration assay; CRISPR-Cas9 endogenous deletion/editing; ChIP; In vivo phenotyping
E_01275	2024	38602103	Coronary Artery Disease Risk Variant Dampens the Expression of CALCRL by Reducing HSF Binding to Shear Stress Responsive Enhancer in Endothelial Cells In Vitro	Homo sapiens	hg19	chr2	188184262	188184791	HSF1	CALCRL	Enhancer	Active	Disease	coronary artery disorder	MONDO:0005010	DOID:3393	blood vessel	UBERON:0001981	Human aortic endothelial cells (HAECs)	NA	endothelial cell	CL:0000115	Enhancer activity assay; Functional perturbation assay; TF binding assay	ATAC-seq; RNA-seq; ChIP-seq; STARR-seq	Luciferase reporter assay; CRISPR-Cas9 enhancer deletion; ChIP-qPCR; EMSA; RT-qPCR; Reporter assay; siRNA knockdown
E_01276	2024	39606421	Single cell variant to enhancer to gene map for coronary artery disease	Homo sapiens	hg38	chr3	134460112	134466940	NA	AMOTL2	Enhancer	Active	Disease	coronary artery disorder	MONDO:0005010	DOID:3393	coronary artery	UBERON:0001621	Human coronary artery tissue smooth muscle cell compartment	NA	smooth muscle cell of the coronary artery	CL:0002592	Chromatin interaction assay; Chromatin accessibility assay; Variant-to-enhancer-to-gene mapping; Enhancer activity profiling	Single-nucleus Multiome RNA+ATAC-seq; snATAC-seq; genome-wide Hi-C; H3K27ac ChIP-seq (coronary artery reference integration); Hi-C	CRISPRi
E_01277	2023	36889906	Interactive enhancer hubs (iHUBs) mediate transcriptional reprogramming and adaptive resistance in pancreatic cancer	Homo sapiens	hg19	chr22	39666991	39667170	JUND	LIF	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	Paclitaxel-resistant PDAC derivative (PacR)	NA	malignant cell	CL:0001064	In vivo functional validation; Functional enhancer perturbation; TF binding; enhancer-hub chromatin interaction	JUND/H3K27ac ChIP-seq; ATAC-seq; H3K27ac HiChIP; leChRO-seq; RNA-seq	CRISPR-Cas9 enhancer deletion; 4C-seq/targeted 4C; RT-qPCR; drug-response assays; In vivo phenotyping
E_01278	2023	36889906	Interactive enhancer hubs (iHUBs) mediate transcriptional reprogramming and adaptive resistance in pancreatic cancer	Homo sapiens	hg19	chr22	39666991	39667170	JUND	LIF	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	L3.6pl	CVCL_0384	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; In vivo functional validation	ChIP-seq; ATAC-seq, HiChIP, leChRO-seq	CRISPR knockout; 4C-seq; RT-qPCR; In vivo phenotyping
E_01279	2016	27803105	BET Inhibitors Suppress ALDH Activity by Targeting ALDH1A1 Super-Enhancer in Ovarian Cancer	Homo sapiens	hg19	chr9	133401000	133404500	BRD4	ALDH1A1	Enhancer	Active	Disease	ovarian carcinoma	MONDO:0005140	DOID:4001	breast	UBERON:0000310	ZR-75-1	CVCL_0588	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; In vivo functional validation	ChIP-seq; RNA-seq, 3C	Luciferase reporter assay, CRISPR knockout; RT-qPCR; In vivo phenotyping
E_01280	2024	38602103	Coronary Artery Disease Risk Variant Dampens the Expression of CALCRL by Reducing HSF Binding to Shear Stress Responsive Enhancer in Endothelial Cells In Vitro	Homo sapiens	hg38	chr2	188184700	188185000	HSF1	CALCRL	Enhancer	Active	Normal	NA	NA	NA	artery	UBERON:0001637	Endothelial cells	NA	endothelial cell	CL:0000115	Enhancer activity assay; Functional perturbation assay	ChIP-seq; RNA-seq; ATAC-seq	Luciferase reporter assay; EMSA; CRISPR knockout; CRISPR-Cas9 enhancer deletion; Reporter assay; ChIP-qPCR; siRNA knockdown
E_01281	2018	30146478	Combinatorial CRISPR/Cas9 Approach to Elucidate a Far-Upstream Enhancer Complex for Tissue-Specific Sox9 Expression	Mus musculus	mm10	chr11	111838889	111839334	Stat3	Sox9	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Cartilage	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR; Transgenic/LacZ assay
E_01282	2018	30590035	The TFAP2C-Regulated OCT4 Naive Enhancer Is Involved in Human Germline Formation	Homo sapiens	hg19	chr6	31140556	31141204	TFAP2C	POU5F1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Human Primordial Germ Cell	NA	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; ATAC-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01283	2017	28982762	A dynamic interplay of enhancer elements regulates Klf4 expression in na?ve pluripotency	Mus musculus	mm10	chr4	55449628	55461828	Pou5f1	Klf4	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_01284	2017	28982762	A dynamic interplay of enhancer elements regulates Klf4 expression in na?ve pluripotency	Mus musculus	mm10	chr4	55449628	55461828	Sox2	Klf4	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_01285	2017	28982762	A dynamic interplay of enhancer elements regulates Klf4 expression in na?ve pluripotency	Mus musculus	mm10	chr4	55449628	55461828	Stat3	Klf4	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_01286	2017	28982762	A dynamic interplay of enhancer elements regulates Klf4 expression in na?ve pluripotency	Mus musculus	mm10	chr4	55453628	55465828	Pou5f1	Klf4	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_01287	2017	28982762	A dynamic interplay of enhancer elements regulates Klf4 expression in na?ve pluripotency	Mus musculus	mm10	chr4	55453628	55465828	Sox2	Klf4	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_01288	2017	28982762	A dynamic interplay of enhancer elements regulates Klf4 expression in na?ve pluripotency	Mus musculus	mm10	chr4	55453628	55465828	Stat3	Klf4	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_01289	2018	30146478	Combinatorial CRISPR/Cas9 Approach to Elucidate a Far-Upstream Enhancer Complex for Tissue-Specific Sox9 Expression	Mus musculus	mm10	chr11	111838889	111839334	Stat3	Sox9	Enhancer	Active	Normal	NA	NA	NA	cartilage tissue	UBERON:0002418	primary chondrocytes	NA	chondrocyte	CL:0000138	Promoter-enhancer complex capture; TF identification; epigenetic silencing; enhancer-deletion mouse validation	dCas9 promoter-complex capture with sequencing; mass spectrometry; ChIP-seq	SIN3A-dCas9 enhancer silencing; CRISPR enhancer-deletion mice; 3C; ChIP-qPCR; RT-qPCR; skeletal phenotyping; CRISPR-Cas9
E_01290	2024	38528203	Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development	Mus musculus	mm10	chr1	92390990	92393985	Dlx5	Prox1	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	Mouse embryonic GE progenitor	NA	neural progenitor cell	CL:0011020	Enhancer activity assay; TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation	ChIP-seq	Transgenic reporter assay; ChIP; Site-directed/motif mutagenesis; In vivo phenotyping
E_01291	2024	38528203	Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development	Mus musculus	mm10	chr1	92390990	92393985	Lhx6	Prox1	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	Mouse embryonic GE progenitor	NA	neural progenitor cell	CL:0011020	Enhancer activity assay; TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation	ChIP-seq	Transgenic reporter assay; ChIP; Site-directed/motif mutagenesis; In vivo phenotyping
E_01292	2024	38528203	Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development	Mus musculus	mm10	chr1	92390990	92393985	Meis2	Prox1	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	Mouse embryonic GE progenitor	NA	neural progenitor cell	CL:0011020	Enhancer activity assay; TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation	ChIP-seq	Transgenic reporter assay; ChIP; Site-directed/motif mutagenesis; In vivo phenotyping
E_01293	2024	38528203	Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development	Mus musculus	mm10	chr12	39300010	39302995	Dlx5	Prkd1	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	Mouse embryonic GE progenitor	NA	neural progenitor cell	CL:0011020	Enhancer activity assay; TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation	ChIP-seq	Transgenic reporter assay; ChIP; Site-directed/motif mutagenesis; In vivo phenotyping
E_01294	2024	38528203	Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development	Mus musculus	mm10	chr12	39300010	39302995	Lhx6	Prkd1	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	Mouse embryonic GE progenitor	NA	neural progenitor cell	CL:0011020	Enhancer activity assay; TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation	ChIP-seq	Transgenic reporter assay; ChIP; Site-directed/motif mutagenesis; In vivo phenotyping
E_01295	2024	38528203	Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development	Mus musculus	mm10	chr12	39300010	39302995	Meis2	Prkd1	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	Mouse embryonic GE progenitor	NA	neural progenitor cell	CL:0011020	Enhancer activity assay; TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation	ChIP-seq	Transgenic reporter assay; ChIP; Site-directed/motif mutagenesis; In vivo phenotyping
E_01296	2017	29149598	Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene	Homo sapiens	hg19	chr12	47732000	47733500	FOSL2	AMIGO2	Enhancer	Active	Disease	cutaneous melanoma	MONDO:0005012	DOID:8923	zone of skin	UBERON:0000014	SK-MEL-147	CVCL_3876	melanoma cell	NA	Enhancer activity assay; Functional perturbation assay	ChIP-seq; ATAC-seq; RNA-seq	Luciferase reporter assay; CRISPR knockout; RT-qPCR
E_01297	2014	24157522	A novel regulatory element for Shh expression in the lung and gut of mouse embryos	Mus musculus	mm10	chr5	28476034	28479024	Rbfox3	Shh	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	Colon Adenocarcinoma Cell Lines	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C
E_01298	2014	24157522	A novel regulatory element for Shh expression in the lung and gut of mouse embryos	Mus musculus	mm10	chr5	28476034	28479024	Socs1	Shh	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	Colon Adenocarcinoma Cell Lines	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C
E_01299	2014	24157522	A novel regulatory element for Shh expression in the lung and gut of mouse embryos	Mus musculus	mm10	chr5	28495262	28497421	Rbfox3	Shh	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	Colon Adenocarcinoma Cell Lines	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C
E_01300	2014	24157522	A novel regulatory element for Shh expression in the lung and gut of mouse embryos	Mus musculus	mm10	chr5	28495262	28497421	Socs1	Shh	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	Colon Adenocarcinoma Cell Lines	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C
E_01301	2014	24157522	A novel regulatory element for Shh expression in the lung and gut of mouse embryos	Mus musculus	mm10	chr5	28500370	28502363	Rbfox3	Shh	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	Colon Adenocarcinoma Cell Lines	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C
E_01302	2014	24157522	A novel regulatory element for Shh expression in the lung and gut of mouse embryos	Mus musculus	mm10	chr5	28500370	28502363	Socs1	Shh	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	Colon Adenocarcinoma Cell Lines	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C
E_01303	2014	24157522	A novel regulatory element for Shh expression in the lung and gut of mouse embryos	Mus musculus	mm10	chr5	28561915	28564905	Rbfox3	Shh	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	Colon Adenocarcinoma Cell Lines	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C
E_01304	2014	24157522	A novel regulatory element for Shh expression in the lung and gut of mouse embryos	Mus musculus	mm10	chr5	28561915	28564905	Socs1	Shh	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	Colon Adenocarcinoma Cell Lines	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C
E_01305	2018	30146478	Combinatorial CRISPR/Cas9 Approach to Elucidate a Far-Upstream Enhancer Complex for Tissue-Specific Sox9 Expression	Mus musculus	mm10	chr11	111838889	111839334	Stat3	Sox9	Enhancer	Active	Normal	NA	NA	NA	cartilage tissue	UBERON:0002418	ATDC-5	CVCL_3894	chondrocyte	CL:0000138	Promoter-enhancer complex capture; TF identification; epigenetic silencing; enhancer-deletion mouse validation	dCas9 promoter-complex capture with sequencing; mass spectrometry; ChIP-seq	SIN3A-dCas9 enhancer silencing; CRISPR enhancer-deletion mice; 3C; ChIP-qPCR; RT-qPCR; skeletal phenotyping; CRISPR-Cas9
E_01306	2017	29149598	Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene	Homo sapiens	hg19	chr12	47483742	47503742	FOSL2	AMIGO2	Enhancer	Active	Disease	metastatic melanoma	MONDO:0005191	DOID:4358	skin	UBERON:0002097	SK-MEL-147	CVCL_3876	melanoma cell line; primary/short-term melanoma culture	NA	super-enhancer constituent validation and endogenous constituent deletion	RNA-seq; BRD2 ChIP-seq; BRD4 ChIP-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; ATAC-seq; FOSL2/TEAD4 ChIP-seq; ROSE super-enhancer calling	E1-E5 and E3A-C luciferase assays; CRISPR-Cas9 deletion of E2-E3 and E4-E5; E3A FOSL2/TEAD motif deletion; FOSL2 or TEAD4/TEAD1 perturbation; qRT-PCR; immunoblot; proliferation/apoptosis assays
E_01307	2017	29149598	Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene	Homo sapiens	hg19	chr12	47483742	47503742	FOSL2	AMIGO2	Enhancer	Active	Disease	metastatic melanoma	MONDO:0005191	DOID:4358	skin	UBERON:0002097	additional melanoma cell lines	NA	melanoma cell line; primary/short-term melanoma culture	NA	super-enhancer constituent validation and endogenous constituent deletion	RNA-seq; BRD2 ChIP-seq; BRD4 ChIP-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; ATAC-seq; FOSL2/TEAD4 ChIP-seq; ROSE super-enhancer calling	E1-E5 and E3A-C luciferase assays; CRISPR-Cas9 deletion of E2-E3 and E4-E5; E3A FOSL2/TEAD motif deletion; FOSL2 or TEAD4/TEAD1 perturbation; qRT-PCR; immunoblot; proliferation/apoptosis assays
E_01308	2017	29149598	Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene	Homo sapiens	hg19	chr12	47483742	47503742	FOSL2	AMIGO2	Enhancer	Active	Disease	metastatic melanoma	MONDO:0005191	DOID:4358	skin	UBERON:0002097	short-term melanoma cultures	NA	melanoma cell line; primary/short-term melanoma culture	NA	super-enhancer constituent validation and endogenous constituent deletion	RNA-seq; BRD2 ChIP-seq; BRD4 ChIP-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; ATAC-seq; FOSL2/TEAD4 ChIP-seq; ROSE super-enhancer calling	E1-E5 and E3A-C luciferase assays; CRISPR-Cas9 deletion of E2-E3 and E4-E5; E3A FOSL2/TEAD motif deletion; FOSL2 or TEAD4/TEAD1 perturbation; qRT-PCR; immunoblot; proliferation/apoptosis assays
E_01309	2017	29149598	Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene	Homo sapiens	hg19	chr12	47483742	47503742	FOSL2	AMIGO2	Enhancer	Active	Disease	metastatic melanoma	MONDO:0005191	DOID:4358	skin	UBERON:0002097	normal human melanocyte controls	NA	melanoma cell line; primary/short-term melanoma culture	NA	super-enhancer constituent validation and endogenous constituent deletion	RNA-seq; BRD2 ChIP-seq; BRD4 ChIP-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; ATAC-seq; FOSL2/TEAD4 ChIP-seq; ROSE super-enhancer calling	E1-E5 and E3A-C luciferase assays; CRISPR-Cas9 deletion of E2-E3 and E4-E5; E3A FOSL2/TEAD motif deletion; FOSL2 or TEAD4/TEAD1 perturbation; qRT-PCR; immunoblot; proliferation/apoptosis assays
E_01310	2017	29149598	Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene	Homo sapiens	hg19	chr12	47483742	47503742	TEAD4	AMIGO2	Enhancer	Active	Disease	metastatic melanoma	MONDO:0005191	DOID:4358	skin	UBERON:0002097	SK-MEL-147	CVCL_3876	melanoma cell line; primary/short-term melanoma culture	NA	super-enhancer constituent validation and endogenous constituent deletion	RNA-seq; BRD2 ChIP-seq; BRD4 ChIP-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; ATAC-seq; FOSL2/TEAD4 ChIP-seq; ROSE super-enhancer calling	E1-E5 and E3A-C luciferase assays; CRISPR-Cas9 deletion of E2-E3 and E4-E5; E3A FOSL2/TEAD motif deletion; FOSL2 or TEAD4/TEAD1 perturbation; qRT-PCR; immunoblot; proliferation/apoptosis assays
E_01311	2017	29149598	Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene	Homo sapiens	hg19	chr12	47483742	47503742	TEAD4	AMIGO2	Enhancer	Active	Disease	metastatic melanoma	MONDO:0005191	DOID:4358	skin	UBERON:0002097	additional melanoma cell lines	NA	melanoma cell line; primary/short-term melanoma culture	NA	super-enhancer constituent validation and endogenous constituent deletion	RNA-seq; BRD2 ChIP-seq; BRD4 ChIP-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; ATAC-seq; FOSL2/TEAD4 ChIP-seq; ROSE super-enhancer calling	E1-E5 and E3A-C luciferase assays; CRISPR-Cas9 deletion of E2-E3 and E4-E5; E3A FOSL2/TEAD motif deletion; FOSL2 or TEAD4/TEAD1 perturbation; qRT-PCR; immunoblot; proliferation/apoptosis assays
E_01312	2017	29149598	Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene	Homo sapiens	hg19	chr12	47483742	47503742	TEAD4	AMIGO2	Enhancer	Active	Disease	metastatic melanoma	MONDO:0005191	DOID:4358	skin	UBERON:0002097	short-term melanoma cultures	NA	melanoma cell line; primary/short-term melanoma culture	NA	super-enhancer constituent validation and endogenous constituent deletion	RNA-seq; BRD2 ChIP-seq; BRD4 ChIP-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; ATAC-seq; FOSL2/TEAD4 ChIP-seq; ROSE super-enhancer calling	E1-E5 and E3A-C luciferase assays; CRISPR-Cas9 deletion of E2-E3 and E4-E5; E3A FOSL2/TEAD motif deletion; FOSL2 or TEAD4/TEAD1 perturbation; qRT-PCR; immunoblot; proliferation/apoptosis assays
E_01313	2017	29149598	Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene	Homo sapiens	hg19	chr12	47483742	47503742	TEAD4	AMIGO2	Enhancer	Active	Disease	metastatic melanoma	MONDO:0005191	DOID:4358	skin	UBERON:0002097	normal human melanocyte controls	NA	melanoma cell line; primary/short-term melanoma culture	NA	super-enhancer constituent validation and endogenous constituent deletion	RNA-seq; BRD2 ChIP-seq; BRD4 ChIP-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; ATAC-seq; FOSL2/TEAD4 ChIP-seq; ROSE super-enhancer calling	E1-E5 and E3A-C luciferase assays; CRISPR-Cas9 deletion of E2-E3 and E4-E5; E3A FOSL2/TEAD motif deletion; FOSL2 or TEAD4/TEAD1 perturbation; qRT-PCR; immunoblot; proliferation/apoptosis assays
E_01314	2024	39606421	Single cell variant to enhancer to gene map for coronary artery disease	Homo sapiens	hg38	chr3	134460112	134466940	NA	AMOTL2	Enhancer	Active	Disease	coronary artery disorder	MONDO:0005010	DOID:3393	coronary artery	UBERON:0001621	Primary human coronary artery smooth muscle cells (HCASMC)	NA	smooth muscle cell of the coronary artery	CL:0002592	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Cell-type-specific enhancer validation	H3K27ac ChIP-seq; HiChIP-seq; snATAC-seq; Hi-C	CRISPRi (dCas9-KRAB; two independent enhancer-targeting sgRNAs); RT-PCR; CRISPRi
E_01315	2018	30146478	Combinatorial CRISPR/Cas9 Approach to Elucidate a Far-Upstream Enhancer Complex for Tissue-Specific Sox9 Expression	Mus musculus	mm10	chr11	111838889	111839334	Stat3	Sox9	Enhancer	Active	Normal	NA	NA	NA	cartilage tissue	UBERON:0002418	primary mouse costal chondrocytes	NA	chondrocyte	CL:0000138	Endogenous enhancer perturbation; Endogenous enhancer deletion; combinatorial enhancer perturbation; TF-binding/functional assay	ChIP-seq and chromatin-conformation data integration	CRISPR-Cas9 enhancer-deletion mouse/cell models; Luciferase reporter; ChIP-qPCR; qRT-PCR; histology; CRISPR-Cas9 endogenous deletion/editing
E_01316	2017	29149598	Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene	Homo sapiens	hg19	chr12	47471429	47487762	FOSL2	AMIGO2	Super-enhancer	Active	Disease	melanoma	MONDO:0005105	DOID:1909	skin	UBERON:0002097	SKmel147	NA	malignant cell	CL:0001064	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq; ATAC-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; Western blot
E_01317	2017	29149598	Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene	Homo sapiens	hg19	chr12	47471429	47487762	TEAD4	AMIGO2	Super-enhancer	Active	Disease	melanoma	MONDO:0005105	DOID:1909	skin	UBERON:0002097	SKmel147	NA	malignant cell	CL:0001064	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq; ATAC-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; Western blot
E_01318	2018	30590035	The TFAP2C-Regulated OCT4 Naive Enhancer Is Involved in Human Germline Formation	Homo sapiens	hg19	chr6	31139519	31140167	TFAP2C	POU5F1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Human Primordial Germ Cell	NA	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; ATAC-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01319	2018	30590035	The TFAP2C-Regulated OCT4 Naive Enhancer Is Involved in Human Germline Formation	Homo sapiens	hg19	chr6	31137056	31138028	TFAP2C	POU5F1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Human Primordial Germ Cell	NA	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; ATAC-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01320	2024	38528203	Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development	Mus musculus	mm10	chr13	53802995	53810985	Dlx5	Drd1	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	Mouse neuroblastoma cell	NA	mouse neuroblastoma cell	NA	Enhancer activity assay; TF binding assay	ChIP-seq	Luciferase reporter assay; Lineage tracing; In vivo CRISPR perturbation
E_01321	2024	38528203	Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development	Mus musculus	mm10	chr13	53802995	53810985	Meis2	Drd1	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	Mouse neuroblastoma cell	NA	mouse neuroblastoma cell	NA	Enhancer activity assay; TF binding assay	ChIP-seq	Luciferase reporter assay; Lineage tracing; In vivo CRISPR perturbation
E_01322	2024	38528203	Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development	Mus musculus	mm10	chr14	23090994	23098987	Dlx5	Zfp503	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	Mouse neuroblastoma cell	NA	mouse neuroblastoma cell	NA	Enhancer activity assay; TF binding assay	ChIP-seq	Luciferase reporter assay; Transgenic reporter assay; Lineage tracing; In vivo CRISPR perturbation
E_01323	2024	38528203	Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development	Mus musculus	mm10	chr14	23090994	23098987	Lhx6	Zfp503	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	Mouse neuroblastoma cell	NA	mouse neuroblastoma cell	NA	Enhancer activity assay; TF binding assay	ChIP-seq	Luciferase reporter assay; Transgenic reporter assay; Lineage tracing; In vivo CRISPR perturbation
E_01324	2024	38528203	Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development	Mus musculus	mm10	chr14	23090994	23098987	Meis2	Zfp503	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	Mouse neuroblastoma cell	NA	mouse neuroblastoma cell	NA	Enhancer activity assay; TF binding assay	ChIP-seq	Luciferase reporter assay; Transgenic reporter assay; Lineage tracing; In vivo CRISPR perturbation
E_01325	2018	30146478	Combinatorial CRISPR/Cas9 Approach to Elucidate a Far-Upstream Enhancer Complex for Tissue-Specific Sox9 Expression	Mus musculus	mm10	chr11	111838889	111839334	Stat3	Sox9	Enhancer	Active	Normal	NA	NA	NA	cartilage tissue	UBERON:0002418	chondrocytes/cartilage	NA	chondrocyte	CL:0000138	Endogenous enhancer perturbation; Critical far-upstream Sox9 cartilage cis-element; STAT3 identified as trans-acting factor	Promoter-enhancer complex NGS; mass spectrometry	dCas9-SIN3A epigenetic silencing; CRISPR/Cas9 enhancer-deletion mouse; reporter/RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_01326	2018	30146478	Combinatorial CRISPR/Cas9 Approach to Elucidate a Far-Upstream Enhancer Complex for Tissue-Specific Sox9 Expression	Mus musculus	mm10	chr11	111838889	111839334	NA	Sox9	Enhancer	Active	Normal	NA	NA	NA	cartilage tissue	UBERON:0002418	enhancer-deletion mouse	NA	chondrocyte	CL:0000138	Endogenous enhancer perturbation; Same defined cartilage enhancer retained as independent deletion-model evidence row	Promoter-enhancer complex NGS	CRISPR/Cas9 enhancer-deletion mouse; skeletal phenotyping; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_01327	2014	24157522	A novel regulatory element for Shh expression in the lung and gut of mouse embryos	Mus musculus	mm10	chr5	28820000	28821700	NA	Shh	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	Embryonic endodermal epithelial cells	NA	endodermal epithelial cell	NA	Enhancer activity assay; Chromatin interaction assay	NA	Transgenic reporter assay; Luciferase reporter assay; 3C assay
E_01328	2024	38849954	An oncogenic enhancer promotes melanoma progression via regulating ETV4 expression	Homo sapiens	hg38	chr17	59785798	59787315	STAT3	ETV4	Enhancer	Active	Disease	cutaneous melanoma	MONDO:0005012	DOID:8923	zone of skin	UBERON:0000014	A-375	CVCL_0132	melanoma cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; Hi-C; CUT&Tag	Luciferase reporter assay; CRISPR knockout, qRT-PCR; Western blot; CRISPR-Cas9; Reporter assay
E_01329	2017	27651453	Identification of a novel distal regulatory element of the human Neuroglobin gene by the chromosome conformation capture approach	Homo sapiens	hg19	chr14	77808992	77809573	GATA2	NGB	Enhancer	Active	Disease	neuroblastoma	MONDO:0005072	DOID:769	brain	UBERON:0000955	SH-SY5Y	CVCL_0019	neuroblastoma cell	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	ChIP-seq	3C-RT-qPCR; ChIP-qPCR; CRISPR knockout; Luciferase reporter assay
E_01330	2017	27651453	Identification of a novel distal regulatory element of the human Neuroglobin gene by the chromosome conformation capture approach	Homo sapiens	hg19	chr14	77635927	77639784	GATA2	NGB	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	NA	NA	SH-SY5Y	CVCL_0019	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RNAi/siRNA/shRNA
E_01331	2019	30872687	Differential transactivation of the upstream aggrecan enhancer regulated by PAX1/9 depends on SOX9-driven transactivation	Mus musculus	mm10	chr7	79042226	79044226	Pax1	Acan	Enhancer	Active	Normal	NA	NA	NA	intervertebral disk	UBERON:0001066	primary mouse annulus fibrosus cells / chondrocytes	NA	chondrocyte	CL:0000138	Enhancer activity assay; In vivo functional validation; TF-site functional dissection; Endogenous enhancer deletion	ChIP-seq data integration	Luciferase reporter assay; TF overexpression; motif mutagenesis; ChIP/EMSA; CRISPR-Cas9 deletion of a 695-bp region containing UE; qRT-PCR; In vivo phenotyping; Reporter assay
E_01332	2019	30872687	Differential transactivation of the upstream aggrecan enhancer regulated by PAX1/9 depends on SOX9-driven transactivation	Mus musculus	mm10	chr7	79042226	79044226	Pax9	Acan	Enhancer	Active	Normal	NA	NA	NA	intervertebral disk	UBERON:0001066	primary mouse annulus fibrosus cells / chondrocytes	NA	chondrocyte	CL:0000138	Enhancer activity assay; In vivo functional validation; TF-site functional dissection; Endogenous enhancer deletion	ChIP-seq data integration	Luciferase reporter assay; TF overexpression; motif mutagenesis; ChIP/EMSA; CRISPR-Cas9 deletion of a 695-bp region containing UE; qRT-PCR; In vivo phenotyping; Reporter assay
E_01333	2019	30872687	Differential transactivation of the upstream aggrecan enhancer regulated by PAX1/9 depends on SOX9-driven transactivation	Mus musculus	mm10	chr7	79042226	79044226	Sox9	Acan	Enhancer	Active	Normal	NA	NA	NA	intervertebral disk	UBERON:0001066	primary mouse annulus fibrosus cells / chondrocytes	NA	chondrocyte	CL:0000138	Enhancer activity assay; In vivo functional validation; TF-site functional dissection; Endogenous enhancer deletion	ChIP-seq data integration	Luciferase reporter assay; TF overexpression; motif mutagenesis; ChIP/EMSA; CRISPR-Cas9 deletion of a 695-bp region containing UE; qRT-PCR; In vivo phenotyping; Reporter assay
E_01334	2018	30537984	Enhancers in the Peril lincRNA locus regulate distant but not local genes	Mus musculus	mm10	chr11	3650000	3652019	NA	Morc2a	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation	MPRA; RNA-seq; Hi-C	qRT-PCR, and ChIP-qPCR; Mouse genetic deletion/knock-in; In vivo phenotyping; Reporter assay
E_01335	2018	30537984	Enhancers in the Peril lincRNA locus regulate distant but not local genes	Mus musculus	mm10	chr13	10543000	10544508	NA	Enc1	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation	MPRA; RNA-seq; Hi-C	qRT-PCR, and ChIP-qPCR; Mouse genetic deletion/knock-in; In vivo phenotyping; Reporter assay
E_01336	2018	30537984	Enhancers in the Peril lincRNA locus regulate distant but not local genes	Mus musculus	mm10	chr17	29065000	29066050	NA	Cdkn1a	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation	MPRA; RNA-seq; Hi-C	qRT-PCR, and ChIP-qPCR; Mouse genetic deletion/knock-in; In vivo phenotyping; Reporter assay
E_01337	2025	39870618	Genetic coupling of enhancer activity and connectivity in gene expression control	Homo sapiens	hg38	chr10	30091300	30093300	NA	SVIL	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary CD14+ monocytes	NA	CD14-positive monocyte	CL:0001054	Enhancer activity assay; Chromatin interaction assay	Capture Hi-C; ATAC-seq; RNA-seq; Hi-C; eQTL-Capture Hi-C; eQTL analysis	qRT-PCR, and ChIP-qPCR; CRISPRi
E_01338	2025	39870618	Genetic coupling of enhancer activity and connectivity in gene expression control	Homo sapiens	hg38	chr14	90559777	90561777	NA	KCNK13	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary CD14+ monocytes	NA	CD14-positive monocyte	CL:0001054	Enhancer activity assay; Chromatin interaction assay	Capture Hi-C; ATAC-seq; RNA-seq; Hi-C; eQTL-Capture Hi-C; eQTL analysis	qRT-PCR, and ChIP-qPCR; CRISPRi
E_01339	2025	39870618	Genetic coupling of enhancer activity and connectivity in gene expression control	Homo sapiens	hg38	chr19	54550115	54552115	NA	TFPT	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary CD14+ monocytes	NA	CD14-positive monocyte	CL:0001054	Enhancer activity assay; Chromatin interaction assay	Capture Hi-C; ATAC-seq; RNA-seq; Hi-C; eQTL-Capture Hi-C; eQTL analysis	qRT-PCR, and ChIP-qPCR; CRISPRi
E_01340	2025	39870618	Genetic coupling of enhancer activity and connectivity in gene expression control	Homo sapiens	hg38	chr4	76816412	76818412	NA	NAAA	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary CD14+ monocytes	NA	CD14-positive monocyte	CL:0001054	Enhancer activity assay; Chromatin interaction assay	Capture Hi-C; ATAC-seq; RNA-seq; Hi-C; eQTL-Capture Hi-C; eQTL analysis	qRT-PCR, and ChIP-qPCR; CRISPRi
E_01341	2025	39870618	Genetic coupling of enhancer activity and connectivity in gene expression control	Homo sapiens	hg38	chr7	26134404	26136404	NA	NFE2L3	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary CD14+ monocytes	NA	CD14-positive monocyte	CL:0001054	Enhancer activity assay; Chromatin interaction assay	Capture Hi-C; ATAC-seq; RNA-seq; Hi-C; eQTL-Capture Hi-C; eQTL analysis	qRT-PCR, and ChIP-qPCR; CRISPRi
E_01342	2024	39271656	Exploring the transcriptional cooperation between RUNX2 and its associated elncRNA RAIN	Homo sapiens	hg38	chr10	3773382	3787964	RUNX2	KLF6	Enhancer	Active	Disease	thyroid gland carcinoma	MONDO:0015075	DOID:3963	thyroid gland	UBERON:0002046	MDA-T41	CVCL_W914	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; In vivo functional validation	ChIRP-seq; RNA-seq; ChIP-seq	CRISPRi; RT-qPCR; RIP assay; Western blot; In vivo phenotyping
E_01343	2022	35676472	The renal lineage factor PAX8 controls oncogenic signalling in kidney cancer	Homo sapiens	hg38	chr11	69419632	69420080	PAX8	CCND1	Enhancer	Active	Disease	renal cell carcinoma	MONDO:0005086	DOID:4450	kidney	UBERON:0002113	786-O	CVCL_1051	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis	ChIP-seq; ATAC-seq; RNA-seq	CRISPRi, Luciferase reporter assay; ChIP-qPCR
E_01344	2022	35766871	A risk variant for Barrett's esophagus and esophageal adenocarcinoma at chr8p23.1 affects enhancer activity and implicates multiple gene targets	Homo sapiens	hg19	chr8	11446898	11447336	KLF1	CTSB	Enhancer	Active	Disease	esophageal adenocarcinoma	MONDO:0005028	DOID:4914	esophagus	UBERON:0001043	OE19	CVCL_1622	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis	RNA-seq; ChIP-seq; eQTL analysis; GWAS	Luciferase reporter assay, CRISPR knockout; RT-qPCR; Luciferase reporter assay; Allele-specific reporter assay; Reporter assay
E_01345	2022	35766871	A risk variant for Barrett's esophagus and esophageal adenocarcinoma at chr8p23.1 affects enhancer activity and implicates multiple gene targets	Homo sapiens	hg19	chr8	11446898	11447336	KLF14	CTSB	Enhancer	Active	Disease	esophageal adenocarcinoma	MONDO:0005028	DOID:4914	esophagus	UBERON:0001043	OE19	CVCL_1622	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis	RNA-seq; ChIP-seq; eQTL analysis; GWAS	Luciferase reporter assay, CRISPR knockout; RT-qPCR; Luciferase reporter assay; Allele-specific reporter assay; Reporter assay
E_01346	2022	35766871	A risk variant for Barrett's esophagus and esophageal adenocarcinoma at chr8p23.1 affects enhancer activity and implicates multiple gene targets	Homo sapiens	hg19	chr8	11446898	11447336	KLF16	CTSB	Enhancer	Active	Disease	esophageal adenocarcinoma	MONDO:0005028	DOID:4914	esophagus	UBERON:0001043	OE19	CVCL_1622	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis	RNA-seq; ChIP-seq; eQTL analysis; GWAS	Luciferase reporter assay, CRISPR knockout; RT-qPCR; Luciferase reporter assay; Allele-specific reporter assay; Reporter assay
E_01347	2022	35766871	A risk variant for Barrett's esophagus and esophageal adenocarcinoma at chr8p23.1 affects enhancer activity and implicates multiple gene targets	Homo sapiens	hg19	chr8	11446898	11447336	KLF3	CTSB	Enhancer	Active	Disease	esophageal adenocarcinoma	MONDO:0005028	DOID:4914	esophagus	UBERON:0001043	OE19	CVCL_1622	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis	RNA-seq; ChIP-seq; eQTL analysis; GWAS	Luciferase reporter assay, CRISPR knockout; RT-qPCR; Luciferase reporter assay; Allele-specific reporter assay; Reporter assay
E_01348	2022	35766871	A risk variant for Barrett's esophagus and esophageal adenocarcinoma at chr8p23.1 affects enhancer activity and implicates multiple gene targets	Homo sapiens	hg19	chr8	11446898	11447336	KLF4	CTSB	Enhancer	Active	Disease	esophageal adenocarcinoma	MONDO:0005028	DOID:4914	esophagus	UBERON:0001043	OE19	CVCL_1622	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis	RNA-seq; ChIP-seq; eQTL analysis; GWAS	Luciferase reporter assay, CRISPR knockout; RT-qPCR; Luciferase reporter assay; Allele-specific reporter assay; Reporter assay
E_01349	2022	35766871	A risk variant for Barrett's esophagus and esophageal adenocarcinoma at chr8p23.1 affects enhancer activity and implicates multiple gene targets	Homo sapiens	hg19	chr8	11446898	11447336	KLF9	CTSB	Enhancer	Active	Disease	esophageal adenocarcinoma	MONDO:0005028	DOID:4914	esophagus	UBERON:0001043	OE19	CVCL_1622	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis	RNA-seq; ChIP-seq; eQTL analysis; GWAS	Luciferase reporter assay, CRISPR knockout; RT-qPCR; Luciferase reporter assay; Allele-specific reporter assay; Reporter assay
E_01350	2022	35766871	A risk variant for Barrett's esophagus and esophageal adenocarcinoma at chr8p23.1 affects enhancer activity and implicates multiple gene targets	Homo sapiens	hg19	chr8	11446898	11447336	RUNX1	CTSB	Enhancer	Active	Disease	esophageal adenocarcinoma	MONDO:0005028	DOID:4914	esophagus	UBERON:0001043	OE19	CVCL_1622	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis	RNA-seq; ChIP-seq; eQTL analysis; GWAS	Luciferase reporter assay, CRISPR knockout; RT-qPCR; Luciferase reporter assay; Allele-specific reporter assay; Reporter assay
E_01351	2022	35766871	A risk variant for Barrett's esophagus and esophageal adenocarcinoma at chr8p23.1 affects enhancer activity and implicates multiple gene targets	Homo sapiens	hg19	chr8	11446898	11447336	RUNX2	CTSB	Enhancer	Active	Disease	esophageal adenocarcinoma	MONDO:0005028	DOID:4914	esophagus	UBERON:0001043	OE19	CVCL_1622	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis	RNA-seq; ChIP-seq; eQTL analysis; GWAS	Luciferase reporter assay, CRISPR knockout; RT-qPCR; Luciferase reporter assay; Allele-specific reporter assay; Reporter assay
E_01352	2022	35766871	A risk variant for Barrett's esophagus and esophageal adenocarcinoma at chr8p23.1 affects enhancer activity and implicates multiple gene targets	Homo sapiens	hg19	chr8	11446898	11447336	ZEB1	CTSB	Enhancer	Active	Disease	esophageal adenocarcinoma	MONDO:0005028	DOID:4914	esophagus	UBERON:0001043	OE19	CVCL_1622	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis	RNA-seq; ChIP-seq; eQTL analysis; GWAS	Luciferase reporter assay, CRISPR knockout; RT-qPCR; Luciferase reporter assay; Allele-specific reporter assay; Reporter assay
E_01353	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60722300	60722700	GATA1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	hematopoietic system	UBERON:0002390	HUDEP-2	CVCL_VI06	erythroid progenitor cell	CL:0000038	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation	ChIP-seq; RNA-seq; ATAC-seq	Luciferase reporter assay, CRISPR knockout; ChIP-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_01354	2024	39271656	Exploring the transcriptional cooperation between RUNX2 and its associated elncRNA RAIN	Homo sapiens	hg38	chr6	45407433	45444666	RUNX2	RUNX2	Enhancer	Active	Disease	thyroid gland carcinoma	MONDO:0015075	DOID:3963	thyroid gland	UBERON:0002046	MDA-T41	CVCL_W914	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; In vivo functional validation	ChIP-seq; RNA-seq	ChIP-qPCR, qRT-PCR; Western blot, CRISPR knockout, CRISPRi; In vivo phenotyping
E_01355	2024	39271656	Exploring the transcriptional cooperation between RUNX2 and its associated elncRNA RAIN	Homo sapiens	hg38	chr7	13905623	13926156	RUNX2	ETV1	Enhancer	Active	Disease	thyroid gland carcinoma	MONDO:0015075	DOID:3963	thyroid gland	UBERON:0002046	MDA-T41	CVCL_W914	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; In vivo functional validation	ChIRP-seq; RNA-seq; ChIP-seq	CRISPRi; RT-qPCR; RIP assay; Western blot; In vivo phenotyping
E_01356	2024	39271656	Exploring the transcriptional cooperation between RUNX2 and its associated elncRNA RAIN	Homo sapiens	hg38	chr1	218337520	218379240	RUNX2	TGFB2	Enhancer	Active	Disease	thyroid gland carcinoma	MONDO:0015075	DOID:3963	thyroid gland	UBERON:0002046	MDA-T41	CVCL_W914	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin interaction assay; In vivo functional validation	ChIRP-seq; RNA-seq; ChIP-seq	RT-qPCR; RIP assay; Western blot; In vivo phenotyping
E_01357	2024	39271656	Exploring the transcriptional cooperation between RUNX2 and its associated elncRNA RAIN	Homo sapiens	hg38	chr5	151674321	151709808	RUNX2	SPARC	Enhancer	Active	Disease	thyroid gland carcinoma	MONDO:0015075	DOID:3963	thyroid gland	UBERON:0002046	MDA-T41	CVCL_W914	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin interaction assay; In vivo functional validation	ChIRP-seq; RNA-seq; ChIP-seq	RT-qPCR; RIP assay; Western blot; In vivo phenotyping
E_01358	2018	30537984	Enhancers in the Peril lincRNA locus regulate distant but not local genes	Mus musculus	mm10	chr3	34765000	34767361	NA	Exosc9	Enhancer	Active	Normal	NA	NA	NA	embryonic stem-cell culture / multiple mouse tissues	NA	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	MPRA enhancer discovery; endogenous deletion; long-range target validation	MPRA; RNA-seq; Hi-C	Enhancer deletion; qRT-PCR; RNA polymerase II ChIP-qPCR; Reporter assay
E_01359	2022	35676472	The renal lineage factor PAX8 controls oncogenic signalling in kidney cancer	Homo sapiens	hg38	chr11	69419632	69420080	PAX8	CCND1	Enhancer	Active	Disease	osteosarcoma	MONDO:0009807	DOID:3347	bone element	UBERON:0001474	OS-LM1	NA	osteosarcoma cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; ATAC-seq; RNA-seq	Luciferase reporter assay; CRISPRi; ChIP-qPCR; RT-qPCR; EMSA
E_01360	2022	35676472	The renal lineage factor PAX8 controls oncogenic signalling in kidney cancer	Homo sapiens	hg19	chr8	128132902	128133724	HNF1B	MYC	Enhancer	Active	Disease	renal cell carcinoma	MONDO:0005086	DOID:4450	kidney	UBERON:0002113	Human renal cell carcinoma cell	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Disease-variant functional analysis	ChIP-seq; ATAC-seq; RNA-seq	CRISPRi; ChIP-qPCR; RT-qPCR
E_01361	2022	35676472	The renal lineage factor PAX8 controls oncogenic signalling in kidney cancer	Homo sapiens	hg19	chr8	128526339	128526710	HNF1B	MYC	Enhancer	Active	Disease	renal cell carcinoma	MONDO:0005086	DOID:4450	kidney	UBERON:0002113	Human renal cell carcinoma cell	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Disease-variant functional analysis	ChIP-seq; ATAC-seq; RNA-seq	CRISPRi; ChIP-qPCR; RT-qPCR
E_01362	2022	35676472	The renal lineage factor PAX8 controls oncogenic signalling in kidney cancer	Homo sapiens	hg38	chr11	69419632	69420080	EPAS1	MYEOV	Enhancer	Active	Disease	renal cell carcinoma	MONDO:0005086	DOID:4450	kidney	UBERON:0002113	786-M1A	CVCL_VR30	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Disease-variant functional analysis	Pooled in vivo CRISPRi screen; ATAC-seq; ChIP-seq	CRISPRi; RT-qPCR; ChIP-qPCR
E_01363	2022	35676472	The renal lineage factor PAX8 controls oncogenic signalling in kidney cancer	Homo sapiens	hg38	chr11	69419632	69420080	PAX8	MYEOV	Enhancer	Active	Disease	renal cell carcinoma	MONDO:0005086	DOID:4450	kidney	UBERON:0002113	786-M1A	CVCL_VR30	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Disease-variant functional analysis	Pooled in vivo CRISPRi screen; ATAC-seq; ChIP-seq	CRISPRi; RT-qPCR; ChIP-qPCR
E_01364	2024	39271656	Exploring the transcriptional cooperation between RUNX2 and its associated elncRNA RAIN	Homo sapiens	hg38	chr1	218337520	218379240	RUNX2	TGFB2	Enhancer	Active	Disease	thyroid gland carcinoma	MONDO:0015075	DOID:3963	thyroid gland	UBERON:0002046	TPC-1	CVCL_6298	malignant cell	CL:0001064	Functional perturbation assay; TF binding assay; In vivo functional validation; RNA-chromatin association assay	ChIRP-seq; RUNX2 ChIP-seq; RNA-seq; H3K4me1/H3K4me3/H3K27ac ChIP-seq	RUNX2 ChIP-qPCR; RIP-qPCR; RAIN CRISPRi; In vivo phenotyping
E_01365	2024	39271656	Exploring the transcriptional cooperation between RUNX2 and its associated elncRNA RAIN	Homo sapiens	hg38	chr5	151674321	151709808	RUNX2	SPARC	Enhancer	Active	Disease	thyroid gland carcinoma	MONDO:0015075	DOID:3963	thyroid gland	UBERON:0002046	TPC-1	CVCL_6298	malignant cell	CL:0001064	Functional perturbation assay; TF binding assay; In vivo functional validation; RNA-chromatin association assay	ChIRP-seq; RUNX2 ChIP-seq; RNA-seq; H3K4me1/H3K4me3/H3K27ac ChIP-seq	RUNX2 ChIP-qPCR; RIP-qPCR; RAIN CRISPRi; In vivo phenotyping
E_01366	2024	39271656	Exploring the transcriptional cooperation between RUNX2 and its associated elncRNA RAIN	Homo sapiens	hg38	chr10	3773382	3787964	NA	KLF6	Enhancer	Active	Disease	thyroid gland carcinoma	MONDO:0015075	DOID:3963	thyroid gland	UBERON:0002046	TPC-1	CVCL_6298	malignant cell	CL:0001064	Functional perturbation assay; In vivo functional validation; RNA-chromatin association assay	ChIRP-seq; RNA-seq; H3K4me1/H3K4me3/H3K27ac ChIP-seq	RAIN CRISPRi; In vivo phenotyping
E_01367	2019	30872687	Differential transactivation of the upstream aggrecan enhancer regulated by PAX1/9 depends on SOX9-driven transactivation	Mus musculus	mm10	chr7	94261534	94261892	Pax1	Acan	Enhancer	Active	Normal	NA	NA	NA	intervertebral disk	UBERON:0001066	Annulus fibrosus	NA	annulus fibrosus cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	RNA-seq	Luciferase reporter assay; CRISPR knockout; ChIP-qPCR; EMSA; RT-qPCR; co-immunoprecipitation; Transgenic reporter assay; CRISPR-Cas9
E_01368	2019	30872687	Differential transactivation of the upstream aggrecan enhancer regulated by PAX1/9 depends on SOX9-driven transactivation	Mus musculus	mm10	chr7	94290200	94290707	Pax1	Acan	Enhancer	Active	Normal	NA	NA	NA	intervertebral disk	UBERON:0001066	Annulus fibrosus	NA	annulus fibrosus cell	NA	Enhancer activity assay; TF binding assay	RNA-seq	Luciferase reporter assay; EMSA; RT-qPCR; CRISPR-Cas9
E_01369	2025	39870618	Genetic coupling of enhancer activity and connectivity in gene expression control	Homo sapiens	hg38	chr15	39315234	39315720	NA	THBS1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary CD14+ monocytes	NA	CD14-positive monocyte	CL:0001054	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	Capture Hi-C; ATAC-seq; RNA-seq; 4C-seq; Hi-C; eQTL-Capture Hi-C; eQTL analysis	CRISPRi; qRT-PCR
E_01370	2025	39870618	Genetic coupling of enhancer activity and connectivity in gene expression control	Homo sapiens	hg38	chr15	89000000	89002500	NA	ABHD2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary monocytes	NA	monocyte	CL:0000576	Enhancer activity assay; Chromatin interaction assay	ATAC-seq; Capture Hi-C; RNA-seq; Hi-C; eQTL-Capture Hi-C; eQTL analysis	CRISPRi, qRT-PCR; CRISPRi
E_01371	2025	39870618	Genetic coupling of enhancer activity and connectivity in gene expression control	Homo sapiens	hg38	chr4	76815143	76817143	NA	NAAA	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary CD14+ monocytes	NA	CD14-positive monocyte	CL:0001054	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	Capture Hi-C; ATAC-seq; RNA-seq; 4C-seq; Hi-C; eQTL-Capture Hi-C; eQTL analysis	CRISPRi
E_01372	2025	39870618	Genetic coupling of enhancer activity and connectivity in gene expression control	Homo sapiens	hg38	chr7	1209755	1211755	NA	CHLSN	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary CD14+ monocytes	NA	CD14-positive monocyte	CL:0001054	Enhancer activity assay; Chromatin interaction assay	Capture Hi-C; ATAC-seq; RNA-seq; Hi-C; eQTL-Capture Hi-C; eQTL analysis	qRT-PCR; CRISPRi
E_01373	2018	30537984	Enhancers in the Peril lincRNA locus regulate distant but not local genes	Mus musculus	mm10	chr11	3650000	3652019	NA	NA	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; MPRA functional screening	MPRA; RNA-seq; Hi-C	Transient transfection; GFP minimal-promoter reporter readout; Mouse genetic deletion/knock-in; In vivo phenotyping; Reporter assay
E_01374	2024	39271656	Exploring the transcriptional cooperation between RUNX2 and its associated elncRNA RAIN	Homo sapiens	hg38	chr6	45407433	45444666	NA	RUNX2	Enhancer	Active	Disease	thyroid gland carcinoma	MONDO:0015075	DOID:3963	thyroid gland	UBERON:0002046	TPC-1	CVCL_6298	malignant cell	CL:0001064	Functional perturbation assay; In vivo functional validation; RNA-chromatin association assay	ChIRP-seq; RNA-seq; H3K4me1/H3K4me3/H3K27ac ChIP-seq	qRT-PCR; RAIN CRISPRi; Western blot; In vivo phenotyping
E_01375	2022	35766871	A risk variant for Barrett's esophagus and esophageal adenocarcinoma at chr8p23.1 affects enhancer activity and implicates multiple gene targets	Homo sapiens	hg19	chr8	11446898	11447336	NA	BLK	Enhancer	Active	Disease	esophageal adenocarcinoma	MONDO:0005028	DOID:4914	esophagus	UBERON:0001043	OE19	CVCL_1622	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis	eQTL analysis; GWAS	Luciferase reporter assay; CRISPR-Cas9 enhancer deletion; PCR validation; RT-qPCR; Allele-specific reporter assay; Reporter assay
E_01376	2022	35766871	A risk variant for Barrett's esophagus and esophageal adenocarcinoma at chr8p23.1 affects enhancer activity and implicates multiple gene targets	Homo sapiens	hg19	chr8	11446898	11447336	NA	BLK	Enhancer	Active	Disease	esophageal adenocarcinoma	MONDO:0005028	DOID:4914	esophagus	UBERON:0001043	OE33	CVCL_0471	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis	eQTL analysis; GWAS	Luciferase reporter assay; CRISPR-Cas9 enhancer deletion; PCR validation; RT-qPCR; Allele-specific reporter assay; Reporter assay
E_01377	2022	35766871	A risk variant for Barrett's esophagus and esophageal adenocarcinoma at chr8p23.1 affects enhancer activity and implicates multiple gene targets	Homo sapiens	hg19	chr8	11446898	11447336	NA	NEIL2	Enhancer	Active	Disease	esophageal adenocarcinoma	MONDO:0005028	DOID:4914	esophagus	UBERON:0001043	OE19	CVCL_1622	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis	eQTL analysis; GWAS	Luciferase reporter assay; CRISPR-Cas9 enhancer deletion; PCR validation; RT-qPCR; Allele-specific reporter assay; Reporter assay
E_01378	2022	35766871	A risk variant for Barrett's esophagus and esophageal adenocarcinoma at chr8p23.1 affects enhancer activity and implicates multiple gene targets	Homo sapiens	hg19	chr8	11446898	11447336	NA	NEIL2	Enhancer	Active	Disease	esophageal adenocarcinoma	MONDO:0005028	DOID:4914	esophagus	UBERON:0001043	OE33	CVCL_0471	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis	eQTL analysis; GWAS	Luciferase reporter assay; CRISPR-Cas9 enhancer deletion; PCR validation; RT-qPCR; Allele-specific reporter assay; Reporter assay
E_01379	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr6	139766548	139767000	NA	CITED2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Functional validation	scRNA-seq; RNA-seq, Hi-C; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPRi, CRISPR KO; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_01380	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60722238	60722466	GATA1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	primary CD34+ hematopoietic progenitors differentiated toward erythroblasts	NA	erythroid progenitor cell	CL:0000038	Endogenous Cas9 saturating mutagenesis of BCL11A erythroid enhancer; TF-site functional mapping; therapeutic HbF validation	Pooled CRISPR-Cas9 in situ saturating mutagenesis with deep sequencing; chromatin accessibility/TF-occupancy integration	Targeted amplicon validation; primary CD34+ editing; BCL11A expression assays; HbF/F-cell flow cytometry; hemoglobin quantification
E_01381	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60722238	60722466	GATA1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	primary CD34+ hematopoietic progenitors differentiated toward erythroblasts	NA	erythroid progenitor cell	CL:0000038	Endogenous Cas9 saturating mutagenesis of BCL11A erythroid enhancer; TF-site functional mapping; therapeutic HbF validation	Pooled CRISPR-Cas9 in situ saturating mutagenesis with deep sequencing; chromatin accessibility/TF-occupancy integration	Targeted amplicon validation; primary CD34+ editing; BCL11A expression assays; HbF/F-cell flow cytometry; hemoglobin quantification
E_01382	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60725424	60725688	GATA1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	primary CD34+ hematopoietic progenitors differentiated toward erythroblasts	NA	erythroid progenitor cell	CL:0000038	Endogenous Cas9 saturating mutagenesis of BCL11A erythroid enhancer; TF-site functional mapping; therapeutic HbF validation	Pooled CRISPR-Cas9 in situ saturating mutagenesis with deep sequencing; chromatin accessibility/TF-occupancy integration	Targeted amplicon validation; primary CD34+ editing; BCL11A expression assays; HbF/F-cell flow cytometry; hemoglobin quantification
E_01383	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60725424	60725688	GATA1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	primary CD34+ hematopoietic progenitors differentiated toward erythroblasts	NA	erythroid progenitor cell	CL:0000038	Endogenous Cas9 saturating mutagenesis of BCL11A erythroid enhancer; TF-site functional mapping; therapeutic HbF validation	Pooled CRISPR-Cas9 in situ saturating mutagenesis with deep sequencing; chromatin accessibility/TF-occupancy integration	Targeted amplicon validation; primary CD34+ editing; BCL11A expression assays; HbF/F-cell flow cytometry; hemoglobin quantification
E_01384	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	primary CD34+ hematopoietic progenitors differentiated toward erythroblasts	NA	erythroid progenitor cell	CL:0000038	Endogenous Cas9 saturating mutagenesis of BCL11A erythroid enhancer; TF-site functional mapping; therapeutic HbF validation	Pooled CRISPR-Cas9 in situ saturating mutagenesis with deep sequencing; chromatin accessibility/TF-occupancy integration	Targeted amplicon validation; primary CD34+ editing; BCL11A expression assays; HbF/F-cell flow cytometry; hemoglobin quantification
E_01385	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	primary CD34+ hematopoietic progenitors differentiated toward erythroblasts	NA	erythroid progenitor cell	CL:0000038	Endogenous Cas9 saturating mutagenesis of BCL11A erythroid enhancer; TF-site functional mapping; therapeutic HbF validation	Pooled CRISPR-Cas9 in situ saturating mutagenesis with deep sequencing; chromatin accessibility/TF-occupancy integration	Targeted amplicon validation; primary CD34+ editing; BCL11A expression assays; HbF/F-cell flow cytometry; hemoglobin quantification
E_01386	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60722238	60722466	GATA1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	primary CD34+ hematopoietic progenitors differentiated toward erythroblasts	NA	erythroid progenitor cell	CL:0000038	Endogenous Cas9 saturating mutagenesis; enhancer functional mapping; TF-site mapping; therapeutic HbF validation	Pooled CRISPR-Cas9 in situ saturating mutagenesis with deep sequencing; chromatin accessibility/TF-occupancy integration	Targeted amplicon validation; primary CD34+ editing; BCL11A expression assay; HbF/F-cell flow cytometry; hemoglobin quantification
E_01387	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60722238	60722466	GATA1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	primary CD34+ hematopoietic progenitors differentiated toward erythroblasts	NA	erythroid progenitor cell	CL:0000038	Endogenous Cas9 saturating mutagenesis; enhancer functional mapping; TF-site mapping; therapeutic HbF validation	Pooled CRISPR-Cas9 in situ saturating mutagenesis with deep sequencing; chromatin accessibility/TF-occupancy integration	Targeted amplicon validation; primary CD34+ editing; BCL11A expression assay; HbF/F-cell flow cytometry; hemoglobin quantification
E_01388	2022	35676472	The renal lineage factor PAX8 controls oncogenic signalling in kidney cancer	Homo sapiens	hg19	chr8	128132902	128133724	HNF1B	MYC	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	Kidney proximal tubule epithelial cell	NA	kidney proximal tubule epithelial cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; ATAC-seq; RNA-seq	CRISPRi; ChIP-qPCR; RT-qPCR
E_01389	2022	35676472	The renal lineage factor PAX8 controls oncogenic signalling in kidney cancer	Homo sapiens	hg19	chr8	128526339	128526710	HNF1B	MYC	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	Kidney proximal tubule epithelial cell	NA	kidney proximal tubule epithelial cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; ATAC-seq; RNA-seq	CRISPRi; ChIP-qPCR; RT-qPCR
E_01390	2015	25801169	Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers	Mus musculus	mm10	chr1	13041306	13127367	Nanog	Prdm14	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_01391	2015	25801169	Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers	Mus musculus	mm10	chr1	13041306	13127367	Pou5f1	Prdm14	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_01392	2015	25801169	Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers	Mus musculus	mm10	chr1	13041306	13127367	Sox2	Prdm14	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_01393	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr18	9876906	9877723	NA	RAB31	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	T cell leukemia cell	NA	T cell	CL:0000084	Disease-variant functional analysis; Endogenous enhancer perturbation; Functional validation	scRNA-seq; ChIP-seq; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPRi; CRISPR-Cas9 endogenous deletion/editing
E_01394	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60722238	60722466	GATA1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	HUDEP-2/human erythroid cells	NA	erythroid progenitor cell	CL:0000038	Endogenous Cas9 saturating mutagenesis of BCL11A erythroid enhancer; TF-site functional mapping; therapeutic HbF validation	Pooled CRISPR-Cas9 in situ saturating mutagenesis with deep sequencing; chromatin accessibility/TF-occupancy integration	Targeted amplicon validation; primary CD34+ editing; BCL11A expression assays; HbF/F-cell flow cytometry; hemoglobin quantification
E_01395	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60722238	60722466	GATA1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	HUDEP-2/human erythroid cells	NA	erythroid progenitor cell	CL:0000038	Endogenous Cas9 saturating mutagenesis of BCL11A erythroid enhancer; TF-site functional mapping; therapeutic HbF validation	Pooled CRISPR-Cas9 in situ saturating mutagenesis with deep sequencing; chromatin accessibility/TF-occupancy integration	Targeted amplicon validation; primary CD34+ editing; BCL11A expression assays; HbF/F-cell flow cytometry; hemoglobin quantification
E_01396	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60725424	60725688	GATA1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	HUDEP-2/human erythroid cells	NA	erythroid progenitor cell	CL:0000038	Endogenous Cas9 saturating mutagenesis of BCL11A erythroid enhancer; TF-site functional mapping; therapeutic HbF validation	Pooled CRISPR-Cas9 in situ saturating mutagenesis with deep sequencing; chromatin accessibility/TF-occupancy integration	Targeted amplicon validation; primary CD34+ editing; BCL11A expression assays; HbF/F-cell flow cytometry; hemoglobin quantification
E_01397	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60725424	60725688	GATA1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	HUDEP-2/human erythroid cells	NA	erythroid progenitor cell	CL:0000038	Endogenous Cas9 saturating mutagenesis of BCL11A erythroid enhancer; TF-site functional mapping; therapeutic HbF validation	Pooled CRISPR-Cas9 in situ saturating mutagenesis with deep sequencing; chromatin accessibility/TF-occupancy integration	Targeted amplicon validation; primary CD34+ editing; BCL11A expression assays; HbF/F-cell flow cytometry; hemoglobin quantification
E_01398	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	HUDEP-2/human erythroid cells	NA	erythroid progenitor cell	CL:0000038	Endogenous Cas9 saturating mutagenesis of BCL11A erythroid enhancer; TF-site functional mapping; therapeutic HbF validation	Pooled CRISPR-Cas9 in situ saturating mutagenesis with deep sequencing; chromatin accessibility/TF-occupancy integration	Targeted amplicon validation; primary CD34+ editing; BCL11A expression assays; HbF/F-cell flow cytometry; hemoglobin quantification
E_01399	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	HUDEP-2/human erythroid cells	NA	erythroid progenitor cell	CL:0000038	Endogenous Cas9 saturating mutagenesis of BCL11A erythroid enhancer; TF-site functional mapping; therapeutic HbF validation	Pooled CRISPR-Cas9 in situ saturating mutagenesis with deep sequencing; chromatin accessibility/TF-occupancy integration	Targeted amplicon validation; primary CD34+ editing; BCL11A expression assays; HbF/F-cell flow cytometry; hemoglobin quantification
E_01400	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60722238	60722466	GATA1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	Human erythroid cells	NA	erythroid progenitor cell	CL:0000038	Endogenous Cas9 saturating mutagenesis; enhancer functional mapping; TF-site mapping; therapeutic HbF validation	Pooled CRISPR-Cas9 in situ saturating mutagenesis with deep sequencing; chromatin accessibility/TF-occupancy integration	Targeted amplicon validation; primary CD34+ editing; BCL11A expression assay; HbF/F-cell flow cytometry; hemoglobin quantification
E_01401	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60722238	60722466	GATA1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	Human erythroid cells	NA	erythroid progenitor cell	CL:0000038	Endogenous Cas9 saturating mutagenesis; enhancer functional mapping; TF-site mapping; therapeutic HbF validation	Pooled CRISPR-Cas9 in situ saturating mutagenesis with deep sequencing; chromatin accessibility/TF-occupancy integration	Targeted amplicon validation; primary CD34+ editing; BCL11A expression assay; HbF/F-cell flow cytometry; hemoglobin quantification
E_01402	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60722238	60722466	GATA1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	Human erythroid cells and primary CD34+ haematopoietic progenitors differentiated toward erythroblasts	NA	erythroid progenitor cell	CL:0000038	Endogenous enhancer perturbation; Endogenous saturation mutagenesis; enhancer functional mapping; therapeutic perturbation validation	Pooled CRISPR-Cas9 in situ saturating mutagenesis with deep sequencing; chromatin-accessibility/TF-occupancy data integration	Targeted amplicon validation; primary CD34+ editing; BCL11A expression assay; HbF/F-cell flow cytometry; haemoglobin quantification; CRISPR-Cas9 endogenous deletion/editing
E_01403	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60722238	60722466	GATA1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	Human erythroid cells and primary CD34+ haematopoietic progenitors differentiated toward erythroblasts	NA	erythroid progenitor cell	CL:0000038	Endogenous enhancer perturbation; Endogenous saturation mutagenesis; enhancer functional mapping; therapeutic perturbation validation	Pooled CRISPR-Cas9 in situ saturating mutagenesis with deep sequencing; chromatin-accessibility/TF-occupancy data integration	Targeted amplicon validation; primary CD34+ editing; BCL11A expression assay; HbF/F-cell flow cytometry; haemoglobin quantification; CRISPR-Cas9 endogenous deletion/editing
E_01404	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60725424	60725688	GATA1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	Human erythroid cells and primary CD34+ haematopoietic progenitors differentiated toward erythroblasts	NA	erythroid progenitor cell	CL:0000038	Endogenous enhancer perturbation; Endogenous saturation mutagenesis; enhancer functional mapping; therapeutic perturbation validation	Pooled CRISPR-Cas9 in situ saturating mutagenesis with deep sequencing; chromatin-accessibility/TF-occupancy data integration	Targeted amplicon validation; primary CD34+ editing; BCL11A expression assay; HbF/F-cell flow cytometry; haemoglobin quantification; CRISPR-Cas9 endogenous deletion/editing
E_01405	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60725424	60725688	GATA1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	Human erythroid cells and primary CD34+ haematopoietic progenitors differentiated toward erythroblasts	NA	erythroid progenitor cell	CL:0000038	Endogenous enhancer perturbation; Endogenous saturation mutagenesis; enhancer functional mapping; therapeutic perturbation validation	Pooled CRISPR-Cas9 in situ saturating mutagenesis with deep sequencing; chromatin-accessibility/TF-occupancy data integration	Targeted amplicon validation; primary CD34+ editing; BCL11A expression assay; HbF/F-cell flow cytometry; haemoglobin quantification; CRISPR-Cas9 endogenous deletion/editing
E_01406	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	bone marrow	UBERON:0002371	Human erythroid cells and primary CD34+ haematopoietic progenitors differentiated toward erythroblasts	NA	erythroid progenitor cell	CL:0000038	Endogenous enhancer perturbation; Endogenous saturation mutagenesis; enhancer functional mapping; therapeutic perturbation validation	Pooled CRISPR-Cas9 in situ saturating mutagenesis with deep sequencing; chromatin-accessibility/TF-occupancy data integration	Targeted amplicon validation; primary CD34+ editing; BCL11A expression assay; HbF/F-cell flow cytometry; haemoglobin quantification; CRISPR-Cas9 endogenous deletion/editing
E_01407	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60725424	60725688	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	Human erythroid cells and primary CD34+ haematopoietic progenitors differentiated toward erythroblasts	NA	erythroid progenitor cell	CL:0000038	Endogenous enhancer perturbation; Endogenous saturation mutagenesis; enhancer functional mapping; therapeutic perturbation validation	Pooled CRISPR-Cas9 in situ saturating mutagenesis with deep sequencing; chromatin-accessibility/TF-occupancy data integration	Targeted amplicon validation; primary CD34+ editing; BCL11A expression assay; HbF/F-cell flow cytometry; haemoglobin quantification; CRISPR-Cas9 endogenous deletion/editing
E_01408	2015	25801169	Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers	Mus musculus	mm10	chr17	35501272	35506872	NA	Pou5f1	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion
E_01409	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr19	12994425	12994945	NA	DNASE2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; High-throughput enhancer-gene mapping; endogenous CRISPRi validation	Multiplex CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	Singleton CRISPRi; RNA FlowFISH; reporter-supported enhancer validation; CRISPR-Cas9 endogenous deletion/editing
E_01410	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr4	56595855	56596581	NA	NMU	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Functional validation	scRNA-seq; RNA-seq; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPRi, CRISPR KO; RT-qPCR, FlowFISH; CRISPR-Cas9 endogenous deletion/editing
E_01411	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr4	56596632	56597095	NA	NMU	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Functional validation	scRNA-seq; RNA-seq; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPRi, CRISPR KO; RT-qPCR, FlowFISH; CRISPR-Cas9 endogenous deletion/editing
E_01412	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr4	56600029	56600394	NA	NMU	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Functional validation	scRNA-seq; RNA-seq; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPRi, CRISPR KO; RT-qPCR, FlowFISH; CRISPR-Cas9 endogenous deletion/editing
E_01413	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr1	71140581	71141097	NA	PTGER3	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Functional validation	scRNA-seq; RNA-seq; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPRi; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_01414	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr1	182308166	182308458	NA	GLUL	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Functional validation	scRNA-seq; RNA-seq; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPRi, CRISPR KO; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_01415	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr11	85862307	85862817	NA	PICALM	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping; singleton replication	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	Singleton CRISPRi plus bulk RNA-seq; CRISPR-Cas9 endogenous deletion/editing
E_01416	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr16	23833191	23833694	NA	PRKCB	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Functional validation	scRNA-seq; RNA-seq; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPRi; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_01417	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr2	8665160	8666881	NA	ID2	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01418	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr2	10437938	10438550	NA	HPCAL1	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01419	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr2	39369017	39369469	NA	SRSF7	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01420	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr2	127402697	127403360	NA	GYPC	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Functional validation	scRNA-seq; RNA-seq; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPRi; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_01421	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr2	220526749	220526916	NA	CHPF	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01422	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr2	236369078	236369902	NA	AGAP1	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01423	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr3	20064352	20064799	NA	KAT2B	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01424	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr3	138594478	138595211	NA	PIK3CB	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01425	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr4	1786615	1787989	NA	FGFR3	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01426	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr4	48483630	48484025	NA	SLC10A4	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01427	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr4	56589677	56589836	NA	NMU	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; cis-regulatory element-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01428	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr4	75196204	75196503	NA	EREG	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01429	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr4	79612721	79612827	NA	BMP2K	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01430	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr4	79612993	79613671	NA	BMP2K	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01431	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr4	79642177	79642661	NA	BMP2K	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01432	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr4	79653654	79654287	NA	BMP2K	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01433	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr4	81100680	81101328	NA	ANTXR2	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01434	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr4	99603807	99604262	NA	TSPAN5	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01435	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr4	99607997	99608423	NA	TSPAN5	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01436	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr4	123670867	123671008	NA	BBS12	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01437	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr4	140099709	140099833	NA	MGARP	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01438	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr4	164414180	164414451	NA	TMA16	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01439	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr6	3162748	3163640	NA	TUBB2A	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01440	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr6	27156121	27157007	NA	H4C8	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01441	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr6	27636220	27636738	NA	ZKSCAN8	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01442	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr6	32099282	32099729	NA	FKBPL	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01443	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr7	2439538	2440225	NA	CHST12	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01444	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr7	5613818	5614929	NA	FSCN1	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01445	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr7	7144678	7144795	NA	C1GALT1	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01446	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr7	7188420	7188897	NA	C1GALT1	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01447	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr7	12762340	12762740	NA	ARL4A	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01448	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr7	22721481	22722093	NA	IL6	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01449	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr7	43796195	43796962	NA	BLVRA	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01450	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr7	64309754	64310337	NA	ZNF273	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01451	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr7	92634200	92634655	NA	CDK6	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01452	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr7	100130956	100131300	NA	VGF	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01453	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr7	100290947	100292440	NA	GIGYF1	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01454	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr7	103636422	103637017	NA	RELN	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01455	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr7	106618759	106619430	NA	PRKAR2B	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01456	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr7	106619602	106619915	NA	PRKAR2B	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01457	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr7	106620127	106620526	NA	PRKAR2B	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01458	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr7	106647453	106648219	NA	PRKAR2B	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01459	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr7	106650504	106650972	NA	PRKAR2B	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01460	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr7	106666076	106666272	NA	PRKAR2B	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01461	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr7	106675810	106676245	NA	PRKAR2B	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01462	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr7	155082665	155083264	NA	INSIG1	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01463	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr8	11736787	11737581	NA	CTSB	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01464	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr8	23366136	23366992	NA	SLC25A37	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping; singleton replication	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	Singleton CRISPRi plus bulk RNA-seq; CRISPR-Cas9 endogenous deletion/editing
E_01465	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr8	30769348	30770834	NA	TEX15	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01466	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr8	56760398	56760957	NA	LYN	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous CRISPRi cis-regulatory perturbation; enhancer-gene mapping	Multiplexed dCas9-KRAB CRISPRi screen; single-cell RNA-seq; RNA-seq; eQTL analysis	CRISPR-Cas9 endogenous deletion/editing
E_01467	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr1	182307087	182307634	NA	GLUL	Enhancer	Active	Normal	NA	NA	NA	cerebellum	UBERON:0002037	Mouse Embryonic Cerebellum	NA	mouse embryonic cerebellum	NA	Functional validation	scRNA-seq; RNA-seq; single-cell RNA-seq; eQTL analysis	CRISPRi; CRISPR KO; RT-qPCR; CRISPR-Cas9
E_01468	2015	25801169	Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers	Mus musculus	mm10	chr17	31794375	31829875	NA	Sik1	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion
E_01469	2015	25801169	Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers	Mus musculus	mm10	chr7	3183157	3229407	NA	NA	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion
E_01470	2015	25801169	Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers	Mus musculus	mm10	chr17	35501113	35507015	NA	Pou5f1	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_01471	2025	40089598	In vivo deletion of a GWAS-identified Myb distal enhancer acts on Myb expression, globin switching, and clinical erythroid parameters in β-thalassemia	Mus musculus	mm10	chr10	21241829	21242175	Gata1	Myb	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Erythroid progenitor	NA	erythroid progenitor cell	CL:0000038	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; ATAC-seq; Capture-C; RNA-seq	CRISPR knockout, qRT-PCR; Flow cytometry
E_01472	2025	40378239	C/EBPα activates Irf8 expression in myeloid progenitors at the +56-kb enhancer to initiate cDC1 development	Mus musculus	mm10	chr8	120792731	120793053	Cebpb	Irf8	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary mouse bone marrow hematopoietic progenitors (LMPP/MDP/CDP)	NA	hematopoietic precursor cell	CL:0008001	Enhancer activity assay; TF binding assay; In vivo functional validation; Enhancer epigenetic-state assay	C/EBPα/C/EBPβ ChIP-seq reanalysis; ATAC-seq reanalysis	Retroviral GFP enhancer reporter assay; Site-directed mutagenesis of C/EBP binding site 1; EMSA; Flow cytometry; In vivo phenotyping
E_01473	2025	41125440	A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress	Homo sapiens	hg38	chr14	23379863	23380961	CTCF	MYH6	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	human iPSC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Endogenous enhancer perturbation	ATAC-seq; RNA-seq, Hi-C; ChIP-seq	CRISPRi, CRISPRa; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_01474	2024	38493444	Integrative regulation of hLMR1 by dietary and genetic factors in nonalcoholic fatty liver disease and hyperlipidemia	Homo sapiens	hg38	chr3	142940163	142943066	SREBF1	HLMR1	Enhancer	Active	Disease	metabolic dysfunction-associated steatotic liver disease	MONDO:0013209	DOID:0080208	liver	UBERON:0002107	Hep-G2	CVCL_0027	hepatoblast	CL:0005026	Enhancer activity assay; Functional perturbation assay; TF binding assay; Disease-variant functional analysis; Allele-specific functional assay	SREBF1 ChIP-seq (ENCODE, public); H3K4me1 ChIP-seq (human liver, public); H3K27ac ChIP-seq (human liver, public); RNA-seq (published human NAFLD liver dataset); RNA-seq; GWAS	Luciferase reporter assay; SREBF1 siRNA knockdown; SREBF1 ChIP-qPCR; CRISPR base editing of rs9653945 G>A; Sanger sequencing; RT-qPCR
E_01475	2021	33982894	Lupus Susceptibility Region Containing CDKN1B rs34330 Mechanistically Influences Expression and Function of Multiple Target Genes, Also Linked to Proliferation and Apoptosis	Homo sapiens	hg19	chr12	12874700	12875275	NA	GPR19	Enhancer	Active	Disease	systemic lupus erythematosus	MONDO:0007915	DOID:9074	blood	UBERON:0000178	Primary T cells	NA	T cell	CL:0000084	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Disease-variant functional analysis; Endogenous enhancer perturbation	eQTL analysis; GWAS	Luciferase reporter assay; 3C-RT-qPCR, CRISPR knockout, CRISPRi; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; ChIP; Allele-specific reporter assay
E_01476	2021	34880227	A predominant enhancer co-amplified with the SOX2 oncogene is necessary and sufficient for its expression in squamous cancer	Homo sapiens	hg19	chr3	181624870	181626200	SOX2	SOX2	Enhancer	Active	Disease	squamous cell carcinoma	NA	NA	breast	UBERON:0000310	MDA-MB-231	CVCL_0062	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay	ATAC-seq; ChIP-seq; RNA-seq, Hi-C	CRISPRi, Luciferase reporter assay; RT-qPCR; ChIP-qPCR
E_01477	2017	28123038	Intron 1 GATA site enhances ALAS2 expression indispensably during erythroid differentiation	Homo sapiens	hg19	chrX	55054584	55054678	GATA1	ALAS2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	erythroid progenitor cell	CL:0000038	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_01478	2017	28123038	Intron 1 GATA site enhances ALAS2 expression indispensably during erythroid differentiation	Homo sapiens	hg19	chrX	55041578	55041679	GATA1	ALAS2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	erythroid progenitor cell	CL:0000038	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_01479	2015	25486239	Identification of hypothalamic arcuate nucleus-specific enhancer region of Kiss1 gene in mice	Mus musculus	mm10	chr1	133308997	133319722	Esr1	Kiss1	Enhancer	Active	Normal	NA	NA	NA	hypothalamus	UBERON:0001898	primary arcuate nucleus kisspeptin neurons	NA	kisspeptin neuron	CL:4023130	Enhancer activity assay; TF binding assay; Chromatin interaction assay; In vivo functional validation; In vivo reporter assay	NA	Transgenic GFP reporter assay; 5-prime deletion analysis; ESR1 ChIP-PCR; 3C; Immunofluorescence; kisspeptin/GFP colocalization; ChIP; In vivo phenotyping; Reporter assay
E_01480	2015	25486239	Identification of hypothalamic arcuate nucleus-specific enhancer region of Kiss1 gene in mice	Mus musculus	mm10	chr1	133303739	133325138	Eral1	Kiss1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Kisspeptin-Immunoreactive Cell	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	DNase-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; Transgenic/LacZ assay; Histology/immunostaining
E_01481	2024	39107271	DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression	Homo sapiens	hg38	chr10	52442551	52444237	FOSL2	DKK1	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	AsPC-1	CVCL_0152	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; In vivo functional validation	ChIP-seq; ATAC-seq; RNA-seq; DNase-seq	Luciferase reporter assay, CRISPRi, CRISPR knockout; ChIP-qPCR; RT-qPCR; Western blot, DNA pull-down assay; In vivo phenotyping
E_01482	2024	39107271	DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression	Homo sapiens	hg38	chr10	52442551	52444237	FOSL2	DKK1	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	HPAC	CVCL_3517	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; In vivo functional validation	ChIP-seq; ATAC-seq; RNA-seq; DNase-seq	Luciferase reporter assay, CRISPRi, CRISPR knockout; ChIP-qPCR; RT-qPCR; Western blot, DNA pull-down assay; In vivo phenotyping
E_01483	2024	39107271	DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression	Homo sapiens	hg38	chr10	52442551	52444237	FOSL2	DKK1	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	PANC-1	CVCL_0480	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; In vivo functional validation	ChIP-seq; ATAC-seq; RNA-seq; DNase-seq	Luciferase reporter assay, CRISPRi, CRISPR knockout; ChIP-qPCR; RT-qPCR; Western blot, DNA pull-down assay; In vivo phenotyping
E_01484	2024	39107271	DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression	Homo sapiens	hg38	chr10	52442551	52444237	JUND	DKK1	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	AsPC-1	CVCL_0152	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; In vivo functional validation	ChIP-seq; ATAC-seq; RNA-seq; DNase-seq	Luciferase reporter assay, CRISPRi, CRISPR knockout; ChIP-qPCR; RT-qPCR; Western blot, DNA pull-down assay; In vivo phenotyping
E_01485	2024	39107271	DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression	Homo sapiens	hg38	chr10	52442551	52444237	JUND	DKK1	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	HPAC	CVCL_3517	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; In vivo functional validation	ChIP-seq; ATAC-seq; RNA-seq; DNase-seq	Luciferase reporter assay, CRISPRi, CRISPR knockout; ChIP-qPCR; RT-qPCR; Western blot, DNA pull-down assay; In vivo phenotyping
E_01486	2024	39107271	DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression	Homo sapiens	hg38	chr10	52442551	52444237	JUND	DKK1	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	PANC-1	CVCL_0480	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; In vivo functional validation	ChIP-seq; ATAC-seq; RNA-seq; DNase-seq	Luciferase reporter assay, CRISPRi, CRISPR knockout; ChIP-qPCR; RT-qPCR; Western blot, DNA pull-down assay; In vivo phenotyping
E_01487	2023	36869028	An Igh distal enhancer modulates antigen receptor diversity by determining locus conformation	Mus musculus	mm10	chr12	114182511	114183025	Ikzf1	Igh	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary Rag2-/- pro-B cells	NA	pro-B cell	CL:0000826	Enhancer activity; TF occupancy; chromatin-conformation and V(D)J functional perturbation	Hi-C; H3K27ac/H3K4me1 ChIP-seq; ATAC-seq; RNA-seq; V(D)J-seq	CRISPR enhancer deletion; 3C/4C; V(D)J recombination qPCR; ChIP-qPCR; DNA FISH
E_01488	2023	36869028	An Igh distal enhancer modulates antigen receptor diversity by determining locus conformation	Mus musculus	mm10	chr12	114182511	114183025	Irf4	Igh	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary Rag1-/- pro-B cells	NA	pro-B cell	CL:0000826	Enhancer activity; TF occupancy; chromatin-conformation and V(D)J functional perturbation	Hi-C; H3K27ac/H3K4me1 ChIP-seq; ATAC-seq; RNA-seq; V(D)J-seq	CRISPR enhancer deletion; 3C/4C; V(D)J recombination qPCR; ChIP-qPCR; DNA FISH
E_01489	2023	36869028	An Igh distal enhancer modulates antigen receptor diversity by determining locus conformation	Mus musculus	mm10	chr12	114182511	114183025	Tcf3	Igh	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary pro-B cells / EVH1-mutant mouse	NA	pro-B cell	CL:0000826	Enhancer activity; TF occupancy; chromatin-conformation and V(D)J functional perturbation	Hi-C; H3K27ac/H3K4me1 ChIP-seq; ATAC-seq; RNA-seq; V(D)J-seq	CRISPR enhancer deletion; 3C/4C; V(D)J recombination qPCR; ChIP-qPCR; DNA FISH
E_01490	2023	37277355	A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest	Mus musculus	mm10	chr6	50789172	50828639	Hoxa2	Hoxa2	Enhancer	Active	Normal	NA	NA	NA	pharyngeal arch	UBERON:0002539	Cranial neural crest cells	NA	cranial neural crest cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; Hi-C; ATAC-seq	CRISPR knockout; RT-qPCR; Western blot
E_01491	2020	33229569	Chromatin topology and the timing of enhancer function at the HoxD locus	Mus musculus	mm10	chr2	75147318	75148561	NA	Hoxd11	Enhancer	Active	Normal	NA	NA	NA	limb	UBERON:0002101	E9-E12.5 mouse forelimb bud	NA	embryonic limb mesenchyme	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	H3K27ac ChIP-seq; 4C-seq	LacZ transgenic reporter assay; CRISPR deletion; RT-qPCR
E_01492	2020	33229569	Chromatin topology and the timing of enhancer function at the HoxD locus	Mus musculus	mm10	chr2	75439366	75440449	NA	Hoxd11	Enhancer	Active	Normal	NA	NA	NA	limb	UBERON:0002101	E9-E12.5 mouse forelimb bud	NA	embryonic limb mesenchyme	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	H3K27ac ChIP-seq; CTCF ChIP-seq; RAD21 ChIP-seq; 4C-seq	LacZ transgenic reporter assay; CRISPR deletion; RT-qPCR; Whole-mount in situ hybridization
E_01493	2023	37277355	A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest	Mus musculus	mm10	chr6	50913170	51087888	Hoxa2	Hoxa2	Super-enhancer	Active	Normal	NA	NA	NA	pharyngeal arch	UBERON:0002539	E10.5 second pharyngeal arch cranial neural crest cells	NA	neural crest cell	CL:0011012	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; Endogenous functional perturbation assay; TF occupancy analysis	H3K27ac ChIP-seq; Hoxa2 ChIP-seq; ATAC-seq; Hi-C; PCHi-C; RNA-seq	CRISPR/Cas9 deletion of HIRE1 in mice; RT-qPCR; in situ hybridization; skeletal staining; mutant phenotyping; Mouse genetic deletion/knock-in
E_01494	2023	37277355	A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest	Mus musculus	mm10	chr6	50913170	51087888	Hoxa2	Hoxa3	Super-enhancer	Active	Normal	NA	NA	NA	pharyngeal arch	UBERON:0002539	E10.5 PA3/PA4 cranial neural crest cells	NA	neural crest cell	CL:0011012	Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; Endogenous functional perturbation assay; TF occupancy analysis	Hoxa2/H3K27ac ChIP-seq; ATAC-seq; Hi-C; PCHi-C; RNA-seq	CRISPR/Cas9 HIRE1 deletion; Hoxa3 RT-qPCR; in situ hybridization; skeletal phenotyping; Mouse genetic deletion/knock-in
E_01495	2023	37277355	A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest	Mus musculus	mm10	chr6	50913170	51087888	Meis2	Hoxa2	Super-enhancer	Active	Normal	NA	NA	NA	pharyngeal arch	UBERON:0002539	E10.5 second pharyngeal arch cranial neural crest cells	NA	neural crest cell	CL:0011012	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; Endogenous functional perturbation assay; TF occupancy analysis	Meis ChIP-seq; H3K27ac ChIP-seq; ATAC-seq; Hi-C; PCHi-C; RNA-seq	CRISPR/Cas9 HIRE1 deletion; RT-qPCR; in situ hybridization; skeletal staining; Mouse genetic deletion/knock-in
E_01496	2023	37277355	A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest	Mus musculus	mm10	chr6	50913170	51087888	Pbx1	Hoxa2	Super-enhancer	Active	Normal	NA	NA	NA	pharyngeal arch	UBERON:0002539	E10.5 second pharyngeal arch cranial neural crest cells	NA	neural crest cell	CL:0011012	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; Endogenous functional perturbation assay; TF occupancy analysis	Pbx ChIP-seq; H3K27ac ChIP-seq; ATAC-seq; Hi-C; PCHi-C; RNA-seq	CRISPR/Cas9 HIRE1 deletion; RT-qPCR; in situ hybridization; skeletal staining; Mouse genetic deletion/knock-in
E_01497	2023	37277355	A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest	Mus musculus	mm10	chr6	50913170	51087888	Pbx1	Hoxa3	Super-enhancer	Active	Normal	NA	NA	NA	pharyngeal arch	UBERON:0002539	E10.5 PA3/PA4 cranial neural crest cells	NA	neural crest cell	CL:0011012	Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; Endogenous functional perturbation assay; TF occupancy analysis	Pbx/H3K27ac ChIP-seq; ATAC-seq; Hi-C; PCHi-C; RNA-seq	CRISPR/Cas9 HIRE1 deletion; Hoxa3 RT-qPCR; in situ hybridization; skeletal phenotyping; Mouse genetic deletion/knock-in
E_01498	2025	40404660	Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity	Homo sapiens	hg38	chr1	52662800	52663070	SP2	COA7	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	iPSC-derived excitatory neurons	NA	excitatory neuron	NA	Enhancer activity assay; TF binding assay	ChIP-seq; ATAC-seq; RNA-seq; MPRA	Transgenic reporter assay; RT-qPCR; Reporter assay; Transgenic mouse enhancer assay
E_01499	2025	40404660	Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity	Homo sapiens	hg38	chr5	88396400	88396670	ASCL1	MEF2C	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	iPSC-derived excitatory neurons	NA	excitatory neuron	NA	Enhancer activity assay; TF binding assay	ChIP-seq; ATAC-seq; RNA-seq; MPRA	Transgenic reporter assay; RT-qPCR; Reporter assay; Transgenic mouse enhancer assay
E_01500	2025	40404660	Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity	Homo sapiens	hg38	chr6	97306500	97306770	CDX1	GPR63	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	iPSC-derived excitatory neurons	NA	excitatory neuron	NA	Enhancer activity assay; TF binding assay	ChIP-seq; ATAC-seq; RNA-seq; MPRA	Transgenic reporter assay; RT-qPCR; Reporter assay; Transgenic mouse enhancer assay
E_01501	2025	40404660	Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity	Homo sapiens	hg38	chr6	97306500	97306770	POU4F3	GPR63	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	iPSC-derived excitatory neurons	NA	excitatory neuron	NA	Enhancer activity assay; TF binding assay	ChIP-seq; ATAC-seq; RNA-seq; MPRA	Transgenic reporter assay; RT-qPCR; Reporter assay; Transgenic mouse enhancer assay
E_01502	2025	40404660	Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity	Homo sapiens	hg38	chr6	162856700	162856970	CTCF	QKI	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	iPSC-derived excitatory neurons	NA	excitatory neuron	NA	Enhancer activity assay; TF binding assay	ChIP-seq; ATAC-seq; RNA-seq; MPRA	Transgenic reporter assay, qRT-PCR; Reporter assay; Transgenic mouse enhancer assay
E_01503	2025	40404660	Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity	Homo sapiens	hg38	chr6	162856700	162856970	RORB	QKI	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	iPSC-derived excitatory neurons	NA	excitatory neuron	NA	Enhancer activity assay; TF binding assay	ChIP-seq; ATAC-seq; RNA-seq; MPRA	Transgenic reporter assay, qRT-PCR; Reporter assay; Transgenic mouse enhancer assay
E_01504	2023	36869028	An Igh distal enhancer modulates antigen receptor diversity by determining locus conformation	Mus musculus	mm10	chr12	114182511	114183025	Pax5	Igh	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Abl-transformed Rag1-/- pro-B cells	NA	pro-B cell	CL:0000826	Enhancer activity; TF occupancy; chromatin-conformation and V(D)J functional perturbation	Hi-C; H3K27ac/H3K4me1 ChIP-seq; ATAC-seq; RNA-seq; V(D)J-seq	CRISPR enhancer deletion; 3C/4C; V(D)J recombination qPCR; ChIP-qPCR; DNA FISH
E_01505	2025	40404660	Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity	Homo sapiens	hg38	chr13	80276300	80276570	NA	SPRY2	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	iPSC-derived excitatory neurons	NA	excitatory neuron	NA	Enhancer activity assay; TF binding assay	ChIP-seq; ATAC-seq; RNA-seq; MPRA	Transgenic reporter assay; RT-qPCR; Reporter assay; Transgenic mouse enhancer assay
E_01506	2025	40404660	Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity	Mus musculus	mm10	chr6	97306690	97307260	NA	Gpr63	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Neurons	NA	neuron	CL:0000540	Enhancer activity assay; Chromatin-state profiling; Disease-variant functional analysis; In vivo functional validation	RNA-seq; ATAC-seq; ATAC-seq; MPRA	Transgenic reporter assay; Transgenic enhancer reporter assay; In vivo phenotyping; Reporter assay
E_01507	2025	40378239	C/EBPα activates Irf8 expression in myeloid progenitors at the +56-kb enhancer to initiate cDC1 development	Mus musculus	mm10	chr11	101234567	101235689	Cebpa	Irf8	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Myeloid cells	NA	myeloid cell	CL:0000763	Functional perturbation assay; In vivo functional validation	ChIP-seq; RNA-seq	CRISPR knockout; ChIP-qPCR; In vivo phenotyping
E_01508	2020	33229569	Chromatin topology and the timing of enhancer function at the HoxD locus	Mus musculus	mm10	chr2	74925621	74939634	NA	Hoxd9	Enhancer	Active	Normal	NA	NA	NA	forelimb bud	UBERON:0005417	E9.5/E12.5 mouse forelimb buds	NA	forelimb-bud mesenchymal cells	NA	Functional perturbation assay; Chromatin interaction assay; Gene expression assay	4C-seq; RNA-seq	CRISPR/Cas9 deletion and inversion; qRT-PCR; whole-mount in situ hybridization
E_01509	2020	33229569	Chromatin topology and the timing of enhancer function at the HoxD locus	Mus musculus	mm10	chr2	75208104	75210328	NA	Hoxd11	Enhancer	Active	Normal	NA	NA	NA	limb	UBERON:0002101	E9-E12.5 mouse forelimb bud	NA	embryonic limb mesenchyme	NA	Enhancer activity assay; Chromatin interaction assay	H3K27ac ChIP-seq; 4C-seq	LacZ transgenic reporter assay
E_01510	2020	33229569	Chromatin topology and the timing of enhancer function at the HoxD locus	Mus musculus	mm10	chr2	75081283	75094718	NA	Hoxd9	Enhancer	Active	Normal	NA	NA	NA	limb	UBERON:0002101	E9 mouse forelimb bud	NA	embryonic limb mesenchyme	NA	Enhancer activity assay	H3K27ac ChIP-seq	LacZ transgenic reporter assay
E_01511	2025	39402215	Functional variant rs9344 at 11q13.3 regulates CCND1 expression in multiple myeloma with t(11;14)	Homo sapiens	hg19	chr11	68155000	68173900	PAX5	CCND1	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	HEK293T	CVCL_0063	embryonic kidney cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; ATAC-seq; RNA-seq; Hi-C	CRISPR knockout, qRT-PCR; Western blot; CRISPR-Cas9
E_01512	2025	40880432	Igf2 adult-specific skeletal muscle enhancer activity revealed in mice with intergenic CTCF boundary deletion	Mus musculus	mm10	chr7	142599494	142601493	Myod1	Igf2	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	Skeletal muscle myocytes	NA	skeletal muscle myocyte	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	Capture-C; ChIP-seq; ATAC-seq; RNA-seq	CRISPR knockout, qRT-PCR; Southern blot
E_01513	2023	37185814	Epigenetic landscape reveals MECOM as an endothelial lineage regulator	Homo sapiens	hg38	chr3	169000000	169001000	MECOM	KDR	Enhancer	Active	Normal	NA	NA	NA	umbilical vein	UBERON:0002066	HUVEC-C	CVCL_2959	umbilical vein endothelial cell	NA	Enhancer activity assay; Chromatin interaction assay	ChIP-seq; RNA-seq; 3C-seq; single-cell RNA-seq; RNA-seq; Hi-C	Luciferase reporter assay; CRISPR knockout
E_01514	2022	35039581	Targeting of noncoding RNAs encoded by a novel MYC enhancers inhibits the proliferation of human hepatic carcinoma cells in vitro	Homo sapiens	hg38	chr8	128554145	128555945	NA	MYC	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Huh-7	CVCL_0336	hepatocyte	CL:0000182	Enhancer activity assay; Endogenous enhancer perturbation; enhancer RNA Functional perturbation assay	H3K27ac ChIP-seq; EP300 ChIP-seq; GRO-seq	Dual-luciferase reporter assay; ASO-mediated R2 eRNA inhibition; RT-qPCR; WST-1 assay; spheroid formation assay; CRISPR-Cas9 endogenous deletion/editing; Reporter assay
E_01515	2022	35869079	A multi-omic dissection of super-enhancer driven oncogenic gene expression programs in ovarian cancer	Homo sapiens	hg19	chr1	16162175	16195191	ELF3	EPHA2	Super-enhancer	Active	Disease	ovarian carcinoma	MONDO:0005140	DOID:4001	ovary	UBERON:0000992	OVCAR-3	CVCL_0465	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq, Hi-C; ATAC-seq, scATAC-seq, scRNA-seq; RNA-seq; Hi-C	CRISPR knockout, CRISPRi, qRT-PCR; Western blot, Cell Proliferation Assay, Cell Migration Assay
E_01516	2022	35869079	A multi-omic dissection of super-enhancer driven oncogenic gene expression programs in ovarian cancer	Homo sapiens	hg19	chr20	53730511	53757381	SOX4	RAE1	Super-enhancer	Active	Disease	ovarian carcinoma	MONDO:0005140	DOID:4001	ovary	UBERON:0000992	OVCAR-3	CVCL_0465	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq, Hi-C; ATAC-seq, scATAC-seq, scRNA-seq; RNA-seq; Hi-C	CRISPR knockout, CRISPRi, qRT-PCR; Western blot, Cell Proliferation Assay, Cell Migration Assay
E_01517	2021	33910361	Variant Intronic Enhancer Controls SCN10A-short Expression and Heart Conduction	Mus musculus	mm9	chr9	119540801	119544032	Tbx5	Scn10a	Enhancer	Active	Disease	atrial fibrillation	MONDO:0004981	DOID:0060224	heart	UBERON:0000948	primary mouse atrial cardiomyocytes and ventricular conduction-system cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Endogenous enhancer perturbation assay; regulatory variant analysis; cardiac electrophysiological assay	RNA-seq; TBX5 ChIP-seq; ATAC-seq; GWAS variant mapping; eQTL analysis	CRISPR/Cas9 RE1A/RE1B deletion; 3-bp disruption of the rs6801957 T-box site; RT-qPCR; in situ hybridization; patch-clamp electrophysiology; in vivo electrophysiology; optical mapping; arrhythmia induction; NaV1.8-short functional expression assay; Start/End denote the previously defined mm9 EnhA domain containing the 2021-dissected RE1 elements; CRISPR-Cas9
E_01518	2021	33910361	Variant Intronic Enhancer Controls SCN10A-short Expression and Heart Conduction	Mus musculus	mm9	chr9	119540801	119544032	Tbx5	Scn10a	Enhancer	Active	Disease	Brugada syndrome	MONDO:0015263	DOID:0050451	heart	UBERON:0000948	primary mouse atrial cardiomyocytes and ventricular conduction-system cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Endogenous enhancer perturbation assay; regulatory variant analysis; cardiac electrophysiological assay	RNA-seq; TBX5 ChIP-seq; ATAC-seq; GWAS variant mapping; eQTL analysis	CRISPR/Cas9 RE1A/RE1B deletion; 3-bp disruption of the rs6801957 T-box site; RT-qPCR; in situ hybridization; patch-clamp electrophysiology; in vivo electrophysiology; optical mapping; arrhythmia induction; NaV1.8-short functional expression assay; Start/End denote the previously defined mm9 EnhA domain containing the 2021-dissected RE1 elements; CRISPR-Cas9
E_01519	2020	32086528	Alteration of CTCF-associated chromatin neighborhood inhibits TAL1-driven oncogenic transcription program and leukemogenesis	Homo sapiens	hg19	chr1	47677539	47677958	NA	TAL1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Jurkat	CVCL_0065	T cell	CL:0000084	Chromatin interaction assay; Functional chromatin-architecture perturbation assay	Chromatin accessibility and chromatin-conformation profiling; ChIP-seq; transcriptome profiling	CRISPR/Cas9 deletion/inversion of -31-kb CTCF boundary; chromatin-interaction validation; RT-qPCR; Western blot; leukemogenesis assay
E_01520	2020	32499651	A distal enhancer at risk locus 11q13.5 promotes suppression of colitis by Treg cells	Mus musculus	mm10	chr7	105711382	105713753	NA	Lrrc32	Enhancer	Active	Disease	colitis	MONDO:0005292	DOID:0060180	colon	UBERON:0001155	Primary Treg cells	NA	regulatory T cell	CL:0000815	Enhancer activity assay; Functional perturbation assay; TF binding assay; Disease-variant functional analysis; Endogenous enhancer perturbation	RNA-seq; ChIP-seq; ATAC-seq	CRISPR knockout; ChIP-qPCR, qRT-PCR, Flow Cytometry; CRISPRa
E_01521	2019	31251802	Enhancer-mediated enrichment of interacting JMJD3-DDX21 to ENPP2 locus prevents R-loop formation and promotes transcription	Homo sapiens	hg19	chr8	120733232	120735226	RELA	ENPP2	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	HEK293	CVCL_0045	embryonic kidney cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; Hi-C	Luciferase reporter assay; ChIP-qPCR; CRISPR knockout; RT-qPCR; Western blot; CRISPR-Cas9
E_01522	2020	32499651	A distal enhancer at risk locus 11q13.5 promotes suppression of colitis by Treg cells	Homo sapiens	hg38	chr11	76586431	76600121	NA	LRRC32	Enhancer	Active	Normal	NA	NA	NA	colon	UBERON:0001155	Primary Treg cells	NA	regulatory T cell	CL:0000815	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis; Endogenous enhancer perturbation	ChIP-seq; RNA-seq, HiChIP, hQTL, eQTL	CRISPRa; ChIP-qPCR; RT-qPCR, Flow Cytometry; CRISPRa
E_01523	2025	40997217	Mechanosensitive genomic enhancers potentiate the cellular response to matrix stiffness	Homo sapiens	hg38	chr15	40809500	40810500	NA	BMF	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	WA13	CVCL_9774	embryonic stem cell	CL:0002322	Endogenous enhancer perturbation; CRISPR interference-based functional screen	ATAC-seq; RNA-seq, HiCAR; CRISPRi screening, single-cell RNA-seq; single-cell RNA-seq; RNA-seq	Luciferase reporter assay; RT-qPCR, flow cytometry, caspase assay; CRISPR-Cas9 endogenous deletion/editing
E_01524	2025	40997217	Mechanosensitive genomic enhancers potentiate the cellular response to matrix stiffness	Homo sapiens	hg38	chr17	44542500	44543500	NA	FZD2	Enhancer	Active	Normal	NA	NA	NA	zone of skin	UBERON:0000014	Human neonatal foreskin fibroblasts	NA	fibroblast	CL:0000057	Endogenous enhancer perturbation; CRISPR interference-based functional screen	ATAC-seq; RNA-seq, HiCAR; CRISPRi screening, single-cell RNA-seq; single-cell RNA-seq; RNA-seq	Luciferase reporter assay; RT-qPCR, flow cytometry; CRISPR-Cas9 endogenous deletion/editing
E_01525	2025	40997217	Mechanosensitive genomic enhancers potentiate the cellular response to matrix stiffness	Homo sapiens	hg38	chr22	36656500	36657500	NA	MYH9	Enhancer	Active	Normal	NA	NA	NA	zone of skin	UBERON:0000014	Human neonatal foreskin fibroblasts	NA	fibroblast	CL:0000057	Endogenous enhancer perturbation; CRISPR interference-based functional screen	ATAC-seq; RNA-seq, HiCAR; CRISPRi screening, single-cell RNA-seq; single-cell RNA-seq; RNA-seq	Luciferase reporter assay; RT-qPCR, flow cytometry, immunostaining; CRISPR-Cas9 endogenous deletion/editing
E_01526	2024	38086419	Cell-type-directed design of synthetic enhancers	Homo sapiens	hg38	chr6	396104	396604	SOX10	IRF4	Enhancer	Active	Disease	cutaneous melanoma	MONDO:0005012	DOID:8923	zone of skin	UBERON:0000014	Human melanoma cell	NA	melanoma cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; ATAC-seq	Luciferase reporter assay; CRISPRi; CRISPR knockout; RT-qPCR; ChIP-qPCR
E_01527	2020	33315856	HOX paralogs selectively convert binding of ubiquitous transcription factors into tissue-specific patterns of enhancer activation	Mus musculus	mm9	chr8	28094779	28095609	Hoxa2	Zfp703	Enhancer	Active	Normal	NA	NA	NA	pharyngeal arch	UBERON:0002539	NIH 3T3	CVCL_0594	fibroblast	CL:0000057	Enhancer activity assay; Functional perturbation assay; TF binding assay; In vivo functional validation	Hoxa2 ChIP-seq; Hoxa3 ChIP-seq; PBX ChIP-seq; MEIS ChIP-seq; H3K27ac ChIP-seq	Luciferase reporter assay; ChIP-qPCR; HOX-PBX site-directed mutagenesis; In vivo phenotyping
E_01528	2020	33315856	HOX paralogs selectively convert binding of ubiquitous transcription factors into tissue-specific patterns of enhancer activation	Mus musculus	mm9	chr8	28094779	28095609	Meis2	Zfp703	Enhancer	Active	Normal	NA	NA	NA	pharyngeal arch	UBERON:0002539	NIH 3T3	CVCL_0594	fibroblast	CL:0000057	Enhancer activity assay; Functional perturbation assay; TF binding assay; In vivo functional validation	Hoxa2 ChIP-seq; Hoxa3 ChIP-seq; PBX ChIP-seq; MEIS ChIP-seq; H3K27ac ChIP-seq	Luciferase reporter assay; ChIP-qPCR; HOX-PBX site-directed mutagenesis; In vivo phenotyping
E_01529	2004	15340054	Granulocyte-macrophage colony-stimulating factor enhancer activation requires cooperation between NFAT and AP-1 elements and is associated with extensive nucleosome reorganization	Homo sapiens	hg19	chr5	131406243	131406930	FOS	CSF2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Jurkat	CVCL_0065	T cell	CL:0000084	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin accessibility assay; In vivo functional validation; Chromatin remodeling assay	NA	Site-directed mutagenesis; transient transfection; Luciferase reporter assay; PMA/A23187 stimulation; recombinant c-Jun/c-Fos EMSA; DMS in vivo footprinting; LM-PCR; DNase I hypersensitivity assay; DNase I footprinting; MNase nucleosome mapping; restriction enzyme accessibility assay; In vivo phenotyping
E_01530	2004	15340054	Granulocyte-macrophage colony-stimulating factor enhancer activation requires cooperation between NFAT and AP-1 elements and is associated with extensive nucleosome reorganization	Homo sapiens	hg19	chr5	131406243	131406930	JUN	CSF2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Jurkat	CVCL_0065	T cell	CL:0000084	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin accessibility assay; In vivo functional validation; Chromatin remodeling assay	NA	Site-directed mutagenesis; transient transfection; Luciferase reporter assay; PMA/A23187 stimulation; recombinant c-Jun/c-Fos EMSA; DMS in vivo footprinting; LM-PCR; DNase I hypersensitivity assay; DNase I footprinting; MNase nucleosome mapping; restriction enzyme accessibility assay; In vivo phenotyping
E_01531	2004	15340054	Granulocyte-macrophage colony-stimulating factor enhancer activation requires cooperation between NFAT and AP-1 elements and is associated with extensive nucleosome reorganization	Homo sapiens	hg19	chr5	131406243	131406930	NFATC1	CSF2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Jurkat	CVCL_0065	T cell	CL:0000084	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin accessibility assay; In vivo functional validation; Chromatin remodeling assay	NA	Site-directed mutagenesis; transient transfection; Luciferase reporter assay; PMA/A23187 stimulation; antibody-EMSA; DMS in vivo footprinting; LM-PCR; DNase I hypersensitivity assay; DNase I footprinting; MNase nucleosome mapping; restriction enzyme accessibility assay; In vivo phenotyping
E_01532	2004	15340054	Granulocyte-macrophage colony-stimulating factor enhancer activation requires cooperation between NFAT and AP-1 elements and is associated with extensive nucleosome reorganization	Homo sapiens	hg19	chr5	131406243	131406930	NFATC2	CSF2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Jurkat	CVCL_0065	T cell	CL:0000084	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin accessibility assay; In vivo functional validation; Chromatin remodeling assay	NA	Site-directed mutagenesis; transient transfection; Luciferase reporter assay; PMA/A23187 stimulation; EMSA; recombinant protein EMSA; DMS in vivo footprinting; LM-PCR; DNase I hypersensitivity assay; DNase I footprinting; MNase nucleosome mapping; restriction enzyme accessibility assay; stable transfection; In vivo phenotyping
E_01533	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chr12	54295641	54296181	NA	HNRNPA1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01534	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chr12	54303561	54304061	NA	HNRNPA1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01535	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chr12	54303561	54304061	NA	NFE2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01536	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chr12	54306981	54307501	NA	HNRNPA1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01537	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chr12	54306981	54307501	NA	NFE2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01538	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chr19	12681111	12681611	NA	WDR83OS	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01539	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chr19	12775155	12776011	NA	DNASE2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01540	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chr19	12775155	12776011	NA	PRDX2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01541	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chr19	12782291	12783171	NA	JUNB	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01542	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chr19	12782291	12783171	NA	PRDX2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01543	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chr19	12805831	12806863	NA	PRDX2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01544	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chr19	12880980	12881831	NA	KLF1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01545	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chr19	12883611	12884131	NA	DNASE2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01546	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chr19	12884935	12885511	NA	PRDX2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01547	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chr19	12884935	12885511	NA	RAD23A	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01548	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chr19	12886091	12888153	NA	CALR	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01549	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chr19	12886091	12888153	NA	DHPS	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01550	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chr19	12886091	12888153	NA	JUNB	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01551	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chr19	12886091	12888153	NA	PRDX2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01552	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chr19	12886091	12888153	NA	RAD23A	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01553	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chr19	12886091	12888153	NA	RNASEH2A	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01554	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chr19	12886091	12888153	NA	WDR83OS	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01555	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chr19	12888891	12889391	NA	KLF1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01556	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chr19	48740463	48741888	NA	FUT1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01557	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chr19	48745108	48745628	NA	FUT1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01558	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chr19	48898139	48899488	NA	NUCB1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01559	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chr19	48962199	48962768	NA	FTL	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01560	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chr19	48970828	48971348	NA	FTL	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01561	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chrX	47232664	47233947	NA	HDAC6	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01562	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chrX	48761499	48762241	NA	GATA1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01563	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chrX	48800418	48801257	NA	GATA1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01564	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chrX	48800418	48801257	NA	HDAC6	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01565	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chrX	48800418	48801257	NA	PLP2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01566	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chrX	48941369	48942569	NA	PIM2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01567	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chrX	48941369	48942569	NA	PQBP1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01568	2019	31784727	Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations	Homo sapiens	hg38	chrX	49047157	49047736	NA	PQBP1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Endogenous enhancer perturbation; Genome-scale enhancer-gene perturbation and activity-by-contact modeling	CRISPRi-FlowFISH; DNase-seq; H3K27ac ChIP-seq; Hi-C/ABC modeling	ChIP-qPCR
E_01569	2016	26766440	Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis	Mus musculus	mm10	chr14	69196226	69202226	Gata1	Slc25a37	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	G1ER Erythroid Cell	NA	erythroid progenitor cell	CL:0000038	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01570	2016	26766440	Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis	Mus musculus	mm10	chr14	69196226	69202226	Gata2	Slc25a37	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	G1ER Erythroid Cell	NA	erythroid progenitor cell	CL:0000038	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01571	2016	26766440	Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis	Mus musculus	mm10	chr14	119710660	119714758	Gata1	Slc25a37	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	G1ER Erythroid Cell	NA	erythroid progenitor cell	CL:0000038	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01572	2016	26766440	Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis	Mus musculus	mm10	chr14	119710660	119714758	Gata2	Slc25a37	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	G1ER Erythroid Cell	NA	erythroid progenitor cell	CL:0000038	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01573	2020	33315856	HOX paralogs selectively convert binding of ubiquitous transcription factors into tissue-specific patterns of enhancer activation	Mus musculus	mm9	chr8	28094779	28095609	Hoxa3	Zfp703	Enhancer	Active	Normal	NA	NA	NA	pharyngeal arch	UBERON:0002539	NIH 3T3	CVCL_0594	fibroblast	CL:0000057	Enhancer activity assay; TF binding assay; In vivo functional validation	Hoxa2 ChIP-seq; Hoxa3 ChIP-seq; PBX ChIP-seq; MEIS ChIP-seq; H3K27ac ChIP-seq	Luciferase reporter assay; ChIP-qPCR; In vivo phenotyping
E_01574	2020	33315856	HOX paralogs selectively convert binding of ubiquitous transcription factors into tissue-specific patterns of enhancer activation	Mus musculus	mm10	chr16	18164900	18165100	Pbx1	Zfp703	Enhancer	Active	Normal	NA	NA	NA	pharyngeal arch	UBERON:0002539	NIH 3T3	CVCL_0594	fibroblast	CL:0000057	Enhancer activity assay; TF binding assay; In vivo functional validation	ChIP-seq	Luciferase reporter assay, Transgenic reporter assay; ChIP-qPCR; In vivo phenotyping
E_01575	2020	33315856	HOX paralogs selectively convert binding of ubiquitous transcription factors into tissue-specific patterns of enhancer activation	Mus musculus	mm10	chr2	73389900	73390100	Pbx1	Meis2	Enhancer	Active	Normal	NA	NA	NA	pharyngeal arch	UBERON:0002539	NIH 3T3	CVCL_0594	fibroblast	CL:0000057	Enhancer activity assay; TF binding assay; In vivo functional validation	ChIP-seq	Luciferase reporter assay, Transgenic reporter assay; ChIP-qPCR; In vivo phenotyping
E_01576	2016	26766440	Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis	Homo sapiens	hg19	chr8	23448386	23454886	GATA1	SLC25A37	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Human CD34+ Hematopoietic Stem/Progenitor Cell	NA	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_01577	2016	26766440	Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis	Homo sapiens	hg19	chr8	23448386	23454886	TAL1	SLC25A37	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Human CD34+ Hematopoietic Stem/Progenitor Cell	NA	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_01578	2016	26766440	Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis	Homo sapiens	hg19	chr8	23433011	23439511	GATA1	SLC25A37	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Human CD34+ Hematopoietic Stem/Progenitor Cell	NA	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_01579	2016	26766440	Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis	Homo sapiens	hg19	chr8	23433011	23439511	TAL1	SLC25A37	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Human CD34+ Hematopoietic Stem/Progenitor Cell	NA	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_01580	2016	26766440	Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis	Homo sapiens	hg19	chr8	23422136	23432636	GATA1	SLC25A37	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Human CD34+ Hematopoietic Stem/Progenitor Cell	NA	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_01581	2016	26766440	Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis	Homo sapiens	hg19	chr8	23422136	23432636	TAL1	SLC25A37	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Human CD34+ Hematopoietic Stem/Progenitor Cell	NA	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_01582	2022	35039581	Targeting of noncoding RNAs encoded by a novel MYC enhancers inhibits the proliferation of human hepatic carcinoma cells in vitro	Homo sapiens	hg38	chr8	128556059	128557653	NA	MYC	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Hep-G2	CVCL_0027	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation	ChIP-seq; GRO-seq	Luciferase reporter assay, CRISPR knockout, qRT-PCR; CRISPR-Cas9 endogenous deletion/editing; Reporter assay
E_01583	2026	41237776	FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry	Homo sapiens	hg38	chrX	49273000	49274000	GATA3	FOXP3	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary conventional CD4+ T cells	NA	CD4-positive, alpha-beta T cell	CL:0000624	Enhancer activity assay; Functional perturbation assay; TF binding assay	Pooled CRISPRi locus-tiling screen; pooled CRISPRn TF screen; ATAC-seq; H3K27ac ChIP-seq; GATA3 ChIP-seq	Paired-Cas9 RNP tiled deletion; CRISPRoff targeted epigenetic silencing; GATA3 knockout; FOXP3 flow cytometry; targeted amplicon sequencing; targeted bisulfite sequencing
E_01584	2016	26766440	Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis	Mus musculus	mm10	chr14	69221635	69222851	Gata1	Slc25a37	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	G1ER Erythroid Cell	NA	erythroid progenitor cell	CL:0000038	Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01585	2016	26766440	Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis	Mus musculus	mm10	chr14	69221635	69222851	Gata2	Slc25a37	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	G1ER Erythroid Cell	NA	erythroid progenitor cell	CL:0000038	Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01586	2025	40997217	Mechanosensitive genomic enhancers potentiate the cellular response to matrix stiffness	Homo sapiens	hg38	chr22	36328713	36329931	NA	MYH9	Enhancer	Active	Disease	idiopathic pulmonary fibrosis	MONDO:0800504	DOID:0050156	lung	UBERON:0002048	primary lung fibroblasts from idiopathic pulmonary fibrosis donors	NA	fibroblast	CL:0000057	Endogenous enhancer perturbation; Disease-context functional perturbation assay	single-cell RNA-seq; RNA-seq	dCas9-KRAB CRISPRi; RT-qPCR; alpha-smooth muscle actin immunostaining; CRISPR-Cas9 endogenous deletion/editing
E_01587	2024	38086419	Cell-type-directed design of synthetic enhancers	Drosophila melanogaster	dm6	chr3L	8670850	8671350	NA	NA	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Kenyon cell	NA	Kenyon cell	CL:0000673	Enhancer activity assay	ATAC-seq	Transgenic reporter assay
E_01588	2024	38086419	Cell-type-directed design of synthetic enhancers	Drosophila melanogaster	dm6	chrX	4010500	4011000	NA	NA	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Kenyon cell	NA	Kenyon cell	CL:0000673	Enhancer activity assay	ATAC-seq	Transgenic reporter assay
E_01589	2024	38086419	Cell-type-directed design of synthetic enhancers	Drosophila melanogaster	dm6	chrX	9786300	9786800	NA	NA	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Kenyon cell	NA	Kenyon cell	CL:0000673	Enhancer activity assay	ATAC-seq	Transgenic reporter assay
E_01590	2024	38086419	Cell-type-directed design of synthetic enhancers	Drosophila melanogaster	dm6	chrX	15547650	15548150	NA	NA	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Kenyon cell	NA	Kenyon cell	CL:0000673	Enhancer activity assay	ATAC-seq	Transgenic reporter assay
E_01591	2024	39316719	Focal deletions of a promoter tether activate the IRX3 oncogene in T-cell acute lymphoblastic leukemia	Homo sapiens	hg38	chr16	54926631	54929466	NA	IRX3	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	ALL-SIL	CVCL_1805	T cell	CL:0000084	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Chromatin accessibility assay; Histone modification profiling	H3K27ac HiChIP; H3K27ac ChIP-seq; ATAC-seq; RNA-seq	CRISPR/Cas9 deletion; UMI-4C; qRT-PCR
E_01592	2015	26364592	A highly conserved NF-κB-responsive enhancer is critical for thymic expression of Aire in mice	Mus musculus	mm10	chr10	78046488	78046636	Nfkb1	Aire	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Thymic Medullary Epithelial Cells (mTECs)	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; EMSA/gel-shift assay; 3C; RT-qPCR/qPCR; Histology/immunostaining
E_01593	2025	39796169	Defining Mechanistic Links Between the Non-Coding Variant rs17673553 in CLEC16A and Lupus Susceptibility	Homo sapiens	hg38	chr16	11075000	11075280	CTCF	CLEC16A	Enhancer	Active	Disease	Burkitt lymphoma	MONDO:0007243	DOID:8584	lymph node	UBERON:0000029	Namalwa (B-lymphocyte)	CVCL_0128	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; Luciferase reporter assay	CRISPR knockout, siRNA Knockdown; RT-qPCR; CRISPRa (dCas9-VPR, dCas9-TET1); CRISPRi (dCas9-DNMT3A, dCas9-MeCP2); Western blot; Luciferase reporter assay; Reporter assay; ChIP-qPCR; qPCR; siRNA knockdown
E_01594	2025	39796169	Defining Mechanistic Links Between the Non-Coding Variant rs17673553 in CLEC16A and Lupus Susceptibility	Homo sapiens	hg38	chr16	11075000	11075280	GATA3	CLEC16A	Enhancer	Active	Disease	Burkitt lymphoma	MONDO:0007243	DOID:8584	lymph node	UBERON:0000029	Namalwa (B-lymphocyte)	CVCL_0128	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; Luciferase reporter assay	CRISPR knockout, siRNA Knockdown; RT-qPCR; CRISPRa (dCas9-VPR, dCas9-TET1); CRISPRi (dCas9-DNMT3A, dCas9-MeCP2); Western blot; Luciferase reporter assay; Reporter assay; ChIP-qPCR; qPCR; siRNA knockdown
E_01595	2025	39796169	Defining Mechanistic Links Between the Non-Coding Variant rs17673553 in CLEC16A and Lupus Susceptibility	Homo sapiens	hg38	chr16	11075000	11075280	STAT3	CLEC16A	Enhancer	Active	Disease	Burkitt lymphoma	MONDO:0007243	DOID:8584	lymph node	UBERON:0000029	Namalwa (B-lymphocyte)	CVCL_0128	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; Luciferase reporter assay	CRISPR knockout, siRNA Knockdown; RT-qPCR; CRISPRa (dCas9-VPR, dCas9-TET1); CRISPRi (dCas9-DNMT3A, dCas9-MeCP2); Western blot; Luciferase reporter assay; Reporter assay; ChIP-qPCR; qPCR; siRNA knockdown
E_01596	2025	40433695	Super-Enhancer-Driven HCG20 Promotes Pulmonary Hypertension Through U2AF2 Splicing	Homo sapiens	hg38	chr6	31350000	31355000	USF2	HCG20	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	Human Pulmonary Artery Endothelial Cells	NA	pulmonary artery endothelial cell	CL:1001568	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation	ChIP-seq; RNA-seq; RNA-seq; ChIP-seq	ChIP-qPCR, CRISPR knockout; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; Luciferase reporter assay; ChIP-qPCR; ChIP; RT-qPCR; Reporter assay
E_01597	2025	40433695	Super-Enhancer-Driven HCG20 Promotes Pulmonary Hypertension Through U2AF2 Splicing	Homo sapiens	hg38	chr6	31356000	31361000	USF2	HCG20	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	Human Pulmonary Artery Endothelial Cells	NA	pulmonary artery endothelial cell	CL:1001568	Enhancer activity assay; TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation	ChIP-seq; RNA-seq; RNA-seq; ChIP-seq	ChIP-qPCR; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; Luciferase reporter assay; ChIP-qPCR; ChIP; RT-qPCR; Reporter assay
E_01598	2025	40691407	NKX2-1 drives neuroendocrine transdifferentiation of prostate cancer via epigenetic and 3D chromatin remodeling	Homo sapiens	hg38	chr14	36508249	36509448	FOXA2	NKX2-1	Enhancer	Active	Disease	neuroendocrine prostate cancer	MONDO:0002477	NA	left supraclavicular lymph node	UBERON:8480056	LNCaP	CVCL_0395	malignant cell	CL:0001064	Functional perturbation assay; TF binding assay; Chromatin interaction assay	FOXA2 ChIP-seq; H3K4me1 ChIP-seq; H3K27ac ChIP-seq; Hi-C; ATAC-seq; RNA-seq	FOXA2 knockdown; RT-qPCR; Western blot
E_01599	2025	40691407	NKX2-1 drives neuroendocrine transdifferentiation of prostate cancer via epigenetic and 3D chromatin remodeling	Homo sapiens	hg38	chr14	36514552	36515387	FOXA2	NKX2-1	Enhancer	Active	Disease	neuroendocrine prostate cancer	MONDO:0002477	NA	left supraclavicular lymph node	UBERON:8480056	LNCaP	CVCL_0395	malignant cell	CL:0001064	Functional perturbation assay; TF binding assay; Chromatin interaction assay	FOXA2 ChIP-seq; H3K4me1 ChIP-seq; H3K27ac ChIP-seq; Hi-C; ATAC-seq; RNA-seq	FOXA2 knockdown; RT-qPCR; Western blot
E_01600	2025	41354677	Characterization of a cis-regulatory element upstream of matrix metalloproteinase-9	Homo sapiens	hg38	chr20	46000017	46000761	ARID3A	MMP9	Enhancer	Active	Normal	NA	NA	NA	placenta	UBERON:0001987	HTR-8/SVneo	CVCL_3286	trophoblast	CL:0000358	Enhancer activity assay; Functional perturbation assay; TF-binding/motif analysis	H3K27ac ChIP-seq; comparative epigenomic profiling	Luciferase reporter assay; CRISPR-Cas9 enhancer deletion; RT-qPCR; TF-motif perturbation
E_01601	2025	41354677	Characterization of a cis-regulatory element upstream of matrix metalloproteinase-9	Homo sapiens	hg38	chr20	46000017	46000761	TEAD4	MMP9	Enhancer	Active	Normal	NA	NA	NA	placenta	UBERON:0001987	HTR-8/SVneo	CVCL_3286	trophoblast	CL:0000358	Enhancer activity assay; Functional perturbation assay; TF-binding/motif analysis	H3K27ac ChIP-seq; comparative epigenomic profiling	Luciferase reporter assay; CRISPR-Cas9 enhancer deletion; RT-qPCR; TF-motif perturbation
E_01602	2025	41354677	Characterization of a cis-regulatory element upstream of matrix metalloproteinase-9	Homo sapiens	hg38	chr20	46000017	46000761	TFAP2C	MMP9	Enhancer	Active	Normal	NA	NA	NA	placenta	UBERON:0001987	HTR-8/SVneo	CVCL_3286	trophoblast	CL:0000358	Enhancer activity assay; Functional perturbation assay; TF-binding/motif analysis	H3K27ac ChIP-seq; comparative epigenomic profiling	Luciferase reporter assay; CRISPR-Cas9 enhancer deletion; RT-qPCR; TF-motif perturbation
E_01603	2024	38806452	TAD border deletion at the Kit locus causes tissue-specific ectopic activation of a neighboring gene	Mus musculus	mm10	chr5	75699926	75706926	NA	Kdr	Enhancer	Active	Normal	NA	NA	NA	zone of skin	UBERON:0000014	Primary Melanocytes (Kit ?30k)	NA	melanocyte	CL:0000148	Functional perturbation assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation	Hi-C; RNA-seq; ChIP-seq	CRISPR knockout, qRT-PCR, Immunohistochemistry; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_01604	2024	38806452	TAD border deletion at the Kit locus causes tissue-specific ectopic activation of a neighboring gene	Mus musculus	mm10	chr5	75825926	75832926	NA	Kdr	Enhancer	Active	Normal	NA	NA	NA	zone of skin	UBERON:0000014	Primary Melanocytes (Kit ?30k)	NA	melanocyte	CL:0000148	Functional perturbation assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation	Hi-C; RNA-seq; ChIP-seq	CRISPR knockout, qRT-PCR, Immunohistochemistry; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_01605	2024	38806452	TAD border deletion at the Kit locus causes tissue-specific ectopic activation of a neighboring gene	Mus musculus	mm10	chr5	75699926	75706926	NA	Kit	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary Mast cells	NA	mast cell	CL:0000097	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation; In vivo functional validation	ChIP-seq; RNA-seq, Hi-C	CRISPR knockout, qRT-PCR; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_01606	2024	38806452	TAD border deletion at the Kit locus causes tissue-specific ectopic activation of a neighboring gene	Mus musculus	mm10	chr5	75825926	75832926	NA	Kit	Enhancer	Active	Normal	NA	NA	NA	zone of skin	UBERON:0000014	Primary Melanocytes	NA	melanocyte	CL:0000148	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation; In vivo functional validation	ChIP-seq; RNA-seq, Hi-C	CRISPR knockout, qRT-PCR; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_01607	2023	37772400	An Anterior Second Heart Field Enhancer Regulates the Gene Regulatory Network of the Cardiac Outflow Tract	Mus musculus	mm10	chr17	26850487	26851000	Gata6	Nkx2-5	Enhancer	Active	Disease	conotruncal heart malformations	MONDO:0016581	NA	outflow tract	UBERON:0004145	embryonic mouse anterior second heart field, outflow tract and right ventricular myocardium	NA	cardiac muscle cell	CL:0000746	TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation; Endogenous enhancer deletion assay; TF-enhancer interaction assay; developmental phenotyping; cardiac electrophysiology	RNA-seq; single-cell RNA-seq; GATA6 ChIP-seq; ATAC-seq; ChIP-seq	CRISPR/Cas9 226-bp enhancer deletion; RT-qPCR; ChIP-qPCR; histology; scanning electron microscopy; ECG; echocardiography; optical mapping; Start/End represent the paper-defined -9435 to -8922 functional enhancer interval mapped to mm10; the 226-bp CRISPR deletion is nested within this interval; CRISPR-Cas9 endogenous deletion/editing; ChIP; Site-directed/motif mutagenesis; Mouse genetic deletion/knock-in
E_01608	2023	37772400	An Anterior Second Heart Field Enhancer Regulates the Gene Regulatory Network of the Cardiac Outflow Tract	Mus musculus	mm10	chr17	26850487	26851000	Gata6	Nkx2-5	Enhancer	Active	Disease	conotruncal heart malformations	MONDO:0016581	NA	outflow tract	UBERON:0004145	human iPSC-derived cardiomyocytes for GATA6 chromatin assays	NA	cardiac muscle cell	CL:0000746	TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation; Endogenous enhancer deletion assay; TF-enhancer interaction assay; developmental phenotyping; cardiac electrophysiology	RNA-seq; single-cell RNA-seq; GATA6 ChIP-seq; ATAC-seq; ChIP-seq	CRISPR/Cas9 226-bp enhancer deletion; RT-qPCR; ChIP-qPCR; histology; scanning electron microscopy; ECG; echocardiography; optical mapping; Start/End represent the paper-defined -9435 to -8922 functional enhancer interval mapped to mm10; the 226-bp CRISPR deletion is nested within this interval; CRISPR-Cas9 endogenous deletion/editing; ChIP; Site-directed/motif mutagenesis; Mouse genetic deletion/knock-in
E_01609	2020	33044128	ATAC-Seq Reveals an Isl1 Enhancer That Regulates Sinoatrial Node Development and Function	Mus musculus	mm10	chr1	172411511	172413110	Mef2c	Rgs6	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	NA	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation	ATAC-seq; RNA-seq; ChIP-seq; ATAC-seq	Transgenic reporter assay, X-gal Staining; Transgenic enhancer reporter assay; Mouse genetic deletion/knock-in
E_01610	2020	33044128	ATAC-Seq Reveals an Isl1 Enhancer That Regulates Sinoatrial Node Development and Function	Mus musculus	mm10	chr12	4704343	4706142	Mef2c	Ptgfr	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	NA	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation	ATAC-seq; RNA-seq; ChIP-seq; ATAC-seq	Transgenic reporter assay, X-gal Staining; Transgenic enhancer reporter assay; Mouse genetic deletion/knock-in
E_01611	2020	33044128	ATAC-Seq Reveals an Isl1 Enhancer That Regulates Sinoatrial Node Development and Function	Mus musculus	mm10	chr15	103026344	103028143	Mef2c	Hcn4	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	NA	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Functional perturbation assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation	ATAC-seq; RNA-seq; ChIP-seq; ATAC-seq	Transgenic reporter assay, CRISPR knockout, X-gal Staining; Transgenic enhancer reporter assay; Mouse genetic deletion/knock-in
E_01612	2017	27881681	A Novel Regulatory Mechanism of Type II Collagen Expression via a SOX9-dependent Enhancer in Intron 6	Rattus norvegicus	rn4	chr7	84833410	84834080	Sox5	Col2a1	Enhancer	Active	Normal	NA	NA	NA	cartilage tissue	UBERON:0002418	RCS rat chondrosarcoma cells	NA	chondrocyte	CL:0000138	Enhancer activity assay; TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation	SOX9 ChIP-seq; ChIP-seq	Luciferase reporter assay; stable reporter assay; SOX5/SOX9 transactivation; EMSA/supershift; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; EMSA; ChIP
E_01613	2017	27881681	A Novel Regulatory Mechanism of Type II Collagen Expression via a SOX9-dependent Enhancer in Intron 6	Rattus norvegicus	rn4	chr7	84833410	84834080	Sox9	Col2a1	Enhancer	Active	Normal	NA	NA	NA	cartilage tissue	UBERON:0002418	RCS rat chondrosarcoma cells	NA	chondrocyte	CL:0000138	Enhancer activity assay; TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; Endogenous functional perturbation assay	SOX9 ChIP-seq; ChIP-seq	Luciferase reporter assay; stable reporter assay; CRISPR/Cas9 intron-6 deletion; ChIP-qPCR; EMSA/supershift; RT-qPCR; Western blot; CRISPR-Cas9 endogenous deletion/editing; EMSA; ChIP
E_01614	2016	27866707	A Functional Variant Associated with Atrial Fibrillation Regulates PITX2c Expression through TFAP2a	Homo sapiens	hg19	chr4	111553098	111553222	TFAP2A	PITX2	Enhancer	Active	Disease	atrial fibrillation	MONDO:0004981	DOID:0060224	heart	UBERON:0000948	hESC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	TF binding assay; Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation; Disease-associated enhancer assay	ENCODE and Roadmap epigenomic integration	Dual-luciferase reporter assay; zebrafish enhancer reporter assay; CRISPR-Cas9 enhancer deletion; CRISPR allele editing; TFAP2A binding assay; qRT-PCR; CRISPR-Cas9 endogenous deletion/editing; In vivo phenotyping
E_01615	2011	21486496	Identification of a novel intronic enhancer responsible for the transcriptional regulation of musashi1 in neural stem/progenitor cells	Mus musculus	mm10	chr5	115358083	115360083	Qsox1	Msi1	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_01616	2011	21486496	Identification of a novel intronic enhancer responsible for the transcriptional regulation of musashi1 in neural stem/progenitor cells	Mus musculus	mm10	chr5	115358083	115360083	Tfap2a	Msi1	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_01617	2008	18836447	Regulation of a remote Shh forebrain enhancer by the Six3 homeoprotein	Homo sapiens	hg38	chr7	156268357	156269154	SIX3	SHH	Enhancer	Active	Disease	holoprosencephaly	MONDO:0016296	DOID:4621	hypothalamus	UBERON:0001898	transient transgenic mouse embryos	NA	embryonic forebrain cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Disease-variant assay	DNA affinity-capture LC-MS/MS proteomics	Patient SBE2 sequencing; transgenic LacZ reporter assay; SBE2 C>T site-directed mutagenesis; transient transfection; EMSA; antibody supershift; ChIP; Transgenic mouse enhancer assay
E_01618	2023	37772400	An Anterior Second Heart Field Enhancer Regulates the Gene Regulatory Network of the Cardiac Outflow Tract	Homo sapiens	hg38	chr5	173245543	173245843	GATA6	NKX2-5	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	hiPSC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	TF binding assay; Chromatin accessibility assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation; cross-species enhancer validation	GATA6 ChIP-seq; ATAC-seq; single-cell RNA-seq; RNA-seq; ChIP-seq	ChIP-qPCR / targeted validation; comparison with mouse CRISPR-deletion phenotype; CRISPR-Cas9 endogenous deletion/editing; ChIP; Site-directed/motif mutagenesis; Mouse genetic deletion/knock-in
E_01619	2023	37772400	An Anterior Second Heart Field Enhancer Regulates the Gene Regulatory Network of the Cardiac Outflow Tract	Mus musculus	mm10	chr17	26853910	26854423	Gata6	Nkx2-5	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	Embryonic mouse heart / anterior second heart field	NA	cardiac muscle cell	CL:0000746	TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation; In vivo enhancer deletion; TF binding; developmental functional validation	RNA-seq; single-cell RNA-seq; ChIP-seq	CRISPR-Cas9 226-bp enhancer deletion; RT-qPCR; histology; scanning electron microscopy; echocardiography; optical mapping; CRISPR-Cas9 endogenous deletion/editing; ChIP; Site-directed/motif mutagenesis; Mouse genetic deletion/knock-in
E_01620	2016	27866707	A Functional Variant Associated with Atrial Fibrillation Regulates PITX2c Expression through TFAP2a	Homo sapiens	hg19	chr4	111553081	111553310	TFAP2A	PITX2	Enhancer	Active	Disease	atrial fibrillation	MONDO:0004981	DOID:0060224	heart	UBERON:0000948	WA07	CVCL_9772	cardiac muscle cell	CL:0000746	Enhancer activity assay; Functional perturbation assay; TF binding assay; Gene expression assay; Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation; eRNA assay	NA	CRISPR-Cas9 biallelic enhancer deletion; CRISPR-Cas9 HDR allele editing; Sanger sequencing; RT-qPCR; TFAP2A ChIP-qPCR; Allele-specific ChIP-qPCR; EMSA; TFAP2A siRNA knockdown; Western blot; eRNA RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; In vivo phenotyping
E_01621	2025	40433695	Super-Enhancer-Driven HCG20 Promotes Pulmonary Hypertension Through U2AF2 Splicing	Mus musculus	mm10	chr17	34520000	34525000	NA	Hcg20	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	Mouse Pulmonary Artery Endothelial Cells	NA	pulmonary artery endothelial cell	CL:1001568	Enhancer activity assay; Functional perturbation assay; Chromatin-state profiling; Endogenous enhancer perturbation	ChIP-seq; RNA-seq; RNA-seq; ChIP-seq	RT-qPCR; Western blot; CRISPR-Cas9 endogenous deletion/editing; Luciferase reporter assay; ChIP-qPCR; ChIP; RT-qPCR; Reporter assay
E_01622	2019	31324781	Deletion of a Csf1r enhancer selectively impacts CSF1R expression and development of tissue macrophage populations	Mus musculus	mm10	chr18	60811244	60811580	Spi1	Csf1r	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse primary macrophages	NA	macrophage	CL:0000235	Enhancer activity assay; Functional perturbation assay; TF binding assay; Endogenous enhancer perturbation; In vivo functional validation	ChIP-seq; ATAC-seq; RNA-seq, Microarray	CRISPR knockout; RT-qPCR; Western blot, Flow Cytometry, Immunohistochemistry, Phagocytosis Assay; Mouse genetic deletion/knock-in
E_01623	2015	26214525	GATA2 is required for lymphatic vessel valve development and maintenance	Homo sapiens	hg19	chr1	214150511	214151337	GATA2	PROX1	Enhancer	Active	Disease	lymphedema	MONDO:0019297	DOID:4977	dermis	UBERON:0002067	Primary adult human dermal lymphatic endothelial cells (hLECs)	NA	endothelial cell	CL:0000115	Enhancer activity assay; Functional perturbation assay; TF binding assay	GATA2 ChIP-seq; ENCODE regulatory annotation integration	Luciferase reporter assay; GATA-site mutagenesis; ChIP-qPCR; WEMSA; GATA2 siRNA knockdown; RT-qPCR
E_01624	2012	22303449	ISL1 directly regulates FGF10 transcription during human cardiac outflow formation	Homo sapiens	hg38	chr5	44385696	44386743	ISL1	FGF10	Enhancer	Active	Normal	NA	NA	NA	outflow tract	UBERON:0004145	human embryonic cardiac outflow tract tissue	NA	second heart field/cardiac progenitor cell	NA	Enhancer activity assay; TF binding assay; transgenic functional validation	Comparative genomics/conservation analysis	ChIP; EMSA; Luciferase reporter assay; Site-directed mutagenesis; transgenic mouse lacZ reporter assay
E_01625	2008	18836447	Regulation of a remote Shh forebrain enhancer by the Six3 homeoprotein	Homo sapiens	hg38	chr7	155754267	155755366	SIX3	SHH	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	Primary embryonic cells	NA	embryonic cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Transgenic reporter assay; ChIP-qPCR; EMSA; RT-qPCR; Transgenic mouse enhancer assay
E_01626	2012	22303449	ISL1 directly regulates FGF10 transcription during human cardiac outflow formation	Homo sapiens	hg38	chr5	44385696	44386743	GATA4	FGF10	Enhancer	Active	Normal	NA	NA	NA	outflow tract	UBERON:0004145	human embryonic cardiac outflow tract tissue	NA	second heart field/cardiac progenitor cell	NA	Enhancer activity assay; cooperative TF regulation assay; transgenic functional validation	Comparative genomics/conservation analysis	Luciferase reporter assay; transcription-factor co-transfection; transgenic mouse lacZ reporter assay; EMSA
E_01627	2012	22303449	ISL1 directly regulates FGF10 transcription during human cardiac outflow formation	Homo sapiens	hg38	chr5	44385696	44386743	TBX20	FGF10	Enhancer	Active	Normal	NA	NA	NA	outflow tract	UBERON:0004145	human embryonic cardiac outflow tract tissue	NA	second heart field/cardiac progenitor cell	NA	Enhancer activity assay; cooperative TF regulation assay; transgenic functional validation	Comparative genomics/conservation analysis	Luciferase reporter assay; transcription-factor co-transfection; transgenic mouse lacZ reporter assay; EMSA
E_01628	2008	18836447	Regulation of a remote Shh forebrain enhancer by the Six3 homeoprotein	Homo sapiens	hg19	chr7	155595558	155596658	SIX3	SHH	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	COS-1	CVCL_0223	COS-1 fibroblast-like cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	Luciferase reporter assay; ChIP-qPCR; Transgenic reporter assay; Transgenic mouse enhancer assay
E_01629	2017	27881681	A Novel Regulatory Mechanism of Type II Collagen Expression via a SOX9-dependent Enhancer in Intron 6	Mus musculus	mm10	chr7	129554284	129564284	Sox9	Col2a1	Enhancer	Active	Disease	Skeletal Diseases	NA	NA	NA	NA	Rat Chondrosarcoma Cells (RCS cells)	NA	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; EMSA/gel-shift assay; RT-qPCR/qPCR
E_01630	2019	31324781	Deletion of a Csf1r enhancer selectively impacts CSF1R expression and development of tissue macrophage populations	Mus musculus	mm10	chr18	60811244	60811580	Spi1	Csf1r	Enhancer	Active	Normal	NA	NA	NA	multiple tissues	NA	primary mouse macrophages	NA	macrophage	CL:0000235	Functional perturbation assay; Enhancer essentiality assay; In vivo macrophage-development assay	ChIP-seq; ATAC-seq; RNA-seq; microarray	Csf1r FIRE enhancer deletion mouse; Flow cytometry; RT-qPCR; macrophage differentiation assays
E_01631	2019	31324781	Deletion of a Csf1r enhancer selectively impacts CSF1R expression and development of tissue macrophage populations	Mus musculus	mm39	chr18	61241648	61241998	Spi1	Csf1r	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	heart resident macrophages	NA	macrophage	CL:0000235	Endogenous enhancer perturbation; In vivo functional validation; Endogenous enhancer deletion; tissue-specific macrophage-development phenotyping; enhancer/TF chromatin profiling	ATAC-seq; ChIP-seq; RNA expression profiling/microarray	CRISPR/genomic FIRE deletion; transgenic reporter; Flow cytometry; immunohistochemistry; mESC macrophage differentiation; Mouse genetic deletion/knock-in
E_01632	2019	31324781	Deletion of a Csf1r enhancer selectively impacts CSF1R expression and development of tissue macrophage populations	Mus musculus	mm39	chr18	61241648	61241998	Spi1	Csf1r	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	kidney resident macrophages	NA	macrophage	CL:0000235	Endogenous enhancer perturbation; In vivo functional validation; Endogenous enhancer deletion; tissue-specific macrophage-development phenotyping; enhancer/TF chromatin profiling	ATAC-seq; ChIP-seq; RNA expression profiling/microarray	CRISPR/genomic FIRE deletion; transgenic reporter; Flow cytometry; immunohistochemistry; mESC macrophage differentiation; Mouse genetic deletion/knock-in
E_01633	2019	31324781	Deletion of a Csf1r enhancer selectively impacts CSF1R expression and development of tissue macrophage populations	Mus musculus	mm39	chr18	61241648	61241998	Spi1	Csf1r	Enhancer	Active	Normal	NA	NA	NA	peritoneal cavity	UBERON:0001179	peritoneal resident macrophages	NA	macrophage	CL:0000235	Endogenous enhancer perturbation; In vivo functional validation; Endogenous enhancer deletion; tissue-specific macrophage-development phenotyping; enhancer/TF chromatin profiling	ATAC-seq; ChIP-seq; RNA expression profiling/microarray	CRISPR/genomic FIRE deletion; transgenic reporter; Flow cytometry; immunohistochemistry; mESC macrophage differentiation; Mouse genetic deletion/knock-in
E_01634	2019	31324781	Deletion of a Csf1r enhancer selectively impacts CSF1R expression and development of tissue macrophage populations	Mus musculus	mm39	chr18	61241648	61241998	Spi1	Csf1r	Enhancer	Active	Normal	NA	NA	NA	skin	UBERON:0002097	skin resident macrophages	NA	macrophage	CL:0000235	Endogenous enhancer perturbation; In vivo functional validation; Endogenous enhancer deletion; tissue-specific macrophage-development phenotyping; enhancer/TF chromatin profiling	ATAC-seq; ChIP-seq; RNA expression profiling/microarray	CRISPR/genomic FIRE deletion; transgenic reporter; Flow cytometry; immunohistochemistry; mESC macrophage differentiation; Mouse genetic deletion/knock-in
E_01635	2012	22303449	ISL1 directly regulates FGF10 transcription during human cardiac outflow formation	Homo sapiens	hg19	chr5	44385797	44386845	TBX20	FGF10	Enhancer	Active	Normal	NA	NA	NA	outflow tract	UBERON:0004145	C3H/10T1/2 clone 8	CVCL_0190	fibroblast	CL:0000057	Enhancer activity assay	NA	Dual-luciferase reporter assay; transcription-factor co-transfection; transgenic mouse LacZ reporter assay; EMSA
E_01636	2020	33044128	ATAC-Seq Reveals an Isl1 Enhancer That Regulates Sinoatrial Node Development and Function	Mus musculus	mm39	chr13	116322276	116325052	NA	Isl1	Enhancer	Active	Normal	NA	NA	NA	sinoatrial node	UBERON:0002351	FACS-sorted neonatal mouse sinoatrial node pacemaker cells	NA	pacemaker cardiomyocyte	NA	Enhancer discovery assay; In vivo enhancer activity assay; Endogenous enhancer perturbation assay	ATAC-seq	Transgenic mouse enhancer reporter assay; CRISPR/Cas9 2762-bp deletion of Rr303/Isl1-deltaISE; zebrafish enhancer reporter assay; RT-qPCR; histology; ECG; telemetry; cardiac electrophysiology
E_01637	2016	27866707	A Functional Variant Associated with Atrial Fibrillation Regulates PITX2c Expression through TFAP2a	Homo sapiens	hg19	chr4	111553081	111553310	TFAP2A	PITX2	Enhancer	Active	Disease	atrial fibrillation	MONDO:0004981	DOID:0060224	uterine cervix	UBERON:0000002	HeLa	CVCL_0030	NA	NA	TF binding assay; Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation	NA	Allele-specific TFAP2A ChIP-qPCR; CRISPR-Cas9 endogenous deletion/editing; In vivo phenotyping
E_01638	2012	22303449	ISL1 directly regulates FGF10 transcription during human cardiac outflow formation	Homo sapiens	hg19	chr5	44385797	44386845	ISL1	FGF10	Enhancer	Active	Normal	NA	NA	NA	outflow tract	UBERON:0004145	human embryonic outflow tract	NA	cardiac progenitor cell	NA	Enhancer activity assay; TF binding assay	NA	ChIP-qPCR; EMSA; Dual-luciferase reporter assay; transgenic mouse LacZ reporter assay
E_01639	2011	21486496	Identification of a novel intronic enhancer responsible for the transcriptional regulation of musashi1 in neural stem/progenitor cells	Mus musculus	mm10	chr5	115574958	115575553	NA	Msi1	Enhancer	Active	Normal	NA	NA	NA	nervous system	UBERON:0001016	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; cis-regulatory deletion mapping	Public H3K4me1/p300 ChIP-seq epigenomic support used for candidate selection (not study-generated)	BAC deletion mapping; Luciferase reporter assay; neural differentiation reporter assay
E_01640	2011	21486496	Identification of a novel intronic enhancer responsible for the transcriptional regulation of musashi1 in neural stem/progenitor cells	Mus musculus	mm10	chr5	115502658	115512658	NA	Msi1	Enhancer	Active	Normal	NA	NA	NA	nervous system	UBERON:0001016	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Candidate enhancer activity assay; BAC deletion mapping	Public H3K4me1/p300 ChIP-seq epigenomic support used for candidate selection (not study-generated)	BAC deletion mapping; Luciferase reporter assay
E_01641	2019	31324781	Deletion of a Csf1r enhancer selectively impacts CSF1R expression and development of tissue macrophage populations	Mus musculus	mm39	chr18	61241648	61241998	Spi1	Csf1r	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	bone-marrow monocytes and progenitors	NA	monocyte/myeloid progenitor	NA	Endogenous enhancer deletion; tissue-specific macrophage-development phenotyping; enhancer/TF chromatin profiling	ATAC-seq; ChIP-seq; RNA expression profiling/microarray	CRISPR/genomic FIRE deletion; transgenic reporter; Flow cytometry; immunohistochemistry; mESC macrophage differentiation
E_01642	2012	22303449	ISL1 directly regulates FGF10 transcription during human cardiac outflow formation	Homo sapiens	hg19	chr5	44385749	44386845	GATA4	FGF10	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	Human Embryos	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	ChIP-qPCR/ChIP; EMSA/gel-shift assay; Transgenic/LacZ assay
E_01643	2012	22303449	ISL1 directly regulates FGF10 transcription during human cardiac outflow formation	Homo sapiens	hg19	chr5	44385749	44386845	ISL1	FGF10	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	Human Embryos	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	ChIP-qPCR/ChIP; EMSA/gel-shift assay; Transgenic/LacZ assay
E_01644	2012	22303449	ISL1 directly regulates FGF10 transcription during human cardiac outflow formation	Homo sapiens	hg19	chr5	44385749	44386845	TBX20	FGF10	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	Human Embryos	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	ChIP-qPCR/ChIP; EMSA/gel-shift assay; Transgenic/LacZ assay
E_01645	2025	40691407	NKX2-1 drives neuroendocrine transdifferentiation of prostate cancer via epigenetic and 3D chromatin remodeling	Homo sapiens	hg38	chr20	20392790	20394473	NA	INSM1	Enhancer	Active	Disease	neuroendocrine prostate cancer	MONDO:0002477	NA	cervical lymph node	UBERON:0002429	NCI-H660	CVCL_1576	malignant cell	CL:0001064	Chromatin interaction assay; Regulatory element annotation	Hi-C; H3K27ac ChIP-seq; H3K27me3 ChIP-seq; RNA-seq	3C
E_01646	2012	22303449	ISL1 directly regulates FGF10 transcription during human cardiac outflow formation	Homo sapiens	hg19	chr5	44385797	44386845	TBX20	FGF10	Enhancer	Active	Normal	NA	NA	NA	outflow tract	UBERON:0004145	C3H/10T1/2 clone 8	CVCL_0190	fibroblast	CL:0000057	Enhancer activity assay	NA	Dual-luciferase reporter assay; transcription-factor co-transfection; transgenic mouse LacZ reporter assay
E_01647	2016	27866707	A Functional Variant Associated with Atrial Fibrillation Regulates PITX2c Expression through TFAP2a	Homo sapiens	hg19	chr4	111553081	111553310	NA	PITX2	Enhancer	Active	Disease	atrial fibrillation	MONDO:0004981	DOID:0060224	heart	UBERON:0000948	HL-1	CVCL_0303	cardiac muscle cell	CL:0000746	Enhancer activity assay	NA	Allele-specific luciferase reporter assay; CRISPR-Cas9
E_01648	2016	27354268	Dissection of the Major Hematopoietic Quantitative Trait Locus in Chromosome 6q23.3 Identifies miR-3662 as a Player in Hematopoiesis and Acute Myeloid Leukemia	Homo sapiens	hg19	chr6	135418600	135418700	NA	MIR3662	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Primary human CD34+ hematopoietic progenitor cells from non-leukemic donor	NA	hematopoietic progenitor cell	NA	Functional perturbation assay	NA	CRISPR/Cas9 genome editing; RT-qPCR
E_01649	2015	26364592	A highly conserved NF-κB-responsive enhancer is critical for thymic expression of Aire in mice	Mus musculus	mm10	chr10	177510950	177511040	NA	Aire	Enhancer	Active	Normal	NA	NA	NA	thymus	UBERON:0002370	mTEC	NA	medullary thymic epithelial cell	CL:0002365	Enhancer activity assay; Endogenous enhancer perturbation; In vivo functional validation	NA	Luciferase reporter assay; Mouse genetic deletion/knock-in
E_01650	2019	31324781	Deletion of a Csf1r enhancer selectively impacts CSF1R expression and development of tissue macrophage populations	Mus musculus	mm10	chr18	61108475	61108975	NA	Csf1r	Enhancer	Active	Normal	NA	NA	NA	skin	UBERON:0002097	Csf1r enhancer-deletion mouse	NA	macrophage	CL:0000235	Endogenous enhancer perturbation; In vivo functional validation; Canonical Csf1r FIRE enhancer; current mm10 interval standardized to chr18:61108475-61108975; in vivo FIRE deletion phenotype	RNA-seq and macrophage population profiling	Enhancer genome editing mouse; Flow cytometry; immunohistochemistry; expression analysis; Mouse genetic deletion/knock-in
E_01651	2015	26214525	GATA2 is required for lymphatic vessel valve development and maintenance	Homo sapiens	hg19	chr1	214150511	214151337	FOXC2	PROX1	Enhancer	Active	Disease	lymphedema	MONDO:0019297	DOID:4977	dermis	UBERON:0002067	Primary adult human dermal lymphatic endothelial cells (hLECs)	NA	endothelial cell	CL:0000115	Enhancer activity assay; TF binding assay	GATA2 ChIP-seq; ENCODE regulatory annotation integration	ChIP-qPCR; Luciferase reporter assay
E_01652	2015	26214525	GATA2 is required for lymphatic vessel valve development and maintenance	Homo sapiens	hg19	chr1	214150511	214151337	NFATC1	PROX1	Enhancer	Active	Disease	lymphedema	MONDO:0019297	DOID:4977	dermis	UBERON:0002067	Primary adult human dermal lymphatic endothelial cells (hLECs)	NA	endothelial cell	CL:0000115	Enhancer activity assay; TF binding assay	GATA2 ChIP-seq; ENCODE regulatory annotation integration	ChIP-qPCR; Luciferase reporter assay
E_01653	2012	22303449	ISL1 directly regulates FGF10 transcription during human cardiac outflow formation	Homo sapiens	hg19	chr5	44385797	44386845	GATA4	FGF10	Enhancer	Active	Normal	NA	NA	NA	outflow tract	UBERON:0004145	C3H/10T1/2 clone 8	CVCL_0190	fibroblast	CL:0000057	Enhancer activity assay; TF binding assay	NA	EMSA; Dual-luciferase reporter assay; Site-directed mutagenesis
E_01654	2025	41354677	Characterization of a cis-regulatory element upstream of matrix metalloproteinase-9	Mus musculus	mm9	chr2	164763372	164764407	NA	Mmp9	Enhancer	Active	Normal	NA	NA	NA	placenta	UBERON:0001987	ectoplacental cone	NA	trophoblast	CL:0000358	Enhancer activity assay; Cross-species cis-regulatory comparison	H3K27ac ChIP-seq; comparative epigenomic profiling	Luciferase reporter assay; sequence conservation analysis
E_01655	2019	31324781	Deletion of a Csf1r enhancer selectively impacts CSF1R expression and development of tissue macrophage populations	Mus musculus	mm10	chr18	61108475	61108975	NA	Csf1r	Enhancer	Active	Normal	NA	NA	NA	multiple tissues	NA	Csf1r enhancer-deletion mouse	NA	macrophage	CL:0000235	Canonical Csf1r FIRE enhancer; current mm10 interval standardized to chr18:61108475-61108975; in vivo FIRE deletion phenotype	RNA-seq and macrophage population profiling	Enhancer genome editing mouse; Flow cytometry; immunohistochemistry; expression analysis
E_01656	2015	26214525	GATA2 is required for lymphatic vessel valve development and maintenance	Homo sapiens	hg19	chr1	214150511	214151337	FOXC2	PROX1	Enhancer	Active	Disease	lymphedema	MONDO:0019297	DOID:4977	lymphatic vessel	UBERON:0001473	K-562	CVCL_0004	NA	NA	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_01657	2015	26214525	GATA2 is required for lymphatic vessel valve development and maintenance	Homo sapiens	hg19	chr1	214150511	214151337	GATA2	PROX1	Enhancer	Active	Disease	lymphedema	MONDO:0019297	DOID:4977	lymphatic vessel	UBERON:0001473	K-562	CVCL_0004	NA	NA	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_01658	2015	26214525	GATA2 is required for lymphatic vessel valve development and maintenance	Homo sapiens	hg19	chr1	214150511	214151337	NFATC1	PROX1	Enhancer	Active	Disease	lymphedema	MONDO:0019297	DOID:4977	lymphatic vessel	UBERON:0001473	K-562	CVCL_0004	NA	NA	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_01659	2016	27354268	Dissection of the Major Hematopoietic Quantitative Trait Locus in Chromosome 6q23.3 Identifies miR-3662 as a Player in Hematopoiesis and Acute Myeloid Leukemia	Homo sapiens	hg19	chr6	135502600	135502750	NA	MIR3662	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	healthy human cohort	NA	hematopoietic cell	CL:0000988	GWAS-locus association and expression analysis	GWAS genotyping; expression profiling	qRT-PCR
E_01660	2021	34245781	Diet-dependent natriuretic peptide receptor C expression in adipose tissue is mediated by PPARγ via long-range distal enhancers	Mus musculus	mm10	chr16	17253000	17253100	NA	Npr3	Enhancer	Active	Disease	obesity	MONDO:0011122	DOID:9970	adipose tissue	UBERON:0001013	3T3-L1	CVCL_0123	adipocyte	CL:0000136	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	ChIP-seq	Luciferase reporter assay, 3C; ChIP-qPCR; RT-qPCR; Luciferase reporter assay; siRNA knockdown; Reporter assay
E_01661	2021	34245781	Diet-dependent natriuretic peptide receptor C expression in adipose tissue is mediated by PPARγ via long-range distal enhancers	Mus musculus	mm10	chr16	17266000	17266100	NA	Npr3	Enhancer	Active	Disease	obesity	MONDO:0011122	DOID:9970	adipose tissue	UBERON:0001013	3T3-L1	CVCL_0123	adipocyte	CL:0000136	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	ChIP-seq	Luciferase reporter assay, 3C; ChIP-qPCR; RT-qPCR; Luciferase reporter assay; siRNA knockdown; Reporter assay
E_01662	2019	31827084	A primate-specific retroviral enhancer wires the XACT lncRNA into the core pluripotency network in humans	Homo sapiens	hg38	chrX	114038200	114039000	NA	XACT	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	H1-hESC	CVCL_9771	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Endogenous enhancer perturbation	ChIP-seq; RNA-seq, Hi-C; ATAC-seq	CRISPR knockout, CRISPRi; ChIP-qPCR; RT-qPCR, RNA-FISH; Western blot; CRISPR-Cas9 endogenous deletion/editing
E_01663	2019	31891018	A novel enhancer RNA, Hmrhl, positively regulates its host gene, phkb, in chronic myelogenous leukemia	Homo sapiens	hg19	chr16	47657923	47659423	NA	PHKB	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:0081088	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	ChIP-seq, ChIA-PET	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot; Luciferase reporter assay; ChIP-qPCR; ChIP; siRNA knockdown
E_01664	2018	30250174	Identification of a limb enhancer that is removed by pathogenic deletions downstream of the SHOX gene	Homo sapiens	hg19	chrX	827128	827691	NA	SHOX	Enhancer	Active	Disease	acute promyelocytic leukemia	MONDO:0012883	DOID:0060318	lung	UBERON:0002048	Human lung adenocarcinoma cell	NA	malignant cell	CL:0001064	Enhancer activity assay; Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation	NA	qRT-PCR, and ChIP-qPCR; Luciferase reporter assay; Site-directed/motif mutagenesis; Mouse genetic deletion/knock-in
E_01665	2017	28087634	Genome-wide identification of regulatory elements in Sertoli cells	Mus musculus	mm10	chr2	104914099	104915125	NA	Wt1	Enhancer	Active	Normal	NA	NA	NA	testis	UBERON:0000473	Sertoli cells	NA	Sertoli cell	CL:0000216	Enhancer activity assay; Chromatin-state profiling; Endogenous enhancer perturbation	DNase-seq; ChIP-seq; RNA-seq; ChIP-seq	Transgenic reporter assay; Transgenic enhancer reporter assay; ChIP; Site-directed/motif mutagenesis
E_01666	2017	29129929	IL-2 imprints human naive B cell fate towards plasma cell through ERK/ELK1-mediated BACH2 repression	Homo sapiens	hg19	chr6	91004796	91006944	ELK1	BACH2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human naive B cells	NA	B cell	CL:0000236	Enhancer activity assay; TF binding assay; Chromatin-state profiling; Cell-fate functional perturbation assay	RNA-seq; BACH2 ChIP-seq; public FANTOM5/H3K27ac enhancer-data integration; ChIP-seq	ELK1 ChIP-qPCR; histone-mark/p300 ChIP-qPCR; Luciferase reporter assay; IL-2 stimulation; ERK inhibition; RT-qPCR; Flow cytometry; plasma-cell differentiation assay; ChIP
E_01667	2015	25838425	Myocardial Infarction-Associated SNP at 6p24 Interferes With MEF2 Binding and Associates With PHACTR1 Expression Levels in Human Coronary Arteries	Homo sapiens	hg19	chr6	12826550	12826620	MEF2A	PHACTR1	Enhancer	Active	Disease	myocardial infarction	MONDO:0005068	DOID:5844	coronary artery	UBERON:0001621	hESC-derived endothelial cells	NA	endothelial cell	CL:0000115	Enhancer activity assay; Functional perturbation assay; TF binding assay; Regulatory variant functional assay	Genetic fine-mapping; eQTL analysis; epigenomic annotation	Reporter assay; MEF2 DNA-binding assay; CRISPR-Cas9 deletion of MEF2-binding site; RT-qPCR
E_01668	2016	26937964	In Vivo Deletion of the Cebpa +37 kb Enhancer Markedly Reduces Cebpa mRNA in Myeloid Progenitors but Not in Non-Hematopoietic Tissues to Impair Granulopoiesis	Mus musculus	mm10	chr7	35156394	35156899	Cebpa	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary mouse myeloid progenitors	NA	myeloid progenitor cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq evidence integration	Cre-loxP in vivo enhancer deletion; CRISPR/Cas9 Ets-site editing; Reporter assay; EMSA; RT-qPCR; Flow cytometry; colony-forming assay; transplantation assay; CRISPR-Cas9
E_01669	2016	26937964	In Vivo Deletion of the Cebpa +37 kb Enhancer Markedly Reduces Cebpa mRNA in Myeloid Progenitors but Not in Non-Hematopoietic Tissues to Impair Granulopoiesis	Mus musculus	mm10	chr7	35156394	35156899	Gata2	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary mouse myeloid progenitors	NA	myeloid progenitor cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq evidence integration	Cre-loxP in vivo enhancer deletion; CRISPR/Cas9 Ets-site editing; Reporter assay; EMSA; RT-qPCR; Flow cytometry; colony-forming assay; transplantation assay; CRISPR-Cas9
E_01670	2016	26937964	In Vivo Deletion of the Cebpa +37 kb Enhancer Markedly Reduces Cebpa mRNA in Myeloid Progenitors but Not in Non-Hematopoietic Tissues to Impair Granulopoiesis	Mus musculus	mm10	chr7	35156394	35156899	Myb	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary mouse myeloid progenitors	NA	myeloid progenitor cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq evidence integration	Cre-loxP in vivo enhancer deletion; CRISPR/Cas9 Ets-site editing; Reporter assay; EMSA; RT-qPCR; Flow cytometry; colony-forming assay; transplantation assay; CRISPR-Cas9
E_01671	2016	26937964	In Vivo Deletion of the Cebpa +37 kb Enhancer Markedly Reduces Cebpa mRNA in Myeloid Progenitors but Not in Non-Hematopoietic Tissues to Impair Granulopoiesis	Mus musculus	mm10	chr7	35156394	35156899	Runx1	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary mouse myeloid progenitors	NA	myeloid progenitor cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq evidence integration	Cre-loxP in vivo enhancer deletion; CRISPR/Cas9 Ets-site editing; Reporter assay; EMSA; RT-qPCR; Flow cytometry; colony-forming assay; transplantation assay; CRISPR-Cas9
E_01672	2016	26937964	In Vivo Deletion of the Cebpa +37 kb Enhancer Markedly Reduces Cebpa mRNA in Myeloid Progenitors but Not in Non-Hematopoietic Tissues to Impair Granulopoiesis	Mus musculus	mm10	chr7	35156394	35156899	Spi1	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary mouse myeloid progenitors	NA	myeloid progenitor cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq evidence integration	Cre-loxP in vivo enhancer deletion; CRISPR/Cas9 Ets-site editing; Reporter assay; EMSA; RT-qPCR; Flow cytometry; colony-forming assay; transplantation assay; CRISPR-Cas9
E_01673	2016	26937964	In Vivo Deletion of the Cebpa +37 kb Enhancer Markedly Reduces Cebpa mRNA in Myeloid Progenitors but Not in Non-Hematopoietic Tissues to Impair Granulopoiesis	Mus musculus	mm10	chr7	35156394	35156899	Tal1	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary mouse myeloid progenitors	NA	myeloid progenitor cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq evidence integration	Cre-loxP in vivo enhancer deletion; CRISPR/Cas9 Ets-site editing; Reporter assay; EMSA; RT-qPCR; Flow cytometry; colony-forming assay; transplantation assay; CRISPR-Cas9
E_01674	2016	26937964	In Vivo Deletion of the Cebpa +37 kb Enhancer Markedly Reduces Cebpa mRNA in Myeloid Progenitors but Not in Non-Hematopoietic Tissues to Impair Granulopoiesis	Mus musculus	mm10	chr7	35156536	35156974	Cebpa	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary myeloid progenitors	NA	myeloid progenitor cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Cre-loxP in vivo enhancer deletion; ChIP-qPCR; Luciferase reporter assay; RT-qPCR; CRISPR-Cas9
E_01675	2016	26937964	In Vivo Deletion of the Cebpa +37 kb Enhancer Markedly Reduces Cebpa mRNA in Myeloid Progenitors but Not in Non-Hematopoietic Tissues to Impair Granulopoiesis	Mus musculus	mm10	chr7	35156536	35156974	Gata2	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary myeloid progenitors	NA	myeloid progenitor cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Cre-loxP in vivo enhancer deletion; ChIP-qPCR; Luciferase reporter assay; RT-qPCR; CRISPR-Cas9
E_01676	2016	26937964	In Vivo Deletion of the Cebpa +37 kb Enhancer Markedly Reduces Cebpa mRNA in Myeloid Progenitors but Not in Non-Hematopoietic Tissues to Impair Granulopoiesis	Mus musculus	mm10	chr7	35156536	35156974	Myb	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary myeloid progenitors	NA	myeloid progenitor cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Cre-loxP in vivo enhancer deletion; ChIP-qPCR; Luciferase reporter assay; RT-qPCR; CRISPR-Cas9
E_01677	2016	26937964	In Vivo Deletion of the Cebpa +37 kb Enhancer Markedly Reduces Cebpa mRNA in Myeloid Progenitors but Not in Non-Hematopoietic Tissues to Impair Granulopoiesis	Mus musculus	mm10	chr7	35156536	35156974	Runx1	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary myeloid progenitors	NA	myeloid progenitor cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Cre-loxP in vivo enhancer deletion; ChIP-qPCR; Luciferase reporter assay; RT-qPCR; Flow cytometry; Colony-forming assay; Bone marrow transplantation; CRISPR-Cas9
E_01678	2016	26937964	In Vivo Deletion of the Cebpa +37 kb Enhancer Markedly Reduces Cebpa mRNA in Myeloid Progenitors but Not in Non-Hematopoietic Tissues to Impair Granulopoiesis	Mus musculus	mm10	chr7	35156536	35156974	Spi1	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary myeloid progenitors	NA	myeloid progenitor cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Cre-loxP in vivo enhancer deletion; ChIP-qPCR; Luciferase reporter assay; Ets-site mutagenesis; RT-qPCR; Flow cytometry; Colony-forming assay; CRISPR-Cas9
E_01679	2016	26937964	In Vivo Deletion of the Cebpa +37 kb Enhancer Markedly Reduces Cebpa mRNA in Myeloid Progenitors but Not in Non-Hematopoietic Tissues to Impair Granulopoiesis	Mus musculus	mm10	chr7	35156536	35156974	Tal1	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary myeloid progenitors	NA	myeloid progenitor cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Cre-loxP in vivo enhancer deletion; ChIP-qPCR; Luciferase reporter assay; RT-qPCR; CRISPR-Cas9
E_01680	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr13	53463266	53463541	Atf4	Msx2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	C2C12,Primary Bone Marrow-Mesenchymal Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01681	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr13	53463266	53463541	Dlx3	Msx2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	C2C12,Primary Bone Marrow-Mesenchymal Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01682	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr13	53463266	53463541	Dlx5	Msx2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	C2C12,Primary Bone Marrow-Mesenchymal Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01683	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr13	53463266	53463541	Msx2	Msx2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	C2C12,Primary Bone Marrow-Mesenchymal Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01684	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr13	53463266	53463541	Runx2	Msx2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	C2C12,Primary Bone Marrow-Mesenchymal Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01685	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr13	53463266	53463541	Sp7	Msx2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	C2C12,Primary Bone Marrow-Mesenchymal Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01686	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr17	44494486	44495486	Atf4	Runx2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	C2C12,Primary Bone Marrow-Mesenchymal Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01687	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr17	44494486	44495486	Dlx3	Runx2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	C2C12,Primary Bone Marrow-Mesenchymal Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01688	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr17	44494486	44495486	Dlx5	Runx2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	C2C12,Primary Bone Marrow-Mesenchymal Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01689	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr17	44494486	44495486	Msx2	Runx2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	C2C12,Primary Bone Marrow-Mesenchymal Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01690	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr17	44494486	44495486	Runx2	Runx2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	C2C12,Primary Bone Marrow-Mesenchymal Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01691	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr17	44494486	44495486	Sp7	Runx2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	C2C12,Primary Bone Marrow-Mesenchymal Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01692	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr17	44494598	44494816	Atf4	Runx2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	C2C12,Primary Bone Marrow-Mesenchymal Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01693	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr17	44494598	44494816	Dlx3	Runx2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	C2C12,Primary Bone Marrow-Mesenchymal Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01694	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr17	44494598	44494816	Dlx5	Runx2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	C2C12,Primary Bone Marrow-Mesenchymal Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01695	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr17	44494598	44494816	Msx2	Runx2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	C2C12,Primary Bone Marrow-Mesenchymal Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01696	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr17	44494598	44494816	Runx2	Runx2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	C2C12,Primary Bone Marrow-Mesenchymal Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01697	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr17	44494598	44494816	Sp7	Runx2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	C2C12,Primary Bone Marrow-Mesenchymal Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01698	2017	29129929	IL-2 imprints human naive B cell fate towards plasma cell through ERK/ELK1-mediated BACH2 repression	Homo sapiens	hg19	chr6	91004796	91006944	ELK1	BACH2	Enhancer	Repressed	Normal	NA	NA	NA	blood	UBERON:0000178	B Cell	NA	B cell	CL:0000236	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01699	2015	25838425	Myocardial Infarction-Associated SNP at 6p24 Interferes With MEF2 Binding and Associates With PHACTR1 Expression Levels in Human Coronary Arteries	Homo sapiens	hg19	chr6	12826550	12826620	MEF2A	PHACTR1	Enhancer	Repressed	Disease	coronary artery disease	NA	NA	aorta	UBERON:0000947	hESC-derived endothelial cells	NA	endothelial cell	CL:0000115	Enhancer activity assay; Functional perturbation assay; TF binding assay; Disease-variant functional analysis; Endogenous enhancer perturbation	eQTL analysis; GWAS	EMSA, CRISPR knockout; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_01700	2015	25838425	Myocardial Infarction-Associated SNP at 6p24 Interferes With MEF2 Binding and Associates With PHACTR1 Expression Levels in Human Coronary Arteries	Homo sapiens	hg19	chr6	12902957	12904957	MEF2A	PHACTR1	Enhancer	Active	Disease	coronary artery disease	NA	NA	coronary artery	UBERON:0001621	HUVEC and hESC-derived endothelial cells	NA	endothelial cell	CL:0000115	TF binding assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Allele-specific cis-regulatory assay; Functional genome-editing assay	Genetic fine-mapping; coronary-artery eQTL analysis; Roadmap Epigenomics integration; eQTL analysis; GWAS	EMSA/supershift; CRISPR/Cas9 deletion of the MEF2-binding site; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_01701	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr13	53476414	53476689	Smad1	Msx2	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Luciferase reporter assay; Site-directed mutagenesis; ChIP-qPCR; RT-qPCR; Western blot; BMP-2/Wnt3a stimulation; GST pull-down; co-immunoprecipitation
E_01702	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr13	53476414	53476689	Smad4	Msx2	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Luciferase reporter assay; Site-directed mutagenesis; ChIP-qPCR; RT-qPCR; Western blot; BMP-2/Wnt3a stimulation; GST pull-down; co-immunoprecipitation
E_01703	2016	26937964	In Vivo Deletion of the Cebpa +37 kb Enhancer Markedly Reduces Cebpa mRNA in Myeloid Progenitors but Not in Non-Hematopoietic Tissues to Impair Granulopoiesis	Mus musculus	mm10	chr7	35156536	35156974	Cebpa	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary mouse myeloid progenitors	NA	myeloid progenitor cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq evidence integration	Cre-loxP in vivo enhancer deletion; enhancer reporter mutagenesis; EMSA; RT-qPCR; Flow cytometry; colony-forming assay; transplantation assay; CRISPR-Cas9
E_01704	2016	26937964	In Vivo Deletion of the Cebpa +37 kb Enhancer Markedly Reduces Cebpa mRNA in Myeloid Progenitors but Not in Non-Hematopoietic Tissues to Impair Granulopoiesis	Mus musculus	mm10	chr7	35156536	35156974	Gata2	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary mouse myeloid progenitors	NA	myeloid progenitor cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq evidence integration	Cre-loxP in vivo enhancer deletion; enhancer reporter mutagenesis; EMSA; RT-qPCR; Flow cytometry; colony-forming assay; transplantation assay; CRISPR-Cas9
E_01705	2016	26937964	In Vivo Deletion of the Cebpa +37 kb Enhancer Markedly Reduces Cebpa mRNA in Myeloid Progenitors but Not in Non-Hematopoietic Tissues to Impair Granulopoiesis	Mus musculus	mm10	chr7	35156536	35156974	Myb	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary mouse myeloid progenitors	NA	myeloid progenitor cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq evidence integration	Cre-loxP in vivo enhancer deletion; enhancer reporter mutagenesis; EMSA; RT-qPCR; Flow cytometry; colony-forming assay; transplantation assay; CRISPR-Cas9
E_01706	2016	26937964	In Vivo Deletion of the Cebpa +37 kb Enhancer Markedly Reduces Cebpa mRNA in Myeloid Progenitors but Not in Non-Hematopoietic Tissues to Impair Granulopoiesis	Mus musculus	mm10	chr7	35156536	35156974	Runx1	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary mouse myeloid progenitors	NA	myeloid progenitor cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq evidence integration	Cre-loxP in vivo enhancer deletion; enhancer reporter mutagenesis; EMSA; RT-qPCR; Flow cytometry; colony-forming assay; transplantation assay; CRISPR-Cas9
E_01707	2016	26937964	In Vivo Deletion of the Cebpa +37 kb Enhancer Markedly Reduces Cebpa mRNA in Myeloid Progenitors but Not in Non-Hematopoietic Tissues to Impair Granulopoiesis	Mus musculus	mm10	chr7	35156536	35156974	Spi1	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary mouse myeloid progenitors	NA	myeloid progenitor cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq evidence integration	Cre-loxP in vivo enhancer deletion; enhancer reporter mutagenesis; EMSA; RT-qPCR; Flow cytometry; colony-forming assay; transplantation assay; CRISPR-Cas9
E_01708	2016	26937964	In Vivo Deletion of the Cebpa +37 kb Enhancer Markedly Reduces Cebpa mRNA in Myeloid Progenitors but Not in Non-Hematopoietic Tissues to Impair Granulopoiesis	Mus musculus	mm10	chr7	35156536	35156974	Tal1	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary mouse myeloid progenitors	NA	myeloid progenitor cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq evidence integration	Cre-loxP in vivo enhancer deletion; enhancer reporter mutagenesis; EMSA; RT-qPCR; Flow cytometry; colony-forming assay; transplantation assay; CRISPR-Cas9
E_01709	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr17	44815967	44816185	Smad1	Runx2	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Luciferase reporter assay; Smad-binding-site deletion/mutagenesis; ChIP-qPCR; RT-qPCR; Western blot; BMP-2/Wnt3a stimulation; GST pull-down; co-immunoprecipitation
E_01710	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr17	44815967	44816185	Smad4	Runx2	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Luciferase reporter assay; Smad-binding-site deletion/mutagenesis; ChIP-qPCR; RT-qPCR; Western blot; BMP-2/Wnt3a stimulation; GST pull-down; co-immunoprecipitation
E_01711	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr13	53476414	53476689	Tcf7l2	Msx2	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Luciferase reporter assay; TCF/LEF-site mutagenesis; ChIP-qPCR; RT-qPCR; dominant-negative TCF4 perturbation; BMP-2/Wnt3a stimulation; GST pull-down; co-immunoprecipitation
E_01712	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr17	44815967	44816185	Tcf7l2	Runx2	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Luciferase reporter assay; TCF/LEF-site mutagenesis; ChIP-qPCR; RT-qPCR; dominant-negative TCF4 perturbation; activated beta-catenin perturbation; BMP-2/Wnt3a stimulation
E_01713	2016	26937964	In Vivo Deletion of the Cebpa +37 kb Enhancer Markedly Reduces Cebpa mRNA in Myeloid Progenitors but Not in Non-Hematopoietic Tissues to Impair Granulopoiesis	Mus musculus	mm10	chr7	134136598	134137038	Runx1	Cebpa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	32Dcl3	CVCL_0119	myeloid progenitor cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; In vivo enhancer deletion assay	ChIP-seq	CRISPR-Cas9 Ets-site mutagenesis; conditional enhancer deletion; RT-qPCR; Flow cytometry; colony-forming assay; transplantation assay
E_01714	2018	30008316	Targeted Enhancer Activation by a Subunit of the Integrator Complex	Homo sapiens	hg19	chr5	149400000	149401000	EGR1	CSF1R	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Myeloid tissue	NA	myeloid cell	CL:0000763	Functional perturbation assay	ChIP-seq; RNA-seq	qRT-PCR, and ChIP-qPCR
E_01715	2018	30008316	Targeted Enhancer Activation by a Subunit of the Integrator Complex	Homo sapiens	hg19	chr16	29018500	29021500	NA	CD84	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Myeloid tissue	NA	myeloid cell	CL:0000763	Functional perturbation assay	ChIP-seq; RNA-seq	qRT-PCR, and ChIP-qPCR
E_01716	2016	26937964	In Vivo Deletion of the Cebpa +37 kb Enhancer Markedly Reduces Cebpa mRNA in Myeloid Progenitors but Not in Non-Hematopoietic Tissues to Impair Granulopoiesis	Mus musculus	mm10	chr7	35156353	35161233	Runx1	Cebpa	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Myeloid cells	NA	NA	NA	Endogenous enhancer perturbation; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; Western blot; Transgenic/LacZ assay
E_01717	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr6	6770399	6771465	Smad1	Dlx5	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Enhancer activity assay; TF binding assay; Chromatin interaction assay	NA	Luciferase reporter assay; ChIP-qPCR, GST Pull-down, Co-IP; RT-qPCR; Western blot
E_01718	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr6	6770399	6771465	Smad4	Dlx5	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Enhancer activity assay; TF binding assay; Chromatin interaction assay	NA	Luciferase reporter assay; ChIP-qPCR, GST Pull-down, Co-IP; RT-qPCR; Western blot
E_01719	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr6	6770399	6771465	Tcf4	Dlx5	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Enhancer activity assay; TF binding assay; Chromatin interaction assay	NA	Luciferase reporter assay; ChIP-qPCR, GST Pull-down, Co-IP; RT-qPCR; Western blot
E_01720	2017	28087634	Genome-wide identification of regulatory elements in Sertoli cells	Mus musculus	mm10	chr2	105072843	105076843	NA	Wt1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Sertoli cells	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	ChIP-qPCR/ChIP
E_01721	2022	36201590	A noncoding single-nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation	Homo sapiens	hg38	chr8	129631847	129635071	POU5F1	MYC	Enhancer	Active	Disease	IDH-mutant low-grade glioma	MONDO:0021637	DOID:0080829	kidney	UBERON:0002113	HEK293T	CVCL_0063	NA	NA	Enhancer activity assay; Functional perturbation assay	NA	MYC Luciferase reporter assay; POU5F1 Overexpression
E_01722	2019	31891018	A novel enhancer RNA, Hmrhl, positively regulates its host gene, phkb, in chronic myelogenous leukemia	Homo sapiens	hg19	chr16	47658623	47659423	NA	PHKB	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:0081088	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay	ChIP-seq	Luciferase reporter assay; ChIP-qPCR; ChIP; siRNA knockdown
E_01723	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr17	44819323	44819541	Smad1	Runx2	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Enhancer activity assay; TF binding assay	NA	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot
E_01724	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr17	44819323	44819541	Smad1	Runx2	Enhancer	Active	Normal	NA	NA	NA	bone element	UBERON:0001474	MC3T3-E1	CVCL_0409	osteoblast	CL:0000062	Enhancer activity assay; TF binding assay	NA	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot
E_01725	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr17	44819323	44819541	Smad4	Runx2	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Enhancer activity assay; TF binding assay	NA	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot
E_01726	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr17	44819323	44819541	Smad4	Runx2	Enhancer	Active	Normal	NA	NA	NA	bone element	UBERON:0001474	MC3T3-E1	CVCL_0409	osteoblast	CL:0000062	Enhancer activity assay; TF binding assay	NA	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot
E_01727	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr17	44819323	44819541	Tcf4	Runx2	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Enhancer activity assay; TF binding assay	NA	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot
E_01728	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr17	44819323	44819541	Tcf4	Runx2	Enhancer	Active	Normal	NA	NA	NA	bone element	UBERON:0001474	MC3T3-E1	CVCL_0409	osteoblast	CL:0000062	Enhancer activity assay; TF binding assay	NA	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot
E_01729	2011	20878775	Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways	Mus musculus	mm10	chr17	45201170	45201388	NA	Runx2	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Enhancer activity assay	NA	Luciferase reporter assay
E_01730	2024	37728419	Three-Dimensional Chromosomal Landscape Revealing miR-146a Dysfunctional Enhancer in Lupus and Establishing a CRISPR-Mediated Approach to Inhibit the Interferon Pathway	Homo sapiens	hg19	chr5	159927785	159928129	CEBPA	MIR146A	Enhancer	Active	Disease	systemic lupus erythematosus	MONDO:0007915	DOID:9074	blood	UBERON:0000178	primary peripheral blood mononuclear cells from patients with SLE	NA	peripheral blood mononuclear cells	NA	Functional perturbation assay; Chromatin interaction assay; Endogenous enhancer perturbation	Hi-C; ATAC-seq; Hi-C	CRISPR knockout, CRISPRi; RT-qPCR; CRISPRa
E_01731	2024	38443991	KLF7 regulates super-enhancer-driven IGF2BP2 overexpression to promote the progression of head and neck squamous cell carcinoma	Homo sapiens	hg38	chr3	185824281	185824602	KLF7	IGF2BP2	Enhancer	Active	Disease	tongue squamous cell carcinoma	MONDO:0000500	DOID:0050865	tongue	UBERON:0001723	CAL-27	CVCL_1107	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation	ChIP-seq	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot; CRISPR-Cas9 endogenous deletion/editing; Luciferase reporter assay; ChIP-qPCR; ChIP; In vivo phenotyping; Xenograft/xenotransplant; Reporter assay
E_01732	2023	36788209	BRD7 inhibits enhancer activity and expression of BIRC2 to suppress tumor growth and metastasis in nasopharyngeal carcinoma	Homo sapiens	hg38	chr11	102245603	102246344	BRD7	BIRC2	Enhancer	Active	Disease	nasopharyngeal carcinoma	MONDO:0015459	DOID:9261	nasopharynx	UBERON:0001728	5-8F	CVCL_C528	malignant cell	CL:0001064	In vivo functional validation; Enhancer activity; chromatin-regulator binding; functional perturbation; enhancer/reporter validation	BRD7 ChIP-seq; H3K27ac ChIP-seq; RNA-seq	Luciferase reporter assay; BRD7 ChIP-qPCR; BRD7 knockdown/overexpression; RT-qPCR; Western blot; xenograft/metastasis assay; In vivo phenotyping; Xenograft/xenotransplant
E_01733	2023	36788209	BRD7 inhibits enhancer activity and expression of BIRC2 to suppress tumor growth and metastasis in nasopharyngeal carcinoma	Homo sapiens	hg38	chr11	102245603	102246344	BRD7	BIRC2	Enhancer	Active	Disease	nasopharyngeal carcinoma	MONDO:0015459	DOID:9261	nasopharynx	UBERON:0001728	HNE-1	CVCL_0308	malignant cell	CL:0001064	In vivo functional validation; Enhancer activity; chromatin-regulator binding; functional perturbation; enhancer/reporter validation	BRD7 ChIP-seq; H3K27ac ChIP-seq; RNA-seq	Luciferase reporter assay; BRD7 ChIP-qPCR; BRD7 knockdown/overexpression; RT-qPCR; Western blot; xenograft/metastasis assay; In vivo phenotyping; Xenograft/xenotransplant
E_01734	2021	32594099	Gata2 -77 enhancer regulates adult hematopoietic stem cell survival	Mus musculus	mm10	chr6	88093745	88094001	Gata2	Gata2	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary Mouse Bone Marrow Cells	NA	mouse bone marrow cell	NA	Functional perturbation assay; TF binding assay; Chromatin interaction assay	RNA-seq; ChIP-seq	CRISPR knockout; RT-qPCR, 3C Assay
E_01735	2026	41293823	Functional Genomics Link REST to Endothelial Plasticity and Atherosclerosis	Homo sapiens	hg38	chr12	12769300	12769800	REST	CDKN1B	Enhancer	Repressed	Disease	coronary artery disease	NA	NA	aorta	UBERON:0000947	JHU006i-1	CVCL_UA48	aortic endothelial cell	CL:0002544	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation; In vivo functional validation	ChIP-seq, CUT&Tag; RNA-seq; RNA-seq; eQTL analysis; GWAS	Luciferase reporter assay, CRISPRi; RT-qPCR; CRISPRi; Mouse genetic deletion/knock-in
E_01736	2026	41293823	Functional Genomics Link REST to Endothelial Plasticity and Atherosclerosis	Homo sapiens	hg38	chr9	139390200	139390700	REST	NOTCH1	Enhancer	Repressed	Disease	coronary artery disease	NA	NA	aorta	UBERON:0000947	JHU006i-1	CVCL_UA48	aortic endothelial cell	CL:0002544	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation; In vivo functional validation	ChIP-seq, CUT&Tag; RNA-seq; RNA-seq; eQTL analysis; GWAS	Luciferase reporter assay, CRISPRi; RT-qPCR; CRISPRi; Mouse genetic deletion/knock-in
E_01737	2026	41293823	Functional Genomics Link REST to Endothelial Plasticity and Atherosclerosis	Homo sapiens	hg38	chr4	56908277	56909126	NA	REST	Enhancer	Active	Disease	coronary artery disease	NA	NA	aorta	UBERON:0000947	Primary human aortic endothelial cells (HAEC; Lonza CC-25350)	NA	aortic endothelial cell	CL:0002544	Enhancer activity assay; Endogenous enhancer perturbation; In vivo functional validation; Allele-specific regulatory assay; Genetic association assay; eQTL colocalization assay	CAD GWAS; endothelial eQTL meta-analysis; CAFEH multi-trait colocalization; endothelial ATAC-seq (public datasets); RNA-seq; eQTL analysis; GWAS	Dual-luciferase reporter assay using 200-bp rs6853156 CRE1 C/T constructs; Sanger sequencing; CRISPRi; Mouse genetic deletion/knock-in
E_01738	2026	41739921	The conserved noncoding sequence CNS11 is a master control region for Rorc transcription in type 17 immune cells	Mus musculus	mm39	chr3	94294960	94295960	Rorc	Rorc	Enhancer	Active	Normal	NA	NA	NA	small intestine	UBERON:0002108	primary mouse type 17 immune cells (Th17, ILC3, RORγt+ Treg, γδT and APC populations)	NA	type 17 immune cell	NA	Chromatin interaction assay; In vivo causal cis-regulatory deletion; TF-site dissection	ATAC-seq; scATAC-seq; CUT&Tag-seq; 4C-seq	1001-bp endogenous CNS11 deletion; TF-motif mutation; bone-marrow chimera; Flow cytometry; RT-qPCR
E_01739	2026	41739921	The conserved noncoding sequence CNS11 is a master control region for Rorc transcription in type 17 immune cells	Mus musculus	mm39	chr3	94294960	94295960	Runx3	Rorc	Enhancer	Active	Normal	NA	NA	NA	small intestine	UBERON:0002108	primary mouse type 17 immune cells (Th17, ILC3, RORγt+ Treg, γδT and APC populations)	NA	type 17 immune cell	NA	Chromatin interaction assay; In vivo causal cis-regulatory deletion; TF-site dissection	ATAC-seq; scATAC-seq; CUT&Tag-seq; 4C-seq	1001-bp endogenous CNS11 deletion; TF-motif mutation; bone-marrow chimera; Flow cytometry; RT-qPCR
E_01740	2026	41739921	The conserved noncoding sequence CNS11 is a master control region for Rorc transcription in type 17 immune cells	Mus musculus	mm39	chr3	94294960	94295960	Maf	Rorc	Enhancer	Active	Normal	NA	NA	NA	small intestine	UBERON:0002108	primary mouse type 17 immune cells (Th17, ILC3, RORγt+ Treg, γδT and APC populations)	NA	type 17 immune cell	NA	Chromatin interaction assay; In vivo causal cis-regulatory deletion; TF-site dissection	ATAC-seq; scATAC-seq; CUT&Tag-seq; 4C-seq	1001-bp endogenous CNS11 deletion; TF-motif mutation; bone-marrow chimera; Flow cytometry; RT-qPCR
E_01741	2024	39223609	Enhlink infers distal and context-specific enhancer-promoter linkages	Homo sapiens	hg38	chr7	150955147	150956502	NA	KCNH2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary monocytes	NA	monocyte	CL:0000576	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Chromatin-state profiling	single-cell ATAC-seq; ATAC-seq; Hi-C; eQTL analysis	CRISPR knockout
E_01742	2020	31905229	Ligand dependent gene regulation by transient ERα clustered enhancers	Homo sapiens	hg19	chr21	42660000	42661000	ESR1	TFF1	Enhancer	Active	Normal	NA	NA	NA	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Functional perturbation assay; Chromatin interaction assay	ChIP-seq, 5C, ChIA-PET	CRISPR knockout; RT-qPCR, ImmunoFISH
E_01743	2020	31905229	Ligand dependent gene regulation by transient ERα clustered enhancers	Homo sapiens	hg19	chr21	42660000	42661000	ESR1	TFF2	Enhancer	Active	Normal	NA	NA	NA	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Functional perturbation assay; Chromatin interaction assay	ChIP-seq, 5C, ChIA-PET	CRISPR knockout; RT-qPCR, ImmunoFISH
E_01744	2020	31905229	Ligand dependent gene regulation by transient ERα clustered enhancers	Homo sapiens	hg19	chr21	42660000	42661000	ESR1	TFF3	Enhancer	Active	Normal	NA	NA	NA	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Functional perturbation assay; Chromatin interaction assay	ChIP-seq, 5C, ChIA-PET	CRISPR knockout; RT-qPCR, ImmunoFISH
E_01745	2017	28916725	Characterization of enhancers and the role of the transcription factor KLF7 in regulating corneal epithelial differentiation	Homo sapiens	hg19	chr2	226999986	227001986	EHF	IRS1	Enhancer	Active	Disease	corneal astigmatism	NA	NA	cornea	UBERON:0000964	primary human corneal epithelial cells	NA	corneal epithelial cell	CL:0000575	TF binding assay; Disease-associated enhancer variant assay	H3K4me1/H3K27ac/H3K4me3 ChIP-seq; public ChIA-PET integration; expression profiling; ChIP-seq	Wild-type/variant luciferase reporter assay; EHF ChIP; EHF siRNA
E_01746	2014	25030696	The active enhancer network operated by liganded RXR supports angiogenic activity in macrophages	Mus musculus	mm10	chr17	45890060	45890829	Rxra	Vegfa	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Bone marrow-derived macrophages	NA	macrophage	CL:0000235	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; GRO-seq; 3C-seq	ChIP-qPCR; RT-qPCR, Luciferase reporter assay; 3C-RT-qPCR, ELISA, CAM Assay; 3C
E_01747	2012	22728936	TBX5 drives Scn5a expression to regulate cardiac conduction system function	Mus musculus	mm9	chr9	119378051	119379479	Tbx5	Scn5a	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	mouse ventricular conduction system	NA	cardiac muscle cell	CL:0000746	Disease-variant functional analysis; In vivo functional validation; In vivo enhancer validation; TF-site functional dissection	ChIP-seq / cardiac regulatory profiling; GWAS	Transgenic lacZ reporter; luciferase assay; T-box motif mutagenesis; RT-qPCR; In vivo phenotyping
E_01748	2012	22728936	TBX5 drives Scn5a expression to regulate cardiac conduction system function	Mus musculus	mm9	chr9	119378051	119379479	Tbx5	Scn5a	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	HL-1 reporter validation	NA	cardiac muscle cell	CL:0000746	Disease-variant functional analysis; In vivo functional validation; In vivo enhancer validation; TF-site functional dissection	ChIP-seq / cardiac regulatory profiling; GWAS	Transgenic lacZ reporter; luciferase assay; T-box motif mutagenesis; RT-qPCR; In vivo phenotyping
E_01749	2000	10688646	Loading of DNA-binding factors to an erythroid enhancer	Homo sapiens	hg19	chr16	1600000	1600110	NFE2	HBA1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Endogenous enhancer perturbation; In vivo functional validation	NA	Luciferase reporter assay; RT-qPCR, EMSA; ChIP; Site-directed/motif mutagenesis; In vivo phenotyping
E_01750	2023	37821107	Allelic chromatin structure precedes imprinted expression of Kcnk9 during neurogenesis	Mus musculus	mm10	chr15	73142260	73142810	NA	Kcnk9	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	F1 hybrid ESCs / Ngn2-induced neuronal differentiation	NA	embryonic stem cell	CL:0002322	Chromatin interaction assay; Enhancer activation; allele-specific chromatin interaction assay	Region Capture Hi-C; ENCODE H3K27ac/H3K4me1/H3K4me3 ChIP-seq reanalysis; Hi-C	dCas9-VPR CRISPRa; RT-qPCR; RT-ddPCR
E_01751	2023	37821107	Allelic chromatin structure precedes imprinted expression of Kcnk9 during neurogenesis	Mus musculus	mm10	chr15	73142260	73142810	NA	Kcnk9	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	B6--CAST reciprocal-hybrid mouse brain/cortex	NA	neuron	CL:0000540	Enhancer activation assay; allele-specific chromatin interaction assay	Region Capture Hi-C; allele-specific H3K27ac profiling; ENCODE H3K27ac/H3K4me1/H3K4me3/CTCF ChIP-seq reanalysis; Hi-C; Capture Hi-C; DNA methylation profiling	dCas9-VPR CRISPRa; RT-qPCR; allele-specific RT-ddPCR
E_01752	2023	37821107	Allelic chromatin structure precedes imprinted expression of Kcnk9 during neurogenesis	Mus musculus	mm10	chr15	73142260	73142810	NA	Kcnk9	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	F1 hybrid ESCs	NA	neuron	CL:0000540	Enhancer activation assay; allele-specific chromatin interaction assay	Region Capture Hi-C; allele-specific H3K27ac profiling; ENCODE H3K27ac/H3K4me1/H3K4me3/CTCF ChIP-seq reanalysis; Hi-C; Capture Hi-C; DNA methylation profiling	dCas9-VPR CRISPRa; RT-qPCR; allele-specific RT-ddPCR
E_01753	2023	37821107	Allelic chromatin structure precedes imprinted expression of Kcnk9 during neurogenesis	Mus musculus	mm10	chr15	73142260	73142810	NA	Kcnk9	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Ngn2-induced neurons	NA	neuron	CL:0000540	Enhancer activation assay; allele-specific chromatin interaction assay	Region Capture Hi-C; allele-specific H3K27ac profiling; ENCODE H3K27ac/H3K4me1/H3K4me3/CTCF ChIP-seq reanalysis; Hi-C; Capture Hi-C; DNA methylation profiling	dCas9-VPR CRISPRa; RT-qPCR; allele-specific RT-ddPCR
E_01754	2023	37821107	Allelic chromatin structure precedes imprinted expression of Kcnk9 during neurogenesis	Mus musculus	mm10	chr15	73148730	73149280	NA	Kcnk9	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	F1 hybrid ESCs / Ngn2-induced neuronal differentiation	NA	embryonic stem cell	CL:0002322	Chromatin interaction assay; Enhancer activation; allele-specific chromatin interaction assay	Region Capture Hi-C; ENCODE H3K27ac/H3K4me1/H3K4me3 ChIP-seq reanalysis; Hi-C	dCas9-VPR CRISPRa; RT-qPCR; RT-ddPCR
E_01755	2023	37821107	Allelic chromatin structure precedes imprinted expression of Kcnk9 during neurogenesis	Mus musculus	mm10	chr15	73148730	73149280	NA	Kcnk9	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	B6--CAST reciprocal-hybrid mouse brain/cortex	NA	neuron	CL:0000540	Enhancer activation assay; allele-specific chromatin interaction assay	Region Capture Hi-C; allele-specific H3K27ac profiling; ENCODE H3K27ac/H3K4me1/H3K4me3/CTCF ChIP-seq reanalysis; Hi-C; Capture Hi-C; DNA methylation profiling	dCas9-VPR CRISPRa; RT-qPCR; allele-specific RT-ddPCR
E_01756	2023	37821107	Allelic chromatin structure precedes imprinted expression of Kcnk9 during neurogenesis	Mus musculus	mm10	chr15	73148730	73149280	NA	Kcnk9	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	F1 hybrid ESCs	NA	neuron	CL:0000540	Enhancer activation assay; allele-specific chromatin interaction assay	Region Capture Hi-C; allele-specific H3K27ac profiling; ENCODE H3K27ac/H3K4me1/H3K4me3/CTCF ChIP-seq reanalysis; Hi-C; Capture Hi-C; DNA methylation profiling	dCas9-VPR CRISPRa; RT-qPCR; allele-specific RT-ddPCR
E_01757	2023	37821107	Allelic chromatin structure precedes imprinted expression of Kcnk9 during neurogenesis	Mus musculus	mm10	chr15	73148730	73149280	NA	Kcnk9	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Ngn2-induced neurons	NA	neuron	CL:0000540	Enhancer activation assay; allele-specific chromatin interaction assay	Region Capture Hi-C; allele-specific H3K27ac profiling; ENCODE H3K27ac/H3K4me1/H3K4me3/CTCF ChIP-seq reanalysis; Hi-C; Capture Hi-C; DNA methylation profiling	dCas9-VPR CRISPRa; RT-qPCR; allele-specific RT-ddPCR
E_01758	2019	31775028	Global Analysis of Enhancer Targets Reveals Convergent Enhancer-Driven Regulatory Modules	Homo sapiens	hg38	chr6	135323137	135323537	NA	MYB	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Disease-variant functional analysis	scRNA-seq; RNA-seq, Hi-C; ChIP-seq; ATAC-seq	CRISPRi; RT-qPCR
E_01759	2014	24692107	Dlx5 and mef2 regulate a novel runx2 enhancer for osteoblast-specific expression	Mus musculus	mm10	chr17	44839209	44839551	Dlx5	Runx2	Enhancer	Active	Normal	NA	NA	NA	bone element	UBERON:0001474	Primary mouse osteoblasts	NA	osteoblast	CL:0000062	Enhancer activity assay; Functional perturbation assay; TF binding assay; Disease-variant functional analysis	NA	Transgenic reporter assay, Luciferase reporter assay, EMSA; ChIP-qPCR, GST-pulldown, Site-directed Mutagenesis
E_01760	2017	28916725	Characterization of enhancers and the role of the transcription factor KLF7 in regulating corneal epithelial differentiation	Homo sapiens	hg19	chr2	227000886	227001086	EHF	IRS1	Enhancer	Active	Disease	astigmatism	MONDO:0011284	DOID:11782	cornea	UBERON:0000964	primary human corneal epithelial cells	NA	corneal epithelial cell	CL:0000575	Corneal enhancer mapping; allele-specific reporter; TF occupancy/target regulation	H3K27ac/H3K4me1/H3K4me3 ChIP-seq; enhancer/super-enhancer analysis; ChIP-seq	allele-specific luciferase; EHF ChIP; EHF knockdown; qRT-PCR/expression profiling; ChIA-PET target-linkage support
E_01761	2017	28916725	Characterization of enhancers and the role of the transcription factor KLF7 in regulating corneal epithelial differentiation	Homo sapiens	hg19	chr2	226998914	227004586	EHF	IRS1	Enhancer	Active	Normal	NA	NA	NA	cornea	UBERON:0000964	primary human corneal epithelial cells	NA	corneal epithelial cell	CL:0000575	TF binding assay; Chromatin-state profiling; Disease-variant functional analysis; Enhancer profiling	H3K4me1 ChIP-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; ChIA-PET integration; ChIP-seq	Luciferase reporter assay; ChIP; siRNA
E_01762	2019	31775028	Global Analysis of Enhancer Targets Reveals Convergent Enhancer-Driven Regulatory Modules	Homo sapiens	hg38	chr6	135321297	135321697	NA	MYB	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis	scRNA-seq; RNA-seq, Hi-C; ChIP-seq	CRISPRi; RT-qPCR
E_01763	2014	24692107	Dlx5 and mef2 regulate a novel runx2 enhancer for osteoblast-specific expression	Mus musculus	mm10	chr17	44464986	44466986	Ctnnb1	Runx2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Osteoblast-Specific Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay; Transgenic/LacZ assay
E_01764	2014	24692107	Dlx5 and mef2 regulate a novel runx2 enhancer for osteoblast-specific expression	Mus musculus	mm10	chr17	44464986	44466986	Dlx5	Runx2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Osteoblast-Specific Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay; Transgenic/LacZ assay
E_01765	2014	24692107	Dlx5 and mef2 regulate a novel runx2 enhancer for osteoblast-specific expression	Mus musculus	mm10	chr17	44464986	44466986	Mef2c	Runx2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Osteoblast-Specific Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay; Transgenic/LacZ assay
E_01766	2014	24692107	Dlx5 and mef2 regulate a novel runx2 enhancer for osteoblast-specific expression	Mus musculus	mm10	chr17	44464986	44466986	Smad1	Runx2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Osteoblast-Specific Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay; Transgenic/LacZ assay
E_01767	2014	24692107	Dlx5 and mef2 regulate a novel runx2 enhancer for osteoblast-specific expression	Mus musculus	mm10	chr17	44464986	44466986	Sox6	Runx2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Osteoblast-Specific Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay; Transgenic/LacZ assay
E_01768	2014	24692107	Dlx5 and mef2 regulate a novel runx2 enhancer for osteoblast-specific expression	Mus musculus	mm10	chr17	44464986	44466986	Sp7	Runx2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Osteoblast-Specific Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay; Transgenic/LacZ assay
E_01769	2014	24692107	Dlx5 and mef2 regulate a novel runx2 enhancer for osteoblast-specific expression	Mus musculus	mm10	chr17	44464986	44466986	Tcf7	Runx2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Osteoblast-Specific Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay; Transgenic/LacZ assay
E_01770	2012	22728936	TBX5 drives Scn5a expression to regulate cardiac conduction system function	Mus musculus	mm10	chr9	119469800	119469811	Tbx5	Scn5a	Enhancer	Active	Disease	Cardiac Conduction System Disease	NA	DOID:10273	heart	UBERON:0000948	HL-1	CVCL_0303	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_01771	2012	22728936	TBX5 drives Scn5a expression to regulate cardiac conduction system function	Mus musculus	mm10	chr9	119469879	119469890	Tbx5	Scn5a	Enhancer	Active	Disease	Cardiac Conduction System Disease	NA	DOID:10273	heart	UBERON:0000948	HL-1	CVCL_0303	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_01772	2012	22728936	TBX5 drives Scn5a expression to regulate cardiac conduction system function	Mus musculus	mm10	chr9	119469902	119469913	Tbx5	Scn5a	Enhancer	Active	Disease	Cardiac Conduction System Disease	NA	DOID:10273	heart	UBERON:0000948	HL-1	CVCL_0303	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_01773	2026	41293823	Functional Genomics Link REST to Endothelial Plasticity and Atherosclerosis	Homo sapiens	hg38	chr4	56908277	56909126	NA	REST	Enhancer	Active	Disease	coronary artery disease	NA	NA	NA	NA	WTC-CLYBL-dCas9-TagBFP-KRAB-cl391	CVCL_A5ET	endothelial cell	CL:0000115	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation; In vivo functional validation; Genetic association assay; eQTL colocalization assay	CAD GWAS; endothelial eQTL meta-analysis; CAFEH multi-trait colocalization; endothelial ATAC-seq (public datasets); RNA-seq; eQTL analysis; GWAS	CRISPRi (dCas9-KRAB) targeting the rs6853156 proximal CRE; RT-qPCR of REST; CRISPRi; Mouse genetic deletion/knock-in
E_01774	2012	22728936	TBX5 drives Scn5a expression to regulate cardiac conduction system function	Mus musculus	mm9	chr9	119378051	119379479	Tbx5	Scn5a	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	ventricular conduction system in vivo	NA	cardiac conduction system cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; In vivo enhancer reporter assay	Published TBX5 ChIP-seq; p300 ChIP-seq; cardiac enhancer prediction data integration	Dual-luciferase reporter assay in HEK-293T; T-box-site mutagenesis; transient transgenic Hsp68-LacZ enhancer assay; ventricular conduction system-specific Tbx5 conditional knockout; qRT-PCR; Immunofluorescence; electrophysiological analysis
E_01775	2019	31775028	Global Analysis of Enhancer Targets Reveals Convergent Enhancer-Driven Regulatory Modules	Homo sapiens	hg38	chr11	33944788	33945188	NA	NAT10	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Multiplex endogenous enhancer perturbation with single-cell transcriptomic target mapping	Mosaic-seq pooled dCas9-KRAB CRISPRi; single-cell RNA-seq; DNase/H3K4me1/p300 regulatory-element integration	Bulk CRISPRi/RNA-seq or qRT-PCR validation for selected enhancers; pair-specific primary evidence is Mosaic-seq
E_01776	2019	31775028	Global Analysis of Enhancer Targets Reveals Convergent Enhancer-Driven Regulatory Modules	Homo sapiens	hg38	chr11	33944788	33945188	NA	TRIM44	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Multiplex endogenous enhancer perturbation with single-cell transcriptomic target mapping	Mosaic-seq pooled dCas9-KRAB CRISPRi; single-cell RNA-seq; DNase/H3K4me1/p300 regulatory-element integration	Bulk CRISPRi/RNA-seq or qRT-PCR validation for selected enhancers; pair-specific primary evidence is Mosaic-seq
E_01777	2019	31775028	Global Analysis of Enhancer Targets Reveals Convergent Enhancer-Driven Regulatory Modules	Homo sapiens	hg38	chr6	135321297	135321697	NA	AHI1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Multiplex endogenous enhancer perturbation with single-cell transcriptomic target mapping	Mosaic-seq pooled dCas9-KRAB CRISPRi; single-cell RNA-seq; DNase/H3K4me1/p300 regulatory-element integration	Bulk CRISPRi/RNA-seq or qRT-PCR validation for selected enhancers; pair-specific primary evidence is Mosaic-seq
E_01778	2019	31775028	Global Analysis of Enhancer Targets Reveals Convergent Enhancer-Driven Regulatory Modules	Homo sapiens	hg38	chr6	135323137	135323537	NA	AHI1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Disease-variant functional analysis; Multiplex endogenous enhancer perturbation with single-cell transcriptomic target mapping	Mosaic-seq pooled dCas9-KRAB CRISPRi; single-cell RNA-seq; DNase/H3K4me1/p300 regulatory-element integration	Bulk CRISPRi/RNA-seq or qRT-PCR validation for selected enhancers; pair-specific primary evidence is Mosaic-seq
E_01779	2000	10688646	Loading of DNA-binding factors to an erythroid enhancer	Homo sapiens	hg19	chr16	80617	80837	NFE2	GATA1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	erythroid progenitor cell	CL:0000038	In vivo functional validation; TF-binding/chromatin assay	NA	ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_01780	2014	25030696	The active enhancer network operated by liganded RXR supports angiogenic activity in macrophages	Mus musculus	mm10	chr17	31172998	31173656	Rxra	Abcg1	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Bone marrow-derived macrophages	NA	macrophage	CL:0000235	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; GRO-seq; 3C-seq	ChIP-qPCR; RT-qPCR, Luciferase reporter assay; 3C-RT-qPCR; 3C
E_01781	2017	28916725	Characterization of enhancers and the role of the transcription factor KLF7 in regulating corneal epithelial differentiation	Homo sapiens	hg19	chr2	226998914	227004586	EHF	IRS1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Human Corneal Epithelial Cells	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq; ChIA-PET	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RNAi/siRNA/shRNA
E_01782	2014	25030696	The active enhancer network operated by liganded RXR supports angiogenic activity in macrophages	Mus musculus	mm10	chr17	31172998	31173656	Rxra	Abcg1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	COS-1	CVCL_0223	macrophage	CL:0000235	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay	ChIP-seq; RNA-seq; GRO-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_01783	2014	25030696	The active enhancer network operated by liganded RXR supports angiogenic activity in macrophages	Mus musculus	mm10	chr17	45890060	45890829	Rxra	Vegfa	Enhancer	Active	Normal	NA	NA	NA	NA	NA	COS-1	CVCL_0223	macrophage	CL:0000235	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay	ChIP-seq; RNA-seq; GRO-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_01784	2020	31905229	Ligand dependent gene regulation by transient ERα clustered enhancers	Homo sapiens	hg19	chr2	10860000	10861000	ESR1	GREB1	Enhancer	Active	Normal	NA	NA	NA	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Functional perturbation assay	ChIP-seq	CRISPRi; RT-qPCR
E_01785	2024	39223609	Enhlink infers distal and context-specific enhancer-promoter linkages	Homo sapiens	hg38	chr12	110928658	110929096	NA	MYL2	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	Ventricular cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Chromatin interaction assay; Chromatin-state profiling	single-cell ATAC-seq; ATAC-seq; Hi-C; eQTL analysis	qRT-PCR, and ChIP-qPCR
E_01786	2024	39223609	Enhlink infers distal and context-specific enhancer-promoter linkages	Homo sapiens	hg38	chr12	110931149	110931877	NA	MYL2	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	Ventricular cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Chromatin interaction assay; Chromatin-state profiling	single-cell ATAC-seq; ATAC-seq; Hi-C; eQTL analysis	qRT-PCR, and ChIP-qPCR
E_01787	2017	28916725	Characterization of enhancers and the role of the transcription factor KLF7 in regulating corneal epithelial differentiation	Homo sapiens	hg19	chr6	31092587	31094587	NA	PSORS1C1	Enhancer	Active	Disease	Stevens-Johnson syndrome-associated corneal phenotype	NA	NA	cornea	UBERON:0000964	primary human corneal epithelial cells	NA	corneal epithelial cell	CL:0000575	Disease-associated enhancer variant functional assay	H3K4me1/H3K27ac/H3K4me3 ChIP-seq; ChIP-seq	Wild-type/variant luciferase reporter assay
E_01788	2019	31775028	Global Analysis of Enhancer Targets Reveals Convergent Enhancer-Driven Regulatory Modules	Homo sapiens	hg38	chr11	33944788	33945188	NA	LMO2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis	scRNA-seq; RNA-seq; ChIP-seq	CRISPRi; RT-qPCR
E_01789	2019	31775028	Global Analysis of Enhancer Targets Reveals Convergent Enhancer-Driven Regulatory Modules	Homo sapiens	hg38	chr12	54304291	54304691	NA	NFE2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis	scRNA-seq; RNA-seq; ChIP-seq	CRISPRi; RT-qPCR
E_01790	2017	28916725	Characterization of enhancers and the role of the transcription factor KLF7 in regulating corneal epithelial differentiation	Homo sapiens	hg19	chr6	31092587	31094587	NA	PSORS1C1	Enhancer	Active	Normal	NA	NA	NA	cornea	UBERON:0000964	primary human corneal epithelial cells	NA	corneal epithelial cell	CL:0000575	Enhancer activity assay; Chromatin-state profiling; Disease-variant functional analysis; Enhancer profiling	H3K4me1 ChIP-seq; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; ChIP-seq	Luciferase reporter assay; ChIP
E_01791	2014	24692107	Dlx5 and mef2 regulate a novel runx2 enhancer for osteoblast-specific expression	Mus musculus	mm10	chr17	44838751	44840051	Dlx5	Runx2	Enhancer	Active	Normal	NA	NA	NA	bone element	UBERON:0001474	Primary mouse osteoblasts	NA	osteoblast	CL:0000062	Enhancer activity assay; TF binding assay; Disease-variant functional analysis	NA	Transgenic reporter assay, Luciferase reporter assay, EMSA; ChIP-qPCR, GST-pulldown
E_01792	2014	24692107	Dlx5 and mef2 regulate a novel runx2 enhancer for osteoblast-specific expression	Mus musculus	mm10	chr17	44839381	44839469	Dlx5	Runx2	Enhancer	Active	Normal	NA	NA	NA	bone element	UBERON:0001474	Primary mouse osteoblasts	NA	osteoblast	CL:0000062	Enhancer activity assay; TF binding assay; Disease-variant functional analysis	NA	Transgenic reporter assay, Luciferase reporter assay, EMSA; ChIP-qPCR, GST-pulldown
E_01793	2024	39223609	Enhlink infers distal and context-specific enhancer-promoter linkages	Homo sapiens	hg38	chr12	110907461	110909456	NA	MYL2	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	Ventricular cardiomyocytes	NA	ventricular cardiac muscle cell	CL:2000046	Chromatin interaction assay; Chromatin-state profiling; Enhancer-promoter linkage analysis; Chromatin accessibility analysis	snATAC-seq; single-cell ATAC-seq; ATAC-seq; Hi-C; eQTL analysis	RT-qPCR
E_01794	2017	28916725	Characterization of enhancers and the role of the transcription factor KLF7 in regulating corneal epithelial differentiation	Homo sapiens	hg19	chr6	31092587	31094587	NA	PSORS1C1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Human Corneal Epithelial Cells	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_01795	2021	32594099	Gata2 -77 enhancer regulates adult hematopoietic stem cell survival	Mus musculus	mm10	chr6	88116954	88117210	Gata2	Gata2	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary adult mouse splenic HSPCs from WT, Gata2 -77+/-, and Gata2+/- mice	NA	hematopoietic multipotent progenitor cell	CL:0000837	In vivo endogenous enhancer haploinsufficiency analysis; hematopoietic progenitor survival and cell-cycle analysis; hematopoietic compartment phenotyping	NA	Multicolor flow cytometry; Annexin V/DAPI apoptosis assay; Ki67/DAPI cell-cycle assay; qRT-PCR; competitive hematopoietic reconstitution analysis
E_01796	2026	41723158	RORγt+ APCs require a distinct cis-regulatory element to instruct tolerance to dietary antigens	Mus musculus	mm10	chr3	94384282	94384650	Runx3	Rorc	Enhancer	Active	Normal	NA	NA	NA	small intestine	UBERON:0002108	Primary intestinal ILC3 and RORγt+ antigen-presenting cells	NA	group 3 innate lymphoid cell / RORγt+ antigen-presenting cell	NA	OCR369 endogenous enhancer deletion; RUNX3 binding; enhancer-promoter looping; intestinal immune-homeostasis phenotyping	ATAC-seq reanalysis; scRNA-seq; RNA-seq; DNA-pulldown mass spectrometry	369-bp endogenous OCR369 deletion; RUNX3 CUT&RUN-qPCR; 3C-qPCR; RT-qPCR; dual-luciferase reporter; Flow cytometry; bone-marrow chimera; oral-tolerance/allergy phenotyping
E_01797	2024	38365720	A regulatory element associated to NAFLD in the promoter of DIO1 controls LDL-C, HDL-C and triglycerides in hepatic cells	Homo sapiens	hg19	chr1	53893000	53895000	NA	DIO1	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Hep-G2	CVCL_0027	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis; Endogenous enhancer perturbation	RNA-seq, Hi-C; GWAS	Luciferase reporter assay; RT-qPCR; Western blot, CRISPR knockout; CRISPR-Cas9 endogenous deletion/editing; RT-qPCR
E_01798	2016	27587399	Epithelial Expression of Human ABO Blood Group Genes Is Dependent upon a Downstream Regulatory Element Functioning through an Epithelial Cell-specific Transcription Factor, Elf5	Homo sapiens	hg38	chr9	133252439	133252657	ELF5	ABO	Enhancer	Active	Normal	NA	NA	NA	stomach	UBERON:0000945	KATO III	CVCL_0371	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Endogenous enhancer perturbation; Endogenous enhancer deletion; direct TF binding; enhancer activity and TF dependency	ENCODE DNase-seq/chromatin-state integration	CRISPR-Cas9 biallelic enhancer deletion; luciferase; EMSA; ChIP; motif mutation; ELF5 shRNA; Flow cytometry; CRISPR-Cas9 endogenous deletion/editing; Luciferase reporter assay; shRNA knockdown; Allele-specific reporter assay
E_01799	2026	42030388	MYC-bound enhancer RNAs in cis regulate gene transcription and tumorigenesis	Homo sapiens	hg19	chr2	11623044	11625344	NA	GREB1	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	mammary gland	UBERON:0001911	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer functional assay; chromatin remodeling assay	ChIP-seq; ChIP-qPCR; ChIA-PET	Dual-luciferase reporter assay; MERG1 enhancer deletion; EP300 occupancy validation; RT-qPCR
E_01800	2024	39158745	An i-motif-regulated enhancer, eRNA and adjacent lncRNA affect Lhb expression through distinct mechanisms in a sex-specific context	Mus musculus	mm10	chr7	45416017	45418912	Hmgb2	Lhb	Enhancer	Active	Normal	NA	NA	NA	pituitary gland	UBERON:0000007	LbetaT2	CVCL_0398	gonadotrope	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Chromatin regulator binding assay; Non-canonical DNA structure assay	snATAC-seq reanalysis; UMI-4C-seq; LC-MS/MS proteomics	dCas9-KRAB CRISPRi; dCas9-VP64 CRISPRa; H3K4me1 ChIP-qPCR; H3K4me3 ChIP-qPCR; Hmgb2 ChIP-qPCR; BG4 ChIP-qPCR; iMab ChIP-qPCR; shRNA-mediated Hmgb2 knockdown; shRNA-mediated eRNA2 knockdown; RT-qPCR; circular dichroism; fluorescence binding assay; dCas9/FLAG locus-specific chromatin pull-down
E_01801	2022	35210422	A fast Myosin super enhancer dictates muscle fiber phenotype through competitive interactions with Myosin genes	Mus musculus	mm10	chr11	97938123	97980122	NA	Myh1	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	Myofibers	NA	skeletal muscle myofiber	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	ATAC-seq; 4C-seq; RNA-seq; ATAC-seq; 4C-seq; 4C	CRISPR knockout; Transgenic reporter assay; RT-qPCR; CRISPR-Cas9
E_01802	2022	35210422	A fast Myosin super enhancer dictates muscle fiber phenotype through competitive interactions with Myosin genes	Mus musculus	mm10	chr11	97938123	97980122	NA	Myh13	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	Myofibers	NA	skeletal muscle myofiber	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	ATAC-seq; 4C-seq; RNA-seq; ATAC-seq; 4C-seq; 4C	CRISPR knockout; Transgenic reporter assay; RT-qPCR; CRISPR-Cas9
E_01803	2022	35210422	A fast Myosin super enhancer dictates muscle fiber phenotype through competitive interactions with Myosin genes	Mus musculus	mm10	chr11	97938123	97980122	NA	Myh2	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	Myofibers	NA	skeletal muscle myofiber	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	ATAC-seq; 4C-seq; RNA-seq; ATAC-seq; 4C-seq; 4C	CRISPR knockout; Transgenic reporter assay; RT-qPCR; CRISPR-Cas9
E_01804	2022	35210422	A fast Myosin super enhancer dictates muscle fiber phenotype through competitive interactions with Myosin genes	Mus musculus	mm10	chr11	97938123	97980122	NA	Myh4	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	Myofibers	NA	skeletal muscle myofiber	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	ATAC-seq; 4C-seq; RNA-seq; ATAC-seq; 4C-seq; 4C	CRISPR knockout; Transgenic reporter assay; RT-qPCR; CRISPR-Cas9
E_01805	2022	35210422	A fast Myosin super enhancer dictates muscle fiber phenotype through competitive interactions with Myosin genes	Mus musculus	mm10	chr11	97938123	97980122	NA	Myh8	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	Myofibers	NA	skeletal muscle myofiber	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	ATAC-seq; 4C-seq; RNA-seq; ATAC-seq; 4C-seq; 4C	CRISPR knockout; Transgenic reporter assay; RT-qPCR; CRISPR-Cas9
E_01806	2021	34643182	Tbx5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt gene regulatory network coordinating cardiopulmonary development	Mus musculus	mm10	chr9	71241739	71242765	Tbx5	Aldh1a2	Enhancer	Active	Normal	NA	NA	NA	alimentary part of gastrointestinal system	UBERON:0005409	E14.5 fetal lung	NA	cardiopulmonary progenitor cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	Tbx5 ChIP-seq; ATAC-seq	Luciferase reporter assay; GFP transgenic reporter assay; Tbx5 motif mutation assay; RT-qPCR
E_01807	2020	32817485	Global epigenomic analysis of KSHV-infected primary effusion lymphoma identifies functional MYC superenhancers and enhancer RNAs	Homo sapiens	hg19	chr8	129234315	129239315	NA	MYC	Enhancer	Active	Disease	primary effusion lymphoma	MONDO:0018842	DOID:0050748	lymph node	UBERON:0000029	EB5 [Mouse ESC]	CVCL_J648	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	ChIP-seq; RNA-seq; 4C-seq	CRISPR knockout; CRISPRi; RT-qPCR; ChIP-qPCR
E_01808	2020	32817485	Global epigenomic analysis of KSHV-infected primary effusion lymphoma identifies functional MYC superenhancers and enhancer RNAs	Homo sapiens	hg19	chr8	129254315	129259315	NA	MYC	Enhancer	Active	Disease	primary effusion lymphoma	MONDO:0018842	DOID:0050748	lymph node	UBERON:0000029	EB5 [Mouse ESC]	CVCL_J648	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	ChIP-seq; RNA-seq; 4C-seq	CRISPR knockout; CRISPRi; RT-qPCR; ChIP-qPCR
E_01809	2020	32817485	Global epigenomic analysis of KSHV-infected primary effusion lymphoma identifies functional MYC superenhancers and enhancer RNAs	Homo sapiens	hg19	chr8	129278315	129283315	NA	MYC	Enhancer	Active	Disease	primary effusion lymphoma	MONDO:0018842	DOID:0050748	lymph node	UBERON:0000029	EB5 [Mouse ESC]	CVCL_J648	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	ChIP-seq; RNA-seq; 4C-seq	CRISPR knockout; CRISPRi; RT-qPCR; ChIP-qPCR
E_01810	2019	31164884	Mechanistic Characterization of RASGRP1 Variants Identifies an hnRNP-K-Regulated Transcriptional Enhancer Contributing to SLE Susceptibility	Homo sapiens	hg19	chr15	38850262	38850330	HNRNPK	RASGRP1	Enhancer	Active	Disease	systemic lupus erythematosus	MONDO:0007915	DOID:9074	blood	UBERON:0000178	primary human T cells	NA	T cell	CL:0000084	Enhancer activity assay; TF binding assay; Disease-variant functional analysis; Allele-specific enhancer activity; enhancer-binding regulator identification; functional perturbation	Genetic association/meta-analysis; transcriptomic/regulatory integration; eQTL analysis	Luciferase reporter assay; EMSA; mass spectrometry; HNRNPK ChIP-qPCR; HNRNPK perturbation; RT-qPCR; ERK signaling assay; ChIP-qPCR; ChIP; Allele-specific reporter assay; Reporter assay
E_01811	2018	29348663	Enhancer-associated long non-coding RNA LEENE regulates endothelial nitric oxide synthase and endothelial function	Homo sapiens	hg19	chr7	150700000	150705000	KLF2	NOS3	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Endothelial Cells (ECs)	NA	endothelial cell	CL:0000115	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; Hi-C; 4C-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01812	2018	29348663	Enhancer-associated long non-coding RNA LEENE regulates endothelial nitric oxide synthase and endothelial function	Homo sapiens	hg19	chr7	150700000	150705000	KLF4	NOS3	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Endothelial Cells (ECs)	NA	endothelial cell	CL:0000115	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; Hi-C; 4C-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01813	2017	28335007	A class of circadian long non-coding RNAs mark enhancers modulating long-range circadian gene regulation	Mus musculus	mm10	chr5	9034150	9036900	Arntl	Gm40264	Super-enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Liver	NA	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 4C; RT-qPCR/qPCR
E_01814	2017	28335007	A class of circadian long non-coding RNAs mark enhancers modulating long-range circadian gene regulation	Mus musculus	mm10	chr5	9034150	9036900	Nr1d2	Gm40264	Super-enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Liver	NA	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 4C; RT-qPCR/qPCR
E_01815	2017	28335007	A class of circadian long non-coding RNAs mark enhancers modulating long-range circadian gene regulation	Mus musculus	mm10	chr5	9037806	9041881	Arntl	Gm40264	Super-enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Liver	NA	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 4C; RT-qPCR/qPCR
E_01816	2017	28335007	A class of circadian long non-coding RNAs mark enhancers modulating long-range circadian gene regulation	Mus musculus	mm10	chr5	9037806	9041881	Nr1d2	Gm40264	Super-enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Liver	NA	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 4C; RT-qPCR/qPCR
E_01817	2017	28335007	A class of circadian long non-coding RNAs mark enhancers modulating long-range circadian gene regulation	Mus musculus	mm10	chr5	9038118	9038593	Arntl	Gm40264	Super-enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Liver	NA	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 4C; RT-qPCR/qPCR
E_01818	2017	28335007	A class of circadian long non-coding RNAs mark enhancers modulating long-range circadian gene regulation	Mus musculus	mm10	chr5	9038118	9038593	Nr1d2	Gm40264	Super-enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Liver	NA	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 4C; RT-qPCR/qPCR
E_01819	2016	26808502	Lineage-affiliated transcription factors bind the Gata3 Tce1 enhancer to mediate lineage-specific programs	Mus musculus	mm10	chr2	9593387	9600910	Rbpj	Gata3	Enhancer	Active	Normal	NA	NA	NA	thymus	UBERON:0002370	primary mouse thymocytes	NA	thymocyte	CL:0000893	Enhancer activity assay; TF binding assay; Endogenous enhancer perturbation; In vivo functional validation; in vivo functional perturbation assay	NA	Transgenic EGFP reporter assay; CRISPR/Cas9 germline enhancer deletion; ChIP-qPCR; RT-qPCR; Flow cytometry; Transgenic enhancer reporter assay; Mouse genetic deletion/knock-in; In vivo phenotyping
E_01820	2016	26808502	Lineage-affiliated transcription factors bind the Gata3 Tce1 enhancer to mediate lineage-specific programs	Mus musculus	mm10	chr2	9593387	9600910	Tcf12	Gata3	Enhancer	Active	Normal	NA	NA	NA	thymus	UBERON:0002370	primary mouse thymocytes	NA	thymocyte	CL:0000893	Enhancer activity assay; TF binding assay; Endogenous enhancer perturbation; In vivo functional validation; in vivo functional perturbation assay	NA	Transgenic EGFP reporter assay; CRISPR/Cas9 germline enhancer deletion; ChIP-qPCR; RT-qPCR; Flow cytometry; Transgenic enhancer reporter assay; Mouse genetic deletion/knock-in; In vivo phenotyping
E_01821	2026	41723158	RORγt+ APCs require a distinct cis-regulatory element to instruct tolerance to dietary antigens	Mus musculus	mm10	chr3	94384282	94384650	Runx3	Rorc	Enhancer	Active	Normal	NA	NA	NA	small intestine	UBERON:0002108	MNK-3 ILC3-like cells for mechanistic assays	NA	group 3 innate lymphoid cell / RORγt+ antigen-presenting cell	NA	OCR369 endogenous enhancer deletion; RUNX3 binding; enhancer-promoter looping; intestinal immune-homeostasis phenotyping	ATAC-seq reanalysis; scRNA-seq; RNA-seq; DNA-pulldown mass spectrometry	369-bp endogenous OCR369 deletion; RUNX3 CUT&RUN-qPCR; 3C-qPCR; RT-qPCR; dual-luciferase reporter; Flow cytometry; bone-marrow chimera; oral-tolerance/allergy phenotyping
E_01822	2025	39863595	The α-globin super-enhancer acts in an orientation-dependent manner	Mus musculus	mm9	chr11	32145540	32169344	Gata1	Hba-a1	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	ES-E14TG2a	CVCL_9108	primitive erythroid lineage cell	CL:0002417	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	ATAC-seq; ChIP-seq; NG Capture-C; RNA-seq	Cre-mediated super-enhancer inversion; RT-qPCR
E_01823	2025	39863595	The α-globin super-enhancer acts in an orientation-dependent manner	Mus musculus	mm9	chr11	32145540	32169344	Gata1	Hba-a2	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	ES-E14TG2a	CVCL_9108	primitive erythroid lineage cell	CL:0002417	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	ATAC-seq; ChIP-seq; NG Capture-C; RNA-seq	Cre-mediated super-enhancer inversion; RT-qPCR
E_01824	2025	40067173	Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma	Homo sapiens	hg38	chr8	128172101	128172473	POU2F2	MYC	Enhancer	Active	Disease	diffuse large B-cell lymphoma	MONDO:0018905	DOID:0050745	lymph node	UBERON:0000029	SU-DHL-5	CVCL_1735	germinal center B cell	CL:0000844	Enhancer activity assay; Functional perturbation assay	NFR-focused CRISPRi screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; POU2F2 CRISPRi; qRT-PCR; Dual-Glo luciferase reporter assay; OCT2-motif deletion reporter assay; 195B tandem-duplication reporter assay; Western blot
E_01825	2025	40067173	Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma	Homo sapiens	hg38	chr8	128172101	128172473	MEF2B	MYC	Enhancer	Active	Disease	diffuse large B-cell lymphoma	MONDO:0018905	DOID:0050745	lymph node	UBERON:0000029	SU-DHL-5	CVCL_1735	germinal center B cell	CL:0000844	Enhancer activity assay; Functional perturbation assay	NFR-focused CRISPRi screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; MEF2B CRISPRi; qRT-PCR; Dual-Glo luciferase reporter assay; 195B tandem-duplication reporter assay; Western blot
E_01826	2025	40067173	Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma	Homo sapiens	hg38	chr8	128172101	128172473	POU2AF1	MYC	Enhancer	Active	Disease	diffuse large B-cell lymphoma	MONDO:0018905	DOID:0050745	lymph node	UBERON:0000029	SU-DHL-5	CVCL_1735	germinal center B cell	CL:0000844	Enhancer activity assay; Functional perturbation assay	NFR-focused CRISPRi screen; H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; POU2AF1 CRISPRi; qRT-PCR; Dual-Glo luciferase reporter assay; 195B tandem-duplication reporter assay; Western blot
E_01827	2025	40067173	Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma	Homo sapiens	hg38	chr8	128172101	128172473	MEF2B	MYC	Enhancer	Active	Disease	diffuse large B-cell lymphoma	MONDO:0018905	DOID:0050745	ascitic fluid	UBERON:0007795	HT	CVCL_1290	germinal center B cell	CL:0000844	Enhancer activity assay; Functional perturbation assay	H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; MEF2B CRISPRi; qRT-PCR; Dual-Glo luciferase reporter assay; Western blot
E_01828	2025	40067173	Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma	Homo sapiens	hg38	chr8	128172101	128172473	POU2AF1	MYC	Enhancer	Active	Disease	diffuse large B-cell lymphoma	MONDO:0018905	DOID:0050745	ascitic fluid	UBERON:0007795	HT	CVCL_1290	germinal center B cell	CL:0000844	Enhancer activity assay; Functional perturbation assay	H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; POU2AF1 CRISPRi; qRT-PCR; Dual-Glo luciferase reporter assay; reporter assay with concurrent POU2AF1 CRISPRi; Western blot
E_01829	2025	40067173	Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma	Homo sapiens	hg38	chr8	128172101	128172473	POU2F2	MYC	Enhancer	Active	Disease	diffuse large B-cell lymphoma	MONDO:0018905	DOID:0050745	ascitic fluid	UBERON:0007795	HT	CVCL_1290	germinal center B cell	CL:0000844	Enhancer activity assay; Functional perturbation assay	H3K27ac ChIP-seq; ATAC-seq	Individual CRISPRi; POU2F2 CRISPRi; qRT-PCR; Dual-Glo luciferase reporter assay; reporter assay with concurrent POU2F2 CRISPRi; Western blot
E_01830	2025	40067173	Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma	Homo sapiens	hg19	chr8	129180000	129190000	MEF2B	MYC	Enhancer	Active	Disease	diffuse large B-cell lymphoma	MONDO:0018905	DOID:0050745	lymph node	UBERON:0000029	Karpas-422	CVCL_1325	B cell	CL:0000236	Enhancer activity assay; Functional perturbation assay	ChIP-seq; ATAC-seq; RNA-seq	CRISPRi, Luciferase reporter assay; RT-qPCR
E_01831	2025	40067173	Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma	Homo sapiens	hg19	chr8	129180000	129190000	POU2AF1	MYC	Enhancer	Active	Disease	diffuse large B-cell lymphoma	MONDO:0018905	DOID:0050745	lymph node	UBERON:0000029	Karpas-422	CVCL_1325	B cell	CL:0000236	Enhancer activity assay; Functional perturbation assay	ChIP-seq; ATAC-seq; RNA-seq	CRISPRi, Luciferase reporter assay; RT-qPCR
E_01832	2025	40067173	Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma	Homo sapiens	hg19	chr8	129180000	129190000	POU2F2	MYC	Enhancer	Active	Disease	diffuse large B-cell lymphoma	MONDO:0018905	DOID:0050745	lymph node	UBERON:0000029	Karpas-422	CVCL_1325	B cell	CL:0000236	Enhancer activity assay; Functional perturbation assay	ChIP-seq; ATAC-seq; RNA-seq	CRISPRi, Luciferase reporter assay; RT-qPCR
E_01833	2018	29348663	Enhancer-associated long non-coding RNA LEENE regulates endothelial nitric oxide synthase and endothelial function	Homo sapiens	hg19	chr14	56245000	56285000	KLF2	LINC00520	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Endothelial Cells (ECs)	NA	endothelial cell	CL:0000115	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; Hi-C	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01834	2018	29348663	Enhancer-associated long non-coding RNA LEENE regulates endothelial nitric oxide synthase and endothelial function	Homo sapiens	hg19	chr14	56245000	56285000	KLF4	LINC00520	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Endothelial Cells (ECs)	NA	endothelial cell	CL:0000115	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; Hi-C	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01835	2016	26751173	Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9	Homo sapiens	hg19	chr11	69329684	69330954	ESR1	CCND1	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; Endogenous enhancer perturbation; In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR; Western blot; Flow cytometry/FACS
E_01836	2016	26751173	Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9	Homo sapiens	hg19	chr11	69329684	69330954	ESR1	CCND1	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	T-47D	CVCL_0553	malignant cell	CL:0001064	Enhancer activity assay; Endogenous enhancer perturbation; In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR; Western blot; Flow cytometry/FACS
E_01837	2024	38233525	Affinity-optimizing enhancer variants disrupt development	Mus musculus	mm10	chr5	28395077	28395877	Ets1	Shh	Enhancer	Active	Normal	NA	NA	NA	forelimb bud	UBERON:0005417	Embryonic limb bud mesenchymal cells	NA	mesenchymal cell	CL:0008019	Enhancer activity assay; TF binding assay; Disease-variant functional analysis	ChIP-seq; RNA-seq	Transgenic reporter assay, EMSA, in situ hybridization, CRISPR knockout
E_01838	2019	31164884	Mechanistic Characterization of RASGRP1 Variants Identifies an hnRNP-K-Regulated Transcriptional Enhancer Contributing to SLE Susceptibility	Homo sapiens	hg19	chr15	38850262	38850330	HNRNPK	RASGRP1	Enhancer	Active	Disease	systemic lupus erythematosus	MONDO:0007915	DOID:9074	blood	UBERON:0000178	Jurkat E6.1	CVCL_0367	T cell	CL:0000084	Enhancer activity assay; TF binding assay; Disease-variant functional analysis; Allele-specific enhancer activity; enhancer-binding regulator identification; functional perturbation	Genetic association/meta-analysis; transcriptomic/regulatory integration; eQTL analysis	Luciferase reporter assay; EMSA; mass spectrometry; HNRNPK ChIP-qPCR; HNRNPK perturbation; RT-qPCR; ERK signaling assay; ChIP-qPCR; ChIP; Allele-specific reporter assay; Reporter assay
E_01839	2016	26751173	Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9	Homo sapiens	hg19	chr6	36635000	36635100	TP53	CDKN1A	Enhancer	Active	Normal	NA	NA	NA	skin of prepuce of penis	UBERON:0001471	BJ [Human fibroblast]	CVCL_3653	fibroblast	CL:0000057	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation	Pooled CRISPR-Cas9 enhancer screen; RNA-seq; TP53 ChIP-seq data integration; CRISPR-Cas9 tiling screen; CRISPR genetic screen	Individual CRISPR/Cas9 editing; Luciferase reporter assay; TP53 ChIP-qPCR; CEBPB ChIP-qPCR; RT-qPCR; BrdU incorporation; senescence-associated beta-galactosidase assay; CRISPR-Cas9 endogenous deletion/editing; Reporter assay
E_01840	2016	26751173	Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9	Homo sapiens	hg19	chr6	36635000	36635100	TP53	CDKN1A	Enhancer	Active	Normal	NA	NA	NA	skin	UBERON:0002097	BJ-hTERT-indRASG12V fibroblasts	NA	fibroblast	CL:0000057	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation	Pooled CRISPR-Cas9 enhancer screen; RNA-seq; p53 ChIP-seq data integration; CRISPR-Cas9 tiling screen; CRISPR genetic screen	Individual CRISPR/Cas9 editing; Luciferase reporter assay; TP53 ChIP-qPCR; CEBPB ChIP-qPCR; RT-qPCR; BrdU incorporation; senescence-associated beta-galactosidase assay; Western blot; CRISPR-Cas9 endogenous deletion/editing; Reporter assay
E_01841	2016	26751173	Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9	Homo sapiens	hg19	chr11	69329684	69330954	ESR1	CCND1	Enhancer	Active	Normal	NA	NA	NA	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	Enhancer activity assay; Endogenous enhancer perturbation	ChIP-seq; CRISPR-Cas9 tiling screen; CRISPR genetic screen	Luciferase reporter assay, CRISPR knockout; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; Reporter assay
E_01842	2016	26808502	Lineage-affiliated transcription factors bind the Gata3 Tce1 enhancer to mediate lineage-specific programs	Mus musculus	mm10	chr2	9515156	9522270	Tcf7	Gata3	Enhancer	Active	Normal	NA	NA	NA	thymus	UBERON:0002370	Thymocytes (ETP/DN/DP/CD4 SP)	NA	thymocyte	CL:0000893	Enhancer activity assay; Functional perturbation assay; TF binding assay; Endogenous enhancer perturbation; In vivo functional validation	NA	Transgenic reporter assay, CRISPR knockout; ChIP-qPCR; RT-qPCR; Transgenic enhancer reporter assay; Mouse genetic deletion/knock-in; In vivo phenotyping
E_01843	2025	39863595	The α-globin super-enhancer acts in an orientation-dependent manner	Mus musculus	mm9	chr11	32145028	32146147	Gata1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	ES-E14TG2a	CVCL_9108	primitive erythroid lineage cell	CL:0002417	Enhancer activity assay; Functional perturbation assay; TF binding assay	ATAC-seq; published erythroid Gata1 ChIP-seq	CRISPR-Cas9 R1 deletion; RT-qPCR
E_01844	2025	39863595	The α-globin super-enhancer acts in an orientation-dependent manner	Mus musculus	mm9	chr11	32145028	32146147	Gata1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	ES-E14TG2a	CVCL_9108	primitive erythroid lineage cell	CL:0002417	Enhancer activity assay; Functional perturbation assay; TF binding assay	ATAC-seq; published erythroid Gata1 ChIP-seq	CRISPR-Cas9 R1 deletion; RT-qPCR
E_01845	2025	39863595	The α-globin super-enhancer acts in an orientation-dependent manner	Mus musculus	mm9	chr11	32145028	32146147	Klf1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	ES-E14TG2a	CVCL_9108	primitive erythroid lineage cell	CL:0002417	Enhancer activity assay; Functional perturbation assay; TF binding assay	ATAC-seq; published erythroid Klf1 ChIP-seq	CRISPR-Cas9 R1 deletion; RT-qPCR
E_01846	2025	39863595	The α-globin super-enhancer acts in an orientation-dependent manner	Mus musculus	mm9	chr11	32145028	32146147	Klf1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	ES-E14TG2a	CVCL_9108	primitive erythroid lineage cell	CL:0002417	Enhancer activity assay; Functional perturbation assay; TF binding assay	ATAC-seq; published erythroid Klf1 ChIP-seq	CRISPR-Cas9 R1 deletion; RT-qPCR
E_01847	2025	39863595	The α-globin super-enhancer acts in an orientation-dependent manner	Mus musculus	mm9	chr11	32145028	32146147	Nfe2	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	ES-E14TG2a	CVCL_9108	primitive erythroid lineage cell	CL:0002417	Enhancer activity assay; Functional perturbation assay; TF binding assay	ATAC-seq; published erythroid Nfe2 ChIP-seq	CRISPR-Cas9 R1 deletion; RT-qPCR
E_01848	2025	39863595	The α-globin super-enhancer acts in an orientation-dependent manner	Mus musculus	mm9	chr11	32145028	32146147	Nfe2	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	ES-E14TG2a	CVCL_9108	primitive erythroid lineage cell	CL:0002417	Enhancer activity assay; Functional perturbation assay; TF binding assay	ATAC-seq; published erythroid Nfe2 ChIP-seq	CRISPR-Cas9 R1 deletion; RT-qPCR
E_01849	2025	39863595	The α-globin super-enhancer acts in an orientation-dependent manner	Mus musculus	mm9	chr11	32145028	32146147	Tal1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	ES-E14TG2a	CVCL_9108	primitive erythroid lineage cell	CL:0002417	Enhancer activity assay; Functional perturbation assay; TF binding assay	ATAC-seq; published erythroid Tal1 ChIP-seq	CRISPR-Cas9 R1 deletion; RT-qPCR
E_01850	2025	39863595	The α-globin super-enhancer acts in an orientation-dependent manner	Mus musculus	mm9	chr11	32145028	32146147	Tal1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	ES-E14TG2a	CVCL_9108	primitive erythroid lineage cell	CL:0002417	Enhancer activity assay; Functional perturbation assay; TF binding assay	ATAC-seq; published erythroid Tal1 ChIP-seq	CRISPR-Cas9 R1 deletion; RT-qPCR
E_01851	2025	39863595	The α-globin super-enhancer acts in an orientation-dependent manner	Mus musculus	mm9	chr11	32150550	32151858	Gata1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	ES-E14TG2a	CVCL_9108	primitive erythroid lineage cell	CL:0002417	Enhancer activity assay; Functional perturbation assay; TF binding assay	ATAC-seq; published erythroid Gata1 ChIP-seq	CRISPR-Cas9 R2 inversion; RT-qPCR
E_01852	2025	39863595	The α-globin super-enhancer acts in an orientation-dependent manner	Mus musculus	mm9	chr11	32150550	32151858	Gata1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	ES-E14TG2a	CVCL_9108	primitive erythroid lineage cell	CL:0002417	Enhancer activity assay; Functional perturbation assay; TF binding assay	ATAC-seq; published erythroid Gata1 ChIP-seq	CRISPR-Cas9 R2 inversion; RT-qPCR
E_01853	2025	39863595	The α-globin super-enhancer acts in an orientation-dependent manner	Mus musculus	mm9	chr11	32150550	32151858	Klf1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	ES-E14TG2a	CVCL_9108	primitive erythroid lineage cell	CL:0002417	Enhancer activity assay; Functional perturbation assay; TF binding assay	ATAC-seq; published erythroid Klf1 ChIP-seq	CRISPR-Cas9 R2 inversion; RT-qPCR
E_01854	2025	39863595	The α-globin super-enhancer acts in an orientation-dependent manner	Mus musculus	mm9	chr11	32150550	32151858	Klf1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	ES-E14TG2a	CVCL_9108	primitive erythroid lineage cell	CL:0002417	Enhancer activity assay; Functional perturbation assay; TF binding assay	ATAC-seq; published erythroid Klf1 ChIP-seq	CRISPR-Cas9 R2 inversion; RT-qPCR
E_01855	2025	39863595	The α-globin super-enhancer acts in an orientation-dependent manner	Mus musculus	mm9	chr11	32150550	32151858	Nfe2	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	ES-E14TG2a	CVCL_9108	primitive erythroid lineage cell	CL:0002417	Enhancer activity assay; Functional perturbation assay; TF binding assay	ATAC-seq; published erythroid Nfe2 ChIP-seq	CRISPR-Cas9 R2 inversion; RT-qPCR
E_01856	2025	39863595	The α-globin super-enhancer acts in an orientation-dependent manner	Mus musculus	mm9	chr11	32150550	32151858	Nfe2	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	ES-E14TG2a	CVCL_9108	primitive erythroid lineage cell	CL:0002417	Enhancer activity assay; Functional perturbation assay; TF binding assay	ATAC-seq; published erythroid Nfe2 ChIP-seq	CRISPR-Cas9 R2 inversion; RT-qPCR
E_01857	2025	39863595	The α-globin super-enhancer acts in an orientation-dependent manner	Mus musculus	mm9	chr11	32150550	32151858	Tal1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	ES-E14TG2a	CVCL_9108	primitive erythroid lineage cell	CL:0002417	Enhancer activity assay; Functional perturbation assay; TF binding assay	ATAC-seq; published erythroid Tal1 ChIP-seq	CRISPR-Cas9 R2 inversion; RT-qPCR
E_01858	2025	39863595	The α-globin super-enhancer acts in an orientation-dependent manner	Mus musculus	mm9	chr11	32150550	32151858	Tal1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	ES-E14TG2a	CVCL_9108	primitive erythroid lineage cell	CL:0002417	Enhancer activity assay; Functional perturbation assay; TF binding assay	ATAC-seq; published erythroid Tal1 ChIP-seq	CRISPR-Cas9 R2 inversion; RT-qPCR
E_01859	2016	26751173	Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9	Homo sapiens	hg19	chr6	36634056	36636070	TP53	CDKN1A	Enhancer	Active	Normal	NA	NA	NA	skin of prepuce of penis	UBERON:0001471	BJ [Human fibroblast]	CVCL_3653	fibroblast of foreskin	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Enhancer RNA assay; Oncogene-induced senescence assay	CRISPR-p53-enhLib pooled screen; CRISPR-deCDKN1A tiling screen; TP53 ChIP-seq; RNA-seq	Individual sgRNA CRISPR-Cas9 mutagenesis; Luciferase reporter assay; TP53-site mutagenesis; TP53 ChIP-qPCR; eRNA RT-qPCR; CDKN1A RT-qPCR; Western blot; BrdU incorporation; SA-beta-galactosidase assay; CRISPR-Cas9; Reporter assay
E_01860	2016	26751173	Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9	Homo sapiens	hg19	chr6	36634056	36636070	TP53	CDKN1A	Enhancer	Active	Normal	NA	NA	NA	foreskin	NA	BJ [Human fibroblast]	CVCL_3653	fibroblast	CL:0000057	Endogenous enhancer perturbation; Pooled enhancer screen; reporter validation; target-gene and senescence phenotype validation	Pooled CRISPR-Cas9 enhancer screen; TP53 ChIP-seq; RNA-seq	Individual CRISPR-Cas9 targeting; Luciferase reporter assay; TP53 ChIP-qPCR; qRT-PCR; BrdU assay; senescence-associated beta-galactosidase assay; CRISPR-Cas9; Reporter assay
E_01861	2016	26751173	Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9	Homo sapiens	hg19	chr6	36631690	36640853	TP53	CDKN1A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	BJ	NA	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; GRO-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RNAi/siRNA/shRNA
E_01862	2016	26751173	Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9	Homo sapiens	hg19	chr6	36640690	36643070	TP53	CDKN1A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	BJ	NA	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RNAi/siRNA/shRNA
E_01863	2015	25249570	Pi3kcb links Hippo-YAP and PI3K-AKT signaling pathways to promote cardiomyocyte proliferation and survival	Mus musculus	mm9	chr9	99032500	99033051	Tead1	Pik3cb	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	neonatal rat ventricular cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	552-bp luciferase reporter assay; TEAD-site mutagenesis; YAP overexpression; YAP[S94A] mutant assay; qRT-PCR; siRNA/shRNA perturbation; ChIP
E_01864	2025	40067173	Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma	Homo sapiens	hg38	chr8	128172101	128172473	POU2F2	MYC	Enhancer	Active	Disease	diffuse large B-cell lymphoma	MONDO:0018905	DOID:0050745	inguinal part of abdomen	UBERON:0008337	BJAB	CVCL_5711	B cell	CL:0000236	Enhancer activity assay; Functional perturbation assay; TF binding assay	H3K27ac ChIP-seq; ATAC-seq; OCT2 BioChIP-seq (published dataset)	Individual CRISPRi; qRT-PCR; Western blot
E_01865	2024	38233525	Affinity-optimizing enhancer variants disrupt development	Homo sapiens	hg19	chr7	155594277	155595077	ETS1	SHH	Enhancer	Active	Normal	NA	NA	NA	forelimb bud	UBERON:0005417	Embryonic limb bud mesenchymal cells	NA	mesenchymal cell	CL:0008019	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis	MPRA; RNA-seq	CRISPR Knockin, Transgenic reporter assay, EMSA, in situ hybridization, Skeletal staining
E_01866	2019	31164884	Mechanistic Characterization of RASGRP1 Variants Identifies an hnRNP-K-Regulated Transcriptional Enhancer Contributing to SLE Susceptibility	Homo sapiens	hg19	chr15	38850022	38850502	HNRNPK	RASGRP1	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	HEK293	CVCL_0045	embryonic kidney cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; eQTL analysis	Luciferase reporter assay; EMSA; ChIP-qPCR; Western blot; RT-qPCR; Reporter assay; qPCR
E_01867	2016	26446995	An autoregulatory enhancer controls mammary-specific STAT5 functions	Mus musculus	mm10	chr11	100859351	100885169	NA	NA	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mammary Epithelium	NA	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; DNase-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_01868	2016	26808502	Lineage-affiliated transcription factors bind the Gata3 Tce1 enhancer to mediate lineage-specific programs	Mus musculus	mm10	chr2	10136078	10138078	Rbpj	Gata3	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	T Cell	NA	T cell	CL:0000084	Enhancer activity assay; Endogenous enhancer perturbation; In vivo functional validation; TF-binding/chromatin assay	NA	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_01869	2016	26808502	Lineage-affiliated transcription factors bind the Gata3 Tce1 enhancer to mediate lineage-specific programs	Mus musculus	mm10	chr2	10136078	10138078	Tcf12	Gata3	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	T Cell	NA	T cell	CL:0000084	Enhancer activity assay; Endogenous enhancer perturbation; In vivo functional validation; TF-binding/chromatin assay	NA	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_01870	2016	26808502	Lineage-affiliated transcription factors bind the Gata3 Tce1 enhancer to mediate lineage-specific programs	Mus musculus	mm10	chr2	10136078	10138078	Tcf7	Gata3	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	T Cell	NA	T cell	CL:0000084	Enhancer activity assay; Endogenous enhancer perturbation; In vivo functional validation; TF-binding/chromatin assay	NA	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_01871	2012	22665440	Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus	Homo sapiens	hg19	chr17	69107686	69108045	AR	SOX9	Enhancer	Active	Normal	NA	NA	NA	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Genetic-variant functional analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_01872	2012	22665440	Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus	Homo sapiens	hg19	chr17	69107686	69108045	FOXA1	SOX9	Enhancer	Active	Normal	NA	NA	NA	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Genetic-variant functional analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_01873	2012	22665440	Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus	Homo sapiens	hg19	chr17	69108466	69108765	AR	SOX9	Enhancer	Active	Normal	NA	NA	NA	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Genetic-variant functional analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_01874	2012	22665440	Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus	Homo sapiens	hg19	chr17	69108466	69108765	FOXA1	SOX9	Enhancer	Active	Normal	NA	NA	NA	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Genetic-variant functional analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_01875	2021	34643182	Tbx5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt gene regulatory network coordinating cardiopulmonary development	Mus musculus	mm10	chr9	71241739	71242765	Tbx5	Aldh1a2	Enhancer	Active	Normal	NA	NA	NA	alimentary part of gastrointestinal system	UBERON:0005409	mouse embryonic mesendoderm	NA	developing mesodermal progenitor	NA	Enhancer activity assay; TF binding assay	ChIP-seq	Luciferase reporter assay; motif mutation assay; RT-qPCR
E_01876	2019	31164884	Mechanistic Characterization of RASGRP1 Variants Identifies an hnRNP-K-Regulated Transcriptional Enhancer Contributing to SLE Susceptibility	Homo sapiens	hg19	chr15	38845678	38847678	NA	RASGRP1	Enhancer	Active	Disease	systemic lupus erythematosus	MONDO:0007915	DOID:9074	blood	UBERON:0000178	Jurkat E6.1	CVCL_0367	T cell	CL:0000084	Enhancer activity assay; Disease-variant functional analysis; Genetic fine-mapping; allele-specific enhancer activity	Genetic association/meta-analysis; regulatory-epigenomic integration; eQTL analysis	Allele-specific luciferase reporter assay; RT-qPCR; Luciferase reporter assay; EMSA; ChIP-qPCR; ChIP; Allele-specific reporter assay; Reporter assay
E_01877	2021	34643182	Tbx5 drives Aldh1a2 expression to regulate a RA-Hedgehog-Wnt gene regulatory network coordinating cardiopulmonary development	Homo sapiens	hg38	chr15	58038775	58039647	TBX5	ALDH1A2	Enhancer	Active	Normal	NA	NA	NA	alimentary part of gastrointestinal system	UBERON:0005409	NA	NA	embryonic cardiopulmonary progenitor cell	NA	Enhancer activity assay; Comparative enhancer analysis	Mouse ortholog ChIP-seq; sequence conservation	Luciferase reporter assay; enhancer motif mutation assay
E_01878	2018	29142074	STAT3 controls COL1A2 enhancer activation cooperatively with JunB, regulates type I collagen synthesis posttranscriptionally, and is essential for lung myofibroblast differentiation	Homo sapiens	hg19	chr7	94002773	94005073	STAT3	COL1A2	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	Lung Myofibroblast	NA	fibroblast	CL:0000057	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01879	2015	25249570	Pi3kcb links Hippo-YAP and PI3K-AKT signaling pathways to promote cardiomyocyte proliferation and survival	Mus musculus	mm10	chr9	99131669	99132862	Yap1	Pik3cb	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	Ventricular Cardiomyocytes (NRVMs)	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01880	2019	31164884	Mechanistic Characterization of RASGRP1 Variants Identifies an hnRNP-K-Regulated Transcriptional Enhancer Contributing to SLE Susceptibility	Homo sapiens	hg19	chr15	38846389	38846967	NA	RASGRP1	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	HEK293	CVCL_0045	embryonic kidney cell	NA	Enhancer activity assay	ChIP-seq; RNA-seq; eQTL analysis	Luciferase reporter assay; EMSA; ChIP-qPCR; Reporter assay; qPCR
E_01881	2024	39158745	An i-motif-regulated enhancer, eRNA and adjacent lncRNA affect Lhb expression through distinct mechanisms in a sex-specific context	Mus musculus	mm10	chr7	45416017	45418912	NA	Lhb	Enhancer	Active	Normal	NA	NA	NA	pituitary gland	UBERON:0000007	AlphaT3-1	CVCL_0149	gonadotrope	NA	Chromatin interaction assay; Hormonal response assay; Enhancer-associated RNA expression assay	NA	3C; RT-qPCR; estradiol treatment; dihydrotestosterone treatment
E_01882	2026	42030388	MYC-bound enhancer RNAs in cis regulate gene transcription and tumorigenesis	Homo sapiens	hg19	chr2	11623044	11625344	NA	GREB1	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	mammary gland	UBERON:0001911	BT-474	CVCL_0179	malignant cell	CL:0001064	Enhancer functional assay; chromatin remodeling assay	ChIP-qPCR	ASO-mediated MERG1 knockdown; qRT-PCR; Western blot
E_01883	2024	39158745	An i-motif-regulated enhancer, eRNA and adjacent lncRNA affect Lhb expression through distinct mechanisms in a sex-specific context	Mus musculus	mm10	chr7	45416017	45418912	NA	Lhb	Enhancer	Active	Normal	NA	NA	NA	pituitary gland	UBERON:0000007	Primary pituitary gonadotrope-derived cells from male and female mice	NA	gonadotrope	NA	Enhancer-associated eRNA validation; Physiological regulatory assay	snATAC-seq reanalysis	RT-qPCR; chromatin-associated RNA fractionation
E_01884	2024	39122682	Super enhancer acquisition drives expression of oncogenic PPP1R15B that regulates protein homeostasis in multiple myeloma	Homo sapiens	hg38	chr1	204379236	204380236	CEBPB	PPP1R15B	Enhancer	Active	Disease	plasma cell myeloma	MONDO:0009693	DOID:9538	bone marrow	UBERON:0002371	NCI-H929	CVCL_1600	plasma cell	CL:0000786	Functional perturbation assay; Super-enhancer activity assay	ChIP-seq; RNA-seq; HiChIP; ChIA-PET	Luciferase reporter assay; ChIP-qPCR
E_01885	2023	38019918	An injury-responsive mmp14b enhancer is required for heart regeneration	Danio rerio	danRer11	chr2	38181326	38182075	tead3a	mmp14b	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	injured adult zebrafish cardiac endothelial cells	NA	cardiac endothelial cell	CL:0010008	Enhancer activity assay; TF-motif binding assay; Endogenous functional perturbation assay	ATAC-seq; RNA-seq	Tol2 transgenic reporter assay; enhancer deletion scanning; TEAD-site mutagenesis; EMSA with recombinant TEAD3; CRISPR/Cas9 endogenous enhancer deletion; RT-qPCR; RNA in situ hybridization
E_01886	2023	38049665	Noncoding mutations cause super-enhancer retargeting resulting in protein synthesis dysregulation during B cell lymphoma progression	Homo sapiens	hg38	chr9	36980000	37150820	NA	ZCCHC7	Super-enhancer	Active	Disease	diffuse large B-cell lymphoma	MONDO:0018905	DOID:0050745	pleural effusion	UBERON:0000175	SU-DHL-10	CVCL_1889	malignant cell	CL:0001064	Functional perturbation assay; Chromatin interaction assay; Super-enhancer retargeting	whole-genome sequencing; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; RNA-seq; Hi-C; 4C-seq	CRISPR/Cas9 HDR editing of PAX5-TSS2; PAX5-TSS2 deletion; Sanger sequencing; RT-qPCR; northern blot; ribosome/RNA-processing assays
E_01887	2022	36402859	Hnf1b renal expression directed by a distal enhancer responsive to Pax8	Mus musculus	mm10	chr17	63643401	63643706	Pax8	Hnf1b	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	mIMCD3	NA	kidney epithelial cell	CL:0002518	Enhancer activity assay; Functional perturbation assay; TF binding assay; In vivo enhancer editing	ATAC-seq; ChIP-seq; DNase-seq	Luciferase reporter assay; Pax8-site mutagenesis; CRISPR-Cas9 enhancer editing; RT-qPCR; in vivo Xenopus reporter assay
E_01888	2019	31366290	Variation in a Left Ventricle-Specific Hand1 Enhancer Impairs GATA Transcription Factor Binding and Disrupts Conduction System Development and Function	Mus musculus	mm9	chr11	57660605	57661348	Gata4	Hand1	Enhancer	Active	Disease	acute promyelocytic leukemia	MONDO:0012883	DOID:0060318	heart left ventricle	UBERON:0002084	mouse embryonic left ventricular myocardium and ventricular conduction system	NA	cardiac muscle cell	CL:0000746	TF binding assay; Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation; In vivo enhancer activity assay; Endogenous enhancer perturbation assay; Regulatory variant functional assay; cardiac electrophysiology	Public GATA4 ChIP-seq in cardiomyocyte progenitor cells; 1000 Genomes variant and linkage-disequilibrium analysis; GWAS QRS-duration association analysis; GWAS	hsp68-lacZ transgenic reporter assay; X-gal staining; 336-bp minimal enhancer mapping within the 744-bp assayed interval; GATA-site mutagenesis; GATA4 EMSA; CRISPR/Cas9 approximately 750-bp Hand1LV enhancer deletion; whole-mount in situ hybridization; RT-qPCR; immunohistochemistry; surface ECG; Langendorff epicardial optical voltage mapping; CRISPR/Cas9 modeling of rs10076436 and rs10054375; EMSA; Mouse genetic deletion/knock-in
E_01889	2014	24391132	Noninvasive and quantitative live imaging reveals a potential stress-responsive enhancer in the failing heart	Mus musculus	mm10	chr4	147962887	147964479	Ctcf	Nppb	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	HEK293T	CVCL_0063	NA	NA	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; Transgenic/LacZ assay
E_01890	2014	24391132	Noninvasive and quantitative live imaging reveals a potential stress-responsive enhancer in the failing heart	Mus musculus	mm10	chr4	147962887	147964479	Nkx2-5	Nppb	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	HEK293T	CVCL_0063	NA	NA	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; Transgenic/LacZ assay
E_01891	2025	41016515	Super-enhancer-driven ELOVL5 promotes T-ALL progression through the MYC-SERBP1 pathway	Homo sapiens	hg38	chr6	53306407	53314482	NA	ELOVL5	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	Primary pediatric T-ALL bone marrow cells	NA	T cell	CL:0000084	Chromatin-state profiling; In vivo functional validation; Super-enhancer identification assay	H3K27ac ChIP-seq; RNA-seq; ChIP-seq	ChIP; In vivo phenotyping; Xenograft/xenotransplant
E_01892	2022	36402859	Hnf1b renal expression directed by a distal enhancer responsive to Pax8	Homo sapiens	hg19	chr17	37648901	37649206	PAX8	HNF1B	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	Kidney Tubule Primary Cells	NA	kidney tubule epithelial cell	NA	Enhancer activity assay; TF binding assay	DNase-seq; ChIP-seq; ATAC-seq	qRT-PCR, and ChIP-qPCR; CRISPR-Cas9
E_01893	2021	33107387	Genetic Dissection of a Super Enhancer Controlling the Nppa-Nppb Cluster in the Heart	Mus musculus	mm9	chr4	147333142	147344738	Gata4	Nppa	Super-enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	mouse ventricular myocardium	NA	cardiac muscle cell	CL:0000746	Endogenous enhancer perturbation; In vivo functional validation; In vivo enhancer-cluster genetic dissection; chromatin topology analysis; enhancer-subdomain perturbation	4C-seq; RNA-seq; H3K27ac CUT&RUN; epigenomic enhancer-cluster analysis	CRISPR/Cas9 deletion of RE1 and constituent RE1a/RE1b regulatory elements; RT-qPCR; in situ expression analysis; myocardial infarction and hypertrophic-stress phenotyping; Start/End denote the approximately 11.6-kb RE1 functional enhancer-cluster domain rather than a single constituent enhancer; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in; In vivo phenotyping
E_01894	2021	33107387	Genetic Dissection of a Super Enhancer Controlling the Nppa-Nppb Cluster in the Heart	Mus musculus	mm9	chr4	147333142	147344738	Gata4	Nppb	Super-enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	mouse ventricular myocardium	NA	cardiac muscle cell	CL:0000746	Endogenous enhancer perturbation; In vivo functional validation; In vivo enhancer-cluster genetic dissection; chromatin topology analysis; enhancer-subdomain perturbation	4C-seq; RNA-seq; H3K27ac CUT&RUN; epigenomic enhancer-cluster analysis	CRISPR/Cas9 deletion of RE1 and constituent RE1a/RE1b regulatory elements; RT-qPCR; in situ expression analysis; myocardial infarction and hypertrophic-stress phenotyping; Start/End denote the approximately 11.6-kb RE1 functional enhancer-cluster domain rather than a single constituent enhancer; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in; In vivo phenotyping
E_01895	2021	33107387	Genetic Dissection of a Super Enhancer Controlling the Nppa-Nppb Cluster in the Heart	Mus musculus	mm9	chr4	147333142	147344738	Nkx2-5	Nppa	Super-enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	mouse ventricular myocardium	NA	cardiac muscle cell	CL:0000746	Endogenous enhancer perturbation; In vivo functional validation; In vivo enhancer-cluster genetic dissection; chromatin topology analysis; enhancer-subdomain perturbation	4C-seq; RNA-seq; H3K27ac CUT&RUN; epigenomic enhancer-cluster analysis	CRISPR/Cas9 deletion of RE1 and constituent RE1a/RE1b regulatory elements; RT-qPCR; in situ expression analysis; myocardial infarction and hypertrophic-stress phenotyping; Start/End denote the approximately 11.6-kb RE1 functional enhancer-cluster domain rather than a single constituent enhancer; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in; In vivo phenotyping
E_01896	2021	33107387	Genetic Dissection of a Super Enhancer Controlling the Nppa-Nppb Cluster in the Heart	Mus musculus	mm9	chr4	147333142	147344738	Nkx2-5	Nppb	Super-enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	mouse ventricular myocardium	NA	cardiac muscle cell	CL:0000746	Endogenous enhancer perturbation; In vivo functional validation; In vivo enhancer-cluster genetic dissection; chromatin topology analysis; enhancer-subdomain perturbation	4C-seq; RNA-seq; H3K27ac CUT&RUN; epigenomic enhancer-cluster analysis	CRISPR/Cas9 deletion of RE1 and constituent RE1a/RE1b regulatory elements; RT-qPCR; in situ expression analysis; myocardial infarction and hypertrophic-stress phenotyping; Start/End denote the approximately 11.6-kb RE1 functional enhancer-cluster domain rather than a single constituent enhancer; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in; In vivo phenotyping
E_01897	2021	33107387	Genetic Dissection of a Super Enhancer Controlling the Nppa-Nppb Cluster in the Heart	Mus musculus	mm9	chr4	147333142	147344738	Tbx5	Nppa	Super-enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	mouse ventricular myocardium	NA	cardiac muscle cell	CL:0000746	Endogenous enhancer perturbation; In vivo functional validation; In vivo enhancer-cluster genetic dissection; chromatin topology analysis; enhancer-subdomain perturbation	4C-seq; RNA-seq; H3K27ac CUT&RUN; epigenomic enhancer-cluster analysis	CRISPR/Cas9 deletion of RE1 and constituent RE1a/RE1b regulatory elements; RT-qPCR; in situ expression analysis; myocardial infarction and hypertrophic-stress phenotyping; Start/End denote the approximately 11.6-kb RE1 functional enhancer-cluster domain rather than a single constituent enhancer; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in; In vivo phenotyping
E_01898	2021	33107387	Genetic Dissection of a Super Enhancer Controlling the Nppa-Nppb Cluster in the Heart	Mus musculus	mm9	chr4	147333142	147344738	Tbx5	Nppb	Super-enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	mouse ventricular myocardium	NA	cardiac muscle cell	CL:0000746	Endogenous enhancer perturbation; In vivo functional validation; In vivo enhancer-cluster genetic dissection; chromatin topology analysis; enhancer-subdomain perturbation	4C-seq; RNA-seq; H3K27ac CUT&RUN; epigenomic enhancer-cluster analysis	CRISPR/Cas9 deletion of RE1 and constituent RE1a/RE1b regulatory elements; RT-qPCR; in situ expression analysis; myocardial infarction and hypertrophic-stress phenotyping; Start/End denote the approximately 11.6-kb RE1 functional enhancer-cluster domain rather than a single constituent enhancer; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in; In vivo phenotyping
E_01899	2009	19458616	Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus	Homo sapiens	hg19	chr12	68434020	68435020	CTCF	IFNG	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	CCR5+ Th1 effector memory CD4+ T cells	NA	T helper 1 cell	CL:0000545	Functional perturbation assay; TF binding assay; Chromatin interaction assay	NA	CTCF/RAD21 ChIP-qPCR; 3C; 3D-FISH; siRNA knockdown; RT-qPCR
E_01900	2009	19458616	Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus	Homo sapiens	hg19	chr12	68551520	68552520	CTCF	IFNG	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	CCR5+ Th1 effector memory CD4+ T cells	NA	T helper 1 cell	CL:0000545	Functional perturbation assay; TF binding assay; Chromatin interaction assay	NA	CTCF/RAD21 ChIP-qPCR; 3C; 3D-FISH; siRNA knockdown; RT-qPCR
E_01901	2009	19458616	Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus	Homo sapiens	hg19	chr12	68616020	68617020	CTCF	IFNG	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	CCR5+ Th1 effector memory CD4+ T cells	NA	T helper 1 cell	CL:0000545	Functional perturbation assay; TF binding assay; Chromatin interaction assay	NA	CTCF/RAD21 ChIP-qPCR; 3C; 3D-FISH; siRNA knockdown; RT-qPCR
E_01902	2011	21087445	Identification of a novel cell type-specific intronic enhancer of macrophage migration inhibitory factor (MIF) and its regulation by mithramycin	Homo sapiens	hg19	chr22	24236392	24237411	SP1	MIF	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	CCRF-CEM C7A	CVCL_6826	T cell	CL:0000084	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin accessibility assay	NA	DNase I hypersensitivity assay; Southern blot; Luciferase reporter assay; Site-directed mutagenesis; EMSA; mithramycin perturbation; siRNA knockdown
E_01903	2011	21673114	Combinatorial regulation of photoreceptor differentiation factor, neural retina leucine zipper gene NRL, revealed by in vivo promoter analysis	Mus musculus	mm10	chr14	55525638	55525795	Rorb	Nrl	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	mouse retina in vivo	NA	retinal rod cell	CL:0000604	Enhancer activity assay; Functional perturbation assay; TF binding assay; In vivo functional validation	NA	In vivo retinal electroporation reporter assay; EMSA/supershift; Site-directed mutagenesis; Confocal fluorescence analysis; EMSA; In vivo phenotyping
E_01904	2025	41016515	Super-enhancer-driven ELOVL5 promotes T-ALL progression through the MYC-SERBP1 pathway	Homo sapiens	hg38	chr6	53306407	53314482	NA	ELOVL5	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	J.gamma1	CVCL_6410	T cell	CL:0000084	Functional perturbation assay; Chromatin-state profiling; In vivo functional validation; Super-enhancer identification assay; Transcriptomic pathway analysis	H3K27ac ChIP-seq; RNA-seq; ChIP-seq	shRNA-mediated ELOVL5 knockdown; Cell proliferation assay; Apoptosis assay; SERBP1 knockdown; Mouse xenograft tumor-burden and survival assay; ChIP; In vivo phenotyping; Xenograft/xenotransplant
E_01905	2025	41016515	Super-enhancer-driven ELOVL5 promotes T-ALL progression through the MYC-SERBP1 pathway	Homo sapiens	hg38	chr6	53306407	53314482	NA	ELOVL5	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	J.gamma1	CVCL_6410	T cell	CL:0000084	Functional perturbation assay; Chromatin-state profiling; In vivo functional validation; Super-enhancer identification assay; Enhancer chromatin-state assay	H3K27ac ChIP-seq; RNA-seq; ChIP-seq	ELOVL5 knockdown; SERBP1 knockdown; qRT-PCR; Western blot; Cell proliferation assay; Flow-cytometric apoptosis assay; Mouse xenograft assay; ChIP; In vivo phenotyping; Xenograft/xenotransplant
E_01906	2016	26813977	A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening	Homo sapiens	hg19	chr6	31139599	31139921	POU5F1	POU5F1	Enhancer	Active	Normal	NA	NA	NA	embryonic stem-cell culture	NA	H1-hESC	CVCL_9771	embryonic stem cell	CL:0002322	Enhancer activity assay; High-throughput cis-regulatory screen; endogenous functional perturbation	Pooled CRISPR-Cas9 screen; DNase-seq/ENCODE chromatin-data integration; DNA methylation profiling	Individual CRISPR-Cas9 perturbation/deletion; Luciferase reporter assay; Flow cytometry; qRT-PCR; CRISPR-Cas9
E_01907	2011	21673114	Combinatorial regulation of photoreceptor differentiation factor, neural retina leucine zipper gene NRL, revealed by in vivo promoter analysis	Mus musculus	mm10	chr11	75210000	75210304	NA	Nrl	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	Primary Retinal Cells	NA	retinal cell	CL:0009004	Enhancer activity assay; In vivo functional validation	NA	Transgenic reporter assay; EMSA; In vivo phenotyping
E_01908	2011	21673114	Combinatorial regulation of photoreceptor differentiation factor, neural retina leucine zipper gene NRL, revealed by in vivo promoter analysis	Mus musculus	mm10	chr14	55525638	55525795	Creb1	Nrl	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	mouse retina in vivo	NA	retinal rod cell	CL:0000604	Enhancer activity assay; TF binding assay; In vivo functional validation	NA	In vivo retinal electroporation reporter assay; EMSA/supershift; Confocal fluorescence analysis; EMSA; In vivo phenotyping
E_01909	2011	21673114	Combinatorial regulation of photoreceptor differentiation factor, neural retina leucine zipper gene NRL, revealed by in vivo promoter analysis	Mus musculus	mm10	chr14	55525638	55525795	Crx	Nrl	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	mouse retina in vivo	NA	retinal rod cell	CL:0000604	Enhancer activity assay; TF binding assay; In vivo functional validation	NA	In vivo retinal electroporation reporter assay; EMSA/supershift; Confocal fluorescence analysis; EMSA; In vivo phenotyping
E_01910	2011	21673114	Combinatorial regulation of photoreceptor differentiation factor, neural retina leucine zipper gene NRL, revealed by in vivo promoter analysis	Mus musculus	mm10	chr14	55525638	55525795	Otx2	Nrl	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	mouse retina in vivo	NA	retinal rod cell	CL:0000604	Enhancer activity assay; TF binding assay; In vivo functional validation	NA	In vivo retinal electroporation reporter assay; EMSA/supershift; Confocal fluorescence analysis; EMSA; In vivo phenotyping
E_01911	2016	26813977	A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening	Homo sapiens	hg19	chr6	30646843	30647217	NA	POU5F1	Enhancer	Active	Normal	NA	NA	NA	embryonic stem-cell culture	NA	H1-hESC	CVCL_9771	embryonic stem cell	CL:0002322	Enhancer activity assay; High-throughput cis-regulatory screen; endogenous functional perturbation	Pooled CRISPR-Cas9 screen; DNase-seq/ENCODE chromatin-data integration; DNA methylation profiling	Individual CRISPR-Cas9 perturbation/deletion; Luciferase reporter assay; Flow cytometry; qRT-PCR; CRISPR-Cas9
E_01912	2016	26813977	A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening	Homo sapiens	hg19	chr6	31126537	31126685	NA	POU5F1	Enhancer	Active	Normal	NA	NA	NA	embryonic stem-cell culture	NA	H1-hESC	CVCL_9771	embryonic stem cell	CL:0002322	Enhancer activity assay; High-throughput cis-regulatory screen; endogenous functional perturbation	Pooled CRISPR-Cas9 screen; DNase-seq/ENCODE chromatin-data integration; DNA methylation profiling	Individual CRISPR-Cas9 perturbation/deletion; Luciferase reporter assay; Flow cytometry; qRT-PCR; CRISPR-Cas9
E_01913	2016	26813977	A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening	Homo sapiens	hg19	chr6	31139599	31139921	NA	POU5F1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; Genetic-variant functional analysis	4C-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion
E_01914	2016	26813977	A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening	Homo sapiens	hg19	chr6	30904342	30904788	NA	POU5F1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation	4C-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion
E_01915	2016	26813977	A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening	Homo sapiens	hg19	chr6	30646843	30647217	NA	POU5F1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation	4C-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion
E_01916	2016	26813977	A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening	Homo sapiens	hg19	chr6	31126537	31126685	NA	POU5F1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation	4C-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion
E_01917	2009	19458616	Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus	Homo sapiens	hg19	chr12	68482000	68483000	NA	IFNG	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	CD4+ Th1 T Cells	NA	CD4-positive Th1 T cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; 3C-seq; RNA-seq	ChIP-qPCR; RT-qPCR; FISH
E_01918	2009	19458616	Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus	Homo sapiens	hg19	chr12	68546500	68547500	NA	IFNG	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	CD4+ Th1 T Cells	NA	CD4-positive Th1 T cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; 3C-seq; RNA-seq	ChIP-qPCR; RT-qPCR; FISH
E_01919	2009	19458616	Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus	Homo sapiens	hg19	chr12	68664000	68665000	NA	IFNG	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	CD4+ Th1 T Cells	NA	CD4-positive Th1 T cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; 3C-seq; RNA-seq	ChIP-qPCR; RT-qPCR; FISH
E_01920	2016	26813977	A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening	Homo sapiens	hg19	chr6	30754822	30755196	TEAD4	POU5F1	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	H1-hESC	CVCL_9771	embryonic stem cell	CL:0002322	Functional perturbation assay; Endogenous enhancer perturbation; Genetic screen	ChIP-seq; CRISPR genetic screen	CRISPR knockout; CRISPR-Cas9 endogenous deletion/editing
E_01921	2016	26813977	A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening	Homo sapiens	hg19	chr6	30904342	30904788	TEAD4	POU5F1	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	H1-hESC	CVCL_9771	embryonic stem cell	CL:0002322	Functional perturbation assay; Endogenous enhancer perturbation; Genetic screen	ChIP-seq; CRISPR genetic screen	CRISPR knockout; CRISPR-Cas9 endogenous deletion/editing
E_01922	2016	26813977	A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening	Homo sapiens	hg19	chr6	31234516	31234664	CTCF	POU5F1	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	H1-hESC	CVCL_9771	embryonic stem cell	CL:0002322	Functional perturbation assay; Endogenous enhancer perturbation; Genetic screen	ChIP-seq; CRISPR genetic screen	CRISPR knockout; CRISPR-Cas9 endogenous deletion/editing
E_01923	2011	21087445	Identification of a novel cell type-specific intronic enhancer of macrophage migration inhibitory factor (MIF) and its regulation by mithramycin	Homo sapiens	hg19	chr22	24236392	24237411	SP1	MIF	Enhancer	Inactive	Disease	rheumatoid arthritis	MONDO:0008383	DOID:7148	synovium	NA	primary rheumatoid arthritis fibroblast-like synoviocytes	NA	fibroblast-like synoviocyte	NA	Enhancer activity assay; Chromatin accessibility assay	NA	DNase I hypersensitivity assay; Luciferase reporter assay; EMSA; siRNA knockdown
E_01924	2011	21673114	Combinatorial regulation of photoreceptor differentiation factor, neural retina leucine zipper gene NRL, revealed by in vivo promoter analysis	Mus musculus	mm10	chr14	55518040	55518674	Crx	Nrl	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	HEK293	CVCL_0045	NA	NA	In vivo functional validation; TF-binding/chromatin assay	NA	EMSA/gel-shift assay
E_01925	2011	21673114	Combinatorial regulation of photoreceptor differentiation factor, neural retina leucine zipper gene NRL, revealed by in vivo promoter analysis	Mus musculus	mm10	chr14	55518040	55518674	Nr2e3	Nrl	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	HEK293	CVCL_0045	NA	NA	In vivo functional validation; TF-binding/chromatin assay	NA	EMSA/gel-shift assay
E_01926	2011	21673114	Combinatorial regulation of photoreceptor differentiation factor, neural retina leucine zipper gene NRL, revealed by in vivo promoter analysis	Mus musculus	mm10	chr14	55518040	55518674	Nrl	Nrl	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	HEK293	CVCL_0045	NA	NA	In vivo functional validation; TF-binding/chromatin assay	NA	EMSA/gel-shift assay
E_01927	2011	21673114	Combinatorial regulation of photoreceptor differentiation factor, neural retina leucine zipper gene NRL, revealed by in vivo promoter analysis	Mus musculus	mm10	chr14	55518040	55518674	Rorb	Nrl	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	HEK293	CVCL_0045	NA	NA	In vivo functional validation; TF-binding/chromatin assay	NA	EMSA/gel-shift assay
E_01928	2011	21087445	Identification of a novel cell type-specific intronic enhancer of macrophage migration inhibitory factor (MIF) and its regulation by mithramycin	Homo sapiens	hg19	chr22	24236570	24237410	SP1	MIF	Enhancer	Inactive	Disease	rheumatoid arthritis	MONDO:0008383	DOID:7148	layer of synovial tissue	UBERON:0007616	primary rheumatoid-arthritis fibroblast-like synoviocytes / SW982	NA	fibroblast	CL:0000057	TF binding assay; Cell-type-specific intronic enhancer mapping; cis-element mutagenesis	NA	DNase-I hypersensitivity mapping; Luciferase reporter assay; GC-box mutagenesis; EMSA; SP1/SP3 RNAi; mithramycin inhibition; siRNA knockdown
E_01929	2011	21087445	Identification of a novel cell type-specific intronic enhancer of macrophage migration inhibitory factor (MIF) and its regulation by mithramycin	Homo sapiens	hg19	chr22	24236392	24237411	SP1	MIF	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	THP-1	CVCL_0006	monocyte-like cell line	NA	Enhancer activity assay; TF binding assay; Chromatin accessibility assay	NA	DNase I hypersensitivity assay; Southern blot; Luciferase reporter assay; Site-directed mutagenesis; EMSA; siRNA knockdown
E_01930	2011	21673114	Combinatorial regulation of photoreceptor differentiation factor, neural retina leucine zipper gene NRL, revealed by in vivo promoter analysis	Mus musculus	mm10	chr14	55524862	55525285	Creb1	Nrl	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	mouse retina in vivo	NA	rod photoreceptor	NA	Promoter/enhancer cis-regulatory analysis; TF-binding analysis	NA	Retinal reporter electroporation; EMSA/supershift with CREB antibody; cluster A/B deletion analysis
E_01931	2011	21673114	Combinatorial regulation of photoreceptor differentiation factor, neural retina leucine zipper gene NRL, revealed by in vivo promoter analysis	Mus musculus	mm10	chr14	55525638	55525920	Crx	Nrl	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	mouse retina in vivo	NA	rod photoreceptor	NA	In vivo enhancer/promoter dissection; TF-binding analysis	NA	Retinal reporter electroporation; EMSA/supershift; deletion analysis
E_01932	2011	21673114	Combinatorial regulation of photoreceptor differentiation factor, neural retina leucine zipper gene NRL, revealed by in vivo promoter analysis	Mus musculus	mm10	chr14	55525638	55525920	Otx2	Nrl	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	mouse retina in vivo	NA	rod photoreceptor	NA	In vivo enhancer/promoter dissection; TF-binding analysis	NA	Retinal reporter electroporation; EMSA/supershift; deletion analysis
E_01933	2011	21087445	Identification of a novel cell type-specific intronic enhancer of macrophage migration inhibitory factor (MIF) and its regulation by mithramycin	Homo sapiens	hg19	chr22	24236570	24237410	SP1	MIF	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	HEK293T	CVCL_0063	epithelial cell	CL:0000066	TF binding assay; Cell-type-specific intronic enhancer mapping; cis-element mutagenesis	NA	DNase-I hypersensitivity mapping; Luciferase reporter assay; GC-box mutagenesis; EMSA; SP1/SP3 RNAi; mithramycin inhibition; siRNA knockdown
E_01934	2011	21087445	Identification of a novel cell type-specific intronic enhancer of macrophage migration inhibitory factor (MIF) and its regulation by mithramycin	Homo sapiens	hg19	chr22	24236570	24237410	SP1	MIF	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	THP-1	CVCL_0006	monocyte	CL:0000576	TF binding assay; Cell-type-specific intronic enhancer mapping; cis-element mutagenesis	NA	DNase-I hypersensitivity mapping; Luciferase reporter assay; GC-box mutagenesis; EMSA; SP1/SP3 RNAi; mithramycin inhibition; siRNA knockdown
E_01935	2011	21087445	Identification of a novel cell type-specific intronic enhancer of macrophage migration inhibitory factor (MIF) and its regulation by mithramycin	Homo sapiens	hg19	chr22	24236392	24237411	SP1	MIF	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	HEK293T	CVCL_0063	transformed embryonic kidney-derived cell line	NA	Enhancer activity assay; TF binding assay	NA	Luciferase reporter assay; Site-directed mutagenesis; EMSA; siRNA knockdown
E_01936	2011	21087445	Identification of a novel cell type-specific intronic enhancer of macrophage migration inhibitory factor (MIF) and its regulation by mithramycin	Homo sapiens	hg19	chr22	24236392	24237411	SP1	MIF	Enhancer	Inactive	Normal	NA	NA	NA	NA	NA	SW982	CVCL_1734	fibroblast-like sarcoma cell line	NA	Enhancer activity assay	NA	Luciferase reporter assay; EMSA; siRNA knockdown
E_01937	2011	21087445	Identification of a novel cell type-specific intronic enhancer of macrophage migration inhibitory factor (MIF) and its regulation by mithramycin	Homo sapiens	hg19	chr22	24236392	24237411	SP1	MIF	Enhancer	Active	Disease	rheumatoid arthritis	MONDO:0008383	DOID:7148	blood	UBERON:0000178	THP-1	CVCL_0006	NA	NA	Enhancer activity assay	DNaseI-seq; EMSA; siRNA knockdown	qRT-PCR
E_01938	2011	21087445	Identification of a novel cell type-specific intronic enhancer of macrophage migration inhibitory factor (MIF) and its regulation by mithramycin	Homo sapiens	hg19	chr22	24236392	24237411	SP1	MIF	Enhancer	Active	Disease	rheumatoid arthritis	MONDO:0008383	DOID:7148	kidney	UBERON:0002113	HEK293T	CVCL_0063	NA	NA	Enhancer activity assay	DNaseI-seq; EMSA; siRNA knockdown	qRT-PCR
E_01939	2011	21087445	Identification of a novel cell type-specific intronic enhancer of macrophage migration inhibitory factor (MIF) and its regulation by mithramycin	Homo sapiens	hg19	chr22	24236392	24237411	SP1	MIF	Enhancer	Active	Disease	rheumatoid arthritis	MONDO:0008383	DOID:7148	layer of synovial tissue	UBERON:0007616	SW982	CVCL_1734	NA	NA	Enhancer activity assay	DNaseI-seq; EMSA; siRNA knockdown	qRT-PCR
E_01940	2011	21087445	Identification of a novel cell type-specific intronic enhancer of macrophage migration inhibitory factor (MIF) and its regulation by mithramycin	Homo sapiens	hg19	chr22	24236392	24237411	SP1	MIF	Enhancer	Active	Disease	rheumatoid arthritis	MONDO:0008383	DOID:7148	NA	NA	CEMC7A	NA	macrophage	CL:0000235	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; EMSA/gel-shift assay
E_01941	2011	21087445	Identification of a novel cell type-specific intronic enhancer of macrophage migration inhibitory factor (MIF) and its regulation by mithramycin	Homo sapiens	hg19	chr22	24236392	24237411	SP1	MIF	Enhancer	Active	Disease	rheumatoid arthritis	MONDO:0008383	DOID:7148	NA	NA	THP-1	CVCL_0006	monocyte	CL:0000576	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; EMSA/gel-shift assay
E_01942	2011	21087445	Identification of a novel cell type-specific intronic enhancer of macrophage migration inhibitory factor (MIF) and its regulation by mithramycin	Homo sapiens	hg19	chr22	24236392	24237411	SP1	MIF	Enhancer	Active	Disease	rheumatoid arthritis	MONDO:0008383	DOID:7148	NA	NA	HEK293T	CVCL_0063	macrophage	CL:0000235	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; EMSA/gel-shift assay
E_01943	2011	21087445	Identification of a novel cell type-specific intronic enhancer of macrophage migration inhibitory factor (MIF) and its regulation by mithramycin	Homo sapiens	hg19	chr22	24236392	24237411	SP1	MIF	Enhancer	Active	Disease	rheumatoid arthritis	MONDO:0008383	DOID:7148	NA	NA	SW982	CVCL_1734	macrophage	CL:0000235	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; EMSA/gel-shift assay
E_01944	2011	21673114	Combinatorial regulation of photoreceptor differentiation factor, neural retina leucine zipper gene NRL, revealed by in vivo promoter analysis	Mus musculus	mm10	chr14	55525638	55525920	Rorb	Nrl	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	mouse retina in vivo	NA	rod photoreceptor	NA	In vivo enhancer/promoter dissection; TF binding	NA	Neonatal-retina reporter electroporation; EMSA/supershift; RORE mutation at -783/-771 abolishing reporter expression
E_01945	2026	42281194	Super-enhancer-driven KIAA1522 upregulation suppresses ferroptosis in hepatocellular carcinoma	Homo sapiens	hg38	chr1	32753965	32762956	NA	KIAA1522	Super-enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Hep-G2	CVCL_0027	hepatoblast	CL:0005026	Enhancer activity assay; Functional perturbation assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation; Super-enhancer activity assay	H3K27ac ChIP-seq; H3K4me1 ChIP-seq; H3K4me3 ChIP-seq; BRD4 ChIP-seq; RNA-seq; ChIP-seq	Dual-luciferase reporter assay; CRISPRi using dCas9-KRAB; BRD4 ChIP-qPCR; BRD4 knockdown; JQ1 treatment; i-BET151 treatment; RT-qPCR; Western blot; CRISPRi; Luciferase reporter assay; ChIP; In vivo phenotyping; Reporter assay
E_01946	2026	42281194	Super-enhancer-driven KIAA1522 upregulation suppresses ferroptosis in hepatocellular carcinoma	Homo sapiens	hg38	chr1	32753965	32762956	NA	KIAA1522	Super-enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Huh-7	CVCL_0336	hepatocyte	CL:0000182	Enhancer activity assay; Functional perturbation assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation; Super-enhancer activity assay	H3K27ac ChIP-seq; H3K4me1 ChIP-seq; H3K4me3 ChIP-seq; RNA-seq; ChIP-seq	Dual-luciferase reporter assay; CRISPRi using dCas9-KRAB; BRD4 ChIP-qPCR; BRD4 knockdown; JQ1 treatment; i-BET151 treatment; RT-qPCR; Western blot; CRISPRi; Luciferase reporter assay; ChIP; In vivo phenotyping; Reporter assay
E_01947	2025	39827212	GATA4 binding to the Sox9 enhancer mXYSRa/Enh13 is critical for testis differentiation in mouse	Mus musculus	mm10	chr11	112200000	112204700	Gata4	Sox9	Enhancer	Active	Normal	NA	NA	NA	mesonephric smooth muscle tissue	UBERON:0005321	Embryonic gonad cells (E11.5)	NA	embryonic gonad cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ATAC-seq; ChIP-seq; CUT&RUN	Luciferase reporter assay; CRISPR knockout, qRT-PCR
E_01948	2025	40208226	Gain-of-function enhancer variant near KCNB1 causes familial ST-depression syndrome	Homo sapiens	hg38	chr20	49345710	49345732	MEF2A	KCNB1	Enhancer	Active	Disease	familial ST-depression syndrome	NA	NA	heart	UBERON:0000948	AC16 [Human hybrid cardiomyocyte]	CVCL_4U18	cardiac muscle cell	CL:0000746	Enhancer activity assay; Chromatin interaction assay; Disease-variant functional analysis	WGS; RNA-seq; ATAC-seq; RNA-seq; whole-genome sequencing	Luciferase reporter assay, CRISPRa; ChIP-qPCR; 4C
E_01949	2024	38413562	The neutrophil-osteogenic cell axis promotes bone destruction in periodontitis	Mus musculus	mm39	chr14	78613540	78616951	Stat3	Tnfsf11	Enhancer	Active	Disease	periodontitis	MONDO:0005076	DOID:824	bone tissue	UBERON:0002481	Primary calvaria-derived osteoblasts from WT and RL-D4-KO mice	NA	osteoblast	CL:0000062	Endogenous enhancer perturbation; In vivo functional validation; Functional enhancer perturbation assay; Target-gene expression assay; In vivo disease phenotype validation; TF binding evidence	scRNA-seq (mouse periodontal lesions); H3K27ac/H3K4me1/H4K5ac ChIP-seq and ATAC-seq (public osteogenic-cell datasets); single-cell RNA-seq; RNA-seq	CRISPR-Cas9 RL-D4 enhancer deletion; Sanger sequencing; qPCR; ELISA; micro-CT; dynamic bone histomorphometry; TRAP staining; Toluidine blue staining; Mouse genetic deletion/knock-in
E_01950	2024	38413562	The neutrophil-osteogenic cell axis promotes bone destruction in periodontitis	Mus musculus	mm10	chr14	78376100	78379511	Stat3	Tnfsf11	Enhancer	Active	Disease	periodontitis	MONDO:0005076	DOID:824	bone tissue	UBERON:0002481	Primary calvaria-derived osteoblasts from WT and RL-D4-KO mice	NA	osteoblast	CL:0000062	Endogenous enhancer perturbation; In vivo functional validation; Functional enhancer perturbation assay; Target-gene expression assay; In vivo disease phenotype validation; TF binding evidence	scRNA-seq (mouse periodontal lesions); H3K27ac/H3K4me1/H4K5ac ChIP-seq and ATAC-seq (public osteogenic-cell datasets); single-cell RNA-seq; RNA-seq	CRISPR-Cas9 RL-D4 enhancer deletion; Sanger sequencing; qPCR; ELISA; micro-CT; dynamic bone histomorphometry; TRAP staining; Toluidine blue staining; Mouse genetic deletion/knock-in
E_01951	2023	37552875	An Enhancer Within Abcb11 Regulates G6pc2 in C57BL/6 Mouse Pancreatic Islets	Mus musculus	mm10	chr2	169760000	169760653	Mafb	G6pc2	Enhancer	Active	Normal	NA	NA	NA	pancreas	UBERON:0001264	Pancreatic islet cells	NA	pancreatic islet cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ATAC-seq; RNA-seq	CRISPR knockout; Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot
E_01952	2018	29378668	Genome-wide analysis reveals a role for TDG in estrogen receptor-mediated enhancer RNA transcription and 3-dimensional reorganization	Homo sapiens	hg19	chr2	11633299	11641134	TDG	GREB1	Enhancer	Inactive	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	MCF-7	CVCL_0031	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_01953	2017	28871148	Editing an α-globin enhancer in primary human hematopoietic stem cells as a treatment for β-thalassemia	Homo sapiens	hg19	chr16	163380	163907	TAL1	HBA1	Enhancer	Active	Disease	alpha thalassemia spectrum	MONDO:0011399	DOID:1099	blood	UBERON:0000178	Primary human CD34+ HSPC-derived erythroid cells	NA	erythroid progenitor cell	CL:0000038	Enhancer activity assay; Functional perturbation assay; TF binding assay; Gene expression assay; Chromatin-state assay	ChIP-seq	CRISPR-Cas9 MCS-R2 deletion; Sanger sequencing; droplet digital PCR; RT-qPCR; TAL1/SCL ChIP-qPCR; xenograft assay; CRISPR-Cas9
E_01954	2017	28871148	Editing an α-globin enhancer in primary human hematopoietic stem cells as a treatment for β-thalassemia	Homo sapiens	hg19	chr16	163380	163907	TAL1	HBA2	Enhancer	Active	Disease	alpha thalassemia spectrum	MONDO:0011399	DOID:1099	blood	UBERON:0000178	Primary human CD34+ HSPC-derived erythroid cells	NA	erythroid progenitor cell	CL:0000038	Enhancer activity assay; Functional perturbation assay; TF binding assay; Gene expression assay; Chromatin-state assay	ChIP-seq	CRISPR-Cas9 MCS-R2 deletion; Sanger sequencing; droplet digital PCR; RT-qPCR; TAL1/SCL ChIP-qPCR; xenograft assay; CRISPR-Cas9
E_01955	2016	26751080	Up-Regulation of Human Inducible Nitric Oxide Synthase by p300 Transcriptional Complex	Homo sapiens	hg19	chr17	26076200	26076350	NA	NOS2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary human hepatocyte	NA	hepatocyte	CL:0000182	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation	NA	Luciferase reporter assay; ChIP; 3C; Site-directed/motif mutagenesis; In vivo phenotyping
E_01956	2023	37438529	Complementary Alu sequences mediate enhancer-promoter selectivity	Homo sapiens	hg19	chr8	29256000	29256500	NA	PTK2	Enhancer	Active	Normal	NA	NA	NA	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Disease-variant functional analysis	ChIP-seq; RNA-seq, Hi-C; RNA-seq	CRISPR knockout; 3C-RT-qPCR; RT-qPCR, FISH
E_01957	2023	37438529	Complementary Alu sequences mediate enhancer-promoter selectivity	Homo sapiens	hg19	chr12	61890000	61895000	NA	AEBP2	Enhancer	Active	Normal	NA	NA	NA	uterine cervix	UBERON:0000002	Human cervical adenocarcinoma cell	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Disease-variant functional analysis	ChIP-seq; RNA-seq, Hi-C; RNA-seq	CRISPR knockout; 3C-RT-qPCR, qRT-PCR, FISH
E_01958	2023	37438529	Complementary Alu sequences mediate enhancer-promoter selectivity	Homo sapiens	hg19	chr12	61890000	61895000	NA	MGST1	Enhancer	Active	Normal	NA	NA	NA	uterine cervix	UBERON:0000002	Human cervical adenocarcinoma cell	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Disease-variant functional analysis	ChIP-seq; RNA-seq, Hi-C; RNA-seq	CRISPR knockout; 3C-RT-qPCR, qRT-PCR, FISH
E_01959	2023	37438529	Complementary Alu sequences mediate enhancer-promoter selectivity	Homo sapiens	hg19	chr12	61890000	61895000	NA	TUBA1B	Enhancer	Active	Normal	NA	NA	NA	uterine cervix	UBERON:0000002	Human cervical adenocarcinoma cell	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Disease-variant functional analysis	ChIP-seq; RNA-seq, Hi-C; RNA-seq	CRISPR knockout; 3C-RT-qPCR, qRT-PCR, FISH
E_01960	2011	21566115	A distal enhancer in Il12b is the target of transcriptional repression by the STAT3 pathway and requires the basic leucine zipper (B-ZIP) protein NFIL3	Mus musculus	mm10	chr11	44390082	44390626	Nfil3	Il12b	Enhancer	Repressed	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary bone marrow-derived macrophages	NA	macrophage	CL:0000235	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Luciferase reporter assay; enhancer deletion and site-directed mutagenesis; NFIL3 ChIP-qPCR; Nfil3 knockout; RT-qPCR; cytokine measurement
E_01961	2024	38448444	Dynamic enhancer landscapes in human craniofacial development	Mus musculus	mm10	chr7	66375715	66378251	NA	Aldh1a3	Enhancer	Active	Normal	NA	NA	NA	face	UBERON:0001456	Primary mouse embryonic face tissue (E10.5-E15.5; reporter E11.5)	NA	epithelial cell	CL:0000066	Enhancer activity assay; In vivo functional validation; Cell-type-resolved enhancer activity assay	snATAC-seq; scRNA-seq	CRISPR-mediated H11 safe-harbor transgenic lacZ reporter assay; In vivo phenotyping
E_01962	2024	38448444	Dynamic enhancer landscapes in human craniofacial development	Homo sapiens	hg38	chr8	98367000	98370806	NA	NA	Enhancer	Active	Normal	NA	NA	NA	face	UBERON:0001456	Primary human embryonic face tissue (CS13-CS23)	NA	NA	NA	Enhancer activity assay; In vivo functional validation; Cross-species functional comparison	H3K27ac ChIP-seq	CRISPR-mediated H11 safe-harbor transgenic lacZ reporter assay; In vivo phenotyping
E_01963	2024	38448444	Dynamic enhancer landscapes in human craniofacial development	Mus musculus	mm10	chr15	34751000	34754612	NA	NA	Enhancer	Repressed	Normal	NA	NA	NA	face	UBERON:0001456	Primary mouse embryonic face tissue	NA	NA	NA	Enhancer activity assay; In vivo functional validation; Cross-species functional comparison	H3K27ac ChIP-seq	CRISPR-mediated H11 safe-harbor transgenic lacZ reporter assay (negative); In vivo phenotyping
E_01964	2018	29256171	Multiple enhancer regions govern the transcription of CCN2 during embryonic development	Mus musculus	mm9	chr10	24116247	24118247	NA	Ccn2	Enhancer	Active	Normal	NA	NA	NA	cartilage tissue	UBERON:0002418	E15.5 transgenic mouse embryo	NA	hypertrophic chondrocyte	CL:0000743	Enhancer activity assay; In vivo enhancer activity assay	ENCODE H3K4me1/H3K27ac ChIP-seq; DNase-seq; comparative-conservation data integration	Hsp68-LacZ transgenic mouse reporter assay; whole-mount X-gal staining; histological analysis; Transgenic enhancer reporter assay
E_01965	2018	29256171	Multiple enhancer regions govern the transcription of CCN2 during embryonic development	Mus musculus	mm9	chr10	24179247	24181247	NA	Ccn2	Enhancer	Active	Normal	NA	NA	NA	articular cartilage of joint	UBERON:0010996	E15.5 transgenic mouse embryo	NA	articular chondrocyte	CL:1001607	Enhancer activity assay; In vivo enhancer activity assay	ENCODE H3K4me1/H3K27ac ChIP-seq; DNase-seq; comparative-conservation data integration	Hsp68-LacZ transgenic mouse reporter assay; whole-mount X-gal staining; histological analysis; Transgenic enhancer reporter assay
E_01966	2018	29256171	Multiple enhancer regions govern the transcription of CCN2 during embryonic development	Mus musculus	mm9	chr10	24214247	24216247	NA	Ccn2	Enhancer	Active	Normal	NA	NA	NA	dermis	UBERON:0002067	E15.5 transgenic mouse embryo	NA	endothelial cell	CL:0000115	Enhancer activity assay; In vivo enhancer activity assay	ENCODE H3K4me1/H3K27ac ChIP-seq; DNase-seq; comparative-conservation data integration	Hsp68-LacZ transgenic mouse reporter assay; whole-mount X-gal staining; histological analysis; Transgenic enhancer reporter assay
E_01967	2018	29256171	Multiple enhancer regions govern the transcription of CCN2 during embryonic development	Mus musculus	mm9	chr10	24115343	24117739	NA	Ccn2	Enhancer	Active	Normal	NA	NA	NA	cartilage tissue	UBERON:0002418	E15.5 transgenic mouse embryo	NA	hypertrophic chondrocyte	CL:0000743	Enhancer activity assay; In vivo enhancer activity assay	ENCODE H3K4me1 ChIP-seq; H3K27ac ChIP-seq; DNase-seq data integration	Hsp68-LacZ transgenic mouse reporter assay; whole-mount X-gal staining; histological analysis; Transgenic enhancer reporter assay
E_01968	2018	29256171	Multiple enhancer regions govern the transcription of CCN2 during embryonic development	Mus musculus	mm9	chr10	24177496	24180069	NA	Ccn2	Enhancer	Active	Normal	NA	NA	NA	articular cartilage of joint	UBERON:0010996	E15.5 transgenic mouse embryo	NA	articular chondrocyte	CL:1001607	Enhancer activity assay; In vivo enhancer activity assay	ENCODE H3K4me1 ChIP-seq; H3K27ac ChIP-seq; DNase-seq data integration	Hsp68-LacZ transgenic mouse reporter assay; whole-mount X-gal staining; histological analysis; Transgenic enhancer reporter assay
E_01969	2018	29256171	Multiple enhancer regions govern the transcription of CCN2 during embryonic development	Mus musculus	mm9	chr10	24212605	24214888	NA	Ccn2	Enhancer	Active	Normal	NA	NA	NA	dermis	UBERON:0002067	E15.5 transgenic mouse embryo	NA	dermal microvascular endothelial cell	CL:0011030	Enhancer activity assay; In vivo enhancer activity assay	ENCODE H3K4me1 ChIP-seq; H3K27ac ChIP-seq; DNase-seq data integration	Hsp68-LacZ transgenic mouse reporter assay; whole-mount X-gal staining; histological analysis; Transgenic enhancer reporter assay
E_01970	2018	29256171	Multiple enhancer regions govern the transcription of CCN2 during embryonic development	Mus musculus	mm9	chr10	79521460	79522010	NA	Ccn2	Enhancer	Active	Normal	NA	NA	NA	dermis	UBERON:0002067	E15.5 transgenic mouse embryo	NA	dermal microvascular endothelial cell	CL:0011030	Enhancer activity assay; In vivo enhancer activity assay	ENCODE H3K4me1/H3K27ac ChIP-seq and DNase-seq data integration	Hsp68-LacZ transgenic mouse reporter assay; whole-mount X-gal staining; histological analysis; Transgenic enhancer reporter assay
E_01971	2018	29256171	Multiple enhancer regions govern the transcription of CCN2 during embryonic development	Mus musculus	mm9	chr10	79544630	79545180	NA	Ccn2	Enhancer	Active	Normal	NA	NA	NA	articular cartilage of joint	UBERON:0010996	E15.5 transgenic mouse embryo	NA	articular chondrocyte	CL:1001607	Enhancer activity assay; In vivo enhancer activity assay	ENCODE H3K4me1/H3K27ac ChIP-seq and DNase-seq data integration	Hsp68-LacZ transgenic mouse reporter assay; whole-mount X-gal staining; histological analysis; Transgenic enhancer reporter assay
E_01972	2018	29256171	Multiple enhancer regions govern the transcription of CCN2 during embryonic development	Mus musculus	mm9	chr10	79567820	79568370	NA	Ccn2	Enhancer	Active	Normal	NA	NA	NA	cartilage tissue	UBERON:0002418	E15.5 transgenic mouse embryo	NA	hypertrophic chondrocyte	CL:0000743	Enhancer activity assay; In vivo enhancer activity assay	ENCODE H3K4me1/H3K27ac ChIP-seq and DNase-seq data integration	Hsp68-LacZ transgenic mouse reporter assay; whole-mount X-gal staining; histological analysis; Transgenic enhancer reporter assay
E_01973	2012	22543974	Regulatory variation in a TBX5 enhancer leads to isolated congenital heart disease	Homo sapiens	hg19	chr12	114701207	114704691	TAL1	TBX5	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	Primary cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Disease-variant functional analysis; In vivo functional validation	ChIP-seq	Transgenic reporter assay, EMSA; In vivo phenotyping
E_01974	2010	20093418	Glucocorticoid receptor activates poised FKBP51 locus through long-distance interactions	Homo sapiens	hg19	chr6	35505138	35511492	CTCF	FKBP5	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	A-549	CVCL_0023	malignant cell	CL:0001064	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01975	2010	20093418	Glucocorticoid receptor activates poised FKBP51 locus through long-distance interactions	Homo sapiens	hg19	chr6	35505138	35511492	CTCF	FKBP5	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	VCaP	CVCL_2235	malignant cell	CL:0001064	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01976	2010	20093418	Glucocorticoid receptor activates poised FKBP51 locus through long-distance interactions	Homo sapiens	hg19	chr6	35616283	35622638	CTCF	FKBP5	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	A-549	CVCL_0023	malignant cell	CL:0001064	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01977	2010	20093418	Glucocorticoid receptor activates poised FKBP51 locus through long-distance interactions	Homo sapiens	hg19	chr6	35616283	35622638	CTCF	FKBP5	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	VCaP	CVCL_2235	malignant cell	CL:0001064	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01978	2010	20093418	Glucocorticoid receptor activates poised FKBP51 locus through long-distance interactions	Homo sapiens	hg19	chr6	35636622	35642872	CTCF	FKBP5	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	A-549	CVCL_0023	malignant cell	CL:0001064	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01979	2010	20093418	Glucocorticoid receptor activates poised FKBP51 locus through long-distance interactions	Homo sapiens	hg19	chr6	35636622	35642872	CTCF	FKBP5	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	VCaP	CVCL_2235	malignant cell	CL:0001064	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_01980	2009	19212405	ChIP-seq accurately predicts tissue-specific activity of enhancers	Mus musculus	mm9	chr1	41975300	41976076	NA	NA	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	E11.5 mouse embryonic forebrain tissue	NA	NA	NA	Chromatin-state profiling; In vivo functional validation; Enhancer-associated chromatin profiling; In vivo enhancer activity assay	p300 ChIP-seq; ChIP-seq	Hsp68-LacZ transgenic mouse reporter assay using the human orthologous sequence; ChIP; In vivo phenotyping
E_01981	2009	19212405	ChIP-seq accurately predicts tissue-specific activity of enhancers	Mus musculus	mm9	chr1	134976575	134977476	NA	NA	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	E11.5 mouse embryonic forebrain tissue	NA	NA	NA	Chromatin-state profiling; In vivo functional validation; Enhancer-associated chromatin profiling; In vivo enhancer activity assay	p300 ChIP-seq; ChIP-seq	Hsp68-LacZ transgenic mouse reporter assay using the human orthologous sequence; ChIP; In vivo phenotyping
E_01982	2009	19212405	ChIP-seq accurately predicts tissue-specific activity of enhancers	Mus musculus	mm9	chr1	140396600	140397726	NA	NA	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	E11.5 mouse embryonic forebrain tissue	NA	NA	NA	Chromatin-state profiling; In vivo functional validation; Enhancer-associated chromatin profiling; In vivo enhancer activity assay	p300 ChIP-seq; ChIP-seq	Hsp68-LacZ transgenic mouse reporter assay using the human orthologous sequence; ChIP; In vivo phenotyping
E_01983	2009	19212405	ChIP-seq accurately predicts tissue-specific activity of enhancers	Mus musculus	mm9	chr1	165828000	165828801	NA	NA	Enhancer	Active	Normal	NA	NA	NA	midbrain	UBERON:0001891	E11.5 mouse embryonic midbrain tissue	NA	NA	NA	Chromatin-state profiling; In vivo functional validation; Enhancer-associated chromatin profiling; In vivo enhancer activity assay	p300 ChIP-seq; ChIP-seq	Hsp68-LacZ transgenic mouse reporter assay using the human orthologous sequence; ChIP; In vivo phenotyping
E_01984	2009	19212405	ChIP-seq accurately predicts tissue-specific activity of enhancers	Mus musculus	mm9	chr1	167864800	167866051	NA	NA	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	E11.5 mouse embryonic forebrain tissue	NA	NA	NA	Chromatin-state profiling; In vivo functional validation; Enhancer-associated chromatin profiling; In vivo enhancer activity assay	p300 ChIP-seq; ChIP-seq	Hsp68-LacZ transgenic mouse reporter assay using the human orthologous sequence; ChIP; In vivo phenotyping
E_01985	2009	19212405	ChIP-seq accurately predicts tissue-specific activity of enhancers	Mus musculus	mm9	chr1	192551300	192552876	NA	NA	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	E11.5 mouse embryonic forebrain tissue	NA	NA	NA	Chromatin-state profiling; In vivo functional validation; Enhancer-associated chromatin profiling; In vivo enhancer activity assay	p300 ChIP-seq; ChIP-seq	Hsp68-LacZ transgenic mouse reporter assay using the human orthologous sequence; ChIP; In vivo phenotyping
E_01986	2009	19212405	ChIP-seq accurately predicts tissue-specific activity of enhancers	Mus musculus	mm9	chr2	137073600	137074376	NA	NA	Enhancer	Active	Normal	NA	NA	NA	midbrain	UBERON:0001891	E11.5 mouse embryonic midbrain tissue	NA	NA	NA	Chromatin-state profiling; In vivo functional validation; Enhancer-associated chromatin profiling; In vivo enhancer activity assay	p300 ChIP-seq; ChIP-seq	Hsp68-LacZ transgenic mouse reporter assay using the human orthologous sequence; ChIP; In vivo phenotyping
E_01987	2009	19212405	ChIP-seq accurately predicts tissue-specific activity of enhancers	Mus musculus	mm9	chr3	5224600	5225676	NA	NA	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	E11.5 mouse embryonic forebrain tissue	NA	NA	NA	Chromatin-state profiling; In vivo functional validation; Enhancer-associated chromatin profiling; In vivo enhancer activity assay	p300 ChIP-seq; ChIP-seq	Hsp68-LacZ transgenic mouse reporter assay using the human orthologous sequence; ChIP; In vivo phenotyping
E_01988	2009	19212405	ChIP-seq accurately predicts tissue-specific activity of enhancers	Mus musculus	mm9	chr3	30006475	30007726	NA	NA	Enhancer	Active	Normal	NA	NA	NA	midbrain	UBERON:0001891	E11.5 mouse embryonic midbrain tissue	NA	NA	NA	Chromatin-state profiling; In vivo functional validation; Enhancer-associated chromatin profiling; In vivo enhancer activity assay	p300 ChIP-seq; ChIP-seq	Hsp68-LacZ transgenic mouse reporter assay using the human orthologous sequence; ChIP; In vivo phenotyping
E_01989	2009	19212405	ChIP-seq accurately predicts tissue-specific activity of enhancers	Mus musculus	mm9	chr3	34986900	34988201	NA	NA	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	E11.5 mouse embryonic forebrain tissue	NA	NA	NA	Chromatin-state profiling; In vivo functional validation; Enhancer-associated chromatin profiling; In vivo enhancer activity assay	p300 ChIP-seq; ChIP-seq	Hsp68-LacZ transgenic mouse reporter assay using the human orthologous sequence; ChIP; In vivo phenotyping
E_01990	2009	19212405	ChIP-seq accurately predicts tissue-specific activity of enhancers	Mus musculus	mm9	chr3	55558975	55559751	NA	NA	Enhancer	Active	Normal	NA	NA	NA	limb	UBERON:0002101	E11.5 mouse embryonic limb tissue	NA	NA	NA	Chromatin-state profiling; In vivo functional validation; Enhancer-associated chromatin profiling; In vivo enhancer activity assay	p300 ChIP-seq; ChIP-seq	Hsp68-LacZ transgenic mouse reporter assay using the human orthologous sequence; ChIP; In vivo phenotyping
E_01991	2009	19212405	ChIP-seq accurately predicts tissue-specific activity of enhancers	Mus musculus	mm9	chr3	84741550	84742501	NA	NA	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	E11.5 mouse embryonic forebrain tissue	NA	NA	NA	Chromatin-state profiling; In vivo functional validation; Enhancer-associated chromatin profiling; In vivo enhancer activity assay	p300 ChIP-seq; ChIP-seq	Hsp68-LacZ transgenic mouse reporter assay using the human orthologous sequence; ChIP; In vivo phenotyping
E_01992	2009	19212405	ChIP-seq accurately predicts tissue-specific activity of enhancers	Mus musculus	mm9	chr3	141901125	141902126	NA	NA	Enhancer	Active	Normal	NA	NA	NA	midbrain	UBERON:0001891	E11.5 mouse embryonic midbrain tissue	NA	NA	NA	Chromatin-state profiling; In vivo functional validation; Enhancer-associated chromatin profiling; In vivo enhancer activity assay	p300 ChIP-seq; ChIP-seq	Hsp68-LacZ transgenic mouse reporter assay using the human orthologous sequence; ChIP; In vivo phenotyping
E_01993	2009	19212405	ChIP-seq accurately predicts tissue-specific activity of enhancers	Mus musculus	mm9	chr4	5888950	5890926	NA	NA	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	E11.5 mouse embryonic forebrain tissue	NA	NA	NA	Chromatin-state profiling; In vivo functional validation; Enhancer-associated chromatin profiling; In vivo enhancer activity assay	p300 ChIP-seq; ChIP-seq	Hsp68-LacZ transgenic mouse reporter assay using the human orthologous sequence; ChIP; In vivo phenotyping
E_01994	2009	19212405	ChIP-seq accurately predicts tissue-specific activity of enhancers	Mus musculus	mm9	chr4	6840325	6841401	NA	NA	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	E11.5 mouse embryonic forebrain tissue	NA	NA	NA	Chromatin-state profiling; In vivo functional validation; Enhancer-associated chromatin profiling; In vivo enhancer activity assay	p300 ChIP-seq; ChIP-seq	Hsp68-LacZ transgenic mouse reporter assay using the human orthologous sequence; ChIP; In vivo phenotyping
E_01995	2009	19212405	ChIP-seq accurately predicts tissue-specific activity of enhancers	Mus musculus	mm9	chr4	44864575	44865251	NA	NA	Enhancer	Active	Normal	NA	NA	NA	limb	UBERON:0002101	E11.5 mouse embryonic limb tissue	NA	NA	NA	Chromatin-state profiling; In vivo functional validation; Enhancer-associated chromatin profiling; In vivo enhancer activity assay	p300 ChIP-seq; ChIP-seq	Hsp68-LacZ transgenic mouse reporter assay using the human orthologous sequence; ChIP; In vivo phenotyping
E_01996	2009	19212405	ChIP-seq accurately predicts tissue-specific activity of enhancers	Mus musculus	mm9	chr4	71828300	71829751	NA	NA	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	E11.5 mouse embryonic forebrain tissue	NA	NA	NA	Chromatin-state profiling; In vivo functional validation; Enhancer-associated chromatin profiling; In vivo enhancer activity assay	p300 ChIP-seq; ChIP-seq	Hsp68-LacZ transgenic mouse reporter assay using the human orthologous sequence; ChIP; In vivo phenotyping
E_01997	2009	19212405	ChIP-seq accurately predicts tissue-specific activity of enhancers	Mus musculus	mm9	chr4	97774675	97775901	NA	NA	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	E11.5 mouse embryonic forebrain tissue	NA	NA	NA	Chromatin-state profiling; In vivo functional validation; Enhancer-associated chromatin profiling; In vivo enhancer activity assay	p300 ChIP-seq; ChIP-seq	Hsp68-LacZ transgenic mouse reporter assay using the human orthologous sequence; ChIP; In vivo phenotyping
E_01998	2009	19212405	ChIP-seq accurately predicts tissue-specific activity of enhancers	Mus musculus	mm9	chr5	74828975	74829601	NA	NA	Enhancer	Active	Normal	NA	NA	NA	limb	UBERON:0002101	E11.5 mouse embryonic limb tissue	NA	NA	NA	Chromatin-state profiling; In vivo functional validation; Enhancer-associated chromatin profiling; In vivo enhancer activity assay	p300 ChIP-seq; ChIP-seq	Hsp68-LacZ transgenic mouse reporter assay using the human orthologous sequence; ChIP; In vivo phenotyping
E_01999	2009	19212405	ChIP-seq accurately predicts tissue-specific activity of enhancers	Mus musculus	mm9	chr6	28346175	28347126	NA	NA	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	E11.5 mouse embryonic forebrain tissue	NA	NA	NA	Chromatin-state profiling; In vivo functional validation; Enhancer-associated chromatin profiling; In vivo enhancer activity assay	p300 ChIP-seq; ChIP-seq	Hsp68-LacZ transgenic mouse reporter assay using the human orthologous sequence; ChIP; In vivo phenotyping
E_02000	2009	19212405	ChIP-seq accurately predicts tissue-specific activity of enhancers	Mus musculus	mm9	chr6	51026850	51028001	NA	NA	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	E11.5 mouse embryonic forebrain tissue	NA	NA	NA	Chromatin-state profiling; In vivo functional validation; Enhancer-associated chromatin profiling; In vivo enhancer activity assay	p300 ChIP-seq; ChIP-seq	Hsp68-LacZ transgenic mouse reporter assay using the human orthologous sequence; ChIP; In vivo phenotyping
E_02001	2009	19212405	ChIP-seq accurately predicts tissue-specific activity of enhancers	Mus musculus	mm9	chr6	51146275	51148026	NA	NA	Enhancer	Active	Normal	NA	NA	NA	midbrain	UBERON:0001891	E11.5 mouse embryonic midbrain tissue	NA	NA	NA	Chromatin-state profiling; In vivo functional validation; Enhancer-associated chromatin profiling; In vivo enhancer activity assay	p300 ChIP-seq; ChIP-seq	Hsp68-LacZ transgenic mouse reporter assay using the human orthologous sequence; ChIP; In vivo phenotyping
E_02002	2009	19212405	ChIP-seq accurately predicts tissue-specific activity of enhancers	Mus musculus	mm9	chr6	144260800	144262201	NA	NA	Enhancer	Active	Normal	NA	NA	NA	midbrain	UBERON:0001891	E11.5 mouse embryonic midbrain tissue	NA	NA	NA	Chromatin-state profiling; In vivo functional validation; Enhancer-associated chromatin profiling; In vivo enhancer activity assay	p300 ChIP-seq; ChIP-seq	Hsp68-LacZ transgenic mouse reporter assay using the human orthologous sequence; ChIP; In vivo phenotyping
E_02003	2018	29256171	Multiple enhancer regions govern the transcription of CCN2 during embryonic development	Mus musculus	mm9	chr10	24085247	24087247	NA	Ccn2	Enhancer	Active	Normal	NA	NA	NA	periosteum	UBERON:0002515	E15.5 transgenic mouse embryo	NA	periosteal cell	NA	In vivo enhancer activity assay	ENCODE H3K4me1/H3K27ac ChIP-seq; DNase-seq; comparative-conservation data integration	Hsp68-LacZ transgenic mouse reporter assay; whole-mount X-gal staining; histological analysis
E_02004	2018	29256171	Multiple enhancer regions govern the transcription of CCN2 during embryonic development	Mus musculus	mm9	chr10	24084485	24085909	NA	Ccn2	Enhancer	Active	Normal	NA	NA	NA	periosteum	UBERON:0002515	E15.5 transgenic mouse embryo	NA	periosteal cell	NA	In vivo enhancer activity assay	ENCODE H3K4me1 ChIP-seq; H3K27ac ChIP-seq; DNase-seq data integration	Hsp68-LacZ transgenic mouse reporter assay; whole-mount X-gal staining; histological analysis
E_02005	2018	29256171	Multiple enhancer regions govern the transcription of CCN2 during embryonic development	Mus musculus	mm9	chr10	79590140	79590690	NA	Ccn2	Enhancer	Active	Normal	NA	NA	NA	periosteum	UBERON:0002515	E15.5 transgenic mouse embryo	NA	periosteal cell	NA	In vivo enhancer activity assay	ENCODE H3K4me1/H3K27ac ChIP-seq and DNase-seq data integration	Hsp68-LacZ transgenic mouse reporter assay; whole-mount X-gal staining; histological analysis
E_02006	2010	20093418	Glucocorticoid receptor activates poised FKBP51 locus through long-distance interactions	Homo sapiens	hg19	chr6	35574362	35576362	CTCF	FKBP5	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	A-549	CVCL_0023	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02007	2018	30017589	GRHL2-Dependent Enhancer Switching Maintains a Pluripotent Stem Cell Transcriptional Subnetwork after Exit from Naive Pluripotency	Mus musculus	mm10	chr13	30108722	30109111	Grhl2	Dsp	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell,Epiblast-like Cells (EpiLCs)	NA	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; ATAC-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02008	2018	30017589	GRHL2-Dependent Enhancer Switching Maintains a Pluripotent Stem Cell Transcriptional Subnetwork after Exit from Naive Pluripotency	Mus musculus	mm10	chr13	30123333	30124861	Grhl2	Dsp	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell,Epiblast-like Cells (EpiLCs)	NA	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; ATAC-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02009	2018	30017589	GRHL2-Dependent Enhancer Switching Maintains a Pluripotent Stem Cell Transcriptional Subnetwork after Exit from Naive Pluripotency	Mus musculus	mm10	chr13	30144166	30145833	Grhl2	Dsp	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; ATAC-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02010	2018	30017589	GRHL2-Dependent Enhancer Switching Maintains a Pluripotent Stem Cell Transcriptional Subnetwork after Exit from Naive Pluripotency	Mus musculus	mm10	chr8	106608533	106609800	Grhl2	Cdh1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; ATAC-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02011	2018	30017589	GRHL2-Dependent Enhancer Switching Maintains a Pluripotent Stem Cell Transcriptional Subnetwork after Exit from Naive Pluripotency	Mus musculus	mm10	chr8	106610533	106611666	Grhl2	Cdh1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; ATAC-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02012	2011	21566115	A distal enhancer in Il12b is the target of transcriptional repression by the STAT3 pathway and requires the basic leucine zipper (B-ZIP) protein NFIL3	Mus musculus	mm10	chr11	44390069	44390173	Nfil3	Il12b	Enhancer	Repressed	Normal	NA	NA	NA	ascitic fluid	UBERON:0007795	RAW 264.7	CVCL_0493	macrophage	CL:0000235	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Luciferase reporter assay; Stable and transient transfection; Site-directed mutagenesis; IVTT-EMSA; NFIL3 overexpression; qRT-PCR
E_02013	2024	38448444	Dynamic enhancer landscapes in human craniofacial development	Homo sapiens	hg38	chr8	98367000	98370806	NA	NA	Enhancer	Active	Normal	NA	NA	NA	face	UBERON:0001456	transgenic mouse embryo reporter assay (e12.5)	NA	NA	NA	Enhancer activity assay; In vivo functional validation; Cross-species functional comparison	H3K27ac ChIP-seq	CRISPR-mediated H11 safe-harbor transgenic lacZ reporter assay; In vivo phenotyping
E_02014	2024	38448444	Dynamic enhancer landscapes in human craniofacial development	Mus musculus	mm10	chr15	34751000	34754612	NA	NA	Enhancer	Repressed	Normal	NA	NA	NA	face	UBERON:0001456	transgenic mouse embryo reporter assay (e12.5)	NA	NA	NA	Enhancer activity assay; In vivo functional validation; Cross-species functional comparison	H3K27ac ChIP-seq	CRISPR-mediated H11 safe-harbor transgenic lacZ reporter assay (negative); In vivo phenotyping
E_02015	2012	22543974	Regulatory variation in a TBX5 enhancer leads to isolated congenital heart disease	Homo sapiens	hg19	chr12	114463712	114464080	TBX5	TBX5	Enhancer	Active	Disease	Congenital Heart Disease	NA	DOID:1682	heart	UBERON:0000948	HeLa	CVCL_0030	malignant cell	CL:0001064	In vivo functional validation; TF-binding/chromatin assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	ChIP-seq	ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_02016	2012	22543974	Regulatory variation in a TBX5 enhancer leads to isolated congenital heart disease	Homo sapiens	hg19	chr12	114701207	114704691	TBX5	TBX5	Enhancer	Active	Disease	Congenital Heart Disease	NA	DOID:1682	heart	UBERON:0000948	HeLa	CVCL_0030	malignant cell	CL:0001064	In vivo functional validation; TF-binding/chromatin assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	ChIP-seq	ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_02017	2012	22543974	Regulatory variation in a TBX5 enhancer leads to isolated congenital heart disease	Homo sapiens	hg19	chr12	114853271	114858238	TBX5	TBX5	Enhancer	Active	Disease	Congenital Heart Disease	NA	DOID:1682	heart	UBERON:0000948	HeLa	CVCL_0030	malignant cell	CL:0001064	In vivo functional validation; TF-binding/chromatin assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	ChIP-seq	ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_02018	2010	20093418	Glucocorticoid receptor activates poised FKBP51 locus through long-distance interactions	Homo sapiens	hg19	chr6	35505138	35511492	NR3C1	FKBP5	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	A-549	CVCL_0023	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; In vivo functional validation	ChIP-seq	Luciferase reporter assay; ChIP; In vivo phenotyping
E_02019	2012	22543974	Regulatory variation in a TBX5 enhancer leads to isolated congenital heart disease	Homo sapiens	hg19	chr12	114463712	114464080	TBX5	TBX5	Enhancer	Active	Disease	Congenital Heart Disease	NA	DOID:1682	heart	UBERON:0000948	HEK293T	CVCL_0063	NA	NA	In vivo functional validation; TF-binding/chromatin assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	ChIP-seq	ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_02020	2012	22543974	Regulatory variation in a TBX5 enhancer leads to isolated congenital heart disease	Homo sapiens	hg19	chr12	114701207	114704691	TBX5	TBX5	Enhancer	Active	Disease	Congenital Heart Disease	NA	DOID:1682	heart	UBERON:0000948	HEK293T	CVCL_0063	NA	NA	In vivo functional validation; TF-binding/chromatin assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	ChIP-seq	ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_02021	2012	22543974	Regulatory variation in a TBX5 enhancer leads to isolated congenital heart disease	Homo sapiens	hg19	chr12	114853271	114858238	TBX5	TBX5	Enhancer	Active	Disease	Congenital Heart Disease	NA	DOID:1682	heart	UBERON:0000948	HEK293T	CVCL_0063	NA	NA	In vivo functional validation; TF-binding/chromatin assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	ChIP-seq	ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_02022	2010	20093418	Glucocorticoid receptor activates poised FKBP51 locus through long-distance interactions	Homo sapiens	hg19	chr6	35628362	35641362	CTCF	FKBP5	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	A-549	CVCL_0023	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	ChIP-qPCR/ChIP; RT-qPCR/qPCR; Western blot; Transgenic/LacZ assay
E_02023	2018	29284139	Coordinated d-cyclin/Foxd1 activation drives mitogenic activity of the Sonic Hedgehog signaling pathway	Mus musculus	mm10	chr7	143459000	143460200	Foxd1	Cdkn1c	Enhancer	Active	Normal	NA	NA	NA	embryonic craniofacial mesenchyme	NA	immortalized mouse embryonic fibroblasts	NA	embryonic fibroblast	CL:2000042	Enhancer activity assay; Functional signaling perturbation assay	NA	Cdkn1c intron-2 enhancer luciferase reporter assay; Foxd1 CRISPR/Cas9 knockout; FOXD1 overexpression; SHH stimulation; RT-qPCR; proliferation assay
E_02024	2018	29284139	Coordinated d-cyclin/Foxd1 activation drives mitogenic activity of the Sonic Hedgehog signaling pathway	Mus musculus	mm10	chr7	143459172	143459787	Foxd1	Cdkn1c	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Fibroblasts	NA	fibroblast	CL:0000057	Enhancer activity assay; Endogenous enhancer perturbation	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion
E_02025	2018	29284139	Coordinated d-cyclin/Foxd1 activation drives mitogenic activity of the Sonic Hedgehog signaling pathway	Mus musculus	mm10	chr7	143462624	143463585	Gli1	Cdkn1c	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Fibroblasts	NA	fibroblast	CL:0000057	Enhancer activity assay; Endogenous enhancer perturbation	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion
E_02026	2011	21566115	A distal enhancer in Il12b is the target of transcriptional repression by the STAT3 pathway and requires the basic leucine zipper (B-ZIP) protein NFIL3	Mus musculus	mm10	chr11	44390069	44390173	Nfil3	Il12b	Enhancer	Repressed	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Bone marrow-derived macrophages (BMDM)	NA	macrophage	CL:0000235	Functional perturbation assay; TF binding assay	LC-MS proteomics	Enhancer-sequence DNA affinity capture; qRT-PCR; Western blot; ELISA; Nfil3 knockout mouse model
E_02027	2018	29256171	Multiple enhancer regions govern the transcription of CCN2 during embryonic development	Mus musculus	mm10	chr10	24357349	24375452	NA	Ccn2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Limb	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_02028	2018	29256171	Multiple enhancer regions govern the transcription of CCN2 during embryonic development	Mus musculus	mm10	chr10	24449590	24469418	NA	Ccn2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Limb	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_02029	2018	29256171	Multiple enhancer regions govern the transcription of CCN2 during embryonic development	Mus musculus	mm10	chr10	24483642	24503469	NA	Ccn2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Limb	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_02030	2024	38448444	Dynamic enhancer landscapes in human craniofacial development	Homo sapiens	hg38	chr8	48581590	48583174	NA	SNAI2	Enhancer	Active	Normal	NA	NA	NA	face	UBERON:0001456	Primary human embryonic face tissue (CS13-CS23)	NA	multiple craniofacial cell types	NA	Enhancer activity assay; Cell-type-resolved enhancer activity assay	H3K27ac ChIP-seq; ATAC-seq; reporter-coupled scRNA-seq	Transgenic lacZ reporter assay; Transgenic mCherry reporter assay
E_02031	2024	38448444	Dynamic enhancer landscapes in human craniofacial development	Homo sapiens	hg38	chr8	48581590	48583174	NA	SNAI2	Enhancer	Active	Normal	NA	NA	NA	face	UBERON:0001456	transgenic mouse embryonic face reporter tissue (e11.5)	NA	multiple craniofacial cell types	NA	Enhancer activity assay; Cell-type-resolved enhancer activity assay	H3K27ac ChIP-seq; ATAC-seq; reporter-coupled scRNA-seq	Transgenic lacZ reporter assay; Transgenic mCherry reporter assay
E_02032	2016	26751080	Up-Regulation of Human Inducible Nitric Oxide Synthase by p300 Transcriptional Complex	Homo sapiens	hg19	chr17	26077792	26078792	JUND	NOS2	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	A-549	CVCL_0023	NA	NA	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C
E_02033	2018	29256171	Multiple enhancer regions govern the transcription of CCN2 during embryonic development	Mus musculus	mm10	chr10	24386336	24406594	NA	Ccn2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Limb	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_02034	2011	21566115	A distal enhancer in Il12b is the target of transcriptional repression by the STAT3 pathway and requires the basic leucine zipper (B-ZIP) protein NFIL3	Mus musculus	mm10	chr11	44390069	44390173	Nfil3	Il12b	Enhancer	Repressed	Normal	NA	NA	NA	peritoneal cavity	UBERON:0001179	thioglycollate-elicited peritoneal-derived macrophages (PDM)	NA	macrophage	CL:0000235	Functional perturbation assay	NA	qRT-PCR; ELISA; Nfil3 knockout mouse model
E_02035	2018	29256171	Multiple enhancer regions govern the transcription of CCN2 during embryonic development	Mus musculus	mm10	chr10	24102250	24104250	Runx2	Ccn2	Enhancer	Active	Normal	NA	NA	NA	connective tissue	UBERON:0002384	Fibroblasts	NA	fibroblast	CL:0000057	Enhancer activity assay; Transgenic reporter assay; Developmental regulation assay	ChIP-seq	qRT-PCR, and ChIP-qPCR; Transgenic enhancer reporter assay
E_02036	2012	22543974	Regulatory variation in a TBX5 enhancer leads to isolated congenital heart disease	Homo sapiens	hg19	chr12	114463712	114464080	NA	TBX5	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	GM12878	CVCL_7526	B lymphoblastoid cell	NA	Enhancer activity assay	ChIP-seq	Transgenic reporter assay
E_02037	2011	21566115	A distal enhancer in Il12b is the target of transcriptional repression by the STAT3 pathway and requires the basic leucine zipper (B-ZIP) protein NFIL3	Mus musculus	mm10	chr11	44390342	44392251	Nfil3	Il12b	Enhancer	Repressed	Disease	Autoimmune and Inflammatory Diseases	NA	NA	blood	UBERON:0000178	Myeloid Cells,T Cell	NA	T cell	CL:0000084	Enhancer activity assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; RT-qPCR/qPCR
E_02038	2018	29284139	Coordinated d-cyclin/Foxd1 activation drives mitogenic activity of the Sonic Hedgehog signaling pathway	Mus musculus	mm10	chr7	143459000	143459700	Foxd1	Cdkn1c	Enhancer	Active	Normal	NA	NA	NA	facial mesenchyme	UBERON:0009891	O9-1	CVCL_GS42	cranial neural crest cell	NA	Enhancer-associated developmental regulatory validation; signaling perturbation assay	NA	SHH ligand stimulation; RT-qPCR; FOXD1/Cdkn1c expression analysis; proliferation assay
E_02039	2011	21566115	A distal enhancer in Il12b is the target of transcriptional repression by the STAT3 pathway and requires the basic leucine zipper (B-ZIP) protein NFIL3	Mus musculus	mm10	chr11	44389500	44390500	Nfil3	Il12b	Enhancer	Repressed	Normal	NA	NA	NA	blood	UBERON:0000178	RAW 264.7	CVCL_0493	macrophage	CL:0000235	Distal enhancer assay; TF binding assay; cytokine-dependent repression	NA	DNase-hypersensitivity analysis; reporter; 10-bp enhancer-site mutation; NFIL3 ChIP; Nfil3 deficiency; IL-12p40/IL-12p70 assays
E_02040	2019	31028121	Runx1 and RORγt Cooperate to Upregulate IL-22 Expression in Th Cells through Its Distal Enhancer	Mus musculus	mm10	chr12	31875800	31876373	Runx1	Il22	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	CD4+ T cells	NA	CD4-positive, alpha-beta T cell	CL:0000624	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	NA	Luciferase reporter assay; 3C-seq; ChIP-qPCR; RT-qPCR; Reporter assay
E_02041	2019	31028121	Runx1 and RORγt Cooperate to Upregulate IL-22 Expression in Th Cells through Its Distal Enhancer	Mus musculus	mm10	chr10	118172284	118172884	Rorc	Il22	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary naive CD4+ T cells differentiated to Th22 cells	NA	CD4-positive helper T cell	CL:0000492	Enhancer activity assay; TF binding assay; Endogenous enhancer perturbation; differentiation-associated enhancer assay	NA	CNS-32 reporter; RORγt-site mutagenesis; RORγt ChIP; histone H4 acetylation ChIP; co-expression analysis; Site-directed/motif mutagenesis; Reporter assay
E_02042	2018	28860350	Identification of distinct mutational patterns and new driver genes in oesophageal squamous cell carcinomas and adenocarcinomas	Homo sapiens	hg38	chr2	43219398	43221398	ZFP36L2	ZFP36L2	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	BEAS-2B	CVCL_0168	bronchial epithelial cell	CL:0002328	Enhancer activity assay; TF binding assay; In vivo functional validation	ChIP-seq	3C, RT-PCR; RT-qPCR; ChIP; Xenograft/xenotransplant
E_02043	2016	26886256	Embryonic Stem Cell (ES)-Specific Enhancers Specify the Expression Potential of ES Genes in Cancer	Homo sapiens	hg19	chr6	43891400	43898360	NA	VEGFA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; 4C-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_02044	2014	24443471	Enhancer-targeted genome editing selectively blocks innate resistance to oncokinase inhibition	Homo sapiens	hg19	chr7	116735000	116735500	MITF	MET	Enhancer	Active	Disease	melanoma	MONDO:0005105	DOID:1909	prostate gland	UBERON:0002367	LNCaP C4-2B	CVCL_4784	malignant cell	CL:0001064	Functional perturbation assay; Endogenous enhancer perturbation	ChIP-seq	3C; ChIP-qPCR, CRISPR knockout/CRISPRi; RT-qPCR; Western blot; CRISPR-Cas9 endogenous deletion/editing
E_02045	2013	23689137	Immune mediators regulate CFTR expression through a bifunctional airway-selective enhancer	Homo sapiens	hg19	chr7	117085371	117085720	IRF1	CFTR	Enhancer	Active	Normal	NA	NA	NA	bronchus	UBERON:0002185	16HBE14o-	CVCL_0112	bronchial epithelial cell	CL:0002328	Enhancer activity assay; Functional perturbation assay; TF binding assay	H3K4me1 chromatin profiling; DNase hypersensitivity profiling	Luciferase reporter assay; DNase I footprinting; EMSA; ChIP-qPCR; siRNA knockdown; RT-qPCR
E_02046	2025	39736453	Oncogenic HJURP enhancer promotes the aggressive behavior of triple-negative breast cancer in association with p53/E2F1/FOXM1-axis	Homo sapiens	hg19	chr2	234762042	234764060	E2F1	HJURP	Enhancer	Active	Disease	triple-negative breast carcinoma	MONDO:0005494	DOID:0060081	breast	UBERON:0000310	BT-549	CVCL_1092	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	H3K27ac ChIP-seq; RNA-seq; DNase-seq	dCas9-KRAB CRISPRi; ChIP-qPCR; Dual-luciferase reporter assay; RT-qPCR; Western blot; CRISPRi
E_02047	2025	39736453	Oncogenic HJURP enhancer promotes the aggressive behavior of triple-negative breast cancer in association with p53/E2F1/FOXM1-axis	Homo sapiens	hg19	chr2	234762042	234764060	E2F1	HJURP	Enhancer	Active	Disease	triple-negative breast carcinoma	MONDO:0005494	DOID:0060081	breast	UBERON:0000310	MDA-MB-231	CVCL_0062	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	H3K27ac ChIP-seq; RNA-seq; DNase-seq	dCas9-KRAB CRISPRi; ChIP-qPCR; Dual-luciferase reporter assay; RT-qPCR; Western blot; CRISPRi
E_02048	2025	39736453	Oncogenic HJURP enhancer promotes the aggressive behavior of triple-negative breast cancer in association with p53/E2F1/FOXM1-axis	Homo sapiens	hg19	chr2	234762042	234764060	FOXM1	HJURP	Enhancer	Active	Disease	triple-negative breast carcinoma	MONDO:0005494	DOID:0060081	breast	UBERON:0000310	BT-549	CVCL_1092	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	H3K27ac ChIP-seq; RNA-seq; DNase-seq	dCas9-KRAB CRISPRi; ChIP-qPCR; Dual-luciferase reporter assay; RT-qPCR; Western blot; CRISPRi
E_02049	2025	39736453	Oncogenic HJURP enhancer promotes the aggressive behavior of triple-negative breast cancer in association with p53/E2F1/FOXM1-axis	Homo sapiens	hg19	chr2	234762042	234764060	FOXM1	HJURP	Enhancer	Active	Disease	triple-negative breast carcinoma	MONDO:0005494	DOID:0060081	breast	UBERON:0000310	MDA-MB-231	CVCL_0062	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	H3K27ac ChIP-seq; RNA-seq; DNase-seq	dCas9-KRAB CRISPRi; ChIP-qPCR; Dual-luciferase reporter assay; RT-qPCR; Western blot; CRISPRi
E_02050	2025	40167268	Enhancer Extrachromosomal Circular DNA ANKRD28 Elicits Drug Resistance via POU2F2-Mediated Transcriptional Network in Multiple Myeloma	Homo sapiens	hg38	chr3	15768491	15768703	POU2F2	BCL2	Enhancer	Active	Disease	plasma cell myeloma	MONDO:0009693	DOID:9538	blood	UBERON:0000178	Multiple myeloma cells	NA	plasma cell	CL:0000786	Enhancer activity assay	ATAC-seq; ChIP-seq; CUT&Tag; single-cell RNA-seq; RNA-seq	CRISPR knockout; CRISPRi; ChIP-qPCR; FISH; CRISPR-Cas9
E_02051	2025	40167268	Enhancer Extrachromosomal Circular DNA ANKRD28 Elicits Drug Resistance via POU2F2-Mediated Transcriptional Network in Multiple Myeloma	Homo sapiens	hg38	chr3	15768491	15768703	POU2F2	IKZF3	Enhancer	Active	Disease	plasma cell myeloma	MONDO:0009693	DOID:9538	blood	UBERON:0000178	Multiple myeloma cells	NA	plasma cell	CL:0000786	Enhancer activity assay	ATAC-seq; ChIP-seq; CUT&Tag; single-cell RNA-seq; RNA-seq	CRISPR knockout; CRISPRi; ChIP-qPCR; FISH; CRISPR-Cas9
E_02052	2025	40167268	Enhancer Extrachromosomal Circular DNA ANKRD28 Elicits Drug Resistance via POU2F2-Mediated Transcriptional Network in Multiple Myeloma	Homo sapiens	hg38	chr3	15768491	15768703	POU2F2	JUNB	Enhancer	Active	Disease	plasma cell myeloma	MONDO:0009693	DOID:9538	blood	UBERON:0000178	Multiple myeloma cells	NA	plasma cell	CL:0000786	Enhancer activity assay	ATAC-seq; ChIP-seq; CUT&Tag; single-cell RNA-seq; RNA-seq	CRISPR knockout; CRISPRi; ChIP-qPCR; FISH; CRISPR-Cas9
E_02053	2025	40167268	Enhancer Extrachromosomal Circular DNA ANKRD28 Elicits Drug Resistance via POU2F2-Mediated Transcriptional Network in Multiple Myeloma	Homo sapiens	hg38	chr3	15768491	15768703	POU2F2	RUNX3	Enhancer	Active	Disease	plasma cell myeloma	MONDO:0009693	DOID:9538	blood	UBERON:0000178	Multiple myeloma cells	NA	plasma cell	CL:0000786	Enhancer activity assay	ATAC-seq; ChIP-seq; CUT&Tag; single-cell RNA-seq; RNA-seq	CRISPR knockout; CRISPRi; ChIP-qPCR; FISH; CRISPR-Cas9
E_02054	2020	33219226	Enhancer remodeling promotes tumor-initiating activity in NRF2-activated non-small cell lung cancers	Homo sapiens	hg19	chr19	15311000	15312500	CEBPB	NOTCH3	Enhancer	Active	Disease	lung adenocarcinoma	MONDO:0005061	DOID:3910	lung	UBERON:0002048	A-549	CVCL_0023	malignant cell	CL:0001064	Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; ATAC-seq	CRISPR knockout; ChIP-qPCR; RT-qPCR; Western blot
E_02055	2020	33219226	Enhancer remodeling promotes tumor-initiating activity in NRF2-activated non-small cell lung cancers	Homo sapiens	hg19	chr19	15311000	15312500	CEBPB	NOTCH3	Enhancer	Active	Disease	lung adenocarcinoma	MONDO:0005061	DOID:3910	lung	UBERON:0002048	NCI-H460	CVCL_0459	malignant cell	CL:0001064	Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; ATAC-seq	CRISPR knockout; ChIP-qPCR; RT-qPCR; Western blot
E_02056	2020	33219226	Enhancer remodeling promotes tumor-initiating activity in NRF2-activated non-small cell lung cancers	Homo sapiens	hg19	chr19	15311000	15312500	FOSL2	NOTCH3	Enhancer	Active	Disease	lung adenocarcinoma	MONDO:0005061	DOID:3910	lung	UBERON:0002048	A-549	CVCL_0023	malignant cell	CL:0001064	Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; ATAC-seq	CRISPR knockout; ChIP-qPCR; RT-qPCR; Western blot
E_02057	2020	33219226	Enhancer remodeling promotes tumor-initiating activity in NRF2-activated non-small cell lung cancers	Homo sapiens	hg19	chr19	15311000	15312500	FOSL2	NOTCH3	Enhancer	Active	Disease	lung adenocarcinoma	MONDO:0005061	DOID:3910	lung	UBERON:0002048	NCI-H460	CVCL_0459	malignant cell	CL:0001064	Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; ATAC-seq	CRISPR knockout; ChIP-qPCR; RT-qPCR; Western blot
E_02058	2020	33219226	Enhancer remodeling promotes tumor-initiating activity in NRF2-activated non-small cell lung cancers	Homo sapiens	hg19	chr19	15311000	15312500	NFE2L2	NOTCH3	Enhancer	Active	Disease	lung adenocarcinoma	MONDO:0005061	DOID:3910	lung	UBERON:0002048	A-549	CVCL_0023	malignant cell	CL:0001064	Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; ATAC-seq	CRISPR knockout; ChIP-qPCR; RT-qPCR; Western blot
E_02059	2020	33219226	Enhancer remodeling promotes tumor-initiating activity in NRF2-activated non-small cell lung cancers	Homo sapiens	hg19	chr19	15311000	15312500	NFE2L2	NOTCH3	Enhancer	Active	Disease	lung adenocarcinoma	MONDO:0005061	DOID:3910	lung	UBERON:0002048	NCI-H460	CVCL_0459	malignant cell	CL:0001064	Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; ATAC-seq	CRISPR knockout; ChIP-qPCR; RT-qPCR; Western blot
E_02060	2019	31019297	NAD metabolic dependency in cancer is shaped by gene amplification and enhancer remodelling	Homo sapiens	hg19	chr7	105856018	105860658	MYC	NAMPT	Enhancer	Active	Disease	lung adenocarcinoma	MONDO:0005061	DOID:3910	lung	UBERON:0002048	NCI-H460	CVCL_0459	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; In vivo functional validation	ChIP-seq	Luciferase reporter assay, CRISPR knockout, CRISPRi; ChIP-qPCR; RT-qPCR; In vivo phenotyping
E_02061	2018	29641996	Transcriptional Dysregulation of MYC Reveals Common Enhancer-Docking Mechanism	Homo sapiens	hg19	chr8	129046628	129096067	CTCF	MYC	Super-enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; ChIA-PET	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 4C; RT-qPCR/qPCR
E_02062	2018	29641996	Transcriptional Dysregulation of MYC Reveals Common Enhancer-Docking Mechanism	Homo sapiens	hg19	chr8	130569971	130616320	CTCF	MYC	Super-enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; ChIA-PET	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 4C; RT-qPCR/qPCR
E_02063	2018	29641996	Transcriptional Dysregulation of MYC Reveals Common Enhancer-Docking Mechanism	Homo sapiens	hg19	chr8	130693569	130739918	CTCF	MYC	Super-enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; ChIA-PET	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 4C; RT-qPCR/qPCR
E_02064	2017	27895109	Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes	Mus musculus	mm10	chr5	118432886	118452483	NA	Med13l	Enhancer	Active	Normal	NA	NA	NA	extraembryonic ectoderm	UBERON:0004366	Trophoblast Stem Cell	NA	trophoblast stem cell	NA	Functional perturbation assay; Chromatin interaction assay	ChIP-seq; RNA-seq; Hi-C	CRISPR knockout; RT-qPCR; CRISPR-Cas9
E_02065	2017	28737489	NFATc2 enhances tumor-initiating phenotypes through the NFATc2/SOX2/ALDH axis in lung adenocarcinoma	Homo sapiens	hg19	chr3	181465000	181468600	NFATC2	SOX2	Enhancer	Active	Disease	lung adenocarcinoma	MONDO:0005061	DOID:3910	lung	UBERON:0002048	NCI-H1299	CVCL_0060	malignant cell	CL:0001064	Functional perturbation assay; In vivo functional validation	ChIP-seq; RNA-seq	CRISPR knockout, Luciferase reporter assay; In vivo phenotyping
E_02066	2017	28737489	NFATc2 enhances tumor-initiating phenotypes through the NFATc2/SOX2/ALDH axis in lung adenocarcinoma	Homo sapiens	hg19	chr3	181432912	181433312	NFATC2	SOX2	Enhancer	Active	Disease	Lung Cancer	NA	DOID:1324	lung	UBERON:0002048	Lung Adenocarcinoma	NA	malignant cell	CL:0001064	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02067	2014	24443471	Enhancer-targeted genome editing selectively blocks innate resistance to oncokinase inhibition	Homo sapiens	hg19	chr7	116374406	116376406	MITF	MET	Enhancer	Active	Disease	melanoma	MONDO:0005105	DOID:1909	skin	UBERON:0002097	COLO 829	CVCL_1137	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	ChIP-qPCR/ChIP; 3C
E_02068	2014	25185713	The Runx-PU.1 pathway preserves normal and AML/ETO9a leukemic stem cells	Mus musculus	mm10	chr2	91067374	91069374	Runx1	Spi1	Enhancer	Active	Disease	Leukemia	NA	DOID:1240	blood	UBERON:0000178	Bone Marrow Cell,Leukemic Stem Cell,Hematopoietic Stem Cell,416B	NA	NA	NA	Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	ChIP-qPCR/ChIP; 3C; Transgenic/LacZ assay
E_02069	2014	25185713	The Runx-PU.1 pathway preserves normal and AML/ETO9a leukemic stem cells	Mus musculus	mm10	chr2	91067374	91069374	Runx2	Spi1	Enhancer	Active	Disease	Leukemia	NA	DOID:1240	blood	UBERON:0000178	Bone Marrow Cell,Leukemic Stem Cell,Hematopoietic Stem Cell,416B	NA	NA	NA	Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	ChIP-qPCR/ChIP; 3C; Transgenic/LacZ assay
E_02070	2014	25185713	The Runx-PU.1 pathway preserves normal and AML/ETO9a leukemic stem cells	Mus musculus	mm10	chr2	91067374	91069374	Runx3	Spi1	Enhancer	Active	Disease	Leukemia	NA	DOID:1240	blood	UBERON:0000178	Bone Marrow Cell,Leukemic Stem Cell,Hematopoietic Stem Cell,416B	NA	NA	NA	Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	ChIP-qPCR/ChIP; 3C; Transgenic/LacZ assay
E_02071	2013	23302769	Bivalent promoter marks and a latent enhancer may prime the leukaemia oncogene LMO1 for ectopic expression in T-cell leukaemia	Homo sapiens	hg19	chr11	8301851	8303851	GATA3	LMO1	Enhancer	Active	Disease	T-Cell leukemia	NA	DOID:715	blood	UBERON:0000178	T-acute lymphoblastic leukemia (T-ALL)	NA	malignant cell	CL:0001064	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02072	2013	23302769	Bivalent promoter marks and a latent enhancer may prime the leukaemia oncogene LMO1 for ectopic expression in T-cell leukaemia	Homo sapiens	hg19	chr11	8301851	8303851	TAL1	LMO1	Enhancer	Active	Disease	T-Cell leukemia	NA	DOID:715	blood	UBERON:0000178	T-acute lymphoblastic leukemia (T-ALL)	NA	malignant cell	CL:0001064	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02073	2016	26886256	Embryonic Stem Cell (ES)-Specific Enhancers Specify the Expression Potential of ES Genes in Cancer	Homo sapiens	hg19	chr6	43740121	43741621	NA	VEGFA	Enhancer	Active	Disease	hematologic malignancy	MONDO:0002334	DOID:2531	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Functional perturbation assay	4C-seq	Luciferase reporter assay, CRISPR knockout/CRISPRi; RT-qPCR
E_02074	2018	29641996	Transcriptional Dysregulation of MYC Reveals Common Enhancer-Docking Mechanism	Homo sapiens	hg19	chr8	128206162	128314310	CTCF	MYC	Super-enhancer	Active	Normal	NA	NA	NA	colon	UBERON:0001155	HCT 116	CVCL_0291	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; ChIA-PET	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 4C; RT-qPCR/qPCR
E_02075	2025	40167268	Enhancer Extrachromosomal Circular DNA ANKRD28 Elicits Drug Resistance via POU2F2-Mediated Transcriptional Network in Multiple Myeloma	Homo sapiens	hg38	chr3	15768491	15768703	POU2F2	IRF4	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	CD34+ HSPCs	NA	hematopoietic stem and progenitor cell	NA	Enhancer activity assay	ATAC-seq; ChIP-seq; CUT&Tag; single-cell RNA-seq; RNA-seq	CRISPR knockout; CRISPRi; ChIP-qPCR; FISH; CRISPR-Cas9
E_02076	2014	25453760	A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin States	Mus musculus	mm10	chr2	167687771	167689503	Bcl11a	Cebpb	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Monocytes	NA	monocyte	CL:0000576	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq; ATAC-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR; Western blot
E_02077	2014	25453760	A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin States	Mus musculus	mm10	chr2	167687771	167689503	Spib	Cebpb	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Monocytes	NA	monocyte	CL:0000576	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq; ATAC-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR; Western blot
E_02078	2014	25453760	A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin States	Mus musculus	mm10	chr2	167687771	167689503	Tcf4	Cebpb	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Monocytes	NA	monocyte	CL:0000576	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq; ATAC-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR; Western blot
E_02079	2014	25453760	A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin States	Mus musculus	mm10	chr8	120737580	120746913	Bcl11a	Irf8	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Monocytes	NA	monocyte	CL:0000576	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq; ATAC-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR; Western blot
E_02080	2014	25453760	A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin States	Mus musculus	mm10	chr8	120737580	120746913	Spib	Irf8	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Monocytes	NA	monocyte	CL:0000576	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq; ATAC-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR; Western blot
E_02081	2014	25453760	A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin States	Mus musculus	mm10	chr8	120737580	120746913	Tcf4	Irf8	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Monocytes	NA	monocyte	CL:0000576	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq; ATAC-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR; Western blot
E_02082	2014	25453760	A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin States	Mus musculus	mm10	chr4	66837166	66852551	Bcl11a	Tlr4	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Dendritic Cells	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq; ATAC-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR; Western blot
E_02083	2014	25453760	A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin States	Mus musculus	mm10	chr4	66837166	66852551	Spib	Tlr4	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Dendritic Cells	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq; ATAC-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR; Western blot
E_02084	2014	25453760	A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin States	Mus musculus	mm10	chr4	66837166	66852551	Tcf4	Tlr4	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Dendritic Cells	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq; ATAC-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR; Western blot
E_02085	2017	28737489	NFATc2 enhances tumor-initiating phenotypes through the NFATc2/SOX2/ALDH axis in lung adenocarcinoma	Homo sapiens	hg19	chr9	75595800	75602900	SOX2	ALDH1A1	Enhancer	Active	Disease	lung adenocarcinoma	MONDO:0005061	DOID:3910	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; In vivo functional validation	ChIP-seq	Luciferase reporter assay; In vivo phenotyping
E_02086	2020	33219226	Enhancer remodeling promotes tumor-initiating activity in NRF2-activated non-small cell lung cancers	Homo sapiens	hg19	chr19	15311000	15312500	NFE2L2	NOTCH3	Enhancer	Active	Disease	lung adenocarcinoma	MONDO:0005061	DOID:3910	lung	UBERON:0002048	H2023	NA	malignant cell	CL:0001064	Functional perturbation assay; TF binding assay	NRF2 ChIP-seq; H3K27ac ChIP-seq; RNA-seq	NRF2 knockdown; ChIP-qPCR; RT-qPCR
E_02087	2018	28860350	Identification of distinct mutational patterns and new driver genes in oesophageal squamous cell carcinomas and adenocarcinomas	Homo sapiens	hg19	chr2	130135200	130141800	NA	ZFP36L2	Enhancer	Active	Disease	esophageal squamous cell carcinoma	MONDO:0005580	DOID:3748	esophagus	UBERON:0001043	esophageal squamous cell carcinoma samples	NA	malignant cell	CL:0001064	In vivo functional validation; Super-enhancer epigenetic silencing analysis	H3K27ac ChIP-seq; whole-genome bisulfite sequencing; DNA methylation array profiling	ChIP; Xenograft/xenotransplant
E_02088	2017	27895109	Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes	Mus musculus	mm10	chr9	78368337	78376479	NA	Dppa5a	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02089	2017	27895109	Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes	Mus musculus	mm10	chr9	78368337	78376479	NA	Ooep	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02090	2026	41838874	Computational identification of lineage-committed precursors in mammalian organogenesis reveals a novel hematopoietic enhancer regulating Bhlhe41 expression	Mus musculus	mm10	chr6	145855899	145856116	NA	Bhlhe41	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	RAW 264.7	CVCL_0493	macrophage	CL:0000235	Enhancer activity assay; Chromatin-state profiling; In vivo functional validation	DNase-seq; RNA-seq; ChIP-seq; RNA-seq; ATAC-seq; DNase-seq	Luciferase reporter assay; In vivo phenotyping
E_02091	2025	40140585	Genome-wide CRISPR screen in human T cells reveals regulators of FOXP3	Homo sapiens	hg38	chrX	49273000	49274000	RBPJ	FOXP3	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human CD4+ T cells differentiated into iTreg cells	NA	regulatory T cell	CL:0000815	Functional perturbation assay; TF binding assay; Chromatin accessibility assay; Histone modification assay	Genome-wide CRISPR-Cas9 loss-of-function screen; Perturb-icCITE-seq; icRNA-seq; inChIP-seq; inATAC-seq; CUT&RUN	RBPJ CRISPR-Cas9 knockout; RBPJ overexpression; FOXP3 flow cytometry; Repeated TCR/cytokine restimulation stability assay; T-cell suppression assay
E_02092	2025	41057395	Evidence for enhancer activity in intron 1 of TNFRSF1A using CRISPR/Cas9 in human induced pluripotent stem cell-derived macrophages	Homo sapiens	hg19	chr12	6444399	6447744	NA	TNFRSF1A	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	iPSC-derived macrophages	NA	macrophage	CL:0000235	Enhancer activity assay; Chromatin-state profiling; Disease-variant functional analysis; Endogenous enhancer perturbation	ATAC-seq; ChIP-seq; RNA-seq; ATAC-seq; ChIP-seq; GWAS	CRISPR knockout, Luciferase reporter assay; CRISPR-Cas9 endogenous deletion/editing; ChIP
E_02093	2024	38592784	Intergenic sequences harboring potential enhancer elements contribute to Axenfeld-Rieger syndrome by regulating PITX2	Homo sapiens	hg38	chr4	111399594	111399691	NA	PITX2	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Hep-G2	CVCL_0027	malignant cell	CL:0001064	Functional perturbation assay; TF binding assay; Chromatin-state profiling; Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation	RNA-seq; ChIP-seq; whole-genome sequencing	ChIP-qPCR; RT-qPCR; Western blot; ChIP; RT-qPCR; Mouse genetic deletion/knock-in
E_02094	2023	37729434	TP63 fusions drive multicomplex enhancer rewiring, lymphomagenesis, and EZH2 dependence	Homo sapiens	hg19	chr11	85780828	85780847	TP63	EED	Enhancer	Active	Disease	type 2 diabetes mellitus	MONDO:0005148	DOID:9352	lymph node	UBERON:0000029	SMZ-1	CVCL_RL84	plasmacytoid dendritic cell	CL:0000784	In vivo functional validation; Regulatory element functional validation; 3D chromatin interaction mapping	ChIP-seq, HiChIP; PRO-seq; RNA-seq; CRISPR-Cas9 screening	qRT-PCR, and ChIP-qPCR; Xenograft/xenotransplant
E_02095	2023	37729434	TP63 fusions drive multicomplex enhancer rewiring, lymphomagenesis, and EZH2 dependence	Homo sapiens	hg19	chr8	127580017	127580036	TP63	MYC	Enhancer	Active	Disease	type 2 diabetes mellitus	MONDO:0005148	DOID:9352	lymph node	UBERON:0000029	SMZ-1	CVCL_RL84	plasmacytoid dendritic cell	CL:0000784	In vivo functional validation; Regulatory element functional validation; 3D chromatin interaction mapping	ChIP-seq, HiChIP; PRO-seq; RNA-seq; CRISPR-Cas9 screening	qRT-PCR, and ChIP-qPCR; Xenograft/xenotransplant
E_02096	2022	35805969	3D Chromatin Organization Involving MEIS1 Factor in the cis-Regulatory Landscape of GJB2	Homo sapiens	hg19	chr13	20993543	20994585	MEIS1	GJB2	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	HEK293T	CVCL_0063	embryonic kidney cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	4C-seq; ChIP-seq; RNA-seq; 4C	CRISPRi; CRISPRa; ChIP-qPCR; Luciferase reporter assay; RT-qPCR
E_02097	2020	32698000	Cohesin-Dependent and -Independent Mechanisms Mediate Chromosomal Contacts between Promoters and Enhancers	Homo sapiens	hg19	chr12	105800000	105801000	CTCF	NUAK1	Enhancer	Active	Normal	NA	NA	NA	cranial neural crest	UBERON:0003099	hCNCC cells	NA	cranial neural crest cell	NA	Functional perturbation assay; Chromatin interaction assay	Hi-C; ChIP-seq; Capture Hi-C	CRISPRi; Luciferase reporter assay; RT-qPCR
E_02098	2020	32958950	Transcription imparts architecture, function and logic to enhancer units	Homo sapiens	hg38	chr8	128747000	128748000	NA	MYC	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation	ChIP-seq; ATAC-seq; RNA-seq; MPRA	Luciferase reporter assay, CRISPR knockout; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; Reporter assay
E_02099	2025	40140585	Genome-wide CRISPR screen in human T cells reveals regulators of FOXP3	Homo sapiens	hg38	chrX	49260470	49261090	NA	FOXP3	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human CD4+ T cells differentiated into iTreg cells	NA	regulatory T cell	CL:0000815	Functional perturbation assay; Chromatin accessibility assay; Enhancer epigenetic-state assay	Genome-wide CRISPR-Cas9 loss-of-function screen; Perturb-icCITE-seq; icRNA-seq; inChIP-seq; inATAC-seq; H3K9ac/H3K27ac ChIP-seq	RBPJ CRISPR-Cas9 knockout; RBPJ overexpression; Bisulfite sequencing of FOXP3 CNS2 CpGs; FOXP3 flow cytometry; Repeated TCR/cytokine restimulation stability assay; T-cell suppression assay
E_02100	2025	40890402	p300/CBP is an essential driver of pathogenic enhancer activity and gene expression in Ewing sarcoma	Homo sapiens	hg38	chr20	21576001	21577647	EWSR1::FLI1	NKX2-2	Enhancer	Active	Disease	Ewing sarcoma	MONDO:0012817	DOID:3369	muscle organ	UBERON:0001630	A-673-dHALO and A-673 EWSR1::FLI1-knockout derivatives	NA	Ewing sarcoma cell	NA	Enhancer-associated functional perturbation assay	EWSR1::FLI1 ChIP-seq; EP300 ChIP-seq; CREBBP ChIP-seq; H3K27ac ChIP-seq; ribo-depleted RNA-seq	dHalo-mediated EWSR1::FLI1 degradation; CRISPR/Cas9-mediated EWSR1::FLI1 knockout; ChIP-qPCR; enhancer RNA RT-qPCR; NKX2-2 RT-qPCR
E_02101	2017	28446439	PAX3-FOXO1 Establishes Myogenic Super Enhancers and Confers BET Bromodomain Vulnerability	Homo sapiens	hg19	chr2	29880537	29880842	PAX3::FOXO1	ALK	Enhancer	Active	Disease	alveolar rhabdomyosarcoma	MONDO:0009994	DOID:4051	skeletal muscle tissue	UBERON:0001134	RH 4	CVCL_B6EX	rhabdomyosarcoma cell	NA	Enhancer activity assay; Super-enhancer profiling	ChIP-seq; RNA-seq	Luciferase reporter assay; CRISPR knockout
E_02102	2011	21681857	N-carbamylglutamate enhancement of ureagenesis leads to discovery of a novel deleterious mutation in a newly defined enhancer of the NAGS gene and to effective therapy	Homo sapiens	hg19	chr17	42078635	42079129	HNF1A	NAGS	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	hepatocyte	CL:0000182	Enhancer activity assay; TF binding assay; Endogenous enhancer perturbation; Functional variant assay	NA	Luciferase reporter assay; EMSA; Site-directed mutagenesis; Sanger sequencing; Genotyping; Site-directed/motif mutagenesis
E_02103	2010	20061391	Nuclear factor kappaB- and specificity protein 1-dependent p53-mediated bi-directional regulation of the human manganese superoxide dismutase gene	Homo sapiens	hg19	chr6	160112271	160112612	RELA	SOD2	Enhancer	Active	Normal	NA	NA	NA	prostate gland	UBERON:0002367	PC-3	CVCL_0035	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; In vivo functional validation	NA	Luciferase reporter assay; NF-kappaB-site mutagenesis; EMSA; RELA/p65 ChIP-PCR; RELA/p65 siRNA knockdown; RELA/p65 overexpression; TP53 overexpression; TP53 siRNA knockdown; RT-PCR; Western blot; ChIP; In vivo phenotyping
E_02104	2024	38592784	Intergenic sequences harboring potential enhancer elements contribute to Axenfeld-Rieger syndrome by regulating PITX2	Homo sapiens	hg38	chr4	111397892	111402926	NA	PITX2	Enhancer	Active	Disease	Axenfeld-Rieger syndrome	MONDO:0019187	DOID:14686	kidney	UBERON:0002113	HEK293	CVCL_0045	transformed cell line	NA	Enhancer activity assay; Functional perturbation assay	ChIP-seq-supported enhancer annotation; public DNase-seq; public scATAC-seq; ChIP-seq; RNA-seq; whole-genome sequencing	CRISPR-Cas9 LOH-E1 deletion; PCR; Sanger sequencing; RT-qPCR; Western blot; CCK-8 assay; cell-cycle analysis; apoptosis assay; wound-healing assay
E_02105	2019	31406377	An Nfil3-Zeb2-Id2 pathway imposes Irf8 enhancer switching during cDC1 development	Mus musculus	mm39	chr8	121503787	121504483	Tcf4	Irf8	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	plasmacytoid dendritic cells	NA	plasmacytoid dendritic cell	CL:0000784	Enhancer switching; E-box TF input; Endogenous enhancer deletion; lineage-fate analysis	ATAC-seq; ChIP-seq; RNA-seq; scRNA-seq; single-cell RNA-seq	CRISPR/endogenous +41 enhancer deletion; retroviral reporter; Site-directed mutagenesis; RT-qPCR; Flow cytometry
E_02106	2018	29507293	Dissecting super-enhancer hierarchy based on chromatin interactions	Homo sapiens	hg19	chr15	66074477	66098025	EBF1	MYO1D	Super-enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Erythroleukemia Cell,B lymphoblastoid Cell	NA	malignant cell	CL:0001064	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; Hi-C	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_02107	2018	29507293	Dissecting super-enhancer hierarchy based on chromatin interactions	Homo sapiens	hg19	chr15	66074477	66098025	EBF1	SMYD3	Super-enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Erythroleukemia Cell,B lymphoblastoid Cell	NA	malignant cell	CL:0001064	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; Hi-C	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_02108	2018	29507293	Dissecting super-enhancer hierarchy based on chromatin interactions	Homo sapiens	hg19	chr15	66074477	66098025	GATA1	MYO1D	Super-enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Erythroleukemia Cell,B lymphoblastoid Cell	NA	malignant cell	CL:0001064	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; Hi-C	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_02109	2018	29507293	Dissecting super-enhancer hierarchy based on chromatin interactions	Homo sapiens	hg19	chr15	66074477	66098025	GATA1	SMYD3	Super-enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Erythroleukemia Cell,B lymphoblastoid Cell	NA	malignant cell	CL:0001064	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; Hi-C	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_02110	2018	29507293	Dissecting super-enhancer hierarchy based on chromatin interactions	Homo sapiens	hg19	chr15	66074477	66098025	PAX5	MYO1D	Super-enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Erythroleukemia Cell,B lymphoblastoid Cell	NA	malignant cell	CL:0001064	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; Hi-C	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_02111	2018	29507293	Dissecting super-enhancer hierarchy based on chromatin interactions	Homo sapiens	hg19	chr15	66074477	66098025	PAX5	SMYD3	Super-enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Erythroleukemia Cell,B lymphoblastoid Cell	NA	malignant cell	CL:0001064	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; Hi-C	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_02112	2018	29507293	Dissecting super-enhancer hierarchy based on chromatin interactions	Homo sapiens	hg19	chr15	66074477	66098025	TAL1	MYO1D	Super-enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Erythroleukemia Cell,B lymphoblastoid Cell	NA	malignant cell	CL:0001064	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; Hi-C	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_02113	2018	29507293	Dissecting super-enhancer hierarchy based on chromatin interactions	Homo sapiens	hg19	chr15	66074477	66098025	TAL1	SMYD3	Super-enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Erythroleukemia Cell,B lymphoblastoid Cell	NA	malignant cell	CL:0001064	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; Hi-C	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_02114	2018	29507293	Dissecting super-enhancer hierarchy based on chromatin interactions	Homo sapiens	hg19	chr17	31209116	31240452	EBF1	MYO1D	Super-enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Erythroleukemia Cell,B lymphoblastoid Cell	NA	malignant cell	CL:0001064	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; Hi-C	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_02115	2018	29507293	Dissecting super-enhancer hierarchy based on chromatin interactions	Homo sapiens	hg19	chr17	31209116	31240452	EBF1	SMYD3	Super-enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Erythroleukemia Cell,B lymphoblastoid Cell	NA	malignant cell	CL:0001064	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; Hi-C	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_02116	2018	29507293	Dissecting super-enhancer hierarchy based on chromatin interactions	Homo sapiens	hg19	chr17	31209116	31240452	GATA1	MYO1D	Super-enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Erythroleukemia Cell,B lymphoblastoid Cell	NA	malignant cell	CL:0001064	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; Hi-C	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_02117	2018	29507293	Dissecting super-enhancer hierarchy based on chromatin interactions	Homo sapiens	hg19	chr17	31209116	31240452	GATA1	SMYD3	Super-enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Erythroleukemia Cell,B lymphoblastoid Cell	NA	malignant cell	CL:0001064	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; Hi-C	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_02118	2018	29507293	Dissecting super-enhancer hierarchy based on chromatin interactions	Homo sapiens	hg19	chr17	31209116	31240452	PAX5	MYO1D	Super-enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Erythroleukemia Cell,B lymphoblastoid Cell	NA	malignant cell	CL:0001064	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; Hi-C	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_02119	2018	29507293	Dissecting super-enhancer hierarchy based on chromatin interactions	Homo sapiens	hg19	chr17	31209116	31240452	PAX5	SMYD3	Super-enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Erythroleukemia Cell,B lymphoblastoid Cell	NA	malignant cell	CL:0001064	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; Hi-C	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_02120	2018	29507293	Dissecting super-enhancer hierarchy based on chromatin interactions	Homo sapiens	hg19	chr17	31209116	31240452	TAL1	MYO1D	Super-enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Erythroleukemia Cell,B lymphoblastoid Cell	NA	malignant cell	CL:0001064	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; Hi-C	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_02121	2018	29507293	Dissecting super-enhancer hierarchy based on chromatin interactions	Homo sapiens	hg19	chr17	31209116	31240452	TAL1	SMYD3	Super-enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Erythroleukemia Cell,B lymphoblastoid Cell	NA	malignant cell	CL:0001064	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; Hi-C	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_02122	2014	25223790	Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers	Mus musculus	mm10	chr17	35502632	35504632	Klf4	NA	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02123	2014	25223790	Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers	Mus musculus	mm10	chr17	35502632	35504632	Nanog	NA	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02124	2014	25223790	Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers	Mus musculus	mm10	chr17	35502632	35504632	Pou5f1	NA	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02125	2014	25223790	Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers	Mus musculus	mm10	chr17	35502632	35504632	Sox2	NA	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02126	2014	25223790	Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers	Mus musculus	mm10	chr6	122700483	122702483	Klf4	Nanog	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02127	2014	25223790	Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers	Mus musculus	mm10	chr6	122700483	122702483	Nanog	Nanog	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02128	2014	25223790	Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers	Mus musculus	mm10	chr6	122700483	122702483	Pou5f1	Nanog	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02129	2014	25223790	Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers	Mus musculus	mm10	chr6	122700483	122702483	Sox2	Nanog	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02130	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Homo sapiens	hg19	chr21	39823183	39825183	ERG	ERG	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	MOLT-4	CVCL_0013	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF occupancy assay; In vivo enhancer reporter assay	NA	Stable luciferase reporter assay; E-box/ETS/GATA motif mutagenesis; ChIP-PCR; ERG knockdown; RT-qPCR; Western blot; proliferation assay; transgenic mouse enhancer reporter assay
E_02131	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Homo sapiens	hg19	chr21	39823183	39825183	FLI1	ERG	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	MOLT-4	CVCL_0013	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF occupancy assay; In vivo enhancer reporter assay	NA	Stable luciferase reporter assay; E-box/ETS/GATA motif mutagenesis; ChIP-PCR; ERG knockdown; RT-qPCR; Western blot; proliferation assay; transgenic mouse enhancer reporter assay
E_02132	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Homo sapiens	hg19	chr21	39823183	39825183	GATA3	ERG	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	MOLT-4	CVCL_0013	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF occupancy assay; In vivo enhancer reporter assay	NA	Stable luciferase reporter assay; E-box/ETS/GATA motif mutagenesis; ChIP-PCR; ERG knockdown; RT-qPCR; Western blot; proliferation assay; transgenic mouse enhancer reporter assay
E_02133	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Homo sapiens	hg19	chr21	39823183	39825183	LMO2	ERG	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	MOLT-4	CVCL_0013	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF occupancy assay; In vivo enhancer reporter assay	NA	Stable luciferase reporter assay; E-box/ETS/GATA motif mutagenesis; ChIP-PCR; ERG knockdown; RT-qPCR; Western blot; proliferation assay; transgenic mouse enhancer reporter assay
E_02134	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Homo sapiens	hg19	chr21	39823183	39825183	LYL1	ERG	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	MOLT-4	CVCL_0013	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF occupancy assay; In vivo enhancer reporter assay	NA	Stable luciferase reporter assay; E-box/ETS/GATA motif mutagenesis; ChIP-PCR; ERG knockdown; RT-qPCR; Western blot; proliferation assay; transgenic mouse enhancer reporter assay
E_02135	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Homo sapiens	hg19	chr21	39823183	39825183	TAL1	ERG	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	MOLT-4	CVCL_0013	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF occupancy assay; In vivo enhancer reporter assay	NA	Stable luciferase reporter assay; E-box/ETS/GATA motif mutagenesis; ChIP-PCR; ERG knockdown; RT-qPCR; Western blot; proliferation assay; transgenic mouse enhancer reporter assay
E_02136	2022	35805969	3D Chromatin Organization Involving MEIS1 Factor in the cis-Regulatory Landscape of GJB2	Homo sapiens	hg19	chr13	20993543	20994585	MEIS1	GJB2	Enhancer	Active	Normal	NA	NA	NA	respiratory airway	UBERON:0001005	Small airway epithelial cells (SAEC)	NA	respiratory epithelial cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	4C-seq; 4C	CRISPRi; MEIS1 ChIP-PCR; RT-qPCR; Endpoint RT-PCR
E_02137	2019	31406377	An Nfil3-Zeb2-Id2 pathway imposes Irf8 enhancer switching during cDC1 development	Mus musculus	mm39	chr8	121503787	121504483	Tcf3	Irf8	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	common dendritic cell progenitors	NA	dendritic cell progenitor	NA	Enhancer switching; E-box TF input; Endogenous enhancer deletion; lineage-fate analysis	ATAC-seq; ChIP-seq; RNA-seq; scRNA-seq; single-cell RNA-seq	CRISPR/endogenous +41 enhancer deletion; retroviral reporter; Site-directed mutagenesis; RT-qPCR; Flow cytometry
E_02138	2019	31406377	An Nfil3-Zeb2-Id2 pathway imposes Irf8 enhancer switching during cDC1 development	Mus musculus	mm39	chr8	121503787	121504483	Tcf3	Irf8	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	pre-cDC1	NA	conventional dendritic cell precursor	NA	Enhancer switching; E-box TF input; Endogenous enhancer deletion; lineage-fate analysis	ATAC-seq; ChIP-seq; RNA-seq; scRNA-seq; single-cell RNA-seq	CRISPR/endogenous +41 enhancer deletion; retroviral reporter; Site-directed mutagenesis; RT-qPCR; Flow cytometry
E_02139	2019	31406377	An Nfil3-Zeb2-Id2 pathway imposes Irf8 enhancer switching during cDC1 development	Mus musculus	mm39	chr8	121503787	121504483	Tcf4	Irf8	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	pre-cDC1	NA	conventional dendritic cell precursor	NA	Enhancer switching; E-box TF input; Endogenous enhancer deletion; lineage-fate analysis	ATAC-seq; ChIP-seq; RNA-seq; scRNA-seq; single-cell RNA-seq	CRISPR/endogenous +41 enhancer deletion; retroviral reporter; Site-directed mutagenesis; RT-qPCR; Flow cytometry
E_02140	2025	40890402	p300/CBP is an essential driver of pathogenic enhancer activity and gene expression in Ewing sarcoma	Homo sapiens	hg38	chr11	69622001	69622601	EWSR1::FLI1	CCND1	Enhancer	Active	Disease	Ewing sarcoma	MONDO:0012817	DOID:3369	orbital region	UBERON:0004088	SK-N-MC	CVCL_0530	malignant cell	CL:0001064	In vivo functional validation; Enhancer-associated functional perturbation assay; in vivo xenograft assay	EWSR1::FLI1 ChIP-seq; histone-acetylation ChIP-seq; ribo-depleted RNA-seq	A-485 treatment; dCBP-1 treatment; CCS1477 treatment; ChIP-qPCR; enhancer RNA RT-qPCR; CCND1 RT-qPCR; SK-N-MC xenograft tumor-growth assay; In vivo phenotyping
E_02141	2025	40890402	p300/CBP is an essential driver of pathogenic enhancer activity and gene expression in Ewing sarcoma	Homo sapiens	hg38	chr20	21576001	21577647	EWSR1::FLI1	NKX2-2	Enhancer	Active	Disease	Ewing sarcoma	MONDO:0012817	DOID:3369	orbital region	UBERON:0004088	SK-N-MC	CVCL_0530	malignant cell	CL:0001064	In vivo functional validation; Enhancer-associated functional perturbation assay; in vivo xenograft assay	EWSR1::FLI1 ChIP-seq; histone-acetylation ChIP-seq; ribo-depleted RNA-seq	A-485 treatment; dCBP-1 treatment; CCS1477 treatment; ChIP-qPCR; enhancer RNA RT-qPCR; NKX2-2 RT-qPCR; SK-N-MC xenograft tumor-growth assay; In vivo phenotyping
E_02142	2025	40890402	p300/CBP is an essential driver of pathogenic enhancer activity and gene expression in Ewing sarcoma	Homo sapiens	hg38	chr12	54624604	54625309	EWSR1::FLI1	PPP1R1A	Enhancer	Active	Disease	Ewing sarcoma	MONDO:0012817	DOID:3369	orbital region	UBERON:0004088	SK-N-MC	CVCL_0530	malignant cell	CL:0001064	In vivo functional validation; Enhancer-associated functional perturbation assay	EWSR1::FLI1 ChIP-seq; histone-acetylation ChIP-seq; ribo-depleted RNA-seq	A-485 treatment; dCBP-1 treatment; CCS1477 treatment; enhancer RNA RT-qPCR; PPP1R1A RT-qPCR; In vivo phenotyping
E_02143	2025	40890402	p300/CBP is an essential driver of pathogenic enhancer activity and gene expression in Ewing sarcoma	Homo sapiens	hg38	chr20	21576001	21577647	EWSR1::FLI1	NKX2-2	Enhancer	Active	Disease	Ewing sarcoma	MONDO:0012817	DOID:3369	NA	NA	EWS-502 dTAG derivative	NA	Ewing sarcoma cell	NA	Enhancer-associated functional perturbation assay	EWSR1::FLI1 ChIP-seq; EP300 ChIP-seq; CREBBP ChIP-seq; H3K27ac ChIP-seq; ribo-depleted RNA-seq	dTAG-mediated EWSR1::FLI1 degradation; ChIP-qPCR; enhancer RNA RT-qPCR; NKX2-2 RT-qPCR
E_02144	2017	28446439	PAX3-FOXO1 Establishes Myogenic Super Enhancers and Confers BET Bromodomain Vulnerability	Homo sapiens	hg19	chr11	17666830	17677080	FOXO1	MYOD1	Super-enhancer	Active	Disease	alveolar rhabdomyosarcoma	MONDO:0009994	DOID:4051	blood	UBERON:0000178	Human Fibroblast Cell Lines	NA	fibroblast	CL:0000057	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 4C; RT-qPCR/qPCR
E_02145	2017	28446439	PAX3-FOXO1 Establishes Myogenic Super Enhancers and Confers BET Bromodomain Vulnerability	Homo sapiens	hg19	chr11	17666830	17677080	PAX3	MYOD1	Super-enhancer	Active	Disease	alveolar rhabdomyosarcoma	MONDO:0009994	DOID:4051	blood	UBERON:0000178	Human Fibroblast Cell Lines	NA	fibroblast	CL:0000057	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 4C; RT-qPCR/qPCR
E_02146	2011	21681857	N-carbamylglutamate enhancement of ureagenesis leads to discovery of a novel deleterious mutation in a newly defined enhancer of the NAGS gene and to effective therapy	Homo sapiens	hg19	chr17	42078768	42079095	HNF1A	NAGS	Enhancer	Active	Disease	hyperammonemia due to N-acetylglutamate synthase deficiency	MONDO:0009377	DOID:0112258	liver	UBERON:0002107	patient genomic DNA	NA	hepatocyte-lineage cell	NA	Disease-variant enhancer activity; TF binding assay	None (focal candidate-locus study); 4C	Sanger sequencing; Luciferase reporter; HNF1 DNA-binding assay; stable isotope ureagenesis; N-carbamylglutamate therapeutic response
E_02147	2014	25223790	Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers	Mus musculus	mm10	chr6	122702344	122703335	NA	Nanog	Enhancer	Active	Normal	NA	NA	NA	epiblast (generic)	UBERON:0002532	mouse epiblast stem cells	NA	epiblast cell	CL:0000352	Enhancer activity assay; Functional perturbation assay; Enhancer activation assay	NA	TALE-VP64 activation; CRISPR/dCas9-VP64 activation; Luciferase reporter assay; RT-qPCR; reprogramming assay
E_02148	2014	25223790	Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers	Mus musculus	mm10	chr6	122702344	122703335	NA	Nanog	Enhancer	Active	Normal	NA	NA	NA	epiblast (generic)	UBERON:0002532	mouse epiblast stem cells	NA	epiblast cell	CL:0000352	Enhancer activity assay; Functional perturbation assay; Enhancer activation assay	NA	TALE-VP64 enhancer activation; CRISPR/dCas9-VP64 enhancer activation; Luciferase reporter assay; RT-qPCR; reprogramming assay
E_02149	2011	21681857	N-carbamylglutamate enhancement of ureagenesis leads to discovery of a novel deleterious mutation in a newly defined enhancer of the NAGS gene and to effective therapy	Homo sapiens	hg19	chr17	42078768	42079095	HNF1A	NAGS	Enhancer	Active	Disease	hyperammonemia due to N-acetylglutamate synthase deficiency	MONDO:0009377	DOID:0112258	liver	UBERON:0002107	HepG2 enhancer-reporter model	NA	malignant cell	CL:0001064	Disease-variant enhancer activity; TF binding assay	None (focal candidate-locus study); 4C	Sanger sequencing; Luciferase reporter; HNF1 DNA-binding assay; stable isotope ureagenesis; N-carbamylglutamate therapeutic response
E_02150	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Homo sapiens	hg19	chr21	39823183	39825183	GATA2	ERG	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	T-acute lymphoblastic leukemia (T-ALL),Molt4,REH,416B	NA	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02151	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Homo sapiens	hg19	chr21	39823183	39825183	LMO2	ERG	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	T-acute lymphoblastic leukemia (T-ALL),Molt4,REH,416B	NA	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02152	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Homo sapiens	hg19	chr21	39823183	39825183	LYL1	ERG	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	T-acute lymphoblastic leukemia (T-ALL),Molt4,REH,416B	NA	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02153	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Homo sapiens	hg19	chr21	39823183	39825183	TAL1	ERG	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	T-acute lymphoblastic leukemia (T-ALL),Molt4,REH,416B	NA	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02154	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Mus musculus	mm10	chr16	95439106	95439643	Tal1	Erg	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	mouse hematopoietic enhancer reporter/transgenic models	NA	hematopoietic stem/progenitor and T-lineage leukemia cells	NA	Enhancer reporter/transgenic validation; leukemia regulatory mechanism	ChIP-seq/chromatin occupancy profiling	Reporter assay; transgenic enhancer assay; TF-binding validation; leukemia growth/transformation assays
E_02155	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Mus musculus	mm10	chr16	95439106	95439643	Tal1	Erg	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	human T-ALL cells	NA	hematopoietic stem/progenitor and T-lineage leukemia cells	NA	Enhancer reporter/transgenic validation; leukemia regulatory mechanism	ChIP-seq/chromatin occupancy profiling	Reporter assay; transgenic enhancer assay; TF-binding validation; leukemia growth/transformation assays
E_02156	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Mus musculus	mm10	chr16	95439106	95439643	Tal1	Erg	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	thymus	UBERON:0002370	mouse hematopoietic enhancer reporter/transgenic models	NA	hematopoietic stem/progenitor and T-lineage leukemia cells	NA	Enhancer reporter/transgenic validation; leukemia regulatory mechanism	ChIP-seq/chromatin occupancy profiling	Reporter assay; transgenic enhancer assay; TF-binding validation; leukemia growth/transformation assays
E_02157	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Mus musculus	mm10	chr16	95439106	95439643	Tal1	Erg	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	thymus	UBERON:0002370	human T-ALL cells	NA	hematopoietic stem/progenitor and T-lineage leukemia cells	NA	Enhancer reporter/transgenic validation; leukemia regulatory mechanism	ChIP-seq/chromatin occupancy profiling	Reporter assay; transgenic enhancer assay; TF-binding validation; leukemia growth/transformation assays
E_02158	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Mus musculus	mm10	chr16	95439106	95439643	Lyl1	Erg	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	mouse hematopoietic enhancer reporter/transgenic models	NA	hematopoietic stem/progenitor and T-lineage leukemia cells	NA	Enhancer reporter/transgenic validation; leukemia regulatory mechanism	ChIP-seq/chromatin occupancy profiling	Reporter assay; transgenic enhancer assay; TF-binding validation; leukemia growth/transformation assays
E_02159	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Mus musculus	mm10	chr16	95439106	95439643	Lyl1	Erg	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	human T-ALL cells	NA	hematopoietic stem/progenitor and T-lineage leukemia cells	NA	Enhancer reporter/transgenic validation; leukemia regulatory mechanism	ChIP-seq/chromatin occupancy profiling	Reporter assay; transgenic enhancer assay; TF-binding validation; leukemia growth/transformation assays
E_02160	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Mus musculus	mm10	chr16	95439106	95439643	Lyl1	Erg	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	thymus	UBERON:0002370	mouse hematopoietic enhancer reporter/transgenic models	NA	hematopoietic stem/progenitor and T-lineage leukemia cells	NA	Enhancer reporter/transgenic validation; leukemia regulatory mechanism	ChIP-seq/chromatin occupancy profiling	Reporter assay; transgenic enhancer assay; TF-binding validation; leukemia growth/transformation assays
E_02161	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Mus musculus	mm10	chr16	95439106	95439643	Lyl1	Erg	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	thymus	UBERON:0002370	human T-ALL cells	NA	hematopoietic stem/progenitor and T-lineage leukemia cells	NA	Enhancer reporter/transgenic validation; leukemia regulatory mechanism	ChIP-seq/chromatin occupancy profiling	Reporter assay; transgenic enhancer assay; TF-binding validation; leukemia growth/transformation assays
E_02162	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Mus musculus	mm10	chr16	95439106	95439643	Erg	Erg	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	mouse hematopoietic enhancer reporter/transgenic models	NA	hematopoietic stem/progenitor and T-lineage leukemia cells	NA	Enhancer reporter/transgenic validation; leukemia regulatory mechanism	ChIP-seq/chromatin occupancy profiling	Reporter assay; transgenic enhancer assay; TF-binding validation; leukemia growth/transformation assays
E_02163	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Mus musculus	mm10	chr16	95439106	95439643	Erg	Erg	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	human T-ALL cells	NA	hematopoietic stem/progenitor and T-lineage leukemia cells	NA	Enhancer reporter/transgenic validation; leukemia regulatory mechanism	ChIP-seq/chromatin occupancy profiling	Reporter assay; transgenic enhancer assay; TF-binding validation; leukemia growth/transformation assays
E_02164	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Mus musculus	mm10	chr16	95439106	95439643	Erg	Erg	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	thymus	UBERON:0002370	mouse hematopoietic enhancer reporter/transgenic models	NA	hematopoietic stem/progenitor and T-lineage leukemia cells	NA	Enhancer reporter/transgenic validation; leukemia regulatory mechanism	ChIP-seq/chromatin occupancy profiling	Reporter assay; transgenic enhancer assay; TF-binding validation; leukemia growth/transformation assays
E_02165	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Mus musculus	mm10	chr16	95439106	95439643	Erg	Erg	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	thymus	UBERON:0002370	human T-ALL cells	NA	hematopoietic stem/progenitor and T-lineage leukemia cells	NA	Enhancer reporter/transgenic validation; leukemia regulatory mechanism	ChIP-seq/chromatin occupancy profiling	Reporter assay; transgenic enhancer assay; TF-binding validation; leukemia growth/transformation assays
E_02166	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Mus musculus	mm10	chr16	95439106	95439643	Fli1	Erg	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	mouse hematopoietic enhancer reporter/transgenic models	NA	hematopoietic stem/progenitor and T-lineage leukemia cells	NA	Enhancer reporter/transgenic validation; leukemia regulatory mechanism	ChIP-seq/chromatin occupancy profiling	Reporter assay; transgenic enhancer assay; TF-binding validation; leukemia growth/transformation assays
E_02167	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Mus musculus	mm10	chr16	95439106	95439643	Fli1	Erg	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	human T-ALL cells	NA	hematopoietic stem/progenitor and T-lineage leukemia cells	NA	Enhancer reporter/transgenic validation; leukemia regulatory mechanism	ChIP-seq/chromatin occupancy profiling	Reporter assay; transgenic enhancer assay; TF-binding validation; leukemia growth/transformation assays
E_02168	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Mus musculus	mm10	chr16	95439106	95439643	Fli1	Erg	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	thymus	UBERON:0002370	mouse hematopoietic enhancer reporter/transgenic models	NA	hematopoietic stem/progenitor and T-lineage leukemia cells	NA	Enhancer reporter/transgenic validation; leukemia regulatory mechanism	ChIP-seq/chromatin occupancy profiling	Reporter assay; transgenic enhancer assay; TF-binding validation; leukemia growth/transformation assays
E_02169	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Mus musculus	mm10	chr16	95439106	95439643	Fli1	Erg	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	thymus	UBERON:0002370	human T-ALL cells	NA	hematopoietic stem/progenitor and T-lineage leukemia cells	NA	Enhancer reporter/transgenic validation; leukemia regulatory mechanism	ChIP-seq/chromatin occupancy profiling	Reporter assay; transgenic enhancer assay; TF-binding validation; leukemia growth/transformation assays
E_02170	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Mus musculus	mm10	chr16	95439106	95439643	Gata3	Erg	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	mouse hematopoietic enhancer reporter/transgenic models	NA	hematopoietic stem/progenitor and T-lineage leukemia cells	NA	Enhancer reporter/transgenic validation; leukemia regulatory mechanism	ChIP-seq/chromatin occupancy profiling	Reporter assay; transgenic enhancer assay; TF-binding validation; leukemia growth/transformation assays
E_02171	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Mus musculus	mm10	chr16	95439106	95439643	Gata3	Erg	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	human T-ALL cells	NA	hematopoietic stem/progenitor and T-lineage leukemia cells	NA	Enhancer reporter/transgenic validation; leukemia regulatory mechanism	ChIP-seq/chromatin occupancy profiling	Reporter assay; transgenic enhancer assay; TF-binding validation; leukemia growth/transformation assays
E_02172	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Mus musculus	mm10	chr16	95439106	95439643	Gata3	Erg	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	thymus	UBERON:0002370	mouse hematopoietic enhancer reporter/transgenic models	NA	hematopoietic stem/progenitor and T-lineage leukemia cells	NA	Enhancer reporter/transgenic validation; leukemia regulatory mechanism	ChIP-seq/chromatin occupancy profiling	Reporter assay; transgenic enhancer assay; TF-binding validation; leukemia growth/transformation assays
E_02173	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Mus musculus	mm10	chr16	95439106	95439643	Gata3	Erg	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	thymus	UBERON:0002370	human T-ALL cells	NA	hematopoietic stem/progenitor and T-lineage leukemia cells	NA	Enhancer reporter/transgenic validation; leukemia regulatory mechanism	ChIP-seq/chromatin occupancy profiling	Reporter assay; transgenic enhancer assay; TF-binding validation; leukemia growth/transformation assays
E_02174	2010	20061391	Nuclear factor kappaB- and specificity protein 1-dependent p53-mediated bi-directional regulation of the human manganese superoxide dismutase gene	Homo sapiens	hg19	chr6	160101620	160102231	TP53	SOD2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	PC-3	CVCL_0035	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_02175	2010	20061391	Nuclear factor kappaB- and specificity protein 1-dependent p53-mediated bi-directional regulation of the human manganese superoxide dismutase gene	Homo sapiens	hg19	chr6	160101890	160102231	SP1	SOD2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	PC-3	CVCL_0035	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_02176	1999	10523648	Structural and functional cross-talk between a distant enhancer and the epsilon-globin gene promoter shows interdependence of the two elements in chromatin	Homo sapiens	hg19	chr11	5266021	5266708	GATA1	HBE1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Experimentally supported enhancer study	NA	3C
E_02177	1999	10523648	Structural and functional cross-talk between a distant enhancer and the epsilon-globin gene promoter shows interdependence of the two elements in chromatin	Homo sapiens	hg19	chr11	5266021	5266708	NFE2	HBE1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Experimentally supported enhancer study	NA	3C
E_02178	2019	31406377	An Nfil3-Zeb2-Id2 pathway imposes Irf8 enhancer switching during cDC1 development	Mus musculus	mm10	chr8	120777048	120777744	Tcf3	Irf8	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	common dendritic cell progenitor / pre-cDC1	NA	dendritic cell progenitor	NA	Stage-specific enhancer assay; enhancer genetic perturbation; E-box mutagenesis	single-cell RNA-seq; ATAC-seq	Enhancer reporter; E-box mutagenesis; genetic epistasis; Flow cytometry; enhancer-null mouse analysis
E_02179	2019	31406377	An Nfil3-Zeb2-Id2 pathway imposes Irf8 enhancer switching during cDC1 development	Mus musculus	mm10	chr8	120768340	120768887	Batf3	Irf8	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	pre-cDC1 / mature cDC1	NA	conventional dendritic cell type 1	NA	Stage-specific enhancer switching; genetic perturbation	single-cell RNA-seq; ATAC-seq	Genetic epistasis; enhancer-function analysis; Flow cytometry
E_02180	1999	10523648	Structural and functional cross-talk between a distant enhancer and the epsilon-globin gene promoter shows interdependence of the two elements in chromatin	Homo sapiens	hg19	chr11	5266021	5266708	GATA1	HBE1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	erythroid lineage cell	CL:0000764	Enhancer activity assay	NA	Transfection; RNase protection assay; DNase I hypersensitivity assay; enhancer-promoter mutagenesis; chromatinized reporter assay
E_02181	1999	10523648	Structural and functional cross-talk between a distant enhancer and the epsilon-globin gene promoter shows interdependence of the two elements in chromatin	Homo sapiens	hg19	chr11	5266021	5266708	NFE2	HBE1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	erythroid lineage cell	CL:0000764	Enhancer activity assay	NA	Transfection; RNase protection assay; DNase I hypersensitivity assay; enhancer-promoter mutagenesis; chromatinized reporter assay
E_02182	2011	21681857	N-carbamylglutamate enhancement of ureagenesis leads to discovery of a novel deleterious mutation in a newly defined enhancer of the NAGS gene and to effective therapy	Homo sapiens	hg19	chr17	42078932	42079032	HNF1A	NAGS	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Ureagenesis	NA	NA	NA	Enhancer activity assay	NA	Luciferase reporter assay; Reporter assay
E_02183	2018	29385519	Genomic dissection of enhancers uncovers principles of combinatorial regulation and cell type-specific wiring of enhancer-promoter contacts	Homo sapiens	hg19	chrX	106959618	106962917	NR3C1	TSC22D3	Enhancer	Active	Normal	NA	NA	NA	NA	NA	U-2 OS	CVCL_0042	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 4C; RT-qPCR/qPCR
E_02184	2018	29385519	Genomic dissection of enhancers uncovers principles of combinatorial regulation and cell type-specific wiring of enhancer-promoter contacts	Homo sapiens	hg19	chrX	106960488	106960865	NR3C1	TSC22D3	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	A-549	CVCL_0023	epithelial cell	CL:0000066	Endogenous enhancer perturbation; GR-bound GILZ/TSC22D3 GBS1 enhancer interval; endogenous deletion and cell-type-specific wiring	GR ChIP-seq; 4C-seq; Hi-C integration	CRISPR/Cas9 GR-binding-site deletion; qPCR; CTCF ChIP-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_02185	2024	38228888	An ancient polymorphic regulatory region within the BDNF gene associated with obesity modulates anxiety-like behaviour in mice and humans	Homo sapiens	hg19	chr11	27725730	27726223	NA	BDNF-AS	Enhancer	Active	Disease	obesity	MONDO:0011122	DOID:9970	nucleus accumbens	UBERON:0001882	GTEx human nucleus accumbens tissue	NA	NA	NA	Enhancer activity assay; Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation; Genetic association analysis; eQTL/sQTL target-linking analysis	GWAS; GTEx eQTL analysis; GTEx sQTL analysis; eQTL analysis	Dual-luciferase reporter assay and rs10767664 site-directed mutagenesis establish BE5.1 enhancer function; no direct human BDNF-AS perturbation was performed; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_02186	2023	37345431	Identification and functional validation of an enhancer variant in the 9p21.3 locus associated with glaucoma risk and elevated expression of p16INK4a	Homo sapiens	hg19	chr9	21980404	21981404	YY1	CDKN2A	Enhancer	Active	Disease	glaucoma	MONDO:0005041	DOID:1686	uterine cervix	UBERON:0000002	HeLa	CVCL_0030	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Disease-variant functional analysis	GWAS	Luciferase reporter assay, EMSA; ChIP-qPCR; RT-qPCR
E_02187	2020	31658410	A distal enhancer that directs Otx2 expression in the retinal pigment epithelium and neuroretina	Homo sapiens	hg19	chr14	57419008	57421445	NA	OTX2	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	Transgenic mouse embryo carrying human enhancer	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay	VISTA enhancer screen; Hi-C; DNase hypersensitivity analysis	Transgenic reporter assay; qRT-PCR; Immunohistochemistry; Transgenic mouse enhancer assay
E_02188	2017	28045957	Normal Levels of Sox9 Expression in the Developing Mouse Testis Depend on the TES/TESCO Enhancer, but This Does Not Act Alone	Mus musculus	mm10	chr11	112635500	112636792	Sry	Sox9	Enhancer	Active	Normal	NA	NA	NA	testis	UBERON:0000473	Sertoli cells	NA	Sertoli cell	CL:0000216	Enhancer activity assay; Functional perturbation assay; TF binding assay; Endogenous enhancer perturbation; In vivo functional validation	RNA-seq	CRISPR knockout; RT-qPCR, Immunofluorescence; ChIP-qPCR, Transgenic reporter assay; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_02189	2014	25209250	A regulatory network controls nephrocan expression and midgut patterning	Mus musculus	mm10	chr10	52388022	52388224	Sox17	Nepn	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	P19	CVCL_2153	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; In vivo functional validation; Functional cis-element perturbation assay	NA	Promoter/enhancer deletion luciferase assay; SOX17 site-A mutagenesis/deletion; EMSA; Sox17 perturbation; RT-qPCR; whole-mount in situ hybridization; In vivo phenotyping
E_02190	2014	25209250	A regulatory network controls nephrocan expression and midgut patterning	Mus musculus	mm10	chr10	52388022	52388224	Sox17	Nepn	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	P19	CVCL_2153	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; In vivo functional validation; Functional cis-element perturbation assay	NA	Deletion-mapping luciferase assay; SOX17 site-A mutagenesis/deletion; EMSA; Sox17 perturbation; RT-qPCR; In vivo phenotyping
E_02191	2014	25209250	A regulatory network controls nephrocan expression and midgut patterning	Mus musculus	mm10	chr11	96200000	96202300	Rara	Nepn	Enhancer	Active	Normal	NA	NA	NA	endoderm	UBERON:0000925	OMEGA-E	CVCL_2151	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; In vivo functional validation; Transgenic reporter assay	NA	Luciferase reporter assay, EMSA, Transgenic reporter assay; RT-qPCR; In vivo phenotyping
E_02192	2014	25209250	A regulatory network controls nephrocan expression and midgut patterning	Mus musculus	mm10	chr11	96201500	96202300	Sox17	Nepn	Enhancer	Active	Normal	NA	NA	NA	endoderm	UBERON:0000925	OMEGA-E	CVCL_2151	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; In vivo functional validation	NA	Luciferase reporter assay, EMSA; RT-qPCR; In vivo phenotyping
E_02193	2013	24014243	The control of hematopoietic stem cell maintenance, self-renewal, and differentiation by Mysm1-mediated epigenetic regulation	Mus musculus	mm10	chr5	107680655	107682655	Gata2	Gfi1	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Mysm1-deficient HSCs	NA	hematopoietic stem cell	CL:0000037	Endogenous enhancer perturbation; In vivo functional validation; Epigenetic enhancer regulation; TF occupancy; functional transactivation	ChIP-seq / expression profiling	ChIP-qPCR; enhancer reporter assay; TF transactivation; RT-qPCR; Mouse genetic deletion/knock-in
E_02194	2013	24014243	The control of hematopoietic stem cell maintenance, self-renewal, and differentiation by Mysm1-mediated epigenetic regulation	Mus musculus	mm10	chr5	107680655	107682655	Gata2	Gfi1	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	wild-type HSCs	NA	hematopoietic stem cell	CL:0000037	Endogenous enhancer perturbation; In vivo functional validation; Epigenetic enhancer regulation; TF occupancy; functional transactivation	ChIP-seq / expression profiling	ChIP-qPCR; enhancer reporter assay; TF transactivation; RT-qPCR; Mouse genetic deletion/knock-in
E_02195	2013	24014243	The control of hematopoietic stem cell maintenance, self-renewal, and differentiation by Mysm1-mediated epigenetic regulation	Mus musculus	mm10	chr5	107680655	107682655	Runx1	Gfi1	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Mysm1-deficient HSCs	NA	hematopoietic stem cell	CL:0000037	Endogenous enhancer perturbation; In vivo functional validation; Epigenetic enhancer regulation; TF occupancy; functional transactivation	ChIP-seq / expression profiling	ChIP-qPCR; enhancer reporter assay; TF transactivation; RT-qPCR; Mouse genetic deletion/knock-in
E_02196	2013	24014243	The control of hematopoietic stem cell maintenance, self-renewal, and differentiation by Mysm1-mediated epigenetic regulation	Mus musculus	mm10	chr5	107680655	107682655	Runx1	Gfi1	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	wild-type HSCs	NA	hematopoietic stem cell	CL:0000037	Endogenous enhancer perturbation; In vivo functional validation; Epigenetic enhancer regulation; TF occupancy; functional transactivation	ChIP-seq / expression profiling	ChIP-qPCR; enhancer reporter assay; TF transactivation; RT-qPCR; Mouse genetic deletion/knock-in
E_02197	2012	22253448	Role of runt-related transcription factor 3 (RUNX3) in transcription regulation of natural cytotoxicity receptor 1 (NCR1/NKp46), an activating natural killer (NK) cell receptor	Homo sapiens	hg19	chr19	55417234	55417304	RUNX3	NCR1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	NK-92	CVCL_2142	natural killer cell	CL:0000623	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin-state assay	NA	Luciferase reporter assay; RUNX-site mutagenesis; EMSA; ChIP-qPCR; RUNX3 overexpression; dominant-negative RUNX perturbation; RT-qPCR; RT-PCR; Western blot; histone ChIP-qPCR
E_02198	2022	35778390	B cell receptor signaling drives APOBEC3 expression via direct enhancer regulation in chronic lymphocytic leukemia B cells	Homo sapiens	hg19	chr22	38686443	38686999	NA	APOBEC3C	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	B cells	NA	B cell	CL:0000236	Enhancer activity assay; Functional perturbation assay; TF binding assay; Endogenous enhancer perturbation	ATAC-seq, CUT&Tag; RNA-seq	CRISPR knockout, CRISPRi, qRT-PCR; Western blot; CRISPR-Cas9 endogenous deletion/editing
E_02199	2022	35778390	B cell receptor signaling drives APOBEC3 expression via direct enhancer regulation in chronic lymphocytic leukemia B cells	Homo sapiens	hg19	chr22	38687301	38687766	NA	APOBEC3C	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	B cells	NA	B cell	CL:0000236	Enhancer activity assay; Functional perturbation assay; TF binding assay; Endogenous enhancer perturbation	ATAC-seq, CUT&Tag; RNA-seq	CRISPR knockout, CRISPRi, qRT-PCR; Western blot; CRISPR-Cas9 endogenous deletion/editing
E_02200	2022	35778390	B cell receptor signaling drives APOBEC3 expression via direct enhancer regulation in chronic lymphocytic leukemia B cells	Homo sapiens	hg19	chr22	38688102	38688577	NA	APOBEC3C	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	B cells	NA	B cell	CL:0000236	Enhancer activity assay; Functional perturbation assay; TF binding assay; Endogenous enhancer perturbation	ATAC-seq, CUT&Tag; RNA-seq	CRISPR knockout, CRISPRi; RT-qPCR; Western blot; CRISPR-Cas9 endogenous deletion/editing
E_02201	2022	36243007	Transcription factor RORα enforces stability of the Th17 cell effector program by binding to a Rorc cis-regulatory element	Mus musculus	mm39	chr3	94294960	94295960	Rora	Rorc	Enhancer	Active	Normal	NA	NA	NA	small intestine	UBERON:0002108	Primary mouse tissue-resident Th17 cells	NA	T-helper 17 cell	CL:0000899	Rorc +11-kb/CNS11 enhancer occupancy by RORα/RORγt; in vivo enhancer-reporter deletion and lineage-maintenance validation	RNA-seq; ATAC-seq; RORα ChIP-seq; RORγt ChIP-seq	Transgenic Rorc reporter; +11-kb enhancer deletion reporter; Rora conditional deletion; RORE CRISPR editing; Flow cytometry; ChIP-qPCR; RT-qPCR; EAE/peripheral inflammatory challenge
E_02202	2022	36243007	Transcription factor RORα enforces stability of the Th17 cell effector program by binding to a Rorc cis-regulatory element	Mus musculus	mm39	chr3	94294960	94295960	Rorc	Rorc	Enhancer	Active	Normal	NA	NA	NA	small intestine	UBERON:0002108	Primary mouse tissue-resident Th17 cells	NA	T-helper 17 cell	CL:0000899	Rorc +11-kb/CNS11 enhancer occupancy by RORα/RORγt; in vivo enhancer-reporter deletion and lineage-maintenance validation	RNA-seq; ATAC-seq; RORα ChIP-seq; RORγt ChIP-seq	Transgenic Rorc reporter; +11-kb enhancer deletion reporter; Rora conditional deletion; RORE CRISPR editing; Flow cytometry; ChIP-qPCR; RT-qPCR; EAE/peripheral inflammatory challenge
E_02203	2022	36243007	Transcription factor RORα enforces stability of the Th17 cell effector program by binding to a Rorc cis-regulatory element	Mus musculus	mm39	chr3	94294960	94295960	Rora	Rorc	Enhancer	Active	Normal	NA	NA	NA	small intestine	UBERON:0002108	Primary small-intestinal lamina propria tissue-resident Th17 cells	NA	T-helper 17 cell	CL:0000899	Rorc CNS11/+11-kb cis-regulatory element; RORα occupancy; in vivo enhancer-reporter deletion and lineage-maintenance validation; exact 1001-bp CNS11 interval independently validated by PMID 41739921	RNA-seq; ATAC-seq; RORα ChIP-seq; RORγt ChIP-seq	BAC/transgenic Rorc reporter; +11-kb element deletion reporter; Rora conditional deletion; RORE CRISPR editing; ChIP-qPCR; RT-qPCR; Flow cytometry; EAE/peripheral inflammatory challenge
E_02204	2022	36243007	Transcription factor RORα enforces stability of the Th17 cell effector program by binding to a Rorc cis-regulatory element	Mus musculus	mm39	chr3	94294960	94295960	Rorc	Rorc	Enhancer	Active	Normal	NA	NA	NA	small intestine	UBERON:0002108	Primary small-intestinal lamina propria tissue-resident Th17 cells	NA	T-helper 17 cell	CL:0000899	Rorc CNS11/+11-kb cis-regulatory element; RORγt occupancy/feed-forward regulation; in vivo enhancer-reporter deletion and lineage-maintenance validation; exact 1001-bp CNS11 interval independently validated by PMID 41739921	RNA-seq; ATAC-seq; RORα ChIP-seq; RORγt ChIP-seq	BAC/transgenic Rorc reporter; +11-kb element deletion reporter; Rora conditional deletion; RORE CRISPR editing; ChIP-qPCR; RT-qPCR; Flow cytometry; EAE/peripheral inflammatory challenge
E_02205	2015	26501517	Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements	Homo sapiens	hg19	chr11	5301862	5302715	NA	HBE1	Enhancer	Repressed	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Functional perturbation assay; Endogenous enhancer perturbation; Epigenome editing assay	RNA-seq; FLAG-dCas9 ChIP-seq; H3K9me3 ChIP-seq; DNase-seq	dCas9-KRAB CRISPR interference; sgRNA screen; RT-qPCR; ChIP-qPCR; Western blot; CRISPR-Cas9 endogenous deletion/editing
E_02206	2015	26501517	Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements	Homo sapiens	hg19	chr11	5301862	5302715	NA	HBG1	Enhancer	Repressed	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Functional perturbation assay; Endogenous enhancer perturbation; Epigenome editing assay	RNA-seq; FLAG-dCas9 ChIP-seq; H3K9me3 ChIP-seq; DNase-seq	dCas9-KRAB CRISPR interference; sgRNA screen; RT-qPCR; ChIP-qPCR; Western blot; CRISPR-Cas9 endogenous deletion/editing
E_02207	2015	26501517	Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements	Homo sapiens	hg19	chr11	5301862	5302715	NA	HBG2	Enhancer	Repressed	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Functional perturbation assay; Endogenous enhancer perturbation; Epigenome editing assay	RNA-seq; FLAG-dCas9 ChIP-seq; H3K9me3 ChIP-seq; DNase-seq	dCas9-KRAB CRISPR interference; sgRNA screen; RT-qPCR; ChIP-qPCR; Western blot; CRISPR-Cas9 endogenous deletion/editing
E_02208	2015	26501517	Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements	Homo sapiens	hg19	chr11	5301862	5302715	NA	HBB	Enhancer	Repressed	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Functional perturbation assay; Endogenous enhancer perturbation; Epigenome editing assay	RNA-seq; FLAG-dCas9 ChIP-seq; H3K9me3 ChIP-seq; DNase-seq	dCas9-KRAB CRISPR interference; sgRNA screen; RT-qPCR; ChIP-qPCR; Western blot; CRISPR-Cas9 endogenous deletion/editing
E_02209	2015	26501517	Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements	Homo sapiens	hg19	chr11	5301862	5302715	NA	HBE1	Enhancer	Repressed	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Functional perturbation assay; Endogenous enhancer perturbation; Epigenome editing assay	RNA-seq; FLAG-dCas9 ChIP-seq; H3K9me3 ChIP-seq; DNase-seq	dCas9-KRAB CRISPR interference; sgRNA targeting; ChIP-qPCR; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_02210	2015	26501517	Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements	Homo sapiens	hg19	chr11	5301862	5302715	NA	HBG1	Enhancer	Repressed	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Functional perturbation assay; Endogenous enhancer perturbation; Epigenome editing assay	RNA-seq; FLAG-dCas9 ChIP-seq; H3K9me3 ChIP-seq; DNase-seq	dCas9-KRAB CRISPR interference; sgRNA targeting; ChIP-qPCR; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_02211	2015	26501517	Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements	Homo sapiens	hg19	chr11	5301862	5302715	NA	HBG2	Enhancer	Repressed	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Functional perturbation assay; Endogenous enhancer perturbation; Epigenome editing assay	RNA-seq; FLAG-dCas9 ChIP-seq; H3K9me3 ChIP-seq; DNase-seq	dCas9-KRAB CRISPR interference; sgRNA targeting; ChIP-qPCR; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_02212	2015	26501517	Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements	Homo sapiens	hg19	chr11	5301862	5302715	NA	HBB	Enhancer	Repressed	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Functional perturbation assay; Endogenous enhancer perturbation; Epigenome editing assay	RNA-seq; FLAG-dCas9 ChIP-seq; H3K9me3 ChIP-seq; DNase-seq	dCas9-KRAB CRISPR interference; sgRNA targeting; ChIP-qPCR; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_02213	2015	26501517	Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements	Homo sapiens	hg38	chr11	5280255	5281665	NA	HBG1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Gene expression assay; Endogenous enhancer perturbation; Chromatin-state assay	RNA-seq; H3K9me3 ChIP-seq; DNase-seq	dCas9-KRAB CRISPRi; RT-qPCR; H3K9me3 ChIP-qPCR; GATA2/FOSL1 ChIP-qPCR; Western blot; CRISPR-Cas9 endogenous deletion/editing
E_02214	2015	26501517	Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements	Homo sapiens	hg38	chr11	5280255	5281665	NA	HBG2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Gene expression assay; Endogenous enhancer perturbation; Chromatin-state assay	RNA-seq; H3K9me3 ChIP-seq; DNase-seq	dCas9-KRAB CRISPRi; RT-qPCR; H3K9me3 ChIP-qPCR; GATA2/FOSL1 ChIP-qPCR; Western blot; CRISPR-Cas9 endogenous deletion/editing
E_02215	2015	26501517	Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements	Homo sapiens	hg19	chr11	5301862	5302715	NA	HBE1	Enhancer	Repressed	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	erythroid-like cell	NA	Functional perturbation assay; Enhancer chromatin-state assay; Epigenome editing assay	RNA-seq; FLAG-dCas9 ChIP-seq; H3K9me3 ChIP-seq; DNase-seq	dCas9-KRAB CRISPRi; sgRNA targeting; ChIP-qPCR; RT-qPCR; CRISPR-Cas9
E_02216	2015	26501517	Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements	Homo sapiens	hg19	chr11	5301862	5302715	NA	HBG1	Enhancer	Repressed	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	erythroid-like cell	NA	Functional perturbation assay; Enhancer chromatin-state assay; Epigenome editing assay	RNA-seq; FLAG-dCas9 ChIP-seq; H3K9me3 ChIP-seq; DNase-seq	dCas9-KRAB CRISPRi; sgRNA targeting; ChIP-qPCR; RT-qPCR; CRISPR-Cas9
E_02217	2015	26501517	Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements	Homo sapiens	hg19	chr11	5301862	5302715	NA	HBG2	Enhancer	Repressed	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	erythroid-like cell	NA	Functional perturbation assay; Enhancer chromatin-state assay; Epigenome editing assay	RNA-seq; FLAG-dCas9 ChIP-seq; H3K9me3 ChIP-seq; DNase-seq	dCas9-KRAB CRISPRi; sgRNA targeting; ChIP-qPCR; RT-qPCR; CRISPR-Cas9
E_02218	2015	26501517	Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements	Homo sapiens	hg19	chr11	5301862	5302715	NA	HBB	Enhancer	Repressed	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	erythroid-like cell	NA	Functional perturbation assay; Enhancer chromatin-state assay; Epigenome editing assay	RNA-seq; FLAG-dCas9 ChIP-seq; H3K9me3 ChIP-seq; DNase-seq	dCas9-KRAB CRISPRi; sgRNA targeting; ChIP-qPCR; RT-qPCR; CRISPR-Cas9
E_02219	2024	38228888	An ancient polymorphic regulatory region within the BDNF gene associated with obesity modulates anxiety-like behaviour in mice and humans	Homo sapiens	hg38	chr11	27725730	27726223	NA	BDNF	Enhancer	Active	Disease	obesity	MONDO:0011122	DOID:9970	brainstem	UBERON:0002298	Cranial motor neurons	NA	motor neuron	CL:0000100	Enhancer activity assay; Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation	GWAS; eQTL analysis	Luciferase reporter assay, qRT-PCR; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_02220	2020	31658410	A distal enhancer that directs Otx2 expression in the retinal pigment epithelium and neuroretina	Homo sapiens	hg19	chr14	57230000	57232400	NA	OTX2	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	Transgenic mouse embryo carrying human enhancer	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay	VISTA enhancer screen; Hi-C; DNase hypersensitivity analysis	Transgenic reporter assay; LacZ reporter assay; Transgenic mouse enhancer assay
E_02221	2014	25209250	A regulatory network controls nephrocan expression and midgut patterning	Mus musculus	mm10	chr10	52388022	52388224	Rara	Nepn	Enhancer	Active	Normal	NA	NA	NA	NA	NA	P19	CVCL_2153	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; EMSA/gel-shift assay
E_02222	2014	25209250	A regulatory network controls nephrocan expression and midgut patterning	Mus musculus	mm10	chr10	52388022	52388224	Sox17	Nepn	Enhancer	Active	Normal	NA	NA	NA	NA	NA	P19	CVCL_2153	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; EMSA/gel-shift assay
E_02223	2012	22253448	Role of runt-related transcription factor 3 (RUNX3) in transcription regulation of natural cytotoxicity receptor 1 (NCR1/NKp46), an activating natural killer (NK) cell receptor	Homo sapiens	hg19	chr19	55412800	55414400	RUNX3	NCR1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	NK-92	CVCL_2142	natural killer cell	CL:0000623	Cis-regulatory activity assay; TF binding assay; transcription-factor perturbation assay	NA	Luciferase reporter assay; deletion mapping; motif mutagenesis; EMSA/DNA-binding assay; RUNX dominant-negative assay; RUNX3 overexpression; RT-PCR; Western blot
E_02224	2022	36243007	Transcription factor RORα enforces stability of the Th17 cell effector program by binding to a Rorc cis-regulatory element	Mus musculus	mm39	chr3	94294960	94295960	Rora	Rorc	Enhancer	Active	Normal	NA	NA	NA	small intestine	UBERON:0002108	transgenic Rorc reporter mice	NA	T-helper 17 cell	CL:0000899	Rorc +11-kb/CNS11 enhancer occupancy by RORα/RORγt; in vivo enhancer-reporter deletion and lineage-maintenance validation	RNA-seq; ATAC-seq; RORα ChIP-seq; RORγt ChIP-seq	Transgenic Rorc reporter; +11-kb enhancer deletion reporter; Rora conditional deletion; RORE CRISPR editing; Flow cytometry; ChIP-qPCR; RT-qPCR; EAE/peripheral inflammatory challenge
E_02225	2022	36243007	Transcription factor RORα enforces stability of the Th17 cell effector program by binding to a Rorc cis-regulatory element	Mus musculus	mm39	chr3	94294960	94295960	Rorc	Rorc	Enhancer	Active	Normal	NA	NA	NA	small intestine	UBERON:0002108	transgenic Rorc reporter mice	NA	T-helper 17 cell	CL:0000899	Rorc +11-kb/CNS11 enhancer occupancy by RORα/RORγt; in vivo enhancer-reporter deletion and lineage-maintenance validation	RNA-seq; ATAC-seq; RORα ChIP-seq; RORγt ChIP-seq	Transgenic Rorc reporter; +11-kb enhancer deletion reporter; Rora conditional deletion; RORE CRISPR editing; Flow cytometry; ChIP-qPCR; RT-qPCR; EAE/peripheral inflammatory challenge
E_02226	2022	36243007	Transcription factor RORα enforces stability of the Th17 cell effector program by binding to a Rorc cis-regulatory element	Mus musculus	mm39	chr3	94294960	94295960	Rora	Rorc	Enhancer	Active	Normal	NA	NA	NA	small intestine	UBERON:0002108	in vitro 2D2tg Th17 cells	NA	T-helper 17 cell	CL:0000899	Rorc CNS11/+11-kb cis-regulatory element; RORα occupancy; in vivo enhancer-reporter deletion and lineage-maintenance validation; exact 1001-bp CNS11 interval independently validated by PMID 41739921	RNA-seq; ATAC-seq; RORα ChIP-seq; RORγt ChIP-seq	BAC/transgenic Rorc reporter; +11-kb element deletion reporter; Rora conditional deletion; RORE CRISPR editing; ChIP-qPCR; RT-qPCR; Flow cytometry; EAE/peripheral inflammatory challenge
E_02227	2022	36243007	Transcription factor RORα enforces stability of the Th17 cell effector program by binding to a Rorc cis-regulatory element	Mus musculus	mm39	chr3	94294960	94295960	Rora	Rorc	Enhancer	Active	Normal	NA	NA	NA	small intestine	UBERON:0002108	transgenic Rorc reporter mice	NA	T-helper 17 cell	CL:0000899	Rorc CNS11/+11-kb cis-regulatory element; RORα occupancy; in vivo enhancer-reporter deletion and lineage-maintenance validation; exact 1001-bp CNS11 interval independently validated by PMID 41739921	RNA-seq; ATAC-seq; RORα ChIP-seq; RORγt ChIP-seq	BAC/transgenic Rorc reporter; +11-kb element deletion reporter; Rora conditional deletion; RORE CRISPR editing; ChIP-qPCR; RT-qPCR; Flow cytometry; EAE/peripheral inflammatory challenge
E_02228	2022	36243007	Transcription factor RORα enforces stability of the Th17 cell effector program by binding to a Rorc cis-regulatory element	Mus musculus	mm39	chr3	94294960	94295960	Rorc	Rorc	Enhancer	Active	Normal	NA	NA	NA	small intestine	UBERON:0002108	in vitro 2D2tg Th17 cells	NA	T-helper 17 cell	CL:0000899	Rorc CNS11/+11-kb cis-regulatory element; RORγt occupancy/feed-forward regulation; in vivo enhancer-reporter deletion and lineage-maintenance validation; exact 1001-bp CNS11 interval independently validated by PMID 41739921	RNA-seq; ATAC-seq; RORα ChIP-seq; RORγt ChIP-seq	BAC/transgenic Rorc reporter; +11-kb element deletion reporter; Rora conditional deletion; RORE CRISPR editing; ChIP-qPCR; RT-qPCR; Flow cytometry; EAE/peripheral inflammatory challenge
E_02229	2022	36243007	Transcription factor RORα enforces stability of the Th17 cell effector program by binding to a Rorc cis-regulatory element	Mus musculus	mm39	chr3	94294960	94295960	Rorc	Rorc	Enhancer	Active	Normal	NA	NA	NA	small intestine	UBERON:0002108	transgenic Rorc reporter mice	NA	T-helper 17 cell	CL:0000899	Rorc CNS11/+11-kb cis-regulatory element; RORγt occupancy/feed-forward regulation; in vivo enhancer-reporter deletion and lineage-maintenance validation; exact 1001-bp CNS11 interval independently validated by PMID 41739921	RNA-seq; ATAC-seq; RORα ChIP-seq; RORγt ChIP-seq	BAC/transgenic Rorc reporter; +11-kb element deletion reporter; Rora conditional deletion; RORE CRISPR editing; ChIP-qPCR; RT-qPCR; Flow cytometry; EAE/peripheral inflammatory challenge
E_02230	2017	28045957	Normal Levels of Sox9 Expression in the Developing Mouse Testis Depend on the TES/TESCO Enhancer, but This Does Not Act Alone	Mus musculus	mm10	chr11	112634637	112637797	Sry	Sox9	Enhancer	Active	Normal	NA	NA	NA	testis	UBERON:0000473	Sertoli cells	NA	Sertoli cell	CL:0000216	Enhancer activity assay; Functional perturbation assay; TF binding assay; Endogenous enhancer perturbation; In vivo functional validation	RNA-seq	CRISPR knockout; RT-qPCR, Immunofluorescence; ChIP-qPCR; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_02231	2012	22253448	Role of runt-related transcription factor 3 (RUNX3) in transcription regulation of natural cytotoxicity receptor 1 (NCR1/NKp46), an activating natural killer (NK) cell receptor	Homo sapiens	hg19	chr19	55417234	55417304	RUNX1	NCR1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	NK-92	CVCL_2142	natural killer cell	CL:0000623	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Luciferase reporter assay; RUNX-site mutagenesis; EMSA; ChIP-qPCR; RT-qPCR; RT-PCR; Western blot
E_02232	2024	38228888	An ancient polymorphic regulatory region within the BDNF gene associated with obesity modulates anxiety-like behaviour in mice and humans	Mus musculus	mm39	chr2	109689202	109690258	NA	Bdnf	Enhancer	Active	Normal	NA	NA	NA	amygdala	UBERON:0001876	Mouse amygdala tissue	NA	mouse amygdala cell	NA	Enhancer activity assay; Functional perturbation assay	RNA-seq; eQTL analysis	CRISPR knockout, qRT-PCR; Transgenic reporter assay; CRISPR-Cas9
E_02233	2024	38228888	An ancient polymorphic regulatory region within the BDNF gene associated with obesity modulates anxiety-like behaviour in mice and humans	Mus musculus	mm10	chr2	109689202	109690258	NA	Bdnf-as	Enhancer	Active	Disease	obesity	MONDO:0011122	DOID:9970	amygdala	UBERON:0001876	Female BE5.1KO mouse amygdala tissue	NA	NA	NA	Functional perturbation assay; Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation; Target-gene expression assay; In vivo phenotypic validation	eQTL analysis; GWAS	CRISPR-Cas9 BE5.1 deletion; qRT-PCR; PCR genotyping; Sanger sequencing; CRISPR off-target validation; Elevated zero maze; Marble-burying test; Diazepam rescue; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_02234	2023	37345431	Identification and functional validation of an enhancer variant in the 9p21.3 locus associated with glaucoma risk and elevated expression of p16INK4a	Homo sapiens	hg19	chr9	21980404	21981404	YY1	CDKN2A	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	HEK293	CVCL_0045	embryonic kidney cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Luciferase reporter assay; EMSA; ChIP-qPCR; RT-qPCR
E_02235	2015	26501517	Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements	Homo sapiens	hg19	chr11	5301600	5302400	TRIM28	HBE1	Enhancer	Repressed	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay	NA	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02236	2015	26501517	Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements	Homo sapiens	hg19	chr11	5301600	5302400	TRIM28	HBG1	Enhancer	Repressed	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay	NA	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02237	2015	26501517	Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements	Homo sapiens	hg19	chr11	5301600	5302400	TRIM28	HBG2	Enhancer	Repressed	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay	NA	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02238	2017	28045957	Normal Levels of Sox9 Expression in the Developing Mouse Testis Depend on the TES/TESCO Enhancer, but This Does Not Act Alone	Mus musculus	mm10	chr11	112769652	112770944	Sox9	Sox9	Enhancer	Active	Normal	NA	NA	NA	testis	UBERON:0000473	primary XY fetal gonadal somatic cells	NA	Sertoli cell precursor	NA	In vivo enhancer loss-of-function; developmental enhancer assay	NA	CRISPR-Cas9 TESCO deletion; qRT-PCR; Immunofluorescence; histology; gonadal phenotyping; CRISPR-Cas9
E_02239	2017	28045957	Normal Levels of Sox9 Expression in the Developing Mouse Testis Depend on the TES/TESCO Enhancer, but This Does Not Act Alone	Mus musculus	mm10	chr11	112769652	112770944	Sry	Sox9	Enhancer	Active	Normal	NA	NA	NA	testis	UBERON:0000473	primary XY fetal gonadal somatic cells	NA	Sertoli cell precursor	NA	In vivo enhancer loss-of-function; developmental enhancer assay	NA	CRISPR-Cas9 TESCO deletion; qRT-PCR; Immunofluorescence; histology; gonadal phenotyping; CRISPR-Cas9
E_02240	2014	25209250	A regulatory network controls nephrocan expression and midgut patterning	Mus musculus	mm10	chr10	52386564	52388864	NA	Nepn	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	transient transgenic mouse embryos	NA	endodermal cell	CL:0000223	In vivo functional validation; Promoter/enhancer-driven transgenic reporter assay	NA	2.3-kb Nepn upstream-region LacZ transgenic reporter assay; whole-mount staining; In vivo phenotyping
E_02241	2020	31658410	A distal enhancer that directs Otx2 expression in the retinal pigment epithelium and neuroretina	Mus musculus	mm10	chr14	48799494	48801489	NA	Otx2	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	E11.5 mouse embryo	NA	NA	NA	Enhancer activity assay; In vivo enhancer validation	VISTA enhancer screen; comparative genomics	Transgenic reporter assay; LacZ reporter assay; Immunohistochemistry; Transgenic mouse enhancer assay
E_02242	2023	37345431	Identification and functional validation of an enhancer variant in the 9p21.3 locus associated with glaucoma risk and elevated expression of p16INK4a	Homo sapiens	hg38	chr9	22050310	22054084	YY1	CDKN2A	Enhancer	Repressed	Disease	glaucoma	MONDO:0005041	DOID:1686	eye	UBERON:0000970	IMR-90	CVCL_0347	fibroblast	CL:0000057	TF binding assay; Disease-variant functional analysis; Allele-specific regulatory-element activity assay; Repressor-function assay	GWAS fine-mapping; ENCODE/epigenomic integration; GWAS	Dual-luciferase reporter; EMSA; YY1 ChIP-qPCR; allele-specific binding; RT-qPCR
E_02243	2023	37345431	Identification and functional validation of an enhancer variant in the 9p21.3 locus associated with glaucoma risk and elevated expression of p16INK4a	Homo sapiens	hg38	chr9	22050310	22054084	YY1	CDKN2A	Enhancer	Repressed	Disease	glaucoma	MONDO:0005041	DOID:1686	eye	UBERON:0000970	human neural stem cells	NA	neural stem cell	CL:0000047	TF binding assay; Disease-variant functional analysis; Allele-specific regulatory-element activity assay; Repressor-function assay	GWAS fine-mapping; ENCODE/epigenomic integration; GWAS	Dual-luciferase reporter; EMSA; YY1 ChIP-qPCR; allele-specific binding; RT-qPCR; senescence-related assays
E_02244	2023	37345431	Identification and functional validation of an enhancer variant in the 9p21.3 locus associated with glaucoma risk and elevated expression of p16INK4a	Homo sapiens	hg38	chr9	22050310	22054084	YY1	CDKN2A	Enhancer	Repressed	Disease	glaucoma	MONDO:0005041	DOID:1686	eye	UBERON:0000970	MCF-7	CVCL_0031	epithelial assay cell	NA	TF binding assay; Allele-specific regulatory-element activity assay; Repressor-function assay	GWAS fine-mapping; ENCODE/epigenomic integration	Dual-luciferase reporter; EMSA; YY1 ChIP-qPCR; allele-specific binding; RT-qPCR
E_02245	2013	24014243	The control of hematopoietic stem cell maintenance, self-renewal, and differentiation by Mysm1-mediated epigenetic regulation	Mus musculus	mm10	chr5	107680655	107682655	Gata2	Gfi1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Hematopoietic Cell,B Cell,T Cell	NA	T cell	CL:0000084	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_02246	2013	24014243	The control of hematopoietic stem cell maintenance, self-renewal, and differentiation by Mysm1-mediated epigenetic regulation	Mus musculus	mm10	chr5	107680655	107682655	Runx1	Gfi1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Hematopoietic Cell,B Cell,T Cell	NA	T cell	CL:0000084	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_02247	2012	22253448	Role of runt-related transcription factor 3 (RUNX3) in transcription regulation of natural cytotoxicity receptor 1 (NCR1/NKp46), an activating natural killer (NK) cell receptor	Mus musculus	mm10	chr7	4340200	4340800	Runx3	Ncr1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	mouse NK cells	NA	natural killer cell	CL:0000623	Cis-regulatory activity assay; conserved regulatory-element analysis; transcription-factor expression assay	Comparative sequence conservation analysis	Reporter assay; RT-PCR; Western blot; RUNX perturbation analysis
E_02248	2023	37506691	High-throughput functional dissection of noncoding SNPs with biased allelic enhancer activity for insulin resistance-relevant phenotypes	Homo sapiens	hg38	chr2	226125612	226127012	NA	IRS1	Enhancer	Active	Normal	NA	NA	NA	adipose tissue	UBERON:0001013	Human Preadipocyte	NA	preadipocyte	CL:0002334	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis	STARR-seq, Hi-C; RNA-seq; STARR-seq; GWAS	qRT-PCR, and ChIP-qPCR; Allele-specific reporter assay
E_02249	2022	36163279	Population-level variation in enhancer expression identifies disease mechanisms in the human brain	Homo sapiens	hg38	chr15	89400200	89400500	NA	ABHD2	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Neural Progenitor Cells (NPCs)	NA	neural progenitor cell	CL:0011020	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis	RNA-seq; ATAC-seq; ChIP-seq, Hi-C; eQTL analysis	CRISPRi, qRT-PCR
E_02250	2022	36163279	Population-level variation in enhancer expression identifies disease mechanisms in the human brain	Homo sapiens	hg38	chr15	89400200	89400500	NA	KIF7	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Neural Progenitor Cells (NPCs)	NA	neural progenitor cell	CL:0011020	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis	RNA-seq; ATAC-seq; ChIP-seq, Hi-C; eQTL analysis	CRISPRi, qRT-PCR
E_02251	2018	29903739	Tbx20 Is Required in Mid-Gestation Cardiomyocytes and Plays a Central Role in Atrial Development	Homo sapiens	hg19	chr15	96725740	96737960	TBX20	NR2F2	Enhancer	Active	Disease	Congenital Heart Disease	NA	DOID:1682	heart	UBERON:0000948	E11.5 Heart	NA	cardiac muscle cell	CL:0000746	Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq; Hi-C	ChIP-qPCR/ChIP
E_02252	2025	40301309	Drug-induced cis-regulatory elements in human hepatocytes affect molecular phenotypes associated with adverse reactions	Homo sapiens	hg38	chr2	233745300	233745811	NR1I2	UGT1A1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	ShP51 (PXR-expressing HepG2 derivative)	NA	hepatocyte-like cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	CAGE; PXR/NR1I2 ChIP-seq (reprocessed primary human hepatocytes)	CRISPR/Cas9-mediated enhancer deletion; Luciferase reporter assay; qRT-PCR; genotyping PCR; DNA sequencing
E_02253	2025	40301309	Drug-induced cis-regulatory elements in human hepatocytes affect molecular phenotypes associated with adverse reactions	Homo sapiens	hg38	chr2	233756747	233757190	NR1I2	UGT1A1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	ShP51 (PXR-expressing HepG2 derivative)	NA	hepatocyte-like cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	CAGE; PXR/NR1I2 ChIP-seq (reprocessed primary human hepatocytes)	CRISPR/Cas9-mediated enhancer deletion; Luciferase reporter assay; qRT-PCR; genotyping PCR; DNA sequencing
E_02254	2024	38378865	Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease	Homo sapiens	hg38	chr9	137494462	137494862	GATA4	COL5A1	Enhancer	Active	Normal	NA	NA	NA	endometrium	UBERON:0001295	1390C1	CVCL_UP48	endometrial stromal cell	NA	CRISPR interference (CRISPRi)	lentiSTARR-seq, lentiMPRA, scATAC-seq; MPRA; whole-genome sequencing	RT-qPCR; FACS; EMSA; Reporter assay
E_02255	2024	38378865	Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease	Homo sapiens	hg38	chr9	137494462	137494862	SMAD3	COL5A1	Enhancer	Active	Normal	NA	NA	NA	endometrium	UBERON:0001295	1390C1	CVCL_UP48	endometrial stromal cell	NA	CRISPR interference (CRISPRi)	lentiSTARR-seq, lentiMPRA, scATAC-seq; MPRA; whole-genome sequencing	RT-qPCR; FACS; EMSA; Reporter assay
E_02256	2024	38378865	Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease	Homo sapiens	hg38	chr9	137494462	137494862	SRF	COL5A1	Enhancer	Active	Normal	NA	NA	NA	endometrium	UBERON:0001295	1390C1	CVCL_UP48	endometrial stromal cell	NA	CRISPR interference (CRISPRi)	lentiSTARR-seq, lentiMPRA, scATAC-seq; MPRA; whole-genome sequencing	RT-qPCR; FACS; EMSA; Reporter assay
E_02257	2024	38378865	Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease	Homo sapiens	hg38	chr9	137494462	137494862	TBX20	COL5A1	Enhancer	Active	Normal	NA	NA	NA	endometrium	UBERON:0001295	1390C1	CVCL_UP48	endometrial stromal cell	NA	CRISPR interference (CRISPRi)	lentiSTARR-seq, lentiMPRA, scATAC-seq; MPRA; whole-genome sequencing	RT-qPCR; FACS; EMSA; Reporter assay
E_02258	2024	38378865	Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease	Homo sapiens	hg38	chr9	137494462	137494862	THRA	COL5A1	Enhancer	Active	Normal	NA	NA	NA	endometrium	UBERON:0001295	1390C1	CVCL_UP48	endometrial stromal cell	NA	CRISPR interference (CRISPRi)	lentiSTARR-seq, lentiMPRA, scATAC-seq; MPRA; whole-genome sequencing	RT-qPCR; FACS; EMSA; Reporter assay
E_02259	2022	35653119	EWS::FLI1 and HOXD13 Control Tumor Cell Plasticity in Ewing Sarcoma	Homo sapiens	hg19	chr2	176265000	176270000	EWSR1::FLI1	HOXD13	Enhancer	Active	Disease	Ewing sarcoma	MONDO:0012817	DOID:3369	bone tissue	UBERON:0002481	A673	NA	Ewing sarcoma cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; CUT&RUN; RNA-seq; HiChIP; CITE-seq	ChIP-qPCR; CRISPRi; RT-qPCR; Western blot; Flow cytometry
E_02260	2022	35653119	EWS::FLI1 and HOXD13 Control Tumor Cell Plasticity in Ewing Sarcoma	Homo sapiens	hg19	chr2	176265000	176270000	EWSR1::FLI1	HOXD13	Enhancer	Active	Disease	Ewing sarcoma	MONDO:0012817	DOID:3369	bone tissue	UBERON:0002481	CHLA10	NA	Ewing sarcoma cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; CUT&RUN; RNA-seq; HiChIP; CITE-seq	ChIP-qPCR; CRISPRi; RT-qPCR; Western blot; Flow cytometry
E_02261	2022	35653119	EWS::FLI1 and HOXD13 Control Tumor Cell Plasticity in Ewing Sarcoma	Homo sapiens	hg19	chr2	176265000	176270000	EWSR1::FLI1	HOXD13	Enhancer	Active	Disease	Ewing sarcoma	MONDO:0012817	DOID:3369	bone tissue	UBERON:0002481	TC32	NA	Ewing sarcoma cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; CUT&RUN; RNA-seq; HiChIP; CITE-seq	ChIP-qPCR; CRISPRi; RT-qPCR; Western blot; Flow cytometry
E_02262	2015	25487574	MyoR modulates cardiac conduction by repressing Gata4	Mus musculus	mm10	chr11	98979280	98979880	Msc	Gjd3	Enhancer	Repressed	Normal	NA	NA	NA	heart	UBERON:0000948	COS-7	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR; Western blot
E_02263	2015	25487574	MyoR modulates cardiac conduction by repressing Gata4	Mus musculus	mm10	chr11	98979280	98979880	Nkx2-5	Gjd3	Enhancer	Repressed	Normal	NA	NA	NA	heart	UBERON:0000948	COS-7	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR; Western blot
E_02264	2015	25487574	MyoR modulates cardiac conduction by repressing Gata4	Mus musculus	mm10	chr11	98979280	98979880	Tbx5	Gjd3	Enhancer	Repressed	Normal	NA	NA	NA	heart	UBERON:0000948	COS-7	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR; Western blot
E_02265	2020	32321991	The interdependence of mammary-specific super-enhancers and their native promoters facilitates gene activation during pregnancy	Mus musculus	mm10	chr11	10070908	10071400	Nfib	Wap	Enhancer	Active	Normal	NA	NA	NA	mammary gland	UBERON:0001911	Primary Mouse Mammary Epithelial	NA	mouse mammary epithelial cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	CRISPR knockout; CRISPRi; RT-qPCR
E_02266	2020	32321991	The interdependence of mammary-specific super-enhancers and their native promoters facilitates gene activation during pregnancy	Mus musculus	mm10	chr11	10070908	10071400	Nr3c1	Wap	Enhancer	Active	Normal	NA	NA	NA	mammary gland	UBERON:0001911	Primary Mouse Mammary Epithelial	NA	mouse mammary epithelial cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	CRISPR knockout; CRISPRi; RT-qPCR
E_02267	2020	32321991	The interdependence of mammary-specific super-enhancers and their native promoters facilitates gene activation during pregnancy	Mus musculus	mm10	chr11	10070908	10071400	Stat5a	Wap	Enhancer	Active	Normal	NA	NA	NA	mammary gland	UBERON:0001911	Primary Mouse Mammary Epithelial	NA	mouse mammary epithelial cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	CRISPR knockout; CRISPRi; RT-qPCR
E_02268	2020	32321991	The interdependence of mammary-specific super-enhancers and their native promoters facilitates gene activation during pregnancy	Mus musculus	mm10	chr11	10077283	10077800	Nfib	Wap	Enhancer	Active	Normal	NA	NA	NA	mammary gland	UBERON:0001911	Primary Mouse Mammary Epithelial	NA	mouse mammary epithelial cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	CRISPR knockout; CRISPRi; RT-qPCR
E_02269	2020	32321991	The interdependence of mammary-specific super-enhancers and their native promoters facilitates gene activation during pregnancy	Mus musculus	mm10	chr11	10077283	10077800	Nr3c1	Wap	Enhancer	Active	Normal	NA	NA	NA	mammary gland	UBERON:0001911	Primary Mouse Mammary Epithelial	NA	mouse mammary epithelial cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	CRISPR knockout; CRISPRi; RT-qPCR
E_02270	2020	32321991	The interdependence of mammary-specific super-enhancers and their native promoters facilitates gene activation during pregnancy	Mus musculus	mm10	chr11	10077283	10077800	Stat5a	Wap	Enhancer	Active	Normal	NA	NA	NA	mammary gland	UBERON:0001911	Primary Mouse Mammary Epithelial	NA	mouse mammary epithelial cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	CRISPR knockout; CRISPRi; RT-qPCR
E_02271	2020	32321991	The interdependence of mammary-specific super-enhancers and their native promoters facilitates gene activation during pregnancy	Mus musculus	mm10	chr11	10081501	10082508	Nfib	Wap	Enhancer	Active	Normal	NA	NA	NA	mammary gland	UBERON:0001911	Primary Mouse Mammary Epithelial	NA	mouse mammary epithelial cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	CRISPR knockout; CRISPRi; RT-qPCR
E_02272	2020	32321991	The interdependence of mammary-specific super-enhancers and their native promoters facilitates gene activation during pregnancy	Mus musculus	mm10	chr11	10081501	10082508	Nr3c1	Wap	Enhancer	Active	Normal	NA	NA	NA	mammary gland	UBERON:0001911	Primary Mouse Mammary Epithelial	NA	mouse mammary epithelial cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	CRISPR knockout; CRISPRi; RT-qPCR
E_02273	2020	32321991	The interdependence of mammary-specific super-enhancers and their native promoters facilitates gene activation during pregnancy	Mus musculus	mm10	chr11	10081501	10082508	Stat5a	Wap	Enhancer	Active	Normal	NA	NA	NA	mammary gland	UBERON:0001911	Primary Mouse Mammary Epithelial	NA	mouse mammary epithelial cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	CRISPR knockout; CRISPRi; RT-qPCR
E_02274	2020	32321991	The interdependence of mammary-specific super-enhancers and their native promoters facilitates gene activation during pregnancy	Mus musculus	mm10	chr11	10070908	10082508	Nfib	Wap	Enhancer	Active	Normal	NA	NA	NA	mammary gland	UBERON:0001911	Primary Mouse Mammary Epithelial	NA	mouse mammary epithelial cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	CRISPR knockout; CRISPRi; RT-qPCR
E_02275	2020	32321991	The interdependence of mammary-specific super-enhancers and their native promoters facilitates gene activation during pregnancy	Mus musculus	mm10	chr11	10070908	10082508	Nr3c1	Wap	Enhancer	Active	Normal	NA	NA	NA	mammary gland	UBERON:0001911	Primary Mouse Mammary Epithelial	NA	mouse mammary epithelial cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	CRISPR knockout; CRISPRi; RT-qPCR
E_02276	2020	32321991	The interdependence of mammary-specific super-enhancers and their native promoters facilitates gene activation during pregnancy	Mus musculus	mm10	chr11	10070908	10082508	Stat5a	Wap	Enhancer	Active	Normal	NA	NA	NA	mammary gland	UBERON:0001911	Primary Mouse Mammary Epithelial	NA	mouse mammary epithelial cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	CRISPR knockout; CRISPRi; RT-qPCR
E_02277	2018	29903739	Tbx20 Is Required in Mid-Gestation Cardiomyocytes and Plays a Central Role in Atrial Development	Homo sapiens	hg19	chr15	93405000	93406000	TBX20	NR2F2	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	hiPSC-CMs	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin-state profiling	ChIP-seq; RNA-seq; ChIP-seq	qRT-PCR, and ChIP-qPCR; ChIP
E_02278	2017	27869826	Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking	Homo sapiens	hg19	chr11	2219531	2239062	NA	IGF2	Super-enhancer	Active	Disease	Lung Cancer	NA	DOID:1324	lung	UBERON:0002048	HCC-15	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq; 4C-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_02279	2025	40301309	Drug-induced cis-regulatory elements in human hepatocytes affect molecular phenotypes associated with adverse reactions	Homo sapiens	hg38	chr11	76772927	76773266	NA	TSKU	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hepatocytes	NA	hepatocyte	CL:0000182	Disease-variant functional analysis; Super-enhancer activity assay	CAGE; GWAS	CRISPR knockout
E_02280	2025	40301309	Drug-induced cis-regulatory elements in human hepatocytes affect molecular phenotypes associated with adverse reactions	Homo sapiens	hg38	chr2	233764355	233764676	NR1I2	UGT1A1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary hepatocytes	NA	hepatocyte	CL:0000182	Enhancer activity assay; Disease-variant functional analysis	CAGE; ChIP-seq; CAGE; GWAS	Luciferase reporter assay
E_02281	2015	25487574	MyoR modulates cardiac conduction by repressing Gata4	Mus musculus	mm10	chr14	63196014	63196614	Msc	Gata4	Enhancer	Repressed	Normal	NA	NA	NA	heart	UBERON:0000948	Cx30.2+ Cells	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR; Western blot
E_02282	2023	37217546	Nicotinamide N-methyltransferase (NNMT) regulates the glucocorticoid signaling pathway during the early phase of adipogenesis	Mus musculus	mm10	chr9	48605113	48605195	Cebpb	Nnmt	Enhancer	Active	Disease	obesity	MONDO:0011122	DOID:9970	adipose tissue	UBERON:0001013	3T3-L1	CVCL_0123	preadipocyte	CL:0002334	Enhancer activity assay; TF binding assay; Endogenous enhancer perturbation	RNA-seq	Luciferase reporter assay; ChIP-qPCR, qRT-PCR; CRISPR-Cas9 endogenous deletion/editing
E_02283	2023	37217546	Nicotinamide N-methyltransferase (NNMT) regulates the glucocorticoid signaling pathway during the early phase of adipogenesis	Mus musculus	mm10	chr9	48606327	48606478	Cebpb	Nnmt	Enhancer	Active	Disease	obesity	MONDO:0011122	DOID:9970	adipose tissue	UBERON:0001013	3T3-L1	CVCL_0123	preadipocyte	CL:0002334	Enhancer activity assay; TF binding assay; Endogenous enhancer perturbation	RNA-seq	Luciferase reporter assay; ChIP-qPCR, qRT-PCR; CRISPR-Cas9 endogenous deletion/editing
E_02284	2022	34859522	The enhancer rare germline variation rs548071605 contributes to lung cancer development	Homo sapiens	hg38	chr22	30195717	30197444	RELA	LIF	Enhancer	Active	Disease	lung carcinoma	MONDO:0005138	DOID:3905	lung	UBERON:0002048	A-549	CVCL_0023	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; In vivo functional validation	ChIP-seq	Luciferase reporter assay; ChIP-qPCR; Xenograft/xenotransplant
E_02285	2022	35349489	FOXK2 promotes ovarian cancer stemness by regulating the unfolded protein response pathway	Homo sapiens	hg38	chr17	64082103	64082506	FOXK2	ERN1	Enhancer	Active	Disease	ovarian carcinoma	MONDO:0005140	DOID:4001	ovary	UBERON:0000992	OVCAR-5	CVCL_1628	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Endogenous enhancer perturbation	ChIP-seq; RNA-seq; ATAC-seq	ChIP-qPCR, CRISPR-dCas9, qRT-PCR; Western blot; CRISPR-Cas9 endogenous deletion/editing; ChIP
E_02286	2022	36263180	HDAC5-mediated Smad7 silencing through MEF2A is critical for fibroblast activation and hypertrophic scar formation	Homo sapiens	hg38	chr18	48949564	48951076	MEF2A	SMAD7	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Huh-7	CVCL_0336	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; In vivo functional validation	NA	Luciferase reporter assay; ChIP-qPCR; Luciferase reporter assay; ChIP-qPCR; ChIP; In vivo phenotyping; Reporter assay
E_02287	2020	31685980	Zfp422 promotes skeletal muscle differentiation by regulating EphA7 to induce appropriate myoblast apoptosis	Mus musculus	mm10	chr4	28176897	28177065	NA	Epha7	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	Primary mouse myoblasts	NA	myoblast	CL:0000056	Enhancer activity assay; Functional perturbation assay	ChIP-seq; RNA-seq	ChIP-PCR; Luciferase reporter assay; CRISPR-Cas9 knockout; RT-qPCR; Western blot
E_02288	2020	32293525	Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection	Homo sapiens	hg19	chr11	5246600	5247600	NA	HBB	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	HEK293T	CVCL_0063	embryonic kidney cell	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	ChIP-seq; RNA-seq; QHR-4C	CRISPR Knock-in
E_02289	2019	30760518	YY1 Complex Promotes Quaking Expression via Super-Enhancer Binding during EMT of Hepatocellular Carcinoma	Homo sapiens	hg19	chr6	163826086	163833600	YY1	QKI	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	PLC/PRF/5	CVCL_0485	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; In vivo functional validation	ChIP-seq; RNA-seq	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot; In vivo phenotyping
E_02290	2015	26423156	CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis	Homo sapiens	hg19	chr5	148785000	148815000	NA	NKX2-5	Super-enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	Cardiac Progenitor Cell	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; Histology/immunostaining
E_02291	2020	31685980	Zfp422 promotes skeletal muscle differentiation by regulating EphA7 to induce appropriate myoblast apoptosis	Mus musculus	mm10	chr4	28176897	28177065	Zfp422	Epha7	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	Satellite cells	NA	satellite cell	NA	Enhancer activity assay; Functional perturbation assay	ChIP-seq; RNA-seq	ChIP-PCR; Luciferase reporter assay; CRISPR-Cas9 knockout; RT-qPCR; Western blot
E_02292	2024	39210046	YY1-controlled regulatory connectivity and transcription are influenced by the cell cycle	Mus musculus	mm10	chr4	140235012	140235389	Yy1	Rcc2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Mouse erythroblast cell	NA	erythroblast	CL:0000765	Functional perturbation assay; Chromatin interaction assay	ChIP-seq, Micro-C; RNA-seq; TT-seq	ChIP-qPCR; Western blot; RT-qPCR
E_02293	2024	39210046	YY1-controlled regulatory connectivity and transcription are influenced by the cell cycle	Mus musculus	mm10	chr4	140385104	140385471	Yy1	Padi3	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Mouse erythroblast cell	NA	erythroblast	CL:0000765	Functional perturbation assay; Chromatin interaction assay	ChIP-seq, Micro-C; RNA-seq; TT-seq	ChIP-qPCR; Western blot; RT-qPCR
E_02294	2023	37641131	SMC3 epigenetic silencing regulates Rab27a expression and drives pancreatic cancer progression	Homo sapiens	hg38	chr15	55288865	55289335	NA	RAB27A	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	MIA PaCa-2	CVCL_0428	pancreatic carcinoma epithelial cell	NA	Enhancer activity assay; Chromatin architectural-protein binding assay; Endogenous functional perturbation assay	Public chromatin-conformation data; SMC3 ChIP-seq integration; TCGA methylation/expression analysis	SMC3 ChIP-qPCR; orientation-independent luciferase assay; CRISPR/Cas9 enhancer targeting; RT-qPCR; Western blot
E_02295	2023	37641131	SMC3 epigenetic silencing regulates Rab27a expression and drives pancreatic cancer progression	Homo sapiens	hg38	chr15	55288865	55289335	NA	RAB27A	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	MIA PaCa-2	CVCL_0428	pancreatic carcinoma epithelial cell	NA	Enhancer activity assay; Chromatin architectural-protein binding assay; Endogenous functional perturbation assay	Public chromatin-conformation data; SMC3 ChIP-seq integration; TCGA methylation/expression analysis	SMC3 ChIP-qPCR; Luciferase reporter assay; combined CRISPR/Cas9 enhancer targeting; RT-qPCR; Western blot
E_02296	2023	37641131	SMC3 epigenetic silencing regulates Rab27a expression and drives pancreatic cancer progression	Homo sapiens	hg38	chr15	55288865	55289335	NA	RAB27A	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	MIA PaCa-2	CVCL_0428	pancreatic carcinoma epithelial cell	NA	Enhancer activity assay; Chromatin architectural-protein binding assay; Endogenous functional perturbation assay	Public chromatin-conformation data; SMC3 ChIP-seq integration; TCGA methylation/expression analysis	SMC3 ChIP-qPCR; Luciferase reporter assay; CRISPR/Cas9 enhancer targeting; RT-qPCR; Western blot
E_02297	2020	32060133	A TGF-β- and p63-Responsive Enhancer Regulates IFN-κ Expression in Human Keratinocytes	Homo sapiens	hg19	chr9	27519197	27520919	TP63	IFNK	Enhancer	Active	Normal	NA	NA	NA	skin	UBERON:0002097	Normal human keratinocytes	NA	keratinocyte	CL:0000312	Enhancer activity assay; Functional perturbation assay	ChIP-seq; ENCODE epigenomic profiling	Luciferase reporter assay; enhancer deletion analysis; siRNA knockdown; ChIP-qPCR; qRT-PCR; Western blot
E_02298	2020	32060133	A TGF-β- and p63-Responsive Enhancer Regulates IFN-κ Expression in Human Keratinocytes	Homo sapiens	hg19	chr9	27519197	27520919	SMAD3	IFNK	Enhancer	Active	Normal	NA	NA	NA	skin	UBERON:0002097	Normal human keratinocytes	NA	keratinocyte	CL:0000312	Enhancer activity assay; Functional perturbation assay	ChIP-seq; ENCODE epigenomic profiling	Luciferase reporter assay; EMSA; siRNA knockdown; ChIP-qPCR; qRT-PCR; Western blot
E_02299	2020	32060133	A TGF-β- and p63-Responsive Enhancer Regulates IFN-κ Expression in Human Keratinocytes	Homo sapiens	hg19	chr9	27519197	27520919	SMAD4	IFNK	Enhancer	Active	Normal	NA	NA	NA	skin	UBERON:0002097	Normal human keratinocytes	NA	keratinocyte	CL:0000312	Enhancer activity assay; Functional perturbation assay	ChIP-seq; ENCODE epigenomic profiling	Luciferase reporter assay; EMSA; siRNA knockdown; ChIP-qPCR; qRT-PCR; Western blot
E_02300	2020	32060133	A TGF-β- and p63-Responsive Enhancer Regulates IFN-κ Expression in Human Keratinocytes	Homo sapiens	hg19	chr9	27519197	27520919	TFAP2C	IFNK	Enhancer	Active	Normal	NA	NA	NA	skin	UBERON:0002097	Normal human keratinocytes	NA	keratinocyte	CL:0000312	Enhancer activity assay; Functional perturbation assay	ChIP-seq; ENCODE epigenomic profiling	Luciferase reporter assay; EMSA; siRNA knockdown; ChIP-qPCR; qRT-PCR; Western blot
E_02301	2015	25651906	Wnt3a signal pathways activate MyoD expression by targeting cis-elements inside and outside its distal enhancer	Mus musculus	mm10	chr7	46351197	46355693	Wnt3a	Myod1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	C2C12	CVCL_0188	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR; Western blot
E_02302	2011	20952403	Chromatin and DNA methylation dynamics during retinoic acid-induced RET gene transcriptional activation in neuroblastoma cells	Homo sapiens	hg19	chr10	43569015	43569494	RARA	RET	Enhancer	Active	Disease	neuroblastoma	MONDO:0005072	DOID:769	NA	NA	SK-N-BE	NA	neuroblastoma cell line	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; DNA methylation assay	DNA methylation profiling	Luciferase reporter assay; ChIP-qPCR; bisulfite sequencing; Sequenom MassARRAY; pyrosequencing; qRT-PCR; siRNA knockdown
E_02303	2022	35849129	Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer-promoter interactions	Homo sapiens	hg38	chr11	5225000	5226000	NA	HBG1	Enhancer	Active	Disease	cervical cancer	MONDO:0002974	DOID:4362	uterine cervix	UBERON:0000002	HeLa	CVCL_0030	malignant cell	CL:0001064	Functional perturbation assay	CUT&RUN	CRISPR knockout; CRISPRi; RT-qPCR; 3C-RT-qPCR; Western blot
E_02304	2022	35849129	Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer-promoter interactions	Homo sapiens	hg38	chr11	5225000	5226000	NA	HBG1	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:0081088	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Functional perturbation assay	CUT&RUN	CRISPR knockout; CRISPRi; RT-qPCR; 3C-RT-qPCR; Western blot
E_02305	2022	35849129	Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer-promoter interactions	Homo sapiens	hg38	chr11	5225000	5226000	NA	HBG1	Enhancer	Active	Disease	osteosarcoma	MONDO:0009807	DOID:3347	bone element	UBERON:0001474	SaOS-2	CVCL_0548	osteosarcoma cell	NA	Functional perturbation assay	CUT&RUN	CRISPR knockout; CRISPRi; RT-qPCR; 3C-RT-qPCR; Western blot
E_02306	2022	35849129	Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer-promoter interactions	Homo sapiens	hg38	chr11	5225000	5226000	NA	HBG1	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	HEK293	CVCL_0045	embryonic kidney cell	NA	Functional perturbation assay	CUT&RUN	CRISPR knockout; CRISPRi; RT-qPCR; 3C-RT-qPCR; Western blot
E_02307	2015	25651906	Wnt3a signal pathways activate MyoD expression by targeting cis-elements inside and outside its distal enhancer	Mus musculus	mm10	chr7	46366985	46368584	Pax7	Myod1	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Enhancer activity assay; TF binding assay; Functional cis-element perturbation assay	NA	Stable and transient luciferase reporter assays; Wnt3a stimulation; Pax3/Pax7-site deletion; Pax7 ChIP-qPCR; RT-qPCR; ChIP
E_02308	2022	35849129	Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer-promoter interactions	Homo sapiens	hg38	chr11	17710000	17711000	NA	MYOD1	Enhancer	Active	Disease	cervical cancer	MONDO:0002974	DOID:4362	uterine cervix	UBERON:0000002	HeLa	CVCL_0030	malignant cell	CL:0001064	Functional perturbation assay	NA	CRISPR knockout; CRISPRi; RT-qPCR
E_02309	2022	35849129	Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer-promoter interactions	Homo sapiens	hg38	chr11	17710000	17711000	NA	MYOD1	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:0081088	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Functional perturbation assay	NA	CRISPR knockout; CRISPRi; RT-qPCR
E_02310	2022	35849129	Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer-promoter interactions	Homo sapiens	hg38	chr6	31130000	31131000	NA	POU5F1	Enhancer	Active	Disease	cervical cancer	MONDO:0002974	DOID:4362	uterine cervix	UBERON:0000002	HeLa	CVCL_0030	malignant cell	CL:0001064	Functional perturbation assay	NA	CRISPR knockout; CRISPRi; RT-qPCR
E_02311	2022	35849129	Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer-promoter interactions	Homo sapiens	hg38	chr6	31130000	31131000	NA	POU5F1	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:0081088	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Functional perturbation assay	NA	CRISPR knockout; CRISPRi; RT-qPCR
E_02312	2017	27920250	Renal Anemia Model Mouse Established by Transgenic Rescue with an Erythropoietin Gene Lacking Kidney-Specific Regulatory Elements	Mus musculus	mm10	chr5	137489416	137503216	NA	Epo	Enhancer	Active	Disease	anemia	MONDO:0002280	DOID:2355	kidney	UBERON:0002113	Renal EPO-producing (REP) cells	NA	fibroblast-like renal EPO-producing cell	NA	Enhancer activity assay; Functional perturbation assay; Gene expression assay; In vivo transgenic rescue assay	NA	BAC transgenic reporter assay; CURE deletion in BAC transgene; transgenic complementation rescue; GFP immunohistochemistry; qRT-PCR; plasma EPO ELISA
E_02313	2024	39210046	YY1-controlled regulatory connectivity and transcription are influenced by the cell cycle	Mus musculus	mm9	chr7	27930056	27930423	Yy1	NA	Enhancer	Active	Normal	NA	NA	NA	NA	NA	G1E-ER4	CVCL_D047	erythroblast	CL:0000765	Functional perturbation assay; TF binding assay	YY1 ChIP-seq	RT-qPCR
E_02314	2022	35849129	Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer-promoter interactions	Homo sapiens	hg38	chr11	17710000	17711000	NA	MYOD1	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	HEK293	CVCL_0045	embryonic kidney cell	NA	Functional perturbation assay	NA	CRISPR knockout; CRISPRi; RT-qPCR
E_02315	2022	35849129	Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer-promoter interactions	Homo sapiens	hg38	chr6	31130000	31131000	NA	POU5F1	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	HEK293	CVCL_0045	embryonic kidney cell	NA	Functional perturbation assay	NA	CRISPR knockout; CRISPRi; RT-qPCR
E_02316	2020	32060133	A TGF-β- and p63-Responsive Enhancer Regulates IFN-κ Expression in Human Keratinocytes	Homo sapiens	hg19	chr9	27519749	27519900	JUNB	IFNK	Enhancer	Active	Normal	NA	NA	NA	zone of skin	UBERON:0000014	Normal human keratinocytes	NA	keratinocyte	CL:0000312	Enhancer activity assay	RNA-seq; ChIP-seq	Luciferase reporter assay, EMSA; ChIP-qPCR, siRNA knockdown, qRT-PCR; Western blot
E_02317	2020	32060133	A TGF-β- and p63-Responsive Enhancer Regulates IFN-κ Expression in Human Keratinocytes	Homo sapiens	hg19	chr9	27520189	27520340	TFAP2A	IFNK	Enhancer	Active	Normal	NA	NA	NA	zone of skin	UBERON:0000014	Normal human keratinocytes	NA	keratinocyte	CL:0000312	Enhancer activity assay	RNA-seq; ChIP-seq	Luciferase reporter assay, EMSA; ChIP-qPCR, siRNA knockdown, qRT-PCR; Western blot
E_02318	2015	26423156	CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis	Homo sapiens	hg19	chr5	148781015	148839604	NA	CARMN	Super-enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	Human fetal cardiac precursor cells	NA	cardiac progenitor cell	NA	Functional perturbation assay; Super-enhancer profiling; lncRNA regulatory assay	RNA-seq; Super-enhancer chromatin-state profiling	GapmeR-mediated CARMN knockdown; RT-qPCR; RNA immunoprecipitation; SUZ12/EZH2 interaction assay; Cardiac differentiation assay
E_02319	2011	20952403	Chromatin and DNA methylation dynamics during retinoic acid-induced RET gene transcriptional activation in neuroblastoma cells	Homo sapiens	hg19	chr10	43569296	43572684	DNMT1	RET	Enhancer	Active	Normal	NA	NA	NA	NA	NA	SK-N-BE	NA	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02320	2011	20952403	Chromatin and DNA methylation dynamics during retinoic acid-induced RET gene transcriptional activation in neuroblastoma cells	Homo sapiens	hg19	chr10	43569296	43572684	EZH2	RET	Enhancer	Active	Normal	NA	NA	NA	NA	NA	SK-N-BE	NA	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02321	2011	20952403	Chromatin and DNA methylation dynamics during retinoic acid-induced RET gene transcriptional activation in neuroblastoma cells	Homo sapiens	hg19	chr10	43569045	43569456	PAX3	RET	Enhancer	Active	Normal	NA	NA	NA	NA	NA	SK-N-BE	NA	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02322	2011	20952403	Chromatin and DNA methylation dynamics during retinoic acid-induced RET gene transcriptional activation in neuroblastoma cells	Homo sapiens	hg19	chr10	43569045	43569456	SOX10	RET	Enhancer	Active	Normal	NA	NA	NA	NA	NA	SK-N-BE	NA	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02323	2015	25651906	Wnt3a signal pathways activate MyoD expression by targeting cis-elements inside and outside its distal enhancer	Mus musculus	mm10	chr7	46351197	46355694	NA	Myod1	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Enhancer activity assay; Chromatin binding assay; Wnt signaling perturbation assay	NA	Stable and transient luciferase reporter assays; Wnt3a stimulation; β-catenin ChIP-qPCR; pathway inhibitor/activator assays; RT-qPCR; ChIP
E_02324	2026	41608622	The castration-resistant prostate cancer-associated SNP rs11067228 facilitates neuroendocrine differentiation through an enhancer-mediated chromatin interaction with SRRM4	Homo sapiens	hg38	chr12	115092472	115096258	NA	SRRM4	Enhancer	Active	Normal	NA	NA	NA	connective tissue	UBERON:0002384	Pluripotent stem cell	NA	pluripotent stem cell	CL:0002248	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	4C-seq; RNA-seq	Luciferase reporter assay; CRISPR knockout; RT-qPCR
E_02325	2024	38992040	The transcriptional co-repressor Runx1t1 is essential for MYCN-driven neuroblastoma tumorigenesis	Homo sapiens	hg38	chr2	44294900	44295100	HAND2	NTRK1	Enhancer	Active	Disease	neuroblastoma	MONDO:0005072	DOID:769	adrenal gland	UBERON:0002369	Kelly	CVCL_2092	neuroblastoma cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; ATAC-seq	ChIP-qPCR; CRISPR knockout, qRT-PCR; Western blot
E_02326	2018	29695788	TFAP2C regulates transcription in human naive pluripotency by opening enhancers	Homo sapiens	hg19	chr6	31137269	31137697	TFAP2C	POU5F1	Enhancer	Repressed	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; ATAC-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_02327	2024	39294132	Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements	Homo sapiens	hg38	chr12	10123456	10124567	NA	ASIC1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation	scRNA-seq; ATAC-seq; ChIP-seq; single-cell RNA-seq; RNA-seq; pooled CRISPRa screen; CRISPR genetic screen	CRISPR knockout, CRISPRi, qRT-PCR; CRISPRa
E_02328	2024	39294132	Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements	Homo sapiens	hg38	chr6	34223538	34224727	NA	HMGA1	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Functional perturbation assay; Endogenous enhancer perturbation; Enhancer activation assay	Multiplex single-cell CRISPRa screen; scRNA-seq; singleton bulk RNA-seq validation; external ENCODE ATAC-seq; external ENCODE H3K27ac ChIP-seq; single-cell RNA-seq; RNA-seq; pooled CRISPRa screen; CRISPR genetic screen	Singleton CRISPRa perturbation; CRISPRa
E_02329	2019	30638865	LRH1-driven transcription factor circuitry for hepatocyte identity: Super-enhancer cistromic analysis	Mus musculus	mm10	chr11	97576234	97587534	Nr5a2	Nr5a2	Super-enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse hepatocytes	NA	hepatocyte	CL:0000182	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; RNA-seq	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot; ChIP; RT-qPCR
E_02330	2019	30638865	LRH1-driven transcription factor circuitry for hepatocyte identity: Super-enhancer cistromic analysis	Mus musculus	mm10	chr15	4422074	4423282	Nr5a2	Ppara	Super-enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse hepatocytes	NA	hepatocyte	CL:0000182	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; RNA-seq	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot; ChIP; RT-qPCR
E_02331	2019	30638865	LRH1-driven transcription factor circuitry for hepatocyte identity: Super-enhancer cistromic analysis	Mus musculus	mm10	chr2	171152164	171153352	Nr5a2	Rxra	Super-enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse hepatocytes	NA	hepatocyte	CL:0000182	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; RNA-seq	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot; ChIP; RT-qPCR
E_02332	2019	30638865	LRH1-driven transcription factor circuitry for hepatocyte identity: Super-enhancer cistromic analysis	Mus musculus	mm10	chr8	56652281	56653526	Nr5a2	Hnf4a	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Primary mouse hepatocytes	NA	hepatocyte	CL:0000182	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; RNA-seq	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot; ChIP; RT-qPCR
E_02333	2011	21549805	Differential regulation of sense and antisense promoter activity at the Csf1R locus in B cells by the transcription factor PAX5	Mus musculus	mm10	chr18	61108475	61108975	Sp3	Csf1r	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary B220+ bone marrow B cells	NA	B cell	CL:0000236	Functional perturbation assay; TF binding assay; Enhancer/antisense-promoter activity assay	NA	Luciferase reporter assay; EMSA; oligonucleotide pull-down; Sp3 knockout; RT-qPCR; ChIP
E_02334	2024	39294132	Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements	Homo sapiens	hg38	chr6	43210000	43211000	NA	HMGA1	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	iPSC-derived excitatory neurons	NA	excitatory neuron	NA	Enhancer activity assay; Functional perturbation assay	scRNA-seq; ATAC-seq; ChIP-seq; single-cell RNA-seq; RNA-seq	CRISPR knockout; CRISPRi, qRT-PCR; Lineage tracing
E_02335	2019	31519704	GATA3-Controlled Nucleosome Eviction Drives MYC Enhancer Activity in T-cell Development and Leukemia	Mus musculus	mm10	chr15	63255515	63256347	Gata3	Myc	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	thymus	UBERON:0002370	N-Me GATA-site mutant mouse DN3 thymocytes	NA	double negative thymocyte	CL:0002489	Endogenous TF-site perturbation; enhancer accessibility assay; enhancer-promoter interaction assay	ATAC-seq; ChIP-seq; 4C-seq	Endogenous GATA-site mutation; Flow cytometry; ChIP-qPCR; DNA FISH; nucleosome occupancy analysis; RT-qPCR
E_02336	2015	25704602	Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci	Homo sapiens	hg19	chr10	123099588	123100426	NA	FGFR2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	GMSM-K (human embry-onic oral epithelial cells)	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; Genetic-variant functional analysis	NA	Luciferase reporter assay; Reporter assay
E_02337	2013	24039598	An enhancer element harboring variants associated with systemic lupus erythematosus engages the TNFAIP3 promoter to influence A20 expression	Homo sapiens	hg19	chr6	138229810	138230149	NFKB1	TNFAIP3	Enhancer	Active	Disease	systemic lupus erythematosus	MONDO:0007915	DOID:9074	bone marrow	UBERON:0002371	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis	ChIP-seq; GWAS	Luciferase reporter assay, EMSA; ChIP-qPCR; EMSA; ChIP; 3C; shRNA knockdown; Reporter assay
E_02338	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm10	chr11	3217000	3222000	NA	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary Murine Erythroblasts	NA	erythroblast	CL:0000765	Enhancer activity assay; TF binding assay; In vivo functional validation	ChIP-chip	ChIP-qPCR; RT-qPCR; In vivo phenotyping
E_02339	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm10	chr11	3222000	3227000	NA	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary Murine Erythroblasts	NA	erythroblast	CL:0000765	Enhancer activity assay; TF binding assay; In vivo functional validation	ChIP-chip	ChIP-qPCR; RT-qPCR; In vivo phenotyping
E_02340	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm10	chr11	3231000	3236000	NA	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary Murine Erythroblasts	NA	erythroblast	CL:0000765	Enhancer activity assay; TF binding assay; In vivo functional validation	ChIP-chip	ChIP-qPCR; RT-qPCR; In vivo phenotyping
E_02341	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm10	chr11	3235000	3240000	NA	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary Murine Erythroblasts	NA	erythroblast	CL:0000765	Enhancer activity assay; TF binding assay; In vivo functional validation	ChIP-chip	ChIP-qPCR; RT-qPCR; In vivo phenotyping
E_02342	2013	24039598	An enhancer element harboring variants associated with systemic lupus erythematosus engages the TNFAIP3 promoter to influence A20 expression	Homo sapiens	hg19	chr6	138229810	138230149	NFKB1	TNFAIP3	Enhancer	Active	Disease	systemic lupus erythematosus	MONDO:0007915	DOID:9074	blood	UBERON:0000178	EBV-transformed lymphoblastoid cells from risk and non-risk donors	NA	B lymphoblastoid cell / monocyte-like cell	NA	Enhancer activity; TF binding; long-range enhancer-promoter looping	NA	EMSA; DNA-affinity pull-down and mass spectrometry; Luciferase reporter assay; ChIP-PCR; 3C; stimulation assays; RT-qPCR
E_02343	2013	24039598	An enhancer element harboring variants associated with systemic lupus erythematosus engages the TNFAIP3 promoter to influence A20 expression	Homo sapiens	hg19	chr6	138229810	138230149	RELA	TNFAIP3	Enhancer	Active	Disease	systemic lupus erythematosus	MONDO:0007915	DOID:9074	blood	UBERON:0000178	EBV-transformed lymphoblastoid cells from risk and non-risk donors	NA	B lymphoblastoid cell / monocyte-like cell	NA	Enhancer activity; TF binding; long-range enhancer-promoter looping	NA	EMSA; DNA-affinity pull-down and mass spectrometry; Luciferase reporter assay; ChIP-PCR; 3C; stimulation assays; RT-qPCR
E_02344	2013	24039598	An enhancer element harboring variants associated with systemic lupus erythematosus engages the TNFAIP3 promoter to influence A20 expression	Homo sapiens	hg19	chr6	138229810	138230149	REL	TNFAIP3	Enhancer	Active	Disease	systemic lupus erythematosus	MONDO:0007915	DOID:9074	blood	UBERON:0000178	EBV-transformed lymphoblastoid cells from risk and non-risk donors	NA	B lymphoblastoid cell / monocyte-like cell	NA	Enhancer activity; TF binding; long-range enhancer-promoter looping	NA	EMSA; DNA-affinity pull-down and mass spectrometry; Luciferase reporter assay; ChIP-PCR; 3C; stimulation assays; RT-qPCR
E_02345	2013	24039598	An enhancer element harboring variants associated with systemic lupus erythematosus engages the TNFAIP3 promoter to influence A20 expression	Homo sapiens	hg19	chr6	138229810	138230149	SATB1	TNFAIP3	Enhancer	Active	Disease	systemic lupus erythematosus	MONDO:0007915	DOID:9074	blood	UBERON:0000178	EBV-transformed lymphoblastoid cells from risk and non-risk donors	NA	B lymphoblastoid cell / monocyte-like cell	NA	Enhancer activity; chromatin organizer dependency; enhancer-promoter looping	NA	EMSA; DNA-affinity pull-down and mass spectrometry; Luciferase reporter assay; ChIP-PCR; 3C; SATB1 shRNA knockdown; RT-qPCR
E_02346	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Homo sapiens	hg18	chr16	94867	95418	GATA1	HBA1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human erythroblasts	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	ChIP-chip	ChIP-qPCR; In vivo phenotyping
E_02347	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Homo sapiens	hg18	chr16	94867	95418	GATA1	HBA2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human erythroblasts	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	ChIP-chip	ChIP-qPCR; In vivo phenotyping
E_02348	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Homo sapiens	hg18	chr16	94867	95418	NFE2	HBA1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human erythroblasts	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	ChIP-chip	ChIP-qPCR; In vivo phenotyping
E_02349	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Homo sapiens	hg18	chr16	94867	95418	NFE2	HBA2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human erythroblasts	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	ChIP-chip	ChIP-qPCR; In vivo phenotyping
E_02350	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Homo sapiens	hg18	chr16	94867	95418	TAL1	HBA1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human erythroblasts	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	ChIP-chip	ChIP-qPCR; In vivo phenotyping
E_02351	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Homo sapiens	hg18	chr16	94867	95418	TAL1	HBA2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human erythroblasts	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	ChIP-chip	ChIP-qPCR; In vivo phenotyping
E_02352	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Homo sapiens	hg18	chr16	103290	103957	GATA1	HBA1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human erythroblasts	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	ChIP-chip	ChIP-qPCR; In vivo phenotyping
E_02353	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Homo sapiens	hg18	chr16	103290	103957	GATA1	HBA2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human erythroblasts	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	ChIP-chip	ChIP-qPCR; In vivo phenotyping
E_02354	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Homo sapiens	hg18	chr16	103290	103957	NFE2	HBA1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human erythroblasts	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	ChIP-chip	ChIP-qPCR; In vivo phenotyping
E_02355	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Homo sapiens	hg18	chr16	103290	103957	NFE2	HBA2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human erythroblasts	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	ChIP-chip	ChIP-qPCR; In vivo phenotyping
E_02356	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Homo sapiens	hg18	chr16	103290	103957	TAL1	HBA1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human erythroblasts	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	ChIP-chip	ChIP-qPCR; In vivo phenotyping
E_02357	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Homo sapiens	hg18	chr16	103290	103957	TAL1	HBA2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human erythroblasts	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	ChIP-chip	ChIP-qPCR; In vivo phenotyping
E_02358	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Homo sapiens	hg18	chr16	109787	110385	GATA1	HBA1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human erythroblasts	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	ChIP-chip	ChIP-qPCR; In vivo phenotyping
E_02359	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Homo sapiens	hg18	chr16	109787	110385	GATA1	HBA2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human erythroblasts	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	ChIP-chip	ChIP-qPCR; In vivo phenotyping
E_02360	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Homo sapiens	hg18	chr16	109787	110385	TAL1	HBA1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human erythroblasts	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	ChIP-chip	ChIP-qPCR; In vivo phenotyping
E_02361	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Homo sapiens	hg18	chr16	109787	110385	TAL1	HBA2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human erythroblasts	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	ChIP-chip	ChIP-qPCR; In vivo phenotyping
E_02362	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Homo sapiens	hg18	chr16	132962	133361	GATA1	HBA1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human erythroblasts	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	ChIP-chip	ChIP-qPCR; In vivo phenotyping
E_02363	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Homo sapiens	hg18	chr16	132962	133361	GATA1	HBA2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human erythroblasts	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	ChIP-chip	ChIP-qPCR; In vivo phenotyping
E_02364	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Homo sapiens	hg18	chr16	132962	133361	TAL1	HBA1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human erythroblasts	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	ChIP-chip	ChIP-qPCR; In vivo phenotyping
E_02365	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Homo sapiens	hg18	chr16	132962	133361	TAL1	HBA2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human erythroblasts	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	ChIP-chip	ChIP-qPCR; In vivo phenotyping
E_02366	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm9	chr11	32145028	32146147	Gata1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary erythroid cells from humanized mouse	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	NA	ChIP-qPCR; In vivo phenotyping
E_02367	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm9	chr11	32145028	32146147	Gata1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary erythroid cells from humanized mouse	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	NA	ChIP-qPCR; In vivo phenotyping
E_02368	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm9	chr11	32145028	32146147	Nfe2	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary erythroid cells from humanized mouse	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	NA	ChIP-qPCR; In vivo phenotyping
E_02369	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm9	chr11	32145028	32146147	Nfe2	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary erythroid cells from humanized mouse	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	NA	ChIP-qPCR; In vivo phenotyping
E_02370	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm9	chr11	32145028	32146147	Tal1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary erythroid cells from humanized mouse	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	NA	ChIP-qPCR; In vivo phenotyping
E_02371	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm9	chr11	32145028	32146147	Tal1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary erythroid cells from humanized mouse	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	NA	ChIP-qPCR; In vivo phenotyping
E_02372	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm9	chr11	32150550	32151858	Gata1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary erythroid cells from humanized mouse	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	NA	ChIP-qPCR; In vivo phenotyping
E_02373	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm9	chr11	32150550	32151858	Gata1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary erythroid cells from humanized mouse	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	NA	ChIP-qPCR; In vivo phenotyping
E_02374	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm9	chr11	32150550	32151858	Nfe2	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary erythroid cells from humanized mouse	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	NA	ChIP-qPCR; In vivo phenotyping
E_02375	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm9	chr11	32150550	32151858	Nfe2	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary erythroid cells from humanized mouse	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	NA	ChIP-qPCR; In vivo phenotyping
E_02376	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm9	chr11	32150550	32151858	Tal1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary erythroid cells from humanized mouse	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	NA	ChIP-qPCR; In vivo phenotyping
E_02377	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm9	chr11	32150550	32151858	Tal1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary erythroid cells from humanized mouse	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	NA	ChIP-qPCR; In vivo phenotyping
E_02378	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm9	chr11	32156048	32157191	Gata1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary erythroid cells from humanized mouse	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	NA	ChIP-qPCR; In vivo phenotyping
E_02379	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm9	chr11	32156048	32157191	Gata1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary erythroid cells from humanized mouse	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	NA	ChIP-qPCR; In vivo phenotyping
E_02380	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm9	chr11	32156048	32157191	Tal1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary erythroid cells from humanized mouse	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	NA	ChIP-qPCR; In vivo phenotyping
E_02381	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm9	chr11	32156048	32157191	Tal1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary erythroid cells from humanized mouse	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	NA	ChIP-qPCR; In vivo phenotyping
E_02382	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm9	chr11	32165011	32165922	Gata1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary erythroid cells from humanized mouse	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	NA	ChIP-qPCR; In vivo phenotyping
E_02383	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm9	chr11	32165011	32165922	Gata1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary erythroid cells from humanized mouse	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	NA	ChIP-qPCR; In vivo phenotyping
E_02384	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm9	chr11	32165011	32165922	Nfe2	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary erythroid cells from humanized mouse	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	NA	ChIP-qPCR; In vivo phenotyping
E_02385	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm9	chr11	32165011	32165922	Nfe2	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary erythroid cells from humanized mouse	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	NA	ChIP-qPCR; In vivo phenotyping
E_02386	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm9	chr11	32165011	32165922	Tal1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary erythroid cells from humanized mouse	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	NA	ChIP-qPCR; In vivo phenotyping
E_02387	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm9	chr11	32165011	32165922	Tal1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary erythroid cells from humanized mouse	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	NA	ChIP-qPCR; In vivo phenotyping
E_02388	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm9	chr11	32168783	32169689	Gata1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary erythroid cells from humanized mouse	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	NA	ChIP-qPCR; In vivo phenotyping
E_02389	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm9	chr11	32168783	32169689	Gata1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary erythroid cells from humanized mouse	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	NA	ChIP-qPCR; In vivo phenotyping
E_02390	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm9	chr11	32168783	32169689	Tal1	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary erythroid cells from humanized mouse	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	NA	ChIP-qPCR; In vivo phenotyping
E_02391	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm9	chr11	32168783	32169689	Tal1	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary erythroid cells from humanized mouse	NA	erythroblast	CL:0000765	TF binding assay; In vivo functional validation; Chromatin modification assay	NA	ChIP-qPCR; In vivo phenotyping
E_02392	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Homo sapiens	hg19	chr16	163406	163841	GATA1	HBA1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human erythroid cells	NA	erythroblast	CL:0000765	In vivo functional validation; Locus-wide enhancer/chromatin-state mapping; TF occupancy analysis	Tiled genomic microarray chromatin profiling	ChIP; histone-modification profiling; expression analysis; In vivo phenotyping
E_02393	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Homo sapiens	hg19	chr16	163406	163841	NFE2	HBA2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human erythroid cells	NA	erythroblast	CL:0000765	In vivo functional validation; Locus-wide enhancer/chromatin-state mapping; TF occupancy analysis	Tiled genomic microarray chromatin profiling	ChIP; histone-modification profiling; expression analysis; In vivo phenotyping
E_02394	2019	31519704	GATA3-Controlled Nucleosome Eviction Drives MYC Enhancer Activity in T-cell Development and Leukemia	Homo sapiens	hg19	chr8	130180065	130180972	GATA3	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Jurkat E6.1	CVCL_0367	malignant cell	CL:0001064	Chromatin accessibility assay; TF-dependent enhancer mechanism; enhancer-promoter interaction assay	ATAC-seq; ChIP-seq; 4C-seq; proteomic DNA-pulldown profiling	GATA-site mutagenesis; ChIP-qPCR; reverse ChIP; DNA FISH; nucleosome assembly assay; RT-qPCR
E_02395	2013	24039598	An enhancer element harboring variants associated with systemic lupus erythematosus engages the TNFAIP3 promoter to influence A20 expression	Homo sapiens	hg19	chr6	138229810	138230149	NFKB1	TNFAIP3	Enhancer	Active	Disease	systemic lupus erythematosus	MONDO:0007915	DOID:9074	blood	UBERON:0000178	THP-1	CVCL_0006	monocyte	CL:0000576	Enhancer activity; TF binding; long-range enhancer-promoter looping	NA	EMSA; DNA-affinity pull-down and mass spectrometry; Luciferase reporter assay; ChIP-PCR; 3C; stimulation assays; RT-qPCR
E_02396	2013	24039598	An enhancer element harboring variants associated with systemic lupus erythematosus engages the TNFAIP3 promoter to influence A20 expression	Homo sapiens	hg19	chr6	138229810	138230149	RELA	TNFAIP3	Enhancer	Active	Disease	systemic lupus erythematosus	MONDO:0007915	DOID:9074	blood	UBERON:0000178	THP-1	CVCL_0006	monocyte	CL:0000576	Enhancer activity; TF binding; long-range enhancer-promoter looping	NA	EMSA; DNA-affinity pull-down and mass spectrometry; Luciferase reporter assay; ChIP-PCR; 3C; stimulation assays; RT-qPCR
E_02397	2013	24039598	An enhancer element harboring variants associated with systemic lupus erythematosus engages the TNFAIP3 promoter to influence A20 expression	Homo sapiens	hg19	chr6	138229810	138230149	REL	TNFAIP3	Enhancer	Active	Disease	systemic lupus erythematosus	MONDO:0007915	DOID:9074	blood	UBERON:0000178	THP-1	CVCL_0006	monocyte	CL:0000576	Enhancer activity; TF binding; long-range enhancer-promoter looping	NA	EMSA; DNA-affinity pull-down and mass spectrometry; Luciferase reporter assay; ChIP-PCR; 3C; stimulation assays; RT-qPCR
E_02398	2013	24039598	An enhancer element harboring variants associated with systemic lupus erythematosus engages the TNFAIP3 promoter to influence A20 expression	Homo sapiens	hg19	chr6	138229810	138230149	SATB1	TNFAIP3	Enhancer	Active	Disease	systemic lupus erythematosus	MONDO:0007915	DOID:9074	blood	UBERON:0000178	THP-1	CVCL_0006	monocyte	CL:0000576	Enhancer activity; chromatin organizer dependency; enhancer-promoter looping	NA	EMSA; DNA-affinity pull-down and mass spectrometry; Luciferase reporter assay; ChIP-PCR; 3C; SATB1 shRNA knockdown; RT-qPCR
E_02399	2013	24039598	An enhancer element harboring variants associated with systemic lupus erythematosus engages the TNFAIP3 promoter to influence A20 expression	Homo sapiens	hg19	chr6	138229810	138230149	NFKB1	TNFAIP3	Enhancer	Active	Disease	systemic lupus erythematosus	MONDO:0007915	DOID:9074	blood	UBERON:0000178	HEK293T	CVCL_0063	B lymphoblastoid cell / monocyte-like cell	NA	Enhancer activity; TF binding; long-range enhancer-promoter looping	NA	EMSA; DNA-affinity pull-down and mass spectrometry; Luciferase reporter assay; ChIP-PCR; 3C; stimulation assays; RT-qPCR
E_02400	2013	24039598	An enhancer element harboring variants associated with systemic lupus erythematosus engages the TNFAIP3 promoter to influence A20 expression	Homo sapiens	hg19	chr6	138229810	138230149	RELA	TNFAIP3	Enhancer	Active	Disease	systemic lupus erythematosus	MONDO:0007915	DOID:9074	blood	UBERON:0000178	HEK293T	CVCL_0063	B lymphoblastoid cell / monocyte-like cell	NA	Enhancer activity; TF binding; long-range enhancer-promoter looping	NA	EMSA; DNA-affinity pull-down and mass spectrometry; Luciferase reporter assay; ChIP-PCR; 3C; stimulation assays; RT-qPCR
E_02401	2013	24039598	An enhancer element harboring variants associated with systemic lupus erythematosus engages the TNFAIP3 promoter to influence A20 expression	Homo sapiens	hg19	chr6	138229810	138230149	REL	TNFAIP3	Enhancer	Active	Disease	systemic lupus erythematosus	MONDO:0007915	DOID:9074	blood	UBERON:0000178	HEK293T	CVCL_0063	B lymphoblastoid cell / monocyte-like cell	NA	Enhancer activity; TF binding; long-range enhancer-promoter looping	NA	EMSA; DNA-affinity pull-down and mass spectrometry; Luciferase reporter assay; ChIP-PCR; 3C; stimulation assays; RT-qPCR
E_02402	2013	24039598	An enhancer element harboring variants associated with systemic lupus erythematosus engages the TNFAIP3 promoter to influence A20 expression	Homo sapiens	hg19	chr6	138229810	138230149	SATB1	TNFAIP3	Enhancer	Active	Disease	systemic lupus erythematosus	MONDO:0007915	DOID:9074	blood	UBERON:0000178	HEK293T	CVCL_0063	B lymphoblastoid cell / monocyte-like cell	NA	Enhancer activity; chromatin organizer dependency; enhancer-promoter looping	NA	EMSA; DNA-affinity pull-down and mass spectrometry; Luciferase reporter assay; ChIP-PCR; 3C; SATB1 shRNA knockdown; RT-qPCR
E_02403	2015	25704602	Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci	Homo sapiens	hg19	chr17	54754755	54758235	NA	NOG	Enhancer	Active	Normal	NA	NA	NA	NA	NA	GMSM-K (human embry-onic oral epithelial cells)	NA	NA	NA	Enhancer activity assay; In vivo functional validation; Genetic-variant functional analysis	NA	Luciferase reporter assay; Reporter assay
E_02404	2015	25704602	Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci	Homo sapiens	hg19	chr17	54775600	54778000	NA	NOG	Enhancer	Active	Normal	NA	NA	NA	NA	NA	GMSM-K (human embry-onic oral epithelial cells)	NA	NA	NA	Enhancer activity assay; In vivo functional validation; Genetic-variant functional analysis	NA	Luciferase reporter assay; Reporter assay
E_02405	2019	31519704	GATA3-Controlled Nucleosome Eviction Drives MYC Enhancer Activity in T-cell Development and Leukemia	Homo sapiens	hg19	chr8	130180065	130180972	GATA3	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	primary T-ALL	NA	T-lineage lymphoblast/leukemia cell	NA	TF-dependent enhancer accessibility; leukemia initiation and maintenance	ATAC-seq; ChIP-seq; RNA-seq	GATA3 perturbation; enhancer accessibility assays; nucleosome occupancy analysis; leukemia initiation and maintenance assays
E_02406	2019	31519704	GATA3-Controlled Nucleosome Eviction Drives MYC Enhancer Activity in T-cell Development and Leukemia	Homo sapiens	hg19	chr8	130180065	130180972	GATA3	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	primary T-ALL	NA	T-lineage lymphoblast/leukemia cell	NA	TF-dependent enhancer accessibility; leukemia initiation and maintenance	ATAC-seq; ChIP-seq; RNA-seq	GATA3 perturbation; enhancer accessibility assays; nucleosome occupancy analysis; leukemia initiation and maintenance assays
E_02407	2019	31519704	GATA3-Controlled Nucleosome Eviction Drives MYC Enhancer Activity in T-cell Development and Leukemia	Homo sapiens	hg19	chr8	130180065	130180972	GATA3	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	human T-ALL cell models	NA	T-lineage lymphoblast/leukemia cell	NA	TF-dependent enhancer accessibility; leukemia initiation and maintenance	ATAC-seq; ChIP-seq; RNA-seq	GATA3 perturbation; enhancer accessibility assays; nucleosome occupancy analysis; leukemia initiation and maintenance assays
E_02408	2019	31519704	GATA3-Controlled Nucleosome Eviction Drives MYC Enhancer Activity in T-cell Development and Leukemia	Homo sapiens	hg19	chr8	130180065	130180972	GATA3	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	mouse T-ALL	NA	T-lineage lymphoblast/leukemia cell	NA	TF-dependent enhancer accessibility; leukemia initiation and maintenance	ATAC-seq; ChIP-seq; RNA-seq	GATA3 perturbation; enhancer accessibility assays; nucleosome occupancy analysis; leukemia initiation and maintenance assays
E_02409	2019	31519704	GATA3-Controlled Nucleosome Eviction Drives MYC Enhancer Activity in T-cell Development and Leukemia	Homo sapiens	hg19	chr8	130180065	130180972	GATA3	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	human T-ALL cell models	NA	T-lineage lymphoblast/leukemia cell	NA	TF-dependent enhancer accessibility; leukemia initiation and maintenance	ATAC-seq; ChIP-seq; RNA-seq	GATA3 perturbation; enhancer accessibility assays; nucleosome occupancy analysis; leukemia initiation and maintenance assays
E_02410	2019	31519704	GATA3-Controlled Nucleosome Eviction Drives MYC Enhancer Activity in T-cell Development and Leukemia	Homo sapiens	hg19	chr8	130180065	130180972	GATA3	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	mouse T-ALL	NA	T-lineage lymphoblast/leukemia cell	NA	TF-dependent enhancer accessibility; leukemia initiation and maintenance	ATAC-seq; ChIP-seq; RNA-seq	GATA3 perturbation; enhancer accessibility assays; nucleosome occupancy analysis; leukemia initiation and maintenance assays
E_02411	2011	21549805	Differential regulation of sense and antisense promoter activity at the Csf1R locus in B cells by the transcription factor PAX5	Mus musculus	mm10	chr18	61235500	61235837	Pax5	Csf1r	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	293T cyno BCMA	CVCL_UE53	pre-B cell	NA	Enhancer activity assay; TF binding assay	NA	Luciferase reporter assay; ChIP-qPCR
E_02412	2011	21549805	Differential regulation of sense and antisense promoter activity at the Csf1R locus in B cells by the transcription factor PAX5	Mus musculus	mm10	chr18	61099404	61099740	Pax5	Csf1r	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	B Cell	NA	B cell	CL:0000236	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_02413	2007	17715390	Tissue-specific histone modification and transcription factor binding in alpha globin gene expression	Mus musculus	mm10	chr11	3210000	3215000	NA	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary Murine Erythroblasts	NA	mouse erythroblast	NA	Enhancer activity assay; TF binding assay	ChIP-chip; microarray	ChIP-qPCR; RT-qPCR
E_02414	2015	25704602	Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci	Homo sapiens	hg19	chr17	54754755	54758235	NA	NOG	Enhancer	Active	Disease	orofacial cleft	MONDO:0000358	DOID:0050567	optic fissure	UBERON:0005412	patient DNA	NA	cranial neural crest/mesenchymal cell	NA	Targeted risk-locus sequencing; functional enhancer-variant validation	targeted high-depth sequencing of GWAS loci	allele-specific reporter; developmental/in vivo enhancer assays; variant functional testing
E_02415	2015	25704602	Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci	Homo sapiens	hg19	chr17	54775600	54778000	NA	NOG	Enhancer	Active	Disease	orofacial cleft	MONDO:0000358	DOID:0050567	optic fissure	UBERON:0005412	patient DNA	NA	cranial neural crest/mesenchymal cell	NA	Targeted risk-locus sequencing; functional enhancer-variant validation	targeted high-depth sequencing of GWAS loci	allele-specific reporter; developmental/in vivo enhancer assays; variant functional testing
E_02416	2015	25704602	Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci	Homo sapiens	hg19	chr10	123099588	123100426	NA	FGFR2	Enhancer	Active	Normal	NA	NA	NA	bone element	UBERON:0001474	MC3T3-E1	CVCL_0409	osteoblast	CL:0000062	Enhancer activity assay	NA	Luciferase reporter assay
E_02417	2015	25704602	Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci	Homo sapiens	hg19	chr17	54776294	54777215	NA	NOG	Enhancer	Active	Normal	NA	NA	NA	Palatal epithelium	UBERON:0006397	GMSM-K	CVCL_6A82	fibroblast	CL:0000057	Enhancer activity assay	NA	Luciferase reporter assay
E_02418	2015	25704602	Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci	Homo sapiens	hg19	chr17	54754755	54758235	NA	NOG	Enhancer	Active	Disease	orofacial cleft	MONDO:0000358	DOID:0050567	optic fissure	UBERON:0005412	embryonic neural-crest/craniofacial enhancer reporter models	NA	cranial neural crest/mesenchymal cell	NA	Targeted risk-locus sequencing; functional enhancer-variant validation	targeted high-depth sequencing of GWAS loci	allele-specific reporter; developmental/in vivo enhancer assays; variant functional testing
E_02419	2015	25704602	Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci	Homo sapiens	hg19	chr17	54775600	54778000	NA	NOG	Enhancer	Active	Disease	orofacial cleft	MONDO:0000358	DOID:0050567	optic fissure	UBERON:0005412	embryonic neural-crest/craniofacial enhancer reporter models	NA	cranial neural crest/mesenchymal cell	NA	Targeted risk-locus sequencing; functional enhancer-variant validation	targeted high-depth sequencing of GWAS loci	allele-specific reporter; developmental/in vivo enhancer assays; variant functional testing
E_02420	2025	40640362	Analysis of biased allelic enhancer activity of schizophrenia-linked common variants	Homo sapiens	hg38	chr3	136050468	136050668	NA	PCCB	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	HEK293	CVCL_0045	embryonic kidney cell	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	Hi-C; STARR-seq	Luciferase reporter assay; CRISPR knockout; RT-qPCR
E_02421	2024	39143563	Comprehensive network modeling approaches unravel dynamic enhancer-promoter interactions across neural differentiation	Homo sapiens	hg19	chr16	30669227	30670310	PAX6	PHKG2	Enhancer	Active	Normal	NA	NA	NA	neural tissue	UBERON:0003714	hESC-derived NPCs	NA	neural progenitor cell	CL:0011020	Enhancer activity assay; Functional perturbation assay; TF binding assay; Disease-variant functional analysis	RNA-seq; ChIP-seq; ATAC-seq; MPRA	TF overexpression assay; RT-qPCR, FIMO motif analysis, permutation test; Reporter assay
E_02422	2024	39143563	Comprehensive network modeling approaches unravel dynamic enhancer-promoter interactions across neural differentiation	Homo sapiens	hg19	chr19	17438298	17439337	PAX6	DDA1	Enhancer	Active	Normal	NA	NA	NA	neural tissue	UBERON:0003714	hESC-derived NPCs	NA	neural progenitor cell	CL:0011020	Enhancer activity assay; Functional perturbation assay; TF binding assay; Disease-variant functional analysis	RNA-seq; ChIP-seq; ATAC-seq; MPRA	TF overexpression assay; RT-qPCR, FIMO motif analysis, permutation test; Reporter assay
E_02423	2023	35930348	An enhancer variant associated with breast cancer susceptibility in Black women regulates TNFSF10 expression and antitumor immunity in triple-negative breast cancer	Homo sapiens	hg38	chr3	172549013	172551013	MYB	TNFSF10	Enhancer	Active	Disease	triple-negative breast carcinoma	MONDO:0005494	DOID:0060081	breast	UBERON:0000310	HCC1806	CVCL_1258	malignant cell	CL:0001064	TF binding assay; Enhancer variant functional assay; Genome editing assay	GWAS; eQTL analysis; ENCODE epigenomic data analysis	CRISPR-Cas9 HDR editing; EMSA; supershift assay; RT-qPCR; Western blot; apoptosis assay
E_02424	2023	37041138	Enhancer hijacking at the ARHGAP36 locus is associated with connective tissue to bone transformation	Homo sapiens	hg19	chr2	69342699	69343679	NA	ARHGAP36	Enhancer	Active	Normal	NA	NA	NA	connective tissue	UBERON:0002384	Primary fibroblasts	NA	fibroblast	CL:0000057	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Disease-variant functional analysis	Hi-C; RNA-seq; ChIP-seq	RT-qPCR; Western blot, Alizarin Red Staining
E_02425	2022	35831318	A SOX17-PDGFB signaling axis regulates aortic root development	Mus musculus	mm10	chr15	79850614	79850824	Sox17	Pdgfb	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	Mouse Cardiac Endothelial Cells (MCECs)	NA	cardiac endothelial cell	CL:0010008	Enhancer activity assay; TF binding assay; Endogenous enhancer perturbation; In vivo functional validation	ChIP-seq; RNA-seq	Luciferase reporter assay; ChIP-qPCR, qRT-PCR; Western blot; Mouse genetic deletion/knock-in
E_02426	2021	34145235	Coordination of two enhancers drives expression of olfactory trace amine-associated receptors	Mus musculus	mm10	chr10	23930200	23931190	NA	NA	Enhancer	Active	Normal	NA	NA	NA	olfactory epithelium	UBERON:0001997	Olfactory sensory neuron (OSN)	NA	olfactory sensory neuron	NA	Enhancer activity assay; In vivo endogenous enhancer deletion; Cis-regulation assay	ATAC-seq; RNA-seq; H3K9me3 ChIP-seq	CRISPR/Cas9 germline enhancer deletion; Transgenic reporter assay; RNA in situ hybridization; genetic cis/trans analysis
E_02427	2021	34145235	Coordination of two enhancers drives expression of olfactory trace amine-associated receptors	Mus musculus	mm10	chr10	23987501	23988362	NA	NA	Enhancer	Active	Normal	NA	NA	NA	olfactory epithelium	UBERON:0001997	Olfactory sensory neuron (OSN)	NA	olfactory sensory neuron	NA	Enhancer activity assay; In vivo endogenous enhancer deletion; Cis-regulation assay	ATAC-seq; RNA-seq; H3K9me3 ChIP-seq	CRISPR/Cas9 germline enhancer deletion; Transgenic reporter assay; RNA in situ hybridization; genetic cis/trans analysis
E_02428	2020	32551799	Genome-Wide Association Study: Functional Variant rs2076295 Regulates Desmoplakin Expression in Airway Epithelial Cells	Homo sapiens	hg19	chr6	7563220	7563274	NA	DSP	Enhancer	Active	Disease	idiopathic pulmonary fibrosis	MONDO:0800504	DOID:0050156	bronchus	UBERON:0002185	Primary normal human bronchial epithelial cells	NA	bronchial epithelial cell	CL:0002328	Disease-variant functional analysis; endogenous enhancer/regulatory-core deletion; CRISPRi; single-base editing; target-gene expression validation	GWAS/eQTL colocalization; RNA-seq; single-cell RNA-seq analysis	CRISPR/Cas9 55-bp regional deletion; CRISPR indel editing; CRISPRi; HDR/single-base editing; RT-qPCR; ddPCR; Sanger sequencing; Luciferase reporter assay
E_02429	2019	30770393	Lmx1a drives Cux2 expression in the cortical hem through activation of a conserved intronic enhancer	Mus musculus	mm10	chr5	135012000	135012856	Lmx1a	Cux2	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	Embryonic neural progenitor	NA	neural progenitor cell	CL:0011020	Enhancer activity assay; TF binding assay; In vivo functional validation	NA	Transgenic reporter assay; ChIP-qPCR; RT-qPCR; In vivo phenotyping
E_02430	2018	29453285	The distal upstream region of insulin-like growth factor-binding protein-1 enhances its expression in endometrial stromal cells during decidualization	Homo sapiens	hg19	chr7	45920458	45923258	FOXO1	IGFBP1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	hepatocyte	CL:0000182	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR; FAIRE
E_02431	2018	30107177	Cooperative Enhancer Activation by TLX1 and STAT5 Drives Development of NUP214-ABL1/TLX1-Positive T Cell Acute Lymphoblastic Leukemia	Homo sapiens	hg19	chr8	130180065	130180972	TLX1	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	NUP214-ABL1/TLX1-positive T-ALL cells	NA	T cell	CL:0000084	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; ATAC-seq; RNA-seq	TLX1 downregulation; STAT5 pathway inhibition; MYC perturbation; BET inhibition; gene-expression assay; cell-death assay
E_02432	2016	27852806	SBE6: a novel long-range enhancer involved in driving sonic hedgehog expression in neural progenitor cells	Mus musculus	mm10	chr5	28889688	28890461	Six3	Shh	Enhancer	Active	Normal	NA	NA	NA	nervous system	UBERON:0001016	Neural progenitor	NA	neural progenitor cell	CL:0011020	Enhancer activity assay; Functional perturbation assay; In vivo functional validation	ChIP-seq; RNA-seq	CRISPR knockout, Transgenic reporter assay; In vivo phenotyping
E_02433	2015	26303528	The DEK Oncoprotein Is a Critical Component of the EKLF/KLF1 Enhancer in Erythroid Cells	Mus musculus	mm10	chr8	87424785	87425735	Dek	Klf1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Mouse erythroid progenitor cells	NA	erythroid progenitor cell	CL:0000038	Enhancer activity assay; Functional perturbation assay; TF binding assay	RNA-seq	ChIP-qPCR, CRISPR knockout, shRNA knockdown; RT-qPCR; Western blot, EMSA, Transgenic reporter assay
E_02434	2011	21331042	Tbx6-dependent Sox2 regulation determines neural or mesodermal fate in axial stem cells	Mus musculus	mm10	chr3	34563695	34565695	Tbx6	Sox2	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Axial Stem Cell	NA	NA	NA	Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay	NA	EMSA/gel-shift assay; Transgenic/LacZ assay
E_02435	2017	28717659	Identification and characterization of variants and a novel 4 bp deletion in the regulatory region of SIX6, a risk factor for primary open-angle glaucoma	Homo sapiens	hg19	chr14	60973427	60975430	NA	SIX6	Enhancer	Active	Disease	Primary Open-Angle Glaucoma	NA	DOID:13550	NA	NA	Eye	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; Transgenic/LacZ assay
E_02436	2017	28905448	Myeloid Zinc Finger 1 and GA Binding Protein Co-Operate with Sox2 in Regulating the Expression of Yes-Associated Protein 1 in Cancer Cells	Homo sapiens	hg19	chr11	109985003	109985222	MZF1	YAP1	Enhancer	Active	Disease	osteosarcoma	MONDO:0009807	DOID:3347	NA	NA	Osteosarcoma Stem Cells	NA	malignant cell	CL:0001064	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_02437	2017	28905448	Myeloid Zinc Finger 1 and GA Binding Protein Co-Operate with Sox2 in Regulating the Expression of Yes-Associated Protein 1 in Cancer Cells	Homo sapiens	hg19	chr11	109985003	109985222	SOX2	YAP1	Enhancer	Active	Disease	osteosarcoma	MONDO:0009807	DOID:3347	NA	NA	Osteosarcoma Stem Cells	NA	malignant cell	CL:0001064	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_02438	2014	24415943	Deletion of a conserved cis-element in the Ifng locus highlights the role of acute histone acetylation in modulating inducible gene transcription	Mus musculus	mm39	chr10	118255061	118255451	Tbx21	Ifng	Enhancer	Active	Normal	NA	NA	NA	NA	NA	primary mouse CD4-positive T cells	NA	T helper 1 cell	CL:0000545	TF binding assay; Endogenous enhancer deletion assay; Epigenetic mechanism assay	DNase-seq/open-chromatin profiling; ChIP-chip	Conditional CNS-22 deletion; cytokine/TCR stimulation; histone H3/H4 acetylation ChIP; RNA polymerase II ChIP; RT-qPCR
E_02439	2014	24415943	Deletion of a conserved cis-element in the Ifng locus highlights the role of acute histone acetylation in modulating inducible gene transcription	Mus musculus	mm39	chr10	118255061	118255451	Runx3	Ifng	Enhancer	Active	Normal	NA	NA	NA	NA	NA	primary mouse CD4-positive T cells	NA	T helper 1 cell	CL:0000545	TF binding assay; Endogenous enhancer deletion assay; Epigenetic mechanism assay	DNase-seq/open-chromatin profiling; ChIP-chip	Conditional CNS-22 deletion; cytokine/TCR stimulation; histone H3/H4 acetylation ChIP; RNA polymerase II ChIP; RT-qPCR
E_02440	2014	24415943	Deletion of a conserved cis-element in the Ifng locus highlights the role of acute histone acetylation in modulating inducible gene transcription	Mus musculus	mm39	chr10	118255061	118255451	Stat4	Ifng	Enhancer	Active	Normal	NA	NA	NA	NA	NA	primary mouse CD4-positive T cells	NA	T helper 1 cell	CL:0000545	TF binding assay; Endogenous enhancer deletion assay; Epigenetic mechanism assay	DNase-seq/open-chromatin profiling; ChIP-chip	Conditional CNS-22 deletion; cytokine/TCR stimulation; histone H3/H4 acetylation ChIP; RNA polymerase II ChIP; RT-qPCR
E_02441	2020	32551799	Genome-Wide Association Study: Functional Variant rs2076295 Regulates Desmoplakin Expression in Airway Epithelial Cells	Homo sapiens	hg19	chr6	7563220	7563274	NA	DSP	Enhancer	Active	Disease	idiopathic pulmonary fibrosis	MONDO:0800504	DOID:0050156	bronchus	UBERON:0002185	16HBE14o-	CVCL_0112	bronchial epithelial cell	CL:0002328	Disease-variant functional analysis; endogenous enhancer/regulatory-core deletion; CRISPRi; single-base editing; target-gene expression validation	GWAS/eQTL colocalization; RNA-seq; single-cell RNA-seq analysis	CRISPR/Cas9 55-bp regional deletion; CRISPR indel editing; CRISPRi; HDR/single-base editing; RT-qPCR; ddPCR; Sanger sequencing; Luciferase reporter assay
E_02442	2011	20942803	The pancreatic islet β-cell-enriched transcription factor Pdx-1 regulates Slc30a8 gene transcription through an intronic enhancer	Mus musculus	mm10	chr15	52316013	52316633	Pdx1	Slc30a8	Enhancer	Active	Normal	NA	NA	NA	islet of Langerhans	UBERON:0000006	Beta-TC-3	CVCL_0172	pancreatic beta cell	CL:0000169	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Luciferase reporter assay; EMSA; ChIP; Site-directed mutagenesis
E_02443	2011	20942803	The pancreatic islet β-cell-enriched transcription factor Pdx-1 regulates Slc30a8 gene transcription through an intronic enhancer	Mus musculus	mm10	chr15	52316213	52316412	Pdx1	Slc30a8	Enhancer	Active	Normal	NA	NA	NA	islet of Langerhans	UBERON:0000006	Beta-TC-3	CVCL_0172	pancreatic beta cell	CL:0000169	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Luciferase reporter assay; EMSA; ChIP; Site-directed mutagenesis
E_02444	2017	28905448	Myeloid Zinc Finger 1 and GA Binding Protein Co-Operate with Sox2 in Regulating the Expression of Yes-Associated Protein 1 in Cancer Cells	Mus musculus	mm10	chr9	60714330	60714960	Gabpa	Yap1	Enhancer	Active	Disease	osteosarcoma	MONDO:0009807	DOID:3347	bone tissue	UBERON:0002481	mOS-482	NA	murine osteosarcoma cell	NA	Enhancer activity assay; TF binding assay	NA	Scanning mutagenesis; Luciferase reporter assay; EMSA/supershift assay; transcription-factor depletion; RT-qPCR; Western blot
E_02445	2017	28905448	Myeloid Zinc Finger 1 and GA Binding Protein Co-Operate with Sox2 in Regulating the Expression of Yes-Associated Protein 1 in Cancer Cells	Mus musculus	mm10	chr1	100900000	100900243	Mzf1	Yap1	Enhancer	Active	Disease	osteosarcoma	MONDO:0009807	DOID:3347	bone element	UBERON:0001474	TASH	CVCL_WT34	osteosarcoma cell	NA	Enhancer activity assay	NA	Luciferase reporter assay; EMSA; ChIP-qPCR; RT-qPCR; Western blot
E_02446	2011	20942803	The pancreatic islet β-cell-enriched transcription factor Pdx-1 regulates Slc30a8 gene transcription through an intronic enhancer	Mus musculus	mm10	chr15	52315678	52316298	Pdx1	Slc30a8	Enhancer	Active	Normal	NA	NA	NA	islet of Langerhans	UBERON:0000006	Beta-TC-3	CVCL_0172	pancreatic beta cell	CL:0000169	Intronic enhancer discovery; cell-type-specific reporter assay; direct TF-binding assay	Comparative VISTA conservation analysis	Dual-luciferase reporter assay; Pdx1 ChIP; EMSA; Pdx1-site mutagenesis; RT-qPCR; developmental immunostaining
E_02447	2017	28905448	Myeloid Zinc Finger 1 and GA Binding Protein Co-Operate with Sox2 in Regulating the Expression of Yes-Associated Protein 1 in Cancer Cells	Mus musculus	mm10	chr9	60714330	60714960	Sox2	Yap1	Enhancer	Active	Disease	osteosarcoma	MONDO:0009807	DOID:3347	bone tissue	UBERON:0002481	murine osteosarcoma cells	NA	murine osteosarcoma cell	NA	Enhancer activity assay; TF binding assay	NA	Luciferase/Venus reporter assay; Sox2-site mutagenesis; ChIP-PCR; Sox2 perturbation
E_02448	2025	40640362	Analysis of biased allelic enhancer activity of schizophrenia-linked common variants	Homo sapiens	hg38	chr8	10368745	10368945	NA	MSRA	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	HEK293	CVCL_0045	embryonic kidney cell	NA	Enhancer activity assay; Chromatin interaction assay	Hi-C; STARR-seq	Luciferase reporter assay
E_02449	2011	20942803	The pancreatic islet β-cell-enriched transcription factor Pdx-1 regulates Slc30a8 gene transcription through an intronic enhancer	Mus musculus	mm10	chr15	52153900	52154520	Pdx1	Slc30a8	Enhancer	Active	Normal	NA	NA	NA	pancreas	UBERON:0001264	NA	NA	pancreatic beta cell	CL:0000169	Enhancer activity assay; cell-type specificity assay; direct TF binding	NA	VISTA conservation; Luciferase reporter; orientation testing; EMSA; PDX1 ChIP; PDX1-site mutagenesis
E_02450	2011	20942803	The pancreatic islet β-cell-enriched transcription factor Pdx-1 regulates Slc30a8 gene transcription through an intronic enhancer	Mus musculus	mm10	chr15	52315878	52316077	Pdx1	Slc30a8	Enhancer	Active	Normal	NA	NA	NA	islet of Langerhans	UBERON:0000006	Beta-TC-3	CVCL_0172	pancreatic beta cell	CL:0000169	Enhancer-core dissection; TF-site mutagenesis; reporter assay	Comparative sequence conservation analysis	Dual-luciferase reporter assay; orientation test; Pdx1-site mutagenesis; EMSA
E_02451	2011	20942803	The pancreatic islet β-cell-enriched transcription factor Pdx-1 regulates Slc30a8 gene transcription through an intronic enhancer	Mus musculus	mm10	chr15	52315678	52316298	Pbx1	Slc30a8	Enhancer	Active	Normal	NA	NA	NA	pancreas	UBERON:0001264	Islet B-Cell	NA	pancreatic beta cell	CL:0000169	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_02452	2017	28717659	Identification and characterization of variants and a novel 4 bp deletion in the regulatory region of SIX6, a risk factor for primary open-angle glaucoma	Homo sapiens	hg19	chr14	60974427	60974430	NA	SIX6	Enhancer	Active	Disease	open-angle glaucoma	MONDO:0005338	DOID:1067	retina	UBERON:0000966	HEK293	CVCL_0045	embryonic kidney-derived transformed cell	NA	Enhancer variant functional assay	NA	Luciferase reporter assay; stable transgenic zebrafish enhancer assay; Sanger sequencing
E_02453	2017	28717659	Identification and characterization of variants and a novel 4 bp deletion in the regulatory region of SIX6, a risk factor for primary open-angle glaucoma	Homo sapiens	hg19	chr14	60974427	60974430	NA	SIX6	Enhancer	Active	Disease	open-angle glaucoma	MONDO:0005338	DOID:1067	eye	UBERON:0000970	HEK293	CVCL_0045	transformed embryonic kidney-derived cell	NA	Enhancer variant functional assay	NA	Luciferase reporter assay; transgenic zebrafish enhancer assay; Sequencing
E_02454	2011	20942803	The pancreatic islet β-cell-enriched transcription factor Pdx-1 regulates Slc30a8 gene transcription through an intronic enhancer	Mus musculus	mm10	chr15	52315678	52316298	Pdx1	Slc30a8	Enhancer	Active	Normal	NA	NA	NA	pancreas	UBERON:0001264	developing mouse pancreatic beta cells	NA	pancreatic beta cell	CL:0000169	Developmental expression correlation plus functionally validated enhancer A	NA	Immunofluorescence; RT-qPCR; enhancer reporter/ChIP evidence from same study
E_02455	2011	20942803	The pancreatic islet β-cell-enriched transcription factor Pdx-1 regulates Slc30a8 gene transcription through an intronic enhancer	Mus musculus	mm10	chr15	52159003	52159479	NA	Slc30a8	Enhancer	Active	Normal	NA	NA	NA	pancreas	UBERON:0001264	NA	NA	pancreatic beta cell	CL:0000169	Enhancer activity assay; cell-type comparison	NA	VISTA conservation; Luciferase reporter; orientation testing
E_02456	2011	20942803	The pancreatic islet β-cell-enriched transcription factor Pdx-1 regulates Slc30a8 gene transcription through an intronic enhancer	Mus musculus	mm10	chr15	52320781	52321257	NA	Slc30a8	Enhancer	Active	Normal	NA	NA	NA	islet of Langerhans	UBERON:0000006	Alpha-TC-6 / Beta-TC-3 comparison	NA	pancreatic endocrine cell	CL:0008024	Comparative intronic enhancer reporter assay	Comparative VISTA conservation analysis	Dual-luciferase reporter assay
E_02457	2011	20942803	The pancreatic islet β-cell-enriched transcription factor Pdx-1 regulates Slc30a8 gene transcription through an intronic enhancer	Mus musculus	mm10	chr15	52321116	52321592	NA	Slc30a8	Enhancer	Active	Normal	NA	NA	NA	islet of Langerhans	UBERON:0000006	Beta-TC-3	CVCL_0172	pancreatic beta cell	CL:0000169	Enhancer activity assay	NA	Luciferase reporter assay
E_02458	2011	20942803	The pancreatic islet β-cell-enriched transcription factor Pdx-1 regulates Slc30a8 gene transcription through an intronic enhancer	Mus musculus	mm10	chr15	52159003	52159479	NA	Slc30a8	Enhancer	Active	Normal	NA	NA	NA	pancreas	UBERON:0001264	NA	NA	pancreatic alpha cell	NA	Enhancer activity assay; cell-type comparison	NA	VISTA conservation; Luciferase reporter
E_02459	2011	20942803	The pancreatic islet β-cell-enriched transcription factor Pdx-1 regulates Slc30a8 gene transcription through an intronic enhancer	Mus musculus	mm10	chr15	52316013	52316633	NA	Slc30a8	Enhancer	Active	Normal	NA	NA	NA	islet of Langerhans	UBERON:0000006	alphaTC1 Clone 6	CVCL_B036	pancreatic alpha cell	NA	Enhancer activity assay	NA	Luciferase reporter assay
E_02460	2011	20942803	The pancreatic islet β-cell-enriched transcription factor Pdx-1 regulates Slc30a8 gene transcription through an intronic enhancer	Mus musculus	mm10	chr15	52321116	52321592	NA	Slc30a8	Enhancer	Active	Normal	NA	NA	NA	islet of Langerhans	UBERON:0000006	alphaTC1 Clone 6	CVCL_B036	pancreatic alpha cell	NA	Enhancer activity assay	NA	Luciferase reporter assay
E_02461	2026	40617410	Redistribution of super-enhancers promotes malignancy in human hepatocellular carcinoma	Homo sapiens	hg38	chr5	133050976	133051978	NA	HSPA4	Super-enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	HCCLM3	CVCL_6832	hepatocyte	CL:0000182	Functional perturbation assay; Endogenous enhancer perturbation; In vivo functional validation; Super-enhancer activity assay	H3K27ac ChIP-seq; RNA-seq	CRISPR-Cas9 deletion of SE-signal regulatory region; H3K27ac ChIP-qPCR; BRD4 ChIP-qPCR; RT-qPCR; Western blot; JQ1 treatment; colony formation assay; migration assay; xenograft assay; HSPA4 rescue assay; CRISPR-Cas9 endogenous deletion/editing; ChIP; Xenograft/xenotransplant
E_02462	2025	40070134	Increasing RB1 Expression by Targeting EZH2 in Triple-Negative Breast Cancer	Homo sapiens	hg19	chr13	48974891	48975426	NA	RB1	Enhancer	Active	Disease	triple-negative breast carcinoma	MONDO:0005494	DOID:0060081	breast	UBERON:0000310	HCC1806	CVCL_1258	malignant cell	CL:0001064	Enhancer functional perturbation assay	ATAC-seq	CRISPR-Cas9 enhancer knockout; RT-qPCR; Western blot; ChIP-qPCR; qPCR
E_02463	2025	40611281	LNP-enclosed NamiRNA inhibits pancreatic cancer proliferation and migration via dual pathways	Homo sapiens	hg38	chr12	6933000	6941000	NA	PTPN6	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	MIA PaCa-2	CVCL_0428	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; In vivo functional validation	ChIP-seq; RNA-seq	Luciferase reporter assay, CRISPR knockout; ChIP-qPCR, qRT-PCR; Western blot; In vivo phenotyping
E_02464	2024	38943090	A specific super-enhancer actuated by berberine regulates EGFR-mediated RAS-RAF1-MEK1/2-ERK1/2 pathway to induce nasopharyngeal carcinoma autophagy	Homo sapiens	hg38	chr7	54960823	54970827	NA	EGFR	Super-enhancer	Active	Disease	nasopharyngeal carcinoma	MONDO:0015459	DOID:9261	nasopharynx	UBERON:0001728	S18	CVCL_B0U9	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin-state profiling; In vivo functional validation	ChIP-seq; RNA-seq; RNA-seq; ChIP-seq	CRISPR knockout, qRT-PCR; Western blot; ChIP; In vivo phenotyping
E_02465	2023	37673892	A super-enhancer-regulated RNA-binding protein cascade drives pancreatic cancer	Homo sapiens	hg19	chr10	102880001	102881789	NA	HNRNPF	Super-enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	MIA PaCa-2	CVCL_0428	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; ATAC-seq; RNA-seq	CRISPR knockout, qRT-PCR; Western blot
E_02466	2022	35998583	Pancreas agenesis mutations disrupt a lead enhancer controlling a developmental enhancer cluster	Homo sapiens	hg19	chr10	23508400	23508721	PDX1	PTF1A	Enhancer	Active	Normal	NA	NA	NA	pancreas	UBERON:0001264	Pancreatic Multipotent Progenitor Cells (MPCs)	NA	pancreatic multipotent progenitor cell	NA	Enhancer activity assay; Functional perturbation assay	ChIP-seq; RNA-seq, scATAC-seq	CRISPR knockout, qRT-PCR; Immunofluorescence
E_02467	2022	35998583	Pancreas agenesis mutations disrupt a lead enhancer controlling a developmental enhancer cluster	Mus musculus	mm10	chr2	14492567	14492959	Pdx1	Ptf1a	Enhancer	Active	Normal	NA	NA	NA	pancreas	UBERON:0001264	Pancreatic Multipotent Progenitor Cells (MPCs)	NA	pancreatic multipotent progenitor cell	NA	Enhancer activity assay; Functional perturbation assay	ChIP-seq, scRNA-seq, scATAC-seq	CRISPR knockout, qRT-PCR; Immunofluorescence
E_02468	2020	32694829	Super-enhancer-driven metabolic reprogramming promotes cystogenesis in autosomal dominant polycystic kidney disease	Mus musculus	mm10	chr8	123455000	123472000	NA	Ampd3	Enhancer	Active	Disease	polycystic kidney disease	MONDO:0020642	DOID:0080322	kidney	UBERON:0002113	Pkd1-null tubule epithelial cells (PN)	NA	kidney epithelial cell	CL:0002518	Enhancer activity assay; Functional perturbation assay	ChIP-seq; RNA-seq; ATAC-seq	ChIP-qPCR; RT-qPCR; Western blot, CRISPR knockout, Flow Cytometry, Immunohistochemistry, HPLC
E_02469	2019	30664630	Enhancer hijacking activates oncogenic transcription factor NR4A3 in acinic cell carcinomas of the salivary glands	Homo sapiens	hg19	chr4	70849125	70849971	NR4A3	NR4A3	Enhancer	Active	Disease	salivary gland acinic cell carcinoma	MONDO:0006400	DOID:0050897	saliva-secreting gland	UBERON:0001044	AciCC primary tumor cells	NA	malignant cell	CL:0001064	Enhancer activity assay	ChIP-seq; RNA-seq; Hi-C; WGS	Luciferase reporter assay; FISH; RT-qPCR; Western blot
E_02470	2016	27863249	Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters	Homo sapiens	hg19	chr11	5241525	5251525	GATA1	HBB	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary erythroblasts	NA	erythroblast	CL:0000765	Enhancer activity assay; Chromatin interaction assay; Disease-variant functional analysis	ChIP-seq; ATAC-seq, Hi-C; Hi-C	Luciferase reporter assay; RT-qPCR
E_02471	2014	24788237	The identification of an ESCC susceptibility SNP rs920778 that regulates the expression of lncRNA HOTAIR via a novel intronic enhancer	Homo sapiens	hg19	chr12	54359946	54360613	NA	HOTAIR	Enhancer	Active	Disease	esophageal squamous cell carcinoma	MONDO:0005580	DOID:3748	esophagus	UBERON:0001043	KYSE-30	CVCL_1351	epithelial cell	CL:0000066	Enhancer activity assay; Disease-variant functional analysis; In vivo functional validation; Functional variant assay; Genetic association study	NA	Dual-luciferase reporter assay; Enhancer deletion mapping; rs920778 allele comparison; Genotyping; HOTAIR RT-qPCR; Allele-specific reporter assay; In vivo phenotyping; Reporter assay
E_02472	2011	21711161	Enhancer-blocking activity is associated with hypersensitive site V sequences in the human growth hormone locus control region	Homo sapiens	hg19	chr17	62028371	62028917	CTCF	GH1	Enhancer	Active	Normal	NA	NA	NA	pituitary gland	UBERON:0000007	HEK293	CVCL_0045	epithelial cell	CL:0000066	Functional perturbation assay; TF binding assay; In vivo functional validation; Enhancer-blocking assay	NA	Enhancer-blocking reporter assay; ChIP; CTCF RNA interference; DNA methylation analysis; In vivo phenotyping
E_02473	2020	32694829	Super-enhancer-driven metabolic reprogramming promotes cystogenesis in autosomal dominant polycystic kidney disease	Mus musculus	mm10	chr8	123455000	123472000	Cdk7	Ampd3	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	Pkd1-heterozygous renal tubular epithelial cells	NA	kidney tubular epithelial cell	NA	Enhancer activity assay; Functional perturbation assay	ChIP-seq; RNA-seq; ATAC-seq	ChIP-qPCR; RT-qPCR; Western blot
E_02474	2011	21711161	Enhancer-blocking activity is associated with hypersensitive site V sequences in the human growth hormone locus control region	Homo sapiens	hg19	chr17	62028371	62028917	YY1	GH1	Enhancer	Active	Normal	NA	NA	NA	pituitary gland	UBERON:0000007	HEK293	CVCL_0045	epithelial cell	CL:0000066	Functional perturbation assay; In vivo functional validation; Enhancer-blocking assay; TF association assay	NA	Enhancer-blocking reporter assay; ChIP; YY1 RNA interference; DNA methylation analysis; In vivo phenotyping
E_02475	2012	22877652	Androgen receptor repression of gonadotropin-releasing hormone gene transcription via enhancer 1	Mus musculus	mm10	chr14	67743318	67743610	Ar	Gnrh1	Enhancer	Repressed	Normal	NA	NA	NA	NA	NA	GT1-7	CVCL_0281	GnRH neuron	CL:0011111	Enhancer activity assay; TF binding assay; Functional cis-element perturbation assay	NA	Luciferase reporter assay; reporter truncation analysis; Site-directed mutagenesis; ChIP-qPCR; EMSA; AR overexpression; AR DNA-binding-domain mutant analysis; R1881 treatment
E_02476	2014	24788237	The identification of an ESCC susceptibility SNP rs920778 that regulates the expression of lncRNA HOTAIR via a novel intronic enhancer	Homo sapiens	hg19	chr12	54357811	54358445	NA	HOTAIR	Enhancer	Active	Disease	esophageal squamous cell carcinoma	MONDO:0005580	DOID:3748	NA	NA	KYSE-30,KESY-150,ESCC	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_02477	2011	21711161	Enhancer-blocking activity is associated with hypersensitive site V sequences in the human growth hormone locus control region	Homo sapiens	hg19	chr17	62028378	62028924	CTCF	GH1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HeLa	CVCL_0030	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_02478	2011	21711161	Enhancer-blocking activity is associated with hypersensitive site V sequences in the human growth hormone locus control region	Homo sapiens	hg19	chr17	62028378	62028924	YY1	GH1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HeLa	CVCL_0030	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_02479	2014	24788237	The identification of an ESCC susceptibility SNP rs920778 that regulates the expression of lncRNA HOTAIR via a novel intronic enhancer	Homo sapiens	hg19	chr12	54359232	54361232	NA	HOTAIR	Enhancer	Active	Disease	esophageal squamous cell carcinoma	MONDO:0005580	DOID:3748	esophagus	UBERON:0001043	ESCC cell lines and human esophageal tissue	NA	esophageal epithelial cell	NA	Disease-associated allele-specific enhancer validation	Case-control genotyping / genetic association	Luciferase reporter; allele-specific expression; RT-qPCR; Reporter assay
E_02480	2011	21711161	Enhancer-blocking activity is associated with hypersensitive site V sequences in the human growth hormone locus control region	Homo sapiens	hg19	chr17	62028378	62028924	CTCF	GH1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HEK293	CVCL_0045	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_02481	2011	21711161	Enhancer-blocking activity is associated with hypersensitive site V sequences in the human growth hormone locus control region	Homo sapiens	hg19	chr17	62028378	62028924	YY1	GH1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HEK293	CVCL_0045	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_02482	2024	38319712	Differential histone acetylation and super-enhancer regulation underlie melanoma cell dedifferentiation	Homo sapiens	hg19	chr17	48110000	48150000	JUNB	ITGA3	Super-enhancer	Active	Disease	cutaneous melanoma	MONDO:0005012	DOID:8923	zone of skin	UBERON:0000014	A-375	CVCL_0132	melanoma cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; ATAC-seq	CRISPR knockout, qRT-PCR; Western blot
E_02483	2024	38513139	RUNX1 C-terminal mutations impair blood cell differentiation by perturbing specific enhancer-promoter networks	Homo sapiens	hg38	chr8	128740000	128750000	FOXK2	MYC	Enhancer	Active	Disease	myeloid malignancy	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; GRID-seq; RNA-seq	CUT&RUN-RT-qPCR, shRNA Knockdown; RT-qPCR; Western blot
E_02484	2024	38513139	RUNX1 C-terminal mutations impair blood cell differentiation by perturbing specific enhancer-promoter networks	Homo sapiens	hg38	chr8	128740000	128750000	RUNX1	MYC	Enhancer	Active	Disease	myeloid malignancy	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; GRID-seq; RNA-seq	CUT&RUN-RT-qPCR, shRNA Knockdown; RT-qPCR; Western blot
E_02485	2018	29440643	Dissection and function of autoimmunity-associated TNFAIP3 (A20) gene enhancers in humanized mouse models	Homo sapiens	hg19	chr6	138226720	138233280	NA	TNFAIP3	Enhancer	Active	Disease	Autoimmune Diseases	NA	NA	blood	UBERON:0000178	B Cell,Monocytes	NA	B cell	CL:0000236	Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq; Hi-C	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_02486	2018	30033119	Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells	Homo sapiens	hg19	chr8	38291071	38304326	POU5F1	FGFR1	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	STARR-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02487	2018	30119690	Functional CRISPR screen identifies AP1-associated enhancer regulating FOXF1 to modulate oncogene-induced senescence	Homo sapiens	hg19	chr16	86422446	86426834	JUN	FOXF1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HEK293	CVCL_0045	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR; Western blot
E_02488	2011	21887706	Runx2 contributes to murine Col10a1 gene regulation through direct interaction with its cis-enhancer	Mus musculus	mm10	chr10	12845744	12845755	Runx2	Col10a1	Enhancer	Active	Normal	NA	NA	NA	cartilage tissue	UBERON:0002418	Hypertrophic MCT chondrocytes	NA	hypertrophic chondrocyte	CL:0000743	Enhancer activity assay; TF binding assay; Endogenous enhancer perturbation; In vivo functional validation	NA	EMSA; Transgenic enhancer reporter assay; ChIP; Site-directed/motif mutagenesis; In vivo phenotyping; Reporter assay
E_02489	1993	8460159	The granulocyte-macrophage colony-stimulating factor/interleukin 3 locus is regulated by an inducible cyclosporin A-sensitive enhancer	Homo sapiens	hg19	chr5	131406243	131406930	NA	CSF2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Jurkat	CVCL_0065	T cell	CL:0000084	Enhancer activity assay; TF binding assay; Chromatin accessibility assay; Cis-regulatory mapping	NA	DNase I hypersensitivity assay; enhancer deletion mapping; restriction mapping; transient transfection; CAT reporter assay; PMA/A23187 stimulation; cyclosporin A inhibition; EMSA; competition EMSA
E_02490	1993	8460159	The granulocyte-macrophage colony-stimulating factor/interleukin 3 locus is regulated by an inducible cyclosporin A-sensitive enhancer	Homo sapiens	hg19	chr5	131406243	131406930	NA	IL3	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Jurkat	CVCL_0065	T cell	CL:0000084	Enhancer activity assay; TF binding assay; Chromatin accessibility assay; Cis-regulatory mapping	NA	DNase I hypersensitivity assay; enhancer deletion mapping; restriction mapping; transient transfection; CAT reporter assay; PMA/A23187 stimulation; cyclosporin A inhibition; EMSA; competition EMSA
E_02491	2022	35741778	Discovery and Functional Characterization of Two Regulatory Variants Underlying Lupus Susceptibility at 2p13.1	Homo sapiens	hg19	chr2	73956813	73957241	ARID3A	DGUOK	Enhancer	Active	Disease	systemic lupus erythematosus	MONDO:0007915	DOID:9074	blood	UBERON:0000178	B Cell	NA	B cell	CL:0000236	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis	Hi-C; eQTL analysis; GWAS	Luciferase reporter assay; ChIP-qPCR; Luciferase reporter assay; ChIP-qPCR; ChIP; Western blot; Allele-specific reporter assay
E_02492	2018	30119690	Functional CRISPR screen identifies AP1-associated enhancer regulating FOXF1 to modulate oncogene-induced senescence	Homo sapiens	hg19	chr16	84000000	84001000	FOS	FOXF1	Enhancer	Active	Disease	oncogene-induced cellular senescence	MONDO:0024500	NA	zone of skin	UBERON:0000014	BJ [Human fibroblast]	CVCL_3653	fibroblast	CL:0000057	Functional perturbation assay; Senescence assay	ChIP-seq; RNA-seq	qRT-PCR, and ChIP-qPCR; CRISPR-Cas9
E_02493	2017	28536097	Dynamic regulation of VEGF-inducible genes by an ERK/ERG/p300 transcriptional network	Homo sapiens	hg19	chr1	22101842	22103407	ERG	HLX	Enhancer	Active	Normal	NA	NA	NA	umbilical vein	UBERON:0002066	HUVEC-C	CVCL_2959	umbilical vein endothelial cell	NA	Enhancer functional assay	ChIP-seq	CRISPR knockout; Luciferase reporter assay
E_02494	2016	26252164	FOXD3 Promotes PAX3 Expression in Melanoma Cells	Homo sapiens	hg19	chr2	223164458	223165065	FOXD3	PAX3	Enhancer	Active	Disease	melanoma	MONDO:0005105	DOID:1909	skin	UBERON:0002097	A-375	CVCL_0132	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Phylogenetic footprinting; Luciferase reporter assay; EMSA; ChIP-qPCR; FOXD3 overexpression; dominant-negative FOXD3; RT-qPCR; Western blot
E_02495	2016	26252164	FOXD3 Promotes PAX3 Expression in Melanoma Cells	Homo sapiens	hg19	chr2	223164458	223165065	FOXD3	PAX3	Enhancer	Active	Disease	melanoma	MONDO:0005105	DOID:1909	skin	UBERON:0002097	SK-MEL-28	CVCL_0526	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Phylogenetic footprinting; Luciferase reporter assay; EMSA; ChIP-qPCR; FOXD3 overexpression; dominant-negative FOXD3; RT-qPCR; Western blot
E_02496	2015	25267720	SRY interference of normal regulation of the RET gene suggests a potential role of the Y-chromosome gene in sexual dimorphism in Hirschsprung disease	Homo sapiens	hg19	chr10	43568986	43571244	PAX3	RET	Enhancer	Active	Disease	Hirschsprung disease	MONDO:0018309	DOID:10487	peripheral nervous system	UBERON:0000010	Neuro-2a	CVCL_0470	neural crest derived neuroblast	CL:0002676	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Luciferase reporter assay; PAX3/SOX10/SRY transfection; ChIP-qPCR; GST pull-down assay; co-immunoprecipitation; mammalian two-hybrid assay; RT-qPCR; Western blot
E_02497	2015	25267720	SRY interference of normal regulation of the RET gene suggests a potential role of the Y-chromosome gene in sexual dimorphism in Hirschsprung disease	Homo sapiens	hg19	chr10	43571244	43572713	NKX2-1	RET	Enhancer	Active	Disease	Hirschsprung disease	MONDO:0018309	DOID:10487	peripheral nervous system	UBERON:0000010	Neuro-2a	CVCL_0470	neural crest derived neuroblast	CL:0002676	Functional perturbation assay; TF binding assay; Promoter-proximal enhancer activity assay	NA	Luciferase reporter assay; NKX2-1/SOX10/SRY transfection; ChIP-qPCR; GST pull-down assay; co-immunoprecipitation; mammalian two-hybrid assay; RT-qPCR; Western blot
E_02498	2015	25769725	Histone Deacetylase Inhibitors Repress Tumoral Expression of the Proinvasive Factor RUNX2	Homo sapiens	hg19	chr6	45413249	45414099	JUN	RUNX2	Enhancer	Active	Disease	thyroid gland papillary carcinoma	MONDO:0005075	DOID:3969	thyroid gland	UBERON:0002046	B-CPAP	CVCL_0153	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	ENCODE regulatory data integration	Luciferase reporter assay; JUN ChIP-qPCR; EMSA/DNA-protein binding assay; JUN perturbation; HDAC inhibitor treatment; RT-qPCR; Western blot
E_02499	2015	25769725	Histone Deacetylase Inhibitors Repress Tumoral Expression of the Proinvasive Factor RUNX2	Homo sapiens	hg19	chr6	45413249	45414099	JUN	RUNX2	Enhancer	Active	Disease	thyroid gland papillary carcinoma	MONDO:0005075	DOID:3969	thyroid gland	UBERON:0002046	TPC-1	CVCL_6298	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	ENCODE regulatory data integration	Luciferase reporter assay; JUN ChIP-qPCR; EMSA/DNA-protein binding assay; JUN perturbation; HDAC inhibitor treatment; RT-qPCR; Western blot
E_02500	2015	26560027	Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism	Homo sapiens	hg19	chr11	8271697	8279492	GATA3	LMO1	Super-enhancer	Active	Disease	neuroblastoma	MONDO:0005072	DOID:769	NA	NA	Neuroblastoma Cell Lines	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RNAi/siRNA/shRNA
E_02501	2013	24285714	Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation	Homo sapiens	hg19	chr8	127047315	127049315	CEBPA	MYC	Enhancer	Active	Disease	Acute Leukemia	NA	DOID:12603	blood	UBERON:0000178	Acute Myeloid Leukemia Cell	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; 4C; RT-qPCR/qPCR; RNAi/siRNA/shRNA
E_02502	2013	24285714	Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation	Homo sapiens	hg19	chr8	127047315	127049315	CEBPB	MYC	Enhancer	Active	Disease	Acute Leukemia	NA	DOID:12603	blood	UBERON:0000178	Acute Myeloid Leukemia Cell	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; 4C; RT-qPCR/qPCR; RNAi/siRNA/shRNA
E_02503	2013	24285714	Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation	Homo sapiens	hg19	chr8	127047315	127049315	ERG	MYC	Enhancer	Active	Disease	Acute Leukemia	NA	DOID:12603	blood	UBERON:0000178	Acute Myeloid Leukemia Cell	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; 4C; RT-qPCR/qPCR; RNAi/siRNA/shRNA
E_02504	2013	24285714	Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation	Homo sapiens	hg19	chr8	127047315	127049315	LMO2	MYC	Enhancer	Active	Disease	Acute Leukemia	NA	DOID:12603	blood	UBERON:0000178	Acute Myeloid Leukemia Cell	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; 4C; RT-qPCR/qPCR; RNAi/siRNA/shRNA
E_02505	2013	24285714	Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation	Homo sapiens	hg19	chr8	127047315	127049315	SMARCA4	MYC	Enhancer	Active	Disease	Acute Leukemia	NA	DOID:12603	blood	UBERON:0000178	Acute Myeloid Leukemia Cell	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; 4C; RT-qPCR/qPCR; RNAi/siRNA/shRNA
E_02506	2017	28536097	Dynamic regulation of VEGF-inducible genes by an ERK/ERG/p300 transcriptional network	Homo sapiens	hg19	chr1	221049243	221051243	ERG	HLX	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HUVEC	NA	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_02507	2017	28536097	Dynamic regulation of VEGF-inducible genes by an ERK/ERG/p300 transcriptional network	Homo sapiens	hg19	chr1	221049243	221051243	NA	HLX	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HUVEC	NA	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_02508	2020	31591481	Oncogenic HOXB8 is driven by MYC-regulated super-enhancer and potentiates colorectal cancer invasiveness via BACH1	Homo sapiens	hg19	chr17	46658000	46660000	MYC	HOXB8	Enhancer	Active	Normal	NA	NA	NA	pulmonary artery	UBERON:0002012	HPAE-26	CVCL_3716	pulmonary artery endothelial cell	CL:1001568	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	CRISPR knockout/CRISPRi; RT-qPCR; ChIP-qPCR
E_02509	2015	26560027	Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism	Homo sapiens	hg19	chr11	8254408	8256408	GATA3	LMO1	Enhancer	Active	Disease	neuroblastoma	MONDO:0005072	DOID:769	sympathetic nervous system	UBERON:0000013	primary neuroblastoma tumors	NA	neuroblastoma cell	NA	GWAS causal-variant fine-mapping; super-enhancer annotation; allele-specific TF binding and cis-expression	GWAS/imputation; DNase-seq integration; H3K27ac/p300/GATA3 ChIP-seq integration; tumor RNA-seq	Direct genotyping; Allele-specific reporter assay; GATA3 binding analysis; allele-specific expression; Reporter assay
E_02510	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr2	180362582	180377003	NA	Mir1a-1	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	myotubes	NA	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02511	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr2	180362582	180377003	NA	Mir133a-2	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	myotubes	NA	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02512	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr2	180361998	180364335	NA	Mir1a-1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	myotubes	NA	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02513	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr2	180361998	180364335	NA	Mir133a-2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	myotubes	NA	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02514	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr2	180366734	180368371	NA	Mir1a-1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	myotubes	NA	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02515	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr2	180366734	180368371	NA	Mir133a-2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	myotubes	NA	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02516	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr2	180367903	180369540	NA	Mir1a-1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	myotubes	NA	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02517	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr2	180367903	180369540	NA	Mir133a-2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	myotubes	NA	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02518	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr2	180375974	180377844	NA	Mir1a-1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	myotubes	NA	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02519	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr2	180375974	180377844	NA	Mir133a-2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	myotubes	NA	NA	NA	Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02520	2014	24671955	Transcription and enhancer profiling in human monocyte subsets	Homo sapiens	hg19	chr5	139970046	139972237	NA	CD14	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Peripheral Blood Monocytes	NA	monocyte	CL:0000576	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_02521	2014	24671955	Transcription and enhancer profiling in human monocyte subsets	Homo sapiens	hg19	chr5	139974521	139975981	NA	CD14	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Peripheral Blood Monocytes	NA	monocyte	CL:0000576	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_02522	2014	24671955	Transcription and enhancer profiling in human monocyte subsets	Homo sapiens	hg19	chr5	139985479	139987671	NA	CD14	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Peripheral Blood Monocytes	NA	monocyte	CL:0000576	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_02523	2014	24671955	Transcription and enhancer profiling in human monocyte subsets	Homo sapiens	hg19	chr5	139987854	139989680	NA	CD14	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Peripheral Blood Monocytes	NA	monocyte	CL:0000576	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_02524	2014	24671955	Transcription and enhancer profiling in human monocyte subsets	Homo sapiens	hg19	chr5	139990822	139992831	NA	CD14	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Peripheral Blood Monocytes	NA	monocyte	CL:0000576	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_02525	2014	24671955	Transcription and enhancer profiling in human monocyte subsets	Homo sapiens	hg19	chr5	140009726	140011735	NA	CD14	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Peripheral Blood Monocytes	NA	monocyte	CL:0000576	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_02526	2022	35741778	Discovery and Functional Characterization of Two Regulatory Variants Underlying Lupus Susceptibility at 2p13.1	Homo sapiens	hg19	chr2	74208162	74208562	ARID3A	DGUOK	Enhancer	Active	Disease	systemic lupus erythematosus	MONDO:0007915	DOID:9074	blood	UBERON:0000178	GM18572	CVCL_P186	B cell	CL:0000236	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis	Hi-C; eQTL analysis; GWAS	Luciferase reporter assay; ChIP-qPCR; Western blot; ChIP; Allele-specific reporter assay
E_02527	2022	35741778	Discovery and Functional Characterization of Two Regulatory Variants Underlying Lupus Susceptibility at 2p13.1	Homo sapiens	hg19	chr2	74213045	74213445	ARID3A	DGUOK	Enhancer	Repressed	Disease	systemic lupus erythematosus	MONDO:0007915	DOID:9074	blood	UBERON:0000178	GM18572	CVCL_P186	B cell	CL:0000236	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis	Hi-C; eQTL analysis; GWAS	Luciferase reporter assay; ChIP-qPCR; Western blot; ChIP; Allele-specific reporter assay
E_02528	2015	26560027	Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism	Homo sapiens	hg19	chr11	8254408	8256408	GATA3	LMO1	Enhancer	Active	Disease	neuroblastoma	MONDO:0005072	DOID:769	sympathetic nervous system	UBERON:0000013	Neuroblastoma Cell Lines	NA	neuroblastoma cell	NA	GWAS causal-variant fine-mapping; super-enhancer annotation; allele-specific TF binding and cis-expression	GWAS/imputation; DNase-seq integration; H3K27ac/p300/GATA3 ChIP-seq integration; tumor RNA-seq	Direct genotyping; Allele-specific reporter assay; GATA3 binding analysis; allele-specific expression; Reporter assay
E_02529	2015	26560027	Genetic predisposition to neuroblastoma mediated by a LMO1 super-enhancer polymorphism	Homo sapiens	hg19	chr11	8255155	8255707	GATA3	LMO1	Enhancer	Active	Disease	neuroblastoma	MONDO:0005072	DOID:769	NA	NA	SK-N-SH	CVCL_0531	neuroblastoma cell	NA	Enhancer activity assay; TF binding assay; Functional variant assay; Genetic association analysis	GWAS/imputation; GATA3 ChIP-seq; H3K27ac ChIP-seq; RNA-seq; DNase-seq	Luciferase reporter assay; Allele-specific reporter assay; Genotyping; Allele-specific expression analysis; ChIP-qPCR; Sanger sequencing; Reporter assay
E_02530	2022	35741778	Discovery and Functional Characterization of Two Regulatory Variants Underlying Lupus Susceptibility at 2p13.1	Homo sapiens	hg19	chr2	73956813	73957241	ARID3A	DGUOK-AS1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	LCL	NA	lymphoblastoid cell line	NA	Enhancer activity assay; TF binding assay; Chromatin interaction assay	Hi-C; Capture Hi-C; eQTL analysis	Luciferase reporter assay; ChIP-qPCR; qPCR; Western blot
E_02531	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr6	51168034	51174811	NA	Mir148a	Super-enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Pro-B cell	NA	B cell	CL:0000236	Endogenous enhancer perturbation; In vivo functional validation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02532	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr6	51117747	51120656	NA	Mir148a	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Pro-B cell	NA	B cell	CL:0000236	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02533	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr6	51168147	51170512	NA	Mir148a	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Pro-B cell	NA	B cell	CL:0000236	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02534	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr6	51171474	51173111	NA	Mir148a	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Pro-B cell	NA	B cell	CL:0000236	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02535	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr6	51173363	51175544	NA	Mir148a	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Pro-B cell	NA	B cell	CL:0000236	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02536	2018	30033119	Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells	Homo sapiens	hg19	chr3	181428000	181429000	NA	SOX2	Enhancer	Active	Normal	NA	NA	NA	inner cell mass	UBERON:0000087	WA13	CVCL_9774	embryonic stem cell	CL:0002322	Enhancer activity assay	ChIP-seq; ATAC-seq; MPRA; STARR-seq	qRT-PCR, and ChIP-qPCR; ChIP; Reporter assay
E_02537	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3199567	3201439	NA	Mir290	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02538	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3199567	3201439	NA	Mir291a	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02539	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3199567	3201439	NA	Mir292	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02540	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3199567	3201439	NA	Mir291b	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02541	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3199567	3201439	NA	Mir293	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02542	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3199567	3201439	NA	Mir294	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02543	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3199567	3201439	NA	Mir295	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02544	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3202646	3204360	NA	Mir290	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02545	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3202646	3204360	NA	Mir291a	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02546	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3202646	3204360	NA	Mir292	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02547	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3202646	3204360	NA	Mir291b	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02548	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3202646	3204360	NA	Mir293	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02549	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3202646	3204360	NA	Mir294	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02550	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3202646	3204360	NA	Mir295	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02551	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3205726	3207280	NA	Mir290	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02552	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3205726	3207280	NA	Mir291a	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02553	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3205726	3207280	NA	Mir292	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02554	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3205726	3207280	NA	Mir291b	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02555	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3205726	3207280	NA	Mir293	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02556	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3205726	3207280	NA	Mir294	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02557	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3205726	3207280	NA	Mir295	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02558	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3209567	3211439	NA	Mir290	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02559	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3209567	3211439	NA	Mir291a	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02560	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3209567	3211439	NA	Mir292	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02561	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3209567	3211439	NA	Mir291b	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02562	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3209567	3211439	NA	Mir293	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02563	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3209567	3211439	NA	Mir294	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02564	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3209567	3211439	NA	Mir295	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02565	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3212448	3214558	NA	Mir290	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02566	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3212448	3214558	NA	Mir291a	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02567	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3212448	3214558	NA	Mir292	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02568	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3212448	3214558	NA	Mir291b	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02569	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3212448	3214558	NA	Mir293	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02570	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3212448	3214558	NA	Mir294	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02571	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3212448	3214558	NA	Mir295	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02572	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3216607	3218399	NA	Mir290	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02573	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3216607	3218399	NA	Mir291a	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02574	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3216607	3218399	NA	Mir292	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02575	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3216607	3218399	NA	Mir291b	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02576	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3216607	3218399	NA	Mir293	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02577	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3216607	3218399	NA	Mir294	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02578	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3216607	3218399	NA	Mir295	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02579	2014	24671955	Transcription and enhancer profiling in human monocyte subsets	Homo sapiens	hg19	chr5	139985479	139987671	NA	CD14	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary classical monocytes	NA	classical monocyte	CL:0000860	Enhancer activity assay; Enhancer landscape assay; Chromatin-state assay	HeliScopeCAGE; H3K4me1 ChIP-seq; H3K27ac ChIP-seq; published PU.1/CEBPB ChIP-seq data integration	Luciferase reporter assay in THP-1 cells; Jurkat negative-control reporter assay
E_02580	2014	24671955	Transcription and enhancer profiling in human monocyte subsets	Homo sapiens	hg19	chr5	139987854	139989680	NA	CD14	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary classical monocytes	NA	classical monocyte	CL:0000860	Enhancer activity assay; Enhancer landscape assay; Chromatin-state assay	HeliScopeCAGE; H3K4me1 ChIP-seq; H3K27ac ChIP-seq; published PU.1/CEBPB ChIP-seq data integration	Luciferase reporter assay in THP-1 cells; Jurkat negative-control reporter assay
E_02581	2014	24671955	Transcription and enhancer profiling in human monocyte subsets	Homo sapiens	hg19	chr5	139990822	139992831	NA	CD14	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary classical monocytes	NA	classical monocyte	CL:0000860	Enhancer activity assay; Enhancer landscape assay; Chromatin-state assay	HeliScopeCAGE; H3K4me1 ChIP-seq; H3K27ac ChIP-seq; published PU.1/CEBPB ChIP-seq data integration	Luciferase reporter assay in THP-1 cells; Jurkat negative-control reporter assay
E_02582	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr6	51108708	51130031	NA	Mir148a	Super-enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Pro-B cell	NA	B cell	CL:0000236	Endogenous enhancer perturbation; In vivo functional validation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02583	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3193003	3218182	NA	Mir290	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation; In vivo functional validation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02584	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3193003	3218182	NA	Mir291a	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation; In vivo functional validation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02585	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3193003	3218182	NA	Mir292	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation; In vivo functional validation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02586	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3193003	3218182	NA	Mir291b	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation; In vivo functional validation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02587	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3193003	3218182	NA	Mir293	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation; In vivo functional validation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02588	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3193003	3218182	NA	Mir294	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation; In vivo functional validation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02589	2016	26855180	Super enhancers at the miR-146a and miR-155 genes contribute to self-regulation of inflammation	Mus musculus	mm10	chr7	3193003	3218182	NA	Mir295	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation; In vivo functional validation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR
E_02590	2014	24671955	Transcription and enhancer profiling in human monocyte subsets	Homo sapiens	hg19	chr5	140657200	140658500	SPI1	CD14	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Classical monocytes	NA	classical monocyte	CL:0000860	Enhancer activity assay	ChIP-seq; CAGE-seq	Luciferase reporter assay; RT-qPCR
E_02591	2014	24671955	Transcription and enhancer profiling in human monocyte subsets	Homo sapiens	hg19	chr5	140659800	140661200	SPI1	CD14	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Classical monocytes	NA	classical monocyte	CL:0000860	Enhancer activity assay	ChIP-seq; CAGE-seq	Luciferase reporter assay; RT-qPCR
E_02592	2014	24671955	Transcription and enhancer profiling in human monocyte subsets	Homo sapiens	hg19	chr5	140662500	140663800	SPI1	CD14	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Classical monocytes	NA	classical monocyte	CL:0000860	Enhancer activity assay	ChIP-seq; CAGE-seq	Luciferase reporter assay; RT-qPCR
E_02593	2016	26252164	FOXD3 Promotes PAX3 Expression in Melanoma Cells	Homo sapiens	hg19	chr2	223164458	223164688	FOXD3	PAX3	Enhancer	Active	Disease	melanoma	MONDO:0005105	DOID:1909	skin	UBERON:0002097	Melanoma	NA	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_02594	2016	26252164	FOXD3 Promotes PAX3 Expression in Melanoma Cells	Homo sapiens	hg19	chr2	223164846	223165065	FOXD3	PAX3	Enhancer	Active	Disease	melanoma	MONDO:0005105	DOID:1909	skin	UBERON:0002097	Melanoma	NA	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_02595	2016	26252164	FOXD3 Promotes PAX3 Expression in Melanoma Cells	Homo sapiens	hg19	chr2	223164458	223164688	FOXD3	PAX3	Enhancer	Active	Disease	cutaneous melanoma	MONDO:0005012	DOID:8923	zone of skin	UBERON:0000014	A-375	CVCL_0132	melanoma cell	NA	Enhancer activity assay	NA	Luciferase reporter assay; EMSA
E_02596	2016	26252164	FOXD3 Promotes PAX3 Expression in Melanoma Cells	Homo sapiens	hg19	chr2	223164846	223165065	FOXD3	PAX3	Enhancer	Active	Disease	cutaneous melanoma	MONDO:0005012	DOID:8923	zone of skin	UBERON:0000014	SK-MEL-28	CVCL_0526	melanoma cell	NA	Enhancer activity assay	NA	Luciferase reporter assay; EMSA
E_02597	2015	25769725	Histone Deacetylase Inhibitors Repress Tumoral Expression of the Proinvasive Factor RUNX2	Homo sapiens	hg19	chr6	45410618	45417584	JUND	RUNX2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	B-CPAP,TPC1	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_02598	2015	25267720	SRY interference of normal regulation of the RET gene suggests a potential role of the Y-chromosome gene in sexual dimorphism in Hirschsprung disease	Homo sapiens	hg19	chr10	43568986	43571244	NKX2-1	RET	Enhancer	Active	Disease	Hirschsprung disease	MONDO:0018309	DOID:10487	blood	UBERON:0000178	Neural Crest Cells	NA	NA	NA	Enhancer activity assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay
E_02599	2015	25267720	SRY interference of normal regulation of the RET gene suggests a potential role of the Y-chromosome gene in sexual dimorphism in Hirschsprung disease	Homo sapiens	hg19	chr10	43568986	43571244	PAX3	RET	Enhancer	Active	Disease	Hirschsprung disease	MONDO:0018309	DOID:10487	blood	UBERON:0000178	Neural Crest Cells	NA	NA	NA	Enhancer activity assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay
E_02600	2015	25267720	SRY interference of normal regulation of the RET gene suggests a potential role of the Y-chromosome gene in sexual dimorphism in Hirschsprung disease	Homo sapiens	hg19	chr10	43571244	43572713	NKX2-1	RET	Enhancer	Active	Disease	Hirschsprung disease	MONDO:0018309	DOID:10487	blood	UBERON:0000178	Neural Crest Cells	NA	NA	NA	Enhancer activity assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay
E_02601	2015	25267720	SRY interference of normal regulation of the RET gene suggests a potential role of the Y-chromosome gene in sexual dimorphism in Hirschsprung disease	Homo sapiens	hg19	chr10	43571244	43572713	PAX3	RET	Enhancer	Active	Disease	Hirschsprung disease	MONDO:0018309	DOID:10487	blood	UBERON:0000178	Neural Crest Cells	NA	NA	NA	Enhancer activity assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay
E_02602	2024	38110836	Engrailed-1 Promotes Pancreatic Cancer Metastasis	Mus musculus	mm10	chr17	26531508	26539010	En1	Dusp1	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	KPC-derived mT3-2D cells	NA	pancreatic ductal cell	CL:0002079	Functional perturbation assay; TF binding assay; In vivo functional validation; Enhancer chromatin-state assay	FLAG-En1 CUT&RUN-seq; H3K27ac CUT&RUN-seq; H3K4me3 CUT&RUN-seq	In vivo phenotyping
E_02603	2023	36749647	Prdm6 drives ductus arteriosus closure by promoting ductus arteriosus smooth muscle cell identity and contractility	Homo sapiens	hg19	chr5	122453050	122453374	NA	PRDM6	Enhancer	Active	Normal	NA	NA	NA	bronchus	UBERON:0002185	Human bronchial smooth muscle cells (HuBrSMCs)	NA	bronchial smooth muscle cell	CL:0002598	Enhancer activity assay; TF binding assay; Disease-variant functional analysis; In vivo functional validation	RNA-seq; GWAS	Luciferase reporter assay; RT-qPCR; ChIP; In vivo phenotyping
E_02604	2020	33193627	Functional Characterization of a Dual Enhancer/Promoter Regulatory Element Leading Human CD69 Expression	Homo sapiens	hg19	chr12	9916938	9918379	NA	CD69	Enhancer	Active	Normal	NA	NA	NA	lymph node	UBERON:0000029	C1R B cells	NA	B cell	CL:0000236	Enhancer activity assay; Functional perturbation assay; TF binding assay; Endogenous enhancer perturbation	RNA-seq; ChIP-seq	Luciferase reporter assay, CRISPR knockout; ChIP-qPCR; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; Luciferase reporter assay
E_02605	2019	31053723	Differential methylation of enhancer at IGF2 is associated with abnormal dopamine synthesis in major psychosis	Mus musculus	mm10	chr7	149796331	149801250	NA	Th	Enhancer	Active	Normal	NA	NA	NA	striatum	UBERON:0002435	Primary mouse cortical neurons	NA	cortical neuron	NA	Functional perturbation assay	Hi-C; RNA-seq; Quantitative mass spectrometry; DNA methylation profiling	CRISPR knockout; RT-qPCR; Western blot; HPLC
E_02606	2024	39413158	Core enhancers of the 3'RR optimize IgH nuclear position and loop conformation for successful oriented class switch recombination	Mus musculus	mm10	chr12	113228270	113228366	NA	Igh	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary splenic B cells (mature resting and LPS-stimulated)	NA	B cell	CL:0000236	Chromatin accessibility assay; Functional genetic perturbation assay; Chromatin topology assay; Nuclear positioning assay; Class switch recombination assay	ATAC-seq; 3C-HTGTS; LAM-HTGTS	Genetic deletion mouse models (Delta3'RR and c3'RR); DNA 3D-FISH; 3C-qPCR; ATAC-qPCR; Flow cytometry
E_02607	2024	39413158	Core enhancers of the 3'RR optimize IgH nuclear position and loop conformation for successful oriented class switch recombination	Mus musculus	mm10	chr12	113232344	113232426	NA	Igh	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary splenic B cells (mature resting and LPS-stimulated)	NA	B cell	CL:0000236	Chromatin accessibility assay; Functional genetic perturbation assay; Chromatin topology assay; Nuclear positioning assay; Class switch recombination assay	ATAC-seq; 3C-HTGTS; LAM-HTGTS	Genetic deletion mouse models (Delta3'RR and c3'RR); DNA 3D-FISH; 3C-qPCR; ATAC-qPCR; Flow cytometry
E_02608	2024	39413158	Core enhancers of the 3'RR optimize IgH nuclear position and loop conformation for successful oriented class switch recombination	Mus musculus	mm10	chr12	113244662	113244744	NA	Igh	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary splenic B cells (mature resting and LPS-stimulated)	NA	B cell	CL:0000236	Chromatin accessibility assay; Functional genetic perturbation assay; Chromatin topology assay; Nuclear positioning assay; Class switch recombination assay	ATAC-seq; 3C-HTGTS; LAM-HTGTS	Genetic deletion mouse models (Delta3'RR and c3'RR); DNA 3D-FISH; 3C-qPCR; ATAC-qPCR; Flow cytometry
E_02609	2024	39413158	Core enhancers of the 3'RR optimize IgH nuclear position and loop conformation for successful oriented class switch recombination	Mus musculus	mm10	chr12	113253846	113254040	NA	Igh	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary splenic B cells (mature resting and LPS-stimulated)	NA	B cell	CL:0000236	Chromatin accessibility assay; Functional genetic perturbation assay; Chromatin topology assay; Nuclear positioning assay; Class switch recombination assay	ATAC-seq; 3C-HTGTS; LAM-HTGTS	Genetic deletion mouse models (Delta3'RR and c3'RR); DNA 3D-FISH; 3C-qPCR; ATAC-qPCR; Flow cytometry
E_02610	2020	32493985	GATA2 Regulates Constitutive PD-L1 and PD-L2 Expression in Brain Tumors	Homo sapiens	hg19	chr9	5459072	5460776	GATA2	CD274	Enhancer	Active	Disease	meningioma	MONDO:0016642	DOID:3565	brain	UBERON:0000955	Brain tumor initiating cells	NA	brain tumor initiating cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	Luciferase reporter assay; RT-qPCR; Flow Cytometry, shRNA Knockdown; Western blot; Flow cytometry
E_02611	2020	32493985	GATA2 Regulates Constitutive PD-L1 and PD-L2 Expression in Brain Tumors	Homo sapiens	hg19	chr9	5504029	5504679	GATA2	PDCD1LG2	Enhancer	Active	Disease	meningioma	MONDO:0016642	DOID:3565	brain	UBERON:0000955	Brain tumor initiating cells	NA	brain tumor initiating cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	Luciferase reporter assay; RT-qPCR; Flow Cytometry, shRNA Knockdown; Western blot; Flow cytometry
E_02612	2015	25259561	Oxidative stress regulates CFTR gene expression in human airway epithelial cells through a distal antioxidant response element	Homo sapiens	hg19	chr7	117075400	117076000	NA	CFTR	Enhancer	Active	Normal	NA	NA	NA	bronchus	UBERON:0002185	16HBE14o-	CVCL_0112	bronchial epithelial cell	CL:0002328	Enhancer activity assay; Endogenous enhancer perturbation	NA	Luciferase reporter assay; RT-qPCR; Site-directed/motif mutagenesis
E_02613	2014	24667089	The PEG13-DMR and brain-specific enhancers dictate imprinted expression within the 8q24 intellectual disability risk locus	Homo sapiens	hg19	chr8	141161900	141175436	CTCF	KCNK9	Enhancer	Active	Disease	Intellectual Disability	NA	DOID:1059	brain	UBERON:0000955	Lymphoblastoid Cell Lines	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_02614	2019	31053723	Differential methylation of enhancer at IGF2 is associated with abnormal dopamine synthesis in major psychosis	Mus musculus	mm10	chr7	149796331	149801250	NA	Igf2	Enhancer	Active	Normal	NA	NA	NA	frontal cortex	UBERON:0001870	striatal neurons	NA	striatal neuron	NA	Functional perturbation assay	Hi-C; RNA-seq; Quantitative mass spectrometry; DNA methylation profiling	CRISPR knockout; RT-qPCR; Western blot; HPLC
E_02615	2018	30285185	Progressing super-enhancer landscape during mammary differentiation controls tissue-specific gene regulation	Mus musculus	mm10	chr11	6639091	6639657	Nr3c1	Wap	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mammary	NA	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02616	2018	30285185	Progressing super-enhancer landscape during mammary differentiation controls tissue-specific gene regulation	Mus musculus	mm10	chr11	6639091	6639657	Stat5a	Wap	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mammary	NA	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02617	2018	30285185	Progressing super-enhancer landscape during mammary differentiation controls tissue-specific gene regulation	Mus musculus	mm10	chr11	6639824	6640424	Nr3c1	Wap	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mammary	NA	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02618	2018	30285185	Progressing super-enhancer landscape during mammary differentiation controls tissue-specific gene regulation	Mus musculus	mm10	chr11	6639824	6640424	Stat5a	Wap	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mammary	NA	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02619	2018	30285185	Progressing super-enhancer landscape during mammary differentiation controls tissue-specific gene regulation	Mus musculus	mm10	chr11	6644257	6644824	Nr3c1	Wap	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Mammary	NA	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02620	2018	30285185	Progressing super-enhancer landscape during mammary differentiation controls tissue-specific gene regulation	Mus musculus	mm10	chr11	6644257	6644824	Stat5a	Wap	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Mammary	NA	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02621	2018	30285185	Progressing super-enhancer landscape during mammary differentiation controls tissue-specific gene regulation	Mus musculus	mm10	chr11	6639029	6644397	Nr3c1	Wap	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Mammary	NA	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02622	2018	30285185	Progressing super-enhancer landscape during mammary differentiation controls tissue-specific gene regulation	Mus musculus	mm10	chr11	6639029	6644397	Stat5a	Wap	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Mammary	NA	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02623	2015	25505291	TGF-β1, but not bone morphogenetic proteins, activates Smad1/5 pathway in primary human macrophages and induces expression of proatherogenic genes	Homo sapiens	hg19	chr1	23881330	23881475	NA	ID3	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human monocyte-derived macrophages	NA	macrophage	CL:0000235	Enhancer activity assay; Signaling perturbation assay	NA	Luciferase reporter assay; ECR deletion analysis; TGF-beta1 stimulation; BMP stimulation; SMAD overexpression; SMAD knockdown; ALK inhibition; RT-qPCR; Western blot; Reporter assay
E_02624	2014	24905168	Reorganization of enhancer patterns in transition from naive to primed pluripotency	Mus musculus	mm10	chr4	124638991	124641160	Otx2	Pou3f1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02625	2014	24905168	Reorganization of enhancer patterns in transition from naive to primed pluripotency	Mus musculus	mm10	chr4	124638991	124641160	Pou5f1	Pou3f1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02626	2014	24905168	Reorganization of enhancer patterns in transition from naive to primed pluripotency	Mus musculus	mm10	chr4	124645999	124647927	Otx2	Pou3f1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02627	2014	24905168	Reorganization of enhancer patterns in transition from naive to primed pluripotency	Mus musculus	mm10	chr4	124645999	124647927	Pou5f1	Pou3f1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02628	2014	24905168	Reorganization of enhancer patterns in transition from naive to primed pluripotency	Mus musculus	mm10	chr5	119677099	119681977	Otx2	Tbx3	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02629	2014	24905168	Reorganization of enhancer patterns in transition from naive to primed pluripotency	Mus musculus	mm10	chr5	119677099	119681977	Pou5f1	Tbx3	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02630	2014	24905168	Reorganization of enhancer patterns in transition from naive to primed pluripotency	Mus musculus	mm10	chr5	119704124	119707831	Otx2	Tbx3	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02631	2014	24905168	Reorganization of enhancer patterns in transition from naive to primed pluripotency	Mus musculus	mm10	chr5	119704124	119707831	Pou5f1	Tbx3	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02632	2014	24905168	Reorganization of enhancer patterns in transition from naive to primed pluripotency	Mus musculus	mm10	chr5	119707931	119710758	Otx2	Tbx3	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02633	2014	24905168	Reorganization of enhancer patterns in transition from naive to primed pluripotency	Mus musculus	mm10	chr5	119707931	119710758	Pou5f1	Tbx3	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02634	2014	24905168	Reorganization of enhancer patterns in transition from naive to primed pluripotency	Mus musculus	mm10	chr5	119710660	119714758	Otx2	Tbx3	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02635	2014	24905168	Reorganization of enhancer patterns in transition from naive to primed pluripotency	Mus musculus	mm10	chr5	119710660	119714758	Pou5f1	Tbx3	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02636	2014	24905168	Reorganization of enhancer patterns in transition from naive to primed pluripotency	Mus musculus	mm10	chr5	98290964	98295647	Otx2	Fgf5	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02637	2014	24905168	Reorganization of enhancer patterns in transition from naive to primed pluripotency	Mus musculus	mm10	chr5	98290964	98295647	Pou5f1	Fgf5	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02638	2014	24905168	Reorganization of enhancer patterns in transition from naive to primed pluripotency	Mus musculus	mm10	chr5	98307793	98312281	Otx2	Fgf5	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02639	2014	24905168	Reorganization of enhancer patterns in transition from naive to primed pluripotency	Mus musculus	mm10	chr5	98307793	98312281	Pou5f1	Fgf5	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02640	2014	24905168	Reorganization of enhancer patterns in transition from naive to primed pluripotency	Mus musculus	mm10	chr5	98310330	98314427	Otx2	Fgf5	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02641	2014	24905168	Reorganization of enhancer patterns in transition from naive to primed pluripotency	Mus musculus	mm10	chr5	98310330	98314427	Pou5f1	Fgf5	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02642	2014	24905168	Reorganization of enhancer patterns in transition from naive to primed pluripotency	Mus musculus	mm10	chr5	98253530	98257713	Otx2	Fgf5	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02643	2014	24905168	Reorganization of enhancer patterns in transition from naive to primed pluripotency	Mus musculus	mm10	chr5	98253530	98257713	Pou5f1	Fgf5	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02644	2014	24667089	The PEG13-DMR and brain-specific enhancers dictate imprinted expression within the 8q24 intellectual disability risk locus	Homo sapiens	hg19	chr8	141161900	141175436	CTCF	PEG13	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	adult human frontal cortex and cerebellum	NA	NA	NA	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Enhancer chromatin-state assay; TF/cohesin binding assay; Imprinting assay	Public CTCF ChIA-PET data integration; published brain H3K4me1/H3K27ac/p300 chromatin-profile data integration	3C-qPCR; CTCF ChIP-qPCR; RAD21 ChIP-qPCR; SMC3 ChIP-qPCR; allele-specific RT-PCR; bisulfite sequencing; ChIP; 3C; Allele-specific reporter assay
E_02645	2014	24667089	The PEG13-DMR and brain-specific enhancers dictate imprinted expression within the 8q24 intellectual disability risk locus	Homo sapiens	hg19	chr8	140900000	140930000	CTCF	KCNK9	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Adult brain tissue	NA	adult brain cell	NA	Enhancer activity assay; Chromatin interaction assay	ChIP-seq; RNA-seq; 3C-seq; 3C; DNA methylation profiling	3C-RT-qPCR; ChIP-qPCR; Luciferase reporter assay
E_02646	2020	32493985	GATA2 Regulates Constitutive PD-L1 and PD-L2 Expression in Brain Tumors	Homo sapiens	hg19	chr9	5459072	5459797	FOS	CD274	Enhancer	Active	Disease	meningioma	MONDO:0016642	DOID:3565	brain	UBERON:0000955	Brain tumor initiating cells	NA	brain tumor initiating cell	NA	Enhancer activity assay	ChIP-seq; RNA-seq	Luciferase reporter assay; RT-qPCR; Flow cytometry
E_02647	2015	25505291	TGF-β1, but not bone morphogenetic proteins, activates Smad1/5 pathway in primary human macrophages and induces expression of proatherogenic genes	Homo sapiens	hg19	chr1	23888938	23889083	NA	ID3	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human monocyte-derived macrophages	NA	macrophage	CL:0000235	Enhancer activity and signaling perturbation	NA	luciferase enhancer reporter; TGF---1/BMP stimulation; Smad pathway inhibition/siRNA; RT-qPCR; immunoblot; Luciferase reporter assay; Reporter assay
E_02648	2015	25259561	Oxidative stress regulates CFTR gene expression in human airway epithelial cells through a distal antioxidant response element	Homo sapiens	hg19	chr7	117075514	117075933	BACH1	CFTR	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Human Bronchial Epithelial Cell	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_02649	2015	25259561	Oxidative stress regulates CFTR gene expression in human airway epithelial cells through a distal antioxidant response element	Homo sapiens	hg19	chr7	117075514	117075933	NFKB1	CFTR	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Human Bronchial Epithelial Cell	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_02650	2015	25505291	TGF-β1, but not bone morphogenetic proteins, activates Smad1/5 pathway in primary human macrophages and induces expression of proatherogenic genes	Homo sapiens	hg19	chr1	23884369	23884886	NA	ID3	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary macrophages	NA	macrophage	CL:0000235	Enhancer activity assay	NA	Luciferase reporter assay; RT-qPCR; Luciferase reporter assay; Reporter assay
E_02651	2015	25505291	TGF-β1, but not bone morphogenetic proteins, activates Smad1/5 pathway in primary human macrophages and induces expression of proatherogenic genes	Homo sapiens	hg19	chr1	23892063	23892208	NA	ID3	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary macrophages	NA	macrophage	CL:0000235	Enhancer activity assay	NA	Luciferase reporter assay; RT-qPCR; Luciferase reporter assay; Reporter assay
E_02652	2015	25505291	TGF-β1, but not bone morphogenetic proteins, activates Smad1/5 pathway in primary human macrophages and induces expression of proatherogenic genes	Mus musculus	mm10	chr4	136148484	136149239	Tgfb1	Id3	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	hepatocyte	CL:0000182	Enhancer activity assay	NA	Luciferase reporter assay; Reporter assay; Western blot; RNAi/siRNA/shRNA
E_02653	2015	25505291	TGF-β1, but not bone morphogenetic proteins, activates Smad1/5 pathway in primary human macrophages and induces expression of proatherogenic genes	Mus musculus	mm10	chr4	136140654	136141162	Tgfb1	Id3	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	hepatocyte	CL:0000182	Enhancer activity assay	NA	Luciferase reporter assay; Reporter assay; Western blot; RNAi/siRNA/shRNA
E_02654	2015	25505291	TGF-β1, but not bone morphogenetic proteins, activates Smad1/5 pathway in primary human macrophages and induces expression of proatherogenic genes	Homo sapiens	hg19	chr1	23881244	23881761	NA	ID3	Enhancer	Active	Disease	Cardiometabolic Disorders	NA	NA	NA	NA	Human Monocytes/Macrophages	NA	macrophage	CL:0000235	Enhancer activity assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay
E_02655	2015	25505291	TGF-β1, but not bone morphogenetic proteins, activates Smad1/5 pathway in primary human macrophages and induces expression of proatherogenic genes	Homo sapiens	hg19	chr1	23888938	23889083	NA	ID3	Enhancer	Active	Disease	Cardiometabolic Disorders	NA	NA	NA	NA	Human Monocytes/Macrophages	NA	macrophage	CL:0000235	Enhancer activity assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay
E_02656	2024	38994563	SMCHD1 activates the expression of genes required for the expansion of human myoblasts	Homo sapiens	hg38	chr12	98515210	98515289	NA	TMPO	Enhancer	Active	Disease	facioscapulohumeral muscular dystrophy 2	MONDO:0008031	DOID:0111193	skeletal muscle tissue	UBERON:0001134	WS234 (donor 15Vbic)	NA	skeletal muscle myoblast	CL:0000515	Functional perturbation assay; Gene expression assay; Enhancer characterization; Chromatin regulator binding assay; Rescue assay	RNA-seq; SMCHD1 ChIP-seq; H3K27ac CUT&Tag; H3K4me1 CUT&Tag; H3K4me3 CUT&Tag; H3K9me3 CUT&Tag; H3K27me3 CUT&Tag	shRNA-mediated SMCHD1 knockdown; shRNA-mediated TMPO/LAP2 knockdown; LAP2β rescue/overexpression; EdU incorporation assay; cell proliferation assay
E_02657	2023	37168287	A genomic enhancer signature associates with hepatocellular carcinoma prognosis	Homo sapiens	hg38	chr5	1294000	1297400	HNF4A	TERT	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	HCC cells	NA	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Chromatin-state profiling	ChIP-seq; RNA-seq; RNA-seq; ChIP-seq; Hi-C; HiChIP	Luciferase reporter assay; ChIP-qPCR; ChIP
E_02658	2021	33828297	Genome-wide enhancer maps link risk variants to disease genes	Homo sapiens	hg19	chr10	81115805	81116305	NA	PPIF	Enhancer	Active	Disease	inflammatory bowel disease	MONDO:0005265	DOID:0050589	blood	UBERON:0000178	THP-1	CVCL_0006	monocyte	CL:0000576	Disease-variant functional analysis; Enhancer-target functional validation; endogenous perturbation; downstream cellular phenotype	ATAC-seq/DNase-seq; H3K27ac profiling; Hi-C; ABC enhancer-gene mapping; GWAS	CRISPRi-FlowFISH; PPIF expression analysis; MitoTracker mitochondrial membrane-potential assay
E_02659	2020	32933554	Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation	Homo sapiens	hg38	chr1	158282456	158282752	CTCF	NA	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	CUTLL1	CVCL_4966	malignant cell	CL:0001064	TF binding assay; Chromatin interaction assay; Chromatin accessibility profiling; Cancer-specific regulatory-site characterization	CTCF ChIP-seq; ATAC-seq; in situ Hi-C; RNA-seq; WGS; DNA methylation profiling	ChIP-qPCR; RT-qPCR; Western blot; NOTCH1-pathway perturbation/validation
E_02660	2020	32933554	Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation	Homo sapiens	hg38	chr1	199217982	199218479	CTCF	NA	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	CUTLL1	CVCL_4966	malignant cell	CL:0001064	TF binding assay; Chromatin interaction assay; Chromatin accessibility profiling; Cancer-specific regulatory-site characterization	CTCF ChIP-seq; ATAC-seq; in situ Hi-C; RNA-seq; WGS; DNA methylation profiling	ChIP-qPCR; RT-qPCR; Western blot; NOTCH1-pathway perturbation/validation
E_02661	2020	33176148	ARID1A Mutations Promote P300-Dependent Endometrial Invasion through Super-Enhancer Hyperacetylation	Homo sapiens	hg38	chr7	100772345	100778921	NA	SERPINE1	Enhancer	Active	Disease	endometriosis	MONDO:0005133	DOID:289	endometrium	UBERON:0001295	RMS-19	CVCL_UG04	endometriotic epithelial cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; ATAC-seq; CUT&RUN	siRNA knockdown; RT-qPCR; Western blot; Flow cytometry
E_02662	2019	31217334	Epigenetic activation and memory at a TGFB2 enhancer in systemic sclerosis	Homo sapiens	hg19	chr1	218299740	218299908	RELA	TGFB2	Enhancer	Active	Normal	NA	NA	NA	zone of skin	UBERON:0000014	Primary human dermal fibroblasts	NA	dermal fibroblast	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ATAC-seq; RNA-seq; ChIP-seq; Chem-seq	ChIP-qPCR; CRISPRa (dCas9-EP300core); CRISPRi (dCas9-KRAB); RT-qPCR; Western blot, mRNA in situ hybridization
E_02663	2017	28683826	Identification and characterization of a FOXA2-regulated transcriptional enhancer at a type 2 diabetes intronic locus that controls GCKR expression in liver cells	Homo sapiens	hg19	chr2	27740600	27741238	FOXA2	GCKR	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	mouse primary hepatocytes	NA	mouse hepatocyte	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	RNA-seq; ChIP-seq	Luciferase reporter assay; ChIP-qPCR; CRISPRa; RT-qPCR; Reporter assay; qPCR
E_02664	2015	26211391	Correlation of the osteoarthritis susceptibility variants that map to chromosome 20q13 with an expression quantitative trait locus operating on NCOA3 and with functional variation at the polymorphism rs116855380	Homo sapiens	hg19	chr20	46120155	46120433	NA	NCOA3	Enhancer	Repressed	Disease	chondrosarcoma	MONDO:0008977	DOID:3371	cartilage tissue	UBERON:0002418	SW1353	CVCL_0543	chondrosarcoma cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Luciferase reporter assay; EMSA; RT-qPCR; Western blot, siRNA-mediated gene knockdown
E_02665	2020	32284612	Therapeutic base editing of human hematopoietic stem cells	Homo sapiens	hg38	chr2	60722150	60722350	GATA1	BCL11A	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	CD34+ hematopoietic stem/progenitor cells	NA	hematopoietic stem cell	CL:0000037	Enhancer activity assay; Functional perturbation assay; TF binding assay; Disease-variant functional analysis; In vivo functional validation	RNA-seq; ChIP-seq	CRISPR knockout, qRT-PCR, Flow Cytometry; In vivo phenotyping
E_02666	2019	30711920	H2AFY promoter deletion causes PITX1 endoactivation and Liebenberg syndrome	Homo sapiens	hg19	chr5	134729406	134737909	NA	PITX1	Enhancer	Active	Disease	brachydactyly-elbow wrist dysplasia syndrome	MONDO:0008520	NA	limb	UBERON:0002101	Liebenberg syndrome patient deletion / orthologous mouse model	NA	progenitor cell	CL:0011026	Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation; Structural-variant/promoter-insulator perturbation revealing enhancer retargeting	whole-genome sequencing; RNA-seq	CRISPR-Cas9 recreation of deletion in mice; RT-qPCR; whole-mount in situ hybridization; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_02667	2011	21652712	Suppression of the pancreatic duodenal homeodomain transcription factor-1 (Pdx-1) promoter by sterol regulatory element-binding protein-1c (SREBP-1c)	Mus musculus	mm10	chr5	147267336	147267640	Pdx1	Pdx1	Enhancer	Active	Normal	NA	NA	NA	islet of Langerhans	UBERON:0000006	INS-1	CVCL_0352	pancreatic beta cell	CL:0000169	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Luciferase reporter assay; EMSA; ChIP-qPCR; GST pull-down; RNAi; qRT-PCR; Western blot
E_02668	2010	20042469	c-Maf activates the promoter and enhancer of the IL-21 gene, and TGF-beta inhibits c-Maf-induced IL-21 production in CD4+ T cells	Mus musculus	mm10	chr3	2931	3443	Maf	Il21	Enhancer	Repressed	Normal	NA	NA	NA	lymph node	UBERON:0000029	CD4+ T	NA	CD4-positive, alpha-beta T cell	CL:0000624	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot; Flow cytometry; Coimmunoprecipitation
E_02669	2010	20042469	c-Maf activates the promoter and enhancer of the IL-21 gene, and TGF-beta inhibits c-Maf-induced IL-21 production in CD4+ T cells	Mus musculus	mm10	chr3	2931	3443	Foxp3	Il21	Enhancer	Repressed	Normal	NA	NA	NA	lymph node	UBERON:0000029	CD4+ T	NA	CD4-positive, alpha-beta T cell	CL:0000624	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot; Flow cytometry; Coimmunoprecipitation
E_02670	2019	30711920	H2AFY promoter deletion causes PITX1 endoactivation and Liebenberg syndrome	Homo sapiens	hg19	chr5	134729406	134737909	NA	PITX1	Enhancer	Active	Disease	brachydactyly-elbow wrist dysplasia syndrome	MONDO:0008520	NA	limb	UBERON:0002101	Liebenberg syndrome patient deletion / orthologous mouse model	NA	NA	NA	Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation; Structural-variant/promoter-insulator perturbation revealing enhancer retargeting	whole-genome sequencing; RNA-seq	CRISPR-Cas9 recreation of deletion in mice; RT-qPCR; whole-mount in situ hybridization; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_02671	2020	32284612	Therapeutic base editing of human hematopoietic stem cells	Homo sapiens	hg38	chr2	60494251	60495546	GATA1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	blood	UBERON:0000178	CD34+ hematopoietic stem and progenitor cells	NA	hematopoietic stem cell	CL:0000037	Functional perturbation assay; Disease-variant functional analysis; In vivo functional validation; enhancer editing assay	Amplicon deep sequencing; Illumina sequencing	CRISPR base editing; RT-qPCR; HbF measurement; HPLC; sickling assay; In vivo phenotyping
E_02672	2020	32284612	Therapeutic base editing of human hematopoietic stem cells	Homo sapiens	hg38	chr2	60494251	60495546	GATA1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	blood	UBERON:0000178	CD34+ hematopoietic stem and progenitor cells	NA	hematopoietic stem cell	CL:0000037	Functional perturbation assay; Disease-variant functional analysis; In vivo functional validation; enhancer editing assay	Amplicon deep sequencing; Illumina sequencing	CRISPR base editing; RT-qPCR; HbF measurement; HPLC; erythroid differentiation assay; In vivo phenotyping
E_02673	2020	32284612	Therapeutic base editing of human hematopoietic stem cells	Homo sapiens	hg38	chr2	60494251	60495546	TAL1	BCL11A	Enhancer	Active	Disease	sickle cell disease	MONDO:0011382	DOID:0081445	blood	UBERON:0000178	CD34+ hematopoietic stem and progenitor cells	NA	hematopoietic stem cell	CL:0000037	Functional perturbation assay; Disease-variant functional analysis; In vivo functional validation; enhancer editing assay	Amplicon deep sequencing; Illumina sequencing	CRISPR base editing; RT-qPCR; HbF measurement; HPLC; sickling assay; In vivo phenotyping
E_02674	2020	32284612	Therapeutic base editing of human hematopoietic stem cells	Homo sapiens	hg38	chr2	60494251	60495546	TAL1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	blood	UBERON:0000178	CD34+ hematopoietic stem and progenitor cells	NA	hematopoietic stem cell	CL:0000037	Functional perturbation assay; Disease-variant functional analysis; In vivo functional validation; enhancer editing assay	Amplicon deep sequencing; Illumina sequencing	CRISPR base editing; RT-qPCR; HbF measurement; HPLC; erythroid differentiation assay; In vivo phenotyping
E_02675	2016	26774474	Deposition of 5-Methylcytosine on Enhancer RNAs Enables the Coactivator Function of PGC-1α	Mus musculus	mm9	chr13	43362622	43364444	NA	Sirt5	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hepa 1-6	CVCL_0327	hepatocyte	CL:0000182	Functional perturbation assay; Enhancer RNA assay; Coactivator occupancy assay	PPARGC1A/PGC-1-- ChIP-seq	ChIP-qPCR; eRNA RT-qPCR; LNA-mediated eRNA knockdown; Luciferase reporter assay; RNA bisulfite sequencing; Western blot
E_02676	2016	26774474	Deposition of 5-Methylcytosine on Enhancer RNAs Enables the Coactivator Function of PGC-1α	Mus musculus	mm9	chr10	77989870	77993100	NA	Pfkl	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hepa 1-6	CVCL_0327	hepatocyte	CL:0000182	Functional perturbation assay; Enhancer RNA assay; Coactivator occupancy assay	PPARGC1A/PGC-1-- ChIP-seq	ChIP-qPCR; eRNA RT-qPCR; RNA immunoprecipitation; RNA EMSA; RT-qPCR
E_02677	2016	26774474	Deposition of 5-Methylcytosine on Enhancer RNAs Enables the Coactivator Function of PGC-1α	Mus musculus	mm9	chr16	4721118	4724819	NA	Hmox2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hepa 1-6	CVCL_0327	hepatocyte	CL:0000182	Functional perturbation assay; Enhancer RNA assay; Coactivator occupancy assay	PPARGC1A/PGC-1-- ChIP-seq	ChIP-qPCR; eRNA RT-qPCR; PPARGC1A/NSUN7 perturbation; RT-qPCR
E_02678	2016	26774474	Deposition of 5-Methylcytosine on Enhancer RNAs Enables the Coactivator Function of PGC-1α	Mus musculus	mm9	chr2	130280565	130281887	NA	Idh3b	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hepa 1-6	CVCL_0327	hepatocyte	CL:0000182	Functional perturbation assay; Enhancer RNA assay; Coactivator occupancy assay	PPARGC1A/PGC-1-- ChIP-seq	ChIP-qPCR; eRNA RT-qPCR; PPARGC1A/NSUN7 perturbation; RT-qPCR
E_02679	2021	33828297	Genome-wide enhancer maps link risk variants to disease genes	Homo sapiens	hg19	chr10	79285696	79287696	NA	PPIF	Enhancer	Active	Disease	inflammatory bowel disease	MONDO:0005265	DOID:0050589	blood	UBERON:0000178	THP-1	CVCL_0006	monocyte	CL:0000576	Functional perturbation assay; Disease-variant functional analysis; enhancer-target validation	CRISPRi-FlowFISH; GWAS	Individual CRISPRi; RT-qPCR; MitoTracker membrane-potential assay
E_02680	2020	32284612	Therapeutic base editing of human hematopoietic stem cells	Homo sapiens	hg38	chr2	6072150	6072450	NA	BCL11A	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	CD34+ hematopoietic stem/progenitor cells	NA	hematopoietic stem cell	CL:0000037	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis; In vivo functional validation	NA	CRISPR knockout, qRT-PCR; In vivo phenotyping
E_02681	2010	20042469	c-Maf activates the promoter and enhancer of the IL-21 gene, and TGF-beta inhibits c-Maf-induced IL-21 production in CD4+ T cells	Mus musculus	mm10	chr3	37229193	37229705	Foxp3	Il21	Enhancer	Active	Normal	NA	NA	NA	NA	NA	EL4	CVCL_0255	T cell	CL:0000084	Enhancer activity assay; Functional perturbation assay	NA	Luciferase reporter assay; Maf and Foxp3 cotransfection; PMA-ionomycin stimulation
E_02682	2010	20042469	c-Maf activates the promoter and enhancer of the IL-21 gene, and TGF-beta inhibits c-Maf-induced IL-21 production in CD4+ T cells	Mus musculus	mm10	chr3	37229193	37229705	Maf	Il21	Enhancer	Active	Normal	NA	NA	NA	NA	NA	EL4	CVCL_0255	T cell	CL:0000084	Enhancer activity assay; Functional perturbation assay	NA	Luciferase reporter assay; Maf overexpression; PMA-ionomycin stimulation
E_02683	2019	30711920	H2AFY promoter deletion causes PITX1 endoactivation and Liebenberg syndrome	Homo sapiens	hg19	chr5	134729406	134737909	NA	PITX1	Enhancer	Active	Disease	brachydactyly-elbow wrist dysplasia syndrome	MONDO:0008520	NA	limb	UBERON:0002101	affected family	NA	limb mesenchymal cell	NA	8.5-kb pathogenic deletion contains H2AFY promoter/first noncoding exon; not an enhancer interval	whole-genome sequencing	Mouse CRISPR recreation; expression analysis; limb phenotyping; CRISPR-Cas9
E_02684	2010	20042469	c-Maf activates the promoter and enhancer of the IL-21 gene, and TGF-beta inhibits c-Maf-induced IL-21 production in CD4+ T cells	Mus musculus	mm10	chr3	37225520	37228865	Maf	Il21	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	CD4+ T Cell	NA	CD4-positive, alpha-beta T cell	CL:0000624	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02685	2010	20042469	c-Maf activates the promoter and enhancer of the IL-21 gene, and TGF-beta inhibits c-Maf-induced IL-21 production in CD4+ T cells	Mus musculus	mm10	chr3	37229193	37229705	Maf	Il21	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HEK293T	CVCL_0063	transformed embryonic kidney-derived cell	NA	Enhancer activity assay; TF-binding-site functional assay	NA	Minimal-promoter luciferase reporter assay; MARE-3/MARE-4 site-directed mutagenesis; Maf overexpression
E_02686	2025	40393811	Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits	Homo sapiens	hg38	chr1	178551259	178551689	NA	RALGPS2	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Adipose-Derived Mesenchymal Stem Cells-01	NA	mesenchymal stem cell	CL:0000134	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis; Endogenous enhancer perturbation	ATAC-seq; RNA-seq; eQTL analysis; GWAS	Luciferase reporter assay, CRISPR knockout, CRISPRi; RT-qPCR; CRISPRi
E_02687	2023	36959177	Mena regulates nesprin-2 to control actin-nuclear lamina associations, trans-nuclear membrane signalling and gene expression	Homo sapiens	hg38	chr3	157437977	157438893	NA	PTX3	Enhancer	Repressed	Disease	skin squamous cell carcinoma	MONDO:0002529	DOID:3151	zone of skin	UBERON:0000014	293T human CD33	CVCL_UE24	malignant cell	CL:0001064	Functional perturbation assay; Chromatin interaction assay	DamID-seq; RNA-seq	CRISPR knockout, qRT-PCR
E_02688	2018	30404006	Genetic Models Reveal cis and trans Immune-Regulatory Activities for lincRNA-Cox2	Mus musculus	mm10	chr1	152006173	152012078	NA	Ptgs2	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	bone marrow-derived macrophages (BMDMs)	NA	macrophage	CL:0000235	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	ChIP-seq; RNA-seq	qRT-PCR, and ChIP-qPCR
E_02689	2017	27986456	Isoform-Specific Expression and Feedback Regulation of E Protein TCF4 Control Dendritic Cell Lineage Specification	Mus musculus	mm10	chr18	69656860	69683465	Tcf4	Tcf4	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	HoxB8-FL cells	NA	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; ATAC-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02690	2017	29038474	A shared Runx1-bound Zbtb16 enhancer directs innate and innate-like lymphoid lineage development	Mus musculus	mm10	chr9	48814346	48815095	Runx1	Zbtb16	Enhancer	Active	Normal	NA	NA	NA	thymus	UBERON:0002370	NKT thymocyte and ILCP	NA	T cell	CL:0000084	Functional perturbation assay; TF binding assay; Chromatin-state profiling; Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation	ATAC-seq; ChIP-seq; ATAC-seq; ChIP-seq	CRISPR knockout; CRISPR-Cas9 endogenous deletion/editing; ChIP; In vivo phenotyping
E_02691	2011	21424707	cAMP target sequences enhCRE and CNRE sense low-salt intake to increase human renin gene expression in vivo	Homo sapiens	hg19	chr1	204123719	204123725	NA	REN	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Calu-6	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02692	2009	19467240	A far-upstream Oct-1 motif regulates cytokine-induced transcription of the human inducible nitric oxide synthase gene	Homo sapiens	hg19	chr17	26072592	26074592	POU2F1	NOS2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	hepatocyte	CL:0000182	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_02693	2023	37563118	Enhancer remodeling activates NOTCH3 signaling to confer chemoresistance in advanced nasopharyngeal carcinoma	Homo sapiens	hg19	chr2	202030000	202040000	NA	FZD7	Enhancer	Active	Disease	nasopharyngeal carcinoma	MONDO:0015459	DOID:9261	nasopharynx	UBERON:0001728	CNE-2	CVCL_6889	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; In vivo functional validation	ChIP-seq; RNA-seq	ChIP-qPCR; RT-qPCR; Western blot; In vivo phenotyping
E_02694	2020	32352029	BCL9/STAT3 regulation of transcriptional enhancer networks promote DCIS progression	Homo sapiens	hg19	chr17	45414208	45414987	NA	ITGB3	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	293T human CLDN18.2	CVCL_UE18	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; In vivo functional validation	ChIP-exo; RNA-seq, RPPA; RNA-seq	ChIP-qPCR, shRNA Knockdown; RT-qPCR; Western blot, In vivo Invasion Assay; ChIP; In vivo phenotyping
E_02695	2020	32352029	BCL9/STAT3 regulation of transcriptional enhancer networks promote DCIS progression	Homo sapiens	hg19	chr17	45436112	45436891	NA	ITGB3	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	293T human CLDN18.2	CVCL_UE18	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; In vivo functional validation	ChIP-exo; RNA-seq, RPPA; RNA-seq	ChIP-qPCR, shRNA Knockdown; RT-qPCR; Western blot, In vivo Invasion Assay; ChIP; In vivo phenotyping
E_02696	2018	29514092	Transcription Factor IRF8 Governs Enhancer Landscape Dynamics in Mononuclear Phagocyte Progenitors	Mus musculus	mm10	chr19	61151074	61161722	Irf8	Csf2ra	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Monocytes,Dendritic Cells	NA	monocyte	CL:0000576	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR; Transgenic/LacZ assay
E_02697	2018	29514092	Transcription Factor IRF8 Governs Enhancer Landscape Dynamics in Mononuclear Phagocyte Progenitors	Mus musculus	mm10	chr19	61158643	61164569	Irf8	Csf2ra	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Monocytes,Dendritic Cells	NA	monocyte	CL:0000576	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR; Transgenic/LacZ assay
E_02698	2018	29514092	Transcription Factor IRF8 Governs Enhancer Landscape Dynamics in Mononuclear Phagocyte Progenitors	Mus musculus	mm10	chr19	61165425	61172555	Irf8	Csf2ra	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Monocytes,Dendritic Cells	NA	monocyte	CL:0000576	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR; Transgenic/LacZ assay
E_02699	2018	29514092	Transcription Factor IRF8 Governs Enhancer Landscape Dynamics in Mononuclear Phagocyte Progenitors	Mus musculus	mm10	chr2	144000110	144014615	Irf8	Bfsp1	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Monocytes,Dendritic Cells	NA	monocyte	CL:0000576	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR; Transgenic/LacZ assay
E_02700	2018	29514092	Transcription Factor IRF8 Governs Enhancer Landscape Dynamics in Mononuclear Phagocyte Progenitors	Mus musculus	mm10	chr2	144014506	144023297	Irf8	Bfsp1	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Monocytes,Dendritic Cells	NA	monocyte	CL:0000576	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR; Transgenic/LacZ assay
E_02701	2018	29514092	Transcription Factor IRF8 Governs Enhancer Landscape Dynamics in Mononuclear Phagocyte Progenitors	Mus musculus	mm10	chr2	103464661	103471206	Irf8	Ehf	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Monocytes,Dendritic Cells	NA	monocyte	CL:0000576	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR; Transgenic/LacZ assay
E_02702	2015	25804738	Genome-wide characterisation of Foxa1 binding sites reveals several mechanisms for regulating neuronal differentiation in midbrain dopamine cells	Mus musculus	mm10	chr3	127641624	127642545	Foxa1	Neurog2	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Embryonic Stem Cell	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR; Transgenic/LacZ assay
E_02703	2015	25804738	Genome-wide characterisation of Foxa1 binding sites reveals several mechanisms for regulating neuronal differentiation in midbrain dopamine cells	Mus musculus	mm10	chr3	127641624	127642545	Foxa2	Neurog2	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Embryonic Stem Cell	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR; Transgenic/LacZ assay
E_02704	2015	25804738	Genome-wide characterisation of Foxa1 binding sites reveals several mechanisms for regulating neuronal differentiation in midbrain dopamine cells	Mus musculus	mm10	chr3	127641624	127642545	Otx2	Neurog2	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Embryonic Stem Cell	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq; RNA-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR; Transgenic/LacZ assay
E_02705	2014	24362753	Genetic determinants of neuroglobin transcription	Homo sapiens	hg19	chr14	77737282	77738405	NA	NGB	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	HEK293	CVCL_0045	transformed embryonic kidney-derived cell line	NA	Promoter activity assay; Cis-regulatory mapping assay; Regulatory variant analysis	Targeted next-generation sequencing; Illumina GoldenGate SNP genotyping; public ENCODE ChIP-seq/DNase-seq data integration	Dual-luciferase reporter assay; deletion mapping; Sanger sequencing
E_02706	2014	24711622	STAT3, STAT4, NFATc1, and CTCF regulate PD-1 through multiple novel regulatory regions in murine T cells	Mus musculus	mm9	chr1	95952661	95952820	Nfatc1	Pdcd1	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary splenic CD8 T cells	NA	CD8-positive, alpha-beta T cell	CL:0000625	Enhancer activity assay; TF binding assay; Chromatin interaction assay	Published STAT/NFAT ChIP-seq data analysis	DNase I hypersensitivity assay; ChIP-qPCR; Luciferase reporter assay; NFAT-site mutagenesis; 3C; RT-qPCR
E_02707	2014	24711622	STAT3, STAT4, NFATc1, and CTCF regulate PD-1 through multiple novel regulatory regions in murine T cells	Mus musculus	mm9	chr1	95952661	95952820	Stat3	Pdcd1	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary splenic CD8 T cells	NA	CD8-positive, alpha-beta T cell	CL:0000625	Enhancer activity assay; TF binding assay; Chromatin interaction assay	Published STAT ChIP-seq data analysis	DNase I hypersensitivity assay; ChIP-qPCR; Luciferase reporter assay; STAT-site mutagenesis; 3C; RT-qPCR
E_02708	2014	24711622	STAT3, STAT4, NFATc1, and CTCF regulate PD-1 through multiple novel regulatory regions in murine T cells	Mus musculus	mm9	chr1	95952661	95952820	Stat4	Pdcd1	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary splenic CD8 T cells	NA	CD8-positive, alpha-beta T cell	CL:0000625	Enhancer activity assay; TF binding assay; Chromatin interaction assay	Published STAT ChIP-seq data analysis	DNase I hypersensitivity assay; ChIP-qPCR; Luciferase reporter assay; STAT-site mutagenesis; 3C; RT-qPCR
E_02709	2014	25321476	Identification and characterization of the novel Col10a1 regulatory mechanism during chondrocyte hypertrophic differentiation	Mus musculus	mm10	chr10	34385685	34385834	Runx2	Col10a1	Enhancer	Active	Disease	Skeletal Diseases	NA	NA	blood	UBERON:0000178	MCT Cells	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	ChIP-qPCR/ChIP; EMSA/gel-shift assay; RT-qPCR/qPCR; Transgenic/LacZ assay
E_02710	2014	24711622	STAT3, STAT4, NFATc1, and CTCF regulate PD-1 through multiple novel regulatory regions in murine T cells	Mus musculus	mm9	chr1	95932003	95932042	Nfatc1	Pdcd1	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary splenic CD8 T cells	NA	CD8-positive, alpha-beta T cell	CL:0000625	Enhancer activity assay; TF binding assay; Chromatin interaction assay	Published STAT/NFAT ChIP-seq data analysis	DNase I hypersensitivity assay; ChIP-qPCR; Luciferase reporter assay; NFAT-site mutagenesis; 3C; RT-qPCR
E_02711	2014	24711622	STAT3, STAT4, NFATc1, and CTCF regulate PD-1 through multiple novel regulatory regions in murine T cells	Mus musculus	mm9	chr1	95932003	95932042	Stat3	Pdcd1	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary splenic CD8 T cells	NA	CD8-positive, alpha-beta T cell	CL:0000625	Enhancer activity assay; TF binding assay; Chromatin interaction assay	Published STAT ChIP-seq data analysis	DNase I hypersensitivity assay; ChIP-qPCR; Luciferase reporter assay; STAT-site mutagenesis; 3C; RT-qPCR
E_02712	2014	24711622	STAT3, STAT4, NFATc1, and CTCF regulate PD-1 through multiple novel regulatory regions in murine T cells	Mus musculus	mm9	chr1	95932003	95932042	Stat4	Pdcd1	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary splenic CD8 T cells	NA	CD8-positive, alpha-beta T cell	CL:0000625	Enhancer activity assay; TF binding assay; Chromatin interaction assay	Published STAT ChIP-seq data analysis	DNase I hypersensitivity assay; ChIP-qPCR; Luciferase reporter assay; STAT-site mutagenesis; 3C; RT-qPCR
E_02713	2014	24362753	Genetic determinants of neuroglobin transcription	Homo sapiens	hg19	chr14	77264349	77265491	NA	NGB	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	human temporal cortex samples	NA	neural cell	CL:0002319	Disease-variant functional analysis; Promoter/enhancer deletion mapping and genetic regulatory analysis	Genotyping / expression association	Luciferase reporter; serial deletion analysis; expression analysis
E_02714	2014	24362753	Genetic determinants of neuroglobin transcription	Homo sapiens	hg19	chr14	77264349	77265491	NA	NGB	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	reporter cell model	NA	neural cell	CL:0002319	Disease-variant functional analysis; Promoter/enhancer deletion mapping and genetic regulatory analysis	Genotyping / expression association	Luciferase reporter; serial deletion analysis; expression analysis
E_02715	2015	25804738	Genome-wide characterisation of Foxa1 binding sites reveals several mechanisms for regulating neuronal differentiation in midbrain dopamine cells	Mus musculus	mm10	chr3	127349185	127349631	Foxa1	Neurog2	Enhancer	Active	Normal	NA	NA	NA	midbrain	UBERON:0001891	mDA progenitors/neurons (E12.5)	NA	dopaminergic neuron	CL:0000700	Enhancer activity assay; TF binding assay; Chromatin-state profiling; TF binding assay (ChIP-supported)	ChIP-seq; RNA-seq; RNA-seq; ChIP-seq	Transgenic reporter assay; ChIP-qPCR; ChIP
E_02716	2012	22408256	Expression of ABO blood-group genes is dependent upon an erythroid cell-specific regulatory element that is deleted in persons with the B(m) phenotype	Homo sapiens	hg19	chr9	133238853	133239354	GATA1	ABO	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay	NA	Luciferase reporter assay, EMSA; RT-qPCR; Luciferase reporter assay
E_02717	2014	24362753	Genetic determinants of neuroglobin transcription	Homo sapiens	hg19	chr14	77264349	77265491	NA	NGB	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	NA	NA	HEK293	CVCL_0045	NA	NA	Enhancer activity assay; TF-binding/chromatin assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_02718	2009	19467240	A far-upstream Oct-1 motif regulates cytokine-induced transcription of the human inducible nitric oxide synthase gene	Homo sapiens	hg19	chr17	26071355	26071455	NA	NOS2	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	HEK293	CVCL_0045	embryonic kidney cell	NA	Enhancer activity assay	NA	Luciferase reporter assay
E_02719	2019	30518632	Eradication of Central Nervous System Leukemia of T-Cell Origin with a Brain-Permeable LSD1 Inhibitor	Homo sapiens	hg19	chr1	47704791	47705107	ZEB2	TAL1	Super-enhancer	Repressed	Disease	Central Nervous System Leukemia	NA	DOID:12969	blood	UBERON:0000178	T-acute lymphoblastic leukemia (T-ALL)	NA	malignant cell	CL:0001064	In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	ChIP-qPCR/ChIP; RT-qPCR/qPCR; Transgenic/LacZ assay
E_02720	2019	30518632	Eradication of Central Nervous System Leukemia of T-Cell Origin with a Brain-Permeable LSD1 Inhibitor	Homo sapiens	hg19	chr19	15308673	15308842	ZEB2	NOTCH3	Super-enhancer	Repressed	Disease	Central Nervous System Leukemia	NA	DOID:12969	blood	UBERON:0000178	T-acute lymphoblastic leukemia (T-ALL)	NA	malignant cell	CL:0001064	In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	ChIP-qPCR/ChIP; RT-qPCR/qPCR; Transgenic/LacZ assay
E_02721	2019	31890812	Expression analysis data of BCL11A and γ-globin genes in KU812 and KG-1 cell lines after CRISPR/Cas9-mediated BCL11A enhancer deletion	Homo sapiens	hg38	chr2	60447611	60449611	NA	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	blood	UBERON:0000178	KG-1	NA	erythroid/myeloid leukemia cell line used for BCL11A enhancer editing	NA	Chromatin interaction assay; Endogenous enhancer perturbation; Enhancer CRISPR perturbation study	NA	3C; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_02722	2019	31890812	Expression analysis data of BCL11A and γ-globin genes in KU812 and KG-1 cell lines after CRISPR/Cas9-mediated BCL11A enhancer deletion	Homo sapiens	hg38	chr2	60447611	60449611	NA	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	blood	UBERON:0000178	KU812	NA	erythroid/myeloid leukemia cell line used for BCL11A enhancer editing	NA	Chromatin interaction assay; Endogenous enhancer perturbation; Enhancer CRISPR perturbation study	NA	3C; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_02723	2017	28652246	MAPK Signaling and Inflammation Link Melanoma Phenotype Switching to Induction of CD73 during Immunotherapy	Homo sapiens	hg19	chr6	86160197	86176777	JUN	NT5E	Enhancer	Active	Disease	melanoma	MONDO:0005105	DOID:1909	skin	UBERON:0002097	Melanoma	NA	malignant cell	CL:0001064	Endogenous enhancer perturbation; In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02724	2013	23307821	Essential and unexpected role of Yin Yang 1 to promote mesodermal cardiac differentiation	Mus musculus	mm10	chr17	26829229	26831311	Yy1	Nkx2-5	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	Cardiac Progenitor Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_02725	2017	28652246	MAPK Signaling and Inflammation Link Melanoma Phenotype Switching to Induction of CD73 during Immunotherapy	Homo sapiens	hg19	chr6	8120004	8120873	JUN	NT5E	Enhancer	Active	Disease	cutaneous melanoma	MONDO:0005012	DOID:8923	zone of skin	UBERON:0000014	SK-MEL-28	CVCL_0526	melanoma cell	NA	Enhancer activity assay; Functional perturbation assay	ChIP-seq	CRISPR knockout; ChIP-qPCR; RT-qPCR
E_02726	2020	32817515	The Atoh7 remote enhancer provides transcriptional robustness during retinal ganglion cell development	Mus musculus	mm10	chr10	72890000	72890392	NA	Atoh7	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	developing retina	NA	retinal progenitor cell	CL:0002672	Enhancer activity assay; Endogenous enhancer perturbation; In vivo functional validation	ATAC-seq	Transgenic reporter assay; CRISPR/Cas9 deletion; RT-PCR; Immunostaining; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_02727	2020	32817515	The Atoh7 remote enhancer provides transcriptional robustness during retinal ganglion cell development	Mus musculus	mm10	chr10	72890000	72890392	NA	Atoh7	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	developing retina	NA	retinal ganglion cell	CL:0000740	Enhancer activity assay; Endogenous enhancer perturbation; In vivo functional validation	ATAC-seq	Transgenic reporter assay; CRISPR/Cas9 deletion; RT-PCR; Immunostaining; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_02728	2020	32817515	The Atoh7 remote enhancer provides transcriptional robustness during retinal ganglion cell development	Mus musculus	mm10	chr10	72894616	72895600	NA	Atoh7	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	developing retina	NA	retinal ganglion cell	CL:0000740	Enhancer activity assay; Endogenous enhancer perturbation; In vivo functional validation	ATAC-seq	Transgenic reporter assay; CRISPR/Cas9 deletion; RT-PCR; Immunostaining; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_02729	2018	30008200	CTCF Regulates Otic Neurogenesis via Histone Modification in the Neurog1 Locus	Mus musculus	mm10	chr13	56243248	56243833	Ctcf	Neurog1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	P19	CVCL_2153	NA	NA	In vivo functional validation; TF-binding/chromatin assay	NA	ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02730	2018	30008200	CTCF Regulates Otic Neurogenesis via Histone Modification in the Neurog1 Locus	Mus musculus	mm10	chr13	56244114	56244357	Ctcf	Neurog1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	P19	CVCL_2153	NA	NA	In vivo functional validation; TF-binding/chromatin assay	NA	ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02731	2018	30008200	CTCF Regulates Otic Neurogenesis via Histone Modification in the Neurog1 Locus	Mus musculus	mm10	chr13	56245174	56245857	Ctcf	Neurog1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	P19	CVCL_2153	NA	NA	In vivo functional validation; TF-binding/chromatin assay	NA	ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02732	2020	32817515	The Atoh7 remote enhancer provides transcriptional robustness during retinal ganglion cell development	Mus musculus	mm10	chr10	72890000	72895600	NA	Atoh7	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	Retinal Progenitor Cells	NA	retinal progenitor cell	CL:0002672	Enhancer activity assay; Enhancer deletion assay; In vivo developmental assay	ATAC-seq; RNA-seq; ChIP-seq	Genome editing of remote enhancer; RT-qPCR; immunostaining; optic-nerve and retinal phenotyping
E_02733	2020	32817515	The Atoh7 remote enhancer provides transcriptional robustness during retinal ganglion cell development	Mus musculus	mm10	chr10	72890000	72895600	NA	Atoh7	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	Retinal Ganglion Cells	NA	retinal ganglion cell	CL:0000740	Enhancer activity assay; Enhancer deletion assay; In vivo developmental assay	ATAC-seq; RNA-seq; ChIP-seq	Genome editing of remote enhancer; RT-qPCR; immunostaining; optic-nerve and retinal phenotyping
E_02734	2020	33239788	A map of cis-regulatory elements and 3D genome structures in zebrafish	Danio rerio	danRer11	chr1	47366207	47368074	NA	NA	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	embryonic heart	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Chromatin interaction assay; Chromatin-state profiling	ChIP-seq; ATAC-seq; single-cell ATAC-seq; RNA-seq; Hi-C	Transgenic reporter assay; ChIP
E_02735	2020	33239788	A map of cis-regulatory elements and 3D genome structures in zebrafish	Danio rerio	danRer11	chr23	5735883	5736938	NA	NA	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	embryonic heart	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Chromatin interaction assay; Chromatin-state profiling	ChIP-seq; ATAC-seq; single-cell ATAC-seq; RNA-seq; Hi-C	Transgenic reporter assay; ChIP
E_02736	2020	33239788	A map of cis-regulatory elements and 3D genome structures in zebrafish	Danio rerio	danRer11	chr5	49025012	49026815	NA	NA	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	embryonic heart	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Chromatin interaction assay; Chromatin-state profiling	ChIP-seq; ATAC-seq; single-cell ATAC-seq; RNA-seq; Hi-C	Transgenic reporter assay; ChIP
E_02737	2020	33239788	A map of cis-regulatory elements and 3D genome structures in zebrafish	Danio rerio	danRer11	chr6	43661350	43663650	NA	NA	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	embryonic brain	NA	neuron	CL:0000540	Enhancer activity assay; Chromatin interaction assay; Chromatin-state profiling	ChIP-seq; ATAC-seq; single-cell ATAC-seq; RNA-seq; Hi-C	Transgenic reporter assay; ChIP
E_02738	2020	33239788	A map of cis-regulatory elements and 3D genome structures in zebrafish	Danio rerio	danRer11	chr8	44088636	44090085	NA	NA	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	embryonic brain	NA	neuron	CL:0000540	Enhancer activity assay; Chromatin interaction assay; Chromatin-state profiling	ChIP-seq; ATAC-seq; single-cell ATAC-seq; RNA-seq; Hi-C	Transgenic reporter assay; ChIP
E_02739	2020	32817515	The Atoh7 remote enhancer provides transcriptional robustness during retinal ganglion cell development	Homo sapiens	hg19	chr10	94770000	94776500	NA	ATOH7	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	Retinal Progenitor Cells	NA	retinal progenitor cell	CL:0002672	Enhancer activity assay; Endogenous enhancer perturbation; In vivo functional validation	NA	Transgenic reporter assay; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_02740	2020	33239788	A map of cis-regulatory elements and 3D genome structures in zebrafish	Danio rerio	danRer11	chr25	17938108	17939563	NA	NA	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	embryonic kidney	NA	embryonic kidney cell	NA	Enhancer activity assay	ChIP-seq; ATAC-seq; Hi-C	Transgenic reporter assay
E_02741	2020	33239788	A map of cis-regulatory elements and 3D genome structures in zebrafish	Danio rerio	danRer11	chr25	17939264	17940252	NA	NA	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	embryonic kidney	NA	embryonic kidney cell	NA	Enhancer activity assay	ChIP-seq; ATAC-seq; Hi-C	Transgenic reporter assay
E_02742	2020	33239788	A map of cis-regulatory elements and 3D genome structures in zebrafish	Danio rerio	danRer11	chr5	61665365	61667095	NA	NA	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	embryonic kidney	NA	embryonic kidney cell	NA	Enhancer activity assay	ChIP-seq; ATAC-seq; Hi-C	Transgenic reporter assay
E_02743	2020	33239788	A map of cis-regulatory elements and 3D genome structures in zebrafish	Danio rerio	danRer11	chr1	7624913	7626890	NA	NA	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle	NA	embryonic myocyte	NA	embryonic myocyte	NA	Enhancer activity assay	ChIP-seq; ATAC-seq; Hi-C	Transgenic reporter assay
E_02744	2020	33239788	A map of cis-regulatory elements and 3D genome structures in zebrafish	Danio rerio	danRer11	chr1	19433791	19434807	NA	NA	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle	NA	embryonic myocyte	NA	embryonic myocyte	NA	Enhancer activity assay	ChIP-seq; ATAC-seq; Hi-C	Transgenic reporter assay
E_02745	2013	23307821	Essential and unexpected role of Yin Yang 1 to promote mesodermal cardiac differentiation	Mus musculus	mm10	chr17	27040383	27042465	Yy1	Nkx2-5	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	Cardiac progenitor cells	NA	cardiac progenitor cell	NA	Enhancer activity assay	ChIP-seq	Luciferase reporter assay; Transgenic reporter assay; ChIP-qPCR
E_02746	2017	28614915	Identification of an Enhancer Critical for the ephirn-A5 Gene Expression in the Posterior Region of the Mesencephalon	Mus musculus	mm10	chr17	62627957	62633457	Ascl1	Efna5	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mesencephalon	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; EMSA/gel-shift assay
E_02747	2017	29326336	ARID5B as a critical downstream target of the TAL1 complex that activates the oncogenic transcriptional program and promotes T-cell leukemogenesis	Homo sapiens	hg19	chr10	63525013	63527013	TAL1	ARID5B	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	T-acute lymphoblastic leukemia (T-ALL)	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIA-PET	CRISPR-Cas9 targeted editing/deletion
E_02748	2015	26659182	The histone chaperone CAF-1 safeguards somatic cell identity	Mus musculus	mm10	chr2	168744572	168752225	Sox2	Sall4	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Induced Pluripotent Stem Cells	NA	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; ATAC-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_02749	2011	21689639	A Tcf/Lef element within the enhancer region of the human NANOG gene plays a role in promoter activation	Homo sapiens	hg19	chr12	7940709	7941994	LEF1	NANOG	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	HEK293	CVCL_0045	epithelial cell	CL:0000066	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Luciferase reporter assay; ChIP; Site-directed mutagenesis; shRNA knockdown; Western blot
E_02750	1995	7891702	Human granulocyte-macrophage colony-stimulating factor enhancer function is associated with cooperative interactions between AP-1 and NFATp/c	Homo sapiens	hg19	chr5	131406243	131406930	NFATC2	CSF2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Jurkat	CVCL_0065	T cell	CL:0000084	Enhancer activity assay; TF binding assay; Functional cis-regulatory mapping	NA	Enhancer deletion mapping; CAT reporter assay; transient transfection; PMA/A23187 stimulation; cyclosporin A inhibition; EMSA; competition EMSA; antibody supershift assay; methylation interference assay; DNase I footprinting; synthetic oligonucleotide enhancer assay
E_02751	2015	26659182	The histone chaperone CAF-1 safeguards somatic cell identity	Mus musculus	mm10	chr8	89041889	89090124	Sox2	Sall1	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Induced Pluripotent Stem Cells	NA	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq; ATAC-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_02752	2024	38934080	Core regions in immunoglobulin heavy chain enhancers essential for survival of non-Hodgkin lymphoma cells are identified by a CRISPR interference screen	Homo sapiens	hg19	chr14	106328838	106329184	NA	IGH	Enhancer	Active	Disease	Burkitt lymphoma	MONDO:0007243	DOID:8584	blood	UBERON:0000178	Human Burkitt lymphoma cell	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation	CRISPRi screening; RNA-seq; ATAC-seq; RNA-seq; CRISPR genetic screen	CRISPRi; RT-qPCR; Western blot, Flow Cytometry, GFP competition assay; CRISPRi
E_02753	2023	37858706	YY1 Binding to Regulatory Elements That Lack Enhancer Activity Promotes Locus Folding and Gene Activation	Mus musculus	mm10	chr16	19007329	19008187	Irf4	Iglv1	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	103/BCL-2 pre-B cells	NA	precursor B cell	CL:0000817	Enhancer activity assay; TF binding assay; enhancer-hub / locus-folding analysis	ATAC-seq; ChIP-seq reanalysis	Luciferase reporter assay; ChIP-qPCR; targeted 3C
E_02754	2023	37858706	YY1 Binding to Regulatory Elements That Lack Enhancer Activity Promotes Locus Folding and Gene Activation	Mus musculus	mm10	chr16	19007329	19008187	Spi1	Iglv1	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	103/BCL-2 pre-B cells	NA	precursor B cell	CL:0000817	Enhancer activity assay; TF binding assay; enhancer-hub / locus-folding analysis	ATAC-seq; ChIP-seq reanalysis	Luciferase reporter assay; ChIP-qPCR; targeted 3C
E_02755	2023	37858706	YY1 Binding to Regulatory Elements That Lack Enhancer Activity Promotes Locus Folding and Gene Activation	Mus musculus	mm10	chr16	19007329	19008187	Tcf3	Iglv1	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	103/BCL-2 pre-B cells	NA	precursor B cell	CL:0000817	Enhancer activity assay; TF binding assay; enhancer-hub / locus-folding analysis	ATAC-seq; ChIP-seq reanalysis	Luciferase reporter assay; ChIP-qPCR; targeted 3C
E_02756	2023	37858706	YY1 Binding to Regulatory Elements That Lack Enhancer Activity Promotes Locus Folding and Gene Activation	Mus musculus	mm10	chr16	19007329	19008187	Yy1	Iglv1	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	103/BCL-2 pre-B cells	NA	precursor B cell	CL:0000817	Enhancer activity assay; TF binding assay; enhancer-hub / locus-folding analysis	ATAC-seq; ChIP-seq reanalysis	Luciferase reporter assay; ChIP-qPCR; targeted 3C
E_02757	2019	31767869	LncRNA REG1CP promotes tumorigenesis through an enhancer complex to recruit FANCJ helicase for REG3A transcription	Homo sapiens	hg38	chr2	79272263	79272447	NA	REG3A	Enhancer	Active	Disease	cancer (subtype not defined in abstract)	NA	NA	colon	UBERON:0001155	HT-29	CVCL_0320	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	RNA-seq; ChIP-seq	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot, EMSA, shRNA Knockdown
E_02758	2019	31767869	LncRNA REG1CP promotes tumorigenesis through an enhancer complex to recruit FANCJ helicase for REG3A transcription	Homo sapiens	hg38	chr2	79272263	79272447	NA	REG3A	Enhancer	Active	Disease	cancer (subtype not defined in abstract)	NA	NA	colon	UBERON:0001155	LIM1215	CVCL_2574	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	RNA-seq; ChIP-seq	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot, EMSA, shRNA Knockdown
E_02759	2019	31767869	LncRNA REG1CP promotes tumorigenesis through an enhancer complex to recruit FANCJ helicase for REG3A transcription	Homo sapiens	hg38	chr2	79272263	79272447	NA	REG3A	Enhancer	Active	Disease	cancer (subtype not defined in abstract)	NA	NA	colon	UBERON:0001155	SW480	CVCL_0546	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	RNA-seq; ChIP-seq	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot, EMSA, shRNA Knockdown
E_02760	2017	28378740	A CD47-associated super-enhancer links pro-inflammatory signalling to CD47 upregulation in breast cancer	Homo sapiens	hg19	chr3	107702615	107714185	NFKB1	CD47	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RNAi/siRNA/shRNA
E_02761	2017	28378740	A CD47-associated super-enhancer links pro-inflammatory signalling to CD47 upregulation in breast cancer	Homo sapiens	hg19	chr3	107842838	107845592	NFKB1	CD47	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RNAi/siRNA/shRNA
E_02762	2017	28378740	A CD47-associated super-enhancer links pro-inflammatory signalling to CD47 upregulation in breast cancer	Homo sapiens	hg19	chr3	107846969	107854683	NFKB1	CD47	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RNAi/siRNA/shRNA
E_02763	2016	26787680	Desmin enters the nucleus of cardiac stem cells and modulates Nkx2.5 expression by participating in transcription factor complexes that interact with the nkx2.5 gene	Mus musculus	mm10	chr17	26844119	26844624	NA	Nkx2-5	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	Cardiac progenitor cells from differentiating embryoid bodies	NA	cardiac muscle myoblast	CL:0000513	Enhancer activity assay; Functional perturbation assay; Chromatin occupancy assay	NA	Luciferase reporter assay; ChIP-PCR/ChIP-qPCR; Desmin knockdown/overexpression; RT-qPCR; Western blot; co-immunoprecipitation
E_02764	2016	26787680	Desmin enters the nucleus of cardiac stem cells and modulates Nkx2.5 expression by participating in transcription factor complexes that interact with the nkx2.5 gene	Mus musculus	mm10	chr17	26850487	26850997	NA	Nkx2-5	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	Cardiac progenitor cells from differentiating embryoid bodies	NA	cardiac muscle myoblast	CL:0000513	Enhancer activity assay; Functional perturbation assay; Chromatin occupancy assay	NA	Luciferase reporter assay; ChIP-PCR/ChIP-qPCR; Desmin knockdown/overexpression; RT-qPCR; Western blot; co-immunoprecipitation
E_02765	2000	11395135	Identification and characterization of two CD40-inducible enhancers in the mouse TRAF1 gene locus	Mus musculus	mm10	chr2	34963164	34963369	NA	Traf1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	M12	CVCL_IU99	B cell	CL:0000236	Enhancer activity assay; Functional perturbation assay; TF binding assay; CD40-responsive transcription assay	NA	CD40 stimulation; transient reporter assay; enhancer deletion mapping; NF-kappaB-site-directed mutagenesis; EMSA; competition EMSA
E_02766	2000	11395135	Identification and characterization of two CD40-inducible enhancers in the mouse TRAF1 gene locus	Mus musculus	mm10	chr2	34954556	34954788	NA	Traf1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	M12	CVCL_IU99	B cell	CL:0000236	Enhancer activity assay; Functional perturbation assay; TF binding assay; CD40-responsive transcription assay	NA	CD40 stimulation; transient reporter assay; intronic enhancer mapping; NF-kappaB-site-directed mutagenesis; AP-1-site-directed mutagenesis; combined NF-kappaB/AP-1 mutational analysis; EMSA; competition EMSA
E_02767	2020	33020665	Highly interconnected enhancer communities control lineage-determining genes in human mesenchymal stem cells	Homo sapiens	hg19	chr19	33790000	33792000	CEBPB	CEBPA	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	bone marrow mesenchymal stem	NA	mesenchymal stem cell	CL:0000134	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ECHi-C; ChIP-seq, scATAC-seq; RNA-seq	ChIP-qPCR; RT-qPCR
E_02768	2020	33020665	Highly interconnected enhancer communities control lineage-determining genes in human mesenchymal stem cells	Homo sapiens	hg19	chr3	12335000	12337000	CEBPB	PPARG	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	bone marrow mesenchymal stem	NA	mesenchymal stem cell	CL:0000134	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ECHi-C; ChIP-seq, scATAC-seq; RNA-seq	ChIP-qPCR; RT-qPCR
E_02769	2020	33020665	Highly interconnected enhancer communities control lineage-determining genes in human mesenchymal stem cells	Homo sapiens	hg19	chr3	186560000	186562000	CEBPB	ADIPOQ	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	bone marrow mesenchymal stem	NA	mesenchymal stem cell	CL:0000134	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ECHi-C; ChIP-seq, scATAC-seq; RNA-seq	ChIP-qPCR; RT-qPCR
E_02770	2020	33020665	Highly interconnected enhancer communities control lineage-determining genes in human mesenchymal stem cells	Homo sapiens	hg19	chr4	54950000	54952000	TEAD1	PDGFRA	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	bone marrow mesenchymal stem	NA	mesenchymal stem cell	CL:0000134	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ECHi-C; ChIP-seq, scATAC-seq, scRNA-seq; RNA-seq	ChIP-qPCR; RT-qPCR
E_02771	2020	33020665	Highly interconnected enhancer communities control lineage-determining genes in human mesenchymal stem cells	Homo sapiens	hg19	chr4	54950000	54952000	TEAD4	PDGFRA	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	bone marrow mesenchymal stem	NA	mesenchymal stem cell	CL:0000134	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ECHi-C; ChIP-seq, scATAC-seq, scRNA-seq; RNA-seq	ChIP-qPCR; RT-qPCR
E_02772	2020	33020665	Highly interconnected enhancer communities control lineage-determining genes in human mesenchymal stem cells	Homo sapiens	hg19	chr6	45300000	45302000	RUNX2	RUNX2	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	bone marrow mesenchymal stem	NA	mesenchymal stem cell	CL:0000134	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ECHi-C; ChIP-seq, scATAC-seq; RNA-seq	ChIP-qPCR; RT-qPCR
E_02773	2020	33020665	Highly interconnected enhancer communities control lineage-determining genes in human mesenchymal stem cells	Homo sapiens	hg19	chr6	132200000	132202000	TEAD1	CCN2	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	bone marrow mesenchymal stem	NA	mesenchymal stem cell	CL:0000134	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ECHi-C; ChIP-seq, scATAC-seq, scRNA-seq; RNA-seq	ChIP-qPCR; RT-qPCR
E_02774	2020	33020665	Highly interconnected enhancer communities control lineage-determining genes in human mesenchymal stem cells	Homo sapiens	hg19	chr6	132200000	132202000	TEAD4	CCN2	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	bone marrow mesenchymal stem	NA	mesenchymal stem cell	CL:0000134	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ECHi-C; ChIP-seq, scATAC-seq, scRNA-seq; RNA-seq	ChIP-qPCR; RT-qPCR
E_02775	2017	28378740	A CD47-associated super-enhancer links pro-inflammatory signalling to CD47 upregulation in breast cancer	Homo sapiens	hg19	chr3	107662655	107762655	NFKB1	CD47	Super-enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq; ChIA-PET	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RNAi/siRNA/shRNA
E_02776	2024	38934080	Core regions in immunoglobulin heavy chain enhancers essential for survival of non-Hodgkin lymphoma cells are identified by a CRISPR interference screen	Homo sapiens	hg19	chr14	106032312	106033352	NA	MYC	Enhancer	Active	Disease	Burkitt lymphoma	MONDO:0007243	DOID:8584	blood	UBERON:0000178	Burkitt lymphoma cell line	NA	malignant cell	CL:0001064	Functional perturbation assay; Endogenous enhancer perturbation	CRISPR screen; RNA-seq; CRISPR genetic screen	RT-qPCR; Western blot; CRISPRi
E_02777	2024	38934080	Core regions in immunoglobulin heavy chain enhancers essential for survival of non-Hodgkin lymphoma cells are identified by a CRISPR interference screen	Homo sapiens	hg19	chr14	106041116	106041795	NA	BCL2	Enhancer	Active	Disease	Burkitt lymphoma	MONDO:0007243	DOID:8584	blood	UBERON:0000178	Diffuse large B-cell lymphoma cell line	NA	malignant cell	CL:0001064	Functional perturbation assay; Endogenous enhancer perturbation	CRISPR screen; RNA-seq; CRISPR genetic screen	RT-qPCR; Western blot; CRISPRi
E_02778	2020	33020665	Highly interconnected enhancer communities control lineage-determining genes in human mesenchymal stem cells	Homo sapiens	hg19	chr7	107615000	107635000	NA	LAMB1	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	bone marrow mesenchymal stem	NA	mesenchymal stem cell	CL:0000134	Enhancer activity assay; Chromatin interaction assay; eQTL validation	ECHi-C; ChIP-seq; DNase-seq, scATAC-seq; RNA-seq	RT-qPCR
E_02779	2000	11395135	Identification and characterization of two CD40-inducible enhancers in the mouse TRAF1 gene locus	Mus musculus	mm10	chr9	19188000	19188100	Nfkb1	Traf1	Enhancer	Active	Disease	B-cell non-Hodgkin lymphoma	MONDO:0015759	DOID:164	blood	UBERON:0000178	M12 B cells	NA	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay	NA	Luciferase reporter assay; EMSA; RT-qPCR
E_02780	2000	11395135	Identification and characterization of two CD40-inducible enhancers in the mouse TRAF1 gene locus	Mus musculus	mm10	chr9	19196000	19196100	Nfkb1	Traf1	Enhancer	Active	Disease	B-cell non-Hodgkin lymphoma	MONDO:0015759	DOID:164	blood	UBERON:0000178	M12 B cells	NA	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay	NA	Luciferase reporter assay; EMSA; RT-qPCR
E_02781	2024	38934080	Core regions in immunoglobulin heavy chain enhancers essential for survival of non-Hodgkin lymphoma cells are identified by a CRISPR interference screen	Homo sapiens	hg19	chr14	106152156	106153203	NA	MYC	Enhancer	Active	Disease	Burkitt lymphoma	MONDO:0007243	DOID:8584	blood	UBERON:0000178	BL-41	NA	B cell	CL:0000236	IGH 3′RR core peak 1; dense tiling CRISPRi-defined essential enhancer; eRNA-producing region; causal control of translocated MYC and lymphoma-cell survival	Tiling CRISPRi screen with NGS sgRNA quantification; chromatin-enriched RNA-seq	Individual-sgRNA CRISPRi; GFP growth-competition assay; RT-qPCR for eRNA/MYC; BCR surface immunostaining/flow cytometry; MYC-rescue framework
E_02782	2024	38934080	Core regions in immunoglobulin heavy chain enhancers essential for survival of non-Hodgkin lymphoma cells are identified by a CRISPR interference screen	Homo sapiens	hg19	chr14	106152156	106153203	NA	MYC	Enhancer	Active	Disease	Burkitt lymphoma	MONDO:0007243	DOID:8584	blood	UBERON:0000178	study-wide validation also included DG-75, SUDHL4 and lymphoma samples	NA	B cell	CL:0000236	IGH 3′RR core peak 1; dense tiling CRISPRi-defined essential enhancer; eRNA-producing region; causal control of translocated MYC and lymphoma-cell survival	Tiling CRISPRi screen with NGS sgRNA quantification; chromatin-enriched RNA-seq	Individual-sgRNA CRISPRi; GFP growth-competition assay; RT-qPCR for eRNA/MYC; BCR surface immunostaining/flow cytometry; MYC-rescue framework
E_02783	2024	38934080	Core regions in immunoglobulin heavy chain enhancers essential for survival of non-Hodgkin lymphoma cells are identified by a CRISPR interference screen	Homo sapiens	hg19	chr14	106162681	106163347	NA	MYC	Enhancer	Active	Disease	Burkitt lymphoma	MONDO:0007243	DOID:8584	blood	UBERON:0000178	DG-75	NA	B cell	CL:0000236	IGH 3′RR core peak 2; dense tiling CRISPRi-defined essential enhancer; eRNA-producing region; causal control of translocated MYC and lymphoma-cell survival	Tiling CRISPRi screen with NGS sgRNA quantification; chromatin-enriched RNA-seq	Individual-sgRNA CRISPRi; GFP growth-competition assay; RT-qPCR for eRNA/MYC; BCR surface immunostaining/flow cytometry; inducible MYC overexpression rescue
E_02784	2024	38934080	Core regions in immunoglobulin heavy chain enhancers essential for survival of non-Hodgkin lymphoma cells are identified by a CRISPR interference screen	Homo sapiens	hg19	chr14	106162681	106163347	NA	MYC	Enhancer	Active	Disease	Burkitt lymphoma	MONDO:0007243	DOID:8584	blood	UBERON:0000178	study-wide validation also included BL-41, SUDHL4 and lymphoma samples	NA	B cell	CL:0000236	IGH 3′RR core peak 2; dense tiling CRISPRi-defined essential enhancer; eRNA-producing region; causal control of translocated MYC and lymphoma-cell survival	Tiling CRISPRi screen with NGS sgRNA quantification; chromatin-enriched RNA-seq	Individual-sgRNA CRISPRi; GFP growth-competition assay; RT-qPCR for eRNA/MYC; BCR surface immunostaining/flow cytometry; inducible MYC overexpression rescue
E_02785	2017	28614915	Identification of an Enhancer Critical for the ephirn-A5 Gene Expression in the Posterior Region of the Mesencephalon	Mus musculus	mm10	chr1	134714823	134715623	Ascl1	Efna5	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Primary mouse mesencephalic cells	NA	neuron	CL:0000540	Enhancer activity assay; TF binding assay	NA	Transgenic reporter assay, Luciferase reporter assay, EMSA; Transgenic enhancer reporter assay; EMSA
E_02786	2016	26787680	Desmin enters the nucleus of cardiac stem cells and modulates Nkx2.5 expression by participating in transcription factor complexes that interact with the nkx2.5 gene	Mus musculus	mm10	chr17	26829232	26829742	Des	Nkx2-5	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	Cardiac Progenitor Cell	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_02787	2011	21689639	A Tcf/Lef element within the enhancer region of the human NANOG gene plays a role in promoter activation	Homo sapiens	hg19	chr12	7940709	7941994	LEF1	NANOG	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HEK293	CVCL_0045	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_02788	2026	41827844	MGMT Promoter and Enhancer Methylation in Melanoma Brain Metastases and Glioblastoma: Shared and Distinct Features	Homo sapiens	hg38	chr10	129605804	129607046	NA	MGMT	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hepatocyte	NA	hepatocyte	CL:0000182	Enhancer activity assay	DNA methylation profiling	Transgenic reporter assay
E_02789	2025	41081394	Generation and characterization of a knockout mouse of an enhancer of EBF3	Mus musculus	mm10	chr7	136083275	136084434	NA	Ebf3	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	Mouse Embryonic Brain Cells	NA	mouse embryonic brain cell	NA	Functional perturbation assay; Chromatin interaction assay	Hi-C; RNA-seq; PacBio HiFi Whole-Genome Sequencing	CRISPR knockout; RT-qPCR; PCR Genotyping
E_02790	2024	38555298	A conserved NR5A1-responsive enhancer regulates SRY in testis-determination	Homo sapiens	hg38	chrY	2792658	2792907	NR5A1	SRY	Enhancer	Active	Disease	46,XY disorder of sex development	MONDO:0020040	NA	kidney	UBERON:0002113	HEK293T	CVCL_0063	transformed cell line	NA	Enhancer activity assay; Functional perturbation assay	whole-genome sequencing; DNase-seq (ENCODE)	NR5A1 co-transfection luciferase reporter assay; E250 variant reporter assay; NR5A1-motif disruption reporter assay; Sanger sequencing
E_02791	2019	31217582	Noncoding deletions reveal a gene that is critical for intestinal function	Homo sapiens	hg19	chr16	1480850	1482378	NA	PERCC1	Enhancer	Active	Disease	intractable congenital diarrhoea caused by intestine-critical region deletion	NA	NA	intestine	UBERON:0000160	patient-derived intestinal organoids	NA	enteroendocrine cell	CL:0000164	Disease-associated noncoding deletion analysis; transgenic enhancer reporter; endogenous regulatory-region deletion; target-gene rescue; in vivo phenotyping	whole-genome sequencing; whole-exome sequencing; RNA-seq; intestinal single-cell transcriptome re-analysis	Transgenic mouse reporter assay; targeted ICR deletion in mice; RT-qPCR; Immunofluorescence; histology; iPSC-derived intestinal organoid analysis; ICR-driven PERCC1 rescue transgene
E_02792	2019	31290539	A 50-bp enhancer of the mouse acrosomal vesicle protein 1 gene activates round spermatid-specific transcription in vivo?	Mus musculus	mm10	chr9	59048862	59048913	NA	Acrv1	Enhancer	Active	Normal	NA	NA	NA	testis	UBERON:0000473	Round spermatids	NA	spermatid	CL:0000018	Enhancer activity assay; TF binding assay; In vivo functional validation	NA	Transgenic reporter assay, Luciferase reporter assay; Transgenic enhancer reporter assay; In vivo phenotyping; Reporter assay
E_02793	2017	28836200	Characterization of Mesenchymal-Fibroblast Cells Using the Col1a2 Promoter/Enhancer	Mus musculus	mm10	chr6	4438697	4440197	NA	Col1a2	Enhancer	Active	Disease	Fibrotic Disease	NA	NA	blood	UBERON:0000178	Mesenchymal-Fibroblast Cells	NA	fibroblast	CL:0000057	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_02794	2016	26645089	Characterizing a distal muscle enhancer in the mouse Igf2 locus	Mus musculus	mm10	chr7	142580000	142580293	Myod1	Igf2	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C3H10T1/2-derived myoblasts	NA	myoblast	CL:0000056	Enhancer activity assay; Functional perturbation assay; In vivo functional validation; TF binding evidence	Published Myod1 occupancy data integration	BAC recombineering; 294-bp enhancer knockout; enhancer knock-in; stable BAC transfection; Ad-MyoD differentiation; RT-PCR; RT-qPCR; immunocytochemistry; DNA sequencing; In vivo phenotyping
E_02795	2024	38555298	A conserved NR5A1-responsive enhancer regulates SRY in testis-determination	Homo sapiens	hg38	chrY	2792658	2792907	NA	SRY	Enhancer	Repressed	Normal	NA	NA	NA	testis	UBERON:0000473	hiPSC-derived Sertoli-like cells	NA	Sertoli cell	CL:0000216	Enhancer activity assay; Functional perturbation assay; TF binding assay; Disease-variant functional analysis	Whole Genome Sequencing; RNA-seq	Luciferase reporter assay; RT-qPCR; Western blot, Sanger Sequencing
E_02796	2016	26916345	An ankylosing spondylitis-associated genetic variant in the IL23R-IL12RB2 intergenic region modulates enhancer activity and is associated with increased Th1-cell differentiation	Homo sapiens	hg19	chr1	67739940	67741075	TWIST1	NA	Enhancer	Active	Disease	ankylosing spondylitis	MONDO:0005306	DOID:7147	blood	UBERON:0000178	primary CD4-positive T cells	NA	CD4-positive, alpha-beta T cell	CL:0000624	Allele-specific enhancer assay; TF binding assay; phenotype association	GWAS conditional analysis; ENCODE/Roadmap epigenomic integration	Luciferase reporter assay; EMSA; TWIST1 antibody interference; H3K4me1 ChIP-qPCR; qRT-PCR; Flow cytometry; Reporter assay
E_02797	2016	26916345	An ankylosing spondylitis-associated genetic variant in the IL23R-IL12RB2 intergenic region modulates enhancer activity and is associated with increased Th1-cell differentiation	Homo sapiens	hg19	chr1	67739940	67741075	TWIST1	NA	Enhancer	Active	Disease	ankylosing spondylitis	MONDO:0005306	DOID:7147	blood	UBERON:0000178	primary CD4-positive T cells	NA	CD4-positive, alpha-beta T cell	CL:0000624	Enhancer activity assay; TF binding assay; Functional variant assay	ENCODE and Roadmap epigenomic data integration	Luciferase reporter assay; EMSA/supershift; H3K4me1 ChIP-qPCR; RT-qPCR; Flow cytometry; Genotyping; Reporter assay
E_02798	2014	25434007	A rare functional noncoding variant at the GWAS-implicated MIR137/MIR2682 locus might confer risk to schizophrenia and bipolar disorder	Homo sapiens	hg19	chr1	98509888	98511451	YY1	MIR137	Enhancer	Active	Disease	Schizophrenia	MONDO:0005090	DOID:5419	NA	NA	Neuroblastoma Cell Lines	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; EMSA/gel-shift assay; 3C
E_02799	2014	25434007	A rare functional noncoding variant at the GWAS-implicated MIR137/MIR2682 locus might confer risk to schizophrenia and bipolar disorder	Homo sapiens	hg19	chr1	98514701	98515055	YY1	MIR137	Enhancer	Active	Disease	Schizophrenia	MONDO:0005090	DOID:5419	NA	NA	Neuroblastoma Cell Lines	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; EMSA/gel-shift assay; 3C
E_02800	2014	25434007	A rare functional noncoding variant at the GWAS-implicated MIR137/MIR2682 locus might confer risk to schizophrenia and bipolar disorder	Homo sapiens	hg19	chr1	98516486	98522430	YY1	MIR137	Enhancer	Active	Disease	Schizophrenia	MONDO:0005090	DOID:5419	NA	NA	Neuroblastoma Cell Lines	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; EMSA/gel-shift assay; 3C
E_02801	2014	25434007	A rare functional noncoding variant at the GWAS-implicated MIR137/MIR2682 locus might confer risk to schizophrenia and bipolar disorder	Homo sapiens	hg19	chr1	98517055	98517909	YY1	MIR137	Enhancer	Active	Disease	Schizophrenia	MONDO:0005090	DOID:5419	NA	NA	Neuroblastoma Cell Lines	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; EMSA/gel-shift assay; 3C
E_02802	2007	17637499	mNotch1 signaling and erythropoietin cooperate in erythroid differentiation of multipotent progenitor cells and upregulate beta-globin	Homo sapiens	hg38	chr11	5246250	5246637	NA	HBB	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Endogenous enhancer perturbation	NA	Luciferase reporter assay; Site-directed/motif mutagenesis
E_02803	2007	17637499	mNotch1 signaling and erythropoietin cooperate in erythroid differentiation of multipotent progenitor cells and upregulate beta-globin	Homo sapiens	hg38	chr11	5246250	5246637	NA	HBB	Enhancer	Active	Normal	NA	NA	NA	esophagus	UBERON:0001043	KYSE-30	CVCL_1351	malignant cell	CL:0001064	Enhancer activity assay; Endogenous enhancer perturbation	NA	Luciferase reporter assay; Site-directed/motif mutagenesis
E_02804	2019	31217582	Noncoding deletions reveal a gene that is critical for intestinal function	Homo sapiens	hg19	chr16	1480850	1482378	NA	PERCC1	Enhancer	Active	Disease	intractable congenital diarrhoea caused by intestine-critical region deletion	NA	NA	intestine	UBERON:0000160	Developing gastrointestinal tract	NA	enteroendocrine cell	CL:0000164	Disease-associated noncoding deletion analysis; transgenic enhancer reporter; endogenous regulatory-region deletion; target-gene rescue; in vivo phenotyping	whole-genome sequencing; whole-exome sequencing; RNA-seq; intestinal single-cell transcriptome re-analysis	Transgenic mouse reporter assay; targeted ICR deletion in mice; RT-qPCR; Immunofluorescence; histology; iPSC-derived intestinal organoid analysis; ICR-driven PERCC1 rescue transgene
E_02805	2024	39327125	KMT2D deficiency leads to cellular developmental disorders and enhancer dysregulation in neural-crest-containing brain organoids	Homo sapiens	hg38	chr1	228005620	228006224	NA	WNT3A	Enhancer	Active	Disease	Kabuki syndrome	MONDO:0016512	DOID:0060473	brain	UBERON:0000955	HN4-derived cerebral organoids	NA	roof-plate-like neural niche cell; neural-crest/neuronal progenitor context	NA	causal disease-enhancer identification and endogenous enhancer deletion; numeric coordinate supplied only by external database harmonization	RNA-seq; single-cell RNA-seq; single-cell ATAC-seq; single-cell multiome; CUT&Tag; GREE multiomic enhancer-target inference	CRISPR deletion of WNT3A enhancer; KMT2D knockout; organoid differentiation; WNT3A/WNT-pathway rescue; immunostaining; mouse diencephalon validation
E_02806	2024	39327125	KMT2D deficiency leads to cellular developmental disorders and enhancer dysregulation in neural-crest-containing brain organoids	Homo sapiens	hg38	chr1	228005620	228006224	NA	WNT3A	Enhancer	Active	Disease	Kabuki syndrome	MONDO:0016512	DOID:0060473	brain	UBERON:0000955	KMT2D-KO organoids	NA	roof-plate-like neural niche cell; neural-crest/neuronal progenitor context	NA	causal disease-enhancer identification and endogenous enhancer deletion; numeric coordinate supplied only by external database harmonization	RNA-seq; single-cell RNA-seq; single-cell ATAC-seq; single-cell multiome; CUT&Tag; GREE multiomic enhancer-target inference	CRISPR deletion of WNT3A enhancer; KMT2D knockout; organoid differentiation; WNT3A/WNT-pathway rescue; immunostaining; mouse diencephalon validation
E_02807	2024	39327125	KMT2D deficiency leads to cellular developmental disorders and enhancer dysregulation in neural-crest-containing brain organoids	Homo sapiens	hg38	chr1	228005620	228006224	NA	WNT3A	Enhancer	Active	Disease	Kabuki syndrome	MONDO:0016512	DOID:0060473	brain	UBERON:0000955	Kabuki patient-derived iPSC organoids	NA	roof-plate-like neural niche cell; neural-crest/neuronal progenitor context	NA	causal disease-enhancer identification and endogenous enhancer deletion; numeric coordinate supplied only by external database harmonization	RNA-seq; single-cell RNA-seq; single-cell ATAC-seq; single-cell multiome; CUT&Tag; GREE multiomic enhancer-target inference	CRISPR deletion of WNT3A enhancer; KMT2D knockout; organoid differentiation; WNT3A/WNT-pathway rescue; immunostaining; mouse diencephalon validation
E_02808	2024	39327125	KMT2D deficiency leads to cellular developmental disorders and enhancer dysregulation in neural-crest-containing brain organoids	Homo sapiens	hg38	chr1	228005620	228006224	NA	WNT3A	Enhancer	Active	Disease	Kabuki syndrome	MONDO:0016512	DOID:0060473	diencephalon	UBERON:0001894	HN4-derived cerebral organoids	NA	roof-plate-like neural niche cell; neural-crest/neuronal progenitor context	NA	causal disease-enhancer identification and endogenous enhancer deletion; numeric coordinate supplied only by external database harmonization	RNA-seq; single-cell RNA-seq; single-cell ATAC-seq; single-cell multiome; CUT&Tag; GREE multiomic enhancer-target inference	CRISPR deletion of WNT3A enhancer; KMT2D knockout; organoid differentiation; WNT3A/WNT-pathway rescue; immunostaining; mouse diencephalon validation
E_02809	2024	39327125	KMT2D deficiency leads to cellular developmental disorders and enhancer dysregulation in neural-crest-containing brain organoids	Homo sapiens	hg38	chr1	228005620	228006224	NA	WNT3A	Enhancer	Active	Disease	Kabuki syndrome	MONDO:0016512	DOID:0060473	diencephalon	UBERON:0001894	KMT2D-KO organoids	NA	roof-plate-like neural niche cell; neural-crest/neuronal progenitor context	NA	causal disease-enhancer identification and endogenous enhancer deletion; numeric coordinate supplied only by external database harmonization	RNA-seq; single-cell RNA-seq; single-cell ATAC-seq; single-cell multiome; CUT&Tag; GREE multiomic enhancer-target inference	CRISPR deletion of WNT3A enhancer; KMT2D knockout; organoid differentiation; WNT3A/WNT-pathway rescue; immunostaining; mouse diencephalon validation
E_02810	2024	39327125	KMT2D deficiency leads to cellular developmental disorders and enhancer dysregulation in neural-crest-containing brain organoids	Homo sapiens	hg38	chr1	228005620	228006224	NA	WNT3A	Enhancer	Active	Disease	Kabuki syndrome	MONDO:0016512	DOID:0060473	diencephalon	UBERON:0001894	Kabuki patient-derived iPSC organoids	NA	roof-plate-like neural niche cell; neural-crest/neuronal progenitor context	NA	causal disease-enhancer identification and endogenous enhancer deletion; numeric coordinate supplied only by external database harmonization	RNA-seq; single-cell RNA-seq; single-cell ATAC-seq; single-cell multiome; CUT&Tag; GREE multiomic enhancer-target inference	CRISPR deletion of WNT3A enhancer; KMT2D knockout; organoid differentiation; WNT3A/WNT-pathway rescue; immunostaining; mouse diencephalon validation
E_02811	2016	26916345	An ankylosing spondylitis-associated genetic variant in the IL23R-IL12RB2 intergenic region modulates enhancer activity and is associated with increased Th1-cell differentiation	Homo sapiens	hg19	chr1	67739940	67741075	NA	NA	Enhancer	Active	Disease	ankylosing spondylitis	MONDO:0005306	DOID:7147	blood	UBERON:0000178	primary CD4-positive T cells	NA	CD4-positive, alpha-beta T cell	CL:0000624	Enhancer activity assay; Functional variant assay	ENCODE and Roadmap epigenomic data integration	Luciferase reporter assay; H3K4me1 ChIP-qPCR; RT-qPCR; Flow cytometry; Genotyping; Reporter assay
E_02812	2014	25214635	Intersection of population variation and autoimmunity genetics in human T cell activation	Homo sapiens	hg19	chr10	6091181	6091380	YY1	IL2RA	Enhancer	Active	Disease	type 1 diabetes mellitus	MONDO:0005147	DOID:9744	blood	UBERON:0000178	Primary human CD4+ T cells from healthy donors for activation/eQTL mapping	NA	CD4-positive, alpha-beta T cell	CL:0000624	Activation-dependent autoimmune-risk enhancer; eQTL/GWAS fine-mapping; allele-specific YY1 binding and enhancer activity	RNA-seq; activation eQTL mapping; GWAS fine-mapping	Allele-specific luciferase reporter; EMSA; DNA pull-down; YY1 transactivation assay
E_02813	2014	25214635	Intersection of population variation and autoimmunity genetics in human T cell activation	Homo sapiens	hg19	chr10	6091181	6091380	YY1	IL2RA	Enhancer	Active	Disease	multiple sclerosis	MONDO:0005301	DOID:2377	blood	UBERON:0000178	Primary human CD4+ T cells from healthy donors for activation/eQTL mapping	NA	CD4-positive, alpha-beta T cell	CL:0000624	Activation-dependent autoimmune-risk enhancer; eQTL/GWAS fine-mapping; allele-specific YY1 binding and enhancer activity	RNA-seq; activation eQTL mapping; GWAS fine-mapping	Allele-specific luciferase reporter; EMSA; DNA pull-down; YY1 transactivation assay
E_02814	2014	25263596	5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation	Mus musculus	mm10	chr1	182851627	182852853	Nanog	Lefty1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Tet2-/-	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_02815	2014	25263596	5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation	Mus musculus	mm10	chr1	182851627	182852853	Pou5f1	Lefty1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Tet2-/-	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_02816	2014	25263596	5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation	Mus musculus	mm10	chr1	182851627	182852853	Sox4	Lefty1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Tet2-/-	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_02817	2014	25263596	5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation	Mus musculus	mm10	chr1	182852133	182854320	Nanog	Lefty1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Tet2-/-	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_02818	2014	25263596	5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation	Mus musculus	mm10	chr1	182852133	182854320	Pou5f1	Lefty1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Tet2-/-	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_02819	2014	25263596	5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation	Mus musculus	mm10	chr1	182852133	182854320	Sox4	Lefty1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Tet2-/-	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_02820	2014	25263596	5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation	Mus musculus	mm10	chr1	182856227	182857187	Nanog	Lefty1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Tet2-/-	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_02821	2014	25263596	5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation	Mus musculus	mm10	chr1	182856227	182857187	Pou5f1	Lefty1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Tet2-/-	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_02822	2014	25263596	5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation	Mus musculus	mm10	chr1	182856227	182857187	Sox4	Lefty1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Tet2-/-	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_02823	2014	25263596	5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation	Mus musculus	mm10	chr11	35178343	35180368	Nanog	Slit3	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Tet2-/-	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_02824	2014	25263596	5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation	Mus musculus	mm10	chr11	35178343	35180368	Pou5f1	Slit3	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Tet2-/-	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_02825	2014	25263596	5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation	Mus musculus	mm10	chr11	35178343	35180368	Sox2	Slit3	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Tet2-/-	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_02826	2014	25263596	5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation	Mus musculus	mm10	chr11	35813868	35814943	Nanog	Slit3	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Tet2-/-	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_02827	2014	25263596	5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation	Mus musculus	mm10	chr11	35813868	35814943	Pou5f1	Slit3	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Tet2-/-	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_02828	2014	25263596	5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation	Mus musculus	mm10	chr11	35813868	35814943	Sox4	Slit3	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Tet2-/-	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_02829	2009	19285986	Control elements in the neighboring ATPase gene influence spatiotemporal expression of the human agouti-related protein	Mus musculus	mm10	chr8	105528423	105529045	NA	Agrp	Enhancer	Active	Normal	NA	NA	NA	NA	NA	N38	NA	NA	NA	Enhancer activity assay; In vivo functional validation	NA	Luciferase reporter assay; Reporter assay; RT-qPCR/qPCR; Transgenic/LacZ assay
E_02830	2019	31290539	A 50-bp enhancer of the mouse acrosomal vesicle protein 1 gene activates round spermatid-specific transcription in vivo?	Mus musculus	mm10	chr9	110254800	110254851	NA	NA	Enhancer	Active	Normal	NA	NA	NA	testis	UBERON:0000473	Round spermatids	NA	spermatid	CL:0000018	Enhancer activity assay; In vivo functional validation	NA	Transgenic reporter assay, Luciferase reporter assay; Transgenic enhancer reporter assay; In vivo phenotyping; Reporter assay
E_02831	2009	19285986	Control elements in the neighboring ATPase gene influence spatiotemporal expression of the human agouti-related protein	Homo sapiens	hg19	chr16	67520620	67520851	NA	AGRP	Enhancer	Active	Normal	NA	NA	NA	hypothalamus	UBERON:0001898	N38	NA	hypothalamic neuronal cell	NA	Enhancer activity assay; in vivo enhancer validation	NA	Luciferase reporter assay; transgenic mouse reporter assay; in vivo bioluminescence imaging
E_02832	2024	39327125	KMT2D deficiency leads to cellular developmental disorders and enhancer dysregulation in neural-crest-containing brain organoids	Homo sapiens	hg38	chr1	228005620	228006224	NA	WNT3A	Enhancer	Active	Disease	Kabuki syndrome	MONDO:0016512	DOID:0060473	brain	UBERON:0000955	mouse diencephalon	NA	roof-plate-like neural niche cell; neural-crest/neuronal progenitor context	NA	causal disease-enhancer identification and endogenous enhancer deletion; numeric coordinate supplied only by external database harmonization	RNA-seq; single-cell RNA-seq; single-cell ATAC-seq; single-cell multiome; CUT&Tag; GREE multiomic enhancer-target inference	CRISPR deletion of WNT3A enhancer; KMT2D knockout; organoid differentiation; WNT3A/WNT-pathway rescue; immunostaining; mouse diencephalon validation
E_02833	2024	39327125	KMT2D deficiency leads to cellular developmental disorders and enhancer dysregulation in neural-crest-containing brain organoids	Homo sapiens	hg38	chr1	228005620	228006224	NA	WNT3A	Enhancer	Active	Disease	Kabuki syndrome	MONDO:0016512	DOID:0060473	diencephalon	UBERON:0001894	mouse diencephalon	NA	roof-plate-like neural niche cell; neural-crest/neuronal progenitor context	NA	causal disease-enhancer identification and endogenous enhancer deletion; numeric coordinate supplied only by external database harmonization	RNA-seq; single-cell RNA-seq; single-cell ATAC-seq; single-cell multiome; CUT&Tag; GREE multiomic enhancer-target inference	CRISPR deletion of WNT3A enhancer; KMT2D knockout; organoid differentiation; WNT3A/WNT-pathway rescue; immunostaining; mouse diencephalon validation
E_02834	2014	25214635	Intersection of population variation and autoimmunity genetics in human T cell activation	Homo sapiens	hg19	chr10	6091180	6091381	YY1	IL2RA	Enhancer	Active	Disease	autoimmune disease	MONDO:0007179	DOID:417	blood	UBERON:0000178	Jurkat	CVCL_0065	T cell	CL:0000084	Enhancer activity assay; Disease-variant functional analysis; allele-specific TF binding assay; genetic association assay	RNA-seq; eQTL mapping; GWAS fine-mapping	Allele-specific luciferase reporter assay; EMSA; DNA pull-down assay; YY1 transactivation assay
E_02835	2014	25214635	Intersection of population variation and autoimmunity genetics in human T cell activation	Homo sapiens	hg19	chr10	6091181	6091380	YY1	IL2RA	Enhancer	Active	Disease	type 1 diabetes mellitus	MONDO:0005147	DOID:9744	blood	UBERON:0000178	Jurkat	CVCL_0065	T cell	CL:0000084	Activation-dependent autoimmune-risk enhancer; eQTL/GWAS fine-mapping; allele-specific YY1 binding and enhancer activity	RNA-seq; activation eQTL mapping; GWAS fine-mapping	Allele-specific luciferase reporter; EMSA; DNA pull-down; YY1 transactivation assay
E_02836	2014	25214635	Intersection of population variation and autoimmunity genetics in human T cell activation	Homo sapiens	hg19	chr10	6091181	6091380	YY1	IL2RA	Enhancer	Active	Disease	multiple sclerosis	MONDO:0005301	DOID:2377	blood	UBERON:0000178	Jurkat	CVCL_0065	T cell	CL:0000084	Activation-dependent autoimmune-risk enhancer; eQTL/GWAS fine-mapping; allele-specific YY1 binding and enhancer activity	RNA-seq; activation eQTL mapping; GWAS fine-mapping	Allele-specific luciferase reporter; EMSA; DNA pull-down; YY1 transactivation assay
E_02837	2009	19285986	Control elements in the neighboring ATPase gene influence spatiotemporal expression of the human agouti-related protein	Homo sapiens	hg19	chr16	67519201	67519833	NA	AGRP	Enhancer	Active	Normal	NA	NA	NA	NA	NA	H295R,N38	NA	NA	NA	Enhancer activity assay; In vivo functional validation	NA	Luciferase reporter assay; Reporter assay; Transgenic/LacZ assay
E_02838	2009	19285986	Control elements in the neighboring ATPase gene influence spatiotemporal expression of the human agouti-related protein	Homo sapiens	hg19	chr16	67519609	67519833	NA	AGRP	Enhancer	Active	Normal	NA	NA	NA	NA	NA	H295R,N38	NA	NA	NA	Enhancer activity assay; In vivo functional validation	NA	Luciferase reporter assay; Reporter assay; Transgenic/LacZ assay
E_02839	2009	19285986	Control elements in the neighboring ATPase gene influence spatiotemporal expression of the human agouti-related protein	Homo sapiens	hg19	chr16	67520417	67521049	NA	AGRP	Enhancer	Active	Normal	NA	NA	NA	NA	NA	H295R,N38	NA	NA	NA	Enhancer activity assay; In vivo functional validation	NA	Luciferase reporter assay; Reporter assay; Transgenic/LacZ assay
E_02840	2009	19285986	Control elements in the neighboring ATPase gene influence spatiotemporal expression of the human agouti-related protein	Homo sapiens	hg19	chr16	67520417	67520638	NA	AGRP	Enhancer	Active	Normal	NA	NA	NA	NA	NA	AtT-20,N38	NA	NA	NA	Enhancer activity assay; In vivo functional validation	NA	Luciferase reporter assay; Reporter assay; Transgenic/LacZ assay
E_02841	2009	19285986	Control elements in the neighboring ATPase gene influence spatiotemporal expression of the human agouti-related protein	Homo sapiens	hg19	chr16	67520620	67520851	NA	AGRP	Enhancer	Active	Normal	NA	NA	NA	NA	NA	H295R	NA	NA	NA	Enhancer activity assay; In vivo functional validation	NA	Luciferase reporter assay; Reporter assay; Transgenic/LacZ assay
E_02842	2014	25434007	A rare functional noncoding variant at the GWAS-implicated MIR137/MIR2682 locus might confer risk to schizophrenia and bipolar disorder	Homo sapiens	hg19	chr1	98515300	98515700	NA	MIR137	Enhancer	Active	Disease	Schizophrenia	MONDO:0005090	DOID:5419	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; Disease-variant functional analysis	GWAS	Luciferase reporter assay; 3C
E_02843	2016	26916345	An ankylosing spondylitis-associated genetic variant in the IL23R-IL12RB2 intergenic region modulates enhancer activity and is associated with increased Th1-cell differentiation	Homo sapiens	hg19	chr1	67739940	67741075	NA	NA	Enhancer	Active	Disease	ankylosing spondylitis	MONDO:0005306	DOID:7147	blood	UBERON:0000178	primary CD4+ T cells/Th1 phenotyping	NA	CD4-positive, alpha-beta T cell	CL:0000624	Genetic association/fine-mapping; allele-specific enhancer activity; chromatin-state analysis; allele-specific DNA-binding assay; T-cell phenotyping	Genetic association/conditional fine-mapping; epigenomic data integration	Luciferase reporter assay; EMSA/gel-shift assay; H3K4me1 ChIP-qPCR/epigenetic validation; Flow cytometry
E_02844	2009	19285986	Control elements in the neighboring ATPase gene influence spatiotemporal expression of the human agouti-related protein	Homo sapiens	hg19	chr16	67520417	67520638	NA	AGRP	Enhancer	Active	Normal	NA	NA	NA	hypothalamus	UBERON:0001898	mHypoE-38	CVCL_D438	neuron	CL:0000540	Enhancer activity assay; Tissue-selective enhancer assay	NA	Transient transfection; Dual-luciferase reporter assay; enhancer deletion mapping
E_02845	2009	19285986	Control elements in the neighboring ATPase gene influence spatiotemporal expression of the human agouti-related protein	Homo sapiens	hg19	chr16	67520620	67520851	NA	AGRP	Enhancer	Active	Normal	NA	NA	NA	adrenal gland	UBERON:0002369	NCI-H295R	CVCL_0458	cortical cell of adrenal gland	CL:0002097	Enhancer activity assay; Tissue-selective enhancer assay	NA	Transient transfection; Dual-luciferase reporter assay; enhancer deletion mapping
E_02846	2014	25214635	Intersection of population variation and autoimmunity genetics in human T cell activation	Homo sapiens	hg19	chr10	6091181	6091381	YY1	IL2RA	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary activated CD4+ T cells	NA	T cell	CL:0000084	Disease-variant functional analysis; Activation-specific cis-eQTL fine-mapping; allele-specific enhancer and TF-binding validation	Population transcriptomics/eQTL analysis	Luciferase reporter; EMSA/YY1 binding; allele-specific functional assay
E_02847	2009	19285986	Control elements in the neighboring ATPase gene influence spatiotemporal expression of the human agouti-related protein	Homo sapiens	hg19	chr16	67520417	67520638	NA	AGRP	Enhancer	Active	Normal	NA	NA	NA	NA	NA	NCI-H295R	CVCL_0458	adrenocortical cell	NA	Enhancer activity assay	NA	Luciferase reporter assay; enhancer deletion analysis; transfection
E_02848	2016	26916345	An ankylosing spondylitis-associated genetic variant in the IL23R-IL12RB2 intergenic region modulates enhancer activity and is associated with increased Th1-cell differentiation	Homo sapiens	hg19	chr1	67739940	67741075	NA	NA	Enhancer	Active	Disease	ankylosing spondylitis	MONDO:0005306	DOID:7147	blood	UBERON:0000178	HEK293T	CVCL_0063	CD4-positive, alpha-beta T cell	CL:0000624	Genetic association/fine-mapping; allele-specific enhancer activity; chromatin-state analysis; allele-specific DNA-binding assay; T-cell phenotyping	Genetic association/conditional fine-mapping; epigenomic data integration	Luciferase reporter assay; EMSA/gel-shift assay; H3K4me1 ChIP-qPCR/epigenetic validation; Flow cytometry
E_02849	2014	25214635	Intersection of population variation and autoimmunity genetics in human T cell activation	Homo sapiens	hg19	chr10	6091181	6091381	YY1	IL2RA	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Jurkat	CVCL_0065	T cell	CL:0000084	Enhancer activity assay; Disease-variant functional analysis; Allele-specific TF binding assay; Regulatory variant functional assay; Genetic association/eQTL assay	Gene-expression profiling; cis-eQTL mapping; trans-ancestry GWAS fine-mapping	PMA/ionomycin activation; allele-specific luciferase reporter assay; EMSA; DNA pull-down; YY1 transactivation assay
E_02850	2014	25214635	Intersection of population variation and autoimmunity genetics in human T cell activation	Homo sapiens	hg19	chr10	6091181	6091381	YY1	IL2RA	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Jurkat	CVCL_0065	T cell	CL:0000084	Enhancer activity assay; Disease-variant functional analysis; Allele-specific TF binding assay; Regulatory variant functional assay; Genetic association assay	Gene-expression profiling; cis-eQTL mapping; trans-ancestry genetic fine-mapping	Allele-specific luciferase reporter assay; EMSA; DNA pull-down; YY1 transactivation assay; PMA/ionomycin activation
E_02851	2014	25214635	Intersection of population variation and autoimmunity genetics in human T cell activation	Homo sapiens	hg19	chr10	6091181	6091381	YY1	IL2RA	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Jurkat reporter validation	NA	T cell	CL:0000084	Disease-variant functional analysis; Activation-specific cis-eQTL fine-mapping; allele-specific enhancer and TF-binding validation	Population transcriptomics/eQTL analysis	Luciferase reporter; EMSA/YY1 binding; allele-specific functional assay
E_02852	2014	25214635	Intersection of population variation and autoimmunity genetics in human T cell activation	Homo sapiens	hg19	chr10	6064657	6065397	YY1	IL2RA	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	T Cell	NA	T cell	CL:0000084	Enhancer activity assay; TF-binding/chromatin assay; Genetic-variant functional analysis	GWAS/genetic association	Luciferase reporter assay; Reporter assay; EMSA/gel-shift assay
E_02853	2016	26916345	An ankylosing spondylitis-associated genetic variant in the IL23R-IL12RB2 intergenic region modulates enhancer activity and is associated with increased Th1-cell differentiation	Homo sapiens	hg19	chr1	67739940	67741075	NA	NA	Enhancer	Active	Disease	ankylosing spondylitis	MONDO:0005306	DOID:7147	blood	UBERON:0000178	primary CD4-positive T cells	NA	CD4-positive, alpha-beta T cell	CL:0000624	Candidate regulatory-variant analysis	GWAS conditional analysis; ENCODE/Roadmap integration	Luciferase/allelic analysis; weaker functional support than rs11209032; Luciferase reporter assay; Reporter assay
E_02854	2007	17637499	mNotch1 signaling and erythropoietin cooperate in erythroid differentiation of multipotent progenitor cells and upregulate beta-globin	Homo sapiens	hg19	chr11	5211019	5213983	RBPJ	HBB	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	erythroid progenitor cell	CL:0000038	Enhancer activity assay	NA	Luciferase reporter assay; Reporter assay
E_02855	2016	26916345	An ankylosing spondylitis-associated genetic variant in the IL23R-IL12RB2 intergenic region modulates enhancer activity and is associated with increased Th1-cell differentiation	Homo sapiens	hg19	chr1	67739940	67741075	NA	IL23R	Enhancer	Active	Disease	ankylosing spondylitis	MONDO:0005306	DOID:7147	blood	UBERON:0000178	Lymphoblastoid Cell Lines	NA	T helper 1 cell	CL:0000545	Enhancer activity assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay
E_02856	2009	19285986	Control elements in the neighboring ATPase gene influence spatiotemporal expression of the human agouti-related protein	Homo sapiens	hg19	chr16	67520620	67520851	NA	AGRP	Enhancer	Active	Normal	NA	NA	NA	tongue	UBERON:0001723	Transgenic FVB mouse	NA	epithelial cell	CL:0000066	In vivo transgenic enhancer activity assay; Nutrient-responsive enhancer assay	NA	Pronuclear transgenesis; Luciferase reporter assay; in vivo bioluminescence imaging; tissue luminometry; dietary manipulation; overnight fasting; qPCR; immunohistochemistry
E_02857	2009	19285986	Control elements in the neighboring ATPase gene influence spatiotemporal expression of the human agouti-related protein	Homo sapiens	hg19	chr16	67520620	67520851	NA	AGRP	Enhancer	Active	Normal	NA	NA	NA	tongue	UBERON:0001723	transgenic mouse embryo	NA	epithelial cell	CL:0000066	In vivo enhancer activity assay	NA	Transgenic reporter assay; Luciferase reporter assay; immunocytochemistry
E_02858	2009	19285986	Control elements in the neighboring ATPase gene influence spatiotemporal expression of the human agouti-related protein	Homo sapiens	hg19	chr16	67520417	67520638	NA	AGRP	Enhancer	Active	Normal	NA	NA	NA	testis	UBERON:0000473	Transgenic FVB mouse	NA	pachytene spermatocyte	NA	In vivo transgenic enhancer activity assay	NA	Pronuclear transgenesis; Luciferase reporter assay; in vivo bioluminescence imaging; tissue luminometry; qPCR; immunohistochemistry
E_02859	2009	19285986	Control elements in the neighboring ATPase gene influence spatiotemporal expression of the human agouti-related protein	Homo sapiens	hg19	chr16	67520417	67520851	NA	AGRP	Enhancer	Active	Normal	NA	NA	NA	testis	UBERON:0000473	transgenic mouse embryo	NA	pachytene spermatocyte	NA	In vivo enhancer activity assay	NA	Transgenic reporter assay; Luciferase reporter assay; qPCR; immunohistochemistry
E_02860	2025	40216980	Dynamic interaction of MYC enhancer RNA with YEATS2 protein regulates MYC gene transcription in pancreatic cancer	Homo sapiens	hg38	chr8	127247950	127248600	NA	MYC	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	MIA PaCa-2	CVCL_0428	pancreatic ductal cell	CL:0002079	Functional perturbation assay; Enhancer/eRNA functional validation; RNA-protein interaction assay; Chromatin occupancy assay	nascent RNA-seq; H3K27ac ChIP-seq reanalysis; H3K4me1 ChIP-seq reanalysis; ATAC-seq reanalysis	RT-qPCR; Click-iT nascent RNA capture; shRNA-mediated MYC-490-kb eRNA knockdown; MYC-490-kb eRNA overexpression; UV-RIP-qPCR; YEATS2 shRNA knockdown; ZZZ3 ChIP-qPCR; ChIP-IP; Immunoprecipitation; Western blot; In vitro RNA-binding assay; MTT assay; Wound-healing assay
E_02861	2023	37664846	The NR2F2-HAND2 signaling axis regulates progesterone actions in the uterus at early pregnancy	Mus musculus	mm10	chr8	57331591	57335031	Nr2f2	Hand2	Enhancer	Active	Normal	NA	NA	NA	uterus	UBERON:0000995	GD3.5 pregnant mouse uterus / uterine stromal cells	NA	endometrial stromal cell	NA	TF binding assay; enhancer chromatin-state mapping; conditional TF perturbation; enhancer orthology/functional validation	NR2F2 ChIP-seq; RNA-seq	ChIP-qPCR; RT-qPCR; conditional Nr2f2 knockout phenotyping; Western blot
E_02862	2020	32991581	NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure brown and beige adipocyte differentiation	Mus musculus	mm10	chr6	115566900	115569800	Nfia	Pparg	Enhancer	Active	Normal	NA	NA	NA	adipose tissue	UBERON:0001013	C2C12	CVCL_0188	mouse myoblast cell line	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; FAIRE-seq; RNA-seq	ChIP-qPCR; FAIRE-qPCR; CRISPR-dCas9-KRAB; RT-qPCR
E_02863	2019	30672333	The putative Neuronatin imprint control region is an enhancer that also regulates the Blcap gene	Mus musculus	mm10	chr2	150860120	150860367	NA	Blcap	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Primary Mouse Tissues	NA	mouse brain cell	NA	Enhancer activity assay; Functional perturbation assay	DNA methylation profiling	CRISPR knockout; Transgenic reporter assay; ChIP-qPCR; RT-qPCR
E_02864	2019	30672333	The putative Neuronatin imprint control region is an enhancer that also regulates the Blcap gene	Mus musculus	mm10	chr2	150860120	150860367	NA	Nnat	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Primary Mouse Tissues	NA	mouse brain cell	NA	Enhancer activity assay; Functional perturbation assay	DNA methylation profiling	CRISPR knockout; Transgenic reporter assay; ChIP-qPCR; RT-qPCR
E_02865	2014	24705708	YY1 acts as a transcriptional activator of Hoxa5 gene expression in mouse organogenesis	Mus musculus	mm10	chr6	52199038	52200503	Yy1	Vegfa	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	Lung,Stomach	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	NA	ChIP-qPCR/ChIP; EMSA/gel-shift assay; RT-qPCR/qPCR; Transgenic/LacZ assay
E_02866	2026	41843552	Functional interrogation of candidate cis-regulatory elements at the LDLR locus	Homo sapiens	hg38	chr19	11090422	11091028	NA	LDLR	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Huh-7	CVCL_0336	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis; Endogenous enhancer perturbation	CRISPR screen; MPRA; CRISPR genetic screen; GWAS	CRISPR knockout, CRISPRi; RT-qPCR; Reporter assay
E_02867	2023	36639729	Therapeutic adenine base editing of human hematopoietic stem cells	Homo sapiens	hg38	chr11	5225440	5225500	NA	HBG1	Enhancer	Repressed	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	CD34+ hematopoietic stem/progenitor cells	NA	hematopoietic stem cell	CL:0000037	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis; Endogenous enhancer perturbation	RNA-seq	Adenine base editing; RT-qPCR, RP-HPLC; CRISPR-Cas9 endogenous deletion/editing
E_02868	2023	36639729	Therapeutic adenine base editing of human hematopoietic stem cells	Homo sapiens	hg38	chr2	60722750	60722850	NA	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	CD34+ hematopoietic stem/progenitor cells	NA	hematopoietic stem cell	CL:0000037	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis; Endogenous enhancer perturbation	RNA-seq	CRISPR knockout, Adenine base editing; RT-qPCR; Western blot; CRISPR-Cas9 endogenous deletion/editing
E_02869	2022	34049825	Epigenome editing of the CFTR-locus for treatment of cystic fibrosis	Homo sapiens	hg38	chr7	117587146	117589449	NA	CFTR	Enhancer	Active	Normal	NA	NA	NA	colon	UBERON:0001155	HT-29	CVCL_0320	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation	DNase-seq (public genomic accessibility data integration)	CRISPR/dCas9-KRAB epigenome repression; CRISPRi; qRT-PCR; Western blot; CRISPR-Cas9 endogenous deletion/editing
E_02870	2020	33199677	Enhancer hijacking determines extrachromosomal circular MYCN amplicon architecture in neuroblastoma	Homo sapiens	hg19	chr2	16370000	16380000	GATA3	MYCN	Enhancer	Active	Disease	neuroblastoma	MONDO:0005072	DOID:769	adrenal gland	UBERON:0002369	Kelly	CVCL_2092	neuroblastoma cell	NA	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; ATAC-seq; 3C-seq; ATAC-seq; Hi-C; Oxford Nanopore sequencing	qRT-PCR, and ChIP-qPCR
E_02871	2020	33199677	Enhancer hijacking determines extrachromosomal circular MYCN amplicon architecture in neuroblastoma	Homo sapiens	hg19	chr2	16370000	16380000	HAND2	MYCN	Enhancer	Active	Disease	neuroblastoma	MONDO:0005072	DOID:769	adrenal gland	UBERON:0002369	Kelly	CVCL_2092	neuroblastoma cell	NA	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; ATAC-seq; 3C-seq; ATAC-seq; Hi-C; Oxford Nanopore sequencing	qRT-PCR, and ChIP-qPCR
E_02872	2020	33199677	Enhancer hijacking determines extrachromosomal circular MYCN amplicon architecture in neuroblastoma	Homo sapiens	hg19	chr2	16370000	16380000	PHOX2B	MYCN	Enhancer	Active	Disease	neuroblastoma	MONDO:0005072	DOID:769	adrenal gland	UBERON:0002369	Kelly	CVCL_2092	neuroblastoma cell	NA	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; ATAC-seq; 3C-seq; ATAC-seq; Hi-C; Oxford Nanopore sequencing	qRT-PCR, and ChIP-qPCR
E_02873	2020	33199677	Enhancer hijacking determines extrachromosomal circular MYCN amplicon architecture in neuroblastoma	Homo sapiens	hg19	chr2	12600000	12649999	GATA3	MYCN	Enhancer	Active	Disease	neuroblastoma	MONDO:0005072	DOID:769	adrenal gland	UBERON:0002369	IMR-5/75	CVCL_M473	neuroblastoma cell	NA	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; ATAC-seq; Hi-C; Oxford Nanopore sequencing	qRT-PCR, and ChIP-qPCR
E_02874	2020	33199677	Enhancer hijacking determines extrachromosomal circular MYCN amplicon architecture in neuroblastoma	Homo sapiens	hg19	chr2	12600000	12649999	HAND2	MYCN	Enhancer	Active	Disease	neuroblastoma	MONDO:0005072	DOID:769	adrenal gland	UBERON:0002369	IMR-5/75	CVCL_M473	neuroblastoma cell	NA	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; ATAC-seq; Hi-C; Oxford Nanopore sequencing	qRT-PCR, and ChIP-qPCR
E_02875	2020	33199677	Enhancer hijacking determines extrachromosomal circular MYCN amplicon architecture in neuroblastoma	Homo sapiens	hg19	chr2	12600000	12649999	PHOX2B	MYCN	Enhancer	Active	Disease	neuroblastoma	MONDO:0005072	DOID:769	adrenal gland	UBERON:0002369	IMR-5/75	CVCL_M473	neuroblastoma cell	NA	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; ATAC-seq; Hi-C; Oxford Nanopore sequencing	qRT-PCR, and ChIP-qPCR
E_02876	2023	37664846	The NR2F2-HAND2 signaling axis regulates progesterone actions in the uterus at early pregnancy	Homo sapiens	hg38	chr4	173516002	173519662	NR2F2	HAND2	Enhancer	Active	Normal	NA	NA	NA	endometrium	UBERON:0001295	T-HESC immortalized human endometrial stromal cells	NA	endometrial stromal cell	NA	Enhancer activation assay; orthologous enhancer functional validation; endogenous target-gene activation	Mouse NR2F2 ChIP-seq and RNA-seq used to nominate the conserved enhancer	dCas9-VPR CRISPRa with two independent gRNAs; RT-qPCR
E_02877	2026	41843552	Functional interrogation of candidate cis-regulatory elements at the LDLR locus	Homo sapiens	hg38	chr19	11090150	11090715	NA	LDLR	Enhancer	Active	Normal	NA	NA	NA	tongue	UBERON:0001723	SCC-25	CVCL_1682	malignant cell	CL:0001064	Enhancer activity assay; Disease-variant functional analysis; Endogenous enhancer perturbation	MPRA; CRISPR genetic screen; GWAS	Transgenic reporter assay; Reporter assay
E_02878	2026	41843552	Functional interrogation of candidate cis-regulatory elements at the LDLR locus	Homo sapiens	hg38	chr19	11090550	11090678	NA	LDLR	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Huh-7	CVCL_0336	malignant cell	CL:0001064	Enhancer activity assay; Disease-variant functional analysis; Endogenous enhancer perturbation	MPRA; CRISPR genetic screen; GWAS	Luciferase reporter assay; Reporter assay
E_02879	2023	36639729	Therapeutic adenine base editing of human hematopoietic stem cells	Homo sapiens	hg19	chr2	60722238	60722466	GATA1	BCL11A	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	blood	UBERON:0000178	beta-thalassemia patient CD34+ hematopoietic stem/progenitor cells	NA	hematopoietic stem/progenitor cell	NA	Endogenous enhancer base-editing functional perturbation	Targeted amplicon deep sequencing; off-target deep sequencing	ABE8e RNP base editing; erythroid differentiation; RT-qPCR; RP-HPLC; xenotransplantation
E_02880	2022	34049825	Epigenome editing of the CFTR-locus for treatment of cystic fibrosis	Homo sapiens	hg38	chr7	117504671	117505671	NA	CFTR	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	HEK293T	CVCL_0063	embryonic kidney cell	NA	Functional perturbation assay	NA	CRISPR knockout; CRISPRi; RT-qPCR; Western blot; Ussing Chamber Assay
E_02881	2020	32991581	NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure brown and beige adipocyte differentiation	Mus musculus	mm10	chr7	127306000	127309000	Nfia	Myod1	Enhancer	Repressed	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	C2C12	CVCL_0188	myoblast	CL:0000056	Enhancer activity assay; TF binding assay	ChIP-seq; FAIRE-seq; RNA-seq	ChIP-qPCR; FAIRE-qPCR; RT-qPCR
E_02882	1990	2116990	Tandem AP-1-binding sites within the human beta-globin dominant control region function as an inducible enhancer in erythroid cells	Homo sapiens	hg19	chr11	5301983	5302001	FOS	HBG1	Enhancer	Active	Normal	NA	NA	NA	uterine cervix	UBERON:0000002	HeLa	CVCL_0030	epithelial cell	CL:0000066	Enhancer activity assay; TF-DNA binding assay; cis-regulatory mutational mapping	NA	Transient transfection by calcium phosphate; Luciferase reporter assay; CAT internal-control assay; enhancer scrambling/mutational analysis; DNase I footprinting; EMSA; competition EMSA; in vitro c-Jun/c-Fos DNA-binding comparison; primer extension
E_02883	1990	2116990	Tandem AP-1-binding sites within the human beta-globin dominant control region function as an inducible enhancer in erythroid cells	Homo sapiens	hg19	chr11	5301983	5302001	JUN	HBG1	Enhancer	Active	Normal	NA	NA	NA	uterine cervix	UBERON:0000002	HeLa	CVCL_0030	epithelial cell	CL:0000066	Enhancer activity assay; TF-DNA binding assay; cis-regulatory mutational mapping	NA	Transient transfection by calcium phosphate; Luciferase reporter assay; CAT internal-control assay; enhancer scrambling/mutational analysis; DNase I footprinting; EMSA; competition EMSA; in vitro c-Jun/c-Fos DNA-binding comparison; primer extension
E_02884	1990	2116990	Tandem AP-1-binding sites within the human beta-globin dominant control region function as an inducible enhancer in erythroid cells	Homo sapiens	hg19	chr11	5288664	5288684	SP1	HBE1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	erythroid progenitor cell	CL:0000038	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; EMSA/gel-shift assay
E_02885	1990	2116990	Tandem AP-1-binding sites within the human beta-globin dominant control region function as an inducible enhancer in erythroid cells	Homo sapiens	hg19	chr11	5288664	5288684	SP1	HBE1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	HeLa	CVCL_0030	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; EMSA/gel-shift assay
E_02886	2025	40216980	Dynamic interaction of MYC enhancer RNA with YEATS2 protein regulates MYC gene transcription in pancreatic cancer	Homo sapiens	hg38	chr8	127247950	127248600	NA	MYC	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	AsPC-1	CVCL_0152	pancreatic ductal cell	CL:0002079	Enhancer/eRNA expression validation; RNA-protein interaction assay; Chromatin occupancy assay	NA	RT-qPCR; UV-RIP-qPCR; ZZZ3 ChIP-qPCR; YEATS2 immunoprecipitation; Phosphotyrosine Western blot; TNF-alpha stimulation
E_02887	1990	2116990	Tandem AP-1-binding sites within the human beta-globin dominant control region function as an inducible enhancer in erythroid cells	Homo sapiens	hg19	chr11	5288664	5288684	NA	HBE1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	erythroid lineage cell	CL:0000764	Enhancer activity assay	DNase I hypersensitivity assay	Luciferase reporter assay; EMSA; AP-1 binding-site mutagenesis
E_02888	2022	34049825	Epigenome editing of the CFTR-locus for treatment of cystic fibrosis	Homo sapiens	hg38	chr7	117504671	117505671	NA	CFTR	Enhancer	Active	Disease	cystic fibrosis	MONDO:0009061	DOID:1485	lung	UBERON:0002048	UNCCF3T (F508del/F508del human bronchial epithelial cells)	NA	bronchial epithelial cell	CL:0002328	Epigenome editing assay; Functional enhancer perturbation assay	Published epigenomic prioritization of CFTR regulatory regions	dCas9-p300 enhancer activation; dCas9-KRAB enhancer repression; RT-qPCR; CFTR protein assay; Ussing chamber assay
E_02889	1990	2116990	Tandem AP-1-binding sites within the human beta-globin dominant control region function as an inducible enhancer in erythroid cells	Homo sapiens	hg19	chr11	5288664	5288684	NA	HBE1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	erythroblast	CL:0000765	Enhancer activity assay; cis-element functional mapping; TF-complex binding assay	NA	Reporter assay; DNA-protein binding assay; AP-1-site mutagenesis; erythroid induction assay
E_02890	2025	39391988	A Rare Noncoding Enhancer Variant in SCN5A Contributes to the High Prevalence of Brugada Syndrome in Thailand	Homo sapiens	hg38	chr3	38578362	38581496	NA	SCN5A	Enhancer	Active	Disease	Brugada syndrome	MONDO:0015263	DOID:0050451	heart	UBERON:0000948	isogenic human iPSC-derived cardiomyocytes carrying the RE5 enhancer variant	NA	cardiac muscle cell	CL:0000746	Disease-variant functional analysis; Regulatory variant enhancer assay; Genome editing assay; electrophysiological functional assay	whole-genome sequencing; case-control variant enrichment analysis; genotyping	CRISPR/Cas9 heterozygous knock-in of hg38 chr3:38580380 A>C; allele-specific SCN5A expression analysis; luciferase enhancer assay; MEF2-dependent transcriptional assay; cardiac transcription factor cotransfection; patch-clamp sodium-current assay; Start/End represent the full functionally validated RE5/VISTA hs2177 enhancer
E_02891	2016	26771354	BMP Sustains Embryonic Stem Cell Self-Renewal through Distinct Functions of Different Krüppel-like Factors	Mus musculus	mm10	chr2	152735054	152735521	Smad1	Id1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02892	2016	26771354	BMP Sustains Embryonic Stem Cell Self-Renewal through Distinct Functions of Different Krüppel-like Factors	Mus musculus	mm10	chr2	152735054	152735521	Smad5	Id1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_02893	2016	26809031	E2F/Rb Family Proteins Mediate Interferon Induced Repression of Adenovirus Immediate Early Transcription to Promote Persistent Viral Infection	Homo sapiens	hg19	chr12	131949637	131949801	E2F1	EP400	Enhancer	Repressed	Normal	NA	NA	NA	NA	NA	Normal Human Bronchial Epithelial Cells	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	NA	ChIP-qPCR/ChIP; EMSA/gel-shift assay; RT-qPCR/qPCR
E_02894	2016	26809031	E2F/Rb Family Proteins Mediate Interferon Induced Repression of Adenovirus Immediate Early Transcription to Promote Persistent Viral Infection	Homo sapiens	hg19	chr12	131949637	131949801	SP1	EP400	Enhancer	Repressed	Normal	NA	NA	NA	NA	NA	Normal Human Bronchial Epithelial Cells	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	NA	ChIP-qPCR/ChIP; EMSA/gel-shift assay; RT-qPCR/qPCR
E_02895	2012	22701669	An evolutionarily conserved enhancer regulates Bmp4 expression in developing incisor and limb bud	Mus musculus	mm10	chr14	47056226	47056692	Pitx2	Bmp4	Enhancer	Active	Normal	NA	NA	NA	NA	NA	LS-8 Cells	NA	NA	NA	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	ChIP-qPCR/ChIP; EMSA/gel-shift assay; RT-qPCR/qPCR
E_02896	2020	33382813	Decreased sensitivity to the anorectic effects of leptin in mice that lack a Pomc-specific neural enhancer	Mus musculus	mm10	chr12	103024800	103025800	NA	Pomc	Enhancer	Active	Disease	obesity	MONDO:0011122	DOID:9970	hypothalamus	UBERON:0001898	Mouse primary neurons	NA	neuron	CL:0000540	Functional perturbation assay; Endogenous enhancer perturbation; In vivo functional validation	RNA-seq	CRISPR knockout, CRISPRi; RT-qPCR; Mouse genetic deletion/knock-in
E_02897	2018	30404901	Promoter-enhancer looping and shadow enhancers of the mouse αA-crystallin locus	Mus musculus	mm10	chr17	31670439	31671892	Etv5	Cryaa	Enhancer	Active	Normal	NA	NA	NA	lens of camera-type eye	UBERON:0000965	embryonic mouse lens/lens-derived cells	NA	lens epithelial cell	CL:0002224	Chromatin interaction assay; Shadow-enhancer activity; promoter-enhancer looping; developmental reporter validation	RNA-seq/chromatin-profile integration	3C; transgenic LacZ reporter assay; ChIP/ChIP-qPCR; qRT-PCR
E_02898	2018	30404901	Promoter-enhancer looping and shadow enhancers of the mouse αA-crystallin locus	Mus musculus	mm10	chr17	31670439	31671892	Etv5	Cryaa	Enhancer	Active	Normal	NA	NA	NA	lens of camera-type eye	UBERON:0000965	embryonic mouse lens/lens-derived cells	NA	lens fiber cell	CL:0011004	Chromatin interaction assay; Shadow-enhancer activity; promoter-enhancer looping; developmental reporter validation	RNA-seq/chromatin-profile integration	3C; transgenic LacZ reporter assay; ChIP/ChIP-qPCR; qRT-PCR
E_02899	2018	30404901	Promoter-enhancer looping and shadow enhancers of the mouse αA-crystallin locus	Mus musculus	mm10	chr17	31670439	31671892	Jun	Cryaa	Enhancer	Active	Normal	NA	NA	NA	lens of camera-type eye	UBERON:0000965	embryonic mouse lens/lens-derived cells	NA	lens epithelial cell	CL:0002224	Chromatin interaction assay; Shadow-enhancer activity; promoter-enhancer looping; developmental reporter validation	RNA-seq/chromatin-profile integration	3C; transgenic LacZ reporter assay; ChIP/ChIP-qPCR; qRT-PCR
E_02900	2018	30404901	Promoter-enhancer looping and shadow enhancers of the mouse αA-crystallin locus	Mus musculus	mm10	chr17	31670439	31671892	Jun	Cryaa	Enhancer	Active	Normal	NA	NA	NA	lens of camera-type eye	UBERON:0000965	embryonic mouse lens/lens-derived cells	NA	lens fiber cell	CL:0011004	Chromatin interaction assay; Shadow-enhancer activity; promoter-enhancer looping; developmental reporter validation	RNA-seq/chromatin-profile integration	3C; transgenic LacZ reporter assay; ChIP/ChIP-qPCR; qRT-PCR
E_02901	2014	24703844	Evolution of Alu elements toward enhancers	Homo sapiens	hg19	chr3	11249688	11250280	NA	HRH1	Enhancer	Active	Normal	NA	NA	NA	uterine cervix	UBERON:0000002	HeLa	CVCL_0030	epithelial cell	CL:0000066	Enhancer activity assay; Chromatin interaction assay; Enhancer chromatin-state assay; Chromatin interaction analysis	P300 ChIP-seq data integration; H3K4me1 ChIP-seq data integration; H3K27ac ChIP-seq data integration; MNase-seq; Hi-C-seq data integration; Hi-C	Reporter assay
E_02902	2003	14585970	A human globin enhancer causes both discrete and widespread alterations in chromatin structure	Homo sapiens	hg19	chr11	5286080	5288080	NFE2	HBE1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	In vivo functional validation; TF-binding/chromatin assay	NA	ChIP-qPCR/ChIP
E_02903	2018	30404901	Promoter-enhancer looping and shadow enhancers of the mouse αA-crystallin locus	Mus musculus	mm10	chr17	31670439	31671892	Etv5	Cryaa	Enhancer	Active	Normal	NA	NA	NA	lens of camera-type eye	UBERON:0000965	embryonic mouse lens/lens-derived cells	NA	NA	NA	Shadow-enhancer activity; promoter-enhancer looping; developmental reporter validation	RNA-seq/chromatin-profile integration; 3C	3C; transgenic LacZ reporter assay; ChIP/ChIP-qPCR; qRT-PCR
E_02904	2018	30404901	Promoter-enhancer looping and shadow enhancers of the mouse αA-crystallin locus	Mus musculus	mm10	chr17	31670439	31671892	Jun	Cryaa	Enhancer	Active	Normal	NA	NA	NA	lens of camera-type eye	UBERON:0000965	embryonic mouse lens/lens-derived cells	NA	NA	NA	Shadow-enhancer activity; promoter-enhancer looping; developmental reporter validation	RNA-seq/chromatin-profile integration; 3C	3C; transgenic LacZ reporter assay; ChIP/ChIP-qPCR; qRT-PCR
E_02905	2014	24703844	Evolution of Alu elements toward enhancers	Homo sapiens	hg19	chr1	9996966	9997243	NA	LZIC	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	GM12878	CVCL_7526	B-lymphoblastoid cell line	NA	Enhancer chromatin-state assay; Chromatin interaction analysis	P300 ChIP-seq data integration; H3K4me1 ChIP-seq data integration; H3K27ac ChIP-seq data integration; MNase-seq; Hi-C-seq data integration; Hi-C	Reporter assay
E_02906	2003	14585970	A human globin enhancer causes both discrete and widespread alterations in chromatin structure	Homo sapiens	hg19	chr11	5301862	5302715	NFE2	HBE1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Chromatin accessibility assay; In vivo functional validation; Chromatin modification assay	NA	NF-E2-site mutagenesis; DNase I hypersensitivity assay; restriction enzyme accessibility assay; MNase mapping; ChIP; RNase protection assay; In vivo phenotyping
E_02907	2018	29300379	The role of SMAD3 in the genetic predisposition to papillary thyroid carcinoma	Homo sapiens	hg19	chr15	67301270	67301820	NA	SMAD3	Enhancer	Active	Disease	thyroid gland papillary carcinoma	MONDO:0005075	DOID:3969	thyroid gland	UBERON:0002046	TPC-1	CVCL_6298	malignant cell	CL:0001064	Enhancer activity assay; Allele-specific regulatory variant assay	Expression microarray; microarray	SNP-centered dual-luciferase reporter assay for rs17293632; siRNA knockdown; ChIP-qPCR; RT-qPCR; Luciferase reporter assay; Reporter assay
E_02908	2018	29300379	The role of SMAD3 in the genetic predisposition to papillary thyroid carcinoma	Homo sapiens	hg19	chr15	67301270	67301820	NA	SMAD3	Enhancer	Active	Disease	thyroid gland papillary carcinoma	MONDO:0005075	DOID:3969	thyroid gland	UBERON:0002046	B-CPAP	CVCL_0153	malignant cell	CL:0001064	Enhancer activity assay; Allele-specific regulatory variant assay	Expression microarray; microarray	SNP-centered dual-luciferase reporter assay for rs17293632; siRNA knockdown; ChIP-qPCR; RT-qPCR; Luciferase reporter assay; Reporter assay
E_02909	2018	29300379	The role of SMAD3 in the genetic predisposition to papillary thyroid carcinoma	Homo sapiens	hg19	chr15	67304460	67305010	NA	SMAD3	Enhancer	Active	Disease	thyroid gland papillary carcinoma	MONDO:0005075	DOID:3969	thyroid gland	UBERON:0002046	TPC-1	CVCL_6298	malignant cell	CL:0001064	Enhancer activity assay; Allele-specific regulatory variant assay	Expression microarray; microarray	SNP-centered dual-luciferase reporter assay for rs4562997; siRNA knockdown; ChIP-qPCR; RT-qPCR; Luciferase reporter assay; Reporter assay
E_02910	2018	29300379	The role of SMAD3 in the genetic predisposition to papillary thyroid carcinoma	Homo sapiens	hg19	chr15	67304460	67305010	NA	SMAD3	Enhancer	Active	Disease	thyroid gland papillary carcinoma	MONDO:0005075	DOID:3969	thyroid gland	UBERON:0002046	B-CPAP	CVCL_0153	malignant cell	CL:0001064	Enhancer activity assay; Allele-specific regulatory variant assay	Expression microarray; microarray	SNP-centered dual-luciferase reporter assay for rs4562997; siRNA knockdown; ChIP-qPCR; RT-qPCR; Luciferase reporter assay; Reporter assay
E_02911	2018	29300379	The role of SMAD3 in the genetic predisposition to papillary thyroid carcinoma	Homo sapiens	hg19	chr15	67441595	67443595	NA	SMAD3	Enhancer	Active	Disease	thyroid gland papillary carcinoma	MONDO:0005075	DOID:3969	thyroid gland	UBERON:0002046	TPC-1	CVCL_6298	malignant cell	CL:0001064	Enhancer activity assay; Allele-specific regulatory variant assay	Expression microarray; microarray	Dual-luciferase reporter assay of 100-200-bp rs17293632-centered constructs; siRNA knockdown; ChIP-qPCR; RT-qPCR; Luciferase reporter assay; Reporter assay
E_02912	2018	29300379	The role of SMAD3 in the genetic predisposition to papillary thyroid carcinoma	Homo sapiens	hg19	chr15	67441595	67443595	NA	SMAD3	Enhancer	Active	Disease	thyroid gland papillary carcinoma	MONDO:0005075	DOID:3969	thyroid gland	UBERON:0002046	B-CPAP	CVCL_0153	malignant cell	CL:0001064	Enhancer activity assay; Allele-specific regulatory variant assay	Expression microarray; microarray	Dual-luciferase reporter assay of 100-200-bp rs17293632-centered constructs; siRNA knockdown; ChIP-qPCR; RT-qPCR; Luciferase reporter assay; Reporter assay
E_02913	2018	29300379	The role of SMAD3 in the genetic predisposition to papillary thyroid carcinoma	Homo sapiens	hg19	chr15	67442496	67442696	NA	SMAD3	Enhancer	Active	Disease	thyroid gland papillary carcinoma	MONDO:0005075	DOID:3969	thyroid gland	UBERON:0002046	TPC-1	CVCL_6298	malignant cell	CL:0001064	Enhancer activity assay; allele-specific regulatory-variant assay	Expression microarray; microarray	SNP-centered dual-luciferase reporter assay for rs17293632; SMAD3 siRNA knockdown; RT-qPCR; downstream SMAD3-network ChIP-qPCR (not enhancer-site ChIP); Luciferase reporter assay; Reporter assay
E_02914	2018	29300379	The role of SMAD3 in the genetic predisposition to papillary thyroid carcinoma	Homo sapiens	hg19	chr15	67442496	67442696	NA	SMAD3	Enhancer	Active	Disease	thyroid gland papillary carcinoma	MONDO:0005075	DOID:3969	thyroid gland	UBERON:0002046	B-CPAP	CVCL_0153	malignant cell	CL:0001064	Enhancer activity assay; allele-specific regulatory-variant assay	Expression microarray; microarray	SNP-centered dual-luciferase reporter assay for rs17293632; SMAD3 siRNA knockdown; RT-qPCR; downstream SMAD3-network ChIP-qPCR (not enhancer-site ChIP); Luciferase reporter assay; Reporter assay
E_02915	2018	29300379	The role of SMAD3 in the genetic predisposition to papillary thyroid carcinoma	Homo sapiens	hg19	chr15	67457151	67459151	NA	SMAD3	Enhancer	Active	Disease	thyroid gland papillary carcinoma	MONDO:0005075	DOID:3969	thyroid gland	UBERON:0002046	TPC-1	CVCL_6298	malignant cell	CL:0001064	Enhancer activity assay; Allele-specific regulatory variant assay	Expression microarray; microarray	Dual-luciferase reporter assay of 100-200-bp rs4562997-centered constructs; siRNA knockdown; ChIP-qPCR; RT-qPCR; Luciferase reporter assay; Reporter assay
E_02916	2018	29300379	The role of SMAD3 in the genetic predisposition to papillary thyroid carcinoma	Homo sapiens	hg19	chr15	67457151	67459151	NA	SMAD3	Enhancer	Active	Disease	thyroid gland papillary carcinoma	MONDO:0005075	DOID:3969	thyroid gland	UBERON:0002046	B-CPAP	CVCL_0153	malignant cell	CL:0001064	Enhancer activity assay; Allele-specific regulatory variant assay	Expression microarray; microarray	Dual-luciferase reporter assay of 100-200-bp rs4562997-centered constructs; siRNA knockdown; ChIP-qPCR; RT-qPCR; Luciferase reporter assay; Reporter assay
E_02917	2018	29300379	The role of SMAD3 in the genetic predisposition to papillary thyroid carcinoma	Homo sapiens	hg19	chr15	67458052	67458252	NA	SMAD3	Enhancer	Active	Disease	thyroid gland papillary carcinoma	MONDO:0005075	DOID:3969	thyroid gland	UBERON:0002046	TPC-1	CVCL_6298	malignant cell	CL:0001064	Enhancer activity assay; allele-specific regulatory-variant assay	Expression microarray; microarray	SNP-centered dual-luciferase reporter assay for rs4562997; SMAD3 siRNA knockdown; RT-qPCR; downstream SMAD3-network ChIP-qPCR (not enhancer-site ChIP); Luciferase reporter assay; Reporter assay
E_02918	2018	29300379	The role of SMAD3 in the genetic predisposition to papillary thyroid carcinoma	Homo sapiens	hg19	chr15	67458052	67458252	NA	SMAD3	Enhancer	Active	Disease	thyroid gland papillary carcinoma	MONDO:0005075	DOID:3969	thyroid gland	UBERON:0002046	B-CPAP	CVCL_0153	malignant cell	CL:0001064	Enhancer activity assay; allele-specific regulatory-variant assay	Expression microarray; microarray	SNP-centered dual-luciferase reporter assay for rs4562997; SMAD3 siRNA knockdown; RT-qPCR; downstream SMAD3-network ChIP-qPCR (not enhancer-site ChIP); Luciferase reporter assay; Reporter assay
E_02919	2016	26829750	An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma	Homo sapiens	hg19	chr9	14538685	14540685	TP63	NFIB	Enhancer	Active	Disease	Adenoid Cystic Carcinoma	NA	DOID:0080202	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C
E_02920	2016	26829750	An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma	Homo sapiens	hg19	chr9	14923979	14925979	TP63	NFIB	Enhancer	Active	Disease	Adenoid Cystic Carcinoma	NA	DOID:0080202	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C
E_02921	2016	26829750	An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma	Homo sapiens	hg19	chr9	15066136	15068136	TP63	NFIB	Enhancer	Active	Disease	Adenoid Cystic Carcinoma	NA	DOID:0080202	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C
E_02922	2016	26829750	An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma	Homo sapiens	hg19	chr1	92170642	92172642	TP63	TGFBR3	Enhancer	Active	Disease	Adenoid Cystic Carcinoma	NA	DOID:0080202	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C
E_02923	2016	26829750	An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma	Homo sapiens	hg19	chr1	92254801	92256801	TP63	TGFBR3	Enhancer	Active	Disease	Adenoid Cystic Carcinoma	NA	DOID:0080202	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C
E_02924	2016	26829750	An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma	Homo sapiens	hg19	chr1	92331533	92333533	TP63	TGFBR3	Enhancer	Active	Disease	Adenoid Cystic Carcinoma	NA	DOID:0080202	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C
E_02925	2016	26829750	An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma	Homo sapiens	hg19	chr1	92359751	92361751	TP63	TGFBR3	Enhancer	Active	Disease	Adenoid Cystic Carcinoma	NA	DOID:0080202	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C
E_02926	2016	26829750	An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma	Homo sapiens	hg19	chr1	92392919	92394919	TP63	TGFBR3	Enhancer	Active	Disease	Adenoid Cystic Carcinoma	NA	DOID:0080202	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C
E_02927	2016	26829750	An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma	Homo sapiens	hg19	chr1	92567177	92569177	TP63	TGFBR3	Enhancer	Active	Disease	Adenoid Cystic Carcinoma	NA	DOID:0080202	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C
E_02928	2020	33382813	Decreased sensitivity to the anorectic effects of leptin in mice that lack a Pomc-specific neural enhancer	Mus musculus	mm10	chr12	3941972	3942627	NA	Pomc	Enhancer	Active	Disease	obesity	MONDO:0011122	DOID:9970	arcuate nucleus of hypothalamus	UBERON:0001932	arcuate nucleus POMC neurons	NA	pro-opiomelanocortin neuron	CL:4042033	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation; In vivo functional validation	NA	Targeted nPE1 enhancer knockout mouse model; in situ hybridization; RT-qPCR; acute leptin challenge; chronic leptin infusion; food intake measurement; body weight phenotyping; Mouse genetic deletion/knock-in
E_02929	2020	33382813	Decreased sensitivity to the anorectic effects of leptin in mice that lack a Pomc-specific neural enhancer	Mus musculus	mm10	chr12	3944600	3944917	NA	Pomc	Enhancer	Active	Disease	obesity	MONDO:0011122	DOID:9970	arcuate nucleus of hypothalamus	UBERON:0001932	arcuate nucleus POMC neurons	NA	pro-opiomelanocortin neuron	CL:4042033	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation; In vivo functional validation	NA	Targeted nPE2 enhancer knockout mouse model; in situ hybridization; RT-qPCR; acute leptin challenge; chronic leptin infusion; food intake measurement; body weight phenotyping; Mouse genetic deletion/knock-in
E_02930	2014	24703844	Evolution of Alu elements toward enhancers	Homo sapiens	hg19	chr1	9996966	9997243	NA	LZIC	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	GM12878,CD4+ T Cell	NA	CD4-positive, alpha-beta T cell	CL:0000624	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay	ChIP-seq; Hi-C	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 4C
E_02931	2014	24703844	Evolution of Alu elements toward enhancers	Homo sapiens	hg19	chr3	11249688	11250280	NA	HRH1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	GM12878,CD4+ T Cell	NA	CD4-positive, alpha-beta T cell	CL:0000624	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay	ChIP-seq; Hi-C	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 4C
E_02932	2018	29300379	The role of SMAD3 in the genetic predisposition to papillary thyroid carcinoma	Homo sapiens	hg19	chr15	67442496	67442696	NA	SMAD3	Enhancer	Active	Disease	thyroid gland papillary carcinoma	MONDO:0005075	DOID:3969	thyroid gland	UBERON:0002046	TPC-1	CVCL_6298	thyroid follicular epithelial cell	NA	Enhancer activity assay; Allele-specific regulatory variant assay	Expression microarray after SMAD3 knockdown; microarray	Dual-luciferase reporter assay using rs17293632-centered 100-200-bp fragments; allele comparison; SMAD3 siRNA; RT-qPCR; Luciferase reporter assay; Reporter assay
E_02933	2018	29300379	The role of SMAD3 in the genetic predisposition to papillary thyroid carcinoma	Homo sapiens	hg19	chr15	67458052	67458252	NA	SMAD3	Enhancer	Active	Disease	thyroid gland papillary carcinoma	MONDO:0005075	DOID:3969	thyroid gland	UBERON:0002046	TPC-1	CVCL_6298	thyroid follicular epithelial cell	NA	Enhancer activity assay; Allele-specific regulatory variant assay	Expression microarray after SMAD3 knockdown; microarray	Dual-luciferase reporter assay using rs4562997-centered 100-200-bp fragments; allele comparison; SMAD3 siRNA; RT-qPCR; Luciferase reporter assay; Reporter assay
E_02934	2018	29300379	The role of SMAD3 in the genetic predisposition to papillary thyroid carcinoma	Homo sapiens	hg19	chr15	67442496	67442696	NA	SMAD3	Enhancer	Active	Disease	thyroid gland papillary carcinoma	MONDO:0005075	DOID:3969	thyroid gland	UBERON:0002046	B-CPAP	CVCL_0153	thyroid follicular epithelial cell	NA	Enhancer activity assay; Allele-specific regulatory variant assay	Expression microarray data integration; microarray	Dual-luciferase reporter assay using rs17293632-centered 100-200-bp fragments; allele comparison; RT-qPCR; Luciferase reporter assay; Reporter assay
E_02935	2018	29300379	The role of SMAD3 in the genetic predisposition to papillary thyroid carcinoma	Homo sapiens	hg19	chr15	67458052	67458252	NA	SMAD3	Enhancer	Active	Disease	thyroid gland papillary carcinoma	MONDO:0005075	DOID:3969	thyroid gland	UBERON:0002046	B-CPAP	CVCL_0153	thyroid follicular epithelial cell	NA	Enhancer activity assay; Allele-specific regulatory variant assay	Expression microarray data integration; microarray	Dual-luciferase reporter assay using rs4562997-centered 100-200-bp fragments; allele comparison; RT-qPCR; Luciferase reporter assay; Reporter assay
E_02936	2003	14585970	A human globin enhancer causes both discrete and widespread alterations in chromatin structure	Homo sapiens	hg19	chr11	5286080	5288080	NFE2	HBE1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	erythroid lineage cell	CL:0000764	Enhancer activity assay; chromatin regulatory assay	Chromatin accessibility analysis	Reporter assay; DNase I hypersensitivity assay; ChIP; enhancer-core mutagenesis; RNase protection assay
E_02937	2014	24703906	A remote GATA2 hematopoietic enhancer drives leukemogenesis in inv(3)(q21;q26) by activating EVI1 expression	Homo sapiens	hg19	chr3	128124000	128125500	GATA2	GATA2	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	HSPCs	NA	hematopoietic stem and progenitor cell	NA	Enhancer activity assay	ChIP-seq	RT-qPCR
E_02938	2026	41355963	Super-enhancer-driven core transcription factor FOXP1 delays endothelial cell senescence via phase separation-mediated SESN3 activation	Homo sapiens	hg19	chr3	70961242	70974816	FOXP1	FOXP1	Super-enhancer	Active	Normal	NA	NA	NA	umbilical vein	UBERON:0002066	HUVEC-C	CVCL_2959	human umbilical vein endothelial cell	NA	dCas9-KRAB CRISPRi loss-of-function; dual-luciferase reporter assay	CUT&Tag(H3K27ac/H3K4me1/H3K4me3); ATAC-seq; RNA-seq; CUT&Tag	dual-luciferase reporter detection; CRISPRi lentiviral transduction; RT-qPCR; Western blot, immunofluorescence staining; CRISPRi
E_02939	2019	30407507	Complex sex-biased antibody responses: estrogen receptors bind estrogen response elements centered within immunoglobulin heavy chain gene enhancers	Mus musculus	mm10	chr12	114640000	114670000	Esr1	Aicda	Enhancer	Active	Disease	Autoimmune Diseases	NA	NA	blood	UBERON:0000178	B Cell	NA	B cell	CL:0000236	In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR; Transgenic/LacZ assay
E_02940	2019	30407507	Complex sex-biased antibody responses: estrogen receptors bind estrogen response elements centered within immunoglobulin heavy chain gene enhancers	Mus musculus	mm10	chr12	114460000	114490000	Esr1	Aicda	Enhancer	Active	Disease	Autoimmune Diseases	NA	NA	blood	UBERON:0000178	B Cell	NA	B cell	CL:0000236	In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR; Transgenic/LacZ assay
E_02941	2013	23273978	eRNAs are required for p53-dependent enhancer activity and gene transcription	Homo sapiens	hg19	chr1	181104024	181104549	TP53	MDM2	Enhancer	Active	Normal	NA	NA	NA	breast	UBERON:0000310	MCF-7	CVCL_0031	NA	NA	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 4C; RT-qPCR/qPCR
E_02942	2013	23273978	eRNAs are required for p53-dependent enhancer activity and gene transcription	Homo sapiens	hg19	chr9	118706130	118707280	TP53	MDM2	Enhancer	Active	Normal	NA	NA	NA	breast	UBERON:0000310	MCF-7	CVCL_0031	NA	NA	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 4C; RT-qPCR/qPCR
E_02943	2017	28578223	SERPINB2 is regulated by dynamic interactions with pause-release proteins and enhancer RNAs	Homo sapiens	hg19	chr18	61274230	61274810	NA	SERPINB2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	hematopoietic cell	CL:0000988	Enhancer reporter assay; eRNA-associated regulatory-element assay	H3K27ac ChIP-seq data integration	Luciferase reporter assay using ncRNA-775-associated enhancer DNA; qRT-PCR; ChIP
E_02944	2013	23273978	eRNAs are required for p53-dependent enhancer activity and gene transcription	Homo sapiens	hg38	chr1	117752000	117754000	TP53	PAPPA	Enhancer	Active	Normal	NA	NA	NA	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay	4C-seq	Luciferase reporter assay; ChIP-qPCR; RT-qPCR
E_02945	2013	23273978	eRNAs are required for p53-dependent enhancer activity and gene transcription	Homo sapiens	hg38	chr1	179369000	179374000	TP53	IER5	Enhancer	Active	Normal	NA	NA	NA	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay	4C-seq	Luciferase reporter assay; ChIP-qPCR; RT-qPCR
E_02946	2017	28578223	SERPINB2 is regulated by dynamic interactions with pause-release proteins and enhancer RNAs	Homo sapiens	hg19	chr18	61274230	61274810	JUN	SERPINB2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Mono-Mac-6	CVCL_1426	monocyte	CL:0000576	Enhancer/eRNA functional assay; TF recruitment assay; Transcriptional pause-release assay	H3K27ac ChIP-seq data integration	LPS stimulation; enhancer-RNA knockdown/overexpression; qRT-PCR; ChIP-qPCR; JUN recruitment assay; RNA immunoprecipitation
E_02947	2022	36427307	XLID syndrome gene Med12 promotes Ig isotype switching through chromatin modification and enhancer RNA regulation	Mus musculus	mm10	chr12	117170000	117198000	NA	Igh	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	CH12F3-2A	CVCL_E068	B cell	CL:0000236	Regulatory element functional validation; super-enhancer activation analysis	NA	CRISPR-dCas9 enhancer activation, siRNA knockdown, ASO-mediated eRNA knockdown; 3C assay; ChIP-qPCR; RT-qPCR, flow cytometry
E_02948	2016	26581162	Potent and Targeted Activation of Latent HIV-1 Using the CRISPR/dCas9 Activator Complex	Homo sapiens	hg19	chr3	108015219	108015290	NFKB1	HHLA2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HEK293T	CVCL_0063	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation	RNA-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion
E_02949	2026	41496593	Neuronal titration of Snca via enhancer disruption mitigates disease onset in a Parkinson's disease mouse model	Mus musculus	mm39	chr6	60769316	60772093	NA	Snca	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Primary midbrain dopaminergic neurons	NA	dopaminergic neuron	CL:0000700	Functional perturbation assay; Endogenous enhancer perturbation; In vivo functional validation	NA	CRISPR knockout, CRISPRi; RT-qPCR; Western blot, FISH; Western blot; Mouse genetic deletion/knock-in
E_02950	2009	19345119	Stepwise activation of enhancer and promoter regions of the B cell commitment gene Pax5 in early lymphopoiesis	Mus musculus	mm10	chr4	44520195	44520234	Irf4	Pax5	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Lymphopoiesis B Cell	NA	B cell	CL:0000236	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	ChIP-qPCR/ChIP; EMSA/gel-shift assay; Transgenic/LacZ assay
E_02951	2009	19345119	Stepwise activation of enhancer and promoter regions of the B cell commitment gene Pax5 in early lymphopoiesis	Mus musculus	mm10	chr4	44520195	44520234	Irf8	Pax5	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Lymphopoiesis B Cell	NA	B cell	CL:0000236	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	ChIP-qPCR/ChIP; EMSA/gel-shift assay; Transgenic/LacZ assay
E_02952	2009	19345119	Stepwise activation of enhancer and promoter regions of the B cell commitment gene Pax5 in early lymphopoiesis	Mus musculus	mm10	chr4	44520195	44520234	Nfkb1	Pax5	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Lymphopoiesis B Cell	NA	B cell	CL:0000236	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	ChIP-qPCR/ChIP; EMSA/gel-shift assay; Transgenic/LacZ assay
E_02953	2009	19345119	Stepwise activation of enhancer and promoter regions of the B cell commitment gene Pax5 in early lymphopoiesis	Mus musculus	mm10	chr4	44520195	44520234	Spi1	Pax5	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Lymphopoiesis B Cell	NA	B cell	CL:0000236	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay	NA	ChIP-qPCR/ChIP; EMSA/gel-shift assay; Transgenic/LacZ assay
E_02954	2004	15371553	An insulator blocks spreading of histone acetylation and interferes with RNA polymerase II transfer between an enhancer and gene	Homo sapiens	hg19	chr11	5225400	5225774	NFE2	HBE1	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	ChIP-qPCR; RT-qPCR, RNase protection assay, DNase I hypersensitivity assay, Restriction enzyme accessibility assay
E_02955	2020	31915147	Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types	Mus musculus	mm10	chr14	48579937	48581029	NA	Otx2	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	Primary Mouse Embryonic Retinal Explant Cells	NA	mouse embryonic retinal cell	NA	Enhancer activity assay	RNA-seq; ATAC-seq; ChIP-seq	Transgenic reporter assay; RT-qPCR
E_02956	2020	31915147	Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types	Mus musculus	mm10	chr14	48584564	48585012	NA	Otx2	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	Primary Mouse Embryonic Retinal Explant Cells	NA	mouse embryonic retinal cell	NA	Enhancer activity assay	RNA-seq; ATAC-seq; ChIP-seq	Transgenic reporter assay; RT-qPCR
E_02957	2020	31915147	Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types	Mus musculus	mm10	chr14	48606973	48608016	NA	Otx2	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	Primary Mouse Embryonic Retinal Explant Cells	NA	mouse embryonic retinal cell	NA	Enhancer activity assay	RNA-seq; ATAC-seq; ChIP-seq	Transgenic reporter assay; RT-qPCR
E_02958	2020	31915147	Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types	Mus musculus	mm10	chr14	48608144	48609697	NA	Otx2	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	Primary Mouse Embryonic Retinal Explant Cells	NA	mouse embryonic retinal cell	NA	Enhancer activity assay	RNA-seq; ATAC-seq; ChIP-seq	Transgenic reporter assay; RT-qPCR
E_02959	2020	31915147	Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types	Mus musculus	mm10	chr14	48616314	48617497	NA	Otx2	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	Primary Mouse Embryonic Retinal Explant Cells	NA	mouse embryonic retinal cell	NA	Enhancer activity assay	RNA-seq; ATAC-seq; ChIP-seq	Transgenic reporter assay; RT-qPCR
E_02960	2020	31915147	Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types	Mus musculus	mm10	chr14	48624486	48626389	NA	Otx2	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	Primary Mouse Embryonic Retinal Explant Cells	NA	mouse embryonic retinal cell	NA	Enhancer activity assay	RNA-seq; ATAC-seq; ChIP-seq	Transgenic reporter assay; RT-qPCR
E_02961	2020	31915147	Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types	Mus musculus	mm10	chr14	48662841	48663211	NA	Otx2	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	Primary Mouse Embryonic Retinal Explant Cells	NA	mouse embryonic retinal cell	NA	Enhancer activity assay	RNA-seq; ATAC-seq; ChIP-seq	Transgenic reporter assay; RT-qPCR
E_02962	2004	15371553	An insulator blocks spreading of histone acetylation and interferes with RNA polymerase II transfer between an enhancer and gene	Homo sapiens	hg19	chr11	5301862	5302715	NA	HBE1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Functional perturbation assay; Enhancer-blocking assay; Chromatin modification assay	NA	cHS4 insulator insertion; CTCF-site deletion; ChIP-qPCR for CBP/P300/RNA polymerase II/histone acetylation; DNase I hypersensitivity assay; restriction enzyme accessibility assay; RNase protection assay
E_02963	2020	31915147	Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types	Mus musculus	mm10	chr14	48593170	48594188	NA	Otx2	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	Primary Mouse Embryonic Retinal Explant Cells	NA	mouse embryonic retinal cell	NA	Enhancer activity assay	RNA-seq; ATAC-seq; ChIP-seq	qRT-PCR, and ChIP-qPCR
E_02964	2009	19345119	Stepwise activation of enhancer and promoter regions of the B cell commitment gene Pax5 in early lymphopoiesis	Mus musculus	mm10	chr4	118656335	118661035	NA	Pax5	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary B cell progenitors	NA	pro-B cell	CL:0000826	Enhancer activity assay; TF binding assay	NA	Transgenic reporter assay, Luciferase reporter assay
E_02965	2026	41496593	Neuronal titration of Snca via enhancer disruption mitigates disease onset in a Parkinson's disease mouse model	Mus musculus	mm39	chr6	60769316	60772093	NA	Snca	Enhancer	Active	Disease	Parkinson disease	MONDO:0005180	DOID:14330	substantia nigra	UBERON:0002038	Genetically engineered C57BL/6J mice	NA	dopaminergic neuron	CL:0000700	In vivo causal neuronal enhancer disruption in a Parkinson disease mouse model	Prior neuronal chromatin-accessibility/enhancer discovery; genomic regulatory analysis	CRISPR-Cas12a enhancer deletion; smFISH/RNAscope; immunohistochemistry; stereology; Western blot; alpha-synuclein PFF challenge; motor assays
E_02966	2026	41496593	Neuronal titration of Snca via enhancer disruption mitigates disease onset in a Parkinson's disease mouse model	Mus musculus	mm39	chr6	60769316	60772093	NA	Snca	Enhancer	Active	Disease	Parkinson disease	MONDO:0005180	DOID:14330	substantia nigra	UBERON:0002038	midbrain dopaminergic neurons	NA	dopaminergic neuron	CL:0000700	In vivo causal neuronal enhancer disruption in a Parkinson disease mouse model	Prior neuronal chromatin-accessibility/enhancer discovery; genomic regulatory analysis	CRISPR-Cas12a enhancer deletion; smFISH/RNAscope; immunohistochemistry; stereology; Western blot; alpha-synuclein PFF challenge; motor assays
E_02967	2004	15371553	An insulator blocks spreading of histone acetylation and interferes with RNA polymerase II transfer between an enhancer and gene	Homo sapiens	hg19	chr11	5271421	5273421	NFE2	HBE1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_02968	2016	26382291	Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development	Homo sapiens	hg19	chr6	1614188	1617051	ZIC1	FOXC1	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Embryonic Stem Cell	NA	NA	NA	Experimentally supported enhancer study	NA	3C
E_02969	2016	26382291	Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development	Homo sapiens	hg19	chr6	1614188	1617051	ZIC1	GMDS	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Embryonic Stem Cell	NA	NA	NA	Experimentally supported enhancer study	NA	3C
E_02970	2016	26382291	Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development	Homo sapiens	hg19	chr6	1615843	1617834	ZIC1	FOXC1	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Embryonic Stem Cell	NA	NA	NA	Experimentally supported enhancer study	NA	3C
E_02971	2016	26382291	Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development	Homo sapiens	hg19	chr6	1615843	1617834	ZIC1	GMDS	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Embryonic Stem Cell	NA	NA	NA	Experimentally supported enhancer study	NA	3C
E_02972	2016	26382291	Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development	Homo sapiens	hg19	chr6	1619348	1621343	ZIC1	FOXC1	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Embryonic Stem Cell	NA	NA	NA	Experimentally supported enhancer study	NA	3C
E_02973	2016	26382291	Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development	Homo sapiens	hg19	chr6	1619348	1621343	ZIC1	GMDS	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Embryonic Stem Cell	NA	NA	NA	Experimentally supported enhancer study	NA	3C
E_02974	2016	26382291	Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development	Homo sapiens	hg19	chr6	1701730	1704441	ZIC1	FOXC1	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Embryonic Stem Cell	NA	NA	NA	Experimentally supported enhancer study	NA	3C
E_02975	2016	26382291	Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development	Homo sapiens	hg19	chr6	1701730	1704441	ZIC1	GMDS	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Embryonic Stem Cell	NA	NA	NA	Experimentally supported enhancer study	NA	3C
E_02976	2024	38504114	Multicenter integrated analysis of noncoding CRISPRi screens	Mus musculus	mm10	chr4	156021490	156022916	NA	Tnfrsf18	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary mouse regulatory T cells	NA	regulatory T cell	CL:0000815	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation	CRISPRi screening; ATAC-seq; pooled CRISPRi screen; CRISPR genetic screen	Flow cytometry; CRISPR-Cas9 endogenous deletion/editing; CRISPRi
E_02977	2024	38636893	CDK5RAP3 is a novel super-enhancer-driven gene activated by master TFs and regulates ER-Phagy in neuroblastoma	Homo sapiens	hg38	chr17	47950000	47955000	HAND2	CDK5RAP3	Enhancer	Active	Disease	neuroblastoma	MONDO:0005072	DOID:769	adrenal gland	UBERON:0002369	SK-N-BE(2)	CVCL_0528	neuroblastoma cell	NA	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ChIP-seq; Hi-C; CUT&Tag; RNA-seq; microarray	Luciferase reporter assay; 3C-RT-qPCR; CUT&RUN-RT-qPCR; RT-qPCR; Western blot
E_02978	2024	38636893	CDK5RAP3 is a novel super-enhancer-driven gene activated by master TFs and regulates ER-Phagy in neuroblastoma	Homo sapiens	hg38	chr17	47950000	47955000	MEIS2	CDK5RAP3	Enhancer	Active	Disease	neuroblastoma	MONDO:0005072	DOID:769	adrenal gland	UBERON:0002369	SK-N-BE(2)	CVCL_0528	neuroblastoma cell	NA	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ChIP-seq; Hi-C; CUT&Tag; RNA-seq; microarray	Luciferase reporter assay; 3C-RT-qPCR; CUT&RUN-RT-qPCR; RT-qPCR; Western blot
E_02979	2021	34739481	The Nestin neural enhancer is essential for normal levels of endogenous Nestin in neuroprogenitors but is not required for embryo development	Mus musculus	mm10	chr10	87376120	87376374	NA	Nes	Enhancer	Active	Normal	NA	NA	NA	central nervous system	UBERON:0001017	Embryonic neuroprogenitor cells	NA	neural progenitor cell	CL:0011020	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation; In vivo functional validation	NA	CRISPR knockout, qRT-PCR, In situ hybridization, Immunohistochemistry; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in; In vivo phenotyping; Reporter assay
E_02980	2018	29511351	HPSE enhancer RNA promotes cancer progression through driving chromatin looping and regulating hnRNPU/p300/EGR1/HPSE axis	Homo sapiens	hg19	chr4	84277627	84281723	EGR1	HPSE	Super-enhancer	Active	Disease	gastric cancer	MONDO:0001056	DOID:10534	NA	NA	AGS	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_02981	2015	25548254	A novel Cd8-cis-regulatory element preferentially directs expression in CD44hiCD62L+ CD8+ T cells and in CD8αα+ dendritic cells	Mus musculus	mm10	chr6	71341692	71345212	Bcl11b	Cd8a	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	CD4+ T Cell	NA	CD4-positive, alpha-beta T cell	CL:0000624	In vivo functional validation; TF-binding/chromatin assay	NA	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_02982	2015	25548254	A novel Cd8-cis-regulatory element preferentially directs expression in CD44hiCD62L+ CD8+ T cells and in CD8αα+ dendritic cells	Mus musculus	mm10	chr6	71341692	71345212	Bcl11b	Cd8b1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	CD4+ T Cell	NA	CD4-positive, alpha-beta T cell	CL:0000624	In vivo functional validation; TF-binding/chromatin assay	NA	ChIP-qPCR/ChIP; Transgenic/LacZ assay
E_02983	2013	23613851	In vivo analysis of Aicda gene regulation: a critical balance between upstream enhancers and intronic silencers governs appropriate expression	Mus musculus	mm10	chr6	122563494	122564540	NA	Aicda	Enhancer	Active	Normal	NA	NA	NA	lymph node	UBERON:0000029	Germinal center B cells	NA	germinal center B cell	CL:0000844	Enhancer activity assay; Functional perturbation assay; In vivo functional validation	NA	Transgenic reporter assay; RT-qPCR, FACS; Transgenic enhancer reporter assay; In vivo phenotyping
E_02984	2013	23613851	In vivo analysis of Aicda gene regulation: a critical balance between upstream enhancers and intronic silencers governs appropriate expression	Mus musculus	mm10	chr6	122573553	122574125	NA	Aicda	Enhancer	Active	Normal	NA	NA	NA	lymph node	UBERON:0000029	Germinal center B cells	NA	germinal center B cell	CL:0000844	Enhancer activity assay; Functional perturbation assay; In vivo functional validation	NA	Transgenic reporter assay; RT-qPCR, FACS; Transgenic enhancer reporter assay; In vivo phenotyping
E_02985	2017	27989796	Altered SOX9 genital tubercle enhancer region in hypospadias	Homo sapiens	hg19	chr17	69541883	69542989	SOX9	SOX9	Enhancer	Active	Normal	NA	NA	NA	NA	NA	TM4	CVCL_4327	NA	NA	Enhancer activity assay; In vivo functional validation	NA	Luciferase reporter assay; Reporter assay; Transgenic/LacZ assay; Histology/immunostaining
E_02986	2017	28082341	The transcription factor GATA1 regulates NBEAL2 expression through a long-distance enhancer	Homo sapiens	hg19	chr3	46988756	46990332	GATA1	NBEAL2	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary human megakaryocytes	NA	megakaryocyte	CL:0000556	Enhancer activity; direct TF occupancy; enhancer-target linkage	GATA1/GATA2 ChIP-seq; histone-mark and chromatin-interaction data integration	Luciferase reporter; GATA-site mutagenesis; ChIP-qPCR; siRNA; RT-qPCR; immunoblot; Luciferase reporter assay
E_02987	2015	25604083	Copy number variation of two separate regulatory regions upstream of SOX9 causes isolated 46,XY or 46,XX disorder of sex development	Homo sapiens	hg19	chr17	69487560	69491400	NR5A1	SOX9	Enhancer	Active	Disease	Disorders Of Sexual Development	NA	NA	NA	NA	HEK293	CVCL_0045	NA	NA	Enhancer activity assay; In vivo functional validation; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; Transgenic/LacZ assay
E_02988	2015	25604083	Copy number variation of two separate regulatory regions upstream of SOX9 causes isolated 46,XY or 46,XX disorder of sex development	Homo sapiens	hg19	chr17	69487560	69491400	WT1	SOX9	Enhancer	Active	Disease	Disorders Of Sexual Development	NA	NA	NA	NA	HEK293	CVCL_0045	NA	NA	Enhancer activity assay; In vivo functional validation; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; Transgenic/LacZ assay
E_02989	2012	22265404	Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation	Homo sapiens	hg19	chr14	90847327	90849327	NA	CALM1	Enhancer	Active	Disease	Congenital Limb Deformity	NA	NA	blood	UBERON:0000178	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_02990	2012	22265404	Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation	Homo sapiens	hg19	chr14	90847327	90849327	NA	CALM1	Enhancer	Active	Disease	Congenital Limb Deformity	NA	NA	blood	UBERON:0000178	HeLa	CVCL_0030	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_02991	2012	22265404	Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation	Homo sapiens	hg19	chr14	90847327	90849327	NA	CALM1	Enhancer	Active	Disease	Congenital Limb Deformity	NA	NA	blood	UBERON:0000178	HCT 116	CVCL_0291	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_02992	2011	21327791	The -14010*C variant associated with lactase persistence is located between an Oct-1 and HNF1α binding site and increases lactase promoter activity	Homo sapiens	hg19	chr2	136608729	136608757	HNF1A	LCT	Enhancer	Active	Normal	NA	NA	NA	colon	UBERON:0001155	Caco-2	CVCL_0025	enterocyte-like epithelial cell line	NA	Enhancer activity assay; TF binding assay	NA	Transient transfection; Luciferase reporter assay; deletion analysis; EMSA; DNA footprinting
E_02993	2011	21327791	The -14010*C variant associated with lactase persistence is located between an Oct-1 and HNF1α binding site and increases lactase promoter activity	Homo sapiens	hg19	chr2	136608729	136608757	POU2F1	LCT	Enhancer	Active	Normal	NA	NA	NA	colon	UBERON:0001155	Caco-2	CVCL_0025	enterocyte-like epithelial cell line	NA	Enhancer activity assay; TF binding assay; Allele-specific functional assay	NA	Transient transfection; Luciferase reporter assay; deletion analysis; EMSA; DNA footprinting
E_02994	2003	12855570	Persistent gamma-globin expression in adult transgenic mice is mediated by HPFH-2, HPFH-3, and HPFH-6 breakpoint sequences	Homo sapiens	hg19	chr11	5191975	5193451	NA	HBG1	Enhancer	Active	Disease	hereditary persistence of fetal hemoglobin	MONDO:0020989	NA	blood	UBERON:0000178	transgenic mouse erythroid cells	NA	erythroid lineage cell	CL:0000764	In vivo enhancer activity assay; disease breakpoint analysis	NA	Transgenic mouse reporter assay; Cre-mediated single-copy transgene conversion; fetal globin expression analysis
E_02995	2003	12855570	Persistent gamma-globin expression in adult transgenic mice is mediated by HPFH-2, HPFH-3, and HPFH-6 breakpoint sequences	Homo sapiens	hg19	chr11	5191975	5193451	NA	HBG2	Enhancer	Active	Disease	hereditary persistence of fetal hemoglobin	MONDO:0020989	NA	blood	UBERON:0000178	transgenic mouse erythroid cells	NA	erythroid lineage cell	CL:0000764	In vivo enhancer activity assay; disease breakpoint analysis	NA	Transgenic mouse reporter assay; Cre-mediated single-copy transgene conversion; fetal globin expression analysis
E_02996	2003	12855570	Persistent gamma-globin expression in adult transgenic mice is mediated by HPFH-2, HPFH-3, and HPFH-6 breakpoint sequences	Homo sapiens	hg19	chr11	5214864	5215676	NA	HBG1	Enhancer	Active	Disease	hereditary persistence of fetal hemoglobin	MONDO:0020989	NA	blood	UBERON:0000178	transgenic mouse erythroid cells	NA	erythroid lineage cell	CL:0000764	In vivo enhancer activity assay; disease breakpoint analysis	NA	Transgenic mouse reporter assay; Cre-mediated single-copy transgene conversion; fetal globin expression analysis
E_02997	2003	12855570	Persistent gamma-globin expression in adult transgenic mice is mediated by HPFH-2, HPFH-3, and HPFH-6 breakpoint sequences	Homo sapiens	hg19	chr11	5214864	5215676	NA	HBG2	Enhancer	Active	Disease	hereditary persistence of fetal hemoglobin	MONDO:0020989	NA	blood	UBERON:0000178	transgenic mouse erythroid cells	NA	erythroid lineage cell	CL:0000764	In vivo enhancer activity assay; disease breakpoint analysis	NA	Transgenic mouse reporter assay; Cre-mediated single-copy transgene conversion; fetal globin expression analysis
E_02998	2003	12855570	Persistent gamma-globin expression in adult transgenic mice is mediated by HPFH-2, HPFH-3, and HPFH-6 breakpoint sequences	Homo sapiens	hg19	chr11	5168384	5181696	NA	HBG1	Enhancer	Active	Disease	hereditary persistence of fetal hemoglobin	MONDO:0020989	NA	blood	UBERON:0000178	transgenic mouse erythroid cells	NA	erythroid lineage cell	CL:0000764	In vivo enhancer activity assay; disease breakpoint analysis	NA	Transgenic mouse reporter assay; Cre-mediated single-copy transgene conversion; fetal globin expression analysis
E_02999	2003	12855570	Persistent gamma-globin expression in adult transgenic mice is mediated by HPFH-2, HPFH-3, and HPFH-6 breakpoint sequences	Homo sapiens	hg19	chr11	5168384	5181696	NA	HBG2	Enhancer	Active	Disease	hereditary persistence of fetal hemoglobin	MONDO:0020989	NA	blood	UBERON:0000178	transgenic mouse erythroid cells	NA	erythroid lineage cell	CL:0000764	In vivo enhancer activity assay; disease breakpoint analysis	NA	Transgenic mouse reporter assay; Cre-mediated single-copy transgene conversion; fetal globin expression analysis
E_03000	2012	22265404	Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation	Homo sapiens	hg19	chr14	90847327	90849327	NA	CALM1	Enhancer	Active	Disease	Congenital Limb Deformity	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_03001	2012	22265404	Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation	Homo sapiens	hg19	chr14	90847327	90849327	NA	CALM1	Enhancer	Active	Disease	Congenital Limb Deformity	NA	NA	blood	UBERON:0000178	NB4	CVCL_0005	NA	NA	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_03002	2017	28082341	The transcription factor GATA1 regulates NBEAL2 expression through a long-distance enhancer	Homo sapiens	hg19	chr3	46988756	46990332	GATA1	NBEAL2	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	K-562	CVCL_0004	megakaryocyte	CL:0000556	Enhancer activity; direct TF occupancy; enhancer-target linkage	GATA1/GATA2 ChIP-seq; histone-mark and chromatin-interaction data integration	Luciferase reporter; GATA-site mutagenesis; ChIP-qPCR; siRNA; RT-qPCR; immunoblot; Luciferase reporter assay
E_03003	2003	12855570	Persistent gamma-globin expression in adult transgenic mice is mediated by HPFH-2, HPFH-3, and HPFH-6 breakpoint sequences	Homo sapiens	hg19	chr11	5191975	5193451	NA	HBG1	Enhancer	Active	Disease	hereditary persistence of fetal hemoglobin	MONDO:0020989	NA	blood	UBERON:0000178	transgenic mouse erythroid cells	NA	erythroid lineage cell	CL:0000764	In vivo enhancer activity assay; Breakpoint-associated enhancer assay	NA	Transgenic mouse enhancer assay; breakpoint mapping; sequence analysis; gamma-globin expression assay
E_03004	2017	28082341	The transcription factor GATA1 regulates NBEAL2 expression through a long-distance enhancer	Homo sapiens	hg19	chr3	46988575	46990242	GATA1	NBEAL2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; Western blot
E_03005	2011	21327791	The -14010*C variant associated with lactase persistence is located between an Oct-1 and HNF1α binding site and increases lactase promoter activity	Homo sapiens	hg19	chr2	136531405	136531505	HNF1A	LCT	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Caco-2	CVCL_0025	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; EMSA/gel-shift assay
E_03006	2011	21327791	The -14010*C variant associated with lactase persistence is located between an Oct-1 and HNF1α binding site and increases lactase promoter activity	Homo sapiens	hg19	chr2	136531405	136531505	POU2F1	LCT	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Caco-2	CVCL_0025	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; EMSA/gel-shift assay
E_03007	2017	27989796	Altered SOX9 genital tubercle enhancer region in hypospadias	Homo sapiens	hg19	chr17	69541883	69542989	NA	SOX9	Enhancer	Active	Disease	hypospadias	MONDO:0005345	DOID:10892	mesonephric mesenchyme	UBERON:0005323	patient DNA	NA	genital-tubercle mesenchymal cell	NA	Enhancer-variant functional assay	None (candidate-locus study)	variant screening; enhancer reporter; developmental/in vivo reporter analysis
E_03008	2015	25604083	Copy number variation of two separate regulatory regions upstream of SOX9 causes isolated 46,XY or 46,XX disorder of sex development	Homo sapiens	hg19	chr17	69498800	69500700	NA	SOX9	Enhancer	Active	Normal	NA	NA	NA	testis	UBERON:0000473	TM4	CVCL_4327	Sertoli cell	CL:0000216	Enhancer activity assay	NA	Luciferase reporter assay
E_03009	2017	27989796	Altered SOX9 genital tubercle enhancer region in hypospadias	Homo sapiens	hg19	chr17	69541883	69542989	NA	SOX9	Enhancer	Active	Disease	hypospadias	MONDO:0005345	DOID:10892	mesonephric mesenchyme	UBERON:0005323	genital-tubercle/developmental enhancer reporter models	NA	genital-tubercle mesenchymal cell	NA	Enhancer-variant functional assay	None (candidate-locus study)	variant screening; enhancer reporter; developmental/in vivo reporter analysis
E_03010	2022	36417539	A pleiotropic hypoxia-sensitive EPAS1 enhancer is disrupted by adaptive alleles in Tibetans	Homo sapiens	hg19	chr2	46578867	46579857	NA	EPAS1	Enhancer	Active	Normal	NA	NA	NA	thoracic aorta	UBERON:0001515	TeloHAEC	CVCL_Z065	endothelial cell of thoracic aorta	NA	Enhancer activity assay; Functional perturbation assay	RNA-seq	Luciferase reporter assay; CRISPR/Cas9 deletion; RT-qPCR
E_03011	2021	34103329	Enhancer Hijacking Drives Oncogenic BCL11B Expression in Lineage-Ambiguous Stem Cell Leukemia	Homo sapiens	hg38	chr14	98541905	98544383	NA	BCL11B	Enhancer	Active	Disease	acute leukemia of ambiguous lineage	MONDO:0019460	NA	bone marrow	UBERON:0002371	Primary lineage-ambiguous leukemia cells	NA	malignant cell	CL:0001064	Chromatin interaction assay; Enhancer hijacking assay; Structural-variant regulatory assay	WGS; RNA-seq; H3K27ac regulatory profiling; chromatin-conformation profiling; structural-variant analysis	DNA/RNA FISH; genomic validation; allele-specific expression validation
E_03012	2019	31096644	A Critical E-box in Barhl1 3' Enhancer Is Essential for Auditory Hair Cell Differentiation	Mus musculus	mm10	chr2	44123800	44124118	NA	Barhl1	Enhancer	Active	Normal	NA	NA	NA	internal ear	UBERON:0001846	mESC differentiated hair cell	NA	hair cell	NA	Enhancer activity assay; Functional perturbation assay	RNA-seq	Luciferase reporter assay; CRISPR knockout; RT-qPCR; CRISPR-Cas9
E_03013	2019	31231131	Ascl1-induced Wnt11 regulates neuroendocrine differentiation, cell proliferation, and E-cadherin expression in small-cell lung cancer and Wnt11 regulates small-cell lung cancer biology	Homo sapiens	hg19	chr11	75928700	75928930	ASCL1	WNT11	Enhancer	Active	Disease	small cell lung carcinoma	MONDO:0008433	DOID:5409	lung	UBERON:0002048	NCI-H920	CVCL_1599	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	ChIP-qPCR, qRT-PCR; Western blot
E_03014	2016	26864944	Enhancer RNA-driven looping enhances the transcription of the long noncoding RNA DHRS4-AS1, a controller of the DHRS4 gene cluster	Homo sapiens	hg19	chr14	22758000	22759600	CEBPB	DHRS4-AS1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin interaction assay; eRNA functional assay	NA	Luciferase reporter assay; 3C-RT-qPCR; ChIP-qPCR; RT-qPCR, 5'/3' RACE, Actinomycin D RNA stability assay; Bisulfite sequencing PCR; 3C
E_03015	2014	24510239	ABCC4 copy number variation is associated with susceptibility to esophageal squamous cell carcinoma	Homo sapiens	hg19	chr13	94663320	94664200	GATA3	ABCC4	Enhancer	Active	Disease	esophageal squamous cell carcinoma	MONDO:0005580	DOID:3748	adrenal gland	UBERON:0002369	NCI-H295R	CVCL_0458	malignant cell	CL:0001064	Enhancer activity assay; Disease-variant functional analysis; CNV functional assay	ChIP-seq	Luciferase reporter assay; RT-qPCR, siRNA
E_03016	2013	23443045	FOXA1 mediates p16(INK4a) activation during cellular senescence	Homo sapiens	hg19	chr9	21816751	21818751	FOXA1	CDKN2A	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Human 2BS Diploid Fibroblast Cells	NA	fibroblast	CL:0000057	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay; 3C; RT-qPCR/qPCR
E_03017	2011	21185279	The Pou5f1/Pou3f-dependent but SoxB-independent regulation of conserved enhancer N2 initiates Sox2 expression during epiblast to neural plate stages in vertebrates	Mus musculus	mm10	chr3	34645597	34646134	Pou5f1	Sox2	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Mouse Embryos	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	NA	ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_03018	2003	12861010	A complex chromatin landscape revealed by patterns of nuclease sensitivity and histone modification within the mouse beta-globin locus	Homo sapiens	hg19	chr11	5293686	5294250	CTCF	NA	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	In vivo functional validation; TF-binding/chromatin assay	NA	ChIP-qPCR/ChIP
E_03019	2013	23443045	FOXA1 mediates p16(INK4a) activation during cellular senescence	Homo sapiens	hg19	chr9	22117000	22118500	FOXA1	CDKN2A	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	NTERA-2	CVCL_0034	fetal lung fibroblast	NA	Enhancer activity assay; Chromatin interaction assay	3C-seq	Luciferase reporter assay; ChIP-qPCR; EMSA; RT-qPCR; Western blot
E_03020	2003	12861010	A complex chromatin landscape revealed by patterns of nuclease sensitivity and histone modification within the mouse beta-globin locus	Mus musculus	mm10	chr7	103771431	103772043	Ctcf	Hbb-ar	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Pleen Cells,MEL cells	NA	NA	NA	In vivo functional validation; TF-binding/chromatin assay	NA	ChIP-qPCR/ChIP
E_03021	2018	29912188	Dissection of Enhancer Function Using Multiplex CRISPR-based Enhancer Interference in Cell Lines	Homo sapiens	hg19	chr12	132285987	132290767	NA	MMP17	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Ishikawa Cell	NA	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_03022	2018	29912188	Dissection of Enhancer Function Using Multiplex CRISPR-based Enhancer Interference in Cell Lines	Homo sapiens	hg19	chr12	132281970	132287430	NA	MMP17	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Ishikawa Cell	NA	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_03023	2018	29912188	Dissection of Enhancer Function Using Multiplex CRISPR-based Enhancer Interference in Cell Lines	Homo sapiens	hg19	chr12	132342570	132347690	NA	MMP17	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Ishikawa Cell	NA	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_03024	2018	30139998	Polycomb complexes associate with enhancers and promote oncogenic transcriptional programs in cancer through multiple mechanisms	Homo sapiens	hg19	chr6	37997692	38001538	RNF2	FOXA1	Super-enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	T-47D	CVCL_0553	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq; ATAC-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_03025	2018	30139998	Polycomb complexes associate with enhancers and promote oncogenic transcriptional programs in cancer through multiple mechanisms	Homo sapiens	hg19	chr6	38010769	38019538	RNF2	FOXA1	Super-enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	T-47D	CVCL_0553	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq; ATAC-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_03026	2018	30139998	Polycomb complexes associate with enhancers and promote oncogenic transcriptional programs in cancer through multiple mechanisms	Homo sapiens	hg19	chr6	38032307	38035230	RNF2	FOXA1	Super-enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	T-47D	CVCL_0553	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq; ATAC-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_03027	2017	28637769	Potential contribution of tandem circadian enhancers to nonlinear oscillations in clock gene expression	Homo sapiens	hg19	chr11	45868494	45868510	CLOCK	CRY2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	U-2 OS	CVCL_0042	osteosarcoma cell line	NA	Enhancer activity assay; TF binding assay; Circadian regulatory-element dissection assay	NA	Luciferase reporter deletion/mutagenesis; real-time bioluminescence monitoring; ARNTL/CLOCK transactivation; EMSA; DNA-binding assay
E_03028	2018	30139998	Polycomb complexes associate with enhancers and promote oncogenic transcriptional programs in cancer through multiple mechanisms	Homo sapiens	hg19	chr20	30244800	30316534	RNF2	BCL2L1	Super-enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	MDA-MB-231	CVCL_0062	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq; ATAC-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_03029	2002	12399963	Disruption of the RanBP17/Hox11L2 region by recombination with the TCRdelta locus in acute lymphoblastic leukemias with t(5;14)(q34;q11)	Homo sapiens	hg19	chr14	22420000	22422000	NA	RANBP17	Enhancer	Active	Normal	NA	NA	NA	thymus	UBERON:0002370	T Lymphocyte Progenitors	NA	T lymphocyte progenitor	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	NA	Southern blot; PCR; Sequencing; Northern Blot; FISH
E_03030	2018	30139998	Polycomb complexes associate with enhancers and promote oncogenic transcriptional programs in cancer through multiple mechanisms	Homo sapiens	hg19	chr6	151917241	152028736	RNF2	ESR1	Super-enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	T-47D	CVCL_0553	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq; ATAC-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_03031	2002	12399963	Disruption of the RanBP17/Hox11L2 region by recombination with the TCRdelta locus in acute lymphoblastic leukemias with t(5;14)(q34;q11)	Homo sapiens	hg19	chr14	22420000	22422000	NA	TRD	Enhancer	Active	Normal	NA	NA	NA	zone of skin	UBERON:0000014	Primary human epidermal keratinocytes (HEKa)	NA	keratinocyte	CL:0000312	Enhancer activity assay; Chromatin interaction assay	NA	Southern blot; PCR; Sequencing; FISH
E_03032	2017	28637769	Potential contribution of tandem circadian enhancers to nonlinear oscillations in clock gene expression	Homo sapiens	hg19	chr11	45846943	45846959	ARNTL	CRY2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	U-2 OS	CVCL_0042	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; EMSA/gel-shift assay
E_03033	2017	28637769	Potential contribution of tandem circadian enhancers to nonlinear oscillations in clock gene expression	Homo sapiens	hg19	chr11	45846943	45846959	CLOCK	CRY2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	U-2 OS	CVCL_0042	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; EMSA/gel-shift assay
E_03034	2022	36417539	A pleiotropic hypoxia-sensitive EPAS1 enhancer is disrupted by adaptive alleles in Tibetans	Homo sapiens	hg19	chr2	46578867	46579857	NA	EPAS1	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	HEK293T	CVCL_0063	HEK293T cell	NA	Enhancer activity assay; Allele-specific functional assay	NA	Luciferase reporter assay; Site-directed mutagenesis; Sanger sequencing
E_03035	2014	24510239	ABCC4 copy number variation is associated with susceptibility to esophageal squamous cell carcinoma	Homo sapiens	hg19	chr13	95865319	95866199	NA	ABCC4	Enhancer	Active	Disease	esophageal squamous cell carcinoma	MONDO:0005580	DOID:3748	NA	NA	Umbilical Vein Endothelial Cell,ESCC	NA	endothelial cell	CL:0000115	Enhancer activity assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; Western blot
E_03036	2021	34890222	Conditionally pathogenic genetic variants of a hematopoietic disease-suppressing enhancer	Mus musculus	mm10	chr6	88180000	88180500	NA	Gata2	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Hematopoietic stem cells, HSPCs	NA	hematopoietic stem cell	CL:0000037	Disease-variant functional analysis; Endogenous enhancer perturbation; Regulatory element functional validation; in vivo mouse model validation	NA	CRISPR-Cas9 point mutation; RT-qPCR, flow cytometry, competitive bone marrow transplantation; Site-directed/motif mutagenesis
E_03037	2019	30328555	STAT5-Driven Enhancers Tightly Control Temporal Expression of Mammary-Specific Genes	Mus musculus	mm10	chr11	100854851	100856851	Stat5a	Stat5a	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mammary	NA	NA	NA	Endogenous enhancer perturbation; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_03038	2017	28416141	Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells	Homo sapiens	hg19	chr11	5278952	5279402	NA	HBG2	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	K-562	CVCL_0004	malignant cell	CL:0001064	CRISPRi-based single-cell enhancer perturbation	Drop-seq single-cell RNA-seq, CRISPR barcoding	qRT-PCR, and ChIP-qPCR
E_03039	1992	1429727	Immunoglobulin kappa gene enhancers synergistically activate gene expression but independently determine chromatin structure	Mus musculus	mm10	chr6	70725951	70726429	NA	Igk	Enhancer	Active	Normal	NA	NA	NA	NA	NA	S194/5.XXO.BU.1	CVCL_4696	plasma cell	CL:0000786	Enhancer activity assay; Functional perturbation assay; Chromatin accessibility assay; Endogenous enhancer perturbation; In vivo functional validation; Chromatin structure assay	NA	Enhancer deletion constructs; transient transfection expression assay; stable transfection/integration assay; DNase I hypersensitivity assay; Northern blot; Southern blot; restriction mapping; Mouse genetic deletion/knock-in
E_03040	1992	1429727	Immunoglobulin kappa gene enhancers synergistically activate gene expression but independently determine chromatin structure	Mus musculus	mm10	chr6	70735260	70736060	NA	Igk	Enhancer	Active	Normal	NA	NA	NA	NA	NA	S194/5.XXO.BU.1	CVCL_4696	plasma cell	CL:0000786	Enhancer activity assay; Functional perturbation assay; Chromatin accessibility assay; Endogenous enhancer perturbation; In vivo functional validation; Chromatin structure assay	NA	Enhancer deletion constructs; transient transfection expression assay; stable transfection/integration assay; DNase I hypersensitivity assay; Northern blot; Southern blot; restriction mapping; Mouse genetic deletion/knock-in
E_03041	2017	28416141	Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells	Homo sapiens	hg19	chr11	5258353	5258721	NA	HBG1	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	CRISPRi-based single-cell endogenous enhancer perturbation	Drop-seq single-cell RNA-seq; sgRNA barcode sequencing	Independent RT-qPCR
E_03042	2017	28416141	Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells	Homo sapiens	hg19	chr6	37151046	37151259	NA	PIM1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Multiplex endogenous enhancer perturbation with single-cell transcriptomic readout	Mosaic-seq pooled dCas9-KRAB CRISPRi; single-cell RNA-seq; DNase/ChIP integration	targeted guide validation; qRT-PCR; endogenous CRISPRi validation
E_03043	1992	1429727	Immunoglobulin kappa gene enhancers synergistically activate gene expression but independently determine chromatin structure	Mus musculus	mm10	chr6	70989543	70989643	NA	Igkc	Enhancer	Active	Disease	plasmacytoma	MONDO:0005615	DOID:3721	blood	UBERON:0000178	LPRB3 112	CVCL_V125	plasmacytoma cell	NA	Functional perturbation assay	NA	RT-qPCR
E_03044	1992	1429727	Immunoglobulin kappa gene enhancers synergistically activate gene expression but independently determine chromatin structure	Mus musculus	mm10	chr6	70999043	70999143	NA	Igkc	Enhancer	Active	Disease	plasmacytoma	MONDO:0005615	DOID:3721	blood	UBERON:0000178	LPRB3 112	CVCL_V125	plasmacytoma cell	NA	Functional perturbation assay	NA	RT-qPCR
E_03045	2017	28790107	RUNX1 is required for oncogenic Myb and Myc enhancer activity in T-cell acute lymphoblastic leukemia	Homo sapiens	hg19	chr8	130180065	130180972	RUNX1	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	human T-ALL cells	NA	T-lineage lymphoblast/leukemia cell	NA	TF requirement for oncogenic enhancer activity	ChIP-seq; chromatin-accessibility profiling; gene-expression profiling	RUNX1 genetic perturbation; ChIP-qPCR; enhancer accessibility analysis; leukemia growth assays
E_03046	2017	28790107	RUNX1 is required for oncogenic Myb and Myc enhancer activity in T-cell acute lymphoblastic leukemia	Homo sapiens	hg19	chr8	130180065	130180972	RUNX1	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	NOTCH1/TAL1 leukemia models	NA	T-lineage lymphoblast/leukemia cell	NA	TF requirement for oncogenic enhancer activity	ChIP-seq; chromatin-accessibility profiling; gene-expression profiling	RUNX1 genetic perturbation; ChIP-qPCR; enhancer accessibility analysis; leukemia growth assays
E_03047	2017	28790107	RUNX1 is required for oncogenic Myb and Myc enhancer activity in T-cell acute lymphoblastic leukemia	Homo sapiens	hg19	chr8	130180065	130180972	RUNX1	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	human T-ALL cells	NA	T-lineage lymphoblast/leukemia cell	NA	TF requirement for oncogenic enhancer activity	ChIP-seq; chromatin-accessibility profiling; gene-expression profiling	RUNX1 genetic perturbation; ChIP-qPCR; enhancer accessibility analysis; leukemia growth assays
E_03048	2017	28790107	RUNX1 is required for oncogenic Myb and Myc enhancer activity in T-cell acute lymphoblastic leukemia	Homo sapiens	hg19	chr8	130180065	130180972	RUNX1	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	NOTCH1/TAL1 leukemia models	NA	T-lineage lymphoblast/leukemia cell	NA	TF requirement for oncogenic enhancer activity	ChIP-seq; chromatin-accessibility profiling; gene-expression profiling	RUNX1 genetic perturbation; ChIP-qPCR; enhancer accessibility analysis; leukemia growth assays
E_03049	2026	40971821	Co-activation of the super-enhancer complex SOX2 and HDAC1 confers temozolomide resistance by promoting PDGFB transcription in glioblastoma	Homo sapiens	hg38	chr22	43901526	43904612	SOX2	PDGFB	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:0081088	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Functional perturbation assay; Super-enhancer activity assay	CUT&Tag; RNA-seq	Luciferase reporter assay; CRISPRi; ChIP-qPCR; Reporter assay
E_03050	2025	40160815	A pooled CRISPR screen identifies the Tα2 enhancer element as a driver of TRA expression in a subset of mature human T lymphocytes	Homo sapiens	hg38	chr14	22556439	22556536	NA	TRAC	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human peripheral blood CD3+ T cells	NA	T cell	CL:0000084	Functional enhancer perturbation assay; Endogenous cis-regulatory element validation	NA	Targeted CRISPR/Cas9 editing of Tα2; Paired-sgRNA Tα2 deletion; Flow cytometry; RT-qPCR; PCR; Sanger sequencing; ICE analysis
E_03051	2024	38311851	DLK1/DIO3 locus upregulation by a β-catenin-dependent enhancer drives cell proliferation and liver tumorigenesis	Homo sapiens	hg19	chr14	101283029	101284356	TCF7L2	MEG3	Enhancer	Active	Disease	hepatoblastoma	MONDO:0018666	DOID:687	liver	UBERON:0002107	HuH-6	CVCL_4381	hepatoblast	CL:0005026	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation; Tumorigenicity assay	NA	CRISPR-Cas9 enhancer deletion; RT-qPCR; Cell proliferation assay; Flow cytometry; Spheroid formation assay; Xenograft assay; Ki-67 immunohistochemistry; Western blot; CRISPR-Cas9 endogenous deletion/editing
E_03052	2019	30487368	PGSE Is a Novel Enhancer Regulating the Proteoglycan Pathway of the Mammalian Golgi Stress Response	Homo sapiens	hg19	chr15	69452739	69453134	NA	GLCE	Enhancer	Active	Normal	NA	NA	NA	cervix-derived cell culture	NA	HeLa	CVCL_0030	epithelial cell	CL:0000066	Motif-defined enhancer discovery; Golgi-stress response assay; reporter/mutagenesis analysis	microarray; RNA-seq	Luciferase reporter assay; promoter/enhancer deletion and motif mutagenesis; Golgi-stress induction; qRT-PCR
E_03053	2011	21464046	Nkx2-5 represses Gata1 gene expression and modulates the cellular fate of cardiac progenitors during embryogenesis	Mus musculus	mm10	chrX	7954360	7956360	Nkx2-5	Gata1	Enhancer	Repressed	Normal	NA	NA	NA	heart	UBERON:0000948	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation	NA	Luciferase reporter assay; Reporter assay
E_03054	2022	36097291	Cohesin is required for long-range enhancer action at the Shh locus	Mus musculus	mm10	chr5	28563148	28563921	NA	Shh	Enhancer	Active	Normal	NA	NA	NA	neural tube	UBERON:0001049	ES-E14	CVCL_C320	embryonic stem cell	CL:0002322	Synthetic enhancer activation assay; Cohesin functional perturbation assay; Chromatin conformation analysis	Hi-C data reanalysis; virtual 4C	TALE-VP64 synthetic enhancer activation; auxin-inducible SCC1/RAD21 degradation; RNA FISH; DNA FISH
E_03055	2022	36097291	Cohesin is required for long-range enhancer action at the Shh locus	Mus musculus	mm10	chr5	28875380	28876679	NA	Shh	Enhancer	Active	Normal	NA	NA	NA	diencephalon	UBERON:0001894	ES-E14	CVCL_C320	embryonic stem cell	CL:0002322	Synthetic enhancer activation assay; Cohesin/CTCF functional perturbation assay; Chromatin conformation analysis	Hi-C data reanalysis; virtual 4C	TALE-VP64 synthetic enhancer activation; auxin-inducible SCC1/RAD21 degradation; auxin-inducible CTCF degradation; RNA FISH; DNA FISH; Immunofluorescence; Flow cytometry
E_03056	2019	30678091	Functional SNPs in the Human Autoimmunity-Associated Locus 17q12-21	Homo sapiens	hg19	chr17	37912040	37913027	NA	NA	Enhancer	Active	Disease	autoimmune disease susceptibility at 17q12-21	NA	NA	blood	UBERON:0000178	MP1 mature B-cell line	NA	B cell	CL:0000236	Disease-variant enhancer reporter assay; GWAS/epigenomic prioritization; site-directed allelic comparison	GWAS/fine-mapping; ENCODE DHS/H3K27ac/TF ChIP-seq integration	Luciferase reporter assay; PCR/site-directed mutagenesis
E_03057	2019	30678091	Functional SNPs in the Human Autoimmunity-Associated Locus 17q12-21	Homo sapiens	hg19	chr17	38050770	38051866	NA	NA	Enhancer	Active	Disease	autoimmune disease susceptibility at 17q12-21	NA	NA	blood	UBERON:0000178	MT-2	NA	T cell	CL:0000084	Disease-variant enhancer reporter assay; GWAS/epigenomic prioritization; site-directed allelic comparison	GWAS/fine-mapping; ENCODE DHS/H3K27ac/TF ChIP-seq integration	Luciferase reporter assay; PCR/site-directed mutagenesis
E_03058	2025	40160815	A pooled CRISPR screen identifies the Tα2 enhancer element as a driver of TRA expression in a subset of mature human T lymphocytes	Homo sapiens	hg38	chr14	22556439	22556536	NA	TRAC	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Jurkat E6.1	CVCL_0367	T cell	CL:0000084	CRISPR-based enhancer screening assay; Functional enhancer perturbation assay	Pooled tiled CRISPR/Cas9 screen; sgRNA amplicon Illumina deep sequencing	Targeted CRISPR/Cas9 editing of Tα2; Paired-sgRNA deletion; Flow cytometry; Single-cell cloning; PCR; Allele-specific Sanger sequencing
E_03059	2019	30678091	Functional SNPs in the Human Autoimmunity-Associated Locus 17q12-21	Homo sapiens	hg19	chr17	37912040	37913027	NA	NA	Enhancer	Active	Disease	autoimmune disease susceptibility at 17q12-21	NA	NA	blood	UBERON:0000178	U-937	CVCL_0007	monocyte-like cell	NA	Disease-variant enhancer reporter assay; GWAS/epigenomic prioritization; site-directed allelic comparison	GWAS/fine-mapping; ENCODE DHS/H3K27ac/TF ChIP-seq integration	Luciferase reporter assay; PCR/site-directed mutagenesis
E_03060	2019	30678091	Functional SNPs in the Human Autoimmunity-Associated Locus 17q12-21	Homo sapiens	hg19	chr17	37912040	37913027	NA	NA	Enhancer	Active	Disease	autoimmune disease susceptibility at 17q12-21	NA	NA	blood	UBERON:0000178	NALM-6	CVCL_0092	B-lymphoblast	CL:0017006	Disease-variant enhancer reporter assay; GWAS/epigenomic prioritization; site-directed allelic comparison	GWAS/fine-mapping; ENCODE DHS/H3K27ac/TF ChIP-seq integration	Luciferase reporter assay; PCR/site-directed mutagenesis
E_03061	2019	30678091	Functional SNPs in the Human Autoimmunity-Associated Locus 17q12-21	Homo sapiens	hg19	chr17	38026822	38029614	NA	NA	Enhancer	Active	Disease	autoimmune disease susceptibility at 17q12-21	NA	NA	blood	UBERON:0000178	U-937	CVCL_0007	monocyte-like cell	NA	Disease-variant enhancer reporter assay; GWAS/epigenomic prioritization; site-directed allelic comparison	GWAS/fine-mapping; ENCODE DHS/H3K27ac/TF ChIP-seq integration	Luciferase reporter assay; PCR/site-directed mutagenesis
E_03062	2011	21464046	Nkx2-5 represses Gata1 gene expression and modulates the cellular fate of cardiac progenitors during embryogenesis	Mus musculus	mm10	chrX	7826505	7830405	NA	Gata1	Enhancer	Repressed	Normal	NA	NA	NA	bone marrow	UBERON:0002371	ES	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; TF binding assay	NA	Luciferase reporter assay, Transgenic reporter assay
E_03063	2017	28405742	CRISPR/Cas9-mediated deletion of lncRNA Gm26878 in the distant Foxf1 enhancer region	Mus musculus	mm10	chr8	120880096	120882492	NA	Foxf1	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	Embryonic lung tissue	NA	embryonic lung cell	NA	Functional perturbation assay	NA	CRISPR knockout; RT-qPCR; Sanger sequencing; CRISPR-Cas9
E_03064	2016	27149122	Discovery of Genetic Variation on Chromosome 5q22 Associated with Mortality in Heart Failure	Homo sapiens	hg19	chr5	110175120	110177136	NHLH1	TSLP	Enhancer	Active	Disease	Heart Failure	NA	NA	heart	UBERON:0000948	Blood	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR; RNAi/siRNA/shRNA
E_03065	1999	10488050	Species-specific differences in positive and negative regulatory elements in the renin gene enhancer	Mus musculus	mm39	chr1	133275546	133275787	NA	Ren1	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	As4.1	CVCL_0151	renin-producing renal cell	NA	Enhancer activity assay; TF binding assay; cis-element functional mapping	NA	Transient-transfection reporter assay; deletion/substitution mutagenesis; EMSA; supershift assay
E_03066	2025	38760567	Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations	Homo sapiens	hg19	chr11	5270500	5271500	NA	HBG1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Functional perturbation assay; Disease-variant functional analysis; Endogenous enhancer perturbation	RNA-seq; pooled CRISPRi screen; CRISPR genetic screen	CRISPRi, qRT-PCR; CRISPRi
E_03067	2025	38760567	Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations	Homo sapiens	hg19	chr11	5301862	5302715	NA	HBG2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	myeloid cell	CL:0000763	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis; Endogenous enhancer perturbation	3' RNA-seq; pooled CRISPRi screen; CRISPR genetic screen	multiAsCas12a-KRAB CRISPRi; RT-qPCR; CRISPRi
E_03068	2025	38760567	Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations	Homo sapiens	hg19	chr8	128910869	128911521	NA	MYC	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Functional perturbation assay; Disease-variant functional analysis; Endogenous enhancer perturbation	RNA-seq; pooled CRISPRi screen; CRISPR genetic screen	CRISPRi, Flow Cytometry, qRT-PCR; CRISPRi
E_03069	2025	38760567	Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations	Homo sapiens	hg19	chr8	128972341	128973219	NA	MYC	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Functional perturbation assay; Disease-variant functional analysis; Endogenous enhancer perturbation	RNA-seq; pooled CRISPRi screen; CRISPR genetic screen	CRISPRi, Flow Cytometry, qRT-PCR; CRISPRi
E_03070	2025	38760567	Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations	Homo sapiens	hg19	chr8	129057272	129057795	NA	MYC	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Functional perturbation assay; Disease-variant functional analysis; Endogenous enhancer perturbation	RNA-seq; pooled CRISPRi screen; CRISPR genetic screen	CRISPRi, Flow Cytometry, qRT-PCR; CRISPRi
E_03071	2013	23631855	Tensile strain increases expression of CCN2 and COL2A1 by activating TGF-β-Smad2/3 pathway in chondrocytic cells	Homo sapiens	hg19	chr12	48369059	48369213	SOX9	COL2A1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	SW 1353	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; Western blot
E_03072	2013	23631855	Tensile strain increases expression of CCN2 and COL2A1 by activating TGF-β-Smad2/3 pathway in chondrocytic cells	Homo sapiens	hg19	chr12	48369059	48369213	SOX9	COL2A1	Enhancer	Active	Normal	NA	NA	NA	cartilage tissue	UBERON:0002418	SW1353	CVCL_0543	chondrocyte	CL:0000138	Enhancer activity assay; TF binding assay; Enhancer occupancy assay; functional response assay	NA	COL2A1 enhancer ChIP-qPCR; co-immunoprecipitation; RT-qPCR; Western blot; cyclic tensile strain assay; Luciferase reporter assay; ChIP; Reporter assay
E_03073	2013	23631855	Tensile strain increases expression of CCN2 and COL2A1 by activating TGF-β-Smad2/3 pathway in chondrocytic cells	Homo sapiens	hg19	chr12	48355000	48355154	SMAD2	COL2A1	Enhancer	Active	Disease	chondrosarcoma	MONDO:0008977	DOID:3371	cartilage tissue	UBERON:0002418	Human chondrosarcoma cell	NA	chondrosarcoma cell	NA	Enhancer activity assay	NA	Luciferase reporter assay; ChIP-qPCR, qRT-PCR; Western blot; Reporter assay
E_03074	2016	27149122	Discovery of Genetic Variation on Chromosome 5q22 Associated with Mortality in Heart Failure	Homo sapiens	hg19	chr5	110175800	110176600	NA	TSLP	Enhancer	Active	Disease	Heart Failure	NA	NA	heart	UBERON:0000948	HEK293T	CVCL_0063	NA	NA	Enhancer activity assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay
E_03075	2025	41027000	ER stress upregulates S100A11 in steatohepatitis models via epigenetic modifications within the lipotoxicity-influenced enhancer	Homo sapiens	hg38	chr1	152019738	152021345	XBP1	S100A11	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Huh-7	CVCL_0336	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin-state profiling	RNA-seq; ATAC-seq; ChIP-seq	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; ChIP-qPCR; ChIP
E_03076	2024	39511411	Super-enhancer MYCNOS-SE promotes chemoresistance in small cell lung cancer by recruiting transcription factors CTCF and KLF15	Homo sapiens	hg38	chr2	16000000	16002000	CTCF	MYCNOS	Enhancer	Active	Disease	small cell lung carcinoma	MONDO:0008433	DOID:5409	lung	UBERON:0002048	H446 cells	CVCL_0049	malignant cell	CL:0001064	Super-enhancer activity assay	ChIP-seq; ATAC-seq	Luciferase reporter assay; RT-qPCR
E_03077	2020	32483258	Skeletal muscle enhancer interactions identify genes controlling whole-body metabolism	Homo sapiens	hg38	chr4	73725619	73726851	NA	CXCL8	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	Human Skeletal Myotubes	NA	skeletal myotube	NA	Enhancer activity assay; Chromatin interaction assay	ChIP-seq; RNA-seq; Hi-C	Luciferase reporter assay; ChIP-qPCR
E_03078	2020	32483258	Skeletal muscle enhancer interactions identify genes controlling whole-body metabolism	Homo sapiens	hg38	chr7	95608432	95609655	NA	PDK4	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	Human Skeletal Myotubes	NA	skeletal myotube	NA	Enhancer activity assay; Chromatin interaction assay	ChIP-seq; RNA-seq; Hi-C	Luciferase reporter assay; ChIP-qPCR
E_03079	2018	30475793	Similarities and differences in the regulation of HoxD genes during chick and mouse limb development	Mus musculus	mm10	chr2	75208104	75210328	NA	Hoxd10	Enhancer	Active	Normal	NA	NA	NA	limb	UBERON:0002101	E10.5-E12.5 limb bud cells	NA	limb bud mesenchymal cell	NA	Enhancer activity assay; Chromatin interaction assay; Developmental gene-regulation assay	RNA-seq; ChIP-seq; 4C-seq	Lentiviral transgenic LacZ reporter assay; X-gal staining; RT-qPCR; whole-mount in situ hybridization
E_03080	2018	30475793	Similarities and differences in the regulation of HoxD genes during chick and mouse limb development	Mus musculus	mm10	chr2	75208104	75210328	NA	Hoxd11	Enhancer	Active	Normal	NA	NA	NA	limb	UBERON:0002101	E10.5-E12.5 limb bud cells	NA	limb bud mesenchymal cell	NA	Enhancer activity assay; Chromatin interaction assay; Developmental gene-regulation assay	RNA-seq; ChIP-seq; 4C-seq	Lentiviral transgenic LacZ reporter assay; X-gal staining; RT-qPCR; whole-mount in situ hybridization
E_03081	2016	26754925	IER5 generates a novel hypo-phosphorylated active form of HSF1 and contributes to tumorigenesis	Homo sapiens	hg19	chr1	181117806	181122451	TP53	IER5	Enhancer	Active	Disease	cervical cancer	MONDO:0002974	DOID:4362	colon	UBERON:0001155	HCT 116	CVCL_0291	NA	NA	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq; 4C-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03082	1996	8977525	Specific versus cooperative regulatory mechanisms of the cytokine genes that are clustered on the same chromosome	Homo sapiens	hg19	chr5	131406243	131406930	NA	CSF2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Jurkat	CVCL_0065	T cell	CL:0000084	TF binding assay; Chromatin accessibility assay; Review-supported enhancer activity assay	NA	DNase I hypersensitivity assay; PMA/A23187 stimulation; cyclosporin A inhibition; transient transfection; CAT reporter assay; EMSA; competition EMSA
E_03083	1996	8977525	Specific versus cooperative regulatory mechanisms of the cytokine genes that are clustered on the same chromosome	Homo sapiens	hg19	chr5	131406243	131406930	NA	IL3	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Jurkat	CVCL_0065	T cell	CL:0000084	TF binding assay; Chromatin accessibility assay; Review-supported enhancer activity assay	NA	DNase I hypersensitivity assay; PMA/A23187 stimulation; cyclosporin A inhibition; transient transfection; CAT reporter assay; EMSA; competition EMSA
E_03084	2022	35202564	Duplications disrupt chromatin architecture and rewire GPR101-enhancer communication in X-linked acrogigantism	Homo sapiens	hg19	chrX	135577559	135581959	NA	GPR101	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	PBMCs	NA	peripheral blood mononuclear cell	CL:2000001	Chromatin interaction assay; Disease-variant functional analysis	4C-seq; Hi-C	Luciferase reporter assay; 4C
E_03085	2022	35202564	Duplications disrupt chromatin architecture and rewire GPR101-enhancer communication in X-linked acrogigantism	Homo sapiens	hg19	chrX	135656769	135660247	NA	GPR101	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	PBMCs	NA	peripheral blood mononuclear cell	CL:2000001	Chromatin interaction assay; Disease-variant functional analysis	4C-seq; Hi-C	Luciferase reporter assay; 4C
E_03086	2022	35202564	Duplications disrupt chromatin architecture and rewire GPR101-enhancer communication in X-linked acrogigantism	Homo sapiens	hg19	chrX	135846959	135851769	NA	GPR101	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	PBMCs	NA	peripheral blood mononuclear cell	CL:2000001	Chromatin interaction assay; Disease-variant functional analysis	4C-seq; Hi-C	Luciferase reporter assay; 4C
E_03087	2022	35202564	Duplications disrupt chromatin architecture and rewire GPR101-enhancer communication in X-linked acrogigantism	Homo sapiens	hg19	chrX	135990759	135994160	NA	GPR101	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	PBMCs	NA	peripheral blood mononuclear cell	CL:2000001	Chromatin interaction assay; Disease-variant functional analysis	4C-seq; Hi-C	Luciferase reporter assay; 4C
E_03088	2022	35202564	Duplications disrupt chromatin architecture and rewire GPR101-enhancer communication in X-linked acrogigantism	Homo sapiens	hg19	chrX	135625877	135641072	NA	GPR101	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	PBMCs	NA	peripheral blood mononuclear cell	CL:2000001	Chromatin interaction assay; Disease-variant functional analysis	4C-seq; Hi-C	Luciferase reporter assay; 4C
E_03089	1996	8977525	Specific versus cooperative regulatory mechanisms of the cytokine genes that are clustered on the same chromosome	Homo sapiens	hg19	chr5	132002000	132008000	NA	CAT	Enhancer	Active	Disease	osteosarcoma	MONDO:0009807	DOID:3347	bone element	UBERON:0001474	MG-63	CVCL_0426	osteosarcoma cell	NA	Enhancer activity assay	NA	CAT Reporter Assay; DNase I Hypersensitivity Assay; EMSA
E_03090	2012	21822303	Sox2 expression in breast tumours and activation in breast cancer stem cells	Mus musculus	mm10	chr3	34646162	34646551	NA	Sox2	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay
E_03091	1996	8977525	Specific versus cooperative regulatory mechanisms of the cytokine genes that are clustered on the same chromosome	Mus musculus	mm10	chr11	53495000	53501000	NA	Cat	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Murine T Lymphocytes	NA	T cell	CL:0000084	Enhancer activity assay	NA	CAT Reporter Assay, DNase I Hypersensitivity Assay
E_03092	2025	40346084	Large-scale discovery of potent, compact and erythroid specific enhancers for gene therapy vectors	Homo sapiens	hg38	chr8	128041672	128043891	NA	PVT1	Enhancer	Active	Disease	beta-thalassemia	MONDO:0019402	DOID:12241	bone marrow	UBERON:0002371	CD34+ cells	NA	hematopoietic stem cell	CL:0000037	Functional perturbation assay	RNA-seq	CRISPR knockout; RT-qPCR
E_03093	2011	21868451	The estrogen-regulated transcription factor PITX1 coordinates gene-specific regulation by estrogen receptor-alpha in breast cancer cells	Homo sapiens	hg19	chr5	134350424	134352424	ESR1	PITX1	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C
E_03094	2005	15798195	Identification of neuronal enhancers of the proopiomelanocortin gene by transgenic mouse analysis and phylogenetic footprinting	Mus musculus	mm10	chr12	103439326	103439476	NA	Pomc	Enhancer	Active	Normal	NA	NA	NA	hypothalamus	UBERON:0001898	POMC Arcuate Neuron	NA	POMC neuron	NA	Enhancer activity assay	NA	Transgenic reporter assay; CRISPR knockout; Transgenic mouse enhancer assay
E_03095	2018	30349647	3'Igh enhancers hs3b/hs4 are dispensable for Myc deregulation in mouse plasmacytomas with T(12;15) translocations	Mus musculus	mm10	chr12	113220000	113233375	NA	Myc	Enhancer	Active	Disease	plasmacytoma	MONDO:0005615	DOID:3721	plasma-cell tumor / hematopoietic tumor context	NA	primary mouse plasmacytoma cells	NA	plasma cell	CL:0000786	Genetic enhancer deletion; tumorigenesis/translocation analysis; Myc-expression assessment	RNA-seq/transcriptome profiling	hs3b/hs4 germline deletion; tumor induction; translocation breakpoint analysis; qRT-PCR; proliferation/cell-death assays
E_03096	2013	23675462	Mitogen- and stress-activated protein kinases 1 and 2 are required for maximal trefoil factor 1 induction	Homo sapiens	hg19	chr21	43770915	43772915	NA	TFF1	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer chromatin-state assay; Enhancer occupancy assay; Transcriptional regulation assay	NA	RPS6KA5/MSK1 ChIP-qPCR; RPS6KA4/MSK2 ChIP-qPCR; H3S10ph ChIP-qPCR; 14-3-3 ChIP-qPCR; SMARCA4/BRG1 ChIP-qPCR; RNA polymerase II ChIP-qPCR; RT-qPCR; siRNA knockdown; TPA stimulation
E_03097	2013	23675462	Mitogen- and stress-activated protein kinases 1 and 2 are required for maximal trefoil factor 1 induction	Homo sapiens	hg19	chr21	43795658	43798708	NA	TFF1	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	MCF-7	CVCL_0031	epithelial cell	CL:0000066	Enhancer-associated chromatin-state assay; Signaling perturbation assay	NA	Mononucleosome ChIP-qPCR; Sequential ChIP; RPS6KA5/RPS6KA4 knockdown; Kinase inhibition; TPA stimulation; RT-qPCR; Western blot
E_03098	2013	23675462	Mitogen- and stress-activated protein kinases 1 and 2 are required for maximal trefoil factor 1 induction	Homo sapiens	hg19	chr21	43796920	43797320	NA	TFF1	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer chromatin-state assay; Chromatin co-occupancy assay; Functional signaling perturbation assay	NA	Mononucleosome ChIP-qPCR; sequential ChIP/Re-ChIP; H3S10ph ChIP-qPCR; H3S10phK14ac ChIP-qPCR; RPS6KA5/MSK1 ChIP-qPCR; RPS6KA4/MSK2 ChIP-qPCR; BRG1 ChIP-qPCR; 14-3-3 ChIP-qPCR; H89 inhibition; TPA stimulation; RT-qPCR; Western blot
E_03099	2013	23675462	Mitogen- and stress-activated protein kinases 1 and 2 are required for maximal trefoil factor 1 induction	Homo sapiens	hg19	chr21	43796920	43797320	NA	TFF1	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer-associated chromatin-state assay; signaling perturbation assay	NA	Mononucleosome ChIP-qPCR; sequential ChIP; RPS6KA5/RPS6KA4 knockdown; kinase inhibition; TPA stimulation; RT-qPCR; Western blot
E_03100	2013	24040411	Identification of an evolutionarily conserved cis-regulatory element controlling the Peg3 imprinted domain	Homo sapiens	hg19	chr19	57566145	57571006	NA	PEG3	Enhancer	Repressed	Normal	NA	NA	NA	NA	NA	HeLa	CVCL_0030	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Genetic-variant functional analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C
E_03101	2013	24040411	Identification of an evolutionarily conserved cis-regulatory element controlling the Peg3 imprinted domain	Mus musculus	mm10	chr7	6502892	6504892	NA	Vegfa	Enhancer	Repressed	Normal	NA	NA	NA	NA	NA	HeLa	CVCL_0030	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C
E_03102	2013	24040411	Identification of an evolutionarily conserved cis-regulatory element controlling the Peg3 imprinted domain	Homo sapiens	hg19	chr19	57566145	57571006	NA	PEG3	Enhancer	Repressed	Normal	NA	NA	NA	NA	NA	HEK293	CVCL_0045	NA	NA	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Genetic-variant functional analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C
E_03103	2013	24040411	Identification of an evolutionarily conserved cis-regulatory element controlling the Peg3 imprinted domain	Mus musculus	mm10	chr7	6502892	6504892	NA	Vegfa	Enhancer	Repressed	Normal	NA	NA	NA	NA	NA	HEK293	CVCL_0045	NA	NA	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C
E_03104	2018	30349647	3'Igh enhancers hs3b/hs4 are dispensable for Myc deregulation in mouse plasmacytomas with T(12;15) translocations	Mus musculus	mm10	chr12	113220000	113233375	NA	Myc	Enhancer	Active	Disease	plasmacytoma	MONDO:0005615	DOID:3721	plasma-cell tumor / hematopoietic tumor context	NA	established T(12;15)+ plasmacytoma cells	NA	plasma cell	CL:0000786	Genetic enhancer deletion; tumorigenesis/translocation analysis; Myc-expression assessment	RNA-seq/transcriptome profiling	hs3b/hs4 germline deletion; tumor induction; translocation breakpoint analysis; qRT-PCR; proliferation/cell-death assays
E_03105	2018	30349647	3'Igh enhancers hs3b/hs4 are dispensable for Myc deregulation in mouse plasmacytomas with T(12;15) translocations	Mus musculus	mm10	chr12	113220000	113255414	NA	Myc	Enhancer	Active	Disease	plasmacytoma	MONDO:0005615	DOID:3721	plasma-cell tumor / hematopoietic tumor context	NA	T(12;15)+ plasmacytoma cells	NA	plasma cell	CL:0000786	Enhancer-cluster deletion; tumor-cell functional perturbation; Myc-expression analysis	RNA-seq/transcriptome profiling	Cre-mediated 3'RR deletion; qRT-PCR; proliferation; cell-death/apoptosis assays
E_03106	2018	30349647	3'Igh enhancers hs3b/hs4 are dispensable for Myc deregulation in mouse plasmacytomas with T(12;15) translocations	Mus musculus	mm10	chr12	113220000	113255414	NA	Myc	Enhancer	Active	Disease	plasmacytoma	MONDO:0005615	DOID:3721	plasma-cell tumor / hematopoietic tumor context	NA	established T(12;15)+ plasmacytoma cells	NA	plasma cell	CL:0000786	Enhancer-cluster deletion; tumor-cell functional perturbation; Myc-expression analysis	RNA-seq/transcriptome profiling	Cre-mediated 3'RR deletion; qRT-PCR; proliferation; cell-death/apoptosis assays
E_03107	2013	23675462	Mitogen- and stress-activated protein kinases 1 and 2 are required for maximal trefoil factor 1 induction	Homo sapiens	hg19	chr21	43770915	43772915	RPS6KA4	TFF1	Enhancer	Active	Normal	NA	NA	NA	breast	UBERON:0000310	MCF-7	CVCL_0031	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	ChIP-qPCR/ChIP
E_03108	2013	23675462	Mitogen- and stress-activated protein kinases 1 and 2 are required for maximal trefoil factor 1 induction	Homo sapiens	hg19	chr21	43770915	43772915	RPS6KA5	TFF1	Enhancer	Active	Normal	NA	NA	NA	breast	UBERON:0000310	MCF-7	CVCL_0031	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	ChIP-qPCR/ChIP
E_03109	2025	40512334	Genomic Locus Tagged by Lung Function GWAS SNV rs12477314 (2q37.3) Acts as a Regulatory Region for a Systemic Inflammatory Phenotype	Homo sapiens	hg19	chr2	239866844	239871938	NA	CXCL2	Enhancer	Active	Disease	chronic obstructive pulmonary disease	MONDO:0005002	DOID:3083	lung	UBERON:0002048	NCI-H460	CVCL_0459	large cell lung carcinoma epithelial cell	NA	Enhancer activity assay; Functional perturbation assay	RNA-seq; DNA methylation profiling	CRISPR/Cas9 deletion; Sanger sequencing; RT-qPCR; CRISPR-Cas9
E_03110	2025	40512334	Genomic Locus Tagged by Lung Function GWAS SNV rs12477314 (2q37.3) Acts as a Regulatory Region for a Systemic Inflammatory Phenotype	Homo sapiens	hg19	chr2	239884251	239900294	NA	CXCL2	Enhancer	Active	Disease	chronic obstructive pulmonary disease	MONDO:0005002	DOID:3083	lung	UBERON:0002048	NCI-H460	CVCL_0459	large cell lung carcinoma epithelial cell	NA	Enhancer activity assay; Functional perturbation assay	RNA-seq; DNA methylation profiling	CRISPR/Cas9 deletion; Sanger sequencing; RT-qPCR; CRISPR-Cas9
E_03111	2024	38438958	Nuclear respiratory factor 1 regulates super enhancer-controlled SPIDR to protect hepatocellular carcinoma cells from oxidative stress	Homo sapiens	hg19	chr2	20628003	20667995	NA	RHOB	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Huh-7	CVCL_0336	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay	ChIP-seq; RNA-seq	ChIP-qPCR; RT-qPCR; Western blot; ChIP-qPCR; ChIP
E_03112	2016	25782671	The disruption of a novel limb cis-regulatory element of SHH is associated with autosomal dominant preaxial polydactyly-hypertrichosis	Homo sapiens	hg19	chr7	155845627	155847652	NA	SHH	Enhancer	Active	Disease	preaxial polydactyly-hypertrichosis	NA	NA	limb	UBERON:0002101	Caco-2	CVCL_0025	malignant cell	CL:0001064	Silencer activity assay; Disease-associated structural-variant assay	SNP-array / array-CGH for deletion discovery	Long-range PCR and sequencing; Luciferase reporter assay; deletion-fragment repression assay
E_03113	2009	19386363	Role of a distal enhancer in the transcriptional responsiveness of the human CD200 gene to interferon-gamma and tumor necrosis factor-alpha	Homo sapiens	hg19	chr3	112045517	112046117	IRF1	CD200	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HUVEC	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR; Site-directed mutagenesis
E_03114	2009	19386363	Role of a distal enhancer in the transcriptional responsiveness of the human CD200 gene to interferon-gamma and tumor necrosis factor-alpha	Homo sapiens	hg19	chr3	112045517	112046117	NFKB1	CD200	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HUVEC	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR; Site-directed mutagenesis
E_03115	2009	19386363	Role of a distal enhancer in the transcriptional responsiveness of the human CD200 gene to interferon-gamma and tumor necrosis factor-alpha	Homo sapiens	hg19	chr3	112045517	112046117	STAT1	CD200	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HUVEC	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR; Site-directed mutagenesis
E_03116	2009	19386363	Role of a distal enhancer in the transcriptional responsiveness of the human CD200 gene to interferon-gamma and tumor necrosis factor-alpha	Homo sapiens	hg19	chr3	112045517	112046117	STAT1	CD200	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Liver sinusoidal endothelial cell	NA	liver sinusoidal endothelial cell	NA	Enhancer activity assay	NA	Luciferase reporter assay; ChIP-qPCR
E_03117	2016	25782671	The disruption of a novel limb cis-regulatory element of SHH is associated with autosomal dominant preaxial polydactyly-hypertrichosis	Homo sapiens	hg19	chr7	155845627	155847652	NA	SHH	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Caco-2	CVCL_0025	NA	NA	Enhancer activity assay	NA	Luciferase reporter assay; Reporter assay
E_03118	2025	39905017	Multi-locus CRISPRi targeting with a single truncated guide RNA	Homo sapiens	hg38	chr1	28883749	28884318	NA	EPB41	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	K-562	CVCL_0004	malignant cell	CL:0001064	Functional perturbation assay; Endogenous enhancer perturbation	CRISPR genetic screen	CRISPRi, qRT-PCR; CRISPRi
E_03119	2023	36969227	A cis-element at the Rorc locus regulates the development of type 3 innate lymphoid cells	Mus musculus	mm10	chr3	93993657	93995818	NA	Rorc	Enhancer	Active	Normal	NA	NA	NA	small intestine	UBERON:0002108	ILC3s	NA	innate lymphoid cell	CL:0001065	Functional perturbation assay	RNA-seq	CRISPR knockout, qRT-PCR
E_03120	2021	33313982	The anxiety and ethanol intake controlling GAL5.1 enhancer is epigenetically modulated by, and controls preference for, high-fat diet	Mus musculus	mm10	chr19	3441054	3441445	NA	Gal	Enhancer	Active	Normal	NA	NA	NA	amygdala	UBERON:0001876	primary amygdala neurons	NA	neuron	CL:0000540	Enhancer activity assay; Functional perturbation assay; Epigenetic modulation assay; DNA methylation profiling	DNA methylation profiling	Reporter assay; EGR1/PKC stimulation; CRISPR enhancer disruption; behavioral phenotyping
E_03121	2021	33313982	The anxiety and ethanol intake controlling GAL5.1 enhancer is epigenetically modulated by, and controls preference for, high-fat diet	Mus musculus	mm10	chr19	3441054	3441445	NA	Gal	Enhancer	Active	Normal	NA	NA	NA	hypothalamus	UBERON:0001898	primary hypothalamic neurons	NA	neuron	CL:0000540	Enhancer activity assay; Functional perturbation assay; Epigenetic modulation assay; DNA methylation profiling	DNA methylation profiling	Reporter assay; EGR1/PKC stimulation; CRISPR enhancer disruption; behavioral phenotyping
E_03122	2018	30552336	Human sex reversal is caused by duplication or deletion of core enhancers upstream of SOX9	Homo sapiens	hg38	chr17	72118256	72120256	SOX9	SOX9	Enhancer	Active	Disease	osteosarcoma	MONDO:0009807	DOID:3347	bone element	UBERON:0001474	MEF GFP-LC3-RFP-LC3deltaG	CVCL_UP52	osteosarcoma cell	NA	Enhancer activity assay; TF binding assay	ChIP-seq	3C; RT-PCR; RT-qPCR
E_03123	2014	24734888	A mouse renin distal enhancer is essential for blood pressure homeostasis in BAC-rescued renin-null mutant mice	Mus musculus	mm10	chr1	133347808	133348049	NA	Ren1	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	juxtaglomerular cells	NA	kidney granular cell	CL:0000648	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation; In vivo functional validation; In vivo physiological assay	NA	BAC transgenesis; distal-enhancer deletion; Ren1-null rescue; Northern blot; RT-qPCR; in situ hybridization; plasma renin activity; angiotensin I assay; blood-pressure measurement; Mouse genetic deletion/knock-in; In vivo phenotyping
E_03124	2024	39272130	Chromatin conformation capture in the clinic: 4C-seq/HiC distinguishes pathogenic from neutral duplications at the GPR101 locus	Homo sapiens	hg19	chrX	135656769	135660247	NA	GPR101	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	PBMCs	NA	peripheral blood mononuclear cell	CL:2000001	Chromatin interaction assay; Disease-variant functional analysis	Hi-C; 4C-seq; 4C-seq	qRT-PCR, and ChIP-qPCR; 4C
E_03125	2024	39272130	Chromatin conformation capture in the clinic: 4C-seq/HiC distinguishes pathogenic from neutral duplications at the GPR101 locus	Homo sapiens	hg19	chrX	135846959	135851769	NA	GPR101	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	PBMCs	NA	peripheral blood mononuclear cell	CL:2000001	Chromatin interaction assay; Disease-variant functional analysis	Hi-C; 4C-seq; 4C-seq	qRT-PCR, and ChIP-qPCR; 4C
E_03126	2024	39272130	Chromatin conformation capture in the clinic: 4C-seq/HiC distinguishes pathogenic from neutral duplications at the GPR101 locus	Homo sapiens	hg19	chrX	135959959	135963959	NA	GPR101	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	PBMCs	NA	peripheral blood mononuclear cell	CL:2000001	Chromatin interaction assay; Disease-variant functional analysis	Hi-C; 4C-seq; 4C-seq	qRT-PCR, and ChIP-qPCR; 4C
E_03127	2024	39272130	Chromatin conformation capture in the clinic: 4C-seq/HiC distinguishes pathogenic from neutral duplications at the GPR101 locus	Homo sapiens	hg19	chrX	135990759	135994160	NA	GPR101	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	PBMCs	NA	peripheral blood mononuclear cell	CL:2000001	Chromatin interaction assay; Disease-variant functional analysis	Hi-C; 4C-seq; 4C-seq	qRT-PCR, and ChIP-qPCR; 4C
E_03128	2020	32814051	Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation	Mus musculus	mm10	chr11	45582000	45582499	NA	Lef1	Enhancer	Active	Normal	NA	NA	NA	thymus	UBERON:0002370	double-negative thymocyte	NA	double negative thymocyte	CL:0002489	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; 3C-seq; STARR-seq	qRT-PCR, and ChIP-qPCR
E_03129	2020	32814051	Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation	Mus musculus	mm10	chr11	45586000	45586499	NA	Lef1	Enhancer	Active	Normal	NA	NA	NA	thymus	UBERON:0002370	double-negative thymocyte	NA	double negative thymocyte	CL:0002489	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; 3C-seq; STARR-seq	qRT-PCR, and ChIP-qPCR
E_03130	2016	26795348	Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus	Homo sapiens	hg19	chr2	202120390	202125986	CTCF	CASP8	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	blood	UBERON:0000178	Human Mammary Epithelial Normal Breast Cell Line	NA	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03131	2016	26795348	Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus	Homo sapiens	hg19	chr2	202120390	202125986	MYC	CASP8	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	blood	UBERON:0000178	Human Mammary Epithelial Normal Breast Cell Line	NA	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03132	2016	26795348	Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus	Homo sapiens	hg19	chr2	202120390	202125986	STAT3	CASP8	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	blood	UBERON:0000178	Human Mammary Epithelial Normal Breast Cell Line	NA	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03133	2015	26232425	Pregnane X Receptor Represses HNF4α Gene to Induce Insulin-Like Growth Factor-Binding Protein IGFBP1 that Alters Morphology of and Migrates HepG2 Cells	Homo sapiens	hg19	chr20	43210000	43212000	NR1I2	HNF4A	Enhancer	Repressed	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Hep-G2	CVCL_0027	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay	ChIP-seq	Luciferase reporter assay; ChIP; Western blot; siRNA knockdown
E_03134	2020	32814051	Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation	Mus musculus	mm10	chr11	45582000	45582499	NA	Lef1	Enhancer	Active	Normal	NA	NA	NA	thymus	UBERON:0002370	double-positive thymocyte	NA	double-positive thymocyte	NA	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; 3C-seq	qRT-PCR, and ChIP-qPCR
E_03135	2020	32814051	Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation	Mus musculus	mm10	chr11	45582000	45582499	NA	Lef1	Enhancer	Active	Normal	NA	NA	NA	thymus	UBERON:0002370	naive CD4-positive T cell	NA	naive CD4-positive T cell	NA	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; 3C-seq	qRT-PCR, and ChIP-qPCR
E_03136	2020	32814051	Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation	Mus musculus	mm10	chr11	45586000	45586499	NA	Lef1	Enhancer	Active	Normal	NA	NA	NA	thymus	UBERON:0002370	double-positive thymocyte	NA	double-positive thymocyte	NA	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; 3C-seq	qRT-PCR, and ChIP-qPCR
E_03137	2014	24734888	A mouse renin distal enhancer is essential for blood pressure homeostasis in BAC-rescued renin-null mutant mice	Mus musculus	mm10	chr1	133347808	133348049	NA	Ren1	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	Kidney	NA	NA	NA	In vivo functional validation	NA	Transgenic/LacZ assay
E_03138	2023	37591883	High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription	Homo sapiens	hg19	chr11	5280741	5280786	NA	HBB	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer transcriptional regulation assay; Activity validation	HiS-NET-seq, ChIP-Rx, HiChIP	qRT-PCR, and ChIP-qPCR
E_03139	2017	28121289	Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq	Homo sapiens	hg38	chr6	88202011	88204330	NA	GATA2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hepatocyte	NA	hepatocyte	CL:0000182	Enhancer activity assay; TF binding assay; Chromatin-state profiling	ChIP-seq	Luciferase reporter assay; Western blot
E_03140	2017	28121289	Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq	Mus musculus	mm10	chr11	32145270	32146411	NA	NA	Enhancer	Active	Normal	NA	NA	NA	blood vessel	UBERON:0001981	Endothelial cells	NA	endothelial cell	CL:0000115	Enhancer activity assay; Chromatin-state profiling	ChIP-seq (Ep300 bioChIP-seq); ChIP-seq	Transgenic reporter assay (LacZ)
E_03141	2017	28121289	Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq	Mus musculus	mm10	chr13	28809515	28811310	NA	NA	Enhancer	Active	Normal	NA	NA	NA	blood vessel	UBERON:0001981	Endothelial cells	NA	endothelial cell	CL:0000115	Enhancer activity assay; Chromatin-state profiling	ChIP-seq (Ep300 bioChIP-seq); ChIP-seq	Transgenic reporter assay (LacZ)
E_03142	2017	28121289	Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq	Mus musculus	mm10	chr17	12982583	12985936	NA	NA	Enhancer	Active	Normal	NA	NA	NA	blood vessel	UBERON:0001981	Endothelial cells	NA	endothelial cell	CL:0000115	Enhancer activity assay; Chromatin-state profiling	ChIP-seq (Ep300 bioChIP-seq); ChIP-seq	Transgenic reporter assay (LacZ)
E_03143	2017	28121289	Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq	Mus musculus	mm10	chr3	87786601	87790798	NA	NA	Enhancer	Active	Normal	NA	NA	NA	blood vessel	UBERON:0001981	Endothelial cells	NA	endothelial cell	CL:0000115	Enhancer activity assay; Chromatin-state profiling	ChIP-seq (Ep300 bioChIP-seq); ChIP-seq	Transgenic reporter assay (LacZ)
E_03144	2017	28121289	Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq	Mus musculus	mm10	chr5	93426293	93427320	NA	NA	Enhancer	Active	Normal	NA	NA	NA	blood vessel	UBERON:0001981	Endothelial cells	NA	endothelial cell	CL:0000115	Enhancer activity assay; Chromatin-state profiling	ChIP-seq (Ep300 bioChIP-seq); ChIP-seq	Transgenic reporter assay (LacZ)
E_03145	2017	28121289	Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq	Mus musculus	mm10	chr7	116256647	116260817	NA	NA	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	Cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; Chromatin-state profiling	ChIP-seq (Ep300 bioChIP-seq); ChIP-seq	Transgenic reporter assay (LacZ)
E_03146	2017	28121289	Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq	Mus musculus	mm10	chr8	28216799	28218903	NA	NA	Enhancer	Active	Normal	NA	NA	NA	blood vessel	UBERON:0001981	Endothelial cells	NA	endothelial cell	CL:0000115	Enhancer activity assay; Chromatin-state profiling	ChIP-seq (Ep300 bioChIP-seq); ChIP-seq	Transgenic reporter assay (LacZ)
E_03147	2017	28121289	Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq	Mus musculus	mm10	chr8	28216817	28218896	NA	NA	Enhancer	Active	Normal	NA	NA	NA	blood vessel	UBERON:0001981	Endothelial cells	NA	endothelial cell	CL:0000115	Enhancer activity assay; Chromatin-state profiling	ChIP-seq (Ep300 bioChIP-seq); ChIP-seq	Transgenic reporter assay (LacZ)
E_03148	2017	28121289	Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq	Mus musculus	mm10	chr4	114743698	114748936	NA	NA	Enhancer	Active	Normal	NA	NA	NA	blood vessel	UBERON:0001981	Endothelial cells	NA	endothelial cell	CL:0000115	Enhancer activity assay; Chromatin-state profiling	ChIP-seq (Ep300 bioChIP-seq); ChIP-seq	Transgenic reporter assay (LacZ)
E_03149	2015	26232425	Pregnane X Receptor Represses HNF4α Gene to Induce Insulin-Like Growth Factor-Binding Protein IGFBP1 that Alters Morphology of and Migrates HepG2 Cells	Homo sapiens	hg19	chr20	42977441	42978040	DR1	HNF4A	Enhancer	Repressed	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Hep-G2	CVCL_0027	hepatocyte	CL:0000182	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03150	2015	26232425	Pregnane X Receptor Represses HNF4α Gene to Induce Insulin-Like Growth Factor-Binding Protein IGFBP1 that Alters Morphology of and Migrates HepG2 Cells	Homo sapiens	hg19	chr20	42977441	42978040	FOXM1	HNF4A	Enhancer	Repressed	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Hep-G2	CVCL_0027	hepatocyte	CL:0000182	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03151	2015	26232425	Pregnane X Receptor Represses HNF4α Gene to Induce Insulin-Like Growth Factor-Binding Protein IGFBP1 that Alters Morphology of and Migrates HepG2 Cells	Homo sapiens	hg19	chr20	42977441	42978040	HNF1A	HNF4A	Enhancer	Repressed	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Hep-G2	CVCL_0027	hepatocyte	CL:0000182	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03152	2017	28121289	Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq	Mus musculus	mm10	chr6	88202011	88204330	Ep300	Gata2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Endothelial Cell	NA	endothelial cell	CL:0000115	Enhancer activity assay; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; Western blot
E_03153	2023	37591883	High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription	Homo sapiens	hg38	chr1	42958018	42958389	NA	NA	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	hematopoietic leukemia-derived cell	NA	Enhancer discovery; Nascent-transcription regulation assay; Reporter-validation panel	HiS-NET-seq; BRD4 ChIP-Rx; GRO-cap; H3K27ac/H3K4me1 chromatin integration	Sense/antisense dual-luciferase reporter panel; candidate retained as candidate until construct-number/activity mapping is attached
E_03154	2023	37591883	High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription	Homo sapiens	hg38	chr1	244970941	244971645	NA	NA	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	hematopoietic leukemia-derived cell	NA	Enhancer discovery; Nascent-transcription regulation assay; Reporter-validation panel	HiS-NET-seq; BRD4 ChIP-Rx; GRO-cap; H3K27ac/H3K4me1 chromatin integration	Sense/antisense dual-luciferase reporter panel; candidate retained as candidate until construct-number/activity mapping is attached
E_03155	2023	37591883	High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription	Homo sapiens	hg38	chr17	51121344	51122474	NA	NA	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	hematopoietic leukemia-derived cell	NA	Enhancer discovery; Nascent-transcription regulation assay; Reporter-validation panel	HiS-NET-seq; BRD4 ChIP-Rx; GRO-cap; H3K27ac/H3K4me1 chromatin integration	Sense/antisense dual-luciferase reporter panel; candidate retained as candidate until construct-number/activity mapping is attached
E_03156	2023	37591883	High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription	Homo sapiens	hg38	chr17	74875718	74876890	NA	NA	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	hematopoietic leukemia-derived cell	NA	Enhancer discovery; Nascent-transcription regulation assay; Reporter-validation panel	HiS-NET-seq; BRD4 ChIP-Rx; GRO-cap; H3K27ac/H3K4me1 chromatin integration	Sense/antisense dual-luciferase reporter panel; candidate retained as candidate until construct-number/activity mapping is attached
E_03157	2023	37591883	High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription	Homo sapiens	hg38	chr19	40464709	40464990	NA	NA	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	hematopoietic leukemia-derived cell	NA	Enhancer discovery; Nascent-transcription regulation assay; Reporter-validation panel	HiS-NET-seq; BRD4 ChIP-Rx; GRO-cap; H3K27ac/H3K4me1 chromatin integration	Sense/antisense dual-luciferase reporter panel; candidate retained as candidate until construct-number/activity mapping is attached
E_03158	2023	37591883	High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription	Homo sapiens	hg38	chr19	43754969	43756655	NA	NA	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	hematopoietic leukemia-derived cell	NA	Enhancer discovery; Nascent-transcription regulation assay; Reporter-validation panel	HiS-NET-seq; BRD4 ChIP-Rx; GRO-cap; H3K27ac/H3K4me1 chromatin integration	Sense/antisense dual-luciferase reporter panel; candidate retained as candidate until construct-number/activity mapping is attached
E_03159	2023	37591883	High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription	Homo sapiens	hg38	chr19	46786236	46786920	NA	NA	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	hematopoietic leukemia-derived cell	NA	Enhancer discovery; Nascent-transcription regulation assay; Reporter-validation panel	HiS-NET-seq; BRD4 ChIP-Rx; GRO-cap; H3K27ac/H3K4me1 chromatin integration	Sense/antisense dual-luciferase reporter panel; candidate retained as candidate until construct-number/activity mapping is attached
E_03160	2023	37591883	High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription	Homo sapiens	hg38	chr19	48872999	48873182	NA	NA	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	hematopoietic leukemia-derived cell	NA	Enhancer discovery; Nascent-transcription regulation assay; Reporter-validation panel	HiS-NET-seq; BRD4 ChIP-Rx; GRO-cap; H3K27ac/H3K4me1 chromatin integration	Sense/antisense dual-luciferase reporter panel; candidate retained as candidate until construct-number/activity mapping is attached
E_03161	2023	37591883	High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription	Homo sapiens	hg38	chr21	46325282	46325509	NA	NA	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	hematopoietic leukemia-derived cell	NA	Enhancer discovery; Nascent-transcription regulation assay; Reporter-validation panel	HiS-NET-seq; BRD4 ChIP-Rx; GRO-cap; H3K27ac/H3K4me1 chromatin integration	Sense/antisense dual-luciferase reporter panel; candidate retained as candidate until construct-number/activity mapping is attached
E_03162	2023	37591883	High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription	Homo sapiens	hg38	chr6	28895115	28896348	NA	NA	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	hematopoietic leukemia-derived cell	NA	Enhancer discovery; Nascent-transcription regulation assay; Reporter-validation panel	HiS-NET-seq; BRD4 ChIP-Rx; GRO-cap; H3K27ac/H3K4me1 chromatin integration	Sense/antisense dual-luciferase reporter panel; candidate retained as candidate until construct-number/activity mapping is attached
E_03163	2025	41338221	Targeting TET3 suppresses group 3 medulloblastoma stemness and progression via impairing hypomethylation of Otx2 super-enhancer	Homo sapiens	hg38	chr14	56793806	56795906	NA	OTX2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Lymphoblastoid	NA	lymphoblastoid cell	NA	Functional perturbation assay; Super-enhancer activity assay	WGBS; CUT&Tag; DNA methylation profiling	Luciferase reporter assay; ChIP-qPCR; RT-qPCR
E_03164	2021	34853798	Multiplex CRISPR/Cas9 genome editing in hematopoietic stem cells for fetal hemoglobin reinduction generates chromosomal translocations	Homo sapiens	hg19	chr2	60495216	60495315	NA	BCL11A	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	CD34+ hematopoietic stem cells	NA	CD34-positive hematopoietic stem cell	NA	Functional perturbation assay	RNA-seq	CRISPR knockout; RT-qPCR; HPLC; Flow cytometry; CRISPR-Cas9
E_03165	2016	27149848	A Polymorphic Antioxidant Response Element Links NRF2/sMAF Binding to Enhanced MAPT Expression and Reduced Risk of Parkinsonian Disorders	Homo sapiens	hg19	chr17	44026548	44026648	NFE2L2	MAPT	Enhancer	Active	Disease	Parkinsonian disorders	NA	NA	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Disease-variant functional analysis	ChIP-seq; RNA-seq	Luciferase reporter assay; RT-qPCR
E_03166	2015	26214589	Chimeric EWSR1-FLI1 regulates the Ewing sarcoma susceptibility gene EGR2 via a GGAA microsatellite	Homo sapiens	hg19	chr10	64737032	64737909	EWSR1::FLI1	EGR2	Enhancer	Active	Disease	Ewing sarcoma	MONDO:0012817	DOID:3369	bone tissue	UBERON:0002481	A-673 and additional Ewing sarcoma models	NA	Ewing sarcoma cell	NA	Enhancer activity; fusion-TF occupancy; susceptibility-variant functional assay	EWSR1::FLI1 ChIP-seq; H3K27ac/chromatin-state profiling; germline association data	GGAA-microsatellite reporter; fusion-TF perturbation; EGR2 knockdown; proliferation and xenograft assays
E_03167	2014	25453756	A role for noncoding variation in schizophrenia	Homo sapiens	hg19	chr12	98559923	98563615	NA	CACNA1C	Enhancer	Active	Disease	Schizophrenia	MONDO:0005090	DOID:5419	NA	NA	Induced Pluripotent Stem Cells	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; 3C
E_03168	2015	26214589	Chimeric EWSR1-FLI1 regulates the Ewing sarcoma susceptibility gene EGR2 via a GGAA microsatellite	Homo sapiens	hg19	chr10	64737032	64737909	EWSR1	EGR2	Enhancer	Active	Disease	Ewing sarcoma	MONDO:0012817	DOID:3369	NA	NA	Mouse Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_03169	2014	25453756	A role for noncoding variation in schizophrenia	Homo sapiens	hg19	chr12	98562692	98566384	NA	CACNA1C	Enhancer	Active	Disease	Schizophrenia	MONDO:0005090	DOID:5419	NA	NA	Induced Pluripotent Stem Cells	NA	NA	NA	Chromatin interaction assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	NA	3C
E_03170	2014	25453756	A role for noncoding variation in schizophrenia	Homo sapiens	hg19	chr12	2350700	2350812	NA	CACNA1C	Enhancer	Active	Disease	neuroblastoma	MONDO:0005072	DOID:769	brain	UBERON:0000955	SH-SY5Y	CVCL_0019	neuroblastoma cell	NA	Enhancer activity assay	eQTL analysis	Luciferase reporter assay
E_03171	2015	26214589	Chimeric EWSR1-FLI1 regulates the Ewing sarcoma susceptibility gene EGR2 via a GGAA microsatellite	Homo sapiens	hg19	chr10	64739850	64739980	NA	EGR2	Enhancer	Active	Disease	Ewing sarcoma	MONDO:0012817	DOID:3369	bone element	UBERON:0001474	A-673	CVCL_0080	Ewing sarcoma cell	NA	Enhancer activity assay	NA	Luciferase reporter assay
E_03172	2022	34525218	Single-base editing of rs12603332 on chromosome 17q21 with a cytosine base editor regulates ORMDL3 and ATF6α expression	Homo sapiens	hg19	chr17	38082607	38083007	TCF3	ORMDL3	Enhancer	Active	Disease	asthma	MONDO:0004979	DOID:2841	blood	UBERON:0000178	Primary human CD4+ T cells	NA	CD4-positive, alpha-beta T cell	CL:0000624	TF binding assay; Endogenous disease-variant base editing; enhancer-context functional validation; Target-gene expression assay	NA	Cytosine base editing; Sanger/ICE editing analysis; RT-qPCR; EMSA; Flow cytometry
E_03173	2017	29151363	Functional assessment of human enhancer activities using whole-genome STARR-sequencing	Homo sapiens	hg19	chr19	34845032	34847032	NA	GPI	Enhancer	Active	Normal	NA	NA	NA	prostate gland	UBERON:0002367	Prostate Cancer Cell Lines	NA	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay	ChIP-seq; RNA-seq; ATAC-seq; STARR-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03174	2013	24204311	The transcription factors Sox10 and Myrf define an essential regulatory network module in differentiating oligodendrocytes	Mus musculus	mm10	chr19	102157620	102158432	Sox10	Myrf	Enhancer	Active	Normal	NA	NA	NA	spinal cord	UBERON:0002240	Primary oligodendrocytes	NA	oligodendrocyte	CL:0000128	Enhancer activity assay; TF binding assay	NA	Luciferase reporter assay, Transgenic reporter assay; ChIP-qPCR, EMSA; RT-qPCR
E_03175	2009	18984737	Methyltransferase Set7/9 maintains transcription and euchromatin structure at islet-enriched genes	Mus musculus	mm10	chr9	107683970	107684232	Pdx1	Setd7	Enhancer	Active	Normal	NA	NA	NA	pancreas	UBERON:0001264	Islet	NA	pancreatic islet cell	NA	Enhancer activity assay; TF binding assay	NA	Luciferase reporter assay; ChIP-qPCR; EMSA; siRNA knockdown
E_03176	2019	30755618	Whole-genome sequencing identifies ADGRG6 enhancer mutations and FRS2 duplications as angiogenesis-related drivers in bladder cancer	Homo sapiens	hg19	chr6	142706180	142706230	NA	ADGRG6	Enhancer	Active	Disease	urinary bladder carcinoma	MONDO:0004986	DOID:4007	urinary bladder	UBERON:0001255	5637	CVCL_0126	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay	RNA-seq; whole-genome sequencing	RT-qPCR; Western blot
E_03177	2019	30755618	Whole-genome sequencing identifies ADGRG6 enhancer mutations and FRS2 duplications as angiogenesis-related drivers in bladder cancer	Homo sapiens	hg19	chr6	142706180	142706230	NA	ADGRG6	Enhancer	Active	Disease	urinary bladder carcinoma	MONDO:0004986	DOID:4007	urinary bladder	UBERON:0001255	SW780	CVCL_1728	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay	RNA-seq; whole-genome sequencing	RT-qPCR; Western blot
E_03178	2012	22383952	Transcriptional regulation of N-acetylglutamate synthase	Homo sapiens	hg19	chr17	42078767	42079095	HNF1A	NAGS	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	epithelial cell	CL:0000066	Enhancer activity assay; TF binding assay	NA	Dual-luciferase reporter assay; Site-directed mutagenesis; DNA-protein pull-down; ChIP-qPCR; HNF1A overexpression
E_03179	2012	22383952	Transcriptional regulation of N-acetylglutamate synthase	Homo sapiens	hg19	chr17	42078767	42079095	NFYA	NAGS	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	epithelial cell	CL:0000066	Enhancer activity assay; TF binding assay	NA	Dual-luciferase reporter assay; Site-directed mutagenesis; DNA-protein pull-down; ChIP-qPCR
E_03180	2010	20363298	Identification of a FOXA-dependent enhancer of human alcohol dehydrogenase 4 (ADH4)	Homo sapiens	hg19	chr4	100078375	100078940	FOXA1	ADH4	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	malignant cell	CL:0001064	Reporter-based enhancer mapping; TF-binding and site-mutation validation	NA	Luciferase reporter assay; EMSA; antibody supershift; site-directed TF-binding-site mutagenesis; haplotype/variant reporter analysis
E_03181	2010	20363298	Identification of a FOXA-dependent enhancer of human alcohol dehydrogenase 4 (ADH4)	Homo sapiens	hg19	chr4	100078375	100078940	FOXA1	ADH4	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	NCI-H1299	CVCL_0060	malignant cell	CL:0001064	Reporter-based enhancer mapping; TF-binding and site-mutation validation	NA	Luciferase reporter assay; EMSA; antibody supershift; site-directed TF-binding-site mutagenesis; haplotype/variant reporter analysis
E_03182	2010	20363298	Identification of a FOXA-dependent enhancer of human alcohol dehydrogenase 4 (ADH4)	Homo sapiens	hg19	chr4	100078375	100078940	FOXA2	ADH4	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	malignant cell	CL:0001064	Reporter-based enhancer mapping; TF-binding and site-mutation validation	NA	Luciferase reporter assay; EMSA; antibody supershift; site-directed TF-binding-site mutagenesis; haplotype/variant reporter analysis
E_03183	2010	20363298	Identification of a FOXA-dependent enhancer of human alcohol dehydrogenase 4 (ADH4)	Homo sapiens	hg19	chr4	100078375	100078940	FOXA2	ADH4	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	NCI-H1299	CVCL_0060	malignant cell	CL:0001064	Reporter-based enhancer mapping; TF-binding and site-mutation validation	NA	Luciferase reporter assay; EMSA; antibody supershift; site-directed TF-binding-site mutagenesis; haplotype/variant reporter analysis
E_03184	2022	34525218	Single-base editing of rs12603332 on chromosome 17q21 with a cytosine base editor regulates ORMDL3 and ATF6α expression	Homo sapiens	hg19	chr17	38082607	38083007	TCF3	ORMDL3	Enhancer	Active	Disease	asthma	MONDO:0004979	DOID:2841	blood	UBERON:0000178	Jurkat	CVCL_0065	T cell	CL:0000084	TF binding assay; Endogenous disease-variant base editing; enhancer-context functional validation; Target-gene expression assay	NA	Cytosine base editing; Sanger/ICE editing analysis; RT-qPCR; EMSA; Flow cytometry
E_03185	2012	22383952	Transcriptional regulation of N-acetylglutamate synthase	Homo sapiens	hg19	chr17	42059156	42059522	HNF1A	NAGS	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay	NA	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; ChIP; Reporter assay
E_03186	2012	22383952	Transcriptional regulation of N-acetylglutamate synthase	Homo sapiens	hg19	chr17	42078865	42079198	HNF1A	NAGS	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	hepatocyte	CL:0000182	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_03187	2012	22383952	Transcriptional regulation of N-acetylglutamate synthase	Homo sapiens	hg19	chr17	42078865	42079198	NA	NAGS	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	hepatocyte	CL:0000182	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_03188	2012	22383952	Transcriptional regulation of N-acetylglutamate synthase	Homo sapiens	hg19	chr17	42078865	42079198	SP1	NAGS	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	hepatocyte	CL:0000182	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_03189	2019	30755618	Whole-genome sequencing identifies ADGRG6 enhancer mutations and FRS2 duplications as angiogenesis-related drivers in bladder cancer	Homo sapiens	hg19	chr6	142706180	142706230	NA	ADGRG6	Enhancer	Active	Normal	NA	NA	NA	umbilical vein	UBERON:0002066	HUVEC-C	CVCL_2959	umbilical vein endothelial cell	NA	Enhancer activity assay; Functional perturbation assay	RNA-seq; whole-genome sequencing	RT-qPCR; Western blot
E_03190	2019	30755618	Whole-genome sequencing identifies ADGRG6 enhancer mutations and FRS2 duplications as angiogenesis-related drivers in bladder cancer	Homo sapiens	hg19	chr6	142706180	142706230	NA	ADGRG6	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Neuro-2a	CVCL_0470	neuroblastoma cell	NA	Enhancer activity assay; Functional perturbation assay	RNA-seq; whole-genome sequencing	RT-qPCR; Western blot
E_03191	2013	24204311	The transcription factors Sox10 and Myrf define an essential regulatory network module in differentiating oligodendrocytes	Mus musculus	mm10	chr19	10215891	10216703	Sox10	Myrf	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Oligodendroglial Cell	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay; RT-qPCR/qPCR
E_03192	2009	18984737	Methyltransferase Set7/9 maintains transcription and euchromatin structure at islet-enriched genes	Mus musculus	mm10	chr3	51508734	51512187	Pdx1	Setd7	Enhancer	Active	Disease	Insulin Deficiency	NA	NA	pancreas	UBERON:0001264	βTC-3,INS-1,αTC1.6,NIH3T3	NA	pancreatic beta cell	CL:0000169	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03193	2012	22383952	Transcriptional regulation of N-acetylglutamate synthase	Homo sapiens	hg19	chr17	42078767	42079095	NA	NAGS	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	epithelial cell	CL:0000066	Enhancer activity assay	NA	Dual-luciferase reporter assay; orientation-independence assay; tissue-specific reporter assay; 5′ RACE
E_03194	2015	26216945	MIR retrotransposon sequences provide insulators to the human genome	Homo sapiens	hg19	chr2	98362566	98364423	NA	ZAP70	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HEK293	CVCL_0045	NA	NA	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay	ChIP-seq; Hi-C	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03195	2010	20393465	Widespread transcription at neuronal activity-regulated enhancers	Mus musculus	mm10	chr12	79240000	79242000	Creb1	Fos	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Primary cortical neurons	NA	cortical neuron	NA	Enhancer activity assay; TF binding assay	ChIP-seq; RNA-seq	Luciferase reporter assay; ChIP-qPCR; RT-qPCR
E_03196	2010	20393465	Widespread transcription at neuronal activity-regulated enhancers	Mus musculus	mm10	chr15	93680000	93682000	Crebbp	Arc	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Primary cortical neurons	NA	cortical neuron	NA	Enhancer activity assay	ChIP-seq; RNA-seq	Luciferase reporter assay; RT-qPCR
E_03197	2018	30295986	Identification of Novel Gata3 Distal Enhancers Active in Mouse Embryonic Lens	Mus musculus	mm10	chr2	9881939	9882773	Gata3	Gata3	Enhancer	Active	Normal	NA	NA	NA	lens of camera-type eye	UBERON:0000965	Lens epithelial cells	NA	lens epithelial cell	CL:0002224	Enhancer activity assay	ChIP-seq	Luciferase reporter assay, Transgenic reporter assay; RT-qPCR
E_03198	2018	30295986	Identification of Novel Gata3 Distal Enhancers Active in Mouse Embryonic Lens	Mus musculus	mm10	chr2	9895741	9896397	Gata3	Gata3	Enhancer	Active	Normal	NA	NA	NA	lens of camera-type eye	UBERON:0000965	Lens epithelial cells	NA	lens epithelial cell	CL:0002224	Enhancer activity assay	ChIP-seq	Luciferase reporter assay, Transgenic reporter assay; RT-qPCR
E_03199	2018	30295986	Identification of Novel Gata3 Distal Enhancers Active in Mouse Embryonic Lens	Mus musculus	mm10	chr2	9895741	9898314	Gata3	Gata3	Enhancer	Active	Normal	NA	NA	NA	lens of camera-type eye	UBERON:0000965	Lens epithelial cells	NA	lens epithelial cell	CL:0002224	Enhancer activity assay	ChIP-seq	Luciferase reporter assay, Transgenic reporter assay; RT-qPCR
E_03200	2018	30295986	Identification of Novel Gata3 Distal Enhancers Active in Mouse Embryonic Lens	Mus musculus	mm10	chr2	9897700	9898314	Gata3	Gata3	Enhancer	Active	Normal	NA	NA	NA	lens of camera-type eye	UBERON:0000965	Lens epithelial cells	NA	lens epithelial cell	CL:0002224	Enhancer activity assay	ChIP-seq	Luciferase reporter assay, Transgenic reporter assay; RT-qPCR
E_03201	2016	26817450	Looking beyond GWAS: allele-specific transcription factor binding drives the association of GALNT2 to HDL-C plasma levels	Homo sapiens	hg19	chr1	230294600	230294900	CEBPB	GALNT2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	malignant cell	CL:0001064	GWAS-linked HDL-C regulatory variant; allele-specific enhancer activity and TF binding	GWAS; ENCODE/ChIP-seq regulatory-data integration	Dual-luciferase/allele-specific reporter; EMSA; ChIP/ChIP-qPCR; RT-qPCR
E_03202	2016	26817450	Looking beyond GWAS: allele-specific transcription factor binding drives the association of GALNT2 to HDL-C plasma levels	Homo sapiens	hg19	chr1	230294600	230294900	NR3C2	GALNT2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	malignant cell	CL:0001064	GWAS-linked HDL-C regulatory variant; allele-specific enhancer activity and TF binding	GWAS; ENCODE/ChIP-seq regulatory-data integration	Dual-luciferase/allele-specific reporter; EMSA; ChIP/ChIP-qPCR; RT-qPCR
E_03203	2016	26817450	Looking beyond GWAS: allele-specific transcription factor binding drives the association of GALNT2 to HDL-C plasma levels	Homo sapiens	hg19	chr1	230294600	230294900	PLAGL1	GALNT2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	malignant cell	CL:0001064	GWAS-linked HDL-C regulatory variant; allele-specific enhancer activity and TF binding	GWAS; ENCODE/ChIP-seq regulatory-data integration	Dual-luciferase/allele-specific reporter; EMSA; ChIP/ChIP-qPCR; RT-qPCR
E_03204	2016	26817450	Looking beyond GWAS: allele-specific transcription factor binding drives the association of GALNT2 to HDL-C plasma levels	Homo sapiens	hg19	chr1	230294600	230294900	ZBTB3	GALNT2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	malignant cell	CL:0001064	GWAS-linked HDL-C regulatory variant; allele-specific enhancer activity and TF binding	GWAS; ENCODE/ChIP-seq regulatory-data integration	Dual-luciferase/allele-specific reporter; EMSA; ChIP/ChIP-qPCR; RT-qPCR
E_03205	2000	11120824	The murine IL-2 promoter contains distal regulatory elements responsive to the Ah receptor, a member of the evolutionarily conserved bHLH-PAS transcription factor family	Mus musculus	mm10	chr3	37126710	37127250	Ahr	Il2	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Primary splenic T cells	NA	T cell	CL:0000084	Enhancer activity assay; TF binding assay; ligand-responsive endogenous target validation; genetic TF-dependence validation	NA	Luciferase reporter assay; EMSA/competition EMSA/supershift; TCDD stimulation; RT-PCR; IL-2 ELISA; Ahr-deficient mouse validation
E_03206	2000	11120824	The murine IL-2 promoter contains distal regulatory elements responsive to the Ah receptor, a member of the evolutionarily conserved bHLH-PAS transcription factor family	Mus musculus	mm10	chr3	37126710	37127250	Ahr	Il2	Enhancer	Active	Normal	NA	NA	NA	thymus	UBERON:0002370	Primary thymocytes	NA	thymocyte	CL:0000893	Enhancer activity assay; TF binding assay; ligand-responsive endogenous target validation; genetic TF-dependence validation	NA	Luciferase reporter assay; EMSA/competition EMSA/supershift; TCDD stimulation; RT-PCR; IL-2 ELISA; Ahr-deficient mouse validation
E_03207	1998	9878258	A long terminal repeat of the human endogenous retrovirus ERV-9 is located in the 5' boundary area of the human beta-globin locus control region	Homo sapiens	hg19	chr11	5196000	5197000	GATA1	HBB	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay	NA	Luciferase reporter assay, EMSA; RT-qPCR
E_03208	2016	26817450	Looking beyond GWAS: allele-specific transcription factor binding drives the association of GALNT2 to HDL-C plasma levels	Homo sapiens	hg19	chr1	230294600	230294900	NA	GALNT2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	malignant cell	CL:0001064	GWAS-linked HDL-C regulatory variant; allele-specific enhancer activity and TF binding	GWAS; ENCODE/ChIP-seq regulatory-data integration	Dual-luciferase/allele-specific reporter; EMSA; ChIP/ChIP-qPCR; RT-qPCR
E_03209	2016	26817450	Looking beyond GWAS: allele-specific transcription factor binding drives the association of GALNT2 to HDL-C plasma levels	Homo sapiens	hg19	chr1	230293530	230305966	ZBTB3	GALNT2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	hepatocyte	CL:0000182	Enhancer activity assay; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq; GWAS/genetic association	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_03210	2000	11120824	The murine IL-2 promoter contains distal regulatory elements responsive to the Ah receptor, a member of the evolutionarily conserved bHLH-PAS transcription factor family	Mus musculus	mm10	chr3	37126710	37127250	Ahr	Il2	Enhancer	Active	Normal	NA	NA	NA	thymus	UBERON:0002370	ET	NA	epithelial cell of thymus	CL:0002293	Enhancer activity assay; TF binding assay; ligand-responsive endogenous target validation; genetic TF-dependence validation	NA	Luciferase reporter assay; EMSA/competition EMSA/supershift; TCDD stimulation; RT-PCR; IL-2 ELISA; Ahr-deficient mouse validation
E_03211	2000	11120824	The murine IL-2 promoter contains distal regulatory elements responsive to the Ah receptor, a member of the evolutionarily conserved bHLH-PAS transcription factor family	Mus musculus	mm10	chr3	37126710	37127250	Ahr	Il2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hepa-1c1c7	CVCL_0328	hepatocyte	CL:0000182	Enhancer activity assay; TF binding assay; ligand-responsive endogenous target validation; genetic TF-dependence validation	NA	Luciferase reporter assay; EMSA/competition EMSA/supershift; TCDD stimulation; RT-PCR; IL-2 ELISA; Ahr-deficient mouse validation
E_03212	2000	11120824	The murine IL-2 promoter contains distal regulatory elements responsive to the Ah receptor, a member of the evolutionarily conserved bHLH-PAS transcription factor family	Mus musculus	mm10	chr3	37126710	37127250	Arnt	Il2	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hepa-1c1c7	CVCL_0328	hepatocyte	CL:0000182	Enhancer activity assay; TF binding assay; ligand-responsive endogenous target validation; genetic TF-dependence validation	NA	Luciferase reporter assay; EMSA/competition EMSA/supershift; TCDD stimulation; RT-PCR; IL-2 ELISA; Ahr-deficient mouse validation
E_03213	1998	9878258	A long terminal repeat of the human endogenous retrovirus ERV-9 is located in the 5' boundary area of the human beta-globin locus control region	Homo sapiens	hg19	chr3	108296550	108297750	NA	HBB	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay	NA	3C
E_03214	2018	30295986	Identification of Novel Gata3 Distal Enhancers Active in Mouse Embryonic Lens	Mus musculus	mm10	chr2	9838078	9840078	NA	Gata3	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mouse Embryos	NA	NA	NA	Enhancer activity assay	NA	Luciferase reporter assay; Reporter assay; RT-qPCR/qPCR
E_03215	2023	37580330	IHH enhancer variant within neighboring NHEJ1 intron causes microphthalmia anophthalmia and coloboma	Homo sapiens	hg19	chr2	219988763	219991870	NA	IHH	Enhancer	Active	Disease	squamous cell lung carcinoma	MONDO:0005097	DOID:3907	lung	UBERON:0002048	Primary human LUSC tumor cells	NA	malignant cell	CL:0001064	Enhancer activity assay; Disease-variant functional analysis	ATAC-seq	Transgenic reporter assay, Sanger Sequencing
E_03216	2016	26968549	Identification of a novel putative mitochondrial protein FAM210B associated with erythroid differentiation	Homo sapiens	hg19	chr20	3508597	3508795	GATA1	FAM210B	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Neural progenitor	NA	neural progenitor cell	CL:0011020	Enhancer activity assay; TF binding assay; Chromatin-state profiling	ChIP-seq	Luciferase reporter assay; ChIP; Western blot
E_03217	2015	26537192	Identification of the 187 bp EphA7 Genomic DNA as the Dorsal Midline-Specific Enhancer of the Diencephalon and Mesencephalon	Mus musculus	mm10	chr4	29119847	29120047	NA	Epha7	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryo	NA	NA	NA	Enhancer activity assay; In vivo functional validation	NA	Transgenic/LacZ assay
E_03218	2011	21419113	Left-right asymmetry in the level of active Nodal protein produced in the node is translated into left-right asymmetry in the lateral plate of mouse embryos	Homo sapiens	hg19	chr1	226065482	226067482	FOXH1	LEFTY1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Perinodal Cells	NA	NA	NA	In vivo functional validation	NA	Transgenic/LacZ assay
E_03219	2016	26968549	Identification of a novel putative mitochondrial protein FAM210B associated with erythroid differentiation	Homo sapiens	hg19	chr20	54937784	54938182	GATA1	FAM210B	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	G1E-ER4 Cells	NA	erythroid progenitor cell	CL:0000038	Enhancer activity assay; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RNAi/siRNA/shRNA
E_03220	2015	26537192	Identification of the 187 bp EphA7 Genomic DNA as the Dorsal Midline-Specific Enhancer of the Diencephalon and Mesencephalon	Mus musculus	mm10	chr4	29115647	29140947	NA	Epha7	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryo	NA	NA	NA	Enhancer activity assay; In vivo functional validation	NA	Transgenic/LacZ assay
E_03221	2018	29967281	SP8 and SP9 coordinately promote D2-type medium spiny neuron production by activating Six3 expression	Mus musculus	mm10	chr17	85527960	85530660	Six3	Six3	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	The Subventricular Zone Of Lateral Ganglionic Eminence??LGE SVZ??	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	ChIP-seq; RNA-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03222	2018	29967281	SP8 and SP9 coordinately promote D2-type medium spiny neuron production by activating Six3 expression	Mus musculus	mm10	chr17	85463916	85466386	Six3	Six3	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	The Subventricular Zone Of Lateral Ganglionic Eminence??LGE SVZ??	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	ChIP-seq; RNA-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03223	2018	29967281	SP8 and SP9 coordinately promote D2-type medium spiny neuron production by activating Six3 expression	Mus musculus	mm10	chr17	85392908	85395234	Six3	Six3	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	The Subventricular Zone Of Lateral Ganglionic Eminence??LGE SVZ??	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	ChIP-seq; RNA-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03224	2017	29272704	AP-1 Transcription Factors and the BAF Complex Mediate Signal-Dependent Enhancer Selection	Mus musculus	mm10	chr10	21410566	21412861	Jun	Lama2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Primary Mouse Embryonic Fibroblasts	NA	fibroblast	CL:0000057	TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq; ATAC-seq	ChIP-qPCR/ChIP
E_03225	2017	29272704	AP-1 Transcription Factors and the BAF Complex Mediate Signal-Dependent Enhancer Selection	Mus musculus	mm10	chr11	19833945	19851027	Jun	Spred2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Primary Mouse Embryonic Fibroblasts	NA	fibroblast	CL:0000057	TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq; ATAC-seq	ChIP-qPCR/ChIP
E_03226	2017	29272704	AP-1 Transcription Factors and the BAF Complex Mediate Signal-Dependent Enhancer Selection	Mus musculus	mm10	chr17	45790442	45800636	Jun	Vegfa	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Primary Mouse Embryonic Fibroblasts	NA	fibroblast	CL:0000057	TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq; ATAC-seq	ChIP-qPCR/ChIP
E_03227	2009	19041414	Smad3 activates the Sox9-dependent transcription on chromatin	Mus musculus	mm10	chr15	98129939	98130247	Sox9	Col2a1	Enhancer	Active	Normal	NA	NA	NA	cartilage tissue	UBERON:0002418	NA	NA	NA	NA	Enhancer activity assay; TF binding assay	NA	ChIP-qPCR, EMSA; Luciferase reporter assay; Reporter assay
E_03228	2007	17053039	Transcriptional control of receptor activator of nuclear factor-kappaB ligand by the protein kinase A activator forskolin and the transmembrane glycoprotein 130-activating cytokine, oncostatin M, is exerted through multiple distal enhancers	Mus musculus	mm10	chr14	75355295	75355954	Creb1	Tnfsf11	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	NA	NA	NA	NA	Enhancer activity assay; TF binding assay	NA	Luciferase reporter assay; ChIP-qPCR, qRT-PCR, EMSA; ChIP
E_03229	2007	17053039	Transcriptional control of receptor activator of nuclear factor-kappaB ligand by the protein kinase A activator forskolin and the transmembrane glycoprotein 130-activating cytokine, oncostatin M, is exerted through multiple distal enhancers	Mus musculus	mm10	chr14	75355955	75357027	Creb1	Tnfsf11	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	NA	NA	NA	NA	Enhancer activity assay; TF binding assay	NA	Luciferase reporter assay; ChIP-qPCR, qRT-PCR, EMSA; ChIP
E_03230	2007	17053039	Transcriptional control of receptor activator of nuclear factor-kappaB ligand by the protein kinase A activator forskolin and the transmembrane glycoprotein 130-activating cytokine, oncostatin M, is exerted through multiple distal enhancers	Mus musculus	mm10	chr14	75363000	75363900	Creb1	Tnfsf11	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	NA	NA	NA	NA	Enhancer activity assay; TF binding assay	NA	Luciferase reporter assay; ChIP-qPCR, qRT-PCR, EMSA; ChIP
E_03231	2007	17053039	Transcriptional control of receptor activator of nuclear factor-kappaB ligand by the protein kinase A activator forskolin and the transmembrane glycoprotein 130-activating cytokine, oncostatin M, is exerted through multiple distal enhancers	Mus musculus	mm10	chr14	75371600	75372700	Creb1	Tnfsf11	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	NA	NA	NA	NA	Enhancer activity assay; TF binding assay	NA	Luciferase reporter assay; ChIP-qPCR, qRT-PCR, EMSA; ChIP
E_03232	2007	17053039	Transcriptional control of receptor activator of nuclear factor-kappaB ligand by the protein kinase A activator forskolin and the transmembrane glycoprotein 130-activating cytokine, oncostatin M, is exerted through multiple distal enhancers	Mus musculus	mm10	chr14	75408900	75410500	Creb1	Tnfsf11	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	NA	NA	NA	NA	Enhancer activity assay; TF binding assay	NA	Luciferase reporter assay; ChIP-qPCR, qRT-PCR, EMSA; ChIP
E_03233	2007	17053039	Transcriptional control of receptor activator of nuclear factor-kappaB ligand by the protein kinase A activator forskolin and the transmembrane glycoprotein 130-activating cytokine, oncostatin M, is exerted through multiple distal enhancers	Mus musculus	mm10	chr14	75415600	75416800	Creb1	Tnfsf11	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	NA	NA	NA	NA	Enhancer activity assay; TF binding assay	NA	Luciferase reporter assay; ChIP-qPCR, qRT-PCR, EMSA; ChIP
E_03234	2009	19041414	Smad3 activates the Sox9-dependent transcription on chromatin	Mus musculus	mm10	chr15	98750000	98750480	Sox9	Col2a1	Enhancer	Active	Disease	chondrosarcoma	MONDO:0008977	DOID:3371	cartilage tissue	UBERON:0002418	SW1353	CVCL_0543	chondrosarcoma cell	NA	Enhancer activity assay; TF binding assay	NA	Luciferase reporter assay; EMSA; In vitro transcription assay; Reporter assay
E_03235	2009	19041414	Smad3 activates the Sox9-dependent transcription on chromatin	Mus musculus	mm10	chr15	97977739	97977942	Sox9	Col2a1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HeLa	CVCL_0030	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; EMSA/gel-shift assay
E_03236	2007	17053039	Transcriptional control of receptor activator of nuclear factor-kappaB ligand by the protein kinase A activator forskolin and the transmembrane glycoprotein 130-activating cytokine, oncostatin M, is exerted through multiple distal enhancers	Homo sapiens	hg18	chr13	41947040	41947582	CREB1	TNFSF11	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	St-2	CVCL_E3YP	bone marrow stromal cell	NA	Enhancer activity assay	NA	Luciferase reporter assay with human hRLD5b; forskolin response assay
E_03237	2026	41253710	The Ets2 super-enhancer modulates endothelial-mesenchymal transition during cardiac ageing	Mus musculus	mm10	chr16	95721049	95979933	NA	Ets2	Super-enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	cardiac endothelial cells	NA	endothelial cell	CL:0000115	Super-enhancer functional perturbation assay; EndoMT assay; In vivo ageing phenotype assay	snRNA-seq; RNA-seq; ATAC-seq	Ets2 super-enhancer deletion mouse; endothelial-specific Ets2 knockout; qRT-PCR; histology; fibrosis and cardiac-function assays
E_03238	2026	41253710	The Ets2 super-enhancer modulates endothelial-mesenchymal transition during cardiac ageing	Mus musculus	mm10	chr16	95721049	95979933	NA	Ets2	Super-enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	aortic endothelial cells	NA	aortic endothelial cell	CL:0002544	Super-enhancer functional perturbation assay; EndoMT assay; In vivo ageing phenotype assay	snRNA-seq; RNA-seq; ATAC-seq	Ets2 super-enhancer deletion mouse; endothelial-specific Ets2 knockout; qRT-PCR; histology; fibrosis and cardiac-function assays
E_03239	2023	37537334	Transcription modulates chromatin dynamics and locus configuration sampling	Mus musculus	mm9	chr2	105444500	105457500	NA	Pax6	Enhancer	Active	Normal	NA	NA	NA	islet of Langerhans	UBERON:0000006	Beta-TC-3	CVCL_0172	pancreatic beta cell	CL:0000169	Chromatin interaction/dynamics assay using previously characterized enhancers	NG Capture-C; ATAC-seq; histone-mark ChIP profiling; 3C	3D DNA FISH; alpha-amanitin transcription inhibition; HiP-HoP computational modeling
E_03240	2023	37537334	Transcription modulates chromatin dynamics and locus configuration sampling	Mus musculus	mm9	chr2	105629500	105640500	NA	Pax6	Enhancer	Active	Normal	NA	NA	NA	islet of Langerhans	UBERON:0000006	Beta-TC-3	CVCL_0172	pancreatic beta cell	CL:0000169	Chromatin interaction/dynamics assay using previously characterized enhancers	NG Capture-C; ATAC-seq; histone-mark ChIP profiling; 3C	3D DNA FISH; alpha-amanitin transcription inhibition; HiP-HoP computational modeling
E_03241	2020	32303558	Leveraging mouse chromatin data for heritability enrichment informs common disease architecture and reveals cortical layer contributions to schizophrenia	Homo sapiens	hg38	chr3	180986412	180988412	NA	SOX2-OT	Enhancer	Active	Disease	type 1 diabetes mellitus	MONDO:0005147	DOID:9744	pancreas	UBERON:0001264	CD8+ T cell	NA	CD8-positive T cell	NA	Enhancer activity assay	ATAC-seq	3C; RT-PCR; RT-qPCR
E_03242	2019	30397001	Cell Cycle and Apoptosis Regulator 1, CCAR1, Regulates Enhancer-Dependent Nuclear Receptor CAR Transactivation	Homo sapiens	hg19	chr2	234665349	234665739	CCAR1	UGT1A1	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	Hep-G2	CVCL_0027	hepatocyte	CL:0000182	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_03243	1995	7641334	Hypoxia regulates vascular endothelial growth factor gene expression in endothelial cells. Identification of a 5' enhancer	Homo sapiens	hg38	chr6	43769226	43769421	NA	VEGFA	Enhancer	Active	Normal	NA	NA	NA	pulmonary artery	UBERON:0002012	bovine pulmonary artery endothelial cells	NA	pulmonary artery endothelial cell	CL:1001568	Hypoxia-responsive enhancer activity assay; cis-element functional mapping	NA	Reporter assay; deletion/mutagenesis; DNA-binding assay; hypoxia induction; RNA-expression assay
E_03244	2025	39934429	An unusual transfusion-dependent hemoglobin H disease caused by a novel complex inverted duplication involving the α-globin regulatory elements and α-thalassemia--SEA deletion	Homo sapiens	hg19	chr16	155136	155210	NA	HBA1	Enhancer	Active	Disease	hemoglobin H disease	MONDO:0013512	DOID:0110031	blood	UBERON:0000178	CD71+ erythroid cells from peripheral blood of the MCS-duplication carrier	NA	erythroid progenitor cell	CL:0000038	Chromatin accessibility assay; structural variant analysis	whole-genome sequencing; optical genome mapping; ATAC-seq	MLPA; long-range PCR; Sanger sequencing; Luciferase reporter assay; Reporter assay
E_03245	2025	39934429	An unusual transfusion-dependent hemoglobin H disease caused by a novel complex inverted duplication involving the α-globin regulatory elements and α-thalassemia--SEA deletion	Homo sapiens	hg19	chr16	155136	155210	NA	HBA2	Enhancer	Active	Disease	hemoglobin H disease	MONDO:0013512	DOID:0110031	blood	UBERON:0000178	CD71+ erythroid cells from peripheral blood of the MCS-duplication carrier	NA	erythroid progenitor cell	CL:0000038	Chromatin accessibility assay; structural variant analysis	whole-genome sequencing; optical genome mapping; ATAC-seq	MLPA; long-range PCR; Sanger sequencing; Luciferase reporter assay; Reporter assay
E_03246	2025	39934429	An unusual transfusion-dependent hemoglobin H disease caused by a novel complex inverted duplication involving the α-globin regulatory elements and α-thalassemia--SEA deletion	Homo sapiens	hg19	chr16	164235	164590	NA	HBA2	Enhancer	Active	Disease	hemoglobin H disease	MONDO:0013512	DOID:0110031	pleural effusion	UBERON:0000175	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; structural variant functional analysis	whole-genome sequencing; optical genome mapping; ATAC-seq	Dual-luciferase reporter assay (356-bp MCS-R2/HS-40 wild-type versus reverse-orientation construct with HBA2 promoter); MLPA; long-range PCR; Sanger sequencing; Luciferase reporter assay; Reporter assay
E_03247	2025	39934429	An unusual transfusion-dependent hemoglobin H disease caused by a novel complex inverted duplication involving the α-globin regulatory elements and α-thalassemia--SEA deletion	Homo sapiens	hg19	chr16	170166	170655	NA	HBA1	Enhancer	Active	Disease	hemoglobin H disease	MONDO:0013512	DOID:0110031	blood	UBERON:0000178	CD71+ erythroid cells from peripheral blood of the MCS-duplication carrier	NA	erythroid progenitor cell	CL:0000038	Chromatin accessibility assay; structural variant analysis	whole-genome sequencing; optical genome mapping; ATAC-seq	MLPA; long-range PCR; Sanger sequencing; Luciferase reporter assay; Reporter assay
E_03248	2025	39934429	An unusual transfusion-dependent hemoglobin H disease caused by a novel complex inverted duplication involving the α-globin regulatory elements and α-thalassemia--SEA deletion	Homo sapiens	hg19	chr16	170166	170655	NA	HBA2	Enhancer	Active	Disease	hemoglobin H disease	MONDO:0013512	DOID:0110031	blood	UBERON:0000178	CD71+ erythroid cells from peripheral blood of the MCS-duplication carrier	NA	erythroid progenitor cell	CL:0000038	Chromatin accessibility assay; structural variant analysis	whole-genome sequencing; optical genome mapping; ATAC-seq	MLPA; long-range PCR; Sanger sequencing; Luciferase reporter assay; Reporter assay
E_03249	2025	39934429	An unusual transfusion-dependent hemoglobin H disease caused by a novel complex inverted duplication involving the α-globin regulatory elements and α-thalassemia--SEA deletion	Homo sapiens	hg19	chr16	193013	193087	NA	HBA1	Enhancer	Active	Disease	hemoglobin H disease	MONDO:0013512	DOID:0110031	blood	UBERON:0000178	CD71+ erythroid cells from peripheral blood of the MCS-duplication carrier	NA	erythroid progenitor cell	CL:0000038	Chromatin accessibility assay; structural variant analysis	whole-genome sequencing; optical genome mapping; ATAC-seq	MLPA; long-range PCR; Sanger sequencing; Luciferase reporter assay; Reporter assay
E_03250	2025	39934429	An unusual transfusion-dependent hemoglobin H disease caused by a novel complex inverted duplication involving the α-globin regulatory elements and α-thalassemia--SEA deletion	Homo sapiens	hg19	chr16	193013	193087	NA	HBA2	Enhancer	Active	Disease	hemoglobin H disease	MONDO:0013512	DOID:0110031	blood	UBERON:0000178	CD71+ erythroid cells from peripheral blood of the MCS-duplication carrier	NA	erythroid progenitor cell	CL:0000038	Chromatin accessibility assay; structural variant analysis	whole-genome sequencing; optical genome mapping; ATAC-seq	MLPA; long-range PCR; Sanger sequencing; Luciferase reporter assay; Reporter assay
E_03251	2011	21527504	Class-C SOX transcription factors control GnRH gene expression via the intronic transcriptional enhancer	Mus musculus	mm10	chr14	67745496	67746000	Sox11	Gnrh1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	GT1-1	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay; RT-qPCR/qPCR
E_03252	2011	21527504	Class-C SOX transcription factors control GnRH gene expression via the intronic transcriptional enhancer	Mus musculus	mm10	chr14	67745496	67746000	Sox12	Gnrh1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	GT1-1	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay; RT-qPCR/qPCR
E_03253	2011	21527504	Class-C SOX transcription factors control GnRH gene expression via the intronic transcriptional enhancer	Mus musculus	mm10	chr14	67745496	67746000	Sox4	Gnrh1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	GT1-1	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay; RT-qPCR/qPCR
E_03254	2011	21527504	Class-C SOX transcription factors control GnRH gene expression via the intronic transcriptional enhancer	Mus musculus	mm10	chr14	67745323	67746327	Qsox1	Gnrh1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	GT1-1	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay; RT-qPCR/qPCR
E_03255	2011	21798992	Characterization of the human SLC30A8 promoter and intronic enhancer	Homo sapiens	hg19	chr8	118163800	118164175	NA	SLC30A8	Enhancer	Active	Normal	NA	NA	NA	islet of Langerhans	UBERON:0000006	Beta-TC-3	CVCL_0172	pancreatic beta cell	CL:0000169	Enhancer activity assay; Functional variant assay	NA	Luciferase reporter assay; EMSA; Stable and transient transfection; Site-directed mutagenesis
E_03256	2019	30397001	Cell Cycle and Apoptosis Regulator 1, CCAR1, Regulates Enhancer-Dependent Nuclear Receptor CAR Transactivation	Homo sapiens	hg19	chr2	234665349	234665739	NR1I3	UGT1A1	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	HepaRG	CVCL_9720	hepatocyte	CL:0000182	Nuclear-receptor enhancer assay; coactivator perturbation; TF/cofactor occupancy	NA	Luciferase reporter assay; CCAR1 siRNA; NR1I3/CAR activation; ChIP; qRT-PCR; Western blot
E_03257	2025	40403729	A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types	Homo sapiens	hg38	chr2	46315253	46315668	NA	EPAS1	Enhancer	Active	Normal	NA	NA	NA	blood vessel	UBERON:0001981	Endothelial cells	NA	endothelial cell	CL:0000115	Enhancer activity assay	ATAC-seq; RNA-seq	Luciferase reporter assay, Transgenic reporter assay; Transgenic enhancer reporter assay
E_03258	2025	40403729	A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types	Mus musculus	mm10	chr10	116270311	116271768	NA	Ptprb	Enhancer	Active	Normal	NA	NA	NA	blood vessel	UBERON:0001981	Endothelial cells	NA	endothelial cell	CL:0000115	Enhancer activity assay	ATAC-seq; RNA-seq	Luciferase reporter assay, Transgenic reporter assay; Transgenic enhancer reporter assay
E_03259	2025	40403729	A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types	Mus musculus	mm10	chr16	18703897	18705643	NA	Cldn5	Enhancer	Active	Normal	NA	NA	NA	blood vessel	UBERON:0001981	Endothelial cells	NA	endothelial cell	CL:0000115	Enhancer activity assay	ATAC-seq; RNA-seq	Luciferase reporter assay, Transgenic reporter assay; Transgenic enhancer reporter assay
E_03260	2025	40403729	A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types	Mus musculus	mm10	chr17	31905602	31906289	NA	Notch4	Enhancer	Active	Normal	NA	NA	NA	blood vessel	UBERON:0001981	Endothelial cells	NA	endothelial cell	CL:0000115	Enhancer activity assay	ATAC-seq; RNA-seq	Luciferase reporter assay, Transgenic reporter assay; Transgenic enhancer reporter assay
E_03261	2025	40403729	A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types	Mus musculus	mm10	chr2	26575785	26576489	NA	Egfl7	Enhancer	Active	Normal	NA	NA	NA	blood vessel	UBERON:0001981	Endothelial cells	NA	endothelial cell	CL:0000115	Enhancer activity assay	ATAC-seq; RNA-seq	Luciferase reporter assay, Transgenic reporter assay; Transgenic enhancer reporter assay
E_03262	2025	40403729	A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types	Mus musculus	mm10	chr4	55670153	55670693	NA	Klf4	Enhancer	Active	Normal	NA	NA	NA	blood vessel	UBERON:0001981	Endothelial cells	NA	endothelial cell	CL:0000115	Enhancer activity assay	ATAC-seq; RNA-seq	Luciferase reporter assay, Transgenic reporter assay; Transgenic enhancer reporter assay
E_03263	2025	40403729	A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types	Mus musculus	mm10	chr4	118489677	118490197	NA	Tie1	Enhancer	Active	Normal	NA	NA	NA	blood vessel	UBERON:0001981	Endothelial cells	NA	endothelial cell	CL:0000115	Enhancer activity assay	ATAC-seq; RNA-seq	Luciferase reporter assay, Transgenic reporter assay; Transgenic enhancer reporter assay
E_03264	2025	40403729	A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types	Mus musculus	mm10	chr9	37400589	37400968	NA	Esam	Enhancer	Active	Normal	NA	NA	NA	blood vessel	UBERON:0001981	Endothelial cells	NA	endothelial cell	CL:0000115	Enhancer activity assay	ATAC-seq; RNA-seq	Luciferase reporter assay, Transgenic reporter assay; Transgenic enhancer reporter assay
E_03265	2025	40403729	A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types	Mus musculus	mm10	chr9	37401768	37402146	NA	Robo4	Enhancer	Active	Normal	NA	NA	NA	blood vessel	UBERON:0001981	Endothelial cells	NA	endothelial cell	CL:0000115	Enhancer activity assay	ATAC-seq; RNA-seq	Luciferase reporter assay, Transgenic reporter assay; Transgenic enhancer reporter assay
E_03266	2013	23872150	Estrogen modulates plasminogen promoter activity	Homo sapiens	hg19	chr6	161119825	161121825	NA	PLG	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_03267	2013	23872150	Estrogen modulates plasminogen promoter activity	Homo sapiens	hg19	chr6	161119825	161121825	NA	PLG	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_03268	2013	23872150	Estrogen modulates plasminogen promoter activity	Homo sapiens	hg19	chr6	161110725	161112725	NA	PLG	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_03269	2013	23872150	Estrogen modulates plasminogen promoter activity	Homo sapiens	hg19	chr6	161110725	161112725	NA	PLG	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_03270	2025	40403729	A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types	Mus musculus	mm10	chr5	104397936	104398396	NA	Tgfbr3	Enhancer	Active	Normal	NA	NA	NA	blood vessel	UBERON:0001981	Vascular smooth muscle cells	NA	vascular smooth muscle cell	NA	Enhancer activity assay	ATAC-seq; RNA-seq	Luciferase reporter assay; Transgenic reporter assay
E_03271	2013	23872150	Estrogen modulates plasminogen promoter activity	Homo sapiens	hg19	chr6	161085524	161086263	NA	PLG	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	malignant cell	CL:0001064	Enhancer activity assay	NA	Luciferase reporter assay; RT-qPCR; Luciferase reporter assay; Reporter assay
E_03272	2013	23872150	Estrogen modulates plasminogen promoter activity	Homo sapiens	hg19	chr6	161092630	161095030	NA	PLG	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	malignant cell	CL:0001064	Enhancer activity assay	NA	Luciferase reporter assay; RT-qPCR; Luciferase reporter assay; Reporter assay
E_03273	2013	23872150	Estrogen modulates plasminogen promoter activity	Homo sapiens	hg19	chr6	161110725	161112725	ESR1	PLG	Enhancer	Active	Normal	NA	NA	NA	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; Hormone-response assay	NA	Luciferase reporter assay; estradiol treatment; Reporter assay
E_03274	2013	23872150	Estrogen modulates plasminogen promoter activity	Homo sapiens	hg19	chr6	161110725	161112725	ESR1	PLG	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	hepatic reporter cell models	NA	hepatocyte	CL:0000182	Enhancer activity assay; Estrogen-responsive enhancer/promoter regulatory assay	NA	Luciferase reporter assay; ERE mutagenesis; estrogen stimulation; Reporter assay
E_03275	2013	23872150	Estrogen modulates plasminogen promoter activity	Homo sapiens	hg19	chr6	161119825	161121825	ESR1	PLG	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	hepatic reporter cell models	NA	hepatocyte	CL:0000182	Enhancer activity assay; Estrogen-responsive enhancer/promoter regulatory assay	NA	Luciferase reporter assay; ERE mutagenesis; estrogen stimulation; Reporter assay
E_03276	2011	21798992	Characterization of the human SLC30A8 promoter and intronic enhancer	Mus musculus	mm10	chr15	52315678	52316298	Pdx1	Slc30a8	Enhancer	Active	Normal	NA	NA	NA	islet of Langerhans	UBERON:0000006	Beta-TC-3	CVCL_0172	pancreatic beta cell	CL:0000169	Enhancer activity assay; cell-type-specific reporter assay	Comparative genomics/VISTA conservation analysis	Luciferase reporter assay; orientation-independence assay; beta-cell versus alpha-cell reporter comparison
E_03277	2013	23872150	Estrogen modulates plasminogen promoter activity	Homo sapiens	hg19	chr6	161110725	161112725	ESR1	PLG	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	hepatoblastoma cell line	NA	Enhancer activity assay; Hormone-response assay	NA	Luciferase reporter assay; ESR1 cotransfection; estradiol treatment; Reporter assay
E_03278	2013	23872150	Estrogen modulates plasminogen promoter activity	Homo sapiens	hg19	chr6	161110725	161112725	NA	PLG	Enhancer	Active	Normal	NA	NA	NA	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; Hormone-response assay	NA	Luciferase reporter assay; estrogen treatment; reporter-construct comparison; Reporter assay
E_03279	2011	21798992	Characterization of the human SLC30A8 promoter and intronic enhancer	Homo sapiens	hg19	chr8	117978845	117979466	NA	SLC30A8	Enhancer	Active	Disease	type 2 diabetes mellitus	MONDO:0005148	DOID:9352	NA	NA	βTC-3,αTC-6	NA	NA	NA	Enhancer activity assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay
E_03280	2011	21798992	Characterization of the human SLC30A8 promoter and intronic enhancer	Mus musculus	mm10	chr15	52315678	52316298	NA	Slc30a8	Enhancer	Active	Disease	type 2 diabetes mellitus	MONDO:0005148	DOID:9352	NA	NA	βTC-3,αTC-6	NA	NA	NA	Enhancer activity assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay
E_03281	2013	23872150	Estrogen modulates plasminogen promoter activity	Homo sapiens	hg19	chr6	161110725	161112725	NA	PLG	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	Hep-G2	CVCL_0027	hepatoblastoma cell line	NA	Enhancer activity assay; Hormone-response assay	NA	Luciferase reporter assay; estrogen treatment; reporter-construct comparison; Reporter assay
E_03282	2011	21798992	Characterization of the human SLC30A8 promoter and intronic enhancer	Mus musculus	mm10	chr15	5249678	5250298	NA	Slc30a8	Enhancer	Active	Normal	NA	NA	NA	NA	NA	βTC-3	NA	NA	NA	Enhancer activity assay	NA	Luciferase reporter assay; Reporter assay
E_03283	2026	41276612	Mendelian randomization facilitates identification of schizophrenia risk enhancer RNAs	Homo sapiens	hg19	chr14	72448647	72451627	NA	NA	Enhancer	Active	Disease	Schizophrenia	MONDO:0005090	DOID:5419	NA	NA	SK-N-SH	CVCL_0531	neuroblastoma cell	NA	Enhancer RNA functional perturbation assay; Transcriptome assay; Neuronal differentiation assay	RNA-seq; eQTL analysis	RGS6e forward/reverse-complement transcript overexpression; lentiviral transduction; ATRA-induced neuronal differentiation; fluorescence microscopy; neurite-length quantification; plasmid direct sequencing
E_03284	2013	23598529	REST negatively and ISGF3 positively regulate the human STAT1 gene in melanoma	Homo sapiens	hg19	chr2	191800000	191801000	IRF1	STAT1	Enhancer	Active	Disease	cutaneous melanoma	MONDO:0005012	DOID:8923	zone of skin	UBERON:0000014	Melanoma cells	NA	melanoma cell	NA	Enhancer activity assay; TF binding assay	ChIP-seq; microarray	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot
E_03285	1997	9314837	Conserved enhancer elements in human and mouse renin genes have different transcriptional effects in As4.1 cells	Mus musculus	mm39	chr1	133275546	133275787	NA	Ren1	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	As4.1	CVCL_0151	renin-producing renal cell	NA	Enhancer activity assay; Cross-species cis-regulatory functional analysis	NA	Transient-transfection reporter assay; enhancer deletion/chimeric construct analysis
E_03286	1983	6409418	A lymphocyte-specific cellular enhancer is located downstream of the joining region in immunoglobulin heavy chain genes	Mus musculus	mm10	chr12	113427251	113427729	NA	Igh	Enhancer	Active	Normal	NA	NA	NA	NA	NA	P3X63Ag8	CVCL_3411	plasma cell	CL:0000786	Enhancer activity assay; Cell-type specificity assay; Functional deletion mapping	NA	Transient transfection; SV40 T-antigen reporter assay; Indirect immunofluorescence; beta-globin transcription reporter assay; S1 nuclease mapping; Restriction-fragment deletion mapping; Bal31 deletion mapping
E_03287	2017	29416716	Robust diagnosis of Ewing sarcoma by immunohistochemical detection of super-enhancer-driven EWSR1-ETS targets	Homo sapiens	hg19	chr14	99770698	99782638	NA	BCL11B	Super-enhancer	Active	Disease	Ewing sarcoma	MONDO:0012817	DOID:3369	NA	NA	A673/TR/shEF1 Cells	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_03288	2017	29416716	Robust diagnosis of Ewing sarcoma by immunohistochemical detection of super-enhancer-driven EWSR1-ETS targets	Homo sapiens	hg19	chr1	116896120	116904325	NA	ATP1A1	Super-enhancer	Active	Disease	Ewing sarcoma	MONDO:0012817	DOID:3369	NA	NA	A673/TR/shEF1 Cells	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_03289	2017	29416716	Robust diagnosis of Ewing sarcoma by immunohistochemical detection of super-enhancer-driven EWSR1-ETS targets	Homo sapiens	hg19	chr16	74568579	74583481	NA	GLG1	Super-enhancer	Active	Disease	Ewing sarcoma	MONDO:0012817	DOID:3369	NA	NA	A673/TR/shEF1 Cells	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_03290	2013	24086551	Identification of an enhancer that increases miR-200b~200a~429 gene expression in breast cancer cells	Homo sapiens	hg19	chr1	1083900	1085900	NA	GIHCG	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	HMLE	NA	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_03291	1989	2542571	Induction of human interferon gene expression is associated with a nuclear factor that interacts with the NF-kappa B site of the human immunodeficiency virus enhancer	Homo sapiens	hg19	chr9	21206044	21206127	NFKB1	IFNB1	Enhancer	Active	Disease	histiocytic lymphoma	MONDO:0004854	DOID:5408	blood	UBERON:0000178	U-937	CVCL_0007	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay	NA	EMSA; Luciferase reporter assay
E_03292	2026	41276612	Mendelian randomization facilitates identification of schizophrenia risk enhancer RNAs	Homo sapiens	hg19	chr14	72448647	72451627	NA	NA	Enhancer	Active	Disease	Schizophrenia	MONDO:0005090	DOID:5419	dorsolateral prefrontal cortex	UBERON:0009834	BrainSeq Phase 1 postmortem dorsolateral prefrontal cortex	NA	NA	NA	Disease-variant functional analysis; Enhancer activity-associated transcription analysis; Genetic association analysis; eQTL analysis; Mendelian randomization analysis	RNA-seq; SNP genotyping and imputation; cis-eQTL mapping; PGC3 schizophrenia GWAS integration; Summary-data-based Mendelian Randomization (SMR); eQTL analysis; GWAS	3C
E_03293	1983	6409418	A lymphocyte-specific cellular enhancer is located downstream of the joining region in immunoglobulin heavy chain genes	Mus musculus	mm10	chr12	114666216	114667377	NA	Igh	Enhancer	Active	Disease	plasmacytoma	MONDO:0005615	DOID:3721	lymphoid tissue	UBERON:0001744	ROV-S	CVCL_3415	plasmacytoma cell	NA	Enhancer activity assay; TF binding assay	NA	Luciferase reporter assay; EMSA
E_03294	2013	23598529	REST negatively and ISGF3 positively regulate the human STAT1 gene in melanoma	Homo sapiens	hg19	chr2	191834162	191834795	NA	STAT1	Enhancer	Repressed	Disease	melanoma	MONDO:0005105	DOID:1909	skin	UBERON:0002097	Mm96	NA	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03295	1989	2542571	Induction of human interferon gene expression is associated with a nuclear factor that interacts with the NF-kappa B site of the human immunodeficiency virus enhancer	Homo sapiens	hg19	chr9	21077976	21078020	NA	IFNB1	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	U-937	CVCL_0007	monoblast	CL:0000040	TF-DNA binding assay; Endogenous gene expression assay; Cis-regulatory element mapping	NA	IFN-alpha2 priming; Sendai virus induction; EMSA; competition EMSA; S1 nuclease protection analysis; biological interferon activity assay
E_03296	1989	2542571	Induction of human interferon gene expression is associated with a nuclear factor that interacts with the NF-kappa B site of the human immunodeficiency virus enhancer	Homo sapiens	hg19	chr9	21077976	21078020	NA	IFNB1	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	HEK293	CVCL_0045	epithelial cell	CL:0000066	Enhancer activity assay; Functional cis-regulatory assay	NA	Calcium phosphate transient transfection; CAT reporter assay; Sendai virus induction
E_03297	1989	2542571	Induction of human interferon gene expression is associated with a nuclear factor that interacts with the NF-kappa B site of the human immunodeficiency virus enhancer	Homo sapiens	hg19	chr9	21077976	21078020	NA	IFNB1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Jurkat	CVCL_0065	T cell	CL:0000084	Enhancer activity assay; Functional cis-regulatory assay	NA	DEAE-dextran transient transfection; CAT reporter assay; PHA/PMA stimulation
E_03298	2026	41651436	Targeting super-enhancer-driven MAB21L2 suppresses neuroblastoma growth and migration	Homo sapiens	hg38	chr4	150577837	150588968	NA	MAB21L2	Super-enhancer	Active	Disease	neuroblastoma	MONDO:0005072	DOID:769	bone marrow	UBERON:0002371	SK-N-BE(2)	CVCL_0528	neuroblastoma cell	NA	Functional perturbation assay; Super-enhancer identification; Transcriptomic analysis; Tumor growth and migration assay	RNA-seq; epigenomic super-enhancer profiling	MAB21L2 knockdown; in vitro proliferation assay; migration assay; in vivo xenograft tumor-growth assay
E_03299	2022	35789143	ASCL1 regulates super-enhancer-associated miRNAs to define molecular subtypes of small cell lung cancer	Homo sapiens	hg19	chr2	16200000	16205000	ASCL1	MIR375	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Monocyte	NA	monocyte	CL:0000576	Super-enhancer activity assay	ChIP-seq; RNA-seq; CUT&Tag	Luciferase reporter assay; RT-qPCR
E_03300	2015	26601269	Cis-regulatory mechanisms governing stem and progenitor cell transitions	Mus musculus	mm39	chr6	88093936	88094192	NA	Gata2	Enhancer	Active	Disease	anemia	MONDO:0002280	DOID:2355	liver	UBERON:0002107	E13.5 fetal liver myeloid progenitors	NA	myeloerythroid progenitor cell	NA	Functional perturbation assay; Gene expression assay; Hematopoietic differentiation assay	RNA-seq	Targeted enhancer deletion; RT-qPCR; Flow cytometry; colony-forming assay
E_03301	2014	24915132	Identification of two regulatory elements controlling Fucosyltransferase 7 transcription in murine CD4+ T cells	Mus musculus	mm10	chr2	25423079	25423874	Ep300	Fut7	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Th1	NA	T helper 1 cell	CL:0000545	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_03302	2012	22996659	Cis-element mutated in GATA2-dependent immunodeficiency governs hematopoiesis and vascular integrity	Mus musculus	mm39	chr6	88180138	88180212	NA	Gata2	Enhancer	Active	Disease	GATA2 deficiency syndrome	MONDO:0042982	NA	liver	UBERON:0002107	E13.5 fetal liver hematopoietic stem/progenitor cells	NA	hematopoietic stem/progenitor cell	NA	Functional perturbation assay; Gene expression assay; In vivo developmental assay	NA	Targeted homologous-recombination enhancer deletion; RT-qPCR; Flow cytometry; colony-forming assay; immunohistochemistry
E_03303	2011	21464207	Genome-wide approaches reveal functional interleukin-4-inducible STAT6 binding to the vascular cell adhesion molecule 1 promoter	Homo sapiens	hg19	chr1	101402363	101412724	STAT6	VCAM1	Enhancer	Active	Disease	atherosclerosis	MONDO:0005311	DOID:1936	NA	NA	HUVEC	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_03304	2011	21527503	Progesterone receptor directly inhibits β-casein gene transcription in mammary epithelial cells through promoting promoter and enhancer repressive chromatin modifications	Homo sapiens	hg19	chr1	33353796	33354196	CEBPB	TMEM54	Enhancer	Repressed	Normal	NA	NA	NA	NA	NA	HC11 Mammary Epithelium	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03305	2011	21527503	Progesterone receptor directly inhibits β-casein gene transcription in mammary epithelial cells through promoting promoter and enhancer repressive chromatin modifications	Homo sapiens	hg19	chr1	33353796	33354196	CEBPB	CSN2	Enhancer	Repressed	Normal	NA	NA	NA	NA	NA	HC11 Mammary Epithelium	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03306	2011	21527503	Progesterone receptor directly inhibits β-casein gene transcription in mammary epithelial cells through promoting promoter and enhancer repressive chromatin modifications	Homo sapiens	hg19	chr1	33353796	33354196	STAT5B	TMEM54	Enhancer	Repressed	Normal	NA	NA	NA	NA	NA	HC11 Mammary Epithelium	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03307	2011	21527503	Progesterone receptor directly inhibits β-casein gene transcription in mammary epithelial cells through promoting promoter and enhancer repressive chromatin modifications	Homo sapiens	hg19	chr1	33353796	33354196	STAT5B	CSN2	Enhancer	Repressed	Normal	NA	NA	NA	NA	NA	HC11 Mammary Epithelium	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03308	2011	21527503	Progesterone receptor directly inhibits β-casein gene transcription in mammary epithelial cells through promoting promoter and enhancer repressive chromatin modifications	Homo sapiens	hg19	chr1	33353796	33354196	YY1	TMEM54	Enhancer	Repressed	Normal	NA	NA	NA	NA	NA	HC11 Mammary Epithelium	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03309	2011	21527503	Progesterone receptor directly inhibits β-casein gene transcription in mammary epithelial cells through promoting promoter and enhancer repressive chromatin modifications	Homo sapiens	hg19	chr1	33353796	33354196	YY1	CSN2	Enhancer	Repressed	Normal	NA	NA	NA	NA	NA	HC11 Mammary Epithelium	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03310	2014	24915132	Identification of two regulatory elements controlling Fucosyltransferase 7 transcription in murine CD4+ T cells	Mus musculus	mm10	chr2	25423970	25424765	NA	Fut7	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary CD4+ Th1 cells	NA	T helper 1 cell	CL:0000545	Enhancer activity assay; Cis-regulatory interaction assay	Histone modification profiling	Luciferase reporter assay using CNS with intragenic minimal promoter; 5' RACE-PCR; RT-qPCR; Luciferase reporter assay; Reporter assay
E_03311	2011	21527503	Progesterone receptor directly inhibits β-casein gene transcription in mammary epithelial cells through promoting promoter and enhancer repressive chromatin modifications	Mus musculus	mm10	chr5	87705429	87705829	Cebpb	Csn2	Enhancer	Active	Normal	NA	NA	NA	mammary gland	UBERON:0001911	HC11	CVCL_0288	epithelial cell of mammary gland	NA	Enhancer occupancy assay; Chromatin modification assay; Functional hormone-response assay	NA	ChIP-qPCR; prolactin/hydrocortisone/R5020 hormone perturbation; histone-modification ChIP; RT-qPCR; Western blot
E_03312	2011	21527503	Progesterone receptor directly inhibits β-casein gene transcription in mammary epithelial cells through promoting promoter and enhancer repressive chromatin modifications	Mus musculus	mm10	chr5	87705429	87705829	Nr3c1	Csn2	Enhancer	Active	Normal	NA	NA	NA	mammary gland	UBERON:0001911	HC11	CVCL_0288	epithelial cell of mammary gland	NA	Enhancer occupancy assay; Chromatin modification assay; Functional hormone-response assay	NA	ChIP-qPCR; prolactin/hydrocortisone/R5020 hormone perturbation; histone-modification ChIP; RT-qPCR; Western blot
E_03313	2011	21527503	Progesterone receptor directly inhibits β-casein gene transcription in mammary epithelial cells through promoting promoter and enhancer repressive chromatin modifications	Mus musculus	mm10	chr5	87705429	87705829	Pgr	Csn2	Enhancer	Repressed	Normal	NA	NA	NA	mammary gland	UBERON:0001911	HC11	CVCL_0288	epithelial cell of mammary gland	NA	Enhancer occupancy assay; Chromatin modification assay; Functional hormone-response assay	NA	ChIP-qPCR; prolactin/hydrocortisone/R5020 hormone perturbation; histone-modification ChIP; RT-qPCR; Western blot
E_03314	2011	21527503	Progesterone receptor directly inhibits β-casein gene transcription in mammary epithelial cells through promoting promoter and enhancer repressive chromatin modifications	Mus musculus	mm10	chr5	87705429	87705829	Stat5a	Csn2	Enhancer	Active	Normal	NA	NA	NA	mammary gland	UBERON:0001911	HC11	CVCL_0288	epithelial cell of mammary gland	NA	Enhancer occupancy assay; Chromatin modification assay; Functional hormone-response assay	NA	ChIP-qPCR; prolactin/hydrocortisone/R5020 hormone perturbation; histone-modification ChIP; RT-qPCR; Western blot
E_03315	2019	31888703	Enhancer polymorphism rs10865710 associated with traumatic sepsis is a regulator of PPARG gene expression	Homo sapiens	hg19	chr3	12311574	12312573	ATF4	PPARG	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	HEK293T	CVCL_0063	embryonic kidney cell	NA	Enhancer activity assay; TF binding assay	NA	Luciferase reporter assay; EMSA; RT-qPCR; Western blot; Reporter assay
E_03316	2014	24321386	Transcriptional regulation of human ferredoxin reductase through an intronic enhancer in steroidogenic cells	Homo sapiens	hg19	chr17	73746447	73746564	NR5A1	FDXR	Enhancer	Active	Normal	NA	NA	NA	islet of Langerhans	UBERON:0000006	Islet	NA	pancreatic islet cell	NA	Enhancer activity assay	ChIP-seq; microarray	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Reporter assay
E_03317	2013	24324617	Transcriptional activation of Mina by Sp1/3 factors	Mus musculus	mm10	chr16	59471850	59472124	Sp1	Riox2	Enhancer	Active	Disease	Pulmonary Inflammation	NA	NA	lung	UBERON:0002048	EL4	CVCL_0255	NA	NA	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay; RT-qPCR/qPCR
E_03318	2013	24324617	Transcriptional activation of Mina by Sp1/3 factors	Mus musculus	mm10	chr16	59471850	59472124	Sp3	Riox2	Enhancer	Active	Disease	Pulmonary Inflammation	NA	NA	lung	UBERON:0002048	EL4	CVCL_0255	NA	NA	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay; RT-qPCR/qPCR
E_03319	2011	21765417	Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters	Mus musculus	mm10	chr6	124835092	124835618	Ets1	Cd4	Enhancer	Active	Normal	NA	NA	NA	thymus	UBERON:0002370	CD4-positive, CD8-positive thymocyte	NA	double-positive thymocyte	NA	Genome-wide regulatory element profiling	ChIP-seq; Strand-specific RNA-seq; FAIRE-seq	qRT-PCR, and ChIP-qPCR
E_03320	2003	12732147	A global control region defines a chromosomal regulatory landscape containing the HoxD cluster	Homo sapiens	hg19	chr2	176760000	176800000	NA	NA	Enhancer	Active	Normal	NA	NA	NA	limb	UBERON:0002101	embryonic limb tissue	NA	NA	NA	Functional perturbation assay; In vivo enhancer activity assay	NA	Transgenic reporter assay; Southern blot
E_03321	2003	12732147	A global control region defines a chromosomal regulatory landscape containing the HoxD cluster	Mus musculus	mm10	chr2	74460000	74500000	NA	NA	Enhancer	Active	Normal	NA	NA	NA	limb	UBERON:0002101	embryonic limb tissue	NA	NA	NA	Functional perturbation assay; In vivo enhancer activity assay	NA	Transgenic reporter assay; Southern blot; whole-mount in situ hybridization
E_03322	2024	38724692	Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters	Mus musculus	mm10	chr3	34757100	34758037	NA	Sox2	Enhancer	Active	Normal	NA	NA	NA	embryoid body	UBERON:0014374	Pluripotent cells from 21-day mouse embryoid bodies	NA	pluripotent stem cell	CL:0002248	Enhancer activity assay; Disease-variant functional analysis	scRNA-seq, scATAC-seq, MPRA	Single-cell Quantitative Expression Reporter Assay (scQers), Luciferase reporter assay; Reporter assay
E_03323	2024	38724692	Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters	Mus musculus	mm10	chr3	34761100	34762000	NA	Sox2	Enhancer	Active	Normal	NA	NA	NA	embryoid body	UBERON:0014374	Pluripotent cells from 21-day mouse embryoid bodies	NA	pluripotent stem cell	CL:0002248	Enhancer activity assay; Disease-variant functional analysis	scRNA-seq, scATAC-seq, MPRA	Single-cell Quantitative Expression Reporter Assay (scQers), Luciferase reporter assay; Reporter assay
E_03324	2024	38724692	Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters	Mus musculus	mm10	chr3	34757100	34758037	NA	Sox2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	ES-C57BL/6	CVCL_5746	embryonic stem cell	CL:0002322	Enhancer activity assay; Disease-variant functional analysis; Singleton reporter validation	bulk MPRA	Singleton scQer-mCherry reporter assay; FACS; Reporter assay
E_03325	2024	38724692	Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters	Mus musculus	mm10	chr3	34761100	34762000	NA	Sox2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	ES-C57BL/6	CVCL_5746	embryonic stem cell	CL:0002322	Enhancer activity assay; Disease-variant functional analysis; Singleton reporter validation	bulk MPRA	Singleton scQer-mCherry reporter assay; FACS; Reporter assay
E_03326	2018	29358049	Ultraconserved Enhancers Are Required for Normal Development	Mus musculus	mm39	chrX	92353371	92355054	NA	Arx	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	mouse embryonic forebrain	NA	NA	NA	Endogenous enhancer knockout; single and combinatorial enhancer deletion; neurodevelopmental phenotyping	Single-cell transcriptomic profiling (Drop-seq) and expression profiling in selected enhancer-mutant tissues	CRISPR/genome-edited mouse enhancer deletion; histology; neuronal population analysis; structural brain phenotyping; developmental reporter evidence
E_03327	2017	28787589	GATA Factor-Regulated Samd14 Enhancer Confers Red Blood Cell Regeneration and Survival in Severe Anemia	Mus musculus	mm39	chr11	94903148	94903180	NA	Samd14	Enhancer	Active	Disease	anemia	MONDO:0002280	DOID:2355	spleen	UBERON:0002106	splenic stress erythroid progenitors	NA	erythroid progenitor cell	CL:0000038	Functional perturbation assay; Gene expression assay; Stress erythropoiesis assay	NA	TALEN-mediated 33-bp enhancer deletion; RT-qPCR; Flow cytometry; BFU-E/CFU-E colony assay; phenylhydrazine anemia challenge
E_03328	2012	22072553	Identification and characterization of Hoxa9 binding sites in hematopoietic cells	Mus musculus	mm10	chr1	38469166	38512500	Hoxa9	Aff3	Enhancer	Repressed	Disease	Acute Leukemia	NA	DOID:12603	blood	UBERON:0000178	BM Cell	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_03329	2012	22072553	Identification and characterization of Hoxa9 binding sites in hematopoietic cells	Mus musculus	mm10	chr1	38469166	38512500	Meis1	Aff3	Enhancer	Repressed	Disease	Acute Leukemia	NA	DOID:12603	blood	UBERON:0000178	BM Cell	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_03330	2015	25622893	Characterization of the human TCAM1P pseudogene and its activation by a potential dual promoter-enhancer: comparison with a protein-coding mouse orthologue	Homo sapiens	hg19	chr17	61927353	61928827	NA	TCAM1P	Enhancer	Active	Normal	NA	NA	NA	testis	UBERON:0000473	HEK293	CVCL_0045	epithelial cell	CL:0000066	Dual promoter-enhancer reporter characterization; evolutionary regulatory comparison	NA	Bidirectional promoter/enhancer reporter; RT-PCR; deletion/mutational analysis
E_03331	2015	25701871	A large genomic deletion leads to enhancer adoption by the lamin B1 gene: a second path to autosomal dominant adult-onset demyelinating leukodystrophy (ADLD)	Homo sapiens	hg19	chr5	125345378	125345495	NA	LMNB1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HIT DH5A cells (RBC)	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay	NA	Luciferase reporter assay; Reporter assay; 4C
E_03332	2015	25701871	A large genomic deletion leads to enhancer adoption by the lamin B1 gene: a second path to autosomal dominant adult-onset demyelinating leukodystrophy (ADLD)	Homo sapiens	hg19	chr5	125995862	125995972	NA	LMNB1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HIT DH5A cells (RBC)	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay	NA	Luciferase reporter assay; Reporter assay; 4C
E_03333	2013	23321477	Hypoxic adaptation engages the CBP/CREST-induced coactivator complex of Creb-HIF-1α in transactivating murine neuroblastic glucose transporter	Mus musculus	mm10	chr11	119715961	119716245	Hif1a	Slc2a3	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Neuro-2a	CVCL_0470	neuroblastoma cell	NA	Enhancer activity assay	NA	Luciferase reporter assay; ChIP-qPCR; EMSA
E_03334	2013	23321477	Hypoxic adaptation engages the CBP/CREST-induced coactivator complex of Creb-HIF-1α in transactivating murine neuroblastic glucose transporter	Mus musculus	mm10	chr6	122726952	122727236	Creb1	Slc2a3	Enhancer	Active	Normal	NA	NA	NA	NA	NA	N2a	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_03335	2013	23321477	Hypoxic adaptation engages the CBP/CREST-induced coactivator complex of Creb-HIF-1α in transactivating murine neuroblastic glucose transporter	Mus musculus	mm10	chr6	122726952	122727236	Hif1a	Slc2a3	Enhancer	Active	Normal	NA	NA	NA	NA	NA	N2a	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_03336	2013	23321477	Hypoxic adaptation engages the CBP/CREST-induced coactivator complex of Creb-HIF-1α in transactivating murine neuroblastic glucose transporter	Mus musculus	mm10	chr6	122727606	122727632	Creb1	Slc2a3	Enhancer	Active	Normal	NA	NA	NA	NA	NA	N2a	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_03337	2013	23321477	Hypoxic adaptation engages the CBP/CREST-induced coactivator complex of Creb-HIF-1α in transactivating murine neuroblastic glucose transporter	Mus musculus	mm10	chr6	122727606	122727632	Hif1a	Slc2a3	Enhancer	Active	Normal	NA	NA	NA	NA	NA	N2a	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_03338	2015	25622893	Characterization of the human TCAM1P pseudogene and its activation by a potential dual promoter-enhancer: comparison with a protein-coding mouse orthologue	Homo sapiens	hg19	chr17	61927353	61928827	NA	TCAM1P	Enhancer	Active	Normal	NA	NA	NA	testis	UBERON:0000473	HEK293T	CVCL_0063	transformed embryonic kidney-derived cell line	NA	Dual promoter-enhancer activity assay; Transcript characterization assay	NA	RT-PCR; 5-prime RACE; 3-prime RACE; genomic PCR; Luciferase reporter assay; orientation-dependent promoter/enhancer construct analysis
E_03339	2015	25701871	A large genomic deletion leads to enhancer adoption by the lamin B1 gene: a second path to autosomal dominant adult-onset demyelinating leukodystrophy (ADLD)	Homo sapiens	hg19	chr5	125344507	125346243	NA	LMNB1	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	Human embryonic kidney cell	NA	embryonic kidney cell	NA	Enhancer activity assay	NA	Luciferase reporter assay
E_03340	2015	25701871	A large genomic deletion leads to enhancer adoption by the lamin B1 gene: a second path to autosomal dominant adult-onset demyelinating leukodystrophy (ADLD)	Homo sapiens	hg19	chr5	125995897	125996243	NA	LMNB1	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	Human embryonic kidney cell	NA	embryonic kidney cell	NA	Enhancer activity assay	NA	Luciferase reporter assay
E_03341	2026	41629326	A common 19 bp APOE enhancer deletion is protective against Alzheimer's disease in African Americans	Homo sapiens	hg19	chr19	44910240	44910647	NA	APOC1	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	HMC3	CVCL_II76	microglial cell	CL:0000129	Enhancer activity assay; TF binding assay	NA	Luciferase reporter assay; RT-qPCR
E_03342	2020	33147208	A genetic variant controls interferon-β gene expression in human myeloid cells by preventing C/EBP-β binding on a conserved enhancer	Mus musculus	mm10	chr4	88070000	88070500	NA	Ifnb1	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	RAW 264.7	CVCL_0493	macrophage	CL:0000235	Enhancer activity assay; TF binding assay; Disease-variant functional analysis	ChIP-seq	Luciferase reporter assay; ChIP-qPCR
E_03343	2019	30833784	Phase separation of ligand-activated enhancers licenses cooperative chromosomal enhancer assembly	Homo sapiens	hg19	chr21	36200000	36210000	ESR1	NRIP1	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay	ChIP-seq	Luciferase reporter assay
E_03344	2013	23644027	Two novel and functional DNA sequence variants within an upstream enhancer of the human NKX2-5 gene in ventricular septal defects	Homo sapiens	hg19	chr5	17483518	17484083	NA	NKX2-5	Enhancer	Active	Disease	ventricular septal defect	MONDO:0002070	DOID:1657	heart	UBERON:0000948	HEK293	CVCL_0045	embryonic kidney cell	NA	Enhancer activity assay	4C	Luciferase reporter assay
E_03345	2022	34987221	Decoding gene regulation in the fly brain	Drosophila melanogaster	dm6	chr2L	20040500	20041072	ey	sNPF	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	NA	NA	gamma Kenyon cell	NA	In vivo reporter assay	NA	Enhancer-GFP reporter; Site-directed mutagenesis
E_03346	2022	34987221	Decoding gene regulation in the fly brain	Drosophila melanogaster	dm6	chr2R	16905793	16906591	ey	Pkc53E	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	NA	NA	gamma Kenyon cell	NA	In vivo reporter assay	NA	Enhancer-GFP reporter; Site-directed mutagenesis
E_03347	2022	34987221	Decoding gene regulation in the fly brain	Drosophila melanogaster	dm6	chr2R	19127550	19127921	ey	CG15117	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	NA	NA	gamma Kenyon cell	NA	In vivo reporter assay	NA	Enhancer-GFP reporter; Site-directed mutagenesis
E_03348	2022	34987221	Decoding gene regulation in the fly brain	Drosophila melanogaster	dm6	chr3R	16286178	16286811	ey	gish	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	NA	NA	gamma Kenyon cell	NA	In vivo reporter assay	NA	Enhancer-GFP reporter; Site-directed mutagenesis
E_03349	2022	34987221	Decoding gene regulation in the fly brain	Drosophila melanogaster	dm6	chrX	534837	535834	ey	Appl	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	NA	NA	gamma Kenyon cell	NA	In vivo reporter assay	NA	Enhancer-GFP reporter; Site-directed mutagenesis
E_03350	2022	34987221	Decoding gene regulation in the fly brain	Drosophila melanogaster	dm6	chrX	18554916	18555296	ey	Bx	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	NA	NA	gamma Kenyon cell	NA	In vivo reporter assay	NA	Enhancer-GFP reporter; Site-directed mutagenesis
E_03351	2022	34987221	Decoding gene regulation in the fly brain	Drosophila melanogaster	dm6	chr2L	20040500	20041072	Mef2	sNPF	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	NA	NA	gamma Kenyon cell	NA	In vivo reporter assay	NA	Enhancer-GFP reporter; Site-directed mutagenesis
E_03352	2022	34987221	Decoding gene regulation in the fly brain	Drosophila melanogaster	dm6	chr2L	20040500	20041072	onecut	sNPF	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	NA	NA	gamma Kenyon cell	NA	In vivo reporter assay	NA	Enhancer-GFP reporter; Site-directed mutagenesis
E_03353	2022	34987221	Decoding gene regulation in the fly brain	Drosophila melanogaster	dm6	chr2L	20040500	20041072	sr	sNPF	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	NA	NA	gamma Kenyon cell	NA	In vivo reporter assay	NA	Enhancer-GFP reporter; Site-directed mutagenesis
E_03354	2022	34987221	Decoding gene regulation in the fly brain	Drosophila melanogaster	dm6	chr2R	16905793	16906591	onecut	Pkc53E	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	NA	NA	gamma Kenyon cell	NA	In vivo reporter assay	NA	Enhancer-GFP reporter; Site-directed mutagenesis
E_03355	2022	34987221	Decoding gene regulation in the fly brain	Drosophila melanogaster	dm6	chr2R	16905793	16906591	toy	Pkc53E	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	NA	NA	gamma Kenyon cell	NA	In vivo reporter assay	NA	Enhancer-GFP reporter; Site-directed mutagenesis
E_03356	2022	34987221	Decoding gene regulation in the fly brain	Drosophila melanogaster	dm6	chr2R	19127550	19127921	Mef2	CG15117	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	NA	NA	gamma Kenyon cell	NA	In vivo reporter assay	NA	Enhancer-GFP reporter; Site-directed mutagenesis
E_03357	2022	34987221	Decoding gene regulation in the fly brain	Drosophila melanogaster	dm6	chr2R	19127550	19127921	onecut	CG15117	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	NA	NA	gamma Kenyon cell	NA	In vivo reporter assay	NA	Enhancer-GFP reporter; Site-directed mutagenesis
E_03358	2022	34987221	Decoding gene regulation in the fly brain	Drosophila melanogaster	dm6	chr3R	16286178	16286811	Mef2	gish	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	NA	NA	gamma Kenyon cell	NA	In vivo reporter assay	NA	Enhancer-GFP reporter; Site-directed mutagenesis
E_03359	2022	34987221	Decoding gene regulation in the fly brain	Drosophila melanogaster	dm6	chr3R	16286178	16286811	onecut	gish	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	NA	NA	gamma Kenyon cell	NA	In vivo reporter assay	NA	Enhancer-GFP reporter; Site-directed mutagenesis
E_03360	2022	34987221	Decoding gene regulation in the fly brain	Drosophila melanogaster	dm6	chrX	534837	535834	onecut	Appl	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	NA	NA	gamma Kenyon cell	NA	In vivo reporter assay	NA	Enhancer-GFP reporter; Site-directed mutagenesis
E_03361	2022	34987221	Decoding gene regulation in the fly brain	Drosophila melanogaster	dm6	chrX	534837	535834	toy	Appl	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	NA	NA	gamma Kenyon cell	NA	In vivo reporter assay	NA	Enhancer-GFP reporter; Site-directed mutagenesis
E_03362	2022	34987221	Decoding gene regulation in the fly brain	Drosophila melanogaster	dm6	chrX	18554916	18555296	lola	Bx	Enhancer	Repressed	Normal	NA	NA	NA	brain	UBERON:0000955	NA	NA	gamma Kenyon cell	NA	In vivo reporter assay	NA	Enhancer-GFP reporter; Site-directed mutagenesis
E_03363	2022	34987221	Decoding gene regulation in the fly brain	Drosophila melanogaster	dm6	chrX	18554916	18555296	mamo	Bx	Enhancer	Repressed	Normal	NA	NA	NA	brain	UBERON:0000955	NA	NA	gamma Kenyon cell	NA	In vivo reporter assay	NA	Enhancer-GFP reporter; Site-directed mutagenesis
E_03364	2022	34987221	Decoding gene regulation in the fly brain	Drosophila melanogaster	dm6	chrX	18554916	18555296	Mef2	Bx	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	NA	NA	gamma Kenyon cell	NA	In vivo reporter assay	NA	Enhancer-GFP reporter; Site-directed mutagenesis
E_03365	2022	34987221	Decoding gene regulation in the fly brain	Drosophila melanogaster	dm6	chrX	18554916	18555296	onecut	Bx	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	NA	NA	gamma Kenyon cell	NA	In vivo reporter assay	NA	Enhancer-GFP reporter; Site-directed mutagenesis
E_03366	2022	34987221	Decoding gene regulation in the fly brain	Drosophila melanogaster	dm6	chrX	18554916	18555296	sr	Bx	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	NA	NA	gamma Kenyon cell	NA	In vivo reporter assay	NA	Enhancer-GFP reporter; Site-directed mutagenesis
E_03367	2022	34987221	Decoding gene regulation in the fly brain	Drosophila melanogaster	dm6	chr3L	9193218	9194041	ey	Rdl	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	NA	NA	gamma Kenyon cell	NA	In vivo reporter assay	NA	Enhancer-GFP reporter
E_03368	2022	34987221	Decoding gene regulation in the fly brain	Drosophila melanogaster	dm6	chr3L	9193218	9194041	Mef2	Rdl	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	NA	NA	gamma Kenyon cell	NA	In vivo reporter assay	NA	Enhancer-GFP reporter
E_03369	2013	23644027	Two novel and functional DNA sequence variants within an upstream enhancer of the human NKX2-5 gene in ventricular septal defects	Homo sapiens	hg19	chr5	172648612	172649177	NA	NKX2-5	Enhancer	Active	Disease	Congenital Heart Disease	NA	DOID:1682	heart	UBERON:0000948	Leukocytes	NA	NA	NA	Enhancer activity assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay
E_03370	2020	32732264	Cross-species analysis of enhancer logic using deep learning	Homo sapiens	hg19	chr6	396135	396636	NA	IRF4	Enhancer	Active	Disease	cutaneous melanoma	MONDO:0005012	DOID:8923	zone of skin	UBERON:0000014	Human melanoma cells	NA	melanoma cell	NA	Enhancer activity assay	MPRA; ATAC-seq; RNA-seq	In silico saturation mutagenesis
E_03371	2020	32318854	Evidence for craniofacial enhancer variation underlying nonsyndromic cleft lip and palate	Homo sapiens	hg19	chr4	4756237	4758006	LEF1	MSX1	Enhancer	Active	Disease	nonsyndromic cleft lip with or without cleft palate	MONDO:0019338	DOID:0060289	cerebellum	UBERON:0002037	Human NSCLP proband blood DNA	NA	craniofacial developmental enhancer	NA	Enhancer variant association study; Functional enhancer validation	Targeted amplicon sequencing (Illumina MiSeq)	VISTA mouse enhancer reporter assay
E_03372	2020	32318854	Evidence for craniofacial enhancer variation underlying nonsyndromic cleft lip and palate	Homo sapiens	hg19	chr4	4756237	4758006	TCF4	MSX1	Enhancer	Active	Disease	nonsyndromic cleft lip with or without cleft palate	MONDO:0019338	DOID:0060289	cerebellum	UBERON:0002037	Human NSCLP proband blood DNA	NA	craniofacial developmental enhancer	NA	Enhancer variant association study; Functional enhancer validation	Targeted amplicon sequencing (Illumina MiSeq)	VISTA mouse enhancer reporter assay
E_03373	2020	32318854	Evidence for craniofacial enhancer variation underlying nonsyndromic cleft lip and palate	Homo sapiens	hg19	chr4	124383428	124386454	MEF2A	SPRY1	Enhancer	Active	Disease	nonsyndromic cleft lip with or without cleft palate	MONDO:0019338	DOID:0060289	cerebellum	UBERON:0002037	Human NSCLP proband blood DNA	NA	craniofacial developmental enhancer	NA	Enhancer variant association study; Functional enhancer validation	Targeted amplicon sequencing (Illumina MiSeq)	VISTA mouse enhancer reporter assay
E_03374	2017	27333824	Regulation of Laminin γ2 Expression by CDX2 in Colonic Epithelial Cells Is Impaired During Active Inflammation	Homo sapiens	hg19	chr1	183149939	183150336	RELA	LAMC2	Enhancer	Active	Normal	NA	NA	NA	colon	UBERON:0001155	Human normal colon epithelial cell	NA	colon epithelial cell	CL:0011108	Enhancer activity assay; TF binding assay	ChIP-seq	Luciferase reporter assay; ChIP; shRNA knockdown
E_03375	2015	25786345	p53-dependent expression of CXCR5 chemokine receptor in MCF-7 breast cancer cells	Homo sapiens	hg19	chr11	118767466	118769582	NFASC	CXCR5	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03376	2013	23184392	Selection of a common multipotent cardiovascular stem cell using the 3.4-kb MesP1 promoter fragment	Homo sapiens	hg19	chr15	90288698	90290698	NA	MESP1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_03377	1991	1827138	Cloning of murine TCF-1, a T cell-specific transcription factor interacting with functional motifs in the CD3-epsilon and T cell receptor alpha enhancers	Mus musculus	mm10	chr11	105000000	105000100	Tcf7	Cd3e	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	EL4	CVCL_0255	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay	NA	EMSA, Luciferase reporter assay
E_03378	1991	1827138	Cloning of murine TCF-1, a T cell-specific transcription factor interacting with functional motifs in the CD3-epsilon and T cell receptor alpha enhancers	Mus musculus	mm10	chr14	54000000	54000100	Tcf7	Tcra	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	EL4	CVCL_0255	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay	NA	EMSA, Luciferase reporter assay
E_03379	2017	27333824	Regulation of Laminin γ2 Expression by CDX2 in Colonic Epithelial Cells Is Impaired During Active Inflammation	Homo sapiens	hg19	chr1	183149939	183150336	CDX2	LAMC2	Enhancer	Active	Normal	NA	NA	NA	small intestine	UBERON:0002108	Intestinal Epithelial Cell	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03380	2018	30568279	High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human	Homo sapiens	hg19	chr14	106327635	106328903	NA	IGHE	Enhancer	Active	Normal	NA	NA	NA	NA	NA	GM12878	CVCL_7526	B cell	CL:0000236	Enhancer activity assay; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03381	2018	30568279	High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human	Homo sapiens	hg19	chr9	126900000	126900625	NA	NEK6	Enhancer	Active	Normal	NA	NA	NA	NA	NA	GM12878	CVCL_7526	B cell	CL:0000236	Enhancer activity assay; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03382	2018	30568279	High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human	Homo sapiens	hg19	chr9	126964375	126965000	NA	NEK6	Enhancer	Active	Normal	NA	NA	NA	NA	NA	GM12878	CVCL_7526	B cell	CL:0000236	Enhancer activity assay; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03383	2018	30568279	High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human	Homo sapiens	hg19	chr9	126980625	126981125	NA	NEK6	Enhancer	Active	Normal	NA	NA	NA	NA	NA	GM12878	CVCL_7526	B cell	CL:0000236	Enhancer activity assay; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03384	2018	30568279	High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human	Homo sapiens	hg19	chr9	127001250	127001875	NA	NEK6	Enhancer	Active	Normal	NA	NA	NA	NA	NA	GM12878	CVCL_7526	B cell	CL:0000236	Enhancer activity assay; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03385	2018	30568279	High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human	Homo sapiens	hg19	chr9	127047500	127048375	NA	NEK6	Enhancer	Active	Normal	NA	NA	NA	NA	NA	GM12878	CVCL_7526	B cell	CL:0000236	Enhancer activity assay; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03386	2011	21494683	Genetic and metabolic characterization of insomnia	Homo sapiens	hg19	chr1	64083756	64083861	PAX6	ROR1	Enhancer	Active	Disease	Insomnia	NA	NA	NA	NA	SK-N-MC	CVCL_0530	NA	NA	TF-binding/chromatin assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	ChIP-seq	ChIP-qPCR/ChIP
E_03387	2011	21494683	Genetic and metabolic characterization of insomnia	Homo sapiens	hg19	chr1	64087305	64087660	PAX6	ROR1	Enhancer	Active	Disease	Insomnia	NA	NA	NA	NA	SK-N-MC	CVCL_0530	NA	NA	TF-binding/chromatin assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	ChIP-seq	ChIP-qPCR/ChIP
E_03388	2011	21494683	Genetic and metabolic characterization of insomnia	Homo sapiens	hg19	chr20	8684437	8686556	PAX6	PLCB1	Enhancer	Active	Disease	Insomnia	NA	NA	NA	NA	SK-N-MC	CVCL_0530	NA	NA	TF-binding/chromatin assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	ChIP-seq	ChIP-qPCR/ChIP
E_03389	2011	21494683	Genetic and metabolic characterization of insomnia	Homo sapiens	hg19	chr20	8687417	8688741	PAX6	PLCB1	Enhancer	Active	Disease	Insomnia	NA	NA	NA	NA	SK-N-MC	CVCL_0530	NA	NA	TF-binding/chromatin assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	ChIP-seq	ChIP-qPCR/ChIP
E_03390	2011	21494683	Genetic and metabolic characterization of insomnia	Homo sapiens	hg19	chr20	8718344	8719933	PAX6	PLCB1	Enhancer	Active	Disease	Insomnia	NA	NA	NA	NA	SK-N-MC	CVCL_0530	NA	NA	TF-binding/chromatin assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	ChIP-seq	ChIP-qPCR/ChIP
E_03391	2007	17277777	Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome	Homo sapiens	hg17	chr21	34091200	34091900	STAT1	NA	Enhancer	Active	Normal	NA	NA	NA	uterine cervix	UBERON:0000002	HeLa	CVCL_0030	epithelial cell	CL:0000066	Enhancer activity assay; TF binding assay; chromatin-signature enhancer validation	ChIP-chip; DNase-chip; gene expression microarray	IFN-gamma stimulation; STAT1 ChIP-chip; quantitative PCR validation; transient transfection; pGL3 luciferase enhancer reporter assay
E_03392	2007	17277777	Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome	Homo sapiens	hg17	chr5	131790596	131791596	STAT1	NA	Enhancer	Active	Normal	NA	NA	NA	uterine cervix	UBERON:0000002	HeLa	CVCL_0030	epithelial cell	CL:0000066	Enhancer activity assay; TF binding assay; chromatin-signature enhancer validation	ChIP-chip; DNase-chip; gene expression microarray	IFN-gamma stimulation; STAT1 ChIP-chip; quantitative PCR validation; transient transfection; pGL3 luciferase enhancer reporter assay
E_03393	2007	17277777	Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome	Homo sapiens	hg17	chr7	115940408	115941408	STAT1	NA	Enhancer	Active	Normal	NA	NA	NA	uterine cervix	UBERON:0000002	HeLa	CVCL_0030	epithelial cell	CL:0000066	Enhancer activity assay; TF binding assay; chromatin-signature enhancer validation	ChIP-chip; DNase-chip; gene expression microarray	IFN-gamma stimulation; STAT1 ChIP-chip; quantitative PCR validation; transient transfection; pGL3 luciferase enhancer reporter assay
E_03394	2007	17277777	Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome	Homo sapiens	hg17	chr9	129175952	129176952	STAT1	NA	Enhancer	Active	Normal	NA	NA	NA	uterine cervix	UBERON:0000002	HeLa	CVCL_0030	epithelial cell	CL:0000066	Enhancer activity assay; TF binding assay; chromatin-signature enhancer validation	ChIP-chip; DNase-chip; gene expression microarray	IFN-gamma stimulation; STAT1 ChIP-chip; quantitative PCR validation; transient transfection; pGL3 luciferase enhancer reporter assay
E_03395	2007	17277777	Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome	Homo sapiens	hg38	chr5	131784000	131784700	NA	SLC22A5	Enhancer	Active	Normal	NA	NA	NA	uterine cervix	UBERON:0000002	HeLa	CVCL_0030	malignant cell	CL:0001064	Enhancer activity assay	ChIP-chip	Luciferase reporter assay; RT-qPCR
E_03396	2007	17277777	Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome	Homo sapiens	hg17	chr5	130999000	131001000	EP300	SLC22A5	Enhancer	Active	Normal	NA	NA	NA	uterine cervix	UBERON:0000002	HeLa	CVCL_0030	epithelial cell	CL:0000066	Enhancer activity assay	ChIP-chip	Luciferase reporter assay
E_03397	2015	27602360	Polymorphism within a Neuronal Activity-Dependent Enhancer of NgR1 Is Associated with Corpus Callosum Morphology in Humans	Homo sapiens	hg19	chr22	20224442	20228467	MYBL2	RTN4R	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	NT2/D1	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay; Genetic-variant functional analysis	NA	Luciferase reporter assay; Reporter assay; EMSA/gel-shift assay
E_03398	2011	21385855	A 3-bp deletion in the HBS1L-MYB intergenic region on chromosome 6q23 is associated with HbF expression	Homo sapiens	hg19	chr6	135459326	135461326	NA	HBG2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03399	2011	21385855	A 3-bp deletion in the HBS1L-MYB intergenic region on chromosome 6q23 is associated with HbF expression	Homo sapiens	hg19	chr6	135459326	135461326	RUNX1	HBG2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03400	2015	27602360	Polymorphism within a Neuronal Activity-Dependent Enhancer of NgR1 Is Associated with Corpus Callosum Morphology in Humans	Homo sapiens	hg19	chr22	20224442	20228467	NA	RTN4R	Enhancer	Repressed	Normal	NA	NA	NA	brain	UBERON:0000955	Neuronal	NA	neuronal cell	NA	Enhancer activity assay	ChIP-seq	Luciferase reporter assay
E_03401	2015	25582196	Dynamic switching of active promoter and enhancer domains regulates Tet1 and Tet2 expression during cell state transitions between pluripotency and differentiation	Mus musculus	mm10	chr10	62893206	62923461	Pou5f1	Tet1	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_03402	2015	25582196	Dynamic switching of active promoter and enhancer domains regulates Tet1 and Tet2 expression during cell state transitions between pluripotency and differentiation	Mus musculus	mm10	chr10	62893206	62923461	Sox2	Tet1	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_03403	2015	25582196	Dynamic switching of active promoter and enhancer domains regulates Tet1 and Tet2 expression during cell state transitions between pluripotency and differentiation	Mus musculus	mm10	chr3	133531418	133563926	Pou5f1	Tet2	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_03404	2015	25582196	Dynamic switching of active promoter and enhancer domains regulates Tet1 and Tet2 expression during cell state transitions between pluripotency and differentiation	Mus musculus	mm10	chr3	133531418	133563926	Sox2	Tet2	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_03405	2017	28751304	A lipodystrophy-causing lamin A mutant alters conformation and epigenetic regulation of the anti-adipogenic MIR335 locus	Homo sapiens	hg19	chr7	129854050	129895632	NA	MIR335	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Adipose Progenitor Cell	NA	NA	NA	Chromatin interaction assay; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	ChIP-qPCR/ChIP
E_03406	2016	26818267	Utility of next-generation RNA-sequencing in identifying chimeric transcription involving human endogenous retroviruses	Homo sapiens	hg19	chr22	18897006	18899006	NA	PRODH	Enhancer	Active	Disease	diffuse large B-cell lymphoma	MONDO:0018905	DOID:0050745	blood	UBERON:0000178	DLBCL cells	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03407	2013	23154183	Regulation of cooperative function of the Il12b enhancer and promoter by the interferon regulatory factors 3 and 5	Mus musculus	mm10	chr11	44390063	44390123	Irf4	Il12b	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HEK293	CVCL_0045	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03408	2013	24391766	A novel SP1/SP3 dependent intronic enhancer governing transcription of the UCP3 gene in brown adipocytes	Mus musculus	mm10	chr7	100474191	100474841	Sp1	Ucp3	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Platinum E cells	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_03409	2013	24391766	A novel SP1/SP3 dependent intronic enhancer governing transcription of the UCP3 gene in brown adipocytes	Mus musculus	mm10	chr7	100474191	100474841	Sp3	Ucp3	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Platinum E cells	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_03410	2012	22378757	NEUROG3 is a critical downstream effector for STAT3-regulated differentiation of mammalian stem and progenitor spermatogonia	Mus musculus	mm10	chr10	62128342	62130342	Stat3	Neurog3	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Germ Cell	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03411	2012	22396734	Mapping and functional characterisation of a CTCF-dependent insulator element at the 3' border of the murine Scl transcriptional domain	Mus musculus	mm10	chr4	115100426	115102426	Ctcf	Tal1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	416B	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_03412	2007	17803355	Deletion of ultraconserved elements yields viable mice	Mus musculus	mm39	chrX	92353371	92355054	NA	Arx	Enhancer	Active	Normal	NA	NA	NA	forebrain	UBERON:0001890	mouse embryo	NA	NA	NA	Endogenous ultraconserved enhancer deletion; in vivo phenotyping	NA	Targeted mouse deletion; viability and developmental phenotyping; prior transgenic enhancer activity evidence
E_03413	2001	11263787	Activation of a fibroblast-specific enhancer of the proalpha2(I) collagen gene in tight-skin mice	Mus musculus	mm10	chr6	122481665	122483665	NA	Col1a2	Enhancer	Active	Disease	scleroderma	MONDO:0019340	DOID:419	zone of skin	UBERON:0000014	Dermal Fibroblast	NA	dermal fibroblast	NA	Enhancer activity assay	NA	Transgenic reporter assay; Luciferase reporter assay
E_03414	2001	11263787	Activation of a fibroblast-specific enhancer of the proalpha2(I) collagen gene in tight-skin mice	Mus musculus	mm10	chr6	122479265	122485265	NA	Col1a2	Enhancer	Active	Disease	scleroderma	MONDO:0019340	DOID:419	zone of skin	UBERON:0000014	Dermal Fibroblast	NA	dermal fibroblast	NA	Enhancer activity assay	NA	Transgenic reporter assay; Luciferase reporter assay
E_03415	2018	28971975	TBX4 is involved in the super-enhancer-driven transcriptional programs underlying features specific to lung fibroblasts	Homo sapiens	hg38	chr17	61449600	61451600	NA	TBX4	Enhancer	Active	Normal	NA	NA	NA	lung	UBERON:0002048	Lung fibroblasts	NA	lung fibroblast	NA	Chromatin interaction assay; Super-enhancer functional study	RNA-seq	3C; RT-qPCR
E_03416	2015	26300977	A chromosomal rearrangement in a child with severe speech and language disorder separates FOXP2 from a functional enhancer	Homo sapiens	hg19	chr7	114541370	114542201	NA	FOXP2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay	ChIP-seq	Luciferase reporter assay
E_03417	2015	26416282	Engagement of the Aryl Hydrocarbon Receptor in Mycobacterium tuberculosis-Infected Macrophages Has Pleiotropic Effects on Innate Immune Signaling	Homo sapiens	hg19	chr12	56728500	56735000	AHR	IL23A	Enhancer	Active	Disease	tuberculosis / Mycobacterium tuberculosis infection	NA	NA	blood	UBERON:0000178	THP-1	CVCL_0006	monocyte	CL:0000576	Macrophage enhancer chromatin profiling; direct AHR enhancer binding; infection-responsive transcriptional regulation; AHR perturbation	Macrophage transcriptome profiling; ChIP-seq	ChIP; AHR depletion/knockdown; RT-qPCR; M. tuberculosis infection assays
E_03418	2015	26416282	Engagement of the Aryl Hydrocarbon Receptor in Mycobacterium tuberculosis-Infected Macrophages Has Pleiotropic Effects on Innate Immune Signaling	Homo sapiens	hg19	chr12	56728500	56735000	AHR	IL23A	Enhancer	Active	Disease	tuberculosis / Mycobacterium tuberculosis infection	NA	NA	blood	UBERON:0000178	human and mouse macrophage validation	NA	macrophage	CL:0000235	Macrophage enhancer chromatin profiling; direct AHR enhancer binding; infection-responsive transcriptional regulation; AHR perturbation	Macrophage transcriptome profiling; ChIP-seq	ChIP; AHR depletion/knockdown; RT-qPCR; M. tuberculosis infection assays
E_03419	2013	23024062	Regulation of cytotoxic T lymphocyte antigen 4 by cyclic AMP	Mus musculus	mm10	chr1	60908875	60908895	Creb1	Ctla4	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	T Cell	NA	T cell	CL:0000084	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03420	2010	20686566	From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus	Homo sapiens	hg19	chr1	109816874	109818905	NA	SORT1	Enhancer	Active	Disease	myocardial infarction susceptibility / LDL-cholesterol trait	NA	NA	liver	UBERON:0002107	primary human hepatocytes	NA	hepatocyte	CL:0000182	Disease-variant functional analysis; Enhancer activity; TF-binding mechanism; in vivo target-gene perturbation	Human GWAS/eQTL and liver expression-genetics integration	Allele-specific transcriptional activity assays; C/EBP binding analysis; siRNA knockdown; viral Sort1 overexpression/knockdown in mouse liver; plasma lipid phenotyping
E_03421	2013	23659698	Finding of IFNγ gene enhancers and their core sequences	Homo sapiens	hg19	chr12	68546200	68546440	NA	IFNG	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary T cells	NA	T cell	CL:0000084	Enhancer activity assay	NA	Luciferase reporter assay
E_03422	2013	23659698	Finding of IFNγ gene enhancers and their core sequences	Homo sapiens	hg19	chr12	21439733	21439973	NA	IFNG	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HeLa	CVCL_0030	NA	NA	Enhancer activity assay	NA	3C
E_03423	2013	23659698	Finding of IFNγ gene enhancers and their core sequences	Homo sapiens	hg19	chr12	68549287	68549545	NA	IFNG	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HeLa	CVCL_0030	NA	NA	Enhancer activity assay	NA	3C
E_03424	2013	23659698	Finding of IFNγ gene enhancers and their core sequences	Homo sapiens	hg19	chr12	68549796	68550055	NA	IFNG	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HeLa	CVCL_0030	NA	NA	Enhancer activity assay	NA	3C
E_03425	2013	23659698	Finding of IFNγ gene enhancers and their core sequences	Homo sapiens	hg19	chr12	68553503	68553754	NA	IFNG	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HeLa	CVCL_0030	NA	NA	Enhancer activity assay	NA	3C
E_03426	2013	23659698	Finding of IFNγ gene enhancers and their core sequences	Homo sapiens	hg19	chr12	68553762	68554012	NA	IFNG	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HeLa	CVCL_0030	NA	NA	Enhancer activity assay	NA	3C
E_03427	2013	23659698	Finding of IFNγ gene enhancers and their core sequences	Homo sapiens	hg19	chr12	68544280	68544520	NA	IFNG	Enhancer	Active	Normal	NA	NA	NA	uterine cervix	UBERON:0000002	HeLa	CVCL_0030	malignant cell	CL:0001064	Enhancer activity assay	NA	Luciferase reporter assay
E_03428	2018	29227829	A long noncoding RNA from the HBS1L-MYB intergenic region on chr6q23 regulates human fetal hemoglobin expression	Homo sapiens	hg38	chr6	135096362	135097644	NA	MYB	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	HUDEP-2 and primary CD34+-derived erythroblasts	NA	erythroblast	CL:0000765	Enhancer-associated lncRNA functional assay; Regulatory-locus perturbation assay	ENCODE RNA polymerase II/transcript data integration	5-prime/3-prime RACE; RT-PCR; qRT-PCR; siRNA knockdown; Western blot; erythroid differentiation assays
E_03429	2015	26110280	An insulator element located at the cyclin B1 interacting protein 1 gene locus is highly conserved among mammalian species	Mus musculus	mm10	chr14	50787449	50787634	NA	Ccnb1ip1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Mitotic Cell	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03430	2014	25153150	Identification and characterization of germ cell genes expressed in the F9 testicular teratoma stem cell line	Mus musculus	mm10	chrX	140806807	140808327	NA	Tex13b	Enhancer	Repressed	Normal	NA	NA	NA	NA	NA	F9	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP
E_03431	2011	21355081	The A/G allele of rs16906252 predicts for MGMT methylation and is selectively silenced in premalignant lesions from smokers and in lung adenocarcinomas	Homo sapiens	hg19	chr10	131265598	131265656	NA	MGMT	Enhancer	Inactive	Disease	lung adenocarcinoma	MONDO:0005061	DOID:3910	lung	UBERON:0002048	Human Bronchial Epithelial Cell,Lung cancer-derived Cell Lines,Glioblastoma Cell Lines	NA	malignant cell	CL:0001064	Enhancer activity assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay
E_03432	2025	39889913	Enhancer RNA from STAT3 locus affects temozolomide chemoresistance of glioblastoma cells	Homo sapiens	hg38	chr17	42409879	42412035	NA	STAT3	Enhancer	Active	Disease	pancreatic ductal adenocarcinoma	MONDO:0005184	DOID:3498	pancreas	UBERON:0001264	PANC-1	CVCL_0480	malignant cell	CL:0001064	Enhancer activity assay	NA	Luciferase reporter assay; RT-qPCR; Reporter assay
E_03433	2022	35918310	A common deletion at BAK1 reduces enhancer activity and confers risk of intracranial germ cell tumors	Homo sapiens	hg19	chr6	33548076	33548616	NA	BAK1	Enhancer	Active	Disease	intracranial germ cell tumor	MONDO:0003000	DOID:4439	kidney	UBERON:0002113	HEK293T	CVCL_0063	transformed embryonic kidney-derived cell	NA	Disease-associated enhancer activity assay; Allele-specific enhancer activity assay; Functional variant validation	Genome-wide association study; Genotype imputation; GTEx eQTL analysis	NanoLuc/Firefly dual-luciferase reporter assay; Sanger sequencing; Reporter assay
E_03434	2015	25522777	Salinomycin inhibits hepatocellular carcinoma cell invasion and migration through JNK/JunD pathway-mediated MMP9 expression	Homo sapiens	hg19	chr20	44639323	44641625	NA	MMP9	Enhancer	Repressed	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	HCCLM3	CVCL_6832	malignant cell	CL:0001064	Enhancer activity assay	NA	Luciferase reporter assay; RT-qPCR; Luciferase reporter assay; Reporter assay
E_03435	2015	25522777	Salinomycin inhibits hepatocellular carcinoma cell invasion and migration through JNK/JunD pathway-mediated MMP9 expression	Homo sapiens	hg19	chr20	44637014	44637468	JUND	MMP9	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	NA	NA	Hepatocellular Carcinoma	NA	malignant cell	CL:0001064	Enhancer activity assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; Western blot
E_03436	2012	22323542	A new hypersensitive site, HS10, and the enhancers, E3' and Ed, differentially regulate Igκ gene expression	Mus musculus	mm9	chr6	70675569	70676084	NA	Igkc	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	MPC-11	CVCL_3857	plasma cell	CL:0000786	Enhancer activity assay	NA	DNase I hypersensitivity assay; Luciferase reporter assay; transient transfection; RT-PCR
E_03437	2012	22323542	A new hypersensitive site, HS10, and the enhancers, E3' and Ed, differentially regulate Igκ gene expression	Mus musculus	mm9	chr6	70685249	70686058	NA	Igkc	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	MPC-11	CVCL_3857	plasma cell	CL:0000786	Enhancer activity assay	NA	DNase I hypersensitivity assay; Luciferase reporter assay; transient transfection; RT-PCR
E_03438	2012	22323542	A new hypersensitive site, HS10, and the enhancers, E3' and Ed, differentially regulate Igκ gene expression	Mus musculus	mm9	chr6	70693703	70694944	NA	Igkc	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	MPC-11	CVCL_3857	plasma cell	CL:0000786	Enhancer activity assay	NA	DNase I hypersensitivity assay; Luciferase reporter assay; transient transfection; RT-PCR
E_03439	2012	22323542	A new hypersensitive site, HS10, and the enhancers, E3' and Ed, differentially regulate Igκ gene expression	Mus musculus	mm9	chr6	70713757	70715084	NA	Igkc	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	MPC-11	CVCL_3857	plasma cell	CL:0000786	Enhancer co-activator assay; DNase I hypersensitivity assay	NA	DNase I hypersensitivity assay; Luciferase reporter assay; transient transfection; RT-PCR
E_03440	2012	22323542	A new hypersensitive site, HS10, and the enhancers, E3' and Ed, differentially regulate Igκ gene expression	Mus musculus	mm10	chr6	70763764	70765090	NA	Igk	Enhancer	Active	Normal	NA	NA	NA	NA	NA	S194,MPC-11	NA	NA	NA	Enhancer activity assay	NA	Luciferase reporter assay; Reporter assay
E_03441	2012	22323542	A new hypersensitive site, HS10, and the enhancers, E3' and Ed, differentially regulate Igκ gene expression	Mus musculus	mm10	chr6	70725576	70726090	NA	Igk	Enhancer	Active	Normal	NA	NA	NA	NA	NA	S194,MPC-11	NA	NA	NA	Enhancer activity assay	NA	Luciferase reporter assay; Reporter assay
E_03442	2012	22323542	A new hypersensitive site, HS10, and the enhancers, E3' and Ed, differentially regulate Igκ gene expression	Mus musculus	mm10	chr6	70743710	70744950	NA	Igk	Enhancer	Active	Normal	NA	NA	NA	NA	NA	S194,MPC-11	NA	NA	NA	Enhancer activity assay	NA	Luciferase reporter assay; Reporter assay
E_03443	2012	22323542	A new hypersensitive site, HS10, and the enhancers, E3' and Ed, differentially regulate Igκ gene expression	Mus musculus	mm10	chr6	70735256	70736064	NA	Igk	Enhancer	Active	Normal	NA	NA	NA	NA	NA	S194,MPC-11	NA	NA	NA	Enhancer activity assay	NA	Luciferase reporter assay; Reporter assay
E_03444	2014	24916375	Human skin color is influenced by an intergenic DNA polymorphism regulating transcription of the nearby BNC2 pigmentation gene	Homo sapiens	hg19	chr9	124638991	124641160	NA	BNC2	Enhancer	Active	Normal	NA	NA	NA	skin	UBERON:0002097	LP89	NA	NA	NA	TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_03445	2011	21378152	TGF-beta1 reduces Wilms' tumor suppressor gene expression in podocytes	Homo sapiens	hg19	chr11	32403489	32405489	SMAD4	WT1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Human Podocyte Cell Line AB8/13	NA	NA	NA	Enhancer activity assay	NA	Luciferase reporter assay; Reporter assay; RT-qPCR/qPCR
E_03446	2014	24916375	Human skin color is influenced by an intergenic DNA polymorphism regulating transcription of the nearby BNC2 pigmentation gene	Homo sapiens	hg19	chr9	16857980	16858579	NA	BNC2	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Primary neurons	NA	neuron	CL:0000540	Enhancer activity assay; Disease-variant functional analysis	NA	Luciferase reporter assay
E_03447	2018	29979962	A Muscle-Specific Enhancer RNA Mediates Cohesin Recruitment and Regulates Transcription In trans	Mus musculus	mm10	chr7	46371356	46373481	NA	Myod1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	C2C12	CVCL_0188	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	ChIP-qPCR/ChIP; RT-qPCR/qPCR; Western blot
E_03448	2015	25523606	Blood group B gene is barely expressed in in vitro erythroid culture of Bm-derived CD34+ cells without an erythroid cell-specific regulatory element	Homo sapiens	hg38	chr9	133267998	133270594	GATA2	ABO	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Bm-derived and control CD34+ erythroid cultures	NA	erythroid progenitor cell	CL:0000038	TF binding assay; Human genotype-to-enhancer functional validation; direct TF occupancy	NA	In vitro erythroid differentiation; Flow cytometry; allele-specific RT-PCR; ChIP
E_03449	2015	25523606	Blood group B gene is barely expressed in in vitro erythroid culture of Bm-derived CD34+ cells without an erythroid cell-specific regulatory element	Homo sapiens	hg38	chr9	133267998	133270594	RUNX1	ABO	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Bm-derived and control CD34+ erythroid cultures	NA	erythroid progenitor cell	CL:0000038	TF binding assay; Human genotype-to-enhancer functional validation; direct TF occupancy	NA	In vitro erythroid differentiation; Flow cytometry; allele-specific RT-PCR; ChIP
E_03450	2017	28213503	Inhibition of Inflammatory Gene Transcription by IL-10 Is Associated with Rapid Suppression of Lipopolysaccharide-Induced Enhancer Activation	Mus musculus	mm10	chr11	44386118	44393090	Stat3	Cxcl2	Enhancer	Active	Disease	Inflammatory Disease	NA	NA	NA	NA	Macrophage	NA	macrophage	CL:0000235	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	ChIP-qPCR/ChIP
E_03451	1995	7870592	Identification of two enhancer elements downstream of the human c-myc gene	Homo sapiens	hg19	chr8	128748315	128750245	NA	MYC	Enhancer	Active	Normal	NA	NA	NA	dermis	UBERON:0002067	Primary Dermal Lymphatic Endothelial Cells (hLECs)	NA	dermal lymphatic endothelial cell	NA	Enhancer activity assay	NA	Luciferase reporter assay
E_03452	1990	2304460	Roles of fetal G gamma-globin promoter elements and the adult beta-globin 3' enhancer in the stage-specific expression of globin genes	Homo sapiens	hg19	chr11	5248824	5249485	NA	HBG1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Blood Cells	NA	NA	NA	Experimentally supported enhancer study	NA	3C
E_03453	1990	2304460	Roles of fetal G gamma-globin promoter elements and the adult beta-globin 3' enhancer in the stage-specific expression of globin genes	Homo sapiens	hg19	chr11	5248824	5249485	NA	HBB	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Blood Cells	NA	NA	NA	Experimentally supported enhancer study	NA	3C
E_03454	2016	26728555	Regulation of the imprinted Dlk1-Dio3 locus by allele-specific enhancer activity	Mus musculus	mm10	chr12	109528035	109532509	Aff3	Meg3	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Embryonic Stem Cell	NA	NA	NA	TF-binding/chromatin assay; Genetic-variant functional analysis	ChIP-seq	ChIP-qPCR/ChIP
E_03455	1990	2339058	A 46 base pair enhancer sequence within the locus activating region is required for induced expression of the gamma-globin gene during erythroid differentiation	Homo sapiens	hg19	chr11	5268575	5268621	NA	HBG1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	erythroid progenitor cell	CL:0000038	Experimentally supported enhancer study	NA	3C
E_03456	2017	28667437	An Elf2-like transcription factor acts as repressor of the mouse ecto-5'-nucleotidase gene expression in hepatic myofibroblasts	Mus musculus	mm10	chr9	88325101	88326201	Elf2	Nt5e	Enhancer	Repressed	Disease	Hepatic Fibrosis	NA	NA	NA	NA	Hepatic Myofibroblasts	NA	fibroblast	CL:0000057	Enhancer activity assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay
E_03457	2026	41793551	Functional characterization of the GWAS lead SNP rs888663 and effects of GDF15 SNPs on GDF15 levels in gestational hypertension and preeclampsia	Homo sapiens	hg38	chr19	18373265	18374622	NA	GDF15	Enhancer	Active	Disease	neuroblastoma	MONDO:0005072	DOID:769	adrenal gland	UBERON:0002369	SK-N-BE(2)	CVCL_0528	neuroblastoma cell	NA	Enhancer activity assay	NA	Luciferase reporter assay; Reporter assay
E_03458	2017	28104492	Constitutively active RAS signaling reduces 1,25 dihydroxyvitamin D-mediated gene transcription in intestinal epithelial cells by reducing vitamin D receptor expression	Mus musculus	mm10	chr15	97898854	97902854	NA	Vdr	Enhancer	Active	Disease	Colon Cancer	NA	DOID:219	colon	UBERON:0001155	YAMC Cell	NA	NA	NA	Enhancer activity assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; Western blot
E_03459	2017	28104492	Constitutively active RAS signaling reduces 1,25 dihydroxyvitamin D-mediated gene transcription in intestinal epithelial cells by reducing vitamin D receptor expression	Mus musculus	mm10	chr15	97911426	97915997	NA	Vdr	Enhancer	Active	Disease	Colon Cancer	NA	DOID:219	colon	UBERON:0001155	YAMC Cell	NA	NA	NA	Enhancer activity assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; Western blot
E_03460	2013	23159876	Osterix induces Col1a1 gene expression through binding to Sp1 sites in the bone enhancer and proximal promoter regions	Homo sapiens	hg19	chr17	48258757	48260757	RUNX2	COL1A1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	C2C12	CVCL_0188	NA	NA	Enhancer activity assay	NA	Luciferase reporter assay; Reporter assay
E_03461	2009	19708858	The human urocortin 2 gene is regulated by hypoxia: identification of a hypoxia-responsive element in the 3'-flanking region	Homo sapiens	hg19	chr3	48598405	48598558	HIF1A	UCN2	Enhancer	Active	Disease	Myocardial Ischemia	NA	NA	NA	NA	TE-671	NA	NA	NA	Enhancer activity assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay
E_03462	2009	19708858	The human urocortin 2 gene is regulated by hypoxia: identification of a hypoxia-responsive element in the 3'-flanking region	Homo sapiens	hg19	chr3	48598405	48598558	NA	UCN2	Enhancer	Active	Normal	NA	NA	NA	umbilical vein	UBERON:0002066	HUVEC-C	CVCL_2959	umbilical vein endothelial cell	NA	Enhancer activity assay	NA	Luciferase reporter assay
E_03463	2019	30664627	C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution	Homo sapiens	hg19	chr17	48105016	48105270	NA	PDK2	Enhancer	Active	Normal	NA	NA	NA	lung cell culture	NA	A-549	CVCL_0023	malignant cell	CL:0001064	Single-cell enhancer-transcription assay; target-gene causality not established	C1 CAGE; single-cell transcriptome profiling; RNA-seq	single-molecule RNA FISH
E_03464	2019	30664627	C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution	Homo sapiens	hg19	chr20	56293544	56293843	NA	PMEPA1	Enhancer	Active	Normal	NA	NA	NA	lung cell culture	NA	A-549	CVCL_0023	malignant cell	CL:0001064	Single-cell enhancer-transcription assay; target-gene causality not established	C1 CAGE; single-cell transcriptome profiling; RNA-seq	single-molecule RNA FISH
E_03465	2019	30664627	C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution	Homo sapiens	hg19	chr10	3929991	3930887	NA	NA	Enhancer	Active	Normal	NA	NA	NA	lung cell culture	NA	A-549	CVCL_0023	malignant cell	CL:0001064	Single-cell enhancer-transcription assay; target-gene causality not established	C1 CAGE; single-cell transcriptome profiling; RNA-seq	single-molecule RNA FISH
E_03466	2011	21445863	Transcriptional regulation and spatial organisation of the human AML1/RUNX1 gene	Homo sapiens	hg19	chr21	35982223	35983306	NA	RUNX1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Acute T-Cell Leukaemia Cell	NA	NA	NA	Enhancer activity assay	NA	Luciferase reporter assay; Reporter assay
E_03467	2011	21445863	Transcriptional regulation and spatial organisation of the human AML1/RUNX1 gene	Homo sapiens	hg19	chr21	36141738	36142821	NA	RUNX1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Acute T-Cell Leukaemia Cell	NA	NA	NA	Enhancer activity assay	NA	Luciferase reporter assay; Reporter assay
E_03468	2025	41208708	Neanderthal-derived variants increase SOX9 enhancer activity in craniofacial progenitors that shape jaw development	Mus musculus	mm39	chr11	111456657	111460228	NA	Sox9	Enhancer	Active	Normal	NA	NA	NA	developing craniofacial mesenchyme / jaw	NA	Human/Neanderthal EC1.45 sequences functionally tested in transgenic zebrafish	NA	cranial neural crest-derived mesenchymal progenitor	NA	EC1.45 evolutionary enhancer-variant functional assay; orthologous canonical enhancer interval; dual reporter; lineage tracing; SOX9 phenocopy	scRNA-seq	Tol2 dual enhancer-reporter; live/confocal imaging; lineage tracing; SOX9 overexpression; craniofacial morphometry
E_03469	2025	41208708	Neanderthal-derived variants increase SOX9 enhancer activity in craniofacial progenitors that shape jaw development	Mus musculus	mm39	chr11	111456657	111460228	NA	Sox9	Enhancer	Active	Normal	NA	NA	NA	developing craniofacial mesenchyme / jaw	NA	canonical orthologous EC1.45 interval represented by mouse Rr80	NA	cranial neural crest-derived mesenchymal progenitor	NA	EC1.45 evolutionary enhancer-variant functional assay; orthologous canonical enhancer interval; dual reporter; lineage tracing; SOX9 phenocopy	scRNA-seq	Tol2 dual enhancer-reporter; live/confocal imaging; lineage tracing; SOX9 overexpression; craniofacial morphometry
E_03470	2016	26443750	Comparison of DNA Methylation and Expression Pattern of S100 and Other Epidermal Differentiation Complex Genes in Differentiating Keratinocytes	Homo sapiens	hg19	chr1	153628434	153632039	NA	LCE1A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	HEKa	NA	NA	NA	Experimentally supported enhancer study	NA	Western blot
E_03471	2021	33637692	Regulation of MYB by distal enhancer elements in human myeloid leukemia	Homo sapiens	hg19	chr6	135468624	135469679	GATA1	MYB	Enhancer	Active	Disease	myeloid leukemia	MONDO:0004643	DOID:8692	NA	NA	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF occupancy assay; TF functional perturbation assay; Epigenome editing assay	4C-seq; public ENCODE ChIP-seq and DNase-seq data analysis	Dual-luciferase reporter assay; H3K4me1/H3K27ac ChIP-qPCR; GATA1 ChIP-qPCR; GATA1 overexpression; GATA1 knockdown; dCas9-p300 epigenome editing; dCas9-DNMT3A epigenome editing; RT-qPCR; Western blot; hemin-induced differentiation
E_03472	2021	33637692	Regulation of MYB by distal enhancer elements in human myeloid leukemia	Homo sapiens	hg19	chr6	135414242	135415630	GATA1	MYB	Enhancer	Active	Disease	myeloid leukemia	MONDO:0004643	DOID:8692	NA	NA	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF occupancy assay; Epigenome editing assay	4C-seq; public ENCODE ChIP-seq and DNase-seq data analysis	Dual-luciferase reporter assay; H3K4me1/H3K27ac ChIP-qPCR; GATA1 ChIP-qPCR; dCas9-p300 epigenome editing; dCas9-DNMT3A epigenome editing; RT-qPCR; Western blot; hemin-induced differentiation
E_03473	2021	33637692	Regulation of MYB by distal enhancer elements in human myeloid leukemia	Homo sapiens	hg19	chr6	135467317	135468351	NA	MYB	Enhancer	Active	Disease	myeloid leukemia	MONDO:0004643	DOID:8692	NA	NA	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; Histone-mark validation	4C-seq; public ENCODE ChIP-seq and DNase-seq data analysis	Dual-luciferase reporter assay; H3K4me1/H3K27ac ChIP-qPCR
E_03474	2021	33637692	Regulation of MYB by distal enhancer elements in human myeloid leukemia	Homo sapiens	hg19	chr6	135467317	135468351	GATA1	MYB	Enhancer	Active	Disease	myeloid leukemia	MONDO:0004643	DOID:8692	NA	NA	HEK293T	CVCL_0063	NA	NA	Enhancer activity assay; TF functional perturbation assay	NA	Dual-luciferase reporter assay; GATA1 overexpression
E_03475	2021	33637692	Regulation of MYB by distal enhancer elements in human myeloid leukemia	Homo sapiens	hg19	chr6	135468624	135469679	TAL1	MYB	Enhancer	Active	Disease	myeloid leukemia	MONDO:0004643	DOID:8692	NA	NA	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF occupancy assay; Epigenome editing assay	4C-seq; public ENCODE ChIP-seq and DNase-seq data analysis	Dual-luciferase reporter assay; H3K4me1/H3K27ac ChIP-qPCR; TAL1 ChIP-qPCR; dCas9-p300 epigenome editing; dCas9-DNMT3A epigenome editing; RT-qPCR; hemin-induced differentiation
E_03476	2021	33637692	Regulation of MYB by distal enhancer elements in human myeloid leukemia	Homo sapiens	hg19	chr6	135468624	135469679	CEBPB	MYB	Enhancer	Active	Disease	myeloid leukemia	MONDO:0004643	DOID:8692	NA	NA	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF occupancy assay	4C-seq; public ENCODE ChIP-seq and DNase-seq data analysis	Dual-luciferase reporter assay; H3K4me1/H3K27ac ChIP-qPCR; CEBPB ChIP-qPCR; hemin-induced differentiation; RT-qPCR; Western blot
E_03477	2021	33637692	Regulation of MYB by distal enhancer elements in human myeloid leukemia	Homo sapiens	hg19	chr6	135414242	135415630	TAL1	MYB	Enhancer	Active	Disease	myeloid leukemia	MONDO:0004643	DOID:8692	NA	NA	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF occupancy assay	4C-seq; public ENCODE ChIP-seq and DNase-seq data analysis	Dual-luciferase reporter assay; H3K4me1/H3K27ac ChIP-qPCR; TAL1 ChIP-qPCR; hemin-induced differentiation
E_03478	2021	33637692	Regulation of MYB by distal enhancer elements in human myeloid leukemia	Homo sapiens	hg19	chr6	135468624	135469679	JUN	MYB	Enhancer	Active	Disease	myeloid leukemia	MONDO:0004643	DOID:8692	NA	NA	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF occupancy assay	4C-seq; public ENCODE ChIP-seq and DNase-seq data analysis	Dual-luciferase reporter assay; JUN ChIP-qPCR; hemin-induced differentiation; RT-qPCR; Western blot
E_03479	2021	33637692	Regulation of MYB by distal enhancer elements in human myeloid leukemia	Homo sapiens	hg19	chr6	135468624	135469679	SPI1	MYB	Enhancer	Active	Disease	myeloid leukemia	MONDO:0004643	DOID:8692	NA	NA	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF occupancy assay	4C-seq; public ENCODE ChIP-seq and DNase-seq data analysis	Dual-luciferase reporter assay; SPI1 ChIP-qPCR; hemin-induced differentiation; RT-qPCR; Western blot
E_03480	2021	33637692	Regulation of MYB by distal enhancer elements in human myeloid leukemia	Homo sapiens	hg19	chr6	135414242	135415630	JUN	MYB	Enhancer	Active	Disease	myeloid leukemia	MONDO:0004643	DOID:8692	NA	NA	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF occupancy assay	4C-seq; public ENCODE ChIP-seq and DNase-seq data analysis	Dual-luciferase reporter assay; JUN ChIP-qPCR; hemin-induced differentiation
E_03481	2021	33637692	Regulation of MYB by distal enhancer elements in human myeloid leukemia	Homo sapiens	hg19	chr6	135414242	135415630	SPI1	MYB	Enhancer	Active	Disease	myeloid leukemia	MONDO:0004643	DOID:8692	NA	NA	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF occupancy assay	4C-seq; public ENCODE ChIP-seq and DNase-seq data analysis	Dual-luciferase reporter assay; SPI1 ChIP-qPCR; hemin-induced differentiation
E_03482	2021	33637692	Regulation of MYB by distal enhancer elements in human myeloid leukemia	Homo sapiens	hg19	chr6	135414242	135415630	CEBPB	MYB	Enhancer	Active	Disease	myeloid leukemia	MONDO:0004643	DOID:8692	NA	NA	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF occupancy assay	4C-seq; public ENCODE ChIP-seq and DNase-seq data analysis	Dual-luciferase reporter assay; CEBPB ChIP-qPCR; hemin-induced differentiation
E_03483	2021	33637692	Regulation of MYB by distal enhancer elements in human myeloid leukemia	Homo sapiens	hg19	chr6	135468624	135469679	GATA1	MYB	Enhancer	Active	Disease	myeloid leukemia	MONDO:0004643	DOID:8692	NA	NA	HEK293T	CVCL_0063	NA	NA	Enhancer activity assay; TF functional perturbation assay	NA	Dual-luciferase reporter assay; GATA1 overexpression
E_03484	2021	33637692	Regulation of MYB by distal enhancer elements in human myeloid leukemia	Homo sapiens	hg19	chr6	135468624	135469679	NA	MYB	Enhancer	Active	Disease	myeloid leukemia	MONDO:0004643	DOID:8692	NA	NA	U-937	CVCL_0007	malignant cell	CL:0001064	Chromatin interaction assay; Differentiation-associated enhancer-promoter dynamics	4C-seq	TPA-induced differentiation; RT-qPCR; Western blot
E_03485	2021	33637692	Regulation of MYB by distal enhancer elements in human myeloid leukemia	Homo sapiens	hg19	chr6	135414242	135415630	NA	MYB	Enhancer	Active	Disease	myeloid leukemia	MONDO:0004643	DOID:8692	NA	NA	U-937	CVCL_0007	malignant cell	CL:0001064	Chromatin interaction assay; Differentiation-associated enhancer-promoter dynamics	4C-seq	TPA-induced differentiation; RT-qPCR; Western blot
E_03486	2021	33637692	Regulation of MYB by distal enhancer elements in human myeloid leukemia	Homo sapiens	hg19	chr6	135468624	135469679	NA	MYB	Enhancer	Active	Disease	myeloid leukemia	MONDO:0004643	DOID:8692	NA	NA	HL-60	CVCL_0002	malignant cell	CL:0001064	Chromatin interaction assay; Differentiation-associated enhancer-promoter dynamics	4C-seq	ATRA-induced differentiation; RT-qPCR; Western blot
E_03487	2021	33637692	Regulation of MYB by distal enhancer elements in human myeloid leukemia	Homo sapiens	hg19	chr6	135414242	135415630	NA	MYB	Enhancer	Active	Disease	myeloid leukemia	MONDO:0004643	DOID:8692	NA	NA	HL-60	CVCL_0002	malignant cell	CL:0001064	Chromatin interaction assay; Differentiation-associated enhancer-promoter dynamics	4C-seq	ATRA-induced differentiation; RT-qPCR; Western blot
E_03488	2021	33637692	Regulation of MYB by distal enhancer elements in human myeloid leukemia	Homo sapiens	hg19	chr6	135467317	135468351	NA	MYB	Enhancer	Active	Disease	myeloid leukemia	MONDO:0004643	DOID:8692	NA	NA	HeLa	CVCL_0030	malignant cell	CL:0001064	Enhancer activity assay; Heterologous reporter validation	NA	Dual-luciferase reporter assay
E_03489	2021	33637692	Regulation of MYB by distal enhancer elements in human myeloid leukemia	Homo sapiens	hg19	chr6	135468624	135469679	NA	MYB	Enhancer	Active	Disease	myeloid leukemia	MONDO:0004643	DOID:8692	NA	NA	HeLa	CVCL_0030	malignant cell	CL:0001064	Enhancer activity assay; Heterologous reporter validation	NA	Dual-luciferase reporter assay
E_03490	2021	33637692	Regulation of MYB by distal enhancer elements in human myeloid leukemia	Homo sapiens	hg19	chr6	135414242	135415630	NA	MYB	Enhancer	Active	Disease	myeloid leukemia	MONDO:0004643	DOID:8692	NA	NA	HeLa	CVCL_0030	malignant cell	CL:0001064	Enhancer activity assay; Heterologous reporter validation	NA	Dual-luciferase reporter assay
E_03491	2026	41237776	FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry	Homo sapiens	hg38	chrX	49260470	49261090	SATB1	FOXP3	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human CD4+CD25hiCD127lo Treg cells	NA	CD4-positive, CD25-positive, alpha-beta regulatory T cell	CL:0000792	Enhancer activity assay; TF binding assay; Functional cis-element perturbation assay; TF perturbation assay; Target-gene expression assay	Pooled CRISPRi locus-tiling screen; pooled CRISPRn TF knockout screen; H3K27ac ChIP-seq; SATB1 ChIP-seq; ATAC-seq reanalysis; PBAT-seq reanalysis	Arrayed SATB1 knockout; FOXP3 flow cytometry; targeted amplicon sequencing
E_03492	2026	41237776	FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry	Homo sapiens	hg38	chrX	49273000	49274000	SATB1	FOXP3	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human CD4+CD25hiCD127lo Treg cells	NA	CD4-positive, CD25-positive, alpha-beta regulatory T cell	CL:0000792	Enhancer activity assay; TF binding assay; Functional cis-element perturbation assay; TF perturbation assay; Target-gene expression assay	Pooled CRISPRi locus-tiling screen; pooled CRISPRn TF knockout screen; H3K27ac ChIP-seq; SATB1 ChIP-seq; ATAC-seq reanalysis	Paired-Cas9 RNP tiled deletion; arrayed SATB1 knockout; FOXP3 flow cytometry; deletion-genotyping PCR/Tapestation; targeted amplicon sequencing
E_03493	2026	41237776	FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry	Homo sapiens	hg38	chrX	49273000	49274000	GATA3	FOXP3	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human CD4+CD25lo Tconv cells	NA	CD4-positive, alpha-beta T cell	CL:0000624	Enhancer activity assay; TF binding assay; Chromatin accessibility assay; Functional cis-element perturbation assay; TF perturbation assay; Target-gene expression assay	Pooled CRISPRi locus-tiling screen; pooled CRISPRn TF knockout screen; H3K27ac ChIP-seq; GATA3 ChIP-seq; ATAC-seq reanalysis; TF-KO ATAC-seq reanalysis	Paired-Cas9 RNP tiled deletion; CRISPRoff targeted epigenetic silencing; arrayed GATA3 knockout; FOXP3 flow cytometry; targeted bisulfite sequencing; targeted amplicon sequencing; deletion-genotyping PCR/Tapestation
E_03494	2026	41237776	FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry	Homo sapiens	hg38	chrX	49273000	49274000	SATB1	FOXP3	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human CD4+CD25lo Tconv cells	NA	CD4-positive, alpha-beta T cell	CL:0000624	Enhancer activity assay; TF binding assay; Functional cis-element perturbation assay; TF perturbation assay; Target-gene expression assay	Pooled CRISPRi locus-tiling screen; pooled CRISPRn TF knockout screen; H3K27ac ChIP-seq; SATB1 ChIP-seq; ATAC-seq reanalysis	Paired-Cas9 RNP tiled deletion; CRISPRoff targeted epigenetic silencing; arrayed SATB1 knockout; FOXP3 flow cytometry; targeted bisulfite sequencing; targeted amplicon sequencing; deletion-genotyping PCR/Tapestation
E_03495	2026	41237776	FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry	Homo sapiens	hg38	chrX	49273000	49274000	EGR2	FOXP3	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human CD4+CD25lo Tconv cells	NA	CD4-positive, alpha-beta T cell	CL:0000624	Enhancer activity assay; TF binding assay; Functional cis-element perturbation assay; TF perturbation assay; Target-gene expression assay	Pooled CRISPRi locus-tiling screen; pooled CRISPRn TF knockout screen; H3K27ac ChIP-seq; EGR2 ChIP-seq; ATAC-seq reanalysis	Paired-Cas9 RNP tiled deletion; CRISPRoff targeted epigenetic silencing; arrayed EGR2 knockout; FOXP3 flow cytometry; targeted bisulfite sequencing; targeted amplicon sequencing; deletion-genotyping PCR/Tapestation
E_03496	2026	41237776	FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry	Homo sapiens	hg38	chrX	49273000	49274000	MBD2	FOXP3	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human CD4+CD25lo Tconv cells	NA	CD4-positive, alpha-beta T cell	CL:0000624	Enhancer activity assay; TF binding assay; Functional cis-element perturbation assay; TF perturbation assay; Target-gene expression assay	Pooled CRISPRi locus-tiling screen; pooled CRISPRn TF knockout screen; H3K27ac ChIP-seq; MBD2 ChIP-seq; ATAC-seq reanalysis	Paired-Cas9 RNP tiled deletion; CRISPRoff targeted epigenetic silencing; arrayed MBD2 knockout; FOXP3 flow cytometry; targeted bisulfite sequencing; targeted amplicon sequencing; deletion-genotyping PCR/Tapestation
E_03497	2026	41237776	FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry	Homo sapiens	hg38	chrX	49276500	49278500	NA	FOXP3	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Primary human CD4+CD25lo Tconv cells	NA	CD4-positive, alpha-beta T cell	CL:0000624	Enhancer activity assay; Chromatin accessibility assay; Functional cis-element perturbation assay; Target-gene expression assay; Histone modification assay	Pooled CRISPRi locus-tiling screen; H3K27ac ChIP-seq; ATAC-seq reanalysis	Paired-Cas9 RNP tiled deletion; CRISPRoff targeted epigenetic silencing; FOXP3 flow cytometry; targeted bisulfite sequencing; deletion-genotyping PCR/Tapestation
E_03498	2018	30012865	Identification of a Novel Enhancer/Chromatin Opening Element Associated with High-Level γ-Globin Gene Expression	Homo sapiens	hg19	chr11	5279732	5280272	EGR1	HBG2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Endogenous enhancer perturbation; Enhancer activity; TF binding; chromatin-opening regulation	Public ENCODE/GEO ChIP-seq; RNA-seq; ATAC-seq; GRO-cap	Synthetic zinc-finger perturbation; CRISPR-Cas9 enhancer deletion; EMSA; ChIP-qPCR; RT-qPCR; Western blot
E_03499	2018	30012865	Identification of a Novel Enhancer/Chromatin Opening Element Associated with High-Level γ-Globin Gene Expression	Homo sapiens	hg19	chr11	5279732	5280272	MAFK	HBG2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Endogenous enhancer perturbation; Enhancer activity; TF binding; chromatin-opening regulation	Public ENCODE/GEO ChIP-seq; RNA-seq; ATAC-seq; GRO-cap	Synthetic zinc-finger perturbation; CRISPR-Cas9 enhancer deletion; EMSA; ChIP-qPCR; RT-qPCR; Western blot
E_03500	2018	30012865	Identification of a Novel Enhancer/Chromatin Opening Element Associated with High-Level γ-Globin Gene Expression	Homo sapiens	hg19	chr11	5279732	5280272	NFE2	HBG2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Endogenous enhancer perturbation; Enhancer activity; TF binding; chromatin-opening regulation	Public ENCODE/GEO ChIP-seq; RNA-seq; ATAC-seq; GRO-cap	Synthetic zinc-finger perturbation; CRISPR-Cas9 enhancer deletion; EMSA; ChIP-qPCR; RT-qPCR; Western blot
E_03501	2018	30012865	Identification of a Novel Enhancer/Chromatin Opening Element Associated with High-Level γ-Globin Gene Expression	Homo sapiens	hg19	chr11	5279732	5280272	USF1	HBG2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Endogenous enhancer perturbation; Enhancer activity; TF binding; chromatin-opening regulation	Public ENCODE/GEO ChIP-seq; RNA-seq; ATAC-seq; GRO-cap	Synthetic zinc-finger perturbation; CRISPR-Cas9 enhancer deletion; EMSA; ChIP-qPCR; RT-qPCR; Western blot
E_03502	2018	30012865	Identification of a Novel Enhancer/Chromatin Opening Element Associated with High-Level γ-Globin Gene Expression	Homo sapiens	hg19	chr11	5279732	5280272	USF2	HBG2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Endogenous enhancer perturbation; Enhancer activity; TF binding; chromatin-opening regulation	Public ENCODE/GEO ChIP-seq; RNA-seq; ATAC-seq; GRO-cap	Synthetic zinc-finger perturbation; CRISPR-Cas9 enhancer deletion; EMSA; ChIP-qPCR; RT-qPCR; Western blot
E_03503	2018	30012865	Identification of a Novel Enhancer/Chromatin Opening Element Associated with High-Level γ-Globin Gene Expression	Homo sapiens	hg19	chr11	5279732	5280272	NA	HBG2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	PBMC-derived primary human erythroid cells	NA	erythroblast	CL:0000765	Enhancer functional perturbation; Target-gene expression assay	NA	Synthetic zinc-finger perturbation; RT-qPCR; Western blot; ChIP-qPCR
E_03504	2019	30545847	CRISPR-mediated activation of a promoter or enhancer rescues obesity caused by haploinsufficiency	Mus musculus	mm10	chr10	50623698	50625698	NA	Sim1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	Neuro-2a	CVCL_0470	neural crest derived neuroblast	CL:0002676	Enhancer activation assay; endogenous target-gene activation; CRISPRa specificity analysis	Cas9 ChIP-seq; RNA-seq	CRISPRa (dCas9-VP64); RT-qPCR
E_03505	2019	30545847	CRISPR-mediated activation of a promoter or enhancer rescues obesity caused by haploinsufficiency	Mus musculus	mm10	chr10	50623698	50625698	NA	Sim1	Enhancer	Active	Disease	obesity	MONDO:0011122	DOID:9970	hypothalamus	UBERON:0001898	Sim1+/- mouse hypothalamus	NA	NA	NA	Enhancer activation assay; in vivo functional perturbation; disease-phenotype rescue	RNA-seq; Cas9 ChIP-seq	Transgenic CRISPRa (dCas9-VP64); SCE2-targeting sgRNA; rAAV CRISPRa delivery; stereotactic hypothalamic injection; RT-qPCR; body-weight measurement; food-intake analysis; body-composition phenotyping; immunostaining
E_03506	2019	31046704	Functional characterization of two enhancers located downstream FOXP2	Homo sapiens	hg19	chr7	114456873	114463136	NA	FOXP2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	SK-N-MC	CVCL_0530	neuroectodermal tumor cell	NA	Enhancer activity assay; Endogenous enhancer deletion assay; Target-gene expression assay	ENCODE DNase-seq; H3K4me1/H3K27ac chromatin-state integration; ENCODE ChIP-seq integration	CRISPR-Cas9 enhancer deletion; clonal genotyping; RT-qPCR; Western blot; gene-expression analysis
E_03507	2019	31046704	Functional characterization of two enhancers located downstream FOXP2	Homo sapiens	hg19	chr7	114541370	114543683	NA	FOXP2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	SK-N-MC	CVCL_0530	neuroectodermal tumor cell	NA	Enhancer activity assay; Endogenous enhancer deletion assay; Target-gene expression assay	ENCODE DNase-seq; H3K4me1/H3K27ac chromatin-state integration; ENCODE ChIP-seq integration	CRISPR-Cas9 enhancer deletion; clonal genotyping; RT-qPCR; Western blot; gene-expression analysis; previously reported luciferase enhancer assay
E_03508	2021	34103329	Enhancer Hijacking Drives Oncogenic BCL11B Expression in Lineage-Ambiguous Stem Cell Leukemia	Homo sapiens	hg38	chr14	98541905	98544383	NA	BCL11B	Super-enhancer	Active	Disease	acute leukemia of ambiguous lineage	MONDO:0019460	NA	NA	NA	primary BCL11B-deregulated leukemia cells	NA	lineage-ambiguous acute leukemia cell	NA	Chromatin interaction assay; De novo super-enhancer formation; enhancer hijacking assay; structural-variant regulatory assay	WGS; RNA-seq; H3K27ac ChIP-seq; H3K27ac HiChIP; PacBio long-read sequencing; super-enhancer analysis; allele-specific expression analysis	Structural-variant validation; DNA/RNA FISH; genomic validation
E_03509	2019	31046704	Functional characterization of two enhancers located downstream FOXP2	Homo sapiens	hg19	chr7	114456873	114463136	NA	FOXP2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	SK-N-MC	CVCL_0530	neuroectodermal tumor cell	NA	Enhancer activity assay; Endogenous enhancer deletion assay; Target-gene expression assay	ENCODE chromatin-state integration; DNase-accessibility and histone-mark integration	CRISPR-Cas9 enhancer deletion; clonal genotyping; RT-qPCR; Western blot; gene-expression analysis
E_03510	2019	31046704	Functional characterization of two enhancers located downstream FOXP2	Homo sapiens	hg19	chr7	114541370	114543683	NA	FOXP2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	SK-N-MC	CVCL_0530	neuroectodermal tumor cell	NA	Enhancer activity assay; Endogenous enhancer deletion assay; Target-gene expression assay	ENCODE chromatin-state integration; DNase-accessibility and histone-mark integration	CRISPR-Cas9 enhancer deletion; clonal genotyping; RT-qPCR; Western blot; gene-expression analysis; Reporter assay
E_03511	2021	34103329	Enhancer Hijacking Drives Oncogenic BCL11B Expression in Lineage-Ambiguous Stem Cell Leukemia	Homo sapiens	hg38	chr14	98541905	98544383	NA	BCL11B	Super-enhancer	Active	Disease	acute leukemia of ambiguous lineage	MONDO:0019460	NA	bone marrow	UBERON:0002371	primary BCL11B-deregulated leukemia cells	NA	lineage-ambiguous acute leukemia cell	NA	Chromatin interaction assay; De novo super-enhancer formation assay; enhancer-hijacking assay; structural-variant regulatory assay	WGS; RNA-seq; H3K27ac ChIP-seq; H3K27ac HiChIP; PacBio long-read sequencing; super-enhancer analysis; allele-specific expression analysis	DNA/RNA FISH; structural-variant validation; genomic validation
E_03512	2016	26957309	Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters	Homo sapiens	hg19	chr1	20173000	20175000	NA	NA	Enhancer	Active	Normal	NA	NA	NA	NA	NA	H1-hESC	CVCL_9771	embryonic stem cell	CL:0002322	Enhancer activity assay; epigenomic characterization	ChIP-seq	Luciferase reporter assay
E_03513	2016	26957309	Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters	Homo sapiens	hg19	chr13	40839693	40853195	NA	LINC00548	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Jurkat E6.1	CVCL_0367	T cell	CL:0000084	Enhancer activity assay; chromatin-state characterization; chromatin-contact analysis	ChIP-seq	Luciferase reporter assay; chromatin interaction analysis
E_03514	2016	26957309	Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters	Homo sapiens	hg19	chr9	4600913	4608373	NA	SLC1A1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Jurkat E6.1	CVCL_0367	T cell	CL:0000084	Enhancer activity assay; chromatin-state characterization; chromatin-contact analysis	ChIP-seq	Luciferase reporter assay; chromatin interaction analysis
E_03515	2014	25194570	A NOTCH1-driven MYC enhancer promotes T cell development, transformation and acute lymphoblastic leukemia	Homo sapiens	hg19	chr8	130180065	130180972	NOTCH1	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	HPB-ALL	CVCL_1820	T cell	CL:0000084	Enhancer activity assay; TF binding assay; chromatin-state characterization; Enhancer-promoter interaction; genetic enhancer functional validation	NOTCH1 ChIP-seq; RBPJ ChIP-seq; H3K27ac profiling	Luciferase reporter assay; 3C; local ChIP; NOTCH pathway inhibition; N-Me knockout mouse; leukemia initiation and maintenance assays
E_03516	2014	25194570	A NOTCH1-driven MYC enhancer promotes T cell development, transformation and acute lymphoblastic leukemia	Homo sapiens	hg19	chr8	130180065	130180972	RBPJ	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	pleural effusion	UBERON:0000175	CUTLL1	CVCL_4966	T cell	CL:0000084	Enhancer activity assay; TF binding assay; Enhancer-promoter interaction; TF-site functional perturbation	NOTCH1 ChIP-seq; RBPJ ChIP-seq	Luciferase reporter assay; RBPJ-binding-site mutagenesis; 3C; NOTCH pathway inhibition
E_03517	2014	25194570	A NOTCH1-driven MYC enhancer promotes T cell development, transformation and acute lymphoblastic leukemia	Homo sapiens	hg19	chr8	130180065	130180972	NOTCH1	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Jurkat	CVCL_0065	T cell	CL:0000084	Enhancer activity assay; signaling-dependent enhancer functional validation	NA	Luciferase reporter assay; orientation-independent reporter assay; gamma-secretase inhibitor treatment; MYC promoter reporter assay
E_03518	2014	25194570	A NOTCH1-driven MYC enhancer promotes T cell development, transformation and acute lymphoblastic leukemia	Homo sapiens	hg19	chr8	130180065	130180972	RBPJ	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Jurkat	CVCL_0065	T cell	CL:0000084	Enhancer activity assay; TF-site functional perturbation	NA	Luciferase reporter assay; RBPJ-binding-site mutagenesis
E_03519	2014	25194570	A NOTCH1-driven MYC enhancer promotes T cell development, transformation and acute lymphoblastic leukemia	Mus musculus	mm10	chr15	63255515	63256347	Notch1	Myc	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	thymus	UBERON:0002370	thymocyte	NA	T cell	CL:0000084	Enhancer activity assay; conserved enhancer functional validation; genetic enhancer knockout; leukemia functional assay	Notch1 ChIP-seq	Luciferase reporter assay; N-Me knockout mouse; thymocyte-development phenotyping; NOTCH1-induced leukemia initiation and maintenance assay
E_03520	2014	25194570	A NOTCH1-driven MYC enhancer promotes T cell development, transformation and acute lymphoblastic leukemia	Mus musculus	mm10	chr15	63255515	63256347	Rbpj	Myc	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	thymus	UBERON:0002370	thymocyte	NA	T cell	CL:0000084	TF-binding evidence; conserved enhancer functional validation	Notch1/Rbpj ChIP-seq	Luciferase reporter assay; Rbpj-binding-site functional analysis
E_03521	2023	36869052	An autoimmune pleiotropic SNP modulates IRF5 alternative promoter usage through ZBTB3-mediated chromatin looping	Homo sapiens	hg19	chr7	128573081	128574098	ZBTB3	IRF5	Enhancer	Active	Disease	autoimmune disease	MONDO:0007179	DOID:417	blood	UBERON:0000178	Primary CD14+ monocytes/macrophages	NA	CD14-positive monocyte / macrophage	NA	Disease-risk variant functional enhancer validation; allele-specific TF binding; chromatin looping; endogenous perturbation	GWAS fine-mapping; ATAC-seq; H3K27ac/H3K4me1 ChIP-seq; ZBTB3/CTCF/RAD21 ChIP-seq; RNA-seq; 4C-seq	Luciferase reporter; 3C; CRISPRa/CRISPRi; CRISPR-Cas9 deletion/knock-in; EMSA; ChIP-qPCR; RT-qPCR; macrophage-polarization assays
E_03522	2016	27774982	Genetic variation at the 8q24.21 renal cancer susceptibility locus affects HIF binding to a MYC enhancer	Homo sapiens	hg19	chr8	128889122	128889450	EPAS1	MYC	Enhancer	Active	Disease	clear cell renal cell carcinoma	MONDO:0005005	DOID:4467	kidney	UBERON:0002113	primary renal tumors and renal-cell validation	NA	clear cell renal cell carcinoma cell / malignant renal epithelial cell	NA	Causal disease-risk enhancer validation; allele-specific HIF binding; chromatin interaction; endogenous HRE editing	HIF ChIP-seq; H3K27ac ChIP-seq; RNA polymerase II ChIP-seq; Capture-C; TCGA RNA-seq/eQTL	Luciferase reporter; allele-specific ChIP-qPCR; FAIRE-qPCR; CRISPR-Cas9 HRE editing; RT-qPCR
E_03523	2025	40758996	Integrated Omics and Multicohort Analyses Identify an Enhancer Variant Linking Ferroptosis to Precision Therapy in Prostate Cancer	Homo sapiens	hg38	chr10	46073046	46074046	ZNF384	NCOA4	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	C4-2	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis; Endogenous enhancer perturbation	ATAC-seq; RNA-seq; Hi-C	Luciferase reporter assay; ChIP-qPCR; 3C-qPCR; CRISPR knockout; CRISPRi; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; Allele-specific reporter assay
E_03524	2025	40758996	Integrated Omics and Multicohort Analyses Identify an Enhancer Variant Linking Ferroptosis to Precision Therapy in Prostate Cancer	Homo sapiens	hg38	chr10	46073046	46074046	ZNF384	NCOA4	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	DU145	CVCL_0105	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis; Endogenous enhancer perturbation	ATAC-seq; RNA-seq; Hi-C	Luciferase reporter assay; ChIP-qPCR; 3C-qPCR; CRISPR knockout; CRISPRi; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; Allele-specific reporter assay
E_03525	2025	40758996	Integrated Omics and Multicohort Analyses Identify an Enhancer Variant Linking Ferroptosis to Precision Therapy in Prostate Cancer	Homo sapiens	hg38	chr10	46073046	46074046	ZNF384	NCOA4	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis; Endogenous enhancer perturbation	ATAC-seq; RNA-seq; Hi-C	Luciferase reporter assay; ChIP-qPCR; 3C-qPCR; CRISPR knockout; CRISPRi; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; Allele-specific reporter assay
E_03526	2025	40830415	Systematic decoding of functional enhancer connectomes and risk variants in human glioma	Homo sapiens	hg38	chr20	63680793	63682109	MEIS1	SOX18	Enhancer	Active	Disease	malignant glioma	MONDO:0100342	NA	brain	UBERON:0000955	U-251MG	CVCL_0021	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin-state profiling; Disease-variant functional analysis; Endogenous enhancer perturbation	H3K27ac HiChIP; H3K27ac ChIP-seq; RNA-seq; GWAS variant mapping; pooled CRISPRi screening; HiChIP; pooled CRISPRi screen	ChIP-qPCR; CRISPR-Cas9 enhancer deletion; base editing; 3C-qPCR; dCas9-CRISPRa; RT-qPCR; Luciferase reporter assay; CRISPR-Cas9 endogenous deletion/editing; CRISPRi
E_03527	2024	39196225	A transcriptional enhancer regulates cardiac maturation	Mus musculus	mm39	chr13	12371881	12373182	Mef2c	Actn2	Enhancer	Active	Disease	heart failure susceptibility	NA	NA	heart	UBERON:0000948	hPSC-derived cardiomyocytes plus endogenous Actn2 enhancer-deletion mouse models	NA	cardiac muscle cell	CL:0000746	Actn2 enh/Rr593 endogenous enhancer deletion; human ortholog CRISPRi/enCRISPRa; direct MEF2C occupancy; maturation and mitochondrial phenotyping	scRNA-seq; RNA-seq; GWAS integration; ATAC-seq; H3K27ac/H3K4me1 ChIP-seq; Hi-C	CRISPR-Cas9 enhancer deletion; CRISPRi; enCRISPRa; Luciferase reporter; ChIP-qPCR; RT-qPCR; Western blot; Seahorse respiration; echocardiography
E_03528	2024	39196225	A transcriptional enhancer regulates cardiac maturation	Mus musculus	mm39	chr13	12371881	12373182	Gata4	Actn2	Enhancer	Active	Disease	heart failure susceptibility	NA	NA	heart	UBERON:0000948	hPSC-derived cardiomyocytes plus endogenous Actn2 enhancer-deletion mouse models	NA	cardiac muscle cell	CL:0000746	Actn2 enh/Rr593 endogenous enhancer deletion; human ortholog CRISPRi/enCRISPRa; direct GATA4 occupancy; maturation and mitochondrial phenotyping	scRNA-seq; RNA-seq; GWAS integration; ATAC-seq; H3K27ac/H3K4me1 ChIP-seq; Hi-C	CRISPR-Cas9 enhancer deletion; CRISPRi; enCRISPRa; Luciferase reporter; ChIP-qPCR; RT-qPCR; Western blot; Seahorse respiration; echocardiography
E_03529	2023	36869052	An autoimmune pleiotropic SNP modulates IRF5 alternative promoter usage through ZBTB3-mediated chromatin looping	Homo sapiens	hg19	chr7	128573081	128574098	ZBTB3	IRF5	Enhancer	Active	Disease	autoimmune disease	MONDO:0007179	DOID:417	blood	UBERON:0000178	293T and SC cells for reporter/mechanistic assays	NA	CD14-positive monocyte / macrophage	NA	Disease-risk variant functional enhancer validation; allele-specific TF binding; chromatin looping; endogenous perturbation	GWAS fine-mapping; ATAC-seq; H3K27ac/H3K4me1 ChIP-seq; ZBTB3/CTCF/RAD21 ChIP-seq; RNA-seq; 4C-seq	Luciferase reporter; 3C; CRISPRa/CRISPRi; CRISPR-Cas9 deletion/knock-in; EMSA; ChIP-qPCR; RT-qPCR; macrophage-polarization assays
E_03530	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23912000	23912961	NKX2-5	MYH7	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	ventricular cardiomyocyte	NA	Enhancer activity assay; Functional perturbation assay; Regulatory variant functional assay; Engineered heart tissue functional assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Luciferase reporter assay; CRISPR-Cas9 enhancer deletion; RT-qPCR; engineered heart tissue functional assay
E_03531	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23912000	23912961	TCF21	MYH7	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	ventricular cardiomyocyte	NA	Enhancer activity assay; Functional perturbation assay; Regulatory variant functional assay; Engineered heart tissue functional assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Luciferase reporter assay; CRISPR-Cas9 enhancer deletion; RT-qPCR; engineered heart tissue functional assay
E_03532	2022	36253360	A local tumor microenvironment acquired super-enhancer induces an oncogenic driver in colorectal carcinoma	Homo sapiens	hg19	chr1	47644434	47659486	NA	PDZK1IP1	Super-enhancer	Active	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	primary colorectal carcinoma epithelial cells	NA	colorectal epithelial cancer cell	NA	Super-enhancer acquisition; tumor-microenvironment-dependent enhancer activation; target-gene regulation; tumor growth and metabolic phenotype	H3K27ac ChIP-seq; RNA-seq; super-enhancer profiling	Cytokine stimulation; xenotransplantation; PDZK1IP1 expression perturbation; glucose uptake assay; glutathione/NADPH assay; oxidative-stress growth assay
E_03533	2024	38233525	Affinity-optimizing enhancer variants disrupt development	Homo sapiens	hg38	chr7	156790708	156793079	NA	SHH	Enhancer	Active	Disease	ZRS-associated preaxial polydactyly	NA	NA	limb bud	NA	embryonic limb bud	NA	limb bud mesenchymal cell	NA	Enhancer variant functional assay; TF-binding affinity assay; enhancer gain-of-function assay; developmental phenotype assay	High-throughput enhancer variant and sequence-function analysis	Enhancer reporter assay; Site-directed mutagenesis; quantitative TF-binding assay; transgenic embryo assay; mouse genome editing; limb developmental phenotyping
E_03534	2025	40644525	Discovery of oligodendrocyte enhancers that regulate Sox10 expression	Mus musculus	mm10	chr15	79192912	79193720	Myrf	Sox10	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Oli-neu cells; primary mouse oligodendrocyte precursor cells	NA	oligodendrocyte lineage cell	NA	Enhancer activity assay; endogenous enhancer epigenetic perturbation; TF binding assay; target-gene regulation	Brain multi-omics; ChIP-seq; ATAC-seq; Hi-C	CRISPRi; RT-qPCR; Luciferase reporter assay; MYRF DNA pull-down assay; MYRF motif mutagenesis; quantitative immunofluorescence
E_03535	2025	40644525	Discovery of oligodendrocyte enhancers that regulate Sox10 expression	Mus musculus	mm10	chr15	79201371	79202190	NA	Sox10	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	Oli-neu cells; primary mouse oligodendrocyte precursor cells	NA	oligodendrocyte lineage cell	NA	Enhancer activity assay; endogenous enhancer epigenetic perturbation; target-gene regulation	Brain multi-omics; ChIP-seq; ATAC-seq; Hi-C	CRISPRi; RT-qPCR; Luciferase reporter assay; quantitative immunofluorescence
E_03536	2020	32771023	Disruption of super-enhancer-driven tumor suppressor gene RCAN1.4 expression promotes the malignancy of breast carcinoma	Homo sapiens	hg19	chr21	36179867	36180107	RUNX3	RCAN1	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	BT-549	CVCL_1092	mammary gland epithelial cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation	H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C; ChIP-seq	Dual-luciferase reporter assay; RUNX3 ChIP-qPCR; RUNX3 siRNA knockdown; RUNX3 motif mutagenesis; double-CRISPR enhancer deletion; RT-qPCR; Western blot; CRISPR-Cas9 endogenous deletion/editing; Luciferase reporter assay; ChIP-qPCR; ChIP; In vivo phenotyping; Reporter assay
E_03537	2020	32771023	Disruption of super-enhancer-driven tumor suppressor gene RCAN1.4 expression promotes the malignancy of breast carcinoma	Homo sapiens	hg19	chr21	36179867	36180107	RUNX3	RCAN1	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	MDA-MB-231	CVCL_0062	mammary gland epithelial cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation	H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C; ChIP-seq	Dual-luciferase reporter assay; RUNX3 ChIP-qPCR; RUNX3 siRNA knockdown; RUNX3 motif mutagenesis; double-CRISPR enhancer deletion; RT-qPCR; Western blot; CRISPR-Cas9 endogenous deletion/editing; Luciferase reporter assay; ChIP-qPCR; ChIP; In vivo phenotyping; Reporter assay
E_03538	2025	40382324	Auricular malformations are driven by copy number variations in a hierarchical enhancer cluster and a dominant enhancer recapitulates human pathogenesis	Homo sapiens	hg38	chr4	8705075	8707510	NA	HMX1	Enhancer	Active	Disease	bilateral constricted ear	NA	NA	external ear	UBERON:0001691	human cranial neural crest cells	NA	cranial neural crest-derived fibroblast	NA	Enhancer activity assay; enhancer-cluster cooperativity assay; copy-number-associated enhancer dysregulation; developmental phenotype assay	Hi-C; ATAC-seq; epigenomic profiling; whole-genome sequencing; target-capture sequencing	LacZ transgenic enhancer reporter assay; combinatorial enhancer reporter assay; CRISPR-Cas9 genome editing; mouse pinna developmental phenotyping
E_03539	2025	40382324	Auricular malformations are driven by copy number variations in a hierarchical enhancer cluster and a dominant enhancer recapitulates human pathogenesis	Homo sapiens	hg38	chr4	8725074	8725674	NA	HMX1	Enhancer	Active	Disease	bilateral constricted ear	NA	NA	external ear	UBERON:0001691	human cranial neural crest cells	NA	cranial neural crest-derived fibroblast	NA	Enhancer activity assay; enhancer-cluster cooperativity assay; copy-number-associated enhancer dysregulation; developmental phenotype assay	Hi-C; ATAC-seq; epigenomic profiling; whole-genome sequencing; target-capture sequencing	LacZ transgenic enhancer reporter assay; combinatorial enhancer reporter assay; CRISPR-Cas9 genome editing; mouse pinna developmental phenotyping
E_03540	2025	40369080	A human-specific enhancer fine-tunes radial glia potency and corticogenesis	Homo sapiens	hg38	chr10	35949193	35950411	NA	FZD8	Enhancer	Active	Normal	NA	NA	NA	cerebral cortex	UBERON:0000956	human neural progenitor cells	NA	radial glial cell	CL:0000681	Enhancer activity assay; endogenous enhancer replacement; species-specific enhancer functional assay; target-gene regulation; cortical developmental phenotype	RNA-seq; single-cell RNA-seq; cortical transcriptomic profiling	CRISPR-mediated genome replacement; HARE5 humanization knock-in; enhancer reporter assay; FZD8 expression analysis; WNT signaling assay; neural progenitor proliferation assay; mouse cortical phenotyping; primate neural progenitor analysis
E_03541	2016	27571262	Noncoding somatic and inherited single-nucleotide variants converge to promote ESR1 expression in breast cancer	Homo sapiens	hg19	chr6	151953109	151955347	GATA3	ESR1	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	breast	UBERON:0000310	T-47D	CVCL_0553	breast carcinoma epithelial cell	NA	Variant-to-enhancer functional validation; Endogenous enhancer deletion; enhancer-target linkage	Tumor whole-genome sequencing; DNase-seq; H3K27ac profiling; transcriptome analysis; POL2 ChIA-PET integration	Luciferase reporter assay; allele-specific GATA3 ChIP-qPCR; CRISPR-Cas9 enhancer deletion; RT-qPCR; chromosome-interaction validation
E_03542	2016	27774982	Genetic variation at the 8q24.21 renal cancer susceptibility locus affects HIF binding to a MYC enhancer	Homo sapiens	hg19	chr8	128889122	128889450	EPAS1	MYC	Enhancer	Active	Disease	clear cell renal cell carcinoma	MONDO:0005005	DOID:4467	kidney	UBERON:0002113	786-O	CVCL_1051	clear cell renal cell carcinoma cell / malignant renal epithelial cell	NA	Causal disease-risk enhancer validation; allele-specific HIF binding; chromatin interaction; endogenous HRE editing	HIF ChIP-seq; H3K27ac ChIP-seq; RNA polymerase II ChIP-seq; Capture-C; TCGA RNA-seq/eQTL	Luciferase reporter; allele-specific ChIP-qPCR; FAIRE-qPCR; CRISPR-Cas9 HRE editing; RT-qPCR
E_03543	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23913940	23915344	NA	MYH7	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	ventricular cardiomyocyte	NA	Enhancer activity assay; Functional perturbation assay; Regulatory variant functional assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Luciferase reporter assay; CRISPR-Cas9 enhancer deletion; RT-qPCR; engineered heart tissue functional assay
E_03544	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23915187	23917391	NA	MYH7	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	ventricular cardiomyocyte	NA	Enhancer activity assay; Functional perturbation assay; Regulatory variant functional assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Luciferase reporter assay; CRISPR-Cas9 enhancer deletion; RT-qPCR; engineered heart tissue functional assay
E_03545	2025	40830415	Systematic decoding of functional enhancer connectomes and risk variants in human glioma	Homo sapiens	hg38	chr20	63680793	63682109	MEIS1	SOX18	Enhancer	Active	Disease	malignant glioma	MONDO:0100342	NA	brain	UBERON:0000955	U-251MG	CVCL_0021	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin-state profiling; Disease-variant functional analysis; Endogenous enhancer perturbation	H3K27ac HiChIP; H3K27ac ChIP-seq; RNA-seq; pooled CRISPRi screening; GWAS variant mapping; HiChIP; pooled CRISPRi screen	CRISPR-Cas9 enhancer deletion; SNP base editing; ChIP-qPCR; 3C-qPCR; MEIS1 CRISPRa; RT-qPCR; rescue assay; CRISPR-Cas9 endogenous deletion/editing; CRISPRi
E_03546	2019	31727856	Brain cell type-specific enhancer-promoter interactome maps and disease-risk association	Homo sapiens	hg19	chr2	127892629	127892991	SPI1	BIN1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	cerebral cortex	UBERON:0000956	H1 hESC-derived microglia	NA	microglial cell	CL:0000129	cell-type-specific enhancer-promoter mapping plus endogenous causal enhancer deletion	H3K27ac ChIP-seq; H3K4me3 ChIP-seq; ATAC-seq; H3K4me3 PLAC-seq; RNA-seq; GWAS fine-mapping/integration	CRISPR-Cas9 363-bp enhancer deletion in two PSC lines; differentiation to microglia, neurons and astrocytes; Western blot; immunohistochemistry
E_03547	2025	40830415	Systematic decoding of functional enhancer connectomes and risk variants in human glioma	Homo sapiens	hg38	chr17	5958900	5960100	NA	VMP1	Enhancer	Active	Disease	malignant glioma	MONDO:0100342	NA	brain	UBERON:0000955	U-251MG	CVCL_0021	malignant cell	CL:0001064	Chromatin interaction assay; Chromatin-state profiling; Disease-variant functional analysis; Endogenous enhancer perturbation; Functional enhancer validation	H3K27ac HiChIP; H3K27ac ChIP-seq; ATAC-seq; RNA-seq; pooled CRISPRi screening; HiChIP; pooled CRISPRi screen	dCas9-KRAB CRISPRi; HiChIP validation; 3C-qPCR; CRISPR-Cas9 endogenous deletion/editing; CRISPRi
E_03548	2025	40830415	Systematic decoding of functional enhancer connectomes and risk variants in human glioma	Homo sapiens	hg38	chr2	18910338	18911438	NA	LAPTM4A	Enhancer	Active	Disease	malignant glioma	MONDO:0100342	NA	brain	UBERON:0000955	U-251MG	CVCL_0021	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Chromatin-state profiling; Disease-variant functional analysis; Endogenous enhancer perturbation	H3K27ac HiChIP; H3K27ac ChIP-seq; RNA-seq; pooled CRISPRi screening; HiChIP; pooled CRISPRi screen	CRISPRi enhancer repression; 3C-qPCR; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; CRISPRi
E_03549	2025	40830415	Systematic decoding of functional enhancer connectomes and risk variants in human glioma	Homo sapiens	hg38	chr2	18910338	18911438	NA	PUM2	Enhancer	Active	Disease	malignant glioma	MONDO:0100342	NA	brain	UBERON:0000955	U-251MG	CVCL_0021	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Chromatin-state profiling; Disease-variant functional analysis; Endogenous enhancer perturbation	H3K27ac HiChIP; H3K27ac ChIP-seq; RNA-seq; pooled CRISPRi screening; HiChIP; pooled CRISPRi screen	CRISPRi enhancer repression; 3C-qPCR; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; CRISPRi
E_03550	2025	40830415	Systematic decoding of functional enhancer connectomes and risk variants in human glioma	Homo sapiens	hg38	chr2	18910338	18911438	NA	RHOB	Enhancer	Active	Disease	malignant glioma	MONDO:0100342	NA	brain	UBERON:0000955	U-251MG	CVCL_0021	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Chromatin-state profiling; Disease-variant functional analysis; Endogenous enhancer perturbation	H3K27ac HiChIP; H3K27ac ChIP-seq; RNA-seq; pooled CRISPRi screening; HiChIP; pooled CRISPRi screen	CRISPRi enhancer repression; 3C-qPCR; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; CRISPRi
E_03551	2025	40830415	Systematic decoding of functional enhancer connectomes and risk variants in human glioma	Homo sapiens	hg38	chr2	18910338	18911438	NA	SDC1	Enhancer	Active	Disease	malignant glioma	MONDO:0100342	NA	brain	UBERON:0000955	U-251MG	CVCL_0021	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Chromatin-state profiling; Disease-variant functional analysis; Endogenous enhancer perturbation	H3K27ac HiChIP; H3K27ac ChIP-seq; RNA-seq; pooled CRISPRi screening; HiChIP; pooled CRISPRi screen	CRISPRi enhancer repression; 3C-qPCR; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; CRISPRi
E_03552	2025	40830415	Systematic decoding of functional enhancer connectomes and risk variants in human glioma	Homo sapiens	hg38	chr17	5958900	5960100	NA	VMP1	Enhancer	Active	Disease	malignant glioma	MONDO:0100342	NA	brain	UBERON:0000955	U-251MG	CVCL_0021	malignant cell	CL:0001064	Chromatin interaction assay; Chromatin-state profiling; Disease-variant functional analysis; Endogenous enhancer perturbation	H3K27ac HiChIP; H3K27ac ChIP-seq; HiChIP; pooled CRISPRi screen	3C-qPCR; CRISPRi; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_03553	2025	40830415	Systematic decoding of functional enhancer connectomes and risk variants in human glioma	Homo sapiens	hg38	chr8	12738300	12744200	NA	MYC	Enhancer	Active	Disease	malignant glioma	MONDO:0100342	NA	brain	UBERON:0000955	U-251MG	CVCL_0021	malignant cell	CL:0001064	Chromatin interaction assay; Chromatin-state profiling; Disease-variant functional analysis; Endogenous enhancer perturbation; Functional enhancer validation	H3K27ac HiChIP; H3K27ac ChIP-seq; RNA-seq; pooled CRISPRi screening; HiChIP; pooled CRISPRi screen	dCas9-KRAB CRISPRi; 3C-qPCR; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; CRISPRi
E_03554	2025	40830415	Systematic decoding of functional enhancer connectomes and risk variants in human glioma	Homo sapiens	hg38	chr8	12738300	12744200	NA	MYC	Enhancer	Active	Disease	malignant glioma	MONDO:0100342	NA	brain	UBERON:0000955	U-251MG	CVCL_0021	malignant cell	CL:0001064	Chromatin interaction assay; Chromatin-state profiling; Disease-variant functional analysis; Endogenous enhancer perturbation; Functional enhancer validation	H3K27ac HiChIP; H3K27ac ChIP-seq; RNA-seq; HiChIP; pooled CRISPRi screen	CRISPRi enhancer repression; 3C-qPCR; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; CRISPRi
E_03555	2020	32771023	Disruption of super-enhancer-driven tumor suppressor gene RCAN1.4 expression promotes the malignancy of breast carcinoma	Homo sapiens	hg19	chr21	36179867	36180107	RUNX3	RCAN1	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	BT-549	CVCL_1092	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation	H3K27ac ChIP-seq data analysis; H3K4me1 ChIP-seq data analysis; ChIP-seq	Dual-luciferase reporter assay; RUNX3 motif mutagenesis; RUNX3 ChIP-qPCR; H3K27ac ChIP-qPCR; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; Luciferase reporter assay; ChIP-qPCR; ChIP; In vivo phenotyping; Reporter assay
E_03556	2020	32771023	Disruption of super-enhancer-driven tumor suppressor gene RCAN1.4 expression promotes the malignancy of breast carcinoma	Homo sapiens	hg19	chr21	36179867	36180107	RUNX3	RCAN1	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	MDA-MB-231	CVCL_0062	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation	H3K27ac ChIP-seq data analysis; H3K4me1 ChIP-seq data analysis; ChIP-seq	Dual-luciferase reporter assay; RUNX3 motif mutagenesis; RUNX3 ChIP-qPCR; H3K27ac ChIP-qPCR; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; Luciferase reporter assay; ChIP-qPCR; ChIP; In vivo phenotyping; Reporter assay
E_03557	2018	29731168	Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element	Homo sapiens	hg19	chr8	128821500	128822500	NA	MYC	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	MDA-MB-231	CVCL_0062	breast carcinoma epithelial cell	NA	Enhancer activity; enhancer-promoter competition; endogenous perturbation	ATAC-seq; H3K27ac ChIP-seq/HiChIP; RNA-seq	Luciferase reporter assay; CRISPRi; PVT1 promoter genome editing; RT-qPCR; Western blot
E_03558	2018	29731168	Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element	Homo sapiens	hg19	chr8	128866000	128867000	NA	MYC	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	MDA-MB-231	CVCL_0062	breast carcinoma epithelial cell	NA	Enhancer activity; enhancer-promoter competition; endogenous perturbation	ATAC-seq; H3K27ac ChIP-seq/HiChIP; RNA-seq	Luciferase reporter assay; CRISPRi; PVT1 promoter genome editing; RT-qPCR; Western blot
E_03559	2018	29731168	Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element	Homo sapiens	hg19	chr8	128912000	128913000	NA	MYC	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	MCF-7	CVCL_0031	breast carcinoma epithelial cell	NA	Enhancer activity; enhancer-promoter competition; endogenous perturbation	ATAC-seq; H3K27ac ChIP-seq/HiChIP; RNA-seq	Luciferase reporter assay; CRISPRi; PVT1 promoter genome editing; RT-qPCR; Western blot
E_03560	2018	29731168	Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element	Homo sapiens	hg19	chr8	128919000	128920000	NA	MYC	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	MDA-MB-231	CVCL_0062	breast carcinoma epithelial cell	NA	Enhancer activity; enhancer-promoter competition; endogenous perturbation	ATAC-seq; H3K27ac ChIP-seq/HiChIP; RNA-seq	Luciferase reporter assay; CRISPRi; PVT1 promoter genome editing; RT-qPCR; Western blot
E_03561	2025	40830415	Systematic decoding of functional enhancer connectomes and risk variants in human glioma	Homo sapiens	hg38	chr2	18910338	18911438	NA	LAPTM4A	Enhancer	Active	Disease	malignant glioma	MONDO:0100342	NA	brain	UBERON:0000955	U-251MG	CVCL_0021	malignant cell	CL:0001064	Chromatin interaction assay; Chromatin-state profiling; Disease-variant functional analysis; Endogenous enhancer perturbation; Functional enhancer validation	H3K27ac HiChIP; RNA-seq; pooled CRISPRi screening; HiChIP; pooled CRISPRi screen	CRISPRi enhancer repression; 3C-qPCR; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; CRISPRi
E_03562	2025	40830415	Systematic decoding of functional enhancer connectomes and risk variants in human glioma	Homo sapiens	hg38	chr2	18910338	18911438	NA	PUM2	Enhancer	Active	Disease	malignant glioma	MONDO:0100342	NA	brain	UBERON:0000955	U-251MG	CVCL_0021	malignant cell	CL:0001064	Chromatin interaction assay; Chromatin-state profiling; Disease-variant functional analysis; Endogenous enhancer perturbation; Functional enhancer validation	H3K27ac HiChIP; RNA-seq; pooled CRISPRi screening; HiChIP; pooled CRISPRi screen	CRISPRi enhancer repression; 3C-qPCR; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; CRISPRi
E_03563	2025	40830415	Systematic decoding of functional enhancer connectomes and risk variants in human glioma	Homo sapiens	hg38	chr2	18910338	18911438	NA	RHOB	Enhancer	Active	Disease	malignant glioma	MONDO:0100342	NA	brain	UBERON:0000955	U-251MG	CVCL_0021	malignant cell	CL:0001064	Chromatin interaction assay; Chromatin-state profiling; Disease-variant functional analysis; Endogenous enhancer perturbation; Functional enhancer validation	H3K27ac HiChIP; RNA-seq; pooled CRISPRi screening; HiChIP; pooled CRISPRi screen	CRISPRi enhancer repression; 3C-qPCR; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; CRISPRi
E_03564	2025	40830415	Systematic decoding of functional enhancer connectomes and risk variants in human glioma	Homo sapiens	hg38	chr2	18910338	18911438	NA	SDC1	Enhancer	Active	Disease	malignant glioma	MONDO:0100342	NA	brain	UBERON:0000955	U-251MG	CVCL_0021	malignant cell	CL:0001064	Chromatin interaction assay; Chromatin-state profiling; Disease-variant functional analysis; Endogenous enhancer perturbation; Functional enhancer validation	H3K27ac HiChIP; RNA-seq; pooled CRISPRi screening; HiChIP; pooled CRISPRi screen	CRISPRi enhancer repression; 3C-qPCR; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; CRISPRi
E_03565	2016	27571262	Noncoding somatic and inherited single-nucleotide variants converge to promote ESR1 expression in breast cancer	Homo sapiens	hg19	chr6	151953109	151955347	NA	ESR1	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	pleural effusion	UBERON:0000175	T-47D	CVCL_0553	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay	DNase-seq; H3K27ac ChIP-seq	CRISPR-Cas9 enhancer deletion; RT-qPCR
E_03566	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23876121	23878188	NKX2-5	MYH6	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	ventricular cardiomyocyte	NA	Enhancer activity assay; Regulatory variant functional assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Luciferase reporter assay in human iPSC-derived cardiomyocytes
E_03567	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23876121	23878188	NKX2-5	MYH7	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	ventricular cardiomyocyte	NA	Enhancer activity assay; Regulatory variant functional assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Luciferase reporter assay in human iPSC-derived cardiomyocytes
E_03568	2018	29731168	Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element	Homo sapiens	hg19	chr8	128821500	128822500	NA	MYC	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	MCF-7 and breast cancer models	NA	malignant cell	CL:0001064	Enhancer-promoter competition/boundary perturbation and chromatin-contact assay	H3K27ac HiChIP/chromatin-contact and chromatin-state profiling	CRISPRi/genome editing; UMI-4C/contact validation; MYC/PVT1 nascent RNA and qRT-PCR; CRISPRi
E_03569	2018	29731168	Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element	Homo sapiens	hg19	chr8	128866000	128867000	NA	MYC	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	MCF-7 and breast cancer models	NA	malignant cell	CL:0001064	Enhancer-promoter competition/boundary perturbation and chromatin-contact assay	H3K27ac HiChIP/chromatin-contact and chromatin-state profiling	CRISPRi/genome editing; UMI-4C/contact validation; MYC/PVT1 nascent RNA and qRT-PCR; CRISPRi
E_03570	2018	29731168	Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element	Homo sapiens	hg19	chr8	128912000	128913000	NA	MYC	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	MCF-7 and breast cancer models	NA	malignant cell	CL:0001064	Enhancer-promoter competition/boundary perturbation and chromatin-contact assay	H3K27ac HiChIP/chromatin-contact and chromatin-state profiling	CRISPRi/genome editing; UMI-4C/contact validation; MYC/PVT1 nascent RNA and qRT-PCR; CRISPRi
E_03571	2018	29731168	Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element	Homo sapiens	hg19	chr8	128919000	128920000	NA	MYC	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	MCF-7 and breast cancer models	NA	malignant cell	CL:0001064	Enhancer-promoter competition/boundary perturbation and chromatin-contact assay	H3K27ac HiChIP/chromatin-contact and chromatin-state profiling	CRISPRi/genome editing; UMI-4C/contact validation; MYC/PVT1 nascent RNA and qRT-PCR; CRISPRi
E_03572	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr1	155936009	155937220	NA	LMNA	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	ventricular cardiomyocyte	NA	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Luciferase reporter assay in human iPSC-derived cardiomyocytes
E_03573	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr1	155937201	155938359	NA	LMNA	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	ventricular cardiomyocyte	NA	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Luciferase reporter assay in human iPSC-derived cardiomyocytes
E_03574	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr1	156073216	156074415	NA	LMNA	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	ventricular cardiomyocyte	NA	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Luciferase reporter assay in human iPSC-derived cardiomyocytes
E_03575	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr1	156074366	156075480	NA	LMNA	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	ventricular cardiomyocyte	NA	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Luciferase reporter assay in human iPSC-derived cardiomyocytes
E_03576	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr1	156092084	156093294	NA	LMNA	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	ventricular cardiomyocyte	NA	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Luciferase reporter assay in human iPSC-derived cardiomyocytes
E_03577	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr1	156093103	156094494	NA	LMNA	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	ventricular cardiomyocyte	NA	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Luciferase reporter assay in human iPSC-derived cardiomyocytes
E_03578	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr1	156095724	156096574	NA	LMNA	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	ventricular cardiomyocyte	NA	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Luciferase reporter assay in human iPSC-derived cardiomyocytes
E_03579	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr1	156099538	156100640	NA	LMNA	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	ventricular cardiomyocyte	NA	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Luciferase reporter assay in human iPSC-derived cardiomyocytes
E_03580	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23870150	23870823	NA	MYH6	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	ventricular cardiomyocyte	NA	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Luciferase reporter assay in human iPSC-derived cardiomyocytes
E_03581	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23870150	23870823	NA	MYH7	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	ventricular cardiomyocyte	NA	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Luciferase reporter assay in human iPSC-derived cardiomyocytes
E_03582	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23870761	23871458	NA	MYH6	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	ventricular cardiomyocyte	NA	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Luciferase reporter assay in human iPSC-derived cardiomyocytes
E_03583	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23870761	23871458	NA	MYH7	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	ventricular cardiomyocyte	NA	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Luciferase reporter assay in human iPSC-derived cardiomyocytes
E_03584	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23871436	23872136	NA	MYH6	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	ventricular cardiomyocyte	NA	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Luciferase reporter assay in human iPSC-derived cardiomyocytes
E_03585	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23871436	23872136	NA	MYH7	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	ventricular cardiomyocyte	NA	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Luciferase reporter assay in human iPSC-derived cardiomyocytes
E_03586	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23876221	23877058	NA	MYH6	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	ventricular cardiomyocyte	NA	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Luciferase reporter assay in human iPSC-derived cardiomyocytes
E_03587	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23876221	23877058	NA	MYH7	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	ventricular cardiomyocyte	NA	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Luciferase reporter assay in human iPSC-derived cardiomyocytes
E_03588	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23876782	23877626	NA	MYH6	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	ventricular cardiomyocyte	NA	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Luciferase reporter assay in human iPSC-derived cardiomyocytes
E_03589	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23876782	23877626	NA	MYH7	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	ventricular cardiomyocyte	NA	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Luciferase reporter assay in human iPSC-derived cardiomyocytes
E_03590	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23877446	23878141	NA	MYH6	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	ventricular cardiomyocyte	NA	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Luciferase reporter assay in human iPSC-derived cardiomyocytes
E_03591	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23877446	23878141	NA	MYH7	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	ventricular cardiomyocyte	NA	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Luciferase reporter assay in human iPSC-derived cardiomyocytes
E_03592	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23922666	23924886	NA	MYH7	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	ventricular cardiomyocyte	NA	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Luciferase reporter assay in human iPSC-derived cardiomyocytes
E_03593	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23923381	23924171	NA	MYH7	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart left ventricle	UBERON:0002084	human iPSC-derived cardiomyocytes	NA	ventricular cardiomyocyte	NA	Enhancer activity assay	promoter capture Hi-C; H3K27ac ChIP-seq; ATAC-seq; H3K4me3 ChIP-seq; CTCF ChIP-seq; cardiac TF ChIP-seq; gnomAD variant filtering; GTEx eQTL analysis	Luciferase reporter assay in human iPSC-derived cardiomyocytes
E_03594	2016	27571262	Noncoding somatic and inherited single-nucleotide variants converge to promote ESR1 expression in breast cancer	Homo sapiens	hg19	chr6	151953109	151955347	GATA3	ESR1	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	HCC1419	CVCL_1251	malignant cell	CL:0001064	TF binding assay; Allele-specific regulatory assay	RNA-seq	Allele-specific GATA3 ChIP-qPCR; Sanger sequencing
E_03595	2014	25394790	Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element	Homo sapiens	hg19	chr1	47704954	47704983	MYB	TAL1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	primary T-ALL specimens	NA	T lymphoblast	NA	Mutation-created oncogenic enhancer; TF recruitment; endogenous allele dependency	H3K27ac ChIP-seq; MYB/RUNX1/GATA3/TAL1/TCF12 ChIP-seq; RNA polymerase II and MED1 profiling; mutation sequencing	Luciferase reporter assay using 400-bp enhancer fragments; MYB siRNA; co-immunoprecipitation; allele-specific CRISPR-Cas9 deletion; qRT-PCR; immunoblotting
E_03596	2014	25394790	Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element	Homo sapiens	hg19	chr1	47704954	47704983	RUNX1	TAL1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	primary T-ALL specimens	NA	T lymphoblast	NA	Mutation-created oncogenic enhancer; TF recruitment; endogenous allele dependency	H3K27ac ChIP-seq; MYB/RUNX1/GATA3/TAL1/TCF12 ChIP-seq; RNA polymerase II and MED1 profiling; mutation sequencing	Luciferase reporter assay using 400-bp enhancer fragments; co-immunoprecipitation; allele-specific CRISPR-Cas9 deletion; qRT-PCR; immunoblotting
E_03597	2014	25394790	Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element	Homo sapiens	hg19	chr1	47704954	47704983	GATA3	TAL1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	primary T-ALL specimens	NA	T lymphoblast	NA	Mutation-created oncogenic enhancer; TF recruitment; endogenous allele dependency	H3K27ac ChIP-seq; MYB/RUNX1/GATA3/TAL1/TCF12 ChIP-seq; RNA polymerase II and MED1 profiling; mutation sequencing	Luciferase reporter assay using 400-bp enhancer fragments; co-immunoprecipitation; allele-specific CRISPR-Cas9 deletion; qRT-PCR; immunoblotting
E_03598	2014	25394790	Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element	Homo sapiens	hg19	chr1	47704954	47704983	TAL1	TAL1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	primary T-ALL specimens	NA	T lymphoblast	NA	Mutation-created oncogenic enhancer; TF recruitment; endogenous allele dependency	H3K27ac ChIP-seq; MYB/RUNX1/GATA3/TAL1/TCF12 ChIP-seq; RNA polymerase II and MED1 profiling; mutation sequencing	Luciferase reporter assay using 400-bp enhancer fragments; co-immunoprecipitation; allele-specific CRISPR-Cas9 deletion; qRT-PCR; immunoblotting
E_03599	2014	25394790	Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element	Homo sapiens	hg19	chr1	47704954	47704983	TCF12	TAL1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	primary T-ALL specimens	NA	T lymphoblast	NA	Mutation-created oncogenic enhancer; TF recruitment; endogenous allele dependency	H3K27ac ChIP-seq; MYB/RUNX1/GATA3/TAL1/TCF12 ChIP-seq; RNA polymerase II and MED1 profiling; mutation sequencing	Luciferase reporter assay using 400-bp enhancer fragments; co-immunoprecipitation; allele-specific CRISPR-Cas9 deletion; qRT-PCR; immunoblotting
E_03600	2014	25394790	Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element	Homo sapiens	hg19	chr1	129180000	129181000	MYB	TAL1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	T-ALL	NA	T lymphoblast	NA	Enhancer activity assay; TF binding assay	ChIP-seq	Luciferase reporter assay; ChIP-qPCR
E_03601	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44420684	44421883	FOXA1	UBE2C	Enhancer	Active	Disease	castration-resistant prostate cancer	NA	NA	bone tissue	UBERON:0002481	PC-3	CVCL_0035	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Histone modification assay	NA	3C-qPCR; Luciferase reporter assay; FOXA1 ChIP-qPCR; H3K4me1/H3K4me2 ChIP-qPCR; FOXA1 siRNA; MED1 siRNA; RT-qPCR; Western blot
E_03602	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44426134	44428433	FOXA1	UBE2C	Enhancer	Active	Disease	castration-resistant prostate cancer	NA	NA	bone tissue	UBERON:0002481	PC-3	CVCL_0035	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Histone modification assay	NA	3C-qPCR; Luciferase reporter assay; FOXA1 ChIP-qPCR; H3K4me1/H3K4me2 ChIP-qPCR; FOXA1 siRNA; MED1 siRNA; RT-qPCR; Western blot
E_03603	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44442384	44444183	FOXA1	UBE2C	Enhancer	Active	Disease	castration-resistant prostate cancer	NA	NA	bone tissue	UBERON:0002481	PC-3	CVCL_0035	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Histone modification assay	NA	3C-qPCR; Luciferase reporter assay; FOXA1 ChIP-qPCR; H3K4me1/H3K4me2 ChIP-qPCR; FOXA1 siRNA; MED1 siRNA; RT-qPCR; Western blot
E_03604	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44420684	44421883	ETS1	UBE2C	Enhancer	Active	Disease	castration-resistant prostate cancer	NA	NA	bone tissue	UBERON:0002481	PC-3	CVCL_0035	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Histone modification assay	NA	3C-qPCR; Luciferase reporter assay; ETS1 ChIP-qPCR; H3K4me1/H3K4me2 ChIP-qPCR
E_03605	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44420684	44421883	GATA2	UBE2C	Enhancer	Active	Disease	castration-resistant prostate cancer	NA	NA	bone tissue	UBERON:0002481	PC-3	CVCL_0035	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Histone modification assay	NA	3C-qPCR; Luciferase reporter assay; GATA2 ChIP-qPCR; H3K4me1/H3K4me2 ChIP-qPCR
E_03606	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44420684	44421883	POU2F1	UBE2C	Enhancer	Active	Disease	castration-resistant prostate cancer	NA	NA	bone tissue	UBERON:0002481	PC-3	CVCL_0035	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Histone modification assay	NA	3C-qPCR; Luciferase reporter assay; POU2F1 ChIP-qPCR; H3K4me1/H3K4me2 ChIP-qPCR
E_03607	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44426134	44428433	ETS1	UBE2C	Enhancer	Active	Disease	castration-resistant prostate cancer	NA	NA	bone tissue	UBERON:0002481	PC-3	CVCL_0035	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Histone modification assay	NA	3C-qPCR; Luciferase reporter assay; ETS1 ChIP-qPCR; H3K4me1/H3K4me2 ChIP-qPCR
E_03608	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44426134	44428433	GATA2	UBE2C	Enhancer	Active	Disease	castration-resistant prostate cancer	NA	NA	bone tissue	UBERON:0002481	PC-3	CVCL_0035	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Histone modification assay	NA	3C-qPCR; Luciferase reporter assay; GATA2 ChIP-qPCR; H3K4me1/H3K4me2 ChIP-qPCR
E_03609	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44426134	44428433	POU2F1	UBE2C	Enhancer	Active	Disease	castration-resistant prostate cancer	NA	NA	bone tissue	UBERON:0002481	PC-3	CVCL_0035	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Histone modification assay	NA	3C-qPCR; Luciferase reporter assay; POU2F1 ChIP-qPCR; H3K4me1/H3K4me2 ChIP-qPCR
E_03610	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44442384	44444183	ETS1	UBE2C	Enhancer	Active	Disease	castration-resistant prostate cancer	NA	NA	bone tissue	UBERON:0002481	PC-3	CVCL_0035	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Histone modification assay	NA	3C-qPCR; Luciferase reporter assay; ETS1 ChIP-qPCR; H3K4me1/H3K4me2 ChIP-qPCR
E_03611	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44442384	44444183	GATA2	UBE2C	Enhancer	Active	Disease	castration-resistant prostate cancer	NA	NA	bone tissue	UBERON:0002481	PC-3	CVCL_0035	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Histone modification assay	NA	3C-qPCR; Luciferase reporter assay; GATA2 ChIP-qPCR; H3K4me1/H3K4me2 ChIP-qPCR
E_03612	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44442384	44444183	POU2F1	UBE2C	Enhancer	Active	Disease	castration-resistant prostate cancer	NA	NA	bone tissue	UBERON:0002481	PC-3	CVCL_0035	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Histone modification assay	NA	3C-qPCR; Luciferase reporter assay; POU2F1 ChIP-qPCR; H3K4me1/H3K4me2 ChIP-qPCR
E_03613	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44430820	44433428	ETS1	UBE2C	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; Western blot
E_03614	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44430820	44433428	ETS1	UBE2C	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	PC-3	CVCL_0035	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; Western blot
E_03615	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44430820	44433428	FOXA1	UBE2C	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; Western blot
E_03616	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44430820	44433428	FOXA1	UBE2C	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	PC-3	CVCL_0035	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; Western blot
E_03617	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44430820	44433428	GATA2	UBE2C	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; Western blot
E_03618	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44430820	44433428	GATA2	UBE2C	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	PC-3	CVCL_0035	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; Western blot
E_03619	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44430820	44433428	POU2F1	UBE2C	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; Western blot
E_03620	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44430820	44433428	POU2F1	UBE2C	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	PC-3	CVCL_0035	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; Western blot
E_03621	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44441255	44444472	ETS1	UBE2C	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; Western blot
E_03622	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44441255	44444472	ETS1	UBE2C	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	PC-3	CVCL_0035	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; Western blot
E_03623	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44441255	44444472	FOXA1	UBE2C	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; Western blot
E_03624	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44441255	44444472	FOXA1	UBE2C	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	PC-3	CVCL_0035	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; Western blot
E_03625	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44441255	44444472	GATA2	UBE2C	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; Western blot
E_03626	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44441255	44444472	GATA2	UBE2C	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	PC-3	CVCL_0035	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; Western blot
E_03627	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44441255	44444472	POU2F1	UBE2C	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; Western blot
E_03628	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44441255	44444472	POU2F1	UBE2C	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	PC-3	CVCL_0035	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; Western blot
E_03629	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44478646	44484559	ETS1	UBE2C	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; Western blot
E_03630	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44478646	44484559	ETS1	UBE2C	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	PC-3	CVCL_0035	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; Western blot
E_03631	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44478646	44484559	FOXA1	UBE2C	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; Western blot
E_03632	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44478646	44484559	FOXA1	UBE2C	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	PC-3	CVCL_0035	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; Western blot
E_03633	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44478646	44484559	GATA2	UBE2C	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; Western blot
E_03634	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44478646	44484559	GATA2	UBE2C	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	PC-3	CVCL_0035	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; Western blot
E_03635	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44478646	44484559	POU2F1	UBE2C	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; Western blot
E_03636	2011	21556051	Phospho-MED1-enhanced UBE2C locus looping drives castration-resistant prostate cancer growth	Homo sapiens	hg19	chr20	44478646	44484559	POU2F1	UBE2C	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	PC-3	CVCL_0035	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; Western blot
E_03637	2022	36159594	A novel oncogenic enhancer of estrogen receptor-positive breast cancer	Homo sapiens	hg38	chr8	127668529	127669329	ESR1	MYC	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay	ChIP-seq	CRISPR knockout; Luciferase reporter assay
E_03638	2023	37591943	TAL1 hijacks MYCN enhancer that induces MYCN expression and dependence on mevalonate pathway in T-cell acute lymphoblastic leukemia	Homo sapiens	hg19	chr2	16619625	16621501	TAL1	MYCN	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Jurkat	CVCL_0065	T lymphoblast	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; ATAC-seq; Hi-C; 4C-seq	Luciferase reporter assay; CRISPR knockout; CRISPRi; ChIP-qPCR; RT-qPCR; Western blot
E_03639	2023	37591943	TAL1 hijacks MYCN enhancer that induces MYCN expression and dependence on mevalonate pathway in T-cell acute lymphoblastic leukemia	Homo sapiens	hg19	chr2	16619625	16621501	TAL1	MYCN	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	RPMI-8402	CVCL_1667	T lymphoblast	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; ATAC-seq; Hi-C; 4C-seq	Luciferase reporter assay; CRISPR knockout; CRISPRi; ChIP-qPCR; RT-qPCR; Western blot
E_03640	2025	40604280	Range extender mediates long-distance enhancer activity	Mus musculus	mm10	chr5	29314881	29315667	Ets1	Shh	Enhancer	Active	Normal	NA	NA	NA	limb bud	NA	Zone of polarizing activity cells	NA	mesenchymal cell	CL:0008019	Enhancer activity assay; Functional perturbation assay	ATAC-seq; ChIP-seq; Hi-C; scATAC-seq/scRNA-seq multiome	Luciferase reporter assay; CRISPR knock-in; CRISPR knockout; whole-mount in situ hybridization; skeletal staining; Knock-in mouse
E_03641	2025	40604280	Range extender mediates long-distance enhancer activity	Mus musculus	mm10	chr5	29314881	29315667	Lhx2	Shh	Enhancer	Active	Normal	NA	NA	NA	limb bud	NA	Zone of polarizing activity cells	NA	mesenchymal cell	CL:0008019	Enhancer activity assay; Functional perturbation assay	ATAC-seq; ChIP-seq; Hi-C; scATAC-seq/scRNA-seq multiome	Luciferase reporter assay; CRISPR knock-in; CRISPR knockout; whole-mount in situ hybridization; skeletal staining; Knock-in mouse
E_03642	2025	40604280	Range extender mediates long-distance enhancer activity	Mus musculus	mm10	chr5	29314881	29315667	Lhx9	Shh	Enhancer	Active	Normal	NA	NA	NA	limb bud	NA	Zone of polarizing activity cells	NA	mesenchymal cell	CL:0008019	Enhancer activity assay; Functional perturbation assay	ATAC-seq; ChIP-seq; Hi-C; scATAC-seq/scRNA-seq multiome	Luciferase reporter assay; CRISPR knock-in; CRISPR knockout; whole-mount in situ hybridization; skeletal staining; Knock-in mouse
E_03643	2020	32680982	A rare variant of African ancestry activates 8q24 lncRNA hub by modulating cancer associated enhancer	Homo sapiens	hg38	chr8	128018000	128023000	FOXA1	PCAT1	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP clone FGC	CVCL_1379	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis	FOXA1 ChIP-seq; AR ChIP-seq; ATAC-seq; DHS; 4C	CRISPRi; RT-qPCR; Luciferase reporter assay
E_03644	2020	32680982	A rare variant of African ancestry activates 8q24 lncRNA hub by modulating cancer associated enhancer	Homo sapiens	hg38	chr8	128018000	128023000	SPDEF	MYC	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP clone FGC	CVCL_1379	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis	AR ChIP-seq; FOXA1 ChIP-seq; H3K27ac ChIP-seq; ATAC-seq; DHS; 4C	Allele-specific Luciferase reporter assay; EMSA; SPDEF knockdown; CRISPRi; RT-qPCR
E_03645	2020	32680982	A rare variant of African ancestry activates 8q24 lncRNA hub by modulating cancer associated enhancer	Homo sapiens	hg38	chr8	128018000	128023000	AR	MYC	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP clone FGC	CVCL_1379	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis	AR ChIP-seq; H3K27ac ChIP-seq; FOXA1 ChIP-seq; 4C	Androgen stimulation; Luciferase reporter assay; RT-qPCR
E_03646	2018	29236325	AML1/ETO trans-activates c-KIT expression through the long range interaction between promoter and intronic enhancer	Homo sapiens	hg19	chr4	55554102	55554596	RUNX1::RUNX1T1	KIT	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	blood	UBERON:0000178	Kasumi-1	CVCL_0589	myeloblast	CL:0000835	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin-state profiling	ChIP-seq data analysis; patient expression-cohort analysis; ChIP-seq	Luciferase reporter assay; ChIP-qPCR; ChIP-3C-qPCR; siRNA knockdown; RT-qPCR; ChIP; 3C; Reporter assay
E_03647	2016	26656844	Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers	Homo sapiens	hg19	chr13	27523026	27544353	NA	USP12	Super-enhancer	Active	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	blood	UBERON:0000178	Colon Crypt Cell	NA	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; Endogenous enhancer perturbation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR; RNAi/siRNA/shRNA
E_03648	2022	34605909	Functional annotation and investigation of the 10q24.33 melanoma risk locus identifies a common variant that influences transcriptional regulation of OBFC1	Homo sapiens	hg19	chr10	105664375	105670803	MEOX2	STN1	Enhancer	Active	Disease	cutaneous melanoma	MONDO:0005012	DOID:8923	skin	UBERON:0002097	Primary melanoma tumor	NA	melanoma tissue	NA	Functional association assay	RNA-seq; eQTL analysis; Hi-C; 3C	qRT-PCR; genotype-expression correlation; CRISPR-Cas9
E_03649	2022	34605909	Functional annotation and investigation of the 10q24.33 melanoma risk locus identifies a common variant that influences transcriptional regulation of OBFC1	Homo sapiens	hg19	chr10	105664375	105670803	MEOX2	STN1	Enhancer	Active	Disease	cutaneous melanoma	MONDO:0005012	DOID:8923	skin	UBERON:0002097	HEK293T	CVCL_0063	epithelial cell line	NA	Functional perturbation assay	Hi-C; 3C	CRISPR-Cas9 enhancer deletion; RT-qPCR; Western blot; CRISPR-Cas9
E_03650	2025	40382324	Auricular malformations are driven by copy number variations in a hierarchical enhancer cluster and a dominant enhancer recapitulates human pathogenesis	Mus musculus	mm39	chr5	35623357	35624110	NA	Hmx1	Enhancer	Active	Disease	BCE-like auricular malformation model	NA	NA	external ear	UBERON:0001691	E14.5 mEC1dup/dup and mEC1del/del pinna	NA	neural crest-derived fibroblast	NA	Enhancer activity assay; Functional perturbation assay; Phenotypic validation assay	scRNA-seq; bulk RNA-seq	Transgenic LacZ reporter assay; mEC1 duplication knock-in; mEC1 deletion; WISH; RT-qPCR; micro-CT
E_03651	2024	38373841	KLF2 enhancer variant rs4808485 increases lupus risk by modulating inflammasome machinery and cellular homoeostasis	Homo sapiens	hg19	chr19	16439455	16439541	NA	KLF2	Enhancer	Repressed	Disease	systemic lupus erythematosus	MONDO:0007915	DOID:9074	blood	UBERON:0000178	primary immune cells from healthy controls and patients with SLE	NA	immune cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis; Endogenous enhancer perturbation	ChIP-seq; RNA-seq; 3C-seq; RNA-seq; eQTL analysis; GWAS	Luciferase reporter assay; ChIP-qPCR, CRISPR knockout, CRISPRi; RT-qPCR; Western blot; CRISPR-Cas9 endogenous deletion/editing; Luciferase reporter assay; ChIP; Allele-specific reporter assay; Reporter assay
E_03652	2021	34040254	Enhancer release and retargeting activates disease-susceptibility genes	Homo sapiens	hg38	chr21	43745000	43747000	ESR1	TFF1	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Endogenous enhancer perturbation	ChIP-seq; GRO-seq, Hi-C, ChIA-PET; RNA-seq; pooled CRISPRi screen; GWAS	CRISPR knockout; RT-qPCR; 4C-seq; ChIP-qPCR; CRISPRi; Site-directed/motif mutagenesis
E_03653	2021	34040254	Enhancer release and retargeting activates disease-susceptibility genes	Homo sapiens	hg19	chr21	43795658	43798708	FOXA1	TFF1	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	MCF-7	CVCL_0031	epithelial cell	CL:0000066	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Endogenous enhancer perturbation	GRO-seq; ChIA-PET; ChIP-seq; pooled CRISPRi screen; GWAS	CRISPR-Cas9 enhancer deletion; 4C-seq; qRT-PCR; ChIP-qPCR; CRISPRi; Site-directed/motif mutagenesis
E_03654	2019	31023702	RUNX1-targeted therapy for AML expressing somatic or germline mutation in RUNX1	Homo sapiens	hg19	chr21	36399106	36399322	RUNX1	RUNX1	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	bone marrow	UBERON:0002371	primary RUNX1-mutant AML	NA	AML cell	NA	Endogenous enhancer editing; enhancer dependency; leukemia survival analysis	ChIP-seq; H3K27ac profiling; RNA-seq; Hi-C data integration	CRISPR/Cas9 eR1 editing-out; qRT-PCR; Western blot; proliferation assay; apoptosis assay; colony-forming assay
E_03655	2019	31023702	RUNX1-targeted therapy for AML expressing somatic or germline mutation in RUNX1	Homo sapiens	hg19	chr21	36399106	36399322	RUNX1	RUNX1	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	bone marrow	UBERON:0002371	OCI-AML5	CVCL_1620	AML cell	NA	Endogenous enhancer editing; enhancer dependency; leukemia survival analysis	ChIP-seq; H3K27ac profiling; RNA-seq; Hi-C data integration	CRISPR/Cas9 eR1 editing-out; qRT-PCR; Western blot; proliferation assay; apoptosis assay; colony-forming assay
E_03656	2023	37904237	Landscape of enhancer disruption and functional screen in melanoma cells	Homo sapiens	hg19	chr10	89875711	89876693	NA	PTEN	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	T-47D	CVCL_0553	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay	ChIP-seq; ATAC-seq; CRISPRi screen; whole-genome sequencing	Luciferase reporter assay; CRISPRi; CRISPRa; RT-qPCR; Western blot; Cell Apoptosis Assay; Colony Formation Assay
E_03657	2019	31023702	RUNX1-targeted therapy for AML expressing somatic or germline mutation in RUNX1	Homo sapiens	hg19	chr21	36399106	36399322	NA	RUNX1	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	bone marrow	UBERON:0002371	primary RUNX1-mutant AML	NA	myeloid leukemia cell	NA	Endogenous enhancer editing; AML survival dependency	H3K27ac/BRD4 chromatin profiling; transcriptomic profiling	CRISPR-Cas9 eR1 editing/deletion; RT-qPCR; immunoblotting; proliferation; apoptosis; colony-forming assays
E_03658	2019	31023702	RUNX1-targeted therapy for AML expressing somatic or germline mutation in RUNX1	Homo sapiens	hg19	chr21	36399106	36399322	NA	RUNX1	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	blood	UBERON:0000178	primary RUNX1-mutant AML	NA	myeloid leukemia cell	NA	Endogenous enhancer editing; AML survival dependency	H3K27ac/BRD4 chromatin profiling; transcriptomic profiling	CRISPR-Cas9 eR1 editing/deletion; RT-qPCR; immunoblotting; proliferation; apoptosis; colony-forming assays
E_03659	2019	31023702	RUNX1-targeted therapy for AML expressing somatic or germline mutation in RUNX1	Homo sapiens	hg19	chr21	36399106	36399322	NA	RUNX1	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	bone marrow	UBERON:0002371	RUNX1-mutant AML cell lines	NA	myeloid leukemia cell	NA	Endogenous enhancer editing; AML survival dependency	H3K27ac/BRD4 chromatin profiling; transcriptomic profiling	CRISPR-Cas9 eR1 editing/deletion; RT-qPCR; immunoblotting; proliferation; apoptosis; colony-forming assays
E_03660	2019	31023702	RUNX1-targeted therapy for AML expressing somatic or germline mutation in RUNX1	Homo sapiens	hg19	chr21	36399106	36399322	NA	RUNX1	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	blood	UBERON:0000178	RUNX1-mutant AML cell lines	NA	myeloid leukemia cell	NA	Endogenous enhancer editing; AML survival dependency	H3K27ac/BRD4 chromatin profiling; transcriptomic profiling	CRISPR-Cas9 eR1 editing/deletion; RT-qPCR; immunoblotting; proliferation; apoptosis; colony-forming assays
E_03661	2025	40378042	Transcription factor cooperativity at a GATA3 tandem DNA sequence determines oncogenic enhancer-mediated activation	Homo sapiens	hg19	chr1	47680000	47681000	GATA3	TAL1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Jurkat	CVCL_0065	T lymphoblast	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ATAC-seq; ChIP-seq; RNA-seq	Luciferase reporter assay; CRISPR knockout; ChIP-qPCR; RT-qPCR; 3C-seq; CRISPR-Cas9
E_03662	2026	41526337	Temporal constraints on enhancer usage shape the regulation of limb gene transcription	Mus musculus	mm39	chr3	66845656	66847450	NA	Shox2	Enhancer	Active	Normal	NA	NA	NA	limb bud	NA	FACS-sorted embryonic limb mesenchymal cells	NA	mesenchymal cell	CL:0008019	Enhancer activity assay; Chromatin interaction assay; Functional enhancer validation; Temporal enhancer profiling	H3K27ac ChIP-seq; Capture-HiC; scRNA-seq; RNA-seq; ATAC-seq integration	In vivo LacZ transgenic reporter assay; CRISPR/Cas9 enhancer deletion evidence; Shox2 in situ hybridization; RT-qPCR; fluorescence reporter imaging; Flow cytometry
E_03663	2026	41526337	Temporal constraints on enhancer usage shape the regulation of limb gene transcription	Mus musculus	mm39	chr3	66977632	66978927	NA	Shox2	Enhancer	Active	Normal	NA	NA	NA	limb bud	NA	FACS-sorted embryonic limb mesenchymal cells	NA	mesenchymal cell	CL:0008019	Enhancer activity assay; Chromatin interaction assay; Functional enhancer validation; Temporal enhancer profiling	H3K27ac ChIP-seq; Capture-HiC; scRNA-seq; RNA-seq; ATAC-seq integration	In vivo LacZ transgenic reporter assay; CRISPR/Cas9 enhancer deletion evidence; Shox2 in situ hybridization; RT-qPCR; fluorescence reporter imaging; Flow cytometry
E_03664	2022	35915089	A Ctnnb1 enhancer regulates neocortical neurogenesis by controlling the abundance of intermediate progenitors	Mus musculus	mm10	chr9	120869062	120871341	NA	Ctnnb1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Mouse Embryonic Stem Cells (ESCs)	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; Hi-C; ATAC-seq	Transgenic reporter assay; Luciferase reporter assay; ChIP-qPCR; CRISPR knockout; CRISPRi; CRISPRa, qRT-PCR; Western blot; CRISPR-Cas9
E_03665	2026	41526337	Temporal constraints on enhancer usage shape the regulation of limb gene transcription	Mus musculus	mm10	chr3	66740432	66749559	NA	Shox2	Enhancer	Active	Normal	NA	NA	NA	limb bud	NA	Embryonic proximal limb mesenchymal cells	NA	mesenchymal cell	CL:0008019	Enhancer activity assay; Chromatin interaction assay; Temporal enhancer profiling	H3K27ac ChIP-seq; Capture-HiC; scRNA-seq; RNA-seq; ATAC-seq integration	In vivo LacZ transgenic reporter assay; stable transgenic reporter analysis; Shox2 expression analysis; fluorescence reporter imaging; Flow cytometry
E_03666	2015	26610392	Functional analysis of the 11q23.3 glioma susceptibility locus implicates PHLDB1 and DDX6 in glioma susceptibility	Homo sapiens	hg19	chr11	118559857	118561857	NA	DDX6	Enhancer	Active	Disease	malignant glioma	MONDO:0100342	NA	brain	UBERON:0000955	U-87MG ATCC	CVCL_0022	glioblastoma-like cell line	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Allele-specific functional assay	ENCODE H3K27ac/H3K4me1/H3K4me3/DHS/FAIRE-seq integration; RNA polymerase II ChIA-PET data integration; 3C	Luciferase enhancer scanning; Allele-specific reporter assay; EMSA; 3C; DDX6 siRNA knockdown; RT-qPCR; neurosphere formation assay; Luciferase reporter assay
E_03667	2019	31406378	Cryptic activation of an Irf8 enhancer governs cDC1 fate specification	Mus musculus	mm10	chr8	120777048	120777744	Tcf3	Irf8	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	Primary mouse MDP/CDP/pre-cDC1 populations	NA	common dendritic progenitor / pre-cDC1	NA	Irf8 +41-kb enhancer chromatin opening; TF binding; Endogenous enhancer deletion; cDC1-lineage specification	ATAC-seq; H3K27ac/H3K4me1 ChIP-seq; TCF3/E2A occupancy integration; transcriptome profiling	CRISPR-Cas9 enhancer deletion in mice; enhancer reporter; Flt3L bone-marrow culture; Flow cytometry; bone-marrow chimera
E_03668	2019	31406378	Cryptic activation of an Irf8 enhancer governs cDC1 fate specification	Mus musculus	mm10	chr8	120777048	120777744	Tcf3	Irf8	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	enhancer-deletion mice	NA	common dendritic progenitor / pre-cDC1	NA	Irf8 +41-kb enhancer chromatin opening; TF binding; Endogenous enhancer deletion; cDC1-lineage specification	ATAC-seq; H3K27ac/H3K4me1 ChIP-seq; TCF3/E2A occupancy integration; transcriptome profiling	CRISPR-Cas9 enhancer deletion in mice; enhancer reporter; Flt3L bone-marrow culture; Flow cytometry; bone-marrow chimera
E_03669	2015	26610392	Functional analysis of the 11q23.3 glioma susceptibility locus implicates PHLDB1 and DDX6 in glioma susceptibility	Homo sapiens	hg19	chr11	118559857	118561857	NA	DDX6	Enhancer	Active	Disease	malignant glioma	MONDO:0100342	NA	brain	UBERON:0000955	hTERT-immortalized normal human astrocytes	NA	astrocyte	CL:0000127	Enhancer activity assay; Chromatin interaction assay; Disease-variant functional analysis; Allele-specific functional assay; Chromatin-state assay	ENCODE H3K27ac/H3K4me1/H3K4me3/DHS/FAIRE-seq integration; GWAS	Luciferase enhancer scanning; Allele-specific reporter assay; EMSA; 3C
E_03670	2015	26610392	Functional analysis of the 11q23.3 glioma susceptibility locus implicates PHLDB1 and DDX6 in glioma susceptibility	Homo sapiens	hg19	chr11	118540532	118575295	NA	DDX6	Enhancer	Active	Disease	glioma	MONDO:0021042	NA	brain	UBERON:0000955	Normal Human Astrocyte	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; 3C
E_03671	2025	41120733	Enhancer activation from transposable elements in extrachromosomal DNA	Homo sapiens	hg19	chr3	111274001	111275000	NA	MYC	Enhancer	Active	Disease	colorectal adenocarcinoma	MONDO:0005008	DOID:0050861	sigmoid colon	UBERON:0001159	COLO 320DM	CVCL_0219	colon epithelial cell, adenocarcinoma-derived	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Endogenous enhancer perturbation	Hi-C; Nanopore ultra-long read sequencing; H3K27ac ChIP-seq; ATAC-seq; RNA-seq; CRISPRi screen	Luciferase reporter assay; CRISPRi dCas9-KRAB; CRISPR-CATCH; RNA-FISH; ORCA imaging; RT-qPCR; CRISPRi; Reporter assay
E_03672	2024	39443808	Chromatin remodelling drives immune cell-fibroblast communication in heart failure	Homo sapiens	hg38	chr17	43589381	43595263	RELA	MEOX1	Enhancer	Active	Disease	Heart Failure	NA	NA	heart	UBERON:0000948	human iPSC-derived cardiac fibroblast	NA	cardiac fibroblast	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	H3K27ac ChIP-seq; p65/RELA ChIP-seq; bulk RNA-seq; 3C	Dual-luciferase reporter assay (HeLa); RELA siRNA knockdown; qRT-PCR
E_03673	2021	34819668	ecDNA hubs drive cooperative intermolecular oncogene expression	Homo sapiens	hg38	chr8	128804981	128806980	NA	MYC	Enhancer	Active	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	COLO 320DM	CVCL_0219	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation	ATAC-seq; ChIP-seq, Hi-C	CRISPRi, Luciferase reporter assay, FISH; RT-qPCR; CRISPRi
E_03674	2025	41120733	Enhancer activation from transposable elements in extrachromosomal DNA	Homo sapiens	hg19	chr3	111274001	111275000	NA	MYC	Enhancer	Active	Disease	colorectal adenocarcinoma	MONDO:0005008	DOID:0050861	sigmoid colon	UBERON:0001159	COLO 320DM	CVCL_0219	colon epithelial cell, adenocarcinoma-derived	NA	Enhancer activity assay; Chromatin-state profiling; Endogenous enhancer perturbation; endogenous epigenetic perturbation; ecDNA structural mapping; chromatin-interaction mapping; 3D spatial interaction analysis; transcriptional imaging; cancer-cell fitness assay	Hi-C; Oxford Nanopore ultra-long-read whole-genome sequencing with CoRAL ecDNA reconstruction; pooled CRISPRi fitness screen with deep sequencing; re-analysis of ATAC-seq; H3K27ac ChIP-seq; BRD4 ChIP-seq	CRISPR-CATCH with PFGE and targeted sequencing; ORCA 3D DNA imaging; DNA-FISH; RNA-FISH; dual-luciferase enhancer assay using MYC and TK promoters; L1PA2/L1M4a1 fragment reporter assays; metaphase-spread ecDNA validation; CRISPRi; CRISPR-CATCH; Reporter assay
E_03675	2022	36516256	PAX5 epigenetically orchestrates CD58 transcription and modulates blinatumomab response in acute lymphoblastic leukemia	Homo sapiens	hg38	chr1	116544766	116545360	PAX5	CD58	Enhancer	Active	Disease	B-cell acute lymphoblastic leukemia	MONDO:0004947	DOID:0080638	bone marrow	UBERON:0002371	primary B-ALL blasts	NA	B-lineage lymphoblast/leukemia cell	NA	Endogenous enhancer perturbation; TF-motif causality; immunotherapy-response validation	genome-wide CRISPR screen; RNA-seq; PAX5 ChIP-seq; histone ChIP-seq; ATAC-seq	CRISPRi; PAX5-motif CRISPR editing; ChIP-qPCR; Luciferase reporter assay; Flow cytometry; blinatumomab cytotoxicity assays
E_03676	2022	36516256	PAX5 epigenetically orchestrates CD58 transcription and modulates blinatumomab response in acute lymphoblastic leukemia	Homo sapiens	hg38	chr1	116544766	116545360	PAX5	CD58	Enhancer	Active	Disease	B-cell acute lymphoblastic leukemia	MONDO:0004947	DOID:0080638	blood	UBERON:0000178	primary B-ALL blasts	NA	B-lineage lymphoblast/leukemia cell	NA	Endogenous enhancer perturbation; TF-motif causality; immunotherapy-response validation	genome-wide CRISPR screen; RNA-seq; PAX5 ChIP-seq; histone ChIP-seq; ATAC-seq	CRISPRi; PAX5-motif CRISPR editing; ChIP-qPCR; Luciferase reporter assay; Flow cytometry; blinatumomab cytotoxicity assays
E_03677	2019	30990414	Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from na?ve pluripotency	Mus musculus	mm10	chr1	63189000	63192000	Pou5f1	Zdbf2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	ES-R1	CVCL_2167	embryonic stem cell	CL:0002322	Enhancer activity assay; TF binding assay; Chromatin interaction assay	4C-seq; ATAC-seq; ChIP-seq; RNA-seq; WGBS; DNA methylation profiling	CRISPR knockout; ChIP-qPCR; RT-qPCR; Bisulfite Pyrosequencing
E_03678	2019	30990414	Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from na?ve pluripotency	Mus musculus	mm10	chr1	63189000	63192000	Pou5f1	Zdbf2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Mouse embryonic stem cells (mESCs)	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; TF binding assay; Chromatin interaction assay	4C-seq; ATAC-seq; ChIP-seq; RNA-seq; WGBS; DNA methylation profiling	CRISPR knockout; ChIP-qPCR; RT-qPCR; Bisulfite Pyrosequencing
E_03679	2019	30990414	Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from na?ve pluripotency	Mus musculus	mm10	chr1	63193000	63196000	Pou5f1	Zdbf2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	ES-R1	CVCL_2167	embryonic stem cell	CL:0002322	Enhancer activity assay; TF binding assay; Chromatin interaction assay	4C-seq; ATAC-seq; ChIP-seq; RNA-seq; WGBS; DNA methylation profiling	CRISPR knockout; ChIP-qPCR; RT-qPCR; Bisulfite Pyrosequencing
E_03680	2019	30990414	Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from na?ve pluripotency	Mus musculus	mm10	chr1	63193000	63196000	Pou5f1	Zdbf2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Mouse embryonic stem cells (mESCs)	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; TF binding assay; Chromatin interaction assay	4C-seq; ATAC-seq; ChIP-seq; RNA-seq; WGBS; DNA methylation profiling	CRISPR knockout; ChIP-qPCR; RT-qPCR; Bisulfite Pyrosequencing
E_03681	2014	25486255	CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells	Mus musculus	mm10	chr3	34755799	34762535	Nanog	Sox2	Super-enhancer	Active	Normal	NA	NA	NA	embryo	NA	F123 mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Functional perturbation assay; TF binding assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; Super-enhancer activity assay	H3K27ac ChIP-seq; H3K4me3 ChIP-seq; RNA-seq; published POU5F1/SOX2/NANOG/MED1 ChIP-seq and Hi-C/5C data integration	Double-CRISPR/Cas9 enhancer deletion; deletion-junction PCR; Sanger sequencing; genomic qPCR; allele-specific RT-qPCR; qRT-PCR; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_03682	2014	25486255	CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells	Mus musculus	mm10	chr3	34755799	34762535	Pou5f1	Sox2	Super-enhancer	Active	Normal	NA	NA	NA	embryo	NA	F123 mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Functional perturbation assay; TF binding assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; Super-enhancer activity assay	H3K27ac ChIP-seq; H3K4me3 ChIP-seq; RNA-seq; published POU5F1/SOX2/NANOG/MED1 ChIP-seq and Hi-C/5C data integration	Double-CRISPR/Cas9 enhancer deletion; deletion-junction PCR; Sanger sequencing; genomic qPCR; allele-specific RT-qPCR; qRT-PCR; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_03683	2014	25486255	CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells	Mus musculus	mm10	chr3	34755799	34762535	Sox2	Sox2	Super-enhancer	Active	Normal	NA	NA	NA	embryo	NA	F123 mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Functional perturbation assay; TF binding assay; Chromatin interaction assay; Endogenous enhancer perturbation; In vivo functional validation; Super-enhancer activity assay	H3K27ac ChIP-seq; H3K4me3 ChIP-seq; RNA-seq; published POU5F1/SOX2/NANOG/MED1 ChIP-seq and Hi-C/5C data integration	Double-CRISPR/Cas9 enhancer deletion; deletion-junction PCR; Sanger sequencing; genomic qPCR; allele-specific RT-qPCR; qRT-PCR; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_03684	2022	36516256	PAX5 epigenetically orchestrates CD58 transcription and modulates blinatumomab response in acute lymphoblastic leukemia	Homo sapiens	hg38	chr1	116544766	116545360	PAX5	CD58	Enhancer	Active	Disease	B-cell acute lymphoblastic leukemia	MONDO:0004947	DOID:0080638	blood	UBERON:0000178	697	CVCL_0079	B-lymphoblast	CL:0017006	Enhancer activity assay; Functional perturbation assay; TF binding assay; Endogenous enhancer perturbation	ChIP-seq; ATAC-seq; RNA-seq	Luciferase reporter assay; ChIP-qPCR, CRISPR knockout, CRISPRi; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_03685	2022	36516256	PAX5 epigenetically orchestrates CD58 transcription and modulates blinatumomab response in acute lymphoblastic leukemia	Homo sapiens	hg38	chr1	116544766	116545360	PAX5	CD58	Enhancer	Active	Disease	B-cell acute lymphoblastic leukemia	MONDO:0004947	DOID:0080638	bone marrow	UBERON:0002371	697	CVCL_0079	B-lineage lymphoblast/leukemia cell	NA	Endogenous enhancer perturbation; TF-motif causality; immunotherapy-response validation	genome-wide CRISPR screen; RNA-seq; PAX5 ChIP-seq; histone ChIP-seq; ATAC-seq	CRISPRi; PAX5-motif CRISPR editing; ChIP-qPCR; Luciferase reporter assay; Flow cytometry; blinatumomab cytotoxicity assays
E_03686	2022	36516256	PAX5 epigenetically orchestrates CD58 transcription and modulates blinatumomab response in acute lymphoblastic leukemia	Homo sapiens	hg38	chr1	116544766	116545360	PAX5	CD58	Enhancer	Active	Disease	B-cell acute lymphoblastic leukemia	MONDO:0004947	DOID:0080638	blood	UBERON:0000178	697	CVCL_0079	B-lineage lymphoblast/leukemia cell	NA	Endogenous enhancer perturbation; TF-motif causality; immunotherapy-response validation	genome-wide CRISPR screen; RNA-seq; PAX5 ChIP-seq; histone ChIP-seq; ATAC-seq	CRISPRi; PAX5-motif CRISPR editing; ChIP-qPCR; Luciferase reporter assay; Flow cytometry; blinatumomab cytotoxicity assays
E_03687	2022	36516256	PAX5 epigenetically orchestrates CD58 transcription and modulates blinatumomab response in acute lymphoblastic leukemia	Homo sapiens	hg38	chr1	116544766	116545360	PAX5	CD58	Enhancer	Active	Disease	B-cell acute lymphoblastic leukemia	MONDO:0004947	DOID:0080638	bone marrow	UBERON:0002371	primary B-ALL blasts	NA	B-lineage lymphoblast	NA	Endogenous TF-site perturbation; enhancer reporter validation; immunotherapy-response functional analysis	genome-wide CRISPR screen; RNA-seq; ChIP-seq/epigenomic profiling	PAX5-motif CRISPR editing; Luciferase reporter assay; Flow cytometry; CD58 expression assay; T-cell activation and blinatumomab cytotoxicity assays
E_03688	2022	36516256	PAX5 epigenetically orchestrates CD58 transcription and modulates blinatumomab response in acute lymphoblastic leukemia	Homo sapiens	hg38	chr1	116544766	116545360	PAX5	CD58	Enhancer	Active	Disease	B-cell acute lymphoblastic leukemia	MONDO:0004947	DOID:0080638	blood	UBERON:0000178	primary B-ALL blasts	NA	B-lineage lymphoblast	NA	Endogenous TF-site perturbation; enhancer reporter validation; immunotherapy-response functional analysis	genome-wide CRISPR screen; RNA-seq; ChIP-seq/epigenomic profiling	PAX5-motif CRISPR editing; Luciferase reporter assay; Flow cytometry; CD58 expression assay; T-cell activation and blinatumomab cytotoxicity assays
E_03689	2023	37832549	Genome-wide CRISPR activation screening in senescent cells reveals SOX5 as a driver and therapeutic target of rejuvenation	Homo sapiens	hg19	chr4	174249537	174250490	SOX5	HMGB2	Enhancer	Active	Disease	Werner syndrome	MONDO:0010196	DOID:5688	connective tissue / articular cartilage	NA	Human mesenchymal precursor cells (WT and progeroid-syndrome model)	NA	mesenchymal stem/progenitor cell	NA	Genome-wide CRISPRa rejuvenation screen; SOX5-dependent HMGB2 enhancer activation; epigenomic remodeling; in vivo osteoarthritis validation	Genome-wide pooled CRISPRa screen; RNA-seq; ATAC-seq; SOX5 ChIP-seq; H3K27ac/H3K4me1 ChIP-seq	SOX5/HMGB2 overexpression; ChIP-qPCR; RT-qPCR; Western blot; senescence assays; lentiviral in vivo cartilage gene therapy; osteoarthritis phenotyping
E_03690	2023	37832549	Genome-wide CRISPR activation screening in senescent cells reveals SOX5 as a driver and therapeutic target of rejuvenation	Homo sapiens	hg19	chr4	174249537	174250490	SOX5	HMGB2	Enhancer	Active	Disease	Werner syndrome	MONDO:0010196	DOID:5688	connective tissue / articular cartilage	NA	aged mouse articular cartilage for in vivo validation	NA	mesenchymal stem/progenitor cell	NA	Genome-wide CRISPRa rejuvenation screen; SOX5-dependent HMGB2 enhancer activation; epigenomic remodeling; in vivo osteoarthritis validation	Genome-wide pooled CRISPRa screen; RNA-seq; ATAC-seq; SOX5 ChIP-seq; H3K27ac/H3K4me1 ChIP-seq	SOX5/HMGB2 overexpression; ChIP-qPCR; RT-qPCR; Western blot; senescence assays; lentiviral in vivo cartilage gene therapy; osteoarthritis phenotyping
E_03691	2023	37832549	Genome-wide CRISPR activation screening in senescent cells reveals SOX5 as a driver and therapeutic target of rejuvenation	Homo sapiens	hg19	chr4	174249537	174250490	SOX5	HMGB2	Enhancer	Active	Disease	osteoarthritis	MONDO:0005178	DOID:8398	connective tissue / articular cartilage	NA	Human mesenchymal precursor cells (WT and progeroid-syndrome model)	NA	mesenchymal stem/progenitor cell	NA	Genome-wide CRISPRa rejuvenation screen; SOX5-dependent HMGB2 enhancer activation; epigenomic remodeling; in vivo osteoarthritis validation	Genome-wide pooled CRISPRa screen; RNA-seq; ATAC-seq; SOX5 ChIP-seq; H3K27ac/H3K4me1 ChIP-seq	SOX5/HMGB2 overexpression; ChIP-qPCR; RT-qPCR; Western blot; senescence assays; lentiviral in vivo cartilage gene therapy; osteoarthritis phenotyping
E_03692	2023	37832549	Genome-wide CRISPR activation screening in senescent cells reveals SOX5 as a driver and therapeutic target of rejuvenation	Homo sapiens	hg19	chr4	174249537	174250490	SOX5	HMGB2	Enhancer	Active	Disease	osteoarthritis	MONDO:0005178	DOID:8398	connective tissue / articular cartilage	NA	aged mouse articular cartilage for in vivo validation	NA	mesenchymal stem/progenitor cell	NA	Genome-wide CRISPRa rejuvenation screen; SOX5-dependent HMGB2 enhancer activation; epigenomic remodeling; in vivo osteoarthritis validation	Genome-wide pooled CRISPRa screen; RNA-seq; ATAC-seq; SOX5 ChIP-seq; H3K27ac/H3K4me1 ChIP-seq	SOX5/HMGB2 overexpression; ChIP-qPCR; RT-qPCR; Western blot; senescence assays; lentiviral in vivo cartilage gene therapy; osteoarthritis phenotyping
E_03693	2022	36516256	PAX5 epigenetically orchestrates CD58 transcription and modulates blinatumomab response in acute lymphoblastic leukemia	Homo sapiens	hg38	chr1	116544766	116545360	PAX5	CD58	Enhancer	Active	Disease	B-cell acute lymphoblastic leukemia	MONDO:0004947	DOID:0080638	bone marrow	UBERON:0002371	697	CVCL_0079	B-lineage lymphoblast	NA	Endogenous TF-site perturbation; enhancer reporter validation; immunotherapy-response functional analysis	genome-wide CRISPR screen; RNA-seq; ChIP-seq/epigenomic profiling	PAX5-motif CRISPR editing; Luciferase reporter assay; Flow cytometry; CD58 expression assay; T-cell activation and blinatumomab cytotoxicity assays
E_03694	2022	36516256	PAX5 epigenetically orchestrates CD58 transcription and modulates blinatumomab response in acute lymphoblastic leukemia	Homo sapiens	hg38	chr1	116544766	116545360	PAX5	CD58	Enhancer	Active	Disease	B-cell acute lymphoblastic leukemia	MONDO:0004947	DOID:0080638	blood	UBERON:0000178	697	CVCL_0079	B-lineage lymphoblast	NA	Endogenous TF-site perturbation; enhancer reporter validation; immunotherapy-response functional analysis	genome-wide CRISPR screen; RNA-seq; ChIP-seq/epigenomic profiling	PAX5-motif CRISPR editing; Luciferase reporter assay; Flow cytometry; CD58 expression assay; T-cell activation and blinatumomab cytotoxicity assays
E_03695	2019	30990414	Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from na?ve pluripotency	Mus musculus	mm10	chr1	63189000	63192000	NA	Zdbf2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Endogenous enhancer perturbation; In vivo functional validation; One of four Zdbf2 regulatory enhancers; duplicated supplied intervals retained as separate experimental-context records	4C-seq; chromatin/epigenomic profiling; RNA-seq	Genetic mutant analysis; RT-qPCR; differentiation assays; Mouse genetic deletion/knock-in
E_03696	2019	30990414	Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from na?ve pluripotency	Mus musculus	mm10	chr1	63193000	63196000	NA	Zdbf2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Endogenous enhancer perturbation; In vivo functional validation; One of four Zdbf2 regulatory enhancers; duplicated supplied intervals retained as separate experimental-context records	4C-seq; chromatin/epigenomic profiling; RNA-seq	Genetic mutant analysis; RT-qPCR; differentiation assays; Mouse genetic deletion/knock-in
E_03697	2017	28753427	A Genetic Variant Associated with Five Vascular Diseases Is a Distal Regulator of Endothelin-1 Gene Expression	Homo sapiens	hg19	chr6	12490000	12590000	NA	EDN1	Super-enhancer	Active	Disease	Coronary Artery Disease,Migraine Headache,Cervical Artery Dissection,Fibromuscular Dysplasia,Hypertension	NA	NA	NA	NA	HUVEC	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; Disease-associated enhancer analysis	RNA-seq; 4C-seq	Luciferase reporter assay; Reporter assay
E_03698	2025	40082405	Enhancer transcription profiling reveals an enhancer RNA-driven ferroptosis and new therapeutic opportunities in prostate cancer	Homo sapiens	hg38	chr3	46453226	46459225	AR	LTF	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	22Rv1	CVCL_1045	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin-state profiling	ATAC-seq; RNA-seq; ChIP-seq; 3C-seq; RNA-seq; ATAC-seq; ChIP-seq	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot, FISH; ChIP
E_03699	2025	40082405	Enhancer transcription profiling reveals an enhancer RNA-driven ferroptosis and new therapeutic opportunities in prostate cancer	Homo sapiens	hg38	chr3	46453226	46459225	AR	LTF	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin-state profiling	ATAC-seq; RNA-seq; ChIP-seq; 3C-seq; RNA-seq; ATAC-seq; ChIP-seq	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot, FISH; ChIP
E_03700	2025	40082405	Enhancer transcription profiling reveals an enhancer RNA-driven ferroptosis and new therapeutic opportunities in prostate cancer	Homo sapiens	hg38	chr3	46453226	46459225	HNRNPF	LTF	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	22Rv1	CVCL_1045	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin-state profiling	ATAC-seq; RNA-seq; ChIP-seq; 3C-seq; RNA-seq; ATAC-seq; ChIP-seq	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot, FISH; ChIP
E_03701	2025	40082405	Enhancer transcription profiling reveals an enhancer RNA-driven ferroptosis and new therapeutic opportunities in prostate cancer	Homo sapiens	hg38	chr3	46453226	46459225	HNRNPF	LTF	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Chromatin-state profiling	ATAC-seq; RNA-seq; ChIP-seq; 3C-seq; RNA-seq; ATAC-seq; ChIP-seq	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Western blot, FISH; ChIP
E_03702	2022	34707247	A stem cell marker KLF5 regulates CCAT1 via three-dimensional genome structure in colorectal cancer cells	Homo sapiens	hg19	chr13	74003796	74004073	KLF5	KLF5	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	HT-29	CVCL_0320	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	in vitro enChIP-seq; public H3K27ac ChIP-seq; public BRD4 ChIP-seq; public DNase-seq	CRISPR/Cas9 heterozygous enhancer deletion; PCR and sequencing validation; KLF5 ChIP-qPCR; qRT-PCR; sphere-formation assay; 5-FU and oxaliplatin cell viability assay; Flow cytometry; ChIP
E_03703	2022	34707247	A stem cell marker KLF5 regulates CCAT1 via three-dimensional genome structure in colorectal cancer cells	Homo sapiens	hg19	chr13	74003796	74004073	MEIS1	KLF5	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	HT-29	CVCL_0320	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin interaction assay	in vitro enChIP-seq; public H3K27ac ChIP-seq; public BRD4 ChIP-seq; public DNase-seq	MEIS1 ChIP-qPCR; CRISPR/Cas9 heterozygous enhancer deletion; qRT-PCR; sphere-formation assay; cell viability assay; Flow cytometry; ChIP
E_03704	2022	34707247	A stem cell marker KLF5 regulates CCAT1 via three-dimensional genome structure in colorectal cancer cells	Homo sapiens	hg19	chr13	74003796	74004073	RHOXF1	KLF5	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	HT-29	CVCL_0320	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin interaction assay	in vitro enChIP-seq; public H3K27ac ChIP-seq; public BRD4 ChIP-seq; public DNase-seq	RHOXF1 ChIP-qPCR; CRISPR/Cas9 heterozygous enhancer deletion; qRT-PCR; sphere-formation assay; cell viability assay; Flow cytometry; ChIP
E_03705	2021	34146516	Functional annotation of the 2q35 breast cancer risk locus implicates a structural variant in influencing activity of a long-range enhancer element	Homo sapiens	hg19	chr2	217994794	217995294	FOXA1	IGFBP5	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Regulatory variant functional assay	ChIP-seq; RNA-seq; DNase-seq/epigenomic profiling	Luciferase reporter assay; CRISPR-Cas9 enhancer perturbation; RT-qPCR
E_03706	2021	34146516	Functional annotation of the 2q35 breast cancer risk locus implicates a structural variant in influencing activity of a long-range enhancer element	Homo sapiens	hg19	chr2	217994794	217995294	FOXA1	IGFBP5	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	T-47D	CVCL_0553	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Regulatory variant functional assay	ChIP-seq; RNA-seq; DNase-seq/epigenomic profiling	Luciferase reporter assay; CRISPR-Cas9 enhancer perturbation; RT-qPCR
E_03707	2014	24778216	Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation	Homo sapiens	hg19	chr19	51352371	51354471	AR	KLK2	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Functional perturbation assay; TF binding assay; Chromatin interaction assay; Enhancer RNA assay	AR/H3K27ac/H3K4me1 ChIP-seq data integration; GRO-seq data integration	DHT treatment; KLK3e RNAi; RT-qPCR; AR/MED1 RIP-qPCR; ChIP-qPCR; 3C/3C-qPCR; orientation-dependent and ARE III deletion luciferase reporter assays
E_03708	2021	33980539	Selective Requirement of MYB for Oncogenic Hyperactivation of a Translocated Enhancer in Leukemia	Homo sapiens	hg19	chr3	128322411	128323124	MYB	MECOM	Enhancer	Active	Disease	Acute myeloid leukemia with MECOM rearrangement [inv(3)(q21;q26.2)/t(3;3)(q21;q26.2)]	NA	NA	bone marrow	UBERON:0002371	MUTZ-3 EVI1-GFP AML model	NA	myeloid leukemia cell	NA	Endogenous enhancer dependency; TF-motif causality; Enhancer hijacking	CRISPR-Cas9 tiling enhancer scan; H3K27ac ChIP-seq; ATAC-seq; deep amplicon sequencing	Individual sgRNA validation; MYB knockout; MYB-motif mutation; qRT-PCR; EVI1-GFP flow cytometry; immunoblotting; differentiation and cell-death assays
E_03709	2019	31422875	Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs	Mus musculus	mm10	chr7	3198900	3202780	Nanog	NA	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Epiblast-like Cells (EpiLCs)	NA	epiblast-like cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; WGBS; Hi-C; DNA methylation profiling	Transgenic reporter assay (RGM); CRISPR knockout; ChIP-qPCR; RT-qPCR; DNA FISH; Immunofluorescence; Confocal Imaging
E_03710	2019	31422875	Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs	Mus musculus	mm10	chr7	3198900	3202780	Pou5f1	NA	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Epiblast-like Cells (EpiLCs)	NA	epiblast-like cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; WGBS; Hi-C; DNA methylation profiling	Transgenic reporter assay (RGM); CRISPR knockout; ChIP-qPCR; RT-qPCR; DNA FISH; Immunofluorescence; Confocal Imaging
E_03711	2021	33980539	Selective Requirement of MYB for Oncogenic Hyperactivation of a Translocated Enhancer in Leukemia	Homo sapiens	hg19	chr3	128322411	128323124	MYB	MECOM	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	bone marrow	UBERON:0002371	primary inv(3)/t(3;3) AML	NA	myeloid leukemia cell	NA	Endogenous enhancer functional validation; TF-site causality; leukemia dependency	CRISPR-Cas9 enhancer scanning; ATAC-seq; ChIP-seq; transcriptomic profiling	individual sgRNA validation; endogenous MYB-site mutation; RT-qPCR; Flow cytometry; differentiation and viability assays
E_03712	2021	33980539	Selective Requirement of MYB for Oncogenic Hyperactivation of a Translocated Enhancer in Leukemia	Homo sapiens	hg19	chr3	128322411	128323124	MYB	MECOM	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	blood	UBERON:0000178	primary inv(3)/t(3;3) AML	NA	myeloid leukemia cell	NA	Endogenous enhancer functional validation; TF-site causality; leukemia dependency	CRISPR-Cas9 enhancer scanning; ATAC-seq; ChIP-seq; transcriptomic profiling	individual sgRNA validation; endogenous MYB-site mutation; RT-qPCR; Flow cytometry; differentiation and viability assays
E_03713	2021	33980539	Selective Requirement of MYB for Oncogenic Hyperactivation of a Translocated Enhancer in Leukemia	Homo sapiens	hg19	chr3	128322411	128323124	MYB	MECOM	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	blood	UBERON:0000178	primary inv(3)/t(3;3) AML	NA	AML hematopoietic progenitor-like leukemia cell	NA	Endogenous enhancer sequence-function mapping; TF-site causality; leukemia fitness and differentiation	CRISPR/Cas9 enhancer scan; ATAC-seq; p300/H3K27ac chromatin profiling; TF chromatin profiling; transcriptomic analysis	individual sgRNA validation; endogenous MYB-motif mutation; MYB knockout; deep amplicon sequencing; qRT-PCR; Flow cytometry; differentiation and viability assays
E_03714	2021	33980539	Selective Requirement of MYB for Oncogenic Hyperactivation of a Translocated Enhancer in Leukemia	Homo sapiens	hg19	chr3	128322411	128323124	MYB	MECOM	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	bone marrow	UBERON:0002371	MUTZ-3	CVCL_1433	malignant cell	CL:0001064	Functional perturbation assay; TF binding assay; Enhancer essentiality assay; Target-gene expression assay	Genome-wide CRISPR/Cas9 enhancer scan; ATAC-seq; H3K27ac ChIP-seq; p300 ChIP-seq; MYB ChIP-seq; CUT&RUN; deep amplicon sequencing	CRISPR/Cas9 MYB-motif mutagenesis; MYB knockout; MYBMIM-mediated MYB-CBP/p300 inhibition; RT-qPCR; Western blot; Flow cytometry; differentiation and cell-viability assays
E_03715	2019	31422875	Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs	Mus musculus	mm10	chr3	34752523	34766449	Nanog	Sox2	Super-enhancer	Active	Normal	NA	NA	NA	embryo	NA	129×CAST F1 mouse ESCs	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; In vivo functional validation; Super-enhancer methylation dynamics; TF/chromatin-state coupling; endogenous allele-specific reporter	H3K27ac ChIP-seq; RNA-seq; WGBS; ATAC-seq	Endogenous allele-specific reporter; targeted enhancer perturbation; ChIP-qPCR; RT-qPCR; DNA FISH; immunofluorescence/confocal imaging; Allele-specific reporter assay; In vivo phenotyping
E_03716	2019	31422875	Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs	Mus musculus	mm10	chr3	34752523	34766449	Nanog	Sox2	Super-enhancer	Active	Normal	NA	NA	NA	embryo	NA	v6.5 mouse ESCs	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; In vivo functional validation; Super-enhancer methylation dynamics; TF/chromatin-state coupling; endogenous allele-specific reporter	H3K27ac ChIP-seq; RNA-seq; WGBS; ATAC-seq	Endogenous allele-specific reporter; targeted enhancer perturbation; ChIP-qPCR; RT-qPCR; DNA FISH; immunofluorescence/confocal imaging; Allele-specific reporter assay; In vivo phenotyping
E_03717	2019	31422875	Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs	Mus musculus	mm10	chr3	34752523	34766449	Pou5f1	Sox2	Super-enhancer	Active	Normal	NA	NA	NA	embryo	NA	129×CAST F1 mouse ESCs	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; In vivo functional validation; Super-enhancer methylation dynamics; TF/chromatin-state coupling; endogenous allele-specific reporter	H3K27ac ChIP-seq; RNA-seq; WGBS; ATAC-seq	Endogenous allele-specific reporter; targeted enhancer perturbation; ChIP-qPCR; RT-qPCR; DNA FISH; immunofluorescence/confocal imaging; Allele-specific reporter assay; In vivo phenotyping
E_03718	2019	31422875	Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs	Mus musculus	mm10	chr3	34752523	34766449	Pou5f1	Sox2	Super-enhancer	Active	Normal	NA	NA	NA	embryo	NA	v6.5 mouse ESCs	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; In vivo functional validation; Super-enhancer methylation dynamics; TF/chromatin-state coupling; endogenous allele-specific reporter	H3K27ac ChIP-seq; RNA-seq; WGBS; ATAC-seq	Endogenous allele-specific reporter; targeted enhancer perturbation; ChIP-qPCR; RT-qPCR; DNA FISH; immunofluorescence/confocal imaging; Allele-specific reporter assay; In vivo phenotyping
E_03719	2019	31422875	Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs	Mus musculus	mm10	chr7	3198900	3202780	Nanog	NA	Super-enhancer	Active	Normal	NA	NA	NA	embryo	NA	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; In vivo functional validation; Super-enhancer methylation dynamics; TF/chromatin-state coupling; endogenous allele-specific reporter	H3K27ac ChIP-seq; RNA-seq; WGBS; ATAC-seq	Endogenous allele-specific reporter; targeted enhancer perturbation; ChIP-qPCR; RT-qPCR; DNA FISH; immunofluorescence/confocal imaging; Allele-specific reporter assay; In vivo phenotyping
E_03720	2019	31422875	Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs	Mus musculus	mm10	chr7	3198900	3202780	Pou5f1	NA	Super-enhancer	Active	Normal	NA	NA	NA	embryo	NA	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; In vivo functional validation; Super-enhancer methylation dynamics; TF/chromatin-state coupling; endogenous allele-specific reporter	H3K27ac ChIP-seq; RNA-seq; WGBS; ATAC-seq	Endogenous allele-specific reporter; targeted enhancer perturbation; ChIP-qPCR; RT-qPCR; DNA FISH; immunofluorescence/confocal imaging; Allele-specific reporter assay; In vivo phenotyping
E_03721	2021	33980539	Selective Requirement of MYB for Oncogenic Hyperactivation of a Translocated Enhancer in Leukemia	Homo sapiens	hg19	chr3	128322411	128323124	MYB	MECOM	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	bone marrow	UBERON:0002371	MUTZ-3/inv(3) AML models	NA	myeloid leukemia cell	NA	Endogenous enhancer functional validation; TF-site causality; leukemia dependency	CRISPR-Cas9 enhancer scanning; ATAC-seq; ChIP-seq; transcriptomic profiling	individual sgRNA validation; endogenous MYB-site mutation; RT-qPCR; Flow cytometry; differentiation and viability assays
E_03722	2021	33980539	Selective Requirement of MYB for Oncogenic Hyperactivation of a Translocated Enhancer in Leukemia	Homo sapiens	hg19	chr3	128322411	128323124	MYB	MECOM	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	blood	UBERON:0000178	MUTZ-3/inv(3) AML models	NA	myeloid leukemia cell	NA	Endogenous enhancer functional validation; TF-site causality; leukemia dependency	CRISPR-Cas9 enhancer scanning; ATAC-seq; ChIP-seq; transcriptomic profiling	individual sgRNA validation; endogenous MYB-site mutation; RT-qPCR; Flow cytometry; differentiation and viability assays
E_03723	2014	25369933	Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia	Mus musculus	mm10	chr15	63254341	63256341	Rbpj	Myc	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	thymus	UBERON:0002370	primary murine T-ALL blasts and T-ALL cell models	NA	T lymphoblast	NA	TF occupancy; long-range enhancer-promoter interaction; drug-response functional assay	NOTCH1/RBPJ/H3K27ac ChIP-seq; chromatin-state profiling	3C/long-range contact assays; enhancer reporter and RBPJ-site mutation; gamma-secretase inhibition; BRD4 inhibition; RT-qPCR
E_03724	2021	33980539	Selective Requirement of MYB for Oncogenic Hyperactivation of a Translocated Enhancer in Leukemia	Homo sapiens	hg19	chr3	128322411	128323124	MYB	MECOM	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	blood	UBERON:0000178	MUTZ-3	CVCL_1433	AML hematopoietic progenitor-like leukemia cell	NA	Endogenous enhancer sequence-function mapping; TF-site causality; leukemia fitness and differentiation	CRISPR/Cas9 enhancer scan; ATAC-seq; p300/H3K27ac chromatin profiling; TF chromatin profiling; transcriptomic analysis	individual sgRNA validation; endogenous MYB-motif mutation; MYB knockout; deep amplicon sequencing; qRT-PCR; Flow cytometry; differentiation and viability assays
E_03725	2022	34707247	A stem cell marker KLF5 regulates CCAT1 via three-dimensional genome structure in colorectal cancer cells	Homo sapiens	hg19	chr13	74003796	74004073	KLF5	KLF5	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	SW48	CVCL_1724	malignant cell	CL:0001064	Functional perturbation assay; TF binding assay; Chromatin interaction assay	NA	KLF5 ChIP-qPCR; BRD4 ChIP-qPCR; MED1 ChIP-qPCR; RAD21 ChIP-qPCR; KLF5 inhibitor ML264 treatment; qRT-PCR; ChIP
E_03726	2021	34146516	Functional annotation of the 2q35 breast cancer risk locus implicates a structural variant in influencing activity of a long-range enhancer element	Homo sapiens	hg19	chr2	217955458	217957767	NA	IGFBP5	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	MDA-MB-231	CVCL_0062	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay	ChIP-seq	Luciferase reporter assay; CRISPR knockout; CRISPRi; RT-qPCR
E_03727	2014	24778216	Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation	Homo sapiens	hg19	chr19	51352419	51358208	AR	KLK2	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Long-range enhancer-RNA-mediated regulation of KLK2; enhancer-promoter looping	AR/H3K27ac/H3K4me1 ChIP-seq integration	DHT stimulation; enhancer-RNA RNAi; 3C; ChIP-qPCR; RT-qPCR; eRNA mapping
E_03728	2014	24778216	Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation	Homo sapiens	hg19	chr19	51352419	51358208	AR	KLK2	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer-RNA perturbation; enhancer-promoter looping; AR occupancy; long-range KLK3e-to-KLK2 promoter regulation	AR/H3K27ac/H3K4me1 ChIP-seq integration	DHT stimulation; eRNA RNAi; 3C; ChIP-qPCR; RT-qPCR; eRNA mapping
E_03729	2014	24778216	Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation	Homo sapiens	hg19	chr19	51358995	51369041	AR	KLK3	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_03730	2014	24778216	Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation	Homo sapiens	hg19	chr19	51358995	51369041	AR	KLK3	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	VCaP	CVCL_2235	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; 3C; RT-qPCR/qPCR
E_03731	2014	25369933	Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia	Mus musculus	mm10	chr15	63254341	63256341	Notch1	Myc	Enhancer	Active	Disease	acute lymphoblastic leukemia	NA	NA	blood	UBERON:0000178	T-acute lymphoblastic leukemia (T-ALL)	NA	T cell	CL:0000084	Enhancer activity assay; Chromatin interaction assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay; 3C; RT-qPCR/qPCR
E_03732	2019	31422875	Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs	Mus musculus	mm10	chr3	34752523	34766449	NA	Sox2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; In vivo functional validation; Sox2 super-enhancer; endogenous allele-specific methylation reporter study	Single-cell/allele-specific methylation and chromatin profiling	Endogenous reporter engineering; differentiation assays; targeted epigenetic manipulation; Allele-specific reporter assay; In vivo phenotyping
E_03733	2014	24778216	Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation	Homo sapiens	hg19	chr19	51347500	51349700	AR	KLK3	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	Primary epithelial	NA	epithelial cell	CL:0000066	Enhancer activity assay	ChIP-seq	Luciferase reporter assay
E_03734	2021	34146516	Functional annotation of the 2q35 breast cancer risk locus implicates a structural variant in influencing activity of a long-range enhancer element	Homo sapiens	hg19	chr2	218305944	218306443	NA	IGFBP5	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	MDA-MB-231	CVCL_0062	malignant cell	CL:0001064	Enhancer activity assay	ChIP-seq	Luciferase reporter assay
E_03735	2021	34153138	A Functional Variant on 9p21.3 Related to Glioma Risk Affects Enhancer Activity and Modulates Expression of CDKN2B-AS1	Homo sapiens	hg19	chr9	22102683	22103683	NA	CDKN2B-AS1	Enhancer	Active	Disease	glioblastoma	MONDO:0018177	NA	brain	UBERON:0000955	U-118MG	CVCL_0633	glioblastoma cell	CL:0001063	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	ChIP-seq; RNA-seq; Hi-C; eQTL analysis	Luciferase reporter assay; CRISPR knockout; RT-qPCR
E_03736	2018	29898989	Disruption of a -35 kb Enhancer Impairs CTCF Binding and MLH1 Expression in Colorectal Cells	Homo sapiens	hg19	chr3	36999364	37001216	NA	MLH1	Enhancer	Active	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	SW620	CVCL_0547	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Disease-variant functional analysis; Endogenous enhancer perturbation	ChIA-PET; RNA-seq; CRISPR genetic screen	qRT-PCR, and ChIP-qPCR; CRISPR-Cas9 endogenous deletion/editing; Luciferase reporter assay; ChIP; 3C; Reporter assay
E_03737	2023	36095844	EVI1 drives leukemogenesis through aberrant ERG activation	Homo sapiens	hg38	chr21	38576000	38577000	MECOM	ERG	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	bone marrow	UBERON:0002371	primary MECOM-rearranged AML cells	NA	myeloblast	CL:0000835	Functional perturbation assay; TF binding assay; In vivo functional validation; Enhancer reporter assay	MECOM/EVI1 ChIP-seq; H3K27ac profiling; ATAC-seq; RNA-seq; leukemia dependency screening	MECOM/EVI1 ChIP-qPCR; ERG+85 luciferase reporter assay; EVI1 knockdown/withdrawal; ERG knockdown and rescue; RT-qPCR; Western blot; differentiation/colony assays; In vivo phenotyping
E_03738	2018	29035388	A novel HER2 gene body enhancer contributes to HER2 expression	Homo sapiens	hg38	chr17	39725049	39725326	TFAP2C	ERBB2	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	primary HER2-positive breast tumors	NA	breast carcinoma cell lines; HEK293T reporter cell	NA	functional gene-body enhancer-core mapping plus TF and epigenetic validation	ENCODE DNase/H3K4me1/H3K27ac integration; TFAP2C ChIP-seq; primary-tumor methylation-expression analysis	serial reporter deletion mapping; luciferase; EMSA/supershift; TFAP2C ChIP-qPCR; TFAP2C siRNA; CRISPR-Cas9 intron-21 editing; dCas9-DNMT3A targeted methylation; bisulfite sequencing; RT-PCR; Western blot
E_03739	2012	22771493	Direct cooperation between androgen receptor and E2F1 reveals a common regulation mechanism for androgen-responsive genes in prostate cells	Homo sapiens	hg19	chr8	124321890	124323890	AR	ATAD2	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	NA	NA	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay; 3C; RT-qPCR/qPCR
E_03740	2012	22771493	Direct cooperation between androgen receptor and E2F1 reveals a common regulation mechanism for androgen-responsive genes in prostate cells	Homo sapiens	hg19	chr8	124321890	124323890	E2F1	ATAD2	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	NA	NA	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay; 3C; RT-qPCR/qPCR
E_03741	2012	22771493	Direct cooperation between androgen receptor and E2F1 reveals a common regulation mechanism for androgen-responsive genes in prostate cells	Homo sapiens	hg19	chr8	124323890	124325890	AR	ATAD2	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	NA	NA	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay; 3C; RT-qPCR/qPCR
E_03742	2012	22771493	Direct cooperation between androgen receptor and E2F1 reveals a common regulation mechanism for androgen-responsive genes in prostate cells	Homo sapiens	hg19	chr8	124323890	124325890	E2F1	ATAD2	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	NA	NA	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay; 3C; RT-qPCR/qPCR
E_03743	2012	22771493	Direct cooperation between androgen receptor and E2F1 reveals a common regulation mechanism for androgen-responsive genes in prostate cells	Homo sapiens	hg19	chr8	124319890	124321890	AR	ATAD2	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	NA	NA	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay; 3C; RT-qPCR/qPCR
E_03744	2012	22771493	Direct cooperation between androgen receptor and E2F1 reveals a common regulation mechanism for androgen-responsive genes in prostate cells	Homo sapiens	hg19	chr8	124319890	124321890	E2F1	ATAD2	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	NA	NA	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay; 3C; RT-qPCR/qPCR
E_03745	2023	36632736	TAL1 activation in T-cell acute lymphoblastic leukemia: a novel oncogenic 3' neo-enhancer	Homo sapiens	hg19	chr1	47677544	47677944	MYB	TAL1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	primary T-ALL UPNT-802	NA	T lymphoblast	NA	Somatic neo-enhancer discovery and functional engineering	WGS; H3K27ac ChIP-seq; H3K4me3 ChIP-seq; RNA-seq	CRISPR engineering; Reporter assay; Sanger sequencing; allele-specific expression analysis
E_03746	2016	26673704	Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus	Homo sapiens	hg19	chr7	117227200	117229503	FOXA2	CFTR	Enhancer	Active	Normal	NA	NA	NA	intestinal epithelium	UBERON:0001277	Caco-2	CVCL_0025	intestinal epithelial cell	CL:0002563	Endogenous enhancer deletion; chromatin interaction; TF occupancy	4C-seq; DNase/open-chromatin and ChIP-seq integration	CRISPR-Cas9 ~1.2-kb enhancer deletion; FOXA2 ChIP-qPCR; RT-qPCR; 3C/4C validation; CRISPR-Cas9; siRNA knockdown
E_03747	2016	26673704	Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus	Homo sapiens	hg19	chr7	117227200	117229503	FOXA2	CFTR	Enhancer	Active	Normal	NA	NA	NA	intestinal epithelium	UBERON:0001277	human epithelial comparison models	NA	intestinal epithelial cell	CL:0002563	Endogenous enhancer deletion; chromatin interaction; TF occupancy	4C-seq; DNase/open-chromatin and ChIP-seq integration	CRISPR-Cas9 ~1.2-kb enhancer deletion; FOXA2 ChIP-qPCR; RT-qPCR; 3C/4C validation; CRISPR-Cas9; siRNA knockdown
E_03748	2018	29035388	A novel HER2 gene body enhancer contributes to HER2 expression	Homo sapiens	hg38	chr17	39725049	39725326	TFAP2C	ERBB2	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	SK-BR-3	CVCL_0033	malignant cell	CL:0001064	functional gene-body enhancer-core mapping plus TF and epigenetic validation	ENCODE DNase/H3K4me1/H3K27ac integration; TFAP2C ChIP-seq; primary-tumor methylation-expression analysis	serial reporter deletion mapping; luciferase; EMSA/supershift; TFAP2C ChIP-qPCR; TFAP2C siRNA; CRISPR-Cas9 intron-21 editing; dCas9-DNMT3A targeted methylation; bisulfite sequencing; RT-PCR; Western blot
E_03749	2018	29035388	A novel HER2 gene body enhancer contributes to HER2 expression	Homo sapiens	hg38	chr17	39725049	39725326	TFAP2C	ERBB2	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	BT-474	CVCL_0179	malignant cell	CL:0001064	functional gene-body enhancer-core mapping plus TF and epigenetic validation	ENCODE DNase/H3K4me1/H3K27ac integration; TFAP2C ChIP-seq; primary-tumor methylation-expression analysis	serial reporter deletion mapping; luciferase; EMSA/supershift; TFAP2C ChIP-qPCR; TFAP2C siRNA; CRISPR-Cas9 intron-21 editing; dCas9-DNMT3A targeted methylation; bisulfite sequencing; RT-PCR; Western blot
E_03750	2018	29035388	A novel HER2 gene body enhancer contributes to HER2 expression	Homo sapiens	hg38	chr17	39725049	39725326	TFAP2C	ERBB2	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	HCC1954	CVCL_1259	malignant cell	CL:0001064	functional gene-body enhancer-core mapping plus TF and epigenetic validation	ENCODE DNase/H3K4me1/H3K27ac integration; TFAP2C ChIP-seq; primary-tumor methylation-expression analysis	serial reporter deletion mapping; luciferase; EMSA/supershift; TFAP2C ChIP-qPCR; TFAP2C siRNA; CRISPR-Cas9 intron-21 editing; dCas9-DNMT3A targeted methylation; bisulfite sequencing; RT-PCR; Western blot
E_03751	2023	36095844	EVI1 drives leukemogenesis through aberrant ERG activation	Homo sapiens	hg38	chr21	38376000	38377000	MECOM	ERG	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	bone marrow	UBERON:0002371	HNT-34	CVCL_2071	malignant cell	CL:0001064	In vivo functional validation; Functional validation; TF binding	ChIP-seq; ATAC-seq; RNA-seq	CRISPR KO, shRNA KD; RT-qPCR; Western blot, Transgenic reporter assay; In vivo phenotyping
E_03752	2023	36095844	EVI1 drives leukemogenesis through aberrant ERG activation	Homo sapiens	hg38	chr21	38576000	38577000	MECOM	ERG	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	bone marrow	UBERON:0002371	EVI1-high human AML cell models	NA	myeloblast	CL:0000835	Functional perturbation assay; TF binding assay; In vivo functional validation; Enhancer reporter assay	MECOM/EVI1 ChIP-seq; H3K27ac profiling; ATAC-seq; RNA-seq; leukemia dependency screening	MECOM/EVI1 ChIP-qPCR; ERG+85 luciferase reporter assay; EVI1 knockdown/withdrawal; ERG knockdown and rescue; RT-qPCR; Western blot; differentiation/colony assays; In vivo phenotyping
E_03753	2018	29035388	A novel HER2 gene body enhancer contributes to HER2 expression	Homo sapiens	hg38	chr17	39725049	39725326	TFAP2C	ERBB2	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	HEK293T	CVCL_0063	breast carcinoma cell lines; HEK293T reporter cell	NA	functional gene-body enhancer-core mapping plus TF and epigenetic validation	ENCODE DNase/H3K4me1/H3K27ac integration; TFAP2C ChIP-seq; primary-tumor methylation-expression analysis	serial reporter deletion mapping; luciferase; EMSA/supershift; TFAP2C ChIP-qPCR; TFAP2C siRNA; CRISPR-Cas9 intron-21 editing; dCas9-DNMT3A targeted methylation; bisulfite sequencing; RT-PCR; Western blot
E_03754	2023	36632736	TAL1 activation in T-cell acute lymphoblastic leukemia: a novel oncogenic 3' neo-enhancer	Homo sapiens	hg19	chr1	47677466	47678021	MYB	TAL1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Jurkat	CVCL_0065	T lymphoblast	NA	Neo-enhancer activity; TF binding; endogenous genetic perturbation	H3K27ac/H3K4me1 ChIP-seq; ACT-seq; RNA-seq	Luciferase reporter assay; CRISPR-Cas9 neo-enhancer engineering; dCas9-KRAB-MECP2 repression; MYB ChIP-qPCR; RT-qPCR; Western blot; Sanger sequencing
E_03755	2023	36632736	TAL1 activation in T-cell acute lymphoblastic leukemia: a novel oncogenic 3' neo-enhancer	Homo sapiens	hg19	chr1	47677466	47678021	MYB	TAL1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	PDX UPNT-613	NA	T lymphoblast	NA	Neo-enhancer activity; TF binding; endogenous genetic perturbation	H3K27ac/H3K4me1 ChIP-seq; ACT-seq; RNA-seq	Luciferase reporter assay; CRISPR-Cas9 neo-enhancer engineering; dCas9-KRAB-MECP2 repression; MYB ChIP-qPCR; RT-qPCR; Western blot; Sanger sequencing
E_03756	2023	36632736	TAL1 activation in T-cell acute lymphoblastic leukemia: a novel oncogenic 3' neo-enhancer	Homo sapiens	hg19	chr1	47677466	47678021	MYB	TAL1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	PDX UPNT-802	NA	T lymphoblast	NA	Neo-enhancer activity; TF binding; endogenous genetic perturbation	H3K27ac/H3K4me1 ChIP-seq; ACT-seq; RNA-seq	Luciferase reporter assay; CRISPR-Cas9 neo-enhancer engineering; dCas9-KRAB-MECP2 repression; MYB ChIP-qPCR; RT-qPCR; Western blot; Sanger sequencing
E_03757	2023	36632736	TAL1 activation in T-cell acute lymphoblastic leukemia: a novel oncogenic 3' neo-enhancer	Homo sapiens	hg19	chr1	47677466	47678021	MYB	TAL1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Peer	CVCL_1913	T lymphoblast	NA	Neo-enhancer activity; TF binding; endogenous genetic perturbation	H3K27ac/H3K4me1 ChIP-seq; ACT-seq; RNA-seq	Luciferase reporter assay; CRISPR-Cas9 neo-enhancer engineering; dCas9-KRAB-MECP2 repression; MYB ChIP-qPCR; RT-qPCR; Western blot; Sanger sequencing
E_03758	2023	36632736	TAL1 activation in T-cell acute lymphoblastic leukemia: a novel oncogenic 3' neo-enhancer	Homo sapiens	hg19	chr1	47677466	47678021	MYB	TAL1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Jurkat	CVCL_0065	T lymphoblast	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	Luciferase reporter assay; CRISPR knockout; ChIP-qPCR; RT-qPCR; Western blot
E_03759	2023	36632736	TAL1 activation in T-cell acute lymphoblastic leukemia: a novel oncogenic 3' neo-enhancer	Homo sapiens	hg19	chr1	47677466	47678021	MYB	TAL1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Peer	CVCL_1913	T lymphoblast	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	Luciferase reporter assay; CRISPR knockout; ChIP-qPCR; RT-qPCR; Western blot
E_03760	2018	29903884	Sex reversal following deletion of a single distal enhancer of Sox9	Mus musculus	mm10	chr11	112217210	112217767	Sry	Sox9	Enhancer	Active	Normal	NA	NA	NA	gonad	NA	Testis	NA	NA	NA	Endogenous enhancer perturbation; In vivo functional validation; TF-binding/chromatin assay	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_03761	2012	22771493	Direct cooperation between androgen receptor and E2F1 reveals a common regulation mechanism for androgen-responsive genes in prostate cells	Homo sapiens	hg19	chr8	124417000	124427000	AR	ATAD2	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ChIP-seq	Luciferase reporter assay; 3C-RT-qPCR; RT-qPCR; ChIP
E_03762	2015	25775043	Functional annotation of native enhancers with a Cas9-histone demethylase fusion	Mus musculus	mm10	chr17	35503912	35504118	NA	Pou5f1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay; Epigenome editing assay	ATAC-seq data integration; gene-expression microarray	dCas9-LSD1 sgRNA targeting of the Pou5f1 distal enhancer; Luciferase reporter assay; colony phenotype assay; RT-qPCR
E_03763	2015	25775043	Functional annotation of native enhancers with a Cas9-histone demethylase fusion	Mus musculus	mm10	chr17	35504981	35505186	NA	Pou5f1	Enhancer	Inactive	Normal	NA	NA	NA	embryo	NA	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Epigenome editing assay; Functional enhancer-state assay	ATAC-seq data integration	dCas9-LSD1 sgRNA targeting of the Pou5f1 proximal enhancer; colony phenotype assay; RT-qPCR
E_03764	2021	34599190	Enhancer-associated H3K4 methylation safeguards in vitro germline competence	Mus musculus	mm10	chr1	13084831	13085465	NA	Prdm14	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	ES-R1	CVCL_2167	embryonic stem cell	CL:0002322	Enhancer chromatin-state profiling; functional enhancer deletion; germline-competence assay	H3K4me1/H3K4me2/H3K4me3/H3K27ac ChIP-seq; ATAC-seq; RNA-seq; DNA methylation profiling; 4C-seq; Capture Hi-C integration; single-cell RNA-seq	CRISPR-Cas9 enhancer deletion; clonal genotyping/Sanger validation; RT-qPCR; CD15/CD61 flow cytometry
E_03765	2021	34599190	Enhancer-associated H3K4 methylation safeguards in vitro germline competence	Mus musculus	mm10	chr1	13093655	13096290	NA	Prdm14	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	ES-R1	CVCL_2167	embryonic stem cell	CL:0002322	Enhancer chromatin-state profiling; functional enhancer deletion; germline-competence assay	H3K4me1/H3K4me2/H3K4me3/H3K27ac ChIP-seq; ATAC-seq; RNA-seq; DNA methylation profiling; 4C-seq; Capture Hi-C integration; single-cell RNA-seq	CRISPR-Cas9 enhancer deletion; clonal genotyping/Sanger validation; RT-qPCR; CD15/CD61 flow cytometry
E_03766	2021	34599190	Enhancer-associated H3K4 methylation safeguards in vitro germline competence	Mus musculus	mm10	chr14	99338943	99341862	NA	Klf5	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	ES-R1	CVCL_2167	embryonic stem cell	CL:0002322	Enhancer chromatin-state profiling; functional enhancer deletion; germline-competence assay	H3K4me1/H3K4me2/H3K4me3/H3K27ac ChIP-seq; ATAC-seq; RNA-seq; DNA methylation profiling; 4C-seq; Capture Hi-C integration; single-cell RNA-seq	CRISPR-Cas9 enhancer deletion; clonal genotyping/Sanger validation; RT-qPCR; CD15/CD61 flow cytometry
E_03767	2021	34599190	Enhancer-associated H3K4 methylation safeguards in vitro germline competence	Mus musculus	mm10	chr12	86497006	86503356	NA	Esrrb	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	ES-R1	CVCL_2167	embryonic stem cell	CL:0002322	Enhancer chromatin-state profiling; functional enhancer deletion; germline-competence assay	H3K4me1/H3K4me2/H3K4me3/H3K27ac ChIP-seq; ATAC-seq; RNA-seq; DNA methylation profiling; 4C-seq; Capture Hi-C integration; single-cell RNA-seq	CRISPR-Cas9 enhancer deletion; clonal genotyping/Sanger validation; RT-qPCR; CD15/CD61 flow cytometry
E_03768	2021	34599190	Enhancer-associated H3K4 methylation safeguards in vitro germline competence	Mus musculus	mm10	chr1	13072129	13076981	NA	Prdm14	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	ES-R1	CVCL_2167	primordial germ cell-like cell	NA	Enhancer chromatin-state profiling; functional enhancer deletion; germline-competence assay	H3K4me1/H3K4me2/H3K4me3/H3K27ac ChIP-seq; ATAC-seq; RNA-seq; DNA methylation profiling; 4C-seq; Capture Hi-C integration; single-cell RNA-seq	CRISPR-Cas9 enhancer deletion; clonal genotyping/Sanger validation; RT-qPCR; CD15/CD61 flow cytometry
E_03769	2021	34599190	Enhancer-associated H3K4 methylation safeguards in vitro germline competence	Mus musculus	mm10	chr1	13072129	13076981	NA	Prdm14	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	ES-R1	CVCL_2167	epiblast-like cell	NA	Enhancer chromatin-state profiling; functional enhancer deletion; germline-competence assay	H3K4me1/H3K4me2/H3K4me3/H3K27ac ChIP-seq; ATAC-seq; RNA-seq; DNA methylation profiling; 4C-seq; Capture Hi-C integration; single-cell RNA-seq	CRISPR-Cas9 enhancer deletion; clonal genotyping/Sanger validation; RT-qPCR; CD15/CD61 flow cytometry
E_03770	2021	34599190	Enhancer-associated H3K4 methylation safeguards in vitro germline competence	Mus musculus	mm10	chr1	13084831	13085465	NA	Prdm14	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	ES-R1	CVCL_2167	primordial germ cell-like cell	NA	Enhancer chromatin-state profiling; functional enhancer deletion; germline-competence assay	H3K4me1/H3K4me2/H3K4me3/H3K27ac ChIP-seq; ATAC-seq; RNA-seq; DNA methylation profiling; 4C-seq; Capture Hi-C integration; single-cell RNA-seq	CRISPR-Cas9 enhancer deletion; clonal genotyping/Sanger validation; RT-qPCR; CD15/CD61 flow cytometry
E_03771	2021	34599190	Enhancer-associated H3K4 methylation safeguards in vitro germline competence	Mus musculus	mm10	chr1	13093655	13096290	NA	Prdm14	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	ES-R1	CVCL_2167	primordial germ cell-like cell	NA	Enhancer chromatin-state profiling; functional enhancer deletion; germline-competence assay	H3K4me1/H3K4me2/H3K4me3/H3K27ac ChIP-seq; ATAC-seq; RNA-seq; DNA methylation profiling; 4C-seq; Capture Hi-C integration; single-cell RNA-seq	CRISPR-Cas9 enhancer deletion; clonal genotyping/Sanger validation; RT-qPCR; CD15/CD61 flow cytometry
E_03772	2021	34599190	Enhancer-associated H3K4 methylation safeguards in vitro germline competence	Mus musculus	mm10	chr1	13093655	13096290	NA	Prdm14	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	ES-R1	CVCL_2167	epiblast-like cell	NA	Enhancer chromatin-state profiling; functional enhancer deletion; germline-competence assay	H3K4me1/H3K4me2/H3K4me3/H3K27ac ChIP-seq; ATAC-seq; RNA-seq; DNA methylation profiling; 4C-seq; Capture Hi-C integration; single-cell RNA-seq	CRISPR-Cas9 enhancer deletion; clonal genotyping/Sanger validation; RT-qPCR; CD15/CD61 flow cytometry
E_03773	2021	34599190	Enhancer-associated H3K4 methylation safeguards in vitro germline competence	Mus musculus	mm10	chr14	99338943	99341862	NA	Klf5	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	ES-R1	CVCL_2167	primordial germ cell-like cell	NA	Enhancer chromatin-state profiling; functional enhancer deletion; germline-competence assay	H3K4me1/H3K4me2/H3K4me3/H3K27ac ChIP-seq; ATAC-seq; RNA-seq; DNA methylation profiling; 4C-seq; Capture Hi-C integration; single-cell RNA-seq	CRISPR-Cas9 enhancer deletion; clonal genotyping/Sanger validation; RT-qPCR; CD15/CD61 flow cytometry
E_03774	2021	34599190	Enhancer-associated H3K4 methylation safeguards in vitro germline competence	Mus musculus	mm10	chr14	99338943	99341862	NA	Klf5	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	ES-R1	CVCL_2167	epiblast-like cell	NA	Enhancer chromatin-state profiling; functional enhancer deletion; germline-competence assay	H3K4me1/H3K4me2/H3K4me3/H3K27ac ChIP-seq; ATAC-seq; RNA-seq; DNA methylation profiling; 4C-seq; Capture Hi-C integration; single-cell RNA-seq	CRISPR-Cas9 enhancer deletion; clonal genotyping/Sanger validation; RT-qPCR; CD15/CD61 flow cytometry
E_03775	2021	34599190	Enhancer-associated H3K4 methylation safeguards in vitro germline competence	Mus musculus	mm10	chr12	86497006	86503356	NA	Esrrb	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	ES-R1	CVCL_2167	primordial germ cell-like cell	NA	Enhancer chromatin-state profiling; functional enhancer deletion; germline-competence assay	H3K4me1/H3K4me2/H3K4me3/H3K27ac ChIP-seq; ATAC-seq; RNA-seq; DNA methylation profiling; 4C-seq; Capture Hi-C integration; single-cell RNA-seq	CRISPR-Cas9 enhancer deletion; clonal genotyping/Sanger validation; RT-qPCR; CD15/CD61 flow cytometry
E_03776	2021	34599190	Enhancer-associated H3K4 methylation safeguards in vitro germline competence	Mus musculus	mm10	chr12	86497006	86503356	NA	Esrrb	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	ES-R1	CVCL_2167	epiblast-like cell	NA	Enhancer chromatin-state profiling; functional enhancer deletion; germline-competence assay	H3K4me1/H3K4me2/H3K4me3/H3K27ac ChIP-seq; ATAC-seq; RNA-seq; DNA methylation profiling; 4C-seq; Capture Hi-C integration; single-cell RNA-seq	CRISPR-Cas9 enhancer deletion; clonal genotyping/Sanger validation; RT-qPCR; CD15/CD61 flow cytometry
E_03777	2022	34059508	Chromatin state dynamics confers specific therapeutic strategies in enhancer subtypes of colorectal cancer	Homo sapiens	hg19	chr11	2233643	2234213	NA	ASCL2	Enhancer	Active	Disease	colorectal adenocarcinoma	MONDO:0005008	DOID:0050861	colon	UBERON:0001155	HCT116/LS513/SW620 HiChIP context	NA	malignant cell	CL:0001064	Chromatin interaction assay; Tumor-specific enhancer mapping; CRISPR epigenomic perturbation	H3K27ac/H3K4me1/H3K4me3/H3K79me2/H3K27me3/H3K9me3 ChIP-seq; RNA-seq; H3K27ac HiChIP	dCas9-KRAB enhancer repression; H3K27ac ChIP-qPCR; 3C; RT-qPCR; proliferation assay
E_03778	2022	34059508	Chromatin state dynamics confers specific therapeutic strategies in enhancer subtypes of colorectal cancer	Homo sapiens	hg19	chr12	130610556	130610854	NA	FZD10	Enhancer	Active	Disease	colorectal adenocarcinoma	MONDO:0005008	DOID:0050861	colon	UBERON:0001155	HCT116/LS513/SW620 HiChIP context	NA	malignant cell	CL:0001064	Chromatin interaction assay; Tumor-specific enhancer mapping; CRISPR epigenomic perturbation	H3K27ac/H3K4me1/H3K4me3/H3K79me2/H3K27me3/H3K9me3 ChIP-seq; RNA-seq; H3K27ac HiChIP	dCas9-KRAB enhancer repression; H3K27ac ChIP-qPCR; 3C; RT-qPCR; proliferation assay
E_03779	2024	38855864	Chromatin profiling identifies chondrocyte-specific Sox9 enhancers important for skeletal development	Mus musculus	mm9	chr11	112334364	112335294	Pitx1	Sox9	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	C3H/10T1/2 clone 8	CVCL_0190	fibroblast	CL:0000057	Enhancer activity assay; Endogenous enhancer perturbation; In vivo functional validation	NA	Luciferase reporter assay; RT-qPCR; Western blot; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_03780	2024	38855864	Chromatin profiling identifies chondrocyte-specific Sox9 enhancers important for skeletal development	Mus musculus	mm9	chr11	112482190	112483273	Pitx1	Sox9	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	C3H/10T1/2 clone 8	CVCL_0190	fibroblast	CL:0000057	Enhancer activity assay; Endogenous enhancer perturbation; In vivo functional validation	NA	Luciferase reporter assay; RT-qPCR; Western blot; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_03781	2024	38965263	TWEAK/Fn14 signalling driven super-enhancer reprogramming promotes pro-metastatic metabolic rewiring in triple-negative breast cancer	Homo sapiens	hg38	chr7	108960000	108961000	MAFG	NAMPT	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	MDA-MB-231	CVCL_0062	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; ATAC-seq; RNA-seq; HiChIP	CRISPR knockout; ChIP-qPCR, qRT-PCR; Western blot
E_03782	2023	37373188	STAT3-Mediated Promoter-Enhancer Interaction Up-Regulates Inhibitor of DNA Binding 1 (ID1) to Promote Colon Cancer Progression	Homo sapiens	hg38	chr20	31595392	31597085	STAT3	ID1	Enhancer	Active	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; GRO-seq	Luciferase reporter assay; ChIP-qPCR; CRISPR knockout, qRT-PCR; Western blot, 3C Assay; CRISPR-Cas9; Reporter assay; RT-qPCR; qPCR; Western blot
E_03783	2022	35575404	Molecular Mechanisms of ARID5B-Mediated Genetic Susceptibility to Acute Lymphoblastic Leukemia	Homo sapiens	hg38	chr10	61960755	61962481	MEF2C	ARID5B	Enhancer	Active	Disease	B-cell acute lymphoblastic leukemia	MONDO:0004947	DOID:0080638	blood	UBERON:0000178	NALM-6	CVCL_0092	B-lymphoblast	CL:0017006	Enhancer activity assay; Functional perturbation assay; TF binding assay; Disease-variant functional analysis	ChIP-seq; ATAC-seq; RNA-seq; GWAS	Luciferase reporter assay; ChIP-qPCR, CRISPR knockout, CRISPRi; RT-qPCR; Western blot; ChIP
E_03784	2018	30590035	The TFAP2C-Regulated OCT4 Naive Enhancer Is Involved in Human Germline Formation	Homo sapiens	hg19	chr6	31132200	31132800	TFAP2C	POU5F1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	human ESC-derived primordial germ cell-like cells and fetal hPGCs	NA	primordial germ cell	CL:0000670	Endogenous enhancer perturbation; Enhancer activity; TF occupancy	ATAC-seq; TFAP2C/chromatin-state ChIP-seq; RNA-seq	CRISPR enhancer deletion; Reporter assay; qRT-PCR; Flow cytometry; germline differentiation assays; CRISPR-Cas9
E_03785	2018	30590035	The TFAP2C-Regulated OCT4 Naive Enhancer Is Involved in Human Germline Formation	Homo sapiens	hg19	chr6	31132200	31132800	TFAP2C	POU5F1	Enhancer	Active	Normal	NA	NA	NA	gonad	NA	human naive pluripotent stem cells / hESC	NA	embryonic stem cell	CL:0002322	Chromatin-state profiling; Endogenous enhancer perturbation; Enhancer activity; TF binding; Endogenous enhancer deletion; germline differentiation assay	ATAC-seq; TFAP2C ChIP-seq integration; RNA-seq	CRISPR-Cas9 enhancer deletion; TFAP2C ChIP-qPCR; qRT-PCR; Flow cytometry; immunofluorescence/hPGCLC differentiation; CRISPR-Cas9 endogenous deletion/editing
E_03786	2018	30590035	The TFAP2C-Regulated OCT4 Naive Enhancer Is Involved in Human Germline Formation	Homo sapiens	hg19	chr6	31132200	31132800	TFAP2C	POU5F1	Enhancer	Active	Normal	NA	NA	NA	gonad	NA	human primordial germ cells (hPGCs)	NA	primordial germ cell	CL:0000670	Chromatin-state profiling; Endogenous enhancer perturbation; Enhancer activity; TF binding; Endogenous enhancer deletion; germline differentiation assay	ATAC-seq; TFAP2C ChIP-seq integration; RNA-seq	CRISPR-Cas9 enhancer deletion; TFAP2C ChIP-qPCR; qRT-PCR; Flow cytometry; immunofluorescence/hPGCLC differentiation; CRISPR-Cas9 endogenous deletion/editing
E_03787	2018	30590035	The TFAP2C-Regulated OCT4 Naive Enhancer Is Involved in Human Germline Formation	Homo sapiens	hg19	chr6	31132200	31132800	TFAP2C	POU5F1	Enhancer	Active	Normal	NA	NA	NA	gonad	NA	human primordial germ cell-like cells (hPGCLCs)	NA	primordial germ cell-like cell	NA	Enhancer activity; TF binding; Endogenous enhancer deletion; germline differentiation assay	ATAC-seq; TFAP2C ChIP-seq integration; RNA-seq	CRISPR-Cas9 enhancer deletion; TFAP2C ChIP-qPCR; qRT-PCR; Flow cytometry; immunofluorescence/hPGCLC differentiation; CRISPR-Cas9
E_03788	2017	28982762	A dynamic interplay of enhancer elements regulates Klf4 expression in na?ve pluripotency	Mus musculus	mm10	chr4	55559000	55560500	Pou5f1	Klf4	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	P3/NS1/1-Ag4.1	CVCL_2155	embryonic stem cell	CL:0002322	Functional perturbation assay	ChIP-exo; ATAC-seq; RNA-seq	CRISPR knockout; Luciferase reporter assay; RT-qPCR; ChIP-qPCR; CRISPR-Cas9
E_03789	2026	41505091	YAP-TEAD regulates the super-enhancer network to control early surface ectoderm commitment	Homo sapiens	hg19	chr8	102449260	102449687	NA	GRHL2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Human embryonic stem cells	NA	embryonic stem cell	CL:0002322	Functional perturbation assay; TF binding assay; Chromatin interaction assay	CUT&Tag-seq; ATAC-seq; RNA-seq, HiChIP	CRISPR knockout, CRISPRi; RT-qPCR; Western blot
E_03790	2026	41505091	YAP-TEAD regulates the super-enhancer network to control early surface ectoderm commitment	Homo sapiens	hg19	chr8	102467180	102467504	NA	GRHL2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Human embryonic stem cells	NA	embryonic stem cell	CL:0002322	Functional perturbation assay; TF binding assay; Chromatin interaction assay	CUT&Tag-seq; ATAC-seq; RNA-seq, HiChIP	CRISPR knockout, CRISPRi; RT-qPCR; Western blot
E_03791	2026	41505091	YAP-TEAD regulates the super-enhancer network to control early surface ectoderm commitment	Homo sapiens	hg19	chr8	102486442	102486801	NA	GRHL2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Human embryonic stem cells	NA	embryonic stem cell	CL:0002322	Functional perturbation assay; TF binding assay; Chromatin interaction assay	CUT&Tag-seq; ATAC-seq; RNA-seq, HiChIP	CRISPR knockout, CRISPRi; RT-qPCR; Western blot
E_03792	2024	38356460	ETV6::ACSL6 translocation-driven super-enhancer activation leads to eosinophilia in acute lymphoblastic leukemia through IL-3 overexpression	Homo sapiens	hg19	chr12	11718965	11902194	NA	ACSL6	Super-enhancer	Active	Disease	B-cell acute lymphoblastic leukemia	MONDO:0004947	DOID:0080638	bone marrow	UBERON:0002371	Primary ETV6::ACSL6 B-ALL cells (RJ-9)	NA	precursor B cell	CL:0000817	Chromatin interaction assay; In vivo functional validation; Super-enhancer activity assay; Enhancer hijacking assay	Hi-C; RNA-seq; H3K27ac CUT&Tag; H3K4me1 CUT&Tag; BRD4 CUT&Tag; Oxford Nanopore long-read sequencing	Luciferase reporter assay (HEK293T; Pro-SE1-derived 3-kb element); In vivo phenotyping; Xenograft/xenotransplant
E_03793	2024	38356460	ETV6::ACSL6 translocation-driven super-enhancer activation leads to eosinophilia in acute lymphoblastic leukemia through IL-3 overexpression	Homo sapiens	hg19	chr12	11718965	11902194	NA	IL3	Super-enhancer	Active	Disease	B-cell acute lymphoblastic leukemia	MONDO:0004947	DOID:0080638	bone marrow	UBERON:0002371	Primary ETV6::ACSL6 B-ALL cells (RJ-9)	NA	precursor B cell	CL:0000817	Functional perturbation assay; Chromatin interaction assay; In vivo functional validation; Super-enhancer activity assay; Enhancer hijacking assay	Hi-C; RNA-seq; scNMT-seq; H3K27ac CUT&Tag; H3K4me1 CUT&Tag; H3K4me3 CUT&Tag; BRD4 CUT&Tag; p300 CUT&Tag; CTCF CUT&Tag; Oxford Nanopore long-read sequencing	Luciferase reporter assay (HEK293T; SE2-derived 3-kb element); RT-qPCR; BET inhibitor JQ1 perturbation; Cytometric Bead Array; In vivo phenotyping; Xenograft/xenotransplant
E_03794	2024	38356460	ETV6::ACSL6 translocation-driven super-enhancer activation leads to eosinophilia in acute lymphoblastic leukemia through IL-3 overexpression	Homo sapiens	hg19	chr12	11718965	11902194	NA	P4HA2	Super-enhancer	Active	Disease	B-cell acute lymphoblastic leukemia	MONDO:0004947	DOID:0080638	bone marrow	UBERON:0002371	Primary ETV6::ACSL6 B-ALL cells (RJ-9)	NA	precursor B cell	CL:0000817	Chromatin interaction assay; In vivo functional validation; Super-enhancer activity assay; Enhancer hijacking assay	Hi-C; RNA-seq; H3K27ac CUT&Tag; BRD4 CUT&Tag	Luciferase reporter assay (HEK293T; SE2-derived 3-kb element); RT-qPCR; In vivo phenotyping; Xenograft/xenotransplant
E_03795	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr16	23819225	23820225	GATA1	PRKCB	Enhancer	Active	Disease	glioblastoma	MONDO:0018177	NA	brain	UBERON:0000955	U-87MG ATCC	CVCL_0022	glioblastoma cell	CL:0001063	Functional perturbation assay	ChIP-seq; ATAC-seq; RNA-seq; single-cell RNA-seq; eQTL analysis	CRISPR knockout; RT-qPCR; CRISPR-Cas9
E_03796	2015	25801169	Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers	Mus musculus	mm9	chr17	31939569	31956756	Nanog	Sik1	Super-enhancer	Active	Normal	NA	NA	NA	embryo	NA	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Super-enhancer profiling; Functional constituent perturbation assay	POU5F1/SOX2/NANOG/MED1 ChIP-seq data integration; H3K27ac ChIP-seq; gene-expression profiling	Constituent luciferase reporter assays; OCT4 shutdown; CRISPR/Cas9 constituent enhancer deletion; RT-qPCR
E_03797	2015	25801169	Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers	Mus musculus	mm9	chr17	31939569	31956756	Pou5f1	Sik1	Super-enhancer	Active	Normal	NA	NA	NA	embryo	NA	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Super-enhancer profiling; Functional constituent perturbation assay	POU5F1/SOX2/NANOG/MED1 ChIP-seq data integration; H3K27ac ChIP-seq; gene-expression profiling	Constituent luciferase reporter assays; OCT4 shutdown; CRISPR/Cas9 constituent enhancer deletion; RT-qPCR
E_03798	2015	25801169	Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers	Mus musculus	mm9	chr17	31939569	31956756	Sox2	Sik1	Super-enhancer	Active	Normal	NA	NA	NA	embryo	NA	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Super-enhancer profiling; Functional constituent perturbation assay	POU5F1/SOX2/NANOG/MED1 ChIP-seq data integration; H3K27ac ChIP-seq; gene-expression profiling	Constituent luciferase reporter assays; OCT4 shutdown; CRISPR/Cas9 constituent enhancer deletion; RT-qPCR
E_03799	2018	30537984	Enhancers in the Peril lincRNA locus regulate distant but not local genes	Mus musculus	mm10	chr3	34765000	34767361	NA	Mccc1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	MPRA; RNA-seq; Hi-C	qRT-PCR, and ChIP-qPCR; Reporter assay
E_03800	2015	25801169	Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers	Mus musculus	mm10	chr17	35600000	35630000	Nanog	Pou5f1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	mouse ESCs	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay	ChIP-seq; RNA-seq	Luciferase reporter assay; CRISPR knockout
E_03801	2015	25801169	Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers	Mus musculus	mm10	chr17	35600000	35630000	Pou5f1	Pou5f1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	mouse ESCs	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay	ChIP-seq; RNA-seq	Luciferase reporter assay; CRISPR knockout
E_03802	2015	25801169	Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers	Mus musculus	mm10	chr17	35600000	35630000	Sox2	Pou5f1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	mouse ESCs	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay	ChIP-seq; RNA-seq	Luciferase reporter assay; CRISPR knockout
E_03803	2015	25801169	Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers	Mus musculus	mm10	chr8	45600000	45640000	Nanog	Klf2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	mouse ESCs	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay	ChIP-seq; RNA-seq	Luciferase reporter assay; CRISPR knockout
E_03804	2015	25801169	Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers	Mus musculus	mm10	chr8	45600000	45640000	Pou5f1	Klf2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	mouse ESCs	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay	ChIP-seq; RNA-seq	Luciferase reporter assay; CRISPR knockout
E_03805	2015	25801169	Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers	Mus musculus	mm10	chr8	45600000	45640000	Sox2	Klf2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	mouse ESCs	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay	ChIP-seq; RNA-seq	Luciferase reporter assay; CRISPR knockout
E_03806	2025	40158221	SWI/SNF complex-mediated ZNF410 cooperative binding maintains chromatin accessibility and enhancer activity	Homo sapiens	hg38	chr12	6612734	6614634	ZNF410	CHD4	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	erythroid lineage cell	CL:0000764	Enhancer activity assay; Functional perturbation assay; TF binding assay	ATAC-seq; ChIP-seq (ZNF410; H3K27ac; H3K4me3; H3K9me3); RNA-seq	Luciferase reporter assay; CRISPR/Cas9 distal enhancer deletion; CRISPRi (dCas9-KRAB); site-directed ZNF410 motif mutagenesis; ChIP-qPCR; RT-qPCR
E_03807	2025	40296153	Rewiring of SINE-MIR enhancer topology and Esrrb modulation in expanded and naive pluripotency	Mus musculus	mm10	chr14	99739099	99739310	Esrrb	Klf5	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	ES-R1	CVCL_2167	embryonic stem cell	CL:0002322	Functional perturbation assay; Chromatin topology assay	Hi-C; H3K27ac HiChIP; ChIP-seq; RNA-seq; ATAC-seq	CRISPR knockout; CRISPRi; ChIP-qPCR; RT-qPCR; Western blot
E_03808	2022	34718356	TCOF1 upregulation in triple-negative breast cancer promotes stemness and tumour growth and correlates with poor prognosis	Homo sapiens	hg19	chr5	149631000	149636000	FOSL1	TCOF1	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	Human breast cancer cell	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; DNase-seq	Luciferase reporter assay; ChIP-qPCR; CRISPR knockout; RT-qPCR; Western blot
E_03809	2022	34718356	TCOF1 upregulation in triple-negative breast cancer promotes stemness and tumour growth and correlates with poor prognosis	Homo sapiens	hg19	chr5	149631000	149636000	MYBL2	TCOF1	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	Human breast cancer cell	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; DNase-seq	Luciferase reporter assay; ChIP-qPCR; CRISPR knockout; RT-qPCR; Western blot
E_03810	2022	34718356	TCOF1 upregulation in triple-negative breast cancer promotes stemness and tumour growth and correlates with poor prognosis	Homo sapiens	hg19	chr5	149631000	149636000	PLAG1	TCOF1	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	Human breast cancer cell	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; DNase-seq	Luciferase reporter assay; ChIP-qPCR; CRISPR knockout; RT-qPCR; Western blot
E_03811	2022	34718356	TCOF1 upregulation in triple-negative breast cancer promotes stemness and tumour growth and correlates with poor prognosis	Homo sapiens	hg19	chr5	149631000	149636000	YY1	TCOF1	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	Human breast cancer cell	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; DNase-seq	Luciferase reporter assay; ChIP-qPCR; CRISPR knockout; RT-qPCR; Western blot
E_03812	2025	40158221	SWI/SNF complex-mediated ZNF410 cooperative binding maintains chromatin accessibility and enhancer activity	Homo sapiens	hg38	chr12	6607234	6609134	ZNF410	CHD4	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	erythroid lineage cell	CL:0000764	Enhancer activity assay; Functional perturbation assay; TF binding assay	ATAC-seq; ChIP-seq (ZNF410; H3K27ac; H3K4me3; H3K9me3); RNA-seq	Luciferase reporter assay; CRISPR/Cas9 proximal enhancer deletion; CRISPRi (dCas9-KRAB); ChIP-qPCR; RT-qPCR
E_03813	2025	40038738	Super-enhancer-hijacking RBBP7 potentiates metastasis and stemness of breast cancer via recruiting NuRD complex subunit LSD1	Homo sapiens	hg38	chrX	16824570	16829407	NA	RBBP7	Super-enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	MCF-7	CVCL_0031	mammary gland epithelial cell	NA	Functional perturbation assay; Super-enhancer activity assay; Histone modification assay	Public H3K27ac ChIP-seq data analysis; Public EP300 ChIP-seq/DNase-seq data analysis; ROSE	CRISPR/Cas9-mediated super-enhancer deletion; H3K27ac ChIP-qPCR; EP300 ChIP-qPCR; p300 siRNA knockdown; RT-qPCR; Western blotting; JQ1 treatment; CCK-8 assay; Colony formation assay; Transwell assay; RBBP7 rescue; CRISPR-Cas9; Luciferase reporter assay; Reporter assay; ChIP-qPCR; qPCR
E_03814	2025	40038738	Super-enhancer-hijacking RBBP7 potentiates metastasis and stemness of breast cancer via recruiting NuRD complex subunit LSD1	Homo sapiens	hg38	chrX	16824570	16829407	NA	RBBP7	Super-enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	T-47D	CVCL_0553	mammary gland epithelial cell	NA	Functional perturbation assay; Super-enhancer activity assay; Histone modification assay	Public H3K27ac ChIP-seq data analysis; Public EP300 ChIP-seq/DNase-seq data analysis; ROSE	CRISPR/Cas9-mediated super-enhancer deletion; H3K27ac ChIP-qPCR; EP300 ChIP-qPCR; p300 siRNA knockdown; RT-qPCR; Western blotting; JQ1 treatment; CCK-8 assay; Colony formation assay; Transwell assay; RBBP7 rescue; CRISPR-Cas9; Luciferase reporter assay; Reporter assay; ChIP-qPCR; qPCR
E_03815	2023	37803333	Epigenomic perturbation of novel EGFR enhancers reduces the proliferative and invasive capacity of glioblastoma and increases sensitivity to temozolomide	Homo sapiens	hg38	chr7	55249000	55251000	NA	EGFR	Enhancer	Active	Disease	glioblastoma	MONDO:0018177	NA	brain	UBERON:0000955	U-251MG	CVCL_0021	malignant cell	CL:0001064	Enhancer activity assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Endogenous enhancer perturbation assay	H3K27ac ChIP-seq; ATAC-seq; RNA-seq	CRISPRi dCas9-KRAB; CRISPR deletion; Luciferase reporter assay; RT-qPCR; Western blot; CRISPR-Cas9 endogenous deletion/editing
E_03816	2022	35316324	Concurrent CDX2 cis-deregulation and UBTF::ATXN7L3 fusion define a novel high-risk subtype of B-cell ALL	Homo sapiens	hg19	chr13	28268000	28270000	NA	CDX2	Enhancer	Active	Disease	B-cell acute lymphoblastic leukemia	MONDO:0004947	DOID:0080638	bone marrow	UBERON:0002371	NALM-16	CVCL_1834	B-lymphoblast	CL:0017006	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Endogenous enhancer perturbation	ChIP-seq; ATAC-seq; 4C-seq; RNA-seq	CRISPR interference; RT-qPCR; Western blot; CRISPRi; 4C
E_03817	2024	39671433	The cells are all-right: Regulation of the Lefty genes by separate enhancers in mouse embryonic stem cells	Mus musculus	mm10	chr1	180887014	180889994	E2f1	Lefty2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Mouse embryonic stem	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; Hi-C	CRISPR knockout; RT-qPCR; CRISPR-Cas9
E_03818	2024	39671433	The cells are all-right: Regulation of the Lefty genes by separate enhancers in mouse embryonic stem cells	Mus musculus	mm10	chr1	180887014	180889994	Esrrb	Lefty2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Mouse embryonic stem	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; Hi-C	CRISPR knockout; RT-qPCR; CRISPR-Cas9
E_03819	2024	39671433	The cells are all-right: Regulation of the Lefty genes by separate enhancers in mouse embryonic stem cells	Mus musculus	mm10	chr1	180887014	180889994	Klf4	Lefty2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Mouse embryonic stem	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; Hi-C	CRISPR knockout; RT-qPCR; CRISPR-Cas9
E_03820	2024	39671433	The cells are all-right: Regulation of the Lefty genes by separate enhancers in mouse embryonic stem cells	Mus musculus	mm10	chr1	180887014	180889994	Nanog	Lefty2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Mouse embryonic stem	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; Hi-C	CRISPR knockout; RT-qPCR; CRISPR-Cas9
E_03821	2024	39671433	The cells are all-right: Regulation of the Lefty genes by separate enhancers in mouse embryonic stem cells	Mus musculus	mm10	chr1	180887014	180889994	Sox2	Lefty2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Mouse embryonic stem	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; Hi-C	CRISPR knockout; RT-qPCR; CRISPR-Cas9
E_03822	2024	39671433	The cells are all-right: Regulation of the Lefty genes by separate enhancers in mouse embryonic stem cells	Mus musculus	mm10	chr1	180887014	180889994	Tfcp2l1	Lefty2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Mouse embryonic stem	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; Hi-C	CRISPR knockout; RT-qPCR; CRISPR-Cas9
E_03823	2024	39671433	The cells are all-right: Regulation of the Lefty genes by separate enhancers in mouse embryonic stem cells	Mus musculus	mm10	chr1	180887014	180889994	Zfx	Lefty2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Mouse embryonic stem	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; Hi-C	CRISPR knockout; RT-qPCR; CRISPR-Cas9
E_03824	2024	39671433	The cells are all-right: Regulation of the Lefty genes by separate enhancers in mouse embryonic stem cells	Mus musculus	mm10	chr1	180924460	180925486	E2f1	Lefty1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Mouse embryonic stem	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; Hi-C	CRISPR knockout; RT-qPCR; CRISPR-Cas9
E_03825	2024	39671433	The cells are all-right: Regulation of the Lefty genes by separate enhancers in mouse embryonic stem cells	Mus musculus	mm10	chr1	180924460	180925486	Esrrb	Lefty1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Mouse embryonic stem	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; Hi-C	CRISPR knockout; RT-qPCR; CRISPR-Cas9
E_03826	2024	39671433	The cells are all-right: Regulation of the Lefty genes by separate enhancers in mouse embryonic stem cells	Mus musculus	mm10	chr1	180924460	180925486	Klf4	Lefty1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Mouse embryonic stem	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; Hi-C	CRISPR knockout; RT-qPCR; CRISPR-Cas9
E_03827	2024	39671433	The cells are all-right: Regulation of the Lefty genes by separate enhancers in mouse embryonic stem cells	Mus musculus	mm10	chr1	180924460	180925486	Nanog	Lefty1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Mouse embryonic stem	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; Hi-C	CRISPR knockout; RT-qPCR; CRISPR-Cas9
E_03828	2024	39671433	The cells are all-right: Regulation of the Lefty genes by separate enhancers in mouse embryonic stem cells	Mus musculus	mm10	chr1	180924460	180925486	Sox2	Lefty1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Mouse embryonic stem	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; Hi-C	CRISPR knockout; RT-qPCR; CRISPR-Cas9
E_03829	2024	39671433	The cells are all-right: Regulation of the Lefty genes by separate enhancers in mouse embryonic stem cells	Mus musculus	mm10	chr1	180924460	180925486	Tfcp2l1	Lefty1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Mouse embryonic stem	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; Hi-C	CRISPR knockout; RT-qPCR; CRISPR-Cas9
E_03830	2024	39671433	The cells are all-right: Regulation of the Lefty genes by separate enhancers in mouse embryonic stem cells	Mus musculus	mm10	chr1	180924460	180925486	Zfx	Lefty1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Mouse embryonic stem	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; Hi-C	CRISPR knockout; RT-qPCR; CRISPR-Cas9
E_03831	2025	40691407	NKX2-1 drives neuroendocrine transdifferentiation of prostate cancer via epigenetic and 3D chromatin remodeling	Homo sapiens	hg38	chr14	36973254	36976254	FOXA2	NKX2-1	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LuCaP93 PDX	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	FOXA2 ChIP-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C; RNA-seq	CRISPR perturbation; qRT-PCR; Western blot
E_03832	2025	40691407	NKX2-1 drives neuroendocrine transdifferentiation of prostate cancer via epigenetic and 3D chromatin remodeling	Homo sapiens	hg38	chr14	36980000	36983000	FOXA2	NKX2-1	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LuCaP93 PDX	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	FOXA2 ChIP-seq; H3K27ac ChIP-seq; Hi-C; ATAC-seq	CRISPR perturbation; qRT-PCR; Western blot
E_03833	2025	40691407	NKX2-1 drives neuroendocrine transdifferentiation of prostate cancer via epigenetic and 3D chromatin remodeling	Homo sapiens	hg38	chr14	36990000	36996211	FOXA2	NKX2-1	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LuCaP93 PDX	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	FOXA2 ChIP-seq; H3K27ac ChIP-seq; Hi-C; RNA-seq	CRISPR perturbation; qRT-PCR; Western blot
E_03834	2023	37932452	GATA transcription factors drive initial Xist upregulation after fertilization through direct activation of long-range enhancers	Mus musculus	mm10	chrX	103578000	103588000	Gata6	Xist	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	GATA6-inducible mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Functional perturbation assay; TF binding assay; Endogenous enhancer perturbation; In vivo functional validation; RE79 long-range enhancer functional validation; database working interval	CUT&Tag; CRISPRa screen; RNA-seq; ATAC-seq; pooled CRISPRa screen	FIREWACh lentiviral enhancer reporter assay; CRISPRi; GATA6 induction; qRT-PCR; RNA-FISH; zygotic CRISPR/Cas9 RE79/RE97 deletion; CRISPRa; Mouse genetic deletion/knock-in
E_03835	2016	27354268	Dissection of the Major Hematopoietic Quantitative Trait Locus in Chromosome 6q23.3 Identifies miR-3662 as a Player in Hematopoiesis and Acute Myeloid Leukemia	Homo sapiens	hg19	chr6	135418600	135418700	GATA1	MIR3662	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	bone marrow	UBERON:0002371	KG-1a	CVCL_1824	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation	Targeted RNA-seq; GWAS	CRISPR knockout, EMSA; RT-qPCR, Luciferase reporter assay; ChIP-qPCR; Western blot, Colony formation assay; CRISPR-Cas9 endogenous deletion/editing; In vivo phenotyping
E_03836	2010	19966299	A beta-catenin/TCF-coordinated chromatin loop at MYC integrates 5' and 3' Wnt responsive enhancers	Homo sapiens	hg19	chr8	127737737	127738437	TCF4	MYC	Enhancer	Active	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq	Luciferase reporter assay, 3C; ChIP-qPCR; RT-qPCR; Western blot; 3C
E_03837	2010	19966299	A beta-catenin/TCF-coordinated chromatin loop at MYC integrates 5' and 3' Wnt responsive enhancers	Homo sapiens	hg19	chr8	127744001	127744701	TCF4	MYC	Enhancer	Active	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq	Luciferase reporter assay, 3C; ChIP-qPCR; RT-qPCR; Western blot; 3C
E_03838	2010	19966299	A beta-catenin/TCF-coordinated chromatin loop at MYC integrates 5' and 3' Wnt responsive enhancers	Homo sapiens	hg19	chr8	128754000	128755000	TCF7L2	MYC	Enhancer	Active	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	NA	3C, Luciferase reporter assay; ChIP-qPCR, shRNA Knockdown; RT-qPCR; Western blot; 3C
E_03839	2010	19966299	A beta-catenin/TCF-coordinated chromatin loop at MYC integrates 5' and 3' Wnt responsive enhancers	Homo sapiens	hg19	chr8	128745000	128745100	TCF7L2	MYC	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	NA	Luciferase reporter assay; 3C-seq; ChIP-qPCR; RT-qPCR; 3C
E_03840	2010	19966299	A beta-catenin/TCF-coordinated chromatin loop at MYC integrates 5' and 3' Wnt responsive enhancers	Homo sapiens	hg19	chr8	128750000	128750100	TCF7L2	MYC	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	NA	Luciferase reporter assay; 3C-seq; ChIP-qPCR; RT-qPCR; 3C
E_03841	2023	37932452	GATA transcription factors drive initial Xist upregulation after fertilization through direct activation of long-range enhancers	Mus musculus	mm10	chrX	103578000	103588000	Gata4	Xist	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	female XEN cells	NA	extraembryonic endoderm cell	NA	RE79 long-range enhancer TF-binding validation; database working interval	GATA4 CUT&Tag; H3K27ac CUT&Tag; RNA-seq; ATAC-seq	FIREWACh enhancer reporter assay; zygotic CRISPR/Cas9 RE79/RE97 deletion; RNA-FISH
E_03842	2019	31324781	Deletion of a Csf1r enhancer selectively impacts CSF1R expression and development of tissue macrophage populations	Mus musculus	mm39	chr18	61241648	61241998	Spi1	Csf1r	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	embryonic macrophages	NA	macrophage	CL:0000235	Endogenous enhancer perturbation; In vivo functional validation; Endogenous enhancer deletion; tissue-specific macrophage-development phenotyping; enhancer/TF chromatin profiling	ATAC-seq; ChIP-seq; RNA expression profiling/microarray	CRISPR/genomic FIRE deletion; transgenic reporter; Flow cytometry; immunohistochemistry; mESC macrophage differentiation; Mouse genetic deletion/knock-in
E_03843	2019	31324781	Deletion of a Csf1r enhancer selectively impacts CSF1R expression and development of tissue macrophage populations	Mus musculus	mm39	chr18	61241648	61241998	Spi1	Csf1r	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	mouse embryonic stem-cell macrophage differentiation	NA	macrophage	CL:0000235	Endogenous enhancer perturbation; In vivo functional validation; Endogenous enhancer deletion; tissue-specific macrophage-development phenotyping; enhancer/TF chromatin profiling	ATAC-seq; ChIP-seq; RNA expression profiling/microarray	CRISPR/genomic FIRE deletion; transgenic reporter; Flow cytometry; immunohistochemistry; mESC macrophage differentiation; Mouse genetic deletion/knock-in
E_03844	2023	37932452	GATA transcription factors drive initial Xist upregulation after fertilization through direct activation of long-range enhancers	Mus musculus	mm10	chrX	103628000	103668000	Gata3	Xist	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	female trophoblast stem cells	NA	trophoblast stem cell	NA	RE97 long-range enhancer TF-binding and in vivo functional validation; database working interval	GATA3 CUT&Tag; H3K27ac CUT&Tag; RNA-seq; ATAC-seq	FIREWACh enhancer reporter assay; zygotic CRISPR/Cas9 RE79/RE97 deletion; RNA-FISH
E_03845	2023	37932452	GATA transcription factors drive initial Xist upregulation after fertilization through direct activation of long-range enhancers	Mus musculus	mm10	chrX	103628000	103668000	Gata6	Xist	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	female XEN cells	NA	extraembryonic endoderm cell	NA	RE97 long-range enhancer TF-binding and in vivo functional validation; database working interval	GATA6 CUT&Tag; H3K27ac CUT&Tag; RNA-seq; ATAC-seq	FIREWACh enhancer reporter assay; zygotic CRISPR/Cas9 RE79/RE97 deletion; RNA-FISH
E_03846	2016	27866707	A Functional Variant Associated with Atrial Fibrillation Regulates PITX2c Expression through TFAP2a	Homo sapiens	hg19	chr4	111544012	111544682	NA	PITX2	Enhancer	Active	Disease	atrial fibrillation	MONDO:0004981	DOID:0060224	embryo	NA	Danio rerio embryos	NA	NA	NA	Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation; In vivo enhancer activity assay	NA	Tol2-mediated transgenic reporter assay; eGFP RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; In vivo phenotyping
E_03847	2016	27866707	A Functional Variant Associated with Atrial Fibrillation Regulates PITX2c Expression through TFAP2a	Homo sapiens	hg19	chr4	111552482	111553989	NA	PITX2	Enhancer	Active	Disease	atrial fibrillation	MONDO:0004981	DOID:0060224	embryo	NA	Danio rerio embryos	NA	NA	NA	Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation; In vivo enhancer activity assay	NA	Tol2-mediated transgenic reporter assay; eGFP RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; In vivo phenotyping
E_03848	2016	27866707	A Functional Variant Associated with Atrial Fibrillation Regulates PITX2c Expression through TFAP2a	Homo sapiens	hg19	chr4	111574843	111575952	NA	PITX2	Enhancer	Active	Disease	atrial fibrillation	MONDO:0004981	DOID:0060224	embryo	NA	Danio rerio embryos	NA	NA	NA	Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation; In vivo enhancer activity assay	NA	Tol2-mediated transgenic reporter assay; eGFP RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; In vivo phenotyping
E_03849	2011	21486496	Identification of a novel intronic enhancer responsible for the transcriptional regulation of musashi1 in neural stem/progenitor cells	Mus musculus	mm10	chr5	115574958	115575553	NA	Msi1	Enhancer	Active	Normal	NA	NA	NA	nervous system	UBERON:0001016	NS/PCs	NA	neural stem/progenitor cell	NA	Enhancer activity assay; cis-regulatory deletion mapping	Public H3K4me1/p300 ChIP-seq epigenomic support used for candidate selection (not study-generated)	BAC deletion mapping; Luciferase reporter assay; neural differentiation reporter assay
E_03850	2011	21486496	Identification of a novel intronic enhancer responsible for the transcriptional regulation of musashi1 in neural stem/progenitor cells	Mus musculus	mm10	chr5	115502658	115512658	NA	Msi1	Enhancer	Active	Normal	NA	NA	NA	nervous system	UBERON:0001016	NS/PCs	NA	neural stem/progenitor cell	NA	Candidate enhancer activity assay; BAC deletion mapping	Public H3K4me1/p300 ChIP-seq epigenomic support used for candidate selection (not study-generated)	BAC deletion mapping; Luciferase reporter assay
E_03851	2016	27354268	Dissection of the Major Hematopoietic Quantitative Trait Locus in Chromosome 6q23.3 Identifies miR-3662 as a Player in Hematopoiesis and Acute Myeloid Leukemia	Homo sapiens	hg19	chr6	135418600	135418700	NA	MIR3662	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	blood	UBERON:0000178	Kasumi-1	CVCL_0589	NA	NA	Functional perturbation assay; Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation	GWAS	CRISPR/Cas9 genome editing; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; In vivo phenotyping
E_03852	2015	26214525	GATA2 is required for lymphatic vessel valve development and maintenance	Homo sapiens	hg19	chr1	214150857	214151185	GATA2	PROX1	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	lymphatic vessel	UBERON:0001473	primary human lymphatic endothelial cells	NA	endothelial cell	CL:0000115	Lymphatic enhancer activity; TF binding; TF-site functional dissection	GATA2 ChIP-seq	GATA2 siRNA; ChIP-qPCR; luciferase; GATA-site mutagenesis; WEMSA; enhancer cooperativity assay
E_03853	2019	31324781	Deletion of a Csf1r enhancer selectively impacts CSF1R expression and development of tissue macrophage populations	Mus musculus	mm10	chr18	61108475	61108975	NA	Csf1r	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Csf1r enhancer-deletion mouse	NA	macrophage	CL:0000235	Endogenous enhancer perturbation; In vivo functional validation; Canonical Csf1r FIRE enhancer; current mm10 interval standardized to chr18:61108475-61108975; in vivo FIRE deletion phenotype	RNA-seq and macrophage population profiling	Enhancer genome editing mouse; Flow cytometry; immunohistochemistry; expression analysis; Mouse genetic deletion/knock-in
E_03854	2015	26214525	GATA2 is required for lymphatic vessel valve development and maintenance	Homo sapiens	hg19	chr1	214150857	214151185	FOXC2	PROX1	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	lymphatic vessel	UBERON:0001473	primary human lymphatic endothelial cells	NA	endothelial cell	CL:0000115	Lymphatic enhancer activity; direct TF occupancy; TF-site functional dissection	GATA2 ChIP-seq / chromatin profiling	ChIP; luciferase; GATA-site mutagenesis; WEMSA; TF perturbation
E_03855	2015	26214525	GATA2 is required for lymphatic vessel valve development and maintenance	Homo sapiens	hg19	chr1	214150857	214151185	FOXC2	PROX1	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	lymphatic vessel	UBERON:0001473	primary human lymphatic endothelial cells	NA	endothelial cell	CL:0000115	Lymphatic enhancer activity and TF occupancy	GATA2 ChIP-seq	FOXC2 ChIP; enhancer reporter; GATA2 perturbation; chromatin-state assays
E_03856	2015	26214525	GATA2 is required for lymphatic vessel valve development and maintenance	Homo sapiens	hg19	chr1	214150857	214151185	GATA2	PROX1	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	lymphatic vessel	UBERON:0001473	primary human lymphatic endothelial cells	NA	endothelial cell	CL:0000115	Lymphatic enhancer activity; direct TF occupancy; TF-site functional dissection	GATA2 ChIP-seq / chromatin profiling	ChIP; luciferase; GATA-site mutagenesis; WEMSA; TF perturbation
E_03857	2015	26214525	GATA2 is required for lymphatic vessel valve development and maintenance	Homo sapiens	hg19	chr1	214150857	214151185	NFATC1	PROX1	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	lymphatic vessel	UBERON:0001473	primary human lymphatic endothelial cells	NA	endothelial cell	CL:0000115	Lymphatic enhancer activity; direct TF occupancy; TF-site functional dissection	GATA2 ChIP-seq / chromatin profiling	ChIP; luciferase; GATA-site mutagenesis; WEMSA; TF perturbation
E_03858	2015	26214525	GATA2 is required for lymphatic vessel valve development and maintenance	Homo sapiens	hg19	chr1	214150857	214151185	NFATC1	PROX1	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	lymphatic vessel	UBERON:0001473	primary human lymphatic endothelial cells	NA	endothelial cell	CL:0000115	Lymphatic enhancer activity and TF occupancy	GATA2 ChIP-seq	NFATC1 ChIP; enhancer reporter; GATA2 perturbation; chromatin-state assays
E_03859	2023	37749132	Genome-wide enhancer-gene regulatory maps link causal variants to target genes underlying human cancer risk	Homo sapiens	hg38	chr20	48682144	48683144	ZEB1	PREX1	Enhancer	Active	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	SW480	CVCL_0546	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Disease-variant functional analysis	ATAC-seq; ChIP-seq; GWAS	Luciferase reporter assay, CRISPR knockout
E_03860	2022	36201590	A noncoding single-nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation	Homo sapiens	hg19	chr8	128748243	128748308	NA	MYC	Enhancer	Active	Disease	malignant glioma	MONDO:0100342	NA	brain	UBERON:0000955	Neural stem	NA	neural stem cell	CL:0000047	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis	RNA-seq, GAM; 4C-seq	Transgenic reporter assay; ChIP-qPCR; RT-qPCR; Western blot, Immunofluorescence
E_03861	2023	37094986	YY1 complex in M2 macrophage promotes prostate cancer progression by upregulating IL-6	Homo sapiens	hg38	chr7	22755717	22757217	YY1	IL6	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	M2 macrophage	NA	macrophage	CL:0000235	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation	ChIP-seq; RNA-seq; RNA-seq; ChIP-seq	Luciferase reporter assay, CRISPR knockout; ChIP-qPCR; CRISPR-Cas9 endogenous deletion/editing; ChIP; In vivo phenotyping
E_03862	2022	36253360	A local tumor microenvironment acquired super-enhancer induces an oncogenic driver in colorectal carcinoma	Homo sapiens	hg19	chr1	47644434	47659486	RELA	PDZK1IP1	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	HT-29	CVCL_0320	malignant cell	CL:0001064	Functional perturbation assay; In vivo functional validation; Super-enhancer activity assay	ChIP-seq; ATAC-seq; RNA-seq	CRISPRi, Luciferase reporter assay; Xenograft/xenotransplant
E_03863	2012	22671145	Transcriptional networks driving enhancer function in the CFTR gene	Homo sapiens	hg19	chr7	117228049	117229449	FOXA1	CFTR	Enhancer	Active	Normal	NA	NA	NA	intestine	UBERON:0000160	Caco-2	CVCL_0025	intestinal epithelial cell	CL:0002563	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-chip/ChIP-seq support; DNase-seq locus context	DNase I footprinting; EMSA; ChIP-qPCR; site-directed motif mutagenesis; Luciferase reporter assay; siRNA; RT-qPCR
E_03864	2012	22671145	Transcriptional networks driving enhancer function in the CFTR gene	Homo sapiens	hg19	chr7	117228049	117229449	FOXA2	CFTR	Enhancer	Active	Normal	NA	NA	NA	intestine	UBERON:0000160	Caco-2	CVCL_0025	intestinal epithelial cell	CL:0002563	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-chip/ChIP-seq support; DNase-seq locus context	DNase I footprinting; EMSA; ChIP-qPCR; site-directed motif mutagenesis; Luciferase reporter assay; siRNA; RT-qPCR
E_03865	2012	22671145	Transcriptional networks driving enhancer function in the CFTR gene	Homo sapiens	hg19	chr7	117228049	117229449	HNF1A	CFTR	Enhancer	Active	Normal	NA	NA	NA	intestine	UBERON:0000160	Caco-2	CVCL_0025	intestinal epithelial cell	CL:0002563	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-chip/ChIP-seq support; DNase-seq locus context	DNase I footprinting; EMSA; ChIP-qPCR; site-directed motif mutagenesis; Luciferase reporter assay; siRNA; RT-qPCR
E_03866	2012	22671145	Transcriptional networks driving enhancer function in the CFTR gene	Homo sapiens	hg19	chr7	117228049	117229449	CDX2	CFTR	Enhancer	Active	Normal	NA	NA	NA	intestine	UBERON:0000160	Caco-2	CVCL_0025	intestinal epithelial cell	CL:0002563	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-chip/ChIP-seq support; DNase-seq locus context	DNase I footprinting; EMSA; ChIP-qPCR; site-directed motif mutagenesis; Luciferase reporter assay; siRNA; RT-qPCR
E_03867	2000	10688646	Loading of DNA-binding factors to an erythroid enhancer	Homo sapiens	hg19	chr16	163380	163907	GATA1	HBA1	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	erythroid lineage cell	CL:0000764	Enhancer activity assay; Functional perturbation assay; TF binding assay; Endogenous enhancer perturbation; In vivo functional validation; TF binding motif functional assay; Enhanceosome assembly assay	NA	Stable genomic integration of wild-type and GATA1-site mutant HS-40 constructs; electroporation; Site-directed mutagenesis; human alpha1-globin promoter-growth hormone reporter assay; growth hormone radioimmunoassay; in vivo DMS genomic footprinting; ligation-mediated PCR; Southern blot copy-number analysis; ChIP; Site-directed/motif mutagenesis; In vivo phenotyping
E_03868	2000	10688646	Loading of DNA-binding factors to an erythroid enhancer	Homo sapiens	hg19	chr16	163380	163907	MAFK	HBA1	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	erythroid lineage cell	CL:0000764	Functional perturbation assay; TF binding assay; Endogenous enhancer perturbation; In vivo functional validation; Enhancer repression assay	NA	3-prime-NA site-directed mutagenesis; recombinant MafK EMSA; MafK antibody EMSA; transient cotransfection; electroporation; human alpha1-globin promoter-growth hormone reporter assay; growth hormone radioimmunoassay; ChIP; Site-directed/motif mutagenesis; In vivo phenotyping
E_03869	2024	38559809	Functional analysis of a first hindlimb positioning enhancer via Gdf11 expression	Mus musculus	mm9	chr10	128326106	128327832	NA	Gdf11	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	posterior embryonic tissues	NA	NA	NA	Enhancer activity assay; Functional perturbation assay	NA	In ovo electroporation EGFP reporter assay in chick embryos; whole-embryo electroporation reporter assay; CRISPR-Cas9 HCR deletion; RT-qPCR; whole-mount in situ hybridization; PCR genotyping and sequencing; skeletal staining
E_03870	2018	29142074	STAT3 controls COL1A2 enhancer activation cooperatively with JunB, regulates type I collagen synthesis posttranscriptionally, and is essential for lung myofibroblast differentiation	Homo sapiens	hg19	chr7	94374796	94376944	STAT3	COL1A2	Enhancer	Active	Disease	systemic sclerosis	NA	NA	lung	UBERON:0002048	primary human lung fibroblasts from systemic sclerosis patients and healthy controls	NA	fibroblast	CL:0000057	Enhancer activity assay; Functional perturbation assay; TF binding assay; Myofibroblast differentiation assay	NA	Luciferase reporter assay; STAT3/JunB ChIP-qPCR; STAT3 inhibition/siRNA; RT-qPCR; Western blot; matrix-remodeling assay
E_03871	2018	29142074	STAT3 controls COL1A2 enhancer activation cooperatively with JunB, regulates type I collagen synthesis posttranscriptionally, and is essential for lung myofibroblast differentiation	Homo sapiens	hg19	chr7	94374796	94376944	JUNB	COL1A2	Enhancer	Active	Disease	systemic sclerosis	NA	NA	lung	UBERON:0002048	primary human lung fibroblasts from systemic sclerosis patients and healthy controls	NA	fibroblast	CL:0000057	Enhancer activity assay; Functional perturbation assay; TF binding assay; Myofibroblast differentiation assay	NA	Luciferase reporter assay; STAT3/JunB ChIP-qPCR; STAT3 inhibition/siRNA; RT-qPCR; Western blot; matrix-remodeling assay
E_03872	2016	26446995	An autoregulatory enhancer controls mammary-specific STAT5 functions	Mus musculus	mm10	chr11	100855351	100856351	Stat5a	Stat5b	Enhancer	Active	Normal	NA	NA	NA	mammary gland	UBERON:0001911	Primary mammary epithelial cells	NA	mammary epithelial cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	H3K27ac ChIP-seq; RNA polymerase II ChIP-seq; MED1 ChIP-seq; GR ChIP-seq; DNase-seq; RNA-seq	CRISPR-Cas9 enhancer deletion; GAS-site deletion; ChIP-qPCR; RT-qPCR; CRISPR-Cas9
E_03873	2015	25303440	Failed degradation of JunB contributes to overproduction of type I collagen and development of dermal fibrosis in patients with systemic sclerosis	Homo sapiens	hg19	chr7	94002773	94005073	JUNB	COL1A2	Enhancer	Active	Disease	systemic sclerosis	NA	NA	skin	UBERON:0002097	Primary human dermal fibroblasts from systemic sclerosis patients	NA	fibroblast	CL:0000057	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Reporter assay; EMSA/supershift; ChIP-qPCR; AP-1 site mutagenesis; JUNB siRNA knockdown; RT-qPCR; Western blot; EMSA; ChIP
E_03874	2024	38233525	Affinity-optimizing enhancer variants disrupt development	Homo sapiens	hg38	chr7	156791087	156791875	ETS1	SHH	Enhancer	Active	Disease	Preaxial polydactyly / triphalangeal thumb-polydactyly spectrum	NA	NA	embryonic limb bud	NA	Embryonic limb bud / zone of polarizing activity mesenchyme	NA	Limb bud mesenchymal cell (ZPA mesenchyme)	NA	Enhancer activity assay; Disease-variant functional analysis; TF binding assay; endogenous functional perturbation; developmental phenotyping	Protein-binding microarray affinity data integration; saturation-mutagenesis MPRA reanalysis	EMSA; CRISPR-Cas9 endogenous knock-in; RNA in situ hybridization for Shh/Ptch1; skeletal staining; transgenic enhancer reporter
E_03875	2024	38233525	Affinity-optimizing enhancer variants disrupt development	Homo sapiens	hg38	chr7	156791087	156791875	ETS1	SHH	Enhancer	Active	Disease	Preaxial polydactyly / triphalangeal thumb-polydactyly spectrum	NA	NA	embryonic limb bud	NA	human ZRS sequence with endogenous mouse ortholog validation	NA	Limb bud mesenchymal cell (ZPA mesenchyme)	NA	Enhancer activity assay; Disease-variant functional analysis; TF binding assay; endogenous functional perturbation; developmental phenotyping	Protein-binding microarray affinity data integration; saturation-mutagenesis MPRA reanalysis	EMSA; CRISPR-Cas9 endogenous knock-in; RNA in situ hybridization for Shh/Ptch1; skeletal staining; transgenic enhancer reporter
E_03876	2024	38233525	Affinity-optimizing enhancer variants disrupt development	Homo sapiens	hg38	chr7	156791087	156791875	ETS1	SHH	Enhancer	Active	Disease	Preaxial polydactyly / triphalangeal thumb-polydactyly spectrum	NA	NA	embryonic limb bud	NA	Embryonic limb-bud/ZPA mesenchyme	NA	limb-bud mesenchymal cell (ZPA domain)	NA	Disease-variant enhancer activity; TF-binding affinity; endogenous developmental perturbation; in vivo phenotyping	Protein-binding microarray integration; saturation-mutagenesis MPRA reanalysis	EMSA; enhancer reporter; CRISPR-Cas9 endogenous knock-in/editing; RNA in situ hybridization for Shh/Ptch1; skeletal staining; developmental phenotyping
E_03877	2024	38233525	Affinity-optimizing enhancer variants disrupt development	Homo sapiens	hg38	chr7	156791087	156791875	ETS1	SHH	Enhancer	Active	Disease	Preaxial polydactyly / triphalangeal thumb-polydactyly spectrum	NA	NA	embryonic limb bud	NA	human ZRS sequence with endogenous mouse developmental validation	NA	limb-bud mesenchymal cell (ZPA domain)	NA	Disease-variant enhancer activity; TF-binding affinity; endogenous developmental perturbation; in vivo phenotyping	Protein-binding microarray integration; saturation-mutagenesis MPRA reanalysis	EMSA; enhancer reporter; CRISPR-Cas9 endogenous knock-in/editing; RNA in situ hybridization for Shh/Ptch1; skeletal staining; developmental phenotyping
E_03878	2024	38233525	Affinity-optimizing enhancer variants disrupt development	Homo sapiens	hg38	chr7	156791087	156791875	HOXA13	SHH	Enhancer	Active	Disease	Preaxial polydactyly / triphalangeal thumb-polydactyly spectrum	NA	NA	embryonic limb bud	NA	Embryonic limb-bud/ZPA mesenchyme	NA	limb-bud mesenchymal cell (ZPA domain)	NA	Disease-variant enhancer activity; TF-binding affinity; endogenous developmental perturbation; in vivo phenotyping	Protein-binding microarray integration; saturation-mutagenesis MPRA reanalysis	EMSA; enhancer reporter; CRISPR-Cas9 endogenous knock-in/editing; RNA in situ hybridization for Shh/Ptch1; skeletal staining; developmental phenotyping
E_03879	2024	38233525	Affinity-optimizing enhancer variants disrupt development	Homo sapiens	hg38	chr7	156791087	156791875	HOXA13	SHH	Enhancer	Active	Disease	Preaxial polydactyly / triphalangeal thumb-polydactyly spectrum	NA	NA	embryonic limb bud	NA	human ZRS sequence with endogenous mouse developmental validation	NA	limb-bud mesenchymal cell (ZPA domain)	NA	Disease-variant enhancer activity; TF-binding affinity; endogenous developmental perturbation; in vivo phenotyping	Protein-binding microarray integration; saturation-mutagenesis MPRA reanalysis	EMSA; enhancer reporter; CRISPR-Cas9 endogenous knock-in/editing; RNA in situ hybridization for Shh/Ptch1; skeletal staining; developmental phenotyping
E_03880	2024	38233525	Affinity-optimizing enhancer variants disrupt development	Homo sapiens	hg38	chr7	156791087	156791875	HOXD13	SHH	Enhancer	Active	Disease	Preaxial polydactyly / triphalangeal thumb-polydactyly spectrum	NA	NA	embryonic limb bud	NA	Embryonic limb-bud/ZPA mesenchyme	NA	limb-bud mesenchymal cell (ZPA domain)	NA	Disease-variant enhancer activity; TF-binding affinity; endogenous developmental perturbation; in vivo phenotyping	Protein-binding microarray integration; saturation-mutagenesis MPRA reanalysis	EMSA; enhancer reporter; CRISPR-Cas9 endogenous knock-in/editing; RNA in situ hybridization for Shh/Ptch1; skeletal staining; developmental phenotyping
E_03881	2024	38233525	Affinity-optimizing enhancer variants disrupt development	Homo sapiens	hg38	chr7	156791087	156791875	HOXD13	SHH	Enhancer	Active	Disease	Preaxial polydactyly / triphalangeal thumb-polydactyly spectrum	NA	NA	embryonic limb bud	NA	human ZRS sequence with endogenous mouse developmental validation	NA	limb-bud mesenchymal cell (ZPA domain)	NA	Disease-variant enhancer activity; TF-binding affinity; endogenous developmental perturbation; in vivo phenotyping	Protein-binding microarray integration; saturation-mutagenesis MPRA reanalysis	EMSA; enhancer reporter; CRISPR-Cas9 endogenous knock-in/editing; RNA in situ hybridization for Shh/Ptch1; skeletal staining; developmental phenotyping
E_03882	2018	29527594	A Novel Distal Enhancer Mediates Inflammation-, PTH-, and Early Onset Murine Kidney Disease-Induced Expression of the Mouse Fgf23 Gene	Mus musculus	mm10	chr6	128542796	128543720	Arnt	Fgf23	Enhancer	Active	Disease	chronic kidney disease	MONDO:0005300	NA	kidney	UBERON:0002113	Conventional dendritic cells	NA	conventional dendritic cell	NA	TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation; Functional genomics assay; Epigenomic profiling assay; Genome editing assay; In vivo functional assay	ChIP-seq, Microarray; ChIP-seq	CRISPR-Cas9 enhancer deletion; RT-qPCR, FGF23 ELISA, Serum biochemical analysis, In vivo LPS stimulation assay, In vivo CKD model assay; CRISPR-Cas9 endogenous deletion/editing; ChIP; Mouse genetic deletion/knock-in
E_03883	2018	29527594	A Novel Distal Enhancer Mediates Inflammation-, PTH-, and Early Onset Murine Kidney Disease-Induced Expression of the Mouse Fgf23 Gene	Mus musculus	mm10	chr6	128542796	128543720	Arntl	Fgf23	Enhancer	Active	Disease	chronic kidney disease	MONDO:0005300	NA	kidney	UBERON:0002113	Conventional dendritic cells	NA	conventional dendritic cell	NA	TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation; Functional genomics assay; Epigenomic profiling assay; Genome editing assay; In vivo functional assay	ChIP-seq, Microarray; ChIP-seq	CRISPR-Cas9 enhancer deletion; RT-qPCR, FGF23 ELISA, Serum biochemical analysis, In vivo LPS stimulation assay, In vivo CKD model assay; CRISPR-Cas9 endogenous deletion/editing; ChIP; Mouse genetic deletion/knock-in
E_03884	2018	29527594	A Novel Distal Enhancer Mediates Inflammation-, PTH-, and Early Onset Murine Kidney Disease-Induced Expression of the Mouse Fgf23 Gene	Mus musculus	mm10	chr6	128542796	128543720	Clock	Fgf23	Enhancer	Active	Disease	chronic kidney disease	MONDO:0005300	NA	kidney	UBERON:0002113	Conventional dendritic cells	NA	conventional dendritic cell	NA	TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation; Functional genomics assay; Epigenomic profiling assay; Genome editing assay; In vivo functional assay	ChIP-seq, Microarray; ChIP-seq	CRISPR-Cas9 enhancer deletion; RT-qPCR, FGF23 ELISA, Serum biochemical analysis, In vivo LPS stimulation assay, In vivo CKD model assay; CRISPR-Cas9 endogenous deletion/editing; ChIP; Mouse genetic deletion/knock-in
E_03885	2018	29527594	A Novel Distal Enhancer Mediates Inflammation-, PTH-, and Early Onset Murine Kidney Disease-Induced Expression of the Mouse Fgf23 Gene	Mus musculus	mm10	chr6	128542796	128543720	Hif1a	Fgf23	Enhancer	Active	Disease	chronic kidney disease	MONDO:0005300	NA	kidney	UBERON:0002113	Conventional dendritic cells	NA	conventional dendritic cell	NA	TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation; Functional genomics assay; Epigenomic profiling assay; Genome editing assay; In vivo functional assay	ChIP-seq, Microarray; ChIP-seq	CRISPR-Cas9 enhancer deletion; RT-qPCR, FGF23 ELISA, Serum biochemical analysis, In vivo LPS stimulation assay, In vivo CKD model assay; CRISPR-Cas9 endogenous deletion/editing; ChIP; Mouse genetic deletion/knock-in
E_03886	2018	29527594	A Novel Distal Enhancer Mediates Inflammation-, PTH-, and Early Onset Murine Kidney Disease-Induced Expression of the Mouse Fgf23 Gene	Mus musculus	mm10	chr6	128542796	128543720	Nfkb1	Fgf23	Enhancer	Active	Disease	chronic kidney disease	MONDO:0005300	NA	kidney	UBERON:0002113	Conventional dendritic cells	NA	conventional dendritic cell	NA	TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation; Functional genomics assay; Epigenomic profiling assay; Genome editing assay; In vivo functional assay	ChIP-seq, Microarray; ChIP-seq	CRISPR-Cas9 enhancer deletion; RT-qPCR, FGF23 ELISA, Serum biochemical analysis, In vivo LPS stimulation assay, In vivo CKD model assay; CRISPR-Cas9 endogenous deletion/editing; ChIP; Mouse genetic deletion/knock-in
E_03887	2018	29527594	A Novel Distal Enhancer Mediates Inflammation-, PTH-, and Early Onset Murine Kidney Disease-Induced Expression of the Mouse Fgf23 Gene	Mus musculus	mm10	chr6	128542796	128543720	Npas2	Fgf23	Enhancer	Active	Disease	chronic kidney disease	MONDO:0005300	NA	kidney	UBERON:0002113	Conventional dendritic cells	NA	conventional dendritic cell	NA	TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation; Functional genomics assay; Epigenomic profiling assay; Genome editing assay; In vivo functional assay	ChIP-seq, Microarray; ChIP-seq	CRISPR-Cas9 enhancer deletion; RT-qPCR, FGF23 ELISA, Serum biochemical analysis, In vivo LPS stimulation assay, In vivo CKD model assay; CRISPR-Cas9 endogenous deletion/editing; ChIP; Mouse genetic deletion/knock-in
E_03888	2018	29527594	A Novel Distal Enhancer Mediates Inflammation-, PTH-, and Early Onset Murine Kidney Disease-Induced Expression of the Mouse Fgf23 Gene	Mus musculus	mm10	chr6	128542796	128543720	Stat3	Fgf23	Enhancer	Active	Disease	chronic kidney disease	MONDO:0005300	NA	kidney	UBERON:0002113	Conventional dendritic cells	NA	conventional dendritic cell	NA	TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation; Functional genomics assay; Epigenomic profiling assay; Genome editing assay; In vivo functional assay	ChIP-seq, Microarray; ChIP-seq	CRISPR-Cas9 enhancer deletion; RT-qPCR, FGF23 ELISA, Serum biochemical analysis, In vivo LPS stimulation assay, In vivo CKD model assay; CRISPR-Cas9 endogenous deletion/editing; ChIP; Mouse genetic deletion/knock-in
E_03889	2018	29527594	A Novel Distal Enhancer Mediates Inflammation-, PTH-, and Early Onset Murine Kidney Disease-Induced Expression of the Mouse Fgf23 Gene	Mus musculus	mm10	chr6	128542796	128543720	Stat5a	Fgf23	Enhancer	Active	Disease	chronic kidney disease	MONDO:0005300	NA	kidney	UBERON:0002113	Conventional dendritic cells	NA	conventional dendritic cell	NA	TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation; Functional genomics assay; Epigenomic profiling assay; Genome editing assay; In vivo functional assay	ChIP-seq, Microarray; ChIP-seq	CRISPR-Cas9 enhancer deletion; RT-qPCR, FGF23 ELISA, Serum biochemical analysis, In vivo LPS stimulation assay, In vivo CKD model assay; CRISPR-Cas9 endogenous deletion/editing; ChIP; Mouse genetic deletion/knock-in
E_03890	2018	29527594	A Novel Distal Enhancer Mediates Inflammation-, PTH-, and Early Onset Murine Kidney Disease-Induced Expression of the Mouse Fgf23 Gene	Mus musculus	mm10	chr6	128542796	128543720	Stat6	Fgf23	Enhancer	Active	Disease	chronic kidney disease	MONDO:0005300	NA	kidney	UBERON:0002113	Conventional dendritic cells	NA	conventional dendritic cell	NA	TF binding assay; Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation; Functional genomics assay; Epigenomic profiling assay; Genome editing assay; In vivo functional assay	ChIP-seq, Microarray; ChIP-seq	CRISPR-Cas9 enhancer deletion; RT-qPCR, FGF23 ELISA, Serum biochemical analysis, In vivo LPS stimulation assay, In vivo CKD model assay; CRISPR-Cas9 endogenous deletion/editing; ChIP; Mouse genetic deletion/knock-in
E_03891	2015	25303440	Failed degradation of JunB contributes to overproduction of type I collagen and development of dermal fibrosis in patients with systemic sclerosis	Homo sapiens	hg19	chr7	94002773	94005073	JUNB	COL1A2	Enhancer	Active	Disease	systemic sclerosis	NA	NA	NA	NA	Fibroblasts	NA	fibroblast	CL:0000057	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay; RNAi/siRNA/shRNA
E_03892	2015	25303440	Failed degradation of JunB contributes to overproduction of type I collagen and development of dermal fibrosis in patients with systemic sclerosis	Homo sapiens	hg19	chr7	94002773	94005073	JUND	COL1A2	Enhancer	Active	Disease	systemic sclerosis	NA	NA	NA	NA	Fibroblasts	NA	fibroblast	CL:0000057	Enhancer activity assay; In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay; RNAi/siRNA/shRNA
E_03893	2012	22665440	Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus	Homo sapiens	hg19	chr17	69107686	69108045	AR	SOX9	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis	ChIP-seq; DNase-seq; 3C-seq; GWAS	Luciferase reporter assay; ChIP-qPCR; 3C-RT-qPCR; Sanger sequencing; Allele-specific reporter assay
E_03894	2009	19433513	Long-range activation of FKBP51 transcription by the androgen receptor via distal intronic enhancers	Homo sapiens	hg18	chr6	35666288	35666763	AR	FKBP5	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; In vivo functional validation	NA	Luciferase reporter assay; EMSA; AR ChIP-qPCR; qRT-PCR; Western blot; androgen stimulation; bicalutamide perturbation; AR overexpression; ChIP; In vivo phenotyping
E_03895	2009	19433513	Long-range activation of FKBP51 transcription by the androgen receptor via distal intronic enhancers	Homo sapiens	hg18	chr6	35666288	35666763	AR	FKBP5	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	VCaP	CVCL_2235	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; In vivo functional validation; Chromatin regulatory assay	NA	Luciferase reporter assay; EMSA; AR ChIP-qPCR; qRT-PCR; Western blot; androgen stimulation; bicalutamide perturbation; RNA polymerase II ChIP-qPCR; BRM/BRG1 ChIP-qPCR; histone ChIP-qPCR; ChIP; In vivo phenotyping
E_03896	2009	19433513	Long-range activation of FKBP51 transcription by the androgen receptor via distal intronic enhancers	Homo sapiens	hg18	chr6	35677658	35677924	AR	FKBP5	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; In vivo functional validation	NA	Luciferase reporter assay; EMSA; ARE-site mutagenesis; AR ChIP-qPCR; qRT-PCR; Western blot; androgen stimulation; bicalutamide perturbation; ChIP; In vivo phenotyping
E_03897	2009	19433513	Long-range activation of FKBP51 transcription by the androgen receptor via distal intronic enhancers	Homo sapiens	hg18	chr6	35677658	35677924	AR	FKBP5	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	VCaP	CVCL_2235	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; In vivo functional validation; Chromatin regulatory assay	NA	Luciferase reporter assay; EMSA; ARE-site mutagenesis; AR ChIP-qPCR; qRT-PCR; Western blot; androgen stimulation; bicalutamide perturbation; RNA polymerase II ChIP-qPCR; BRM/BRG1 ChIP-qPCR; histone ChIP-qPCR; ChIP; In vivo phenotyping
E_03898	2009	19433513	Long-range activation of FKBP51 transcription by the androgen receptor via distal intronic enhancers	Homo sapiens	hg18	chr6	35686677	35687097	AR	FKBP5	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; In vivo functional validation	NA	AR ChIP-qPCR; Luciferase reporter assay; qRT-PCR; androgen stimulation; bicalutamide perturbation; ChIP; In vivo phenotyping
E_03899	2009	19433513	Long-range activation of FKBP51 transcription by the androgen receptor via distal intronic enhancers	Homo sapiens	hg18	chr6	35686677	35687097	AR	FKBP5	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	VCaP	CVCL_2235	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; In vivo functional validation	NA	AR ChIP-qPCR; Luciferase reporter assay; qRT-PCR; androgen stimulation; bicalutamide perturbation; ChIP; In vivo phenotyping
E_03900	2024	38559809	Functional analysis of a first hindlimb positioning enhancer via Gdf11 expression	Mus musculus	mm9	chr10	128326106	128327832	NA	Gdf11	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Mouse embryos (E8.5-E9.5)	NA	NA	NA	Enhancer activity assay; Functional perturbation assay	NA	In ovo electroporation EGFP reporter assay in chick embryos; whole-embryo electroporation reporter assay; CRISPR-Cas9 HCR deletion; RT-qPCR; whole-mount in situ hybridization; PCR genotyping and sequencing; skeletal staining
E_03901	2024	38559809	Functional analysis of a first hindlimb positioning enhancer via Gdf11 expression	Mus musculus	mm9	chr10	128326106	128327832	NA	Gdf11	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Gdf11 WT and HCR-deficient mice	NA	NA	NA	Enhancer activity assay; Functional perturbation assay	NA	In ovo electroporation EGFP reporter assay in chick embryos; whole-embryo electroporation reporter assay; CRISPR-Cas9 HCR deletion; RT-qPCR; whole-mount in situ hybridization; PCR genotyping and sequencing; skeletal staining
E_03902	2019	31164884	Mechanistic Characterization of RASGRP1 Variants Identifies an hnRNP-K-Regulated Transcriptional Enhancer Contributing to SLE Susceptibility	Homo sapiens	hg19	chr15	38850022	38850502	HNRNPK	RASGRP1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Jurkat	CVCL_0065	T lymphoblast	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; eQTL analysis	Luciferase reporter assay; EMSA; ChIP-qPCR; Western blot; RT-qPCR; Reporter assay; qPCR
E_03903	2018	29527594	A Novel Distal Enhancer Mediates Inflammation-, PTH-, and Early Onset Murine Kidney Disease-Induced Expression of the Mouse Fgf23 Gene	Mus musculus	mm10	chr6	127006796	127007720	Nfkb1	Fgf23	Enhancer	Active	Disease	chronic kidney disease	MONDO:0005300	NA	bone	NA	in vivo mouse tissues	NA	osteocyte	CL:0000137	Enhancer discovery; Endogenous enhancer deletion; stimulus-response and in vivo phenotypic validation	ChIP-seq; transcriptomic profiling; comparative conservation analysis	CRISPR-Cas9 enhancer deletion; RT-qPCR; FGF23 ELISA; genotyping/Sanger sequencing; LPS/cytokine/PTH stimulation; CKD mouse model; CRISPR-Cas9
E_03904	2016	26446995	An autoregulatory enhancer controls mammary-specific STAT5 functions	Mus musculus	mm10	chr11	9746900	9747200	Stat5a	Stat5a	Enhancer	Active	Normal	NA	NA	NA	mammary gland	UBERON:0001911	Primary MECs	NA	mammary epithelial cell	NA	Functional perturbation assay	ChIP-seq; RNA-seq	CRISPR knockout; RT-qPCR; CRISPR-Cas9
E_03905	2026	42030388	MYC-bound enhancer RNAs in cis regulate gene transcription and tumorigenesis	Homo sapiens	hg19	chr2	116230440	116232740	BRD4	GREB1	Enhancer	Active	Disease	invasive breast carcinoma	MONDO:0006256	NA	mammary gland	UBERON:0001911	BT-474	CVCL_0179	malignant cell	CL:0001064	Luciferase reporter assay; loss-of-function ASO/shRNA knockdown; ChIP-qPCR; Pol II ChIA-PET chromatin interaction	eCLIP-seq; ChIP-seq; ATAC-seq; RNA-seq; GRO-seq; ChIA-PET; TCGA/CCLE multi-omics	qRT-PCR, dual-luciferase reporter,; RNA FISH super-resolution imaging, subcellular fractionation, xenograft in vivo tumor assay
E_03906	2026	42030388	MYC-bound enhancer RNAs in cis regulate gene transcription and tumorigenesis	Homo sapiens	hg19	chr2	116230440	116232740	BRD4	GREB1	Enhancer	Active	Disease	invasive breast carcinoma	MONDO:0006256	NA	mammary gland	UBERON:0001911	MCF-7	CVCL_0031	malignant cell	CL:0001064	Luciferase reporter assay; loss-of-function ASO/shRNA knockdown; ChIP-qPCR; Pol II ChIA-PET chromatin interaction	eCLIP-seq; ChIP-seq; ATAC-seq; RNA-seq; GRO-seq; ChIA-PET; TCGA/CCLE multi-omics	qRT-PCR, dual-luciferase reporter,; RNA FISH super-resolution imaging, subcellular fractionation, xenograft in vivo tumor assay
E_03907	2026	42030388	MYC-bound enhancer RNAs in cis regulate gene transcription and tumorigenesis	Homo sapiens	hg19	chr2	116230440	116232740	MYC	GREB1	Enhancer	Active	Disease	invasive breast carcinoma	MONDO:0006256	NA	mammary gland	UBERON:0001911	BT-474	CVCL_0179	malignant cell	CL:0001064	Luciferase reporter assay; loss-of-function ASO/shRNA knockdown; ChIP-qPCR; Pol II ChIA-PET chromatin interaction	eCLIP-seq; ChIP-seq; ATAC-seq; RNA-seq; GRO-seq; ChIA-PET; TCGA/CCLE multi-omics	qRT-PCR, dual-luciferase reporter,; RNA FISH super-resolution imaging, subcellular fractionation, xenograft in vivo tumor assay
E_03908	2026	42030388	MYC-bound enhancer RNAs in cis regulate gene transcription and tumorigenesis	Homo sapiens	hg19	chr2	116230440	116232740	MYC	GREB1	Enhancer	Active	Disease	invasive breast carcinoma	MONDO:0006256	NA	mammary gland	UBERON:0001911	MCF-7	CVCL_0031	malignant cell	CL:0001064	Luciferase reporter assay; loss-of-function ASO/shRNA knockdown; ChIP-qPCR; Pol II ChIA-PET chromatin interaction	eCLIP-seq; ChIP-seq; ATAC-seq; RNA-seq; GRO-seq; ChIA-PET; TCGA/CCLE multi-omics	qRT-PCR, dual-luciferase reporter,; RNA FISH super-resolution imaging, subcellular fractionation, xenograft in vivo tumor assay
E_03909	2012	22665440	Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus	Homo sapiens	hg19	chr17	69107686	69108045	AR	SOX9	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	prostate cancer cells and primary prostate tissues	NA	prostate epithelial cell	NA	Risk-enhancer mapping; TF occupancy; enhancer-promoter looping	ChIP-seq; FAIRE-seq; genetic association integration	3C; ChIP-qPCR; allele-specific regulatory assays; Reporter assay
E_03910	2024	38233525	Affinity-optimizing enhancer variants disrupt development	Homo sapiens	hg38	chr7	156791087	156791875	NA	SHH	Enhancer	Active	Disease	polydactyly	NA	DOID:1148	developing limb	NA	ZRS transgenic developmental model	NA	limb bud cell	NA	Enhancer activity assay; TF-binding-affinity assay; enhancer variant functional assay; developmental phenotype assay	MPRA/high-throughput enhancer mutagenesis	Transgenic mouse enhancer assay; Site-directed mutagenesis; TF-binding-affinity assay; embryonic limb reporter analysis; digit phenotype analysis
E_03911	2018	29527594	A Novel Distal Enhancer Mediates Inflammation-, PTH-, and Early Onset Murine Kidney Disease-Induced Expression of the Mouse Fgf23 Gene	Mus musculus	mm10	chr6	127006796	127007720	Arnt	Fgf23	Enhancer	Active	Disease	chronic kidney disease	MONDO:0005300	NA	kidney	UBERON:0002113	Bone marrow-derived mesenchymal stem cells	NA	mesenchymal stromal cell	CL:0000499	Functional genomics assay; Epigenomic profiling assay; Genome editing assay; Transcriptional regulation assay; In vivo functional assay	ChIP-seq; microarray; Comparative genomic conservation analysis	CRISPR-Cas9 enhancer deletion; RT-qPCR; FGF23 ELISA; DXA; Serum biochemical analysis; Genotyping PCR; Sanger sequencing; In vivo LPS stimulation assay; In vivo cytokine stimulation assay; In vivo PTH stimulation assay; In vivo CKD model assay; CRISPR-Cas9
E_03912	2018	29527594	A Novel Distal Enhancer Mediates Inflammation-, PTH-, and Early Onset Murine Kidney Disease-Induced Expression of the Mouse Fgf23 Gene	Mus musculus	mm10	chr6	127006796	127007720	Arntl	Fgf23	Enhancer	Active	Disease	chronic kidney disease	MONDO:0005300	NA	kidney	UBERON:0002113	Bone marrow-derived mesenchymal stem cells	NA	mesenchymal stromal cell	CL:0000499	Functional genomics assay; Epigenomic profiling assay; Genome editing assay; Transcriptional regulation assay; In vivo functional assay	ChIP-seq; microarray; Comparative genomic conservation analysis	CRISPR-Cas9 enhancer deletion; RT-qPCR; FGF23 ELISA; DXA; Serum biochemical analysis; Genotyping PCR; Sanger sequencing; In vivo LPS stimulation assay; In vivo cytokine stimulation assay; In vivo PTH stimulation assay; In vivo CKD model assay; CRISPR-Cas9
E_03913	2018	29527594	A Novel Distal Enhancer Mediates Inflammation-, PTH-, and Early Onset Murine Kidney Disease-Induced Expression of the Mouse Fgf23 Gene	Mus musculus	mm10	chr6	127006796	127007720	Clock	Fgf23	Enhancer	Active	Disease	chronic kidney disease	MONDO:0005300	NA	kidney	UBERON:0002113	Bone marrow-derived mesenchymal stem cells	NA	mesenchymal stromal cell	CL:0000499	Functional genomics assay; Epigenomic profiling assay; Genome editing assay; Transcriptional regulation assay; In vivo functional assay	ChIP-seq; microarray; Comparative genomic conservation analysis	CRISPR-Cas9 enhancer deletion; RT-qPCR; FGF23 ELISA; DXA; Serum biochemical analysis; Genotyping PCR; Sanger sequencing; In vivo LPS stimulation assay; In vivo cytokine stimulation assay; In vivo PTH stimulation assay; In vivo CKD model assay; CRISPR-Cas9
E_03914	2018	29527594	A Novel Distal Enhancer Mediates Inflammation-, PTH-, and Early Onset Murine Kidney Disease-Induced Expression of the Mouse Fgf23 Gene	Mus musculus	mm10	chr6	127006796	127007720	Hif1a	Fgf23	Enhancer	Active	Disease	chronic kidney disease	MONDO:0005300	NA	kidney	UBERON:0002113	Bone marrow-derived mesenchymal stem cells	NA	mesenchymal stromal cell	CL:0000499	Functional genomics assay; Epigenomic profiling assay; Genome editing assay; Transcriptional regulation assay; In vivo functional assay	ChIP-seq; microarray; Comparative genomic conservation analysis	CRISPR-Cas9 enhancer deletion; RT-qPCR; FGF23 ELISA; DXA; Serum biochemical analysis; Genotyping PCR; Sanger sequencing; In vivo LPS stimulation assay; In vivo cytokine stimulation assay; In vivo PTH stimulation assay; In vivo CKD model assay; CRISPR-Cas9
E_03915	2018	29527594	A Novel Distal Enhancer Mediates Inflammation-, PTH-, and Early Onset Murine Kidney Disease-Induced Expression of the Mouse Fgf23 Gene	Mus musculus	mm10	chr6	127006796	127007720	Nfkb1	Fgf23	Enhancer	Active	Disease	chronic kidney disease	MONDO:0005300	NA	kidney	UBERON:0002113	Bone marrow-derived mesenchymal stem cells	NA	mesenchymal stromal cell	CL:0000499	Functional genomics assay; Epigenomic profiling assay; Genome editing assay; Transcriptional regulation assay; In vivo functional assay	ChIP-seq; microarray; Comparative genomic conservation analysis	CRISPR-Cas9 enhancer deletion; RT-qPCR; FGF23 ELISA; DXA; Serum biochemical analysis; Genotyping PCR; Sanger sequencing; In vivo LPS stimulation assay; In vivo cytokine stimulation assay; In vivo PTH stimulation assay; In vivo CKD model assay; CRISPR-Cas9
E_03916	2018	29527594	A Novel Distal Enhancer Mediates Inflammation-, PTH-, and Early Onset Murine Kidney Disease-Induced Expression of the Mouse Fgf23 Gene	Mus musculus	mm10	chr6	127006796	127007720	Npas2	Fgf23	Enhancer	Active	Disease	chronic kidney disease	MONDO:0005300	NA	kidney	UBERON:0002113	Bone marrow-derived mesenchymal stem cells	NA	mesenchymal stromal cell	CL:0000499	Functional genomics assay; Epigenomic profiling assay; Genome editing assay; Transcriptional regulation assay; In vivo functional assay	ChIP-seq; microarray; Comparative genomic conservation analysis	CRISPR-Cas9 enhancer deletion; RT-qPCR; FGF23 ELISA; DXA; Serum biochemical analysis; Genotyping PCR; Sanger sequencing; In vivo LPS stimulation assay; In vivo cytokine stimulation assay; In vivo PTH stimulation assay; In vivo CKD model assay; CRISPR-Cas9
E_03917	2018	29527594	A Novel Distal Enhancer Mediates Inflammation-, PTH-, and Early Onset Murine Kidney Disease-Induced Expression of the Mouse Fgf23 Gene	Mus musculus	mm10	chr6	127006796	127007720	Stat3	Fgf23	Enhancer	Active	Disease	chronic kidney disease	MONDO:0005300	NA	kidney	UBERON:0002113	Bone marrow-derived mesenchymal stem cells	NA	mesenchymal stromal cell	CL:0000499	Functional genomics assay; Epigenomic profiling assay; Genome editing assay; Transcriptional regulation assay; In vivo functional assay	ChIP-seq; microarray; Comparative genomic conservation analysis	CRISPR-Cas9 enhancer deletion; RT-qPCR; FGF23 ELISA; DXA; Serum biochemical analysis; Genotyping PCR; Sanger sequencing; In vivo LPS stimulation assay; In vivo cytokine stimulation assay; In vivo PTH stimulation assay; In vivo CKD model assay; CRISPR-Cas9
E_03918	2018	29527594	A Novel Distal Enhancer Mediates Inflammation-, PTH-, and Early Onset Murine Kidney Disease-Induced Expression of the Mouse Fgf23 Gene	Mus musculus	mm10	chr6	127006796	127007720	Stat5a	Fgf23	Enhancer	Active	Disease	chronic kidney disease	MONDO:0005300	NA	kidney	UBERON:0002113	Bone marrow-derived mesenchymal stem cells	NA	mesenchymal stromal cell	CL:0000499	Functional genomics assay; Epigenomic profiling assay; Genome editing assay; Transcriptional regulation assay; In vivo functional assay	ChIP-seq; microarray; Comparative genomic conservation analysis	CRISPR-Cas9 enhancer deletion; RT-qPCR; FGF23 ELISA; DXA; Serum biochemical analysis; Genotyping PCR; Sanger sequencing; In vivo LPS stimulation assay; In vivo cytokine stimulation assay; In vivo PTH stimulation assay; In vivo CKD model assay; CRISPR-Cas9
E_03919	2018	29527594	A Novel Distal Enhancer Mediates Inflammation-, PTH-, and Early Onset Murine Kidney Disease-Induced Expression of the Mouse Fgf23 Gene	Mus musculus	mm10	chr6	127006796	127007720	Stat6	Fgf23	Enhancer	Active	Disease	chronic kidney disease	MONDO:0005300	NA	kidney	UBERON:0002113	Bone marrow-derived mesenchymal stem cells	NA	mesenchymal stromal cell	CL:0000499	Functional genomics assay; Epigenomic profiling assay; Genome editing assay; Transcriptional regulation assay; In vivo functional assay	ChIP-seq; microarray; Comparative genomic conservation analysis	CRISPR-Cas9 enhancer deletion; RT-qPCR; FGF23 ELISA; DXA; Serum biochemical analysis; Genotyping PCR; Sanger sequencing; In vivo LPS stimulation assay; In vivo cytokine stimulation assay; In vivo PTH stimulation assay; In vivo CKD model assay; CRISPR-Cas9
E_03920	2018	29527594	A Novel Distal Enhancer Mediates Inflammation-, PTH-, and Early Onset Murine Kidney Disease-Induced Expression of the Mouse Fgf23 Gene	Mus musculus	mm9	chr6	126984000	126986000	NA	Fgf23	Enhancer	Active	Disease	chronic kidney disease	MONDO:0005300	NA	bone tissue	UBERON:0002481	IDG-SW3	CVCL_0P23	osteoblast	CL:0000062	Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation; Candidate enhancer identification; Epigenomic profiling	Histone modification ChIP-seq; ChIP-seq	CRISPR-Cas9 endogenous deletion/editing; ChIP; Mouse genetic deletion/knock-in
E_03921	2018	29527594	A Novel Distal Enhancer Mediates Inflammation-, PTH-, and Early Onset Murine Kidney Disease-Induced Expression of the Mouse Fgf23 Gene	Mus musculus	mm9	chr6	127030000	127032000	NA	Fgf23	Enhancer	Active	Disease	chronic kidney disease	MONDO:0005300	NA	bone tissue	UBERON:0002481	IDG-SW3	CVCL_0P23	osteoblast	CL:0000062	Chromatin-state profiling; Endogenous enhancer perturbation; In vivo functional validation; Candidate enhancer identification; Epigenomic profiling	Histone modification ChIP-seq; ChIP-seq	CRISPR-Cas9 endogenous deletion/editing; ChIP; Mouse genetic deletion/knock-in
E_03922	2018	29527594	A Novel Distal Enhancer Mediates Inflammation-, PTH-, and Early Onset Murine Kidney Disease-Induced Expression of the Mouse Fgf23 Gene	Mus musculus	mm10	chr6	127006796	127007720	Nfkb1	Fgf23	Enhancer	Active	Disease	chronic kidney disease	MONDO:0005300	NA	bone	NA	osteocytes	NA	osteocyte	CL:0000137	Enhancer discovery; Endogenous enhancer deletion; stimulus-response and in vivo phenotypic validation	ChIP-seq; transcriptomic profiling; comparative conservation analysis	CRISPR-Cas9 enhancer deletion; RT-qPCR; FGF23 ELISA; genotyping/Sanger sequencing; LPS/cytokine/PTH stimulation; CKD mouse model; CRISPR-Cas9
E_03923	2018	29527594	A Novel Distal Enhancer Mediates Inflammation-, PTH-, and Early Onset Murine Kidney Disease-Induced Expression of the Mouse Fgf23 Gene	Mus musculus	mm10	chr6	127033997	127036097	Hif1a	Fgf23	Enhancer	Active	Disease	chronic kidney disease	MONDO:0005300	NA	kidney	UBERON:0002113	Osteocyte Cell Lines	NA	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_03924	2018	29527594	A Novel Distal Enhancer Mediates Inflammation-, PTH-, and Early Onset Murine Kidney Disease-Induced Expression of the Mouse Fgf23 Gene	Mus musculus	mm10	chr6	127033997	127036097	Nfkb1	Fgf23	Enhancer	Active	Disease	chronic kidney disease	MONDO:0005300	NA	kidney	UBERON:0002113	Osteocyte Cell Lines	NA	NA	NA	Endogenous enhancer perturbation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP
E_03925	2012	22665440	Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus	Homo sapiens	hg19	chr17	69108466	69108765	FOXA1	SOX9	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Disease-variant functional analysis	ChIP-seq; DNase-seq; GWAS	Luciferase reporter assay; ChIP-qPCR; Sanger sequencing; Allele-specific reporter assay
E_03926	2012	22665440	Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus	Homo sapiens	hg19	chr17	69107686	69108045	AR	SOX9	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	VCaP	CVCL_2235	epithelial cell	CL:0000066	Enhancer activity assay; TF binding assay; Disease-variant functional analysis; High-throughput regulatory profiling	ChIP-seq; DNase-seq (public/integrated datasets); GWAS	Allele-specific reporter assay
E_03927	2015	25303440	Failed degradation of JunB contributes to overproduction of type I collagen and development of dermal fibrosis in patients with systemic sclerosis	Homo sapiens	hg19	chr7	94002773	94005073	JUN	COL1A2	Enhancer	Active	Disease	systemic sclerosis	NA	NA	skin	UBERON:0002097	Primary human dermal fibroblasts from systemic sclerosis patients	NA	fibroblast	CL:0000057	Enhancer activity assay; TF binding assay	NA	EMSA/supershift; ChIP-qPCR; Reporter assay; RT-qPCR; EMSA; ChIP; Western blot
E_03928	2015	25303440	Failed degradation of JunB contributes to overproduction of type I collagen and development of dermal fibrosis in patients with systemic sclerosis	Homo sapiens	hg19	chr7	94002773	94005073	JUNB	COL1A2	Enhancer	Active	Disease	systemic sclerosis	NA	NA	connective tissue	UBERON:0002384	primary dermal fibroblasts	NA	fibroblast	CL:0000057	Enhancer activity assay; TF binding assay; Gene-expression perturbation assay	NA	Reporter assay; EMSA; ChIP; RNA interference; RT-qPCR; Western blot; immunohistochemistry
E_03929	2015	25303440	Failed degradation of JunB contributes to overproduction of type I collagen and development of dermal fibrosis in patients with systemic sclerosis	Homo sapiens	hg19	chr7	94002773	94005073	JUND	COL1A2	Enhancer	Active	Disease	systemic sclerosis	NA	NA	connective tissue	UBERON:0002384	primary dermal fibroblasts	NA	fibroblast	CL:0000057	Enhancer activity assay; TF binding assay; Gene-expression perturbation assay	NA	Reporter assay; EMSA; ChIP; RNA interference; RT-qPCR; Western blot; immunohistochemistry
E_03930	2019	31164884	Mechanistic Characterization of RASGRP1 Variants Identifies an hnRNP-K-Regulated Transcriptional Enhancer Contributing to SLE Susceptibility	Homo sapiens	hg19	chr15	38846389	38846967	NA	RASGRP1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Jurkat	CVCL_0065	T lymphoblast	NA	Enhancer activity assay	ChIP-seq; RNA-seq; eQTL analysis	Luciferase reporter assay; EMSA; ChIP-qPCR; Reporter assay; qPCR
E_03931	2009	19433513	Long-range activation of FKBP51 transcription by the androgen receptor via distal intronic enhancers	Homo sapiens	hg38	chr6	35630433	35630733	AR	FKBP5	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	prostate epithelial cell	NA	Androgen-responsive enhancer assay; AR occupancy; chromatin-remodeling analysis; target-gene perturbation	NA	AR ChIP-qPCR; EMSA; Luciferase reporter assay; ARE mutagenesis; AR RNAi; RT-qPCR; histone-density/chromatin-remodeling assays
E_03932	2009	19433513	Long-range activation of FKBP51 transcription by the androgen receptor via distal intronic enhancers	Homo sapiens	hg38	chr6	35630433	35630733	AR	FKBP5	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	prostate epithelial cell	NA	AR enhancer subsite validation; chromatin recruitment analysis	NA	AR ChIP-qPCR; EMSA; Luciferase reporter assay; ARE mutagenesis; RT-qPCR
E_03933	2009	19433513	Long-range activation of FKBP51 transcription by the androgen receptor via distal intronic enhancers	Homo sapiens	hg38	chr6	35630433	35630733	AR	FKBP5	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	VCaP	CVCL_2235	prostate epithelial cell	NA	Androgen-responsive enhancer assay; AR occupancy; chromatin-remodeling analysis; target-gene perturbation	NA	AR ChIP-qPCR; EMSA; Luciferase reporter assay; ARE mutagenesis; AR RNAi; RT-qPCR; histone-density/chromatin-remodeling assays
E_03934	2009	19433513	Long-range activation of FKBP51 transcription by the androgen receptor via distal intronic enhancers	Homo sapiens	hg38	chr6	35630433	35630733	AR	FKBP5	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	VCaP	CVCL_2235	prostate epithelial cell	NA	AR enhancer subsite validation; chromatin recruitment analysis	NA	AR ChIP-qPCR; EMSA; Luciferase reporter assay; ARE mutagenesis; RT-qPCR
E_03935	2009	19433513	Long-range activation of FKBP51 transcription by the androgen receptor via distal intronic enhancers	Homo sapiens	hg38	chr6	35641433	35641733	AR	FKBP5	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	prostate epithelial cell	NA	Androgen-responsive enhancer assay; AR occupancy; chromatin-remodeling analysis; target-gene perturbation	NA	AR ChIP-qPCR; EMSA; Luciferase reporter assay; ARE mutagenesis; AR RNAi; RT-qPCR; histone-density/chromatin-remodeling assays
E_03936	2009	19433513	Long-range activation of FKBP51 transcription by the androgen receptor via distal intronic enhancers	Homo sapiens	hg38	chr6	35641433	35641733	AR	FKBP5	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	prostate epithelial cell	NA	AR enhancer subsite validation; chromatin recruitment analysis	NA	AR ChIP-qPCR; EMSA; Luciferase reporter assay; ARE mutagenesis; RT-qPCR
E_03937	2009	19433513	Long-range activation of FKBP51 transcription by the androgen receptor via distal intronic enhancers	Homo sapiens	hg38	chr6	35641433	35641733	AR	FKBP5	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	VCaP	CVCL_2235	prostate epithelial cell	NA	Androgen-responsive enhancer assay; AR occupancy; chromatin-remodeling analysis; target-gene perturbation	NA	AR ChIP-qPCR; EMSA; Luciferase reporter assay; ARE mutagenesis; AR RNAi; RT-qPCR; histone-density/chromatin-remodeling assays
E_03938	2009	19433513	Long-range activation of FKBP51 transcription by the androgen receptor via distal intronic enhancers	Homo sapiens	hg38	chr6	35641433	35641733	AR	FKBP5	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	VCaP	CVCL_2235	prostate epithelial cell	NA	AR enhancer subsite validation; chromatin recruitment analysis	NA	AR ChIP-qPCR; EMSA; Luciferase reporter assay; ARE mutagenesis; RT-qPCR
E_03939	2024	38233525	Affinity-optimizing enhancer variants disrupt development	Homo sapiens	hg38	chr7	156791087	156791875	HOXA13	SHH	Enhancer	Active	Disease	polydactyly of a triphalangeal thumb	NA	NA	limb bud	NA	NA	NA	NA	NA	TF binding assay; Disease-variant functional analysis; Disease-associated enhancer variant analysis	PBM-based binding-affinity analysis	EMSA of WT and Dutch 2 ZRS sequences with human HOXA13 DNA-binding domain; Sanger sequence verification
E_03940	2024	38233525	Affinity-optimizing enhancer variants disrupt development	Homo sapiens	hg38	chr7	156791087	156791875	HOXD13	SHH	Enhancer	Active	Disease	polydactyly of a triphalangeal thumb	NA	NA	limb bud	NA	NA	NA	NA	NA	TF binding assay; Disease-variant functional analysis; Disease-associated enhancer variant analysis	PBM-based binding-affinity analysis	EMSA of WT and Dutch 2 ZRS sequences with human HOXD13 DNA-binding domain; Sanger sequence verification
E_03941	2023	38016946	Systematic characterization of the HOXA9 downstream targets in MLL-r leukemia by noncoding CRISPR screens	Homo sapiens	hg19	chr13	28840000	28850000	HOXA9	FLT3	Enhancer	Active	Disease	KMT2A-rearranged acute lymphoblastic leukemia	MONDO:0035941	NA	blood	UBERON:0000178	SEM	CVCL_0095	precursor B cell	CL:0000817	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	noncoding CRISPR screen; HOXA9 ChIP-seq; MEIS1 ChIP-seq; ATAC-seq; RNA-seq; Hi-C; Capture-C; ChIP-seq	Cas9 enhancer editing; CRISPRi; RT-qPCR; Western blot; competitive proliferation assay; FLT3 cDNA rescue; Flow cytometry; NSG transplantation
E_03942	2023	38016946	Systematic characterization of the HOXA9 downstream targets in MLL-r leukemia by noncoding CRISPR screens	Homo sapiens	hg19	chr13	28840000	28850000	MEIS1	FLT3	Enhancer	Active	Disease	KMT2A-rearranged acute lymphoblastic leukemia	MONDO:0035941	NA	blood	UBERON:0000178	SEM	CVCL_0095	precursor B cell	CL:0000817	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	noncoding CRISPR screen; HOXA9 ChIP-seq; MEIS1 ChIP-seq; ATAC-seq; RNA-seq; Hi-C; Capture-C; ChIP-seq	Cas9 enhancer editing; CRISPRi; RT-qPCR; Western blot; competitive proliferation assay; FLT3 cDNA rescue; Flow cytometry; NSG transplantation
E_03943	2016	27223305	The MYC 3' Wnt-Responsive Element Drives Oncogenic MYC Expression in Human Colorectal Cancer Cells	Homo sapiens	hg19	chr8	128754419	128756419	TCF7L2	MYC	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	---catenin ChIP-seq; RNA-seq	CRISPR/Cas9 deletion; ChIP-qPCR; qRT-PCR; Western blot; 3C-qPCR; mouse xenograft assay; CRISPR-Cas9
E_03944	2014	23698277	Aberrant TAL1 activation is mediated by an interchromosomal interaction in human T-cell acute lymphoblastic leukemia	Homo sapiens	hg38	chr16	15600300	15601300	MAF	TAL1	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	VCaP	CVCL_2235	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	4C-seq; ChIP-seq	Luciferase reporter assay; ChIP-qPCR, 3C; RT-qPCR, shRNA knockdown; Western blot
E_03945	2016	26813977	A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening	Homo sapiens	hg18	chr6	31247578	31247900	NA	POU5F1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	H1-hESC	CVCL_9771	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation; CRISPR screen	Pooled CRISPR/Cas9 sgRNA screen; amplicon deep sequencing; 4C-seq; Hi-C data integration; CRISPR genetic screen	Locus-specific CRISPR/Cas9 mutagenesis; Luciferase reporter assay; Flow cytometry; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_03946	2016	26813977	A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening	Homo sapiens	hg19	chr6	31139599	31139921	POU5F1	POU5F1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	H1-hESC	CVCL_9771	embryonic stem cell	CL:0002322	Enhancer activity assay; Endogenous enhancer perturbation; High-throughput cis-regulatory screen; Endogenous enhancer deletion	Pooled CRISPR-Cas9 screen; DNase-seq and ENCODE chromatin-data integration; CRISPR genetic screen	Luciferase reporter assay; individual CRISPR-Cas9 enhancer deletion; Flow cytometry; qRT-PCR; CRISPR-Cas9 endogenous deletion/editing
E_03947	2016	26813977	A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening	Homo sapiens	hg19	chr6	30646843	30647217	NA	POU5F1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	H1-hESC	CVCL_9771	embryonic stem cell	CL:0002322	Endogenous enhancer perturbation; High-throughput cis-regulatory screen; endogenous cis-regulatory perturbation	Pooled CRISPR-Cas9 screen; DNase-seq and ENCODE chromatin-data integration; CRISPR genetic screen	Luciferase reporter assay; individual CRISPR-Cas9 deletion; Flow cytometry; qRT-PCR; CRISPR-Cas9 endogenous deletion/editing
E_03948	2016	26813977	A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening	Homo sapiens	hg19	chr6	31126537	31126685	NA	POU5F1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	H1-hESC	CVCL_9771	embryonic stem cell	CL:0002322	Endogenous enhancer perturbation; High-throughput cis-regulatory screen; endogenous cis-regulatory perturbation	Pooled CRISPR-Cas9 screen; DNase-seq and ENCODE chromatin-data integration; CRISPR genetic screen	Luciferase reporter assay; individual CRISPR-Cas9 deletion; Flow cytometry; qRT-PCR; CRISPR-Cas9 endogenous deletion/editing
E_03949	2019	31366290	Variation in a Left Ventricle-Specific Hand1 Enhancer Impairs GATA Transcription Factor Binding and Disrupts Conduction System Development and Function	Mus musculus	mm9	chr11	57660605	57661348	Gata4	Hand1	Enhancer	Active	Normal	NA	NA	NA	heart left ventricle	UBERON:0002084	genetically engineered mouse embryos and adult mice	NA	ventricular cardiomyocyte	NA	TF binding assay; In vivo enhancer activity assay; Functional enhancer deletion assay; Regulatory variant functional assay	1000 Genomes variant analysis; comparative genomics	Transgenic lacZ reporter; CRISPR-Cas9 enhancer deletion; EMSA; SNP knock-in; RT-qPCR; ECG; histology
E_03950	2011	21087445	Identification of a novel cell type-specific intronic enhancer of macrophage migration inhibitory factor (MIF) and its regulation by mithramycin	Homo sapiens	hg19	chr22	24236570	24237410	SP1	MIF	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	CCRF-CEM C7A	CVCL_6826	T lymphoblast	NA	Cell-type-specific intronic enhancer mapping; cis-element mutagenesis; TF binding assay	NA	DNase-I hypersensitivity mapping; Luciferase reporter assay; GC-box mutagenesis; EMSA; SP1/SP3 RNAi; mithramycin inhibition; siRNA knockdown
E_03951	2026	41957362	A single-nucleotide enhancer mutation overrides chromosomal sex to drive XX male development	Mus musculus	mm10	chr11	112217279	112217835	Sox9	Sox9	Enhancer	Active	Normal	NA	NA	NA	gonad	NA	Embryonic gonadal cells	NA	embryonic gonad cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	RNA-seq; ATAC-seq	Luciferase reporter assay; CRISPR knockout; EMSA, qRT-PCR
E_03952	2022	34954189	A β-Catenin-TCF-Sensitive Locus Control Region Mediates GUCY2C Ligand Loss in Colorectal Cancer	Homo sapiens	hg19	chr1	42614062	42616745	NA	GUCA2A	Enhancer	Repressed	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin-state profiling; Endogenous enhancer perturbation	ChIP-seq; RNA-seq; RNA-seq; ChIP-seq	Luciferase reporter assay, CRISPR knockout, CRISPRi, CRISPRa; ChIP-qPCR; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing; Luciferase reporter assay; ChIP
E_03953	2022	34954189	A β-Catenin-TCF-Sensitive Locus Control Region Mediates GUCY2C Ligand Loss in Colorectal Cancer	Homo sapiens	hg19	chr1	42614062	42616745	NA	GUCA2B	Enhancer	Repressed	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	bone marrow	UBERON:0002371	Primary AML blasts	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay	ChIP-seq; RNA-seq	Luciferase reporter assay; CRISPR knockout; CRISPRi; CRISPRa; ChIP-qPCR; RT-qPCR; CRISPR-Cas9
E_03954	2018	29284139	Coordinated d-cyclin/Foxd1 activation drives mitogenic activity of the Sonic Hedgehog signaling pathway	Mus musculus	mm10	chr7	143459000	143459700	Foxd1	Cdkn1c	Enhancer	Active	Normal	NA	NA	NA	embryonic mesenchyme / fibroblast model	NA	Immortalized and primary mouse embryonic fibroblasts	NA	embryonic fibroblast / cranial neural crest-derived cell	NA	FOXD1-responsive Cdkn1c intronic reporter element; candidate enhancer evidence only (no endogenous enhancer deletion in this paper)	Not used for direct enhancer proof in this study	Cdkn1c enh1 luciferase reporter; FOXD1 overexpression; Foxd1 gene CRISPR-Cas9 knockout; SHH stimulation; vismodegib inhibition; RT-qPCR; proliferation assay
E_03955	2018	30017589	GRHL2-Dependent Enhancer Switching Maintains a Pluripotent Stem Cell Transcriptional Subnetwork after Exit from Naive Pluripotency	Mus musculus	mm10	chr18	24562000	24562200	Klf4	Dsp	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	ESCs	NA	embryonic stem cell	CL:0002322	Functional perturbation assay	ChIP-seq; ATAC-seq; RNA-seq	CRISPR knockout; RT-qPCR; Western blot
E_03956	2018	30017589	GRHL2-Dependent Enhancer Switching Maintains a Pluripotent Stem Cell Transcriptional Subnetwork after Exit from Naive Pluripotency	Mus musculus	mm10	chr18	24570000	24570200	Grhl2	Dsp	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	ESCs	NA	embryonic stem cell	CL:0002322	Functional perturbation assay	ChIP-seq; ATAC-seq; RNA-seq	CRISPR knockout; RT-qPCR; Western blot
E_03957	2018	30017589	GRHL2-Dependent Enhancer Switching Maintains a Pluripotent Stem Cell Transcriptional Subnetwork after Exit from Naive Pluripotency	Mus musculus	mm10	chr8	109142000	109142200	Klf4	Cdh1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	ESCs	NA	embryonic stem cell	CL:0002322	Functional perturbation assay	ChIP-seq; ATAC-seq; RNA-seq	CRISPR knockout; RT-qPCR; Western blot
E_03958	2018	30017589	GRHL2-Dependent Enhancer Switching Maintains a Pluripotent Stem Cell Transcriptional Subnetwork after Exit from Naive Pluripotency	Mus musculus	mm10	chr8	109150000	109150200	Grhl2	Cdh1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	ESCs	NA	embryonic stem cell	CL:0002322	Functional perturbation assay	ChIP-seq; ATAC-seq; RNA-seq	CRISPR knockout; RT-qPCR; Western blot
E_03959	2018	29284139	Coordinated d-cyclin/Foxd1 activation drives mitogenic activity of the Sonic Hedgehog signaling pathway	Mus musculus	mm10	chr7	143459000	143459700	Foxd1	Cdkn1c	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	immortalized mouse embryonic fibroblasts	NA	embryonic fibroblast	CL:2000042	Enhancer activity assay; Endogenous enhancer perturbation; In vivo functional validation; transcription-factor-dependent reporter assay; signaling perturbation assay	NA	Cdkn1c enh1 luciferase reporter assay; FOXD1 overexpression; Foxd1 CRISPR-Cas9 knockout; SHH ligand stimulation; vismodegib inhibition; RT-qPCR; cell-proliferation assay; Mouse genetic deletion/knock-in
E_03960	2024	38448444	Dynamic enhancer landscapes in human craniofacial development	Mus musculus	mm10	chr9	55546300	55546600	NA	Isl2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Sensory neurons	NA	sensory neuron	CL:0000101	Enhancer activity assay; In vivo functional validation	snATAC-seq, scRNA-seq	Transgenic reporter assay; In vivo phenotyping
E_03961	2018	29284139	Coordinated d-cyclin/Foxd1 activation drives mitogenic activity of the Sonic Hedgehog signaling pathway	Mus musculus	mm10	chr7	143459000	143459700	Foxd1	Cdkn1c	Enhancer	Active	Normal	NA	NA	NA	embryonic mesenchyme / fibroblast model	NA	O9-1 cranial neural crest cells	NA	embryonic fibroblast / cranial neural crest-derived cell	NA	FOXD1-responsive Cdkn1c intronic reporter element; candidate enhancer evidence only (no endogenous enhancer deletion in this paper)	Not used for direct enhancer proof in this study	Cdkn1c enh1 luciferase reporter; FOXD1 overexpression; Foxd1 gene CRISPR-Cas9 knockout; SHH stimulation; vismodegib inhibition; RT-qPCR; proliferation assay
E_03962	2018	29284139	Coordinated d-cyclin/Foxd1 activation drives mitogenic activity of the Sonic Hedgehog signaling pathway	Mus musculus	mm10	chr7	143112640	143113190	Foxd1	Cdkn1c	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	immortalized mouse embryonic fibroblasts	NA	embryonic fibroblast	CL:2000042	Enhancer activity assay; Endogenous enhancer perturbation; In vivo functional validation; Functional signaling perturbation assay	NA	Cdkn1c intron-2 enhancer luciferase reporter assay; Foxd1 CRISPR/Cas9 knockout; SHH stimulation; RT-qPCR; proliferation assay; Mouse genetic deletion/knock-in
E_03963	2017	29224777	YY1 Is a Structural Regulator of Enhancer-Promoter Loops	Mus musculus	mm10	chr6	115598005	115604631	Yy1	Raf1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Chromatin interaction assay; Structural TF perturbation assay	YY1 ChIP-seq; H3K27ac HiChIP; YY1/CTCF ChIA-PET; RNA-seq; 4C-seq	YY1 depletion/degradation; deletion of YY1 binding sites in functional loci; ChIP-qPCR; RT-qPCR
E_03964	2015	26200345	Non-coding recurrent mutations in chronic lymphocytic leukaemia	Homo sapiens	hg19	chr9	37370916	37371635	NA	PAX5	Enhancer	Active	Disease	B-cell chronic lymphocytic leukemia	MONDO:0004948	NA	blood	UBERON:0000178	Primary CLL cells	NA	B cell	CL:0000236	Chromatin interaction assay; Regulatory variant assay; Functional enhancer perturbation	WGS; RNA-seq; epigenomic profiling; 4C-seq	CRISPR/Cas9 enhancer mutation/deletion; PAX5 expression analysis; targeted validation
E_03965	2021	34362881	Aberrant super-enhancer-driven oncogene ENC1 promotes the radio-resistance of breast carcinoma	Homo sapiens	hg38	chr5	74684243	74687892	TCF4	ENC1	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	Breast Cancer Cell	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	Luciferase reporter assay; ChIP-qPCR, CRISPR knockout; RT-qPCR; Western blot
E_03966	2021	34362881	Aberrant super-enhancer-driven oncogene ENC1 promotes the radio-resistance of breast carcinoma	Homo sapiens	hg38	chr5	74684243	74687892	TCF4	ENC1	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	Breast cancer drug-resistant cell	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	Luciferase reporter assay; ChIP-qPCR, CRISPR knockout; RT-qPCR; Western blot
E_03967	2021	34362881	Aberrant super-enhancer-driven oncogene ENC1 promotes the radio-resistance of breast carcinoma	Homo sapiens	hg38	chr5	74684243	74687892	TCF4	ENC1	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	MDA-MB-231	CVCL_0062	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	Luciferase reporter assay; ChIP-qPCR, CRISPR knockout; RT-qPCR; Western blot
E_03968	2021	34737287	Genome-wide profiling in colorectal cancer identifies PHF19 and TBC1D16 as oncogenic super enhancers	Homo sapiens	hg38	chr17	44421760	44428310	NA	TBC1D16	Super-enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	CRC patient tumor tissue	NA	malignant cell	CL:0001064	Chromatin-state profiling; Disease-variant functional analysis; Super-enhancer identification; Functional validation	H3K27ac ChIP-seq; H3K4me3 ChIP-seq; RNA-seq; whole-genome sequencing; ChIP-seq	CRISPR interference/functional perturbation; qRT-PCR; tumorigenic functional assays; ChIP
E_03969	2021	34737287	Genome-wide profiling in colorectal cancer identifies PHF19 and TBC1D16 as oncogenic super enhancers	Homo sapiens	hg38	chr9	123924740	123931280	NA	PHF19	Super-enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	CRC patient tumor tissue	NA	malignant cell	CL:0001064	Chromatin-state profiling; Disease-variant functional analysis; Super-enhancer identification; Functional validation	H3K27ac ChIP-seq; H3K4me3 ChIP-seq; RNA-seq; whole-genome sequencing; ChIP-seq	CRISPR interference/functional perturbation; qRT-PCR; tumorigenic functional assays; ChIP
E_03970	2019	31019297	NAD metabolic dependency in cancer is shaped by gene amplification and enhancer remodelling	Homo sapiens	hg19	chr7	105856018	105860658	MYC	NAMPT	Enhancer	Active	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; In vivo functional validation	ChIP-seq	Luciferase reporter assay, CRISPR knockout, CRISPRi; ChIP-qPCR; RT-qPCR; In vivo phenotyping
E_03971	2019	31019297	NAD metabolic dependency in cancer is shaped by gene amplification and enhancer remodelling	Homo sapiens	hg19	chr7	105856018	105860658	MYC	NAMPT	Enhancer	Active	Disease	glioblastoma	MONDO:0018177	NA	brain	UBERON:0000955	U-87MG ATCC	CVCL_0022	glioblastoma cell	CL:0001063	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq	Luciferase reporter assay; CRISPR knockout; CRISPRi; ChIP-qPCR; RT-qPCR
E_03972	2017	29155818	SNAIL1-mediated downregulation of FOXA proteins facilitates the inactivation of transcriptional enhancer elements at key epithelial genes in colorectal cancer cells	Homo sapiens	hg19	chr16	68779512	68779800	FOXA1	CDH1	Enhancer	Active	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay	ChIP-seq	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; CRISPR-Cas9
E_03973	2021	34737287	Genome-wide profiling in colorectal cancer identifies PHF19 and TBC1D16 as oncogenic super enhancers	Homo sapiens	hg19	chr17	77922269	77927433	NA	TBC1D16	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	73 paired colorectal-cancer patient tissues	NA	epithelial cell	CL:0000066	Super-enhancer identification; endogenous epigenomic perturbation; oncogenic functional validation	H3K27ac ChIP-seq; H3K4me3 ChIP-seq; RNA-seq; whole-genome sequencing; ROSE super-enhancer analysis; ChIP-seq	dCas9-KRAB CRISPRi; H3K27ac ChIP-qPCR; qRT-PCR; migration/Transwell assay; xenograft assay
E_03974	2021	34737287	Genome-wide profiling in colorectal cancer identifies PHF19 and TBC1D16 as oncogenic super enhancers	Homo sapiens	hg19	chr9	123663103	123669339	NA	PHF19	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	73 paired colorectal-cancer patient tissues	NA	epithelial cell	CL:0000066	Super-enhancer identification; endogenous epigenomic perturbation; oncogenic functional validation	H3K27ac ChIP-seq; H3K4me3 ChIP-seq; RNA-seq; whole-genome sequencing; ROSE super-enhancer analysis; ChIP-seq	dCas9-KRAB CRISPRi; H3K27ac ChIP-qPCR; qRT-PCR; migration/Transwell assay; xenograft assay
E_03975	2014	25185713	The Runx-PU.1 pathway preserves normal and AML/ETO9a leukemic stem cells	Mus musculus	mm10	chr2	28950000	28970000	Runx1	Spi1	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	bone marrow	UBERON:0002371	LSK hematopoietic stem cells	NA	hematopoietic stem cell	CL:0000037	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	NA	3C-RT-qPCR, Luciferase reporter assay; ChIP-qPCR; RT-qPCR
E_03976	2017	27895109	Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes	Mus musculus	mm10	chr11	33524486	33543505	NA	Ranbp17	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Embryonic Stem Cells (mESCs)	NA	embryonic stem cell	CL:0002322	Functional perturbation assay	ChIP-seq; RNA-seq	CRISPR knockout; RT-qPCR; CRISPR-Cas9
E_03977	2017	27895109	Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes	Mus musculus	mm10	chr4	123618309	123637993	NA	Macf1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Embryonic Stem Cells (mESCs)	NA	embryonic stem cell	CL:0002322	Functional perturbation assay	ChIP-seq; RNA-seq	CRISPR knockout; RT-qPCR; CRISPR-Cas9
E_03978	2013	23302769	Bivalent promoter marks and a latent enhancer may prime the leukaemia oncogene LMO1 for ectopic expression in T-cell leukaemia	Homo sapiens	hg19	chr11	8264000	8265500	TAL1	LMO1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Jurkat	CVCL_0065	T lymphoblast	NA	Enhancer activity assay	ChIP-seq	Luciferase reporter assay; Transgenic reporter assay; RT-qPCR
E_03979	2017	29155818	SNAIL1-mediated downregulation of FOXA proteins facilitates the inactivation of transcriptional enhancer elements at key epithelial genes in colorectal cancer cells	Homo sapiens	hg19	chr13	28545205	28547205	FOXA1	CDX2	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	Colorectal Cancer	NA	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_03980	2017	29155818	SNAIL1-mediated downregulation of FOXA proteins facilitates the inactivation of transcriptional enhancer elements at key epithelial genes in colorectal cancer cells	Homo sapiens	hg19	chr16	68777928	68779928	FOXA1	CDH1	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	Colorectal Cancer	NA	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_03981	2017	29155818	SNAIL1-mediated downregulation of FOXA proteins facilitates the inactivation of transcriptional enhancer elements at key epithelial genes in colorectal cancer cells	Homo sapiens	hg19	chr3	184276287	184278287	FOXA1	EPHB3	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	Colorectal Cancer	NA	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_03982	2014	25185713	The Runx-PU.1 pathway preserves normal and AML/ETO9a leukemic stem cells	Homo sapiens	hg38	chr11	47394824	47395023	RUNX1	SPI1	Enhancer	Active	Disease	RUNX1::RUNX1T1-associated acute myeloid leukemia	NA	NA	bone marrow	UBERON:0002371	AML/ETO9a leukemia stem-cell models	NA	leukemia-initiating cell	NA	Endogenous TF-site enhancer perturbation	RNA-seq; hematopoietic profiling	Runx-site mutation; transplantation; leukemia latency analysis; RT-qPCR
E_03983	2018	29909987	A Somatically Acquired Enhancer of the Androgen Receptor Is a Noncoding Driver in Advanced Prostate Cancer	Homo sapiens	hg19	chrX	66118920	66127943	NA	AR	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	22Rv1	CVCL_1045	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Endogenous enhancer perturbation	ChIP-seq	qRT-PCR, and ChIP-qPCR; CRISPR-Cas9 endogenous deletion/editing; ChIP
E_03984	2018	29909987	A Somatically Acquired Enhancer of the Androgen Receptor Is a Noncoding Driver in Advanced Prostate Cancer	Homo sapiens	hg19	chrX	66118920	66127943	NA	AR	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; Endogenous enhancer perturbation	ChIP-seq	qRT-PCR, and ChIP-qPCR; CRISPR-Cas9 endogenous deletion/editing; ChIP
E_03985	1999	10523648	Structural and functional cross-talk between a distant enhancer and the epsilon-globin gene promoter shows interdependence of the two elements in chromatin	Homo sapiens	hg19	chr11	5301801	5302175	GATA1	HBE1	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	erythroid lineage cell	CL:0000764	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin accessibility assay; Endogenous enhancer perturbation; Enhancer-promoter communication assay	NA	Stable EBV-derived episomal minichromosome assay; electroporation; Site-directed mutagenesis; EMSA; RNase protection assay; DNase I hypersensitivity assay; restriction enzyme accessibility assay; Southern blot-based nuclease mapping; Site-directed/motif mutagenesis
E_03986	1999	10523648	Structural and functional cross-talk between a distant enhancer and the epsilon-globin gene promoter shows interdependence of the two elements in chromatin	Homo sapiens	hg19	chr11	5301801	5302175	NFE2	HBE1	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	erythroid lineage cell	CL:0000764	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin accessibility assay; Endogenous enhancer perturbation; Enhancer-promoter communication assay	NA	Stable EBV-derived episomal minichromosome assay; electroporation; NF-E2-site mutational analysis; RNase protection assay; DNase I hypersensitivity assay; restriction enzyme accessibility assay; Southern blot-based nuclease mapping; Site-directed/motif mutagenesis
E_03987	2014	25223790	Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers	Mus musculus	mm10	chr6	122652547	122653538	NA	Nanog	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay	ChIP-seq	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Flow cytometry
E_03988	2014	25223790	Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers	Mus musculus	mm10	chr17	35643073	35645472	NA	Pou5f1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	HMC-1	CVCL_0003	mouse embryonic fibroblast	NA	Enhancer activity assay; Functional perturbation assay	RNA-seq; ChIP-seq	Luciferase reporter assay; ChIP-qPCR; RT-qPCR; Flow cytometry; Alkaline Phosphatase Staining
E_03989	2014	25223790	Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers	Mus musculus	mm10	chr6	122702344	122703335	NA	Nanog	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Nanog-GFP mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay; Enhancer repression assay	NA	TALE-KRAB repression; CRISPR/dCas9-KRAB repression; Flow cytometry; RT-qPCR; Luciferase reporter assay
E_03990	2014	25223790	Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers	Mus musculus	mm10	chr6	122702344	122703335	NA	Nanog	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Nanog-GFP mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay; Enhancer repression assay	NA	TALE-KRAB enhancer repression; CRISPR/dCas9-KRAB enhancer repression; Flow cytometry; RT-qPCR; Luciferase reporter assay
E_03991	2019	31406377	An Nfil3-Zeb2-Id2 pathway imposes Irf8 enhancer switching during cDC1 development	Mus musculus	mm10	chr8	124371000	124371500	Batf3	Irf8	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Mature cDC1	NA	conventional dendritic cell	NA	Enhancer activity assay; TF binding assay	ATAC-seq; ChIP-seq; RNA-seq; single-cell RNA-seq; RNA-seq	ChIP-qPCR; RT-qPCR
E_03992	2019	31406377	An Nfil3-Zeb2-Id2 pathway imposes Irf8 enhancer switching during cDC1 development	Mus musculus	mm10	chr8	124371000	124371500	Irf8	Irf8	Enhancer	Active	Normal	NA	NA	NA	spleen	UBERON:0002106	Mature cDC1	NA	conventional dendritic cell	NA	Enhancer activity assay; TF binding assay	ATAC-seq; ChIP-seq; RNA-seq; single-cell RNA-seq; RNA-seq	ChIP-qPCR; RT-qPCR
E_03993	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Homo sapiens	hg19	chr21	39823183	39825183	GATA2	ERG	Enhancer	Active	Disease	acute lymphoblastic leukemia	NA	NA	blood	UBERON:0000178	MOLT-4	CVCL_0013	T cell	CL:0000084	Enhancer activity assay; High-throughput profiling	ChIP-seq	qRT-PCR
E_03994	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Homo sapiens	hg19	chr21	39823183	39825183	LMO2	ERG	Enhancer	Active	Disease	acute lymphoblastic leukemia	NA	NA	blood	UBERON:0000178	MOLT-4	CVCL_0013	T cell	CL:0000084	Enhancer activity assay; High-throughput profiling	ChIP-seq	qRT-PCR
E_03995	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Homo sapiens	hg19	chr21	39823183	39825183	LYL1	ERG	Enhancer	Active	Disease	acute lymphoblastic leukemia	NA	NA	blood	UBERON:0000178	MOLT-4	CVCL_0013	T cell	CL:0000084	Enhancer activity assay; High-throughput profiling	ChIP-seq	qRT-PCR
E_03996	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Homo sapiens	hg19	chr21	39823183	39825183	TAL1	ERG	Enhancer	Active	Disease	acute lymphoblastic leukemia	NA	NA	blood	UBERON:0000178	MOLT-4	CVCL_0013	T cell	CL:0000084	Enhancer activity assay; High-throughput profiling	ChIP-seq	qRT-PCR
E_03997	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Homo sapiens	hg19	chr21	39823183	39825183	GATA2	ERG	Enhancer	Active	Disease	acute lymphoblastic leukemia	NA	NA	blood	UBERON:0000178	MOLT-4	CVCL_0013	NA	NA	Enhancer activity assay; High-throughput profiling	ChIP-seq	qRT-PCR
E_03998	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Homo sapiens	hg19	chr21	39823183	39825183	LMO2	ERG	Enhancer	Active	Disease	acute lymphoblastic leukemia	NA	NA	blood	UBERON:0000178	MOLT-4	CVCL_0013	NA	NA	Enhancer activity assay; High-throughput profiling	ChIP-seq	qRT-PCR
E_03999	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Homo sapiens	hg19	chr21	39823183	39825183	LYL1	ERG	Enhancer	Active	Disease	acute lymphoblastic leukemia	NA	NA	blood	UBERON:0000178	MOLT-4	CVCL_0013	NA	NA	Enhancer activity assay; High-throughput profiling	ChIP-seq	qRT-PCR
E_04000	2011	21536859	ERG promotes T-acute lymphoblastic leukemia and is transcriptionally regulated in leukemic cells by a stem cell enhancer	Homo sapiens	hg19	chr21	39823183	39825183	TAL1	ERG	Enhancer	Active	Disease	acute lymphoblastic leukemia	NA	NA	blood	UBERON:0000178	MOLT-4	CVCL_0013	NA	NA	Enhancer activity assay; High-throughput profiling	ChIP-seq	qRT-PCR
E_04001	2019	31591447	Distinct enhancer signatures in the mouse gastrula delineate progressive cell fate continuum during embryo development	Mus musculus	mm10	chr16	21480000	21482000	NA	2510009E07Rik	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	mouse gastrula	NA	mouse embryo	NA	Enhancer activity assay; Functional perturbation assay	ATAC-seq; ChIP-seq; RNA-seq	Transgenic reporter assay; CRISPR knockout; CRISPRi
E_04002	2025	40729681	Enhancer heterogeneity in acute lymphoblastic leukemia drives differential gene expression in patients	Homo sapiens	hg38	chr6	45322562	45322863	NA	RUNX2	Enhancer	Active	Disease	acute lymphoblastic leukemia	NA	NA	bone marrow	UBERON:0002371	Primary human KMT2A::AFF1 ALL blast	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	scMultiome ATAC+RNA; H3K27ac CUT&Tag; Micro-Capture-C; single-cell multiome; chromatin profiling	CRISPR enhancer deletion; RT-qPCR
E_04003	2025	40729681	Enhancer heterogeneity in acute lymphoblastic leukemia drives differential gene expression in patients	Homo sapiens	hg38	chr6	45323829	45324130	NA	RUNX2	Enhancer	Active	Disease	acute lymphoblastic leukemia	NA	NA	bone marrow	UBERON:0002371	Primary human KMT2A::AFF1 ALL blast	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	scMultiome ATAC+RNA; H3K27ac CUT&Tag; Micro-Capture-C; single-cell multiome; chromatin profiling	CRISPR enhancer deletion; RT-qPCR
E_04004	2025	40729681	Enhancer heterogeneity in acute lymphoblastic leukemia drives differential gene expression in patients	Homo sapiens	hg38	chr6	45328065	45328366	NA	RUNX2	Enhancer	Active	Disease	acute lymphoblastic leukemia	NA	NA	bone marrow	UBERON:0002371	Primary human KMT2A::AFF1 ALL blast	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	scMultiome ATAC+RNA; H3K27ac CUT&Tag; Micro-Capture-C; single-cell multiome; chromatin profiling	CRISPR enhancer deletion; RT-qPCR
E_04005	2025	40729681	Enhancer heterogeneity in acute lymphoblastic leukemia drives differential gene expression in patients	Homo sapiens	hg38	chr6	45331117	45331418	NA	RUNX2	Enhancer	Active	Disease	acute lymphoblastic leukemia	NA	NA	bone marrow	UBERON:0002371	Primary human KMT2A::AFF1 ALL blast	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	scMultiome ATAC+RNA; H3K27ac CUT&Tag; Micro-Capture-C; single-cell multiome; chromatin profiling	CRISPR enhancer deletion; RT-qPCR
E_04006	2025	40729681	Enhancer heterogeneity in acute lymphoblastic leukemia drives differential gene expression in patients	Homo sapiens	hg38	chr6	45333183	45333484	NA	RUNX2	Enhancer	Active	Disease	acute lymphoblastic leukemia	NA	NA	bone marrow	UBERON:0002371	Primary human KMT2A::AFF1 ALL blast	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	scMultiome ATAC+RNA; H3K27ac CUT&Tag; Micro-Capture-C; single-cell multiome; chromatin profiling	CRISPR enhancer deletion; RT-qPCR
E_04007	2025	40729681	Enhancer heterogeneity in acute lymphoblastic leukemia drives differential gene expression in patients	Homo sapiens	hg38	chr6	45339859	45340160	NA	RUNX2	Enhancer	Active	Disease	acute lymphoblastic leukemia	NA	NA	bone marrow	UBERON:0002371	Primary human KMT2A::AFF1 ALL blast	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	scMultiome ATAC+RNA; H3K27ac CUT&Tag; Micro-Capture-C; single-cell multiome; chromatin profiling	CRISPR enhancer deletion; RT-qPCR
E_04008	2025	40729681	Enhancer heterogeneity in acute lymphoblastic leukemia drives differential gene expression in patients	Homo sapiens	hg38	chr2	66577620	66583740	NA	MEIS1	Enhancer	Active	Disease	acute lymphoblastic leukemia	NA	NA	bone marrow	UBERON:0002371	Primary human KMT2A::AFF1 ALL blast	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	single-cell multiome ATAC+RNA; H3K27ac profiling; Micro-Capture-C; single-cell multiome; chromatin profiling	CRISPR enhancer deletion; RT-qPCR
E_04009	2019	31076442	The enhancer RNA ARIEL activates the oncogenic transcriptional program in T-cell acute lymphoblastic leukemia	Homo sapiens	hg19	chr10	63525013	63527013	TAL1	ARID5B	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Jurkat	CVCL_0065	T lymphoblast	NA	Functional perturbation assay; TF binding assay; Chromatin interaction assay; Enhancer RNA assay	ChIP-seq; RNA-seq; chromatin-interaction profiling; transcriptomic profiling	ARIEL shRNA knockdown; enhancer/eRNA perturbation; ChIP-qPCR; chromatin-interaction validation; RT-qPCR; cell-growth assay; xenograft assay
E_04010	2019	31076442	The enhancer RNA ARIEL activates the oncogenic transcriptional program in T-cell acute lymphoblastic leukemia	Homo sapiens	hg19	chr10	63525013	63527013	GATA3	ARID5B	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Jurkat	CVCL_0065	T lymphoblast	NA	Functional perturbation assay; TF binding assay; Chromatin interaction assay; Enhancer RNA assay	ChIP-seq; RNA-seq; chromatin-interaction profiling; transcriptomic profiling	ARIEL shRNA knockdown; ChIP-qPCR; chromatin-interaction validation; RT-qPCR; cell-growth assay; xenograft assay
E_04011	2019	31076442	The enhancer RNA ARIEL activates the oncogenic transcriptional program in T-cell acute lymphoblastic leukemia	Homo sapiens	hg19	chr10	63525013	63527013	RUNX1	ARID5B	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Jurkat	CVCL_0065	T lymphoblast	NA	Functional perturbation assay; TF binding assay; Chromatin interaction assay; Enhancer RNA assay	ChIP-seq; RNA-seq; chromatin-interaction profiling; transcriptomic profiling	ARIEL shRNA knockdown; ChIP-qPCR; chromatin-interaction validation; RT-qPCR; cell-growth assay; xenograft assay
E_04012	2022	35778390	B cell receptor signaling drives APOBEC3 expression via direct enhancer regulation in chronic lymphocytic leukemia B cells	Homo sapiens	hg38	chr22	39072097	39074320	NA	APOBEC3C	Enhancer	Active	Disease	B-cell chronic lymphocytic leukemia	MONDO:0004948	NA	blood	UBERON:0000178	MEC-1	CVCL_1870	B cell	CL:0000236	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation	CUT&Tag; ATAC-seq	CRISPR-Cas9 enhancer deletion; CRISPRi; PCR validation; RT-qPCR; Western blot; Immunofluorescence; EdU/PI Assay; MTS Cell Viability Assay; CRISPR-Cas9 endogenous deletion/editing
E_04013	2022	35778390	B cell receptor signaling drives APOBEC3 expression via direct enhancer regulation in chronic lymphocytic leukemia B cells	Homo sapiens	hg38	chr22	39072097	39074320	NA	APOBEC3D	Enhancer	Active	Disease	B-cell chronic lymphocytic leukemia	MONDO:0004948	NA	blood	UBERON:0000178	MEC-1	CVCL_1870	B cell	CL:0000236	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation	CUT&Tag; ATAC-seq	CRISPR-Cas9 enhancer deletion; CRISPRi; PCR validation; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_04014	2022	35778390	B cell receptor signaling drives APOBEC3 expression via direct enhancer regulation in chronic lymphocytic leukemia B cells	Homo sapiens	hg38	chr22	39072097	39074320	NA	APOBEC3F	Enhancer	Active	Disease	B-cell chronic lymphocytic leukemia	MONDO:0004948	NA	blood	UBERON:0000178	MEC-1	CVCL_1870	B cell	CL:0000236	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation	CUT&Tag; ATAC-seq	CRISPR-Cas9 enhancer deletion; CRISPRi; PCR validation; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_04015	2022	35778390	B cell receptor signaling drives APOBEC3 expression via direct enhancer regulation in chronic lymphocytic leukemia B cells	Homo sapiens	hg38	chr22	39072097	39074320	NA	APOBEC3G	Enhancer	Active	Disease	B-cell chronic lymphocytic leukemia	MONDO:0004948	NA	blood	UBERON:0000178	MEC-1	CVCL_1870	B cell	CL:0000236	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation	CUT&Tag; ATAC-seq	CRISPR-Cas9 enhancer deletion; CRISPRi; PCR validation; RT-qPCR; Western blot; Immunofluorescence; EdU/PI Assay; MTS Cell Viability Assay; CRISPR-Cas9 endogenous deletion/editing
E_04016	2022	35778390	B cell receptor signaling drives APOBEC3 expression via direct enhancer regulation in chronic lymphocytic leukemia B cells	Homo sapiens	hg38	chr22	39072097	39074320	NA	APOBEC3H	Enhancer	Active	Disease	B-cell chronic lymphocytic leukemia	MONDO:0004948	NA	blood	UBERON:0000178	MEC-1	CVCL_1870	B cell	CL:0000236	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation	CUT&Tag; ATAC-seq	CRISPR-Cas9 enhancer deletion; CRISPRi; PCR validation; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_04017	2022	35778390	B cell receptor signaling drives APOBEC3 expression via direct enhancer regulation in chronic lymphocytic leukemia B cells	Homo sapiens	hg38	chr22	39063777	39068917	NA	APOBEC3C	Enhancer	Active	Disease	B-cell chronic lymphocytic leukemia	MONDO:0004948	NA	blood	UBERON:0000178	MEC-1	CVCL_1870	B cell	CL:0000236	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation	CUT&Tag; ATAC-seq	CRISPR-Cas9 enhancer deletion; CRISPRi; PCR validation; RT-qPCR; Western blot; CRISPR-Cas9 endogenous deletion/editing
E_04018	2022	35778390	B cell receptor signaling drives APOBEC3 expression via direct enhancer regulation in chronic lymphocytic leukemia B cells	Homo sapiens	hg38	chr22	39063777	39068917	NA	APOBEC3D	Enhancer	Active	Disease	B-cell chronic lymphocytic leukemia	MONDO:0004948	NA	blood	UBERON:0000178	MEC-1	CVCL_1870	B cell	CL:0000236	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation	CUT&Tag; ATAC-seq	CRISPR-Cas9 enhancer deletion; CRISPRi; PCR validation; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_04019	2022	35778390	B cell receptor signaling drives APOBEC3 expression via direct enhancer regulation in chronic lymphocytic leukemia B cells	Homo sapiens	hg38	chr22	39063777	39068917	NA	APOBEC3F	Enhancer	Active	Disease	B-cell chronic lymphocytic leukemia	MONDO:0004948	NA	blood	UBERON:0000178	MEC-1	CVCL_1870	B cell	CL:0000236	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation	CUT&Tag; ATAC-seq	CRISPR-Cas9 enhancer deletion; CRISPRi; PCR validation; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_04020	2022	35778390	B cell receptor signaling drives APOBEC3 expression via direct enhancer regulation in chronic lymphocytic leukemia B cells	Homo sapiens	hg38	chr22	39063777	39068917	NA	APOBEC3G	Enhancer	Active	Disease	B-cell chronic lymphocytic leukemia	MONDO:0004948	NA	blood	UBERON:0000178	MEC-1	CVCL_1870	B cell	CL:0000236	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation	CUT&Tag; ATAC-seq	CRISPR-Cas9 enhancer deletion; CRISPRi; PCR validation; RT-qPCR; Western blot; CRISPR-Cas9 endogenous deletion/editing
E_04021	2022	35778390	B cell receptor signaling drives APOBEC3 expression via direct enhancer regulation in chronic lymphocytic leukemia B cells	Homo sapiens	hg38	chr22	39063777	39068917	NA	APOBEC3H	Enhancer	Active	Disease	B-cell chronic lymphocytic leukemia	MONDO:0004948	NA	blood	UBERON:0000178	MEC-1	CVCL_1870	B cell	CL:0000236	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation	CUT&Tag; ATAC-seq	CRISPR-Cas9 enhancer deletion; CRISPRi; PCR validation; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_04022	2022	35778390	B cell receptor signaling drives APOBEC3 expression via direct enhancer regulation in chronic lymphocytic leukemia B cells	Homo sapiens	hg38	chr22	39094134	39100780	NA	APOBEC3C	Enhancer	Active	Disease	B-cell chronic lymphocytic leukemia	MONDO:0004948	NA	blood	UBERON:0000178	MEC-1	CVCL_1870	B cell	CL:0000236	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation	CUT&Tag; ATAC-seq	CRISPR-Cas9 enhancer deletion; CRISPRi; PCR validation; RT-qPCR; Western blot; CRISPR-Cas9 endogenous deletion/editing
E_04023	2022	35778390	B cell receptor signaling drives APOBEC3 expression via direct enhancer regulation in chronic lymphocytic leukemia B cells	Homo sapiens	hg38	chr22	39094134	39100780	NA	APOBEC3D	Enhancer	Active	Disease	B-cell chronic lymphocytic leukemia	MONDO:0004948	NA	blood	UBERON:0000178	MEC-1	CVCL_1870	B cell	CL:0000236	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation	CUT&Tag; ATAC-seq	CRISPR-Cas9 enhancer deletion; CRISPRi; PCR validation; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_04024	2022	35778390	B cell receptor signaling drives APOBEC3 expression via direct enhancer regulation in chronic lymphocytic leukemia B cells	Homo sapiens	hg38	chr22	39094134	39100780	NA	APOBEC3F	Enhancer	Active	Disease	B-cell chronic lymphocytic leukemia	MONDO:0004948	NA	blood	UBERON:0000178	MEC-1	CVCL_1870	B cell	CL:0000236	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation	CUT&Tag; ATAC-seq	CRISPR-Cas9 enhancer deletion; CRISPRi; PCR validation; RT-qPCR; CRISPR-Cas9 endogenous deletion/editing
E_04025	2022	35778390	B cell receptor signaling drives APOBEC3 expression via direct enhancer regulation in chronic lymphocytic leukemia B cells	Homo sapiens	hg38	chr22	39094134	39100780	NA	APOBEC3G	Enhancer	Active	Disease	B-cell chronic lymphocytic leukemia	MONDO:0004948	NA	blood	UBERON:0000178	MEC-1	CVCL_1870	B cell	CL:0000236	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation	CUT&Tag; ATAC-seq	CRISPR-Cas9 enhancer deletion; CRISPRi; PCR validation; RT-qPCR; Western blot; CRISPR-Cas9 endogenous deletion/editing
E_04026	2017	28045957	Normal Levels of Sox9 Expression in the Developing Mouse Testis Depend on the TES/TESCO Enhancer, but This Does Not Act Alone	Mus musculus	mm10	chr11	112769210	112772210	NA	Sox9	Enhancer	Active	Normal	NA	NA	NA	gonad	NA	Testis	NA	NA	NA	Endogenous enhancer perturbation; In vivo functional validation	NA	CRISPR-Cas9 targeted editing/deletion; RT-qPCR/qPCR; Transgenic/LacZ assay
E_04027	2019	31591447	Distinct enhancer signatures in the mouse gastrula delineate progressive cell fate continuum during embryo development	Mus musculus	mm10	chr16	21480000	21482000	NA	2510009E07Rik	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	neural differentiation model	NA	embryonic/neural progenitor cell	NA	Intragenic pre-marked enhancer with ectoderm/future-brain activity and endogenous functional requirement	Spatiotemporal ChIP-seq/ATAC-like epigenomic profiling; RNA-seq	Transgenic enhancer reporter mouse; genome editing; neural differentiation assay
E_04028	2025	39626660	Long-range regulation of transcription scales with genomic distance in a gene-specific manner	Mus musculus	mm10	chr5	98716000	98718000	NA	Fgf5	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	mESCs	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	ChIP-seq; RNA-seq; ORCA; ATAC-seq	CRISPRa; RT-qPCR; ChIP-qPCR
E_04029	2024	39394696	Identification and characterization of an enhancer element regulating expression of Cdkn1c (p57 gene)	Mus musculus	mm10	chr7	142855000	142857000	NA	Cdkn1c	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Mouse embryonic stem cells (mESCs)	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	4C; RNA-seq; ChIP-seq; 4C-seq	CRISPR knockout; CRISPRi; RT-qPCR; Western blot; CRISPR-Cas9
E_04030	2021	34092790	Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes	Homo sapiens	hg38	chr14	37246515	37246652	NA	ETV1	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Functional perturbation assay; Chromatin interaction assay; Endogenous enhancer perturbation	Hi-C; DNase-seq; RNA-seq; Hi-C	CRISPR knockout, qRT-PCR; CRISPR-Cas9 endogenous deletion/editing
E_04031	2021	34092790	Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes	Homo sapiens	hg38	chr14	37278706	37279509	NA	ETV1	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Functional perturbation assay; Chromatin interaction assay; Endogenous enhancer perturbation	Hi-C; DNase-seq; RNA-seq; Hi-C	CRISPR knockout, qRT-PCR; CRISPR-Cas9 endogenous deletion/editing
E_04032	2024	39183203	Multi-omics profiling of retinal pigment epithelium reveals enhancer-driven activation of RANK-NFATc1 signaling in traumatic proliferative vitreoretinopathy	Mus musculus	mm10	chr18	87758000	87762000	Creb5	Nfatc1	Enhancer	Active	Disease	proliferative vitreoretinopathy	NA	DOID:0080067	retina	UBERON:0000966	Primary retinal pigment epithelium (RPE) cells	NA	retinal pigment epithelial cell	CL:0002586	Enhancer activity assay; Functional perturbation assay; TF binding assay	ATAC-seq; ChIP-seq; RNA-seq	ChIP-qPCR; RT-qPCR; Western blot; CRISPRi (shRNA); Immunofluorescence
E_04033	2024	39183203	Multi-omics profiling of retinal pigment epithelium reveals enhancer-driven activation of RANK-NFATc1 signaling in traumatic proliferative vitreoretinopathy	Mus musculus	mm10	chr18	87758000	87762000	Ets1	Nfatc1	Enhancer	Active	Disease	proliferative vitreoretinopathy	NA	DOID:0080067	retina	UBERON:0000966	Primary retinal pigment epithelium (RPE) cells	NA	retinal pigment epithelial cell	CL:0002586	Enhancer activity assay; Functional perturbation assay; TF binding assay	ATAC-seq; ChIP-seq; RNA-seq	ChIP-qPCR; RT-qPCR; Western blot; CRISPRi (shRNA); Immunofluorescence
E_04034	2024	39183203	Multi-omics profiling of retinal pigment epithelium reveals enhancer-driven activation of RANK-NFATc1 signaling in traumatic proliferative vitreoretinopathy	Mus musculus	mm10	chr18	87758000	87762000	Nfatc1	Nfatc1	Enhancer	Active	Disease	proliferative vitreoretinopathy	NA	DOID:0080067	retina	UBERON:0000966	Primary retinal pigment epithelium (RPE) cells	NA	retinal pigment epithelial cell	CL:0002586	Enhancer activity assay; Functional perturbation assay; TF binding assay	ATAC-seq; ChIP-seq; RNA-seq	ChIP-qPCR; RT-qPCR; Western blot; CRISPRi (shRNA); Immunofluorescence
E_04035	2024	39183203	Multi-omics profiling of retinal pigment epithelium reveals enhancer-driven activation of RANK-NFATc1 signaling in traumatic proliferative vitreoretinopathy	Mus musculus	mm10	chr18	87758000	87762000	Smad3	Nfatc1	Enhancer	Active	Disease	proliferative vitreoretinopathy	NA	DOID:0080067	retina	UBERON:0000966	Primary retinal pigment epithelium (RPE) cells	NA	retinal pigment epithelial cell	CL:0002586	Enhancer activity assay; Functional perturbation assay; TF binding assay	ATAC-seq; ChIP-seq; RNA-seq	ChIP-qPCR; RT-qPCR; Western blot; CRISPRi (shRNA); Immunofluorescence
E_04036	2024	39183203	Multi-omics profiling of retinal pigment epithelium reveals enhancer-driven activation of RANK-NFATc1 signaling in traumatic proliferative vitreoretinopathy	Mus musculus	mm10	chr18	87758000	87762000	Tgif1	Nfatc1	Enhancer	Active	Disease	proliferative vitreoretinopathy	NA	DOID:0080067	retina	UBERON:0000966	Primary retinal pigment epithelium (RPE) cells	NA	retinal pigment epithelial cell	CL:0002586	Enhancer activity assay; Functional perturbation assay; TF binding assay	ATAC-seq; ChIP-seq; RNA-seq	ChIP-qPCR; RT-qPCR; Western blot; CRISPRi (shRNA); Immunofluorescence
E_04037	2017	27869826	Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking	Homo sapiens	hg19	chr11	2218986	2222624	NA	IGF2	Super-enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; Structural-variant enhancer-hijacking assay	Pan-cancer SCNA/mRNA-seq/TAD integration; H3K27ac ChIP-seq; 4C-seq; long-insert paired-end sequencing	Dual-luciferase reporter assay in HCT 116 with HeLa control; PCR-based structural-variant validation
E_04038	2017	27869826	Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking	Homo sapiens	hg19	chr11	2227598	2233058	NA	IGF2	Super-enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; Structural-variant enhancer-hijacking assay	Pan-cancer SCNA/mRNA-seq/TAD integration; H3K27ac ChIP-seq; 4C-seq; long-insert paired-end sequencing	Dual-luciferase reporter assay in HCT 116 with HeLa control; PCR-based structural-variant validation
E_04039	2017	27869826	Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking	Homo sapiens	hg19	chr11	2234046	2237062	NA	IGF2	Super-enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; Structural-variant enhancer-hijacking assay	Pan-cancer SCNA/mRNA-seq/TAD integration; H3K27ac ChIP-seq; 4C-seq; long-insert paired-end sequencing	Dual-luciferase reporter assay in HCT 116 with HeLa control; PCR-based structural-variant validation
E_04040	2017	27869826	Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking	Homo sapiens	hg19	chr11	2236031	2239626	NA	IGF2	Super-enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay; Structural-variant enhancer-hijacking assay	Pan-cancer SCNA/mRNA-seq/TAD integration; H3K27ac ChIP-seq; 4C-seq; long-insert paired-end sequencing	Dual-luciferase reporter assay in HCT 116 with HeLa control; PCR-based structural-variant validation
E_04041	2024	39183203	Multi-omics profiling of retinal pigment epithelium reveals enhancer-driven activation of RANK-NFATc1 signaling in traumatic proliferative vitreoretinopathy	Mus musculus	mm9	chr1	107667300	107677300	NA	Tnfrsf11a	Enhancer	Active	Disease	traumatic proliferative vitreoretinopathy	NA	NA	pigmented layer of retina	UBERON:0001782	Primary retinal pigment epithelial cells from traumatic PVR and contralateral control eyes of 8-week-old male C57BL/6J mice	NA	retinal pigment epithelial cell	CL:0002586	Enhancer characterization; Disease-associated chromatin profiling; Functional pathway perturbation assay	ATAC-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; RNA-seq	OPG-Fc-mediated RANKL blockade; RT-qPCR; Western blot; Immunofluorescence; H&E staining; Fundus imaging; OCT
E_04042	2025	40301309	Drug-induced cis-regulatory elements in human hepatocytes affect molecular phenotypes associated with adverse reactions	Homo sapiens	hg38	chr20	54107388	54107945	NA	CYP24A1	Enhancer	Active	Disease	glioblastoma	MONDO:0018177	NA	brain	UBERON:0000955	D-566MG	CVCL_1166	glioblastoma cell	CL:0001063	Super-enhancer activity assay	CAGE	Luciferase reporter assay
E_04043	2022	35773411	YAP1 induces invadopodia formation by transcriptionally activating TIAM1 through enhancer in breast cancer	Homo sapiens	hg19	chr21	32901686	32902140	TEAD4	TIAM1	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	Luciferase reporter assay; ChIP-qPCR; CRISPR knockout; CRISPRi, qRT-PCR; Western blot
E_04044	2020	31770110	A stress-responsive enhancer induces dynamic drug resistance in acute myeloid leukemia	Homo sapiens	hg38	chr7	87574094	87575396	NA	ABCB1	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	bone marrow	UBERON:0002371	Primary AML blasts	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq; 4C-seq	CRISPRi; ChIP-qPCR; RT-qPCR, Flow Cytometry
E_04045	2019	30488457	Sox7 negatively regulates prostate-specific membrane antigen (PSMA) expression through PSMA-enhancer	Homo sapiens	hg19	chr11	33396000	33396331	SOX7	FOLH1	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; In vivo functional validation	NA	Luciferase reporter assay; ChIP-qPCR, EMSA; RT-qPCR; Luciferase reporter assay; EMSA; ChIP; In vivo phenotyping; Reporter assay
E_04046	2017	27920250	Renal Anemia Model Mouse Established by Transgenic Rescue with an Erythropoietin Gene Lacking Kidney-Specific Regulatory Elements	Mus musculus	mm10	chr5	137465620	137479420	NA	Epo	Enhancer	Active	Disease	Renal Anemia	NA	NA	kidney	UBERON:0002113	Renal EPO-producing (REP) cells	NA	NA	NA	Enhancer activity assay; Chromatin interaction assay; In vivo functional validation; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; RT-qPCR/qPCR; Transgenic/LacZ assay
E_04047	2014	24594601	Long-range interaction and correlation between MYC enhancer and oncogenic long noncoding RNA CARLo-5	Homo sapiens	hg19	chr8	128413174	128414429	TCF7L2	CCAT1	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	HCT 116	CVCL_0291	epithelial cell	CL:0000066	Functional perturbation assay; Chromatin interaction assay; Disease-variant functional analysis; Genetic variant-associated regulatory analysis	NanoString nCounter expression profiling; ENCODE chromatin annotation (external data)	3C; SNP genotyping; RT-qPCR; RACE; siRNA knockdown; Flow cytometry; Xenograft assay
E_04048	2023	36717694	Enhancer-promoter interactions can bypass CTCF-mediated boundaries and contribute to phenotypic robustness	Mus musculus	mm10	chr3	34824938	34837938	Nanog	Sox2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	ES-R1	CVCL_2167	embryonic stem cell	CL:0002322	CRISPR deletion functional assay	Capture Hi-C; ChIP-seq; CUT&RUN	RT-qPCR; Immunofluorescence staining
E_04049	2023	36717694	Enhancer-promoter interactions can bypass CTCF-mediated boundaries and contribute to phenotypic robustness	Mus musculus	mm10	chr3	34824938	34837938	Pou5f1	Sox2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	ES-R1	CVCL_2167	embryonic stem cell	CL:0002322	CRISPR deletion functional assay	Capture Hi-C; ChIP-seq; CUT&RUN	RT-qPCR; Immunofluorescence staining
E_04050	2023	36717694	Enhancer-promoter interactions can bypass CTCF-mediated boundaries and contribute to phenotypic robustness	Mus musculus	mm10	chr3	34824938	34837938	Sox2	Sox2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	ES-R1	CVCL_2167	embryonic stem cell	CL:0002322	CRISPR deletion functional assay	Capture Hi-C; ChIP-seq; CUT&RUN	RT-qPCR; Immunofluorescence staining
E_04051	2019	31120998	HoxA9 binds and represses the Cebpa +8 kb enhancer	Mus musculus	mm10	chr7	35156536	35156974	Hoxa9	Cebpa	Enhancer	Active	Disease	acute myeloid leukemia model	NA	NA	bone marrow	UBERON:0002371	primary murine myeloid progenitor cells expressing Hoxa9	NA	myeloid progenitor cell	NA	Enhancer activity assay; TF binding assay; functional perturbation	Hoxa9 ChIP-seq; ChIP-seq	Transgenic enhancer/promoter-hCD4 reporter; Flow cytometry; RT-qPCR; Luciferase reporter assay
E_04052	2014	24990076	Identification of TNF-α-responsive promoters and enhancers in the intestinal epithelial cell model Caco-2	Homo sapiens	hg19	chr1	183149939	183150336	NFKB1	LAMC2	Enhancer	Active	Normal	NA	NA	NA	colon	UBERON:0001155	Caco-2	CVCL_0025	intestinal epithelial cell	CL:0002563	Enhancer activity assay; Functional perturbation assay	CAGE; ENCODE ChIP-seq data integration	Luciferase reporter assay; TNF-alpha stimulation; RELA/NFKB1 co-transfection; NF-kB inhibition; RT-qPCR; Western blot
E_04053	2014	24990076	Identification of TNF-α-responsive promoters and enhancers in the intestinal epithelial cell model Caco-2	Homo sapiens	hg19	chr1	183149939	183150336	NFKB2	LAMC2	Enhancer	Active	Normal	NA	NA	NA	colon	UBERON:0001155	Caco-2	CVCL_0025	intestinal epithelial cell	CL:0002563	Enhancer activity assay; Functional perturbation assay	CAGE; ENCODE ChIP-seq data integration	Luciferase reporter assay; TNF-alpha stimulation; RELA/NFKB2 co-transfection; NF-kB inhibition; RT-qPCR; Western blot
E_04054	2014	24990076	Identification of TNF-α-responsive promoters and enhancers in the intestinal epithelial cell model Caco-2	Homo sapiens	hg19	chr1	183149939	183150336	RELA	LAMC2	Enhancer	Active	Normal	NA	NA	NA	colon	UBERON:0001155	Caco-2	CVCL_0025	intestinal epithelial cell	CL:0002563	Enhancer activity assay; Functional perturbation assay; TF binding assay	CAGE; ENCODE RELA ChIP-seq data integration	Luciferase reporter assay; TNF-alpha stimulation; NF-kB inhibition; RELA/NFKB co-transfection; RT-qPCR; Western blot
E_04055	2019	31120998	HoxA9 binds and represses the Cebpa +8 kb enhancer	Mus musculus	mm10	chr7	35156536	35156974	Hoxa9	Cebpa	Enhancer	Active	Disease	acute myeloid leukemia model	NA	NA	bone marrow	UBERON:0002371	common myeloid progenitors from Vav-NUP98-HOXD13 mice	NA	common myeloid progenitor cell	NA	Enhancer activity assay; TF binding assay; functional perturbation	Hoxa9 ChIP-seq; ChIP-seq	Transgenic enhancer/promoter-hCD4 reporter; Flow cytometry; RT-qPCR; Luciferase reporter assay
E_04056	2019	31120998	HoxA9 binds and represses the Cebpa +8 kb enhancer	Mus musculus	mm9	chr7	35912057	35912683	Hoxa9	Cebpa	Enhancer	Repressed	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	bone marrow	UBERON:0002371	32Dcl3	CVCL_0119	myeloid progenitor cell	NA	Enhancer activity assay	HoxA9 ChIP-seq; ChIP-seq	EMSA; HoxA9-binding-site mutagenesis; Luciferase reporter assay; HoxA9-ER activation; RT-qPCR; cycloheximide test
E_04057	2019	31120998	HoxA9 binds and represses the Cebpa +8 kb enhancer	Mus musculus	mm10	chr7	35156536	35156974	Hoxa9	Cebpa	Enhancer	Repressed	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	bone marrow	UBERON:0002371	NUP98-HOXD13 transgenic mouse marrow progenitors	NA	myeloid progenitor cell	NA	Enhancer activity assay	HoxA9 ChIP-seq; ChIP-seq	+37 enhancer/promoter-hCD4 transgenic reporter assay; Flow cytometry; RT-qPCR; Luciferase reporter assay
E_04058	2019	31120998	HoxA9 binds and represses the Cebpa +8 kb enhancer	Mus musculus	mm9	chr7	35912057	35912683	Cebpa	Cebpa	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	bone marrow	UBERON:0002371	32Dcl3	CVCL_0119	myeloid progenitor cell	NA	Enhancer activity assay	HoxA9 ChIP-seq; ChIP-seq	C/EBPalpha-binding-site mutagenesis; Luciferase reporter assay
E_04059	2023	37749332	Interaction between estrogen receptor-α and PNPLA3 p.I148M variant drives fatty liver disease susceptibility in women	Homo sapiens	hg19	chr22	44315438	44315637	ESR1	PNPLA3	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Jurkat	CVCL_0065	T lymphoblast	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	RNA-seq	Luciferase reporter assay; ChIP-qPCR; CRISPR knockout, qRT-PCR; Western blot; CRISPR-Cas9
E_04060	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322357	128323157	CEBPA	MECOM	Enhancer	Active	Disease	acute myeloid leukemia with inv(3)/t(3; 3); MECOM-rearranged AML	NA	NA	bone marrow	UBERON:0002371	MOLM-1	NA	malignant cell	CL:0001064	Functional dissection of hijacked enhancer TF complex; Enhancer-promoter interaction; TF-site mutagenesis	CEBPA ChIP-seq; RUNX1/CEBPA ChIP-SICAP; RNA-seq; 4C-seq	Luciferase enhancer assay; CEBPA-site mutagenesis; TF perturbation; RT-qPCR; PARP inhibition
E_04061	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322357	128323157	CEBPA	MECOM	Enhancer	Active	Disease	acute myeloid leukemia with inv(3)/t(3; 3); MECOM-rearranged AML	NA	NA	bone marrow	UBERON:0002371	MUTZ-3	CVCL_1433	malignant cell	CL:0001064	Functional dissection of hijacked enhancer TF complex; Enhancer-promoter interaction; TF-site mutagenesis	CEBPA ChIP-seq; RUNX1/CEBPA ChIP-SICAP; RNA-seq; 4C-seq	Luciferase enhancer assay; CEBPA-site mutagenesis; TF perturbation; RT-qPCR; PARP inhibition
E_04062	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322357	128323157	CEBPA	MECOM	Enhancer	Active	Disease	acute myeloid leukemia with inv(3)/t(3; 3); MECOM-rearranged AML	NA	NA	bone marrow	UBERON:0002371	HNT-34	CVCL_2071	malignant cell	CL:0001064	Functional dissection of hijacked enhancer TF complex; Enhancer-promoter interaction; TF-site mutagenesis	CEBPA ChIP-seq; RUNX1/CEBPA ChIP-SICAP; RNA-seq; 4C-seq	Luciferase enhancer assay; CEBPA-site mutagenesis; TF perturbation; RT-qPCR; PARP inhibition
E_04063	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322357	128323157	RUNX1	MECOM	Enhancer	Active	Disease	acute myeloid leukemia with inv(3)/t(3; 3); MECOM-rearranged AML	NA	NA	bone marrow	UBERON:0002371	MOLM-1	NA	malignant cell	CL:0001064	Functional dissection of hijacked enhancer TF complex; Enhancer-promoter interaction; TF-site mutagenesis	CEBPA ChIP-seq; RUNX1/CEBPA ChIP-SICAP; RNA-seq; 4C-seq	Luciferase enhancer assay; RUNX1-site mutagenesis; TF perturbation; RT-qPCR; PARP inhibition
E_04064	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322357	128323157	RUNX1	MECOM	Enhancer	Active	Disease	acute myeloid leukemia with inv(3)/t(3; 3); MECOM-rearranged AML	NA	NA	bone marrow	UBERON:0002371	MUTZ-3	CVCL_1433	malignant cell	CL:0001064	Functional dissection of hijacked enhancer TF complex; Enhancer-promoter interaction; TF-site mutagenesis	CEBPA ChIP-seq; RUNX1/CEBPA ChIP-SICAP; RNA-seq; 4C-seq	Luciferase enhancer assay; RUNX1-site mutagenesis; TF perturbation; RT-qPCR; PARP inhibition
E_04065	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322357	128323157	RUNX1	MECOM	Enhancer	Active	Disease	acute myeloid leukemia with inv(3)/t(3; 3); MECOM-rearranged AML	NA	NA	bone marrow	UBERON:0002371	HNT-34	CVCL_2071	malignant cell	CL:0001064	Functional dissection of hijacked enhancer TF complex; Enhancer-promoter interaction; TF-site mutagenesis	CEBPA ChIP-seq; RUNX1/CEBPA ChIP-SICAP; RNA-seq; 4C-seq	Luciferase enhancer assay; RUNX1-site mutagenesis; TF perturbation; RT-qPCR; PARP inhibition
E_04066	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322357	128323157	CEBPA	MECOM	Enhancer	Active	Disease	MECOM-rearranged acute myeloid leukemia	NA	NA	bone marrow	UBERON:0002371	MOLM-1	NA	malignant cell	CL:0001064	TF-complex dissection at a hijacked enhancer; Enhancer-promoter interaction; functional TF perturbation	CEBPA ChIP-seq; RUNX1/CEBPA ChIP-SICAP; RNA-seq; 4C-seq	Luciferase assay; TF-site mutagenesis; TF knockdown/perturbation; RT-qPCR
E_04067	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322357	128323157	CEBPA	MECOM	Enhancer	Active	Disease	MECOM-rearranged acute myeloid leukemia	NA	NA	bone marrow	UBERON:0002371	MUTZ-3	CVCL_1433	malignant cell	CL:0001064	TF-complex dissection at a hijacked enhancer; Enhancer-promoter interaction; functional TF perturbation	CEBPA ChIP-seq; RUNX1/CEBPA ChIP-SICAP; RNA-seq; 4C-seq	Luciferase assay; TF-site mutagenesis; TF knockdown/perturbation; RT-qPCR
E_04068	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322357	128323157	CEBPA	MECOM	Enhancer	Active	Disease	MECOM-rearranged acute myeloid leukemia	NA	NA	bone marrow	UBERON:0002371	HNT-34	CVCL_2071	malignant cell	CL:0001064	TF-complex dissection at a hijacked enhancer; Enhancer-promoter interaction; functional TF perturbation	CEBPA ChIP-seq; RUNX1/CEBPA ChIP-SICAP; RNA-seq; 4C-seq	Luciferase assay; TF-site mutagenesis; TF knockdown/perturbation; RT-qPCR
E_04069	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322357	128323157	ELK1	MECOM	Enhancer	Active	Disease	MECOM-rearranged acute myeloid leukemia	NA	NA	bone marrow	UBERON:0002371	MOLM-1	NA	malignant cell	CL:0001064	TF-complex dissection at a hijacked enhancer; Enhancer-promoter interaction; functional TF perturbation	CEBPA ChIP-seq; RUNX1/CEBPA ChIP-SICAP; RNA-seq; 4C-seq	Luciferase assay; TF-site mutagenesis; TF knockdown/perturbation; RT-qPCR
E_04070	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322357	128323157	ELK1	MECOM	Enhancer	Active	Disease	MECOM-rearranged acute myeloid leukemia	NA	NA	bone marrow	UBERON:0002371	MUTZ-3	CVCL_1433	malignant cell	CL:0001064	TF-complex dissection at a hijacked enhancer; Enhancer-promoter interaction; functional TF perturbation	CEBPA ChIP-seq; RUNX1/CEBPA ChIP-SICAP; RNA-seq; 4C-seq	Luciferase assay; TF-site mutagenesis; TF knockdown/perturbation; RT-qPCR
E_04071	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322357	128323157	ELK1	MECOM	Enhancer	Active	Disease	MECOM-rearranged acute myeloid leukemia	NA	NA	bone marrow	UBERON:0002371	HNT-34	CVCL_2071	malignant cell	CL:0001064	TF-complex dissection at a hijacked enhancer; Enhancer-promoter interaction; functional TF perturbation	CEBPA ChIP-seq; RUNX1/CEBPA ChIP-SICAP; RNA-seq; 4C-seq	Luciferase assay; TF-site mutagenesis; TF knockdown/perturbation; RT-qPCR
E_04072	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322357	128323157	FLI1	MECOM	Enhancer	Active	Disease	MECOM-rearranged acute myeloid leukemia	NA	NA	bone marrow	UBERON:0002371	MOLM-1	NA	malignant cell	CL:0001064	TF-complex dissection at a hijacked enhancer; Enhancer-promoter interaction; functional TF perturbation	CEBPA ChIP-seq; RUNX1/CEBPA ChIP-SICAP; RNA-seq; 4C-seq	Luciferase assay; TF-site mutagenesis; TF knockdown/perturbation; RT-qPCR
E_04073	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322357	128323157	FLI1	MECOM	Enhancer	Active	Disease	MECOM-rearranged acute myeloid leukemia	NA	NA	bone marrow	UBERON:0002371	MUTZ-3	CVCL_1433	malignant cell	CL:0001064	TF-complex dissection at a hijacked enhancer; Enhancer-promoter interaction; functional TF perturbation	CEBPA ChIP-seq; RUNX1/CEBPA ChIP-SICAP; RNA-seq; 4C-seq	Luciferase assay; TF-site mutagenesis; TF knockdown/perturbation; RT-qPCR
E_04074	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322357	128323157	FLI1	MECOM	Enhancer	Active	Disease	MECOM-rearranged acute myeloid leukemia	NA	NA	bone marrow	UBERON:0002371	HNT-34	CVCL_2071	malignant cell	CL:0001064	TF-complex dissection at a hijacked enhancer; Enhancer-promoter interaction; functional TF perturbation	CEBPA ChIP-seq; RUNX1/CEBPA ChIP-SICAP; RNA-seq; 4C-seq	Luciferase assay; TF-site mutagenesis; TF knockdown/perturbation; RT-qPCR
E_04075	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322357	128323157	GATA2	MECOM	Enhancer	Active	Disease	MECOM-rearranged acute myeloid leukemia	NA	NA	bone marrow	UBERON:0002371	MOLM-1	NA	malignant cell	CL:0001064	TF-complex dissection at a hijacked enhancer; Enhancer-promoter interaction; functional TF perturbation	CEBPA ChIP-seq; RUNX1/CEBPA ChIP-SICAP; RNA-seq; 4C-seq	Luciferase assay; TF-site mutagenesis; TF knockdown/perturbation; RT-qPCR
E_04076	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322357	128323157	GATA2	MECOM	Enhancer	Active	Disease	MECOM-rearranged acute myeloid leukemia	NA	NA	bone marrow	UBERON:0002371	MUTZ-3	CVCL_1433	malignant cell	CL:0001064	TF-complex dissection at a hijacked enhancer; Enhancer-promoter interaction; functional TF perturbation	CEBPA ChIP-seq; RUNX1/CEBPA ChIP-SICAP; RNA-seq; 4C-seq	Luciferase assay; TF-site mutagenesis; TF knockdown/perturbation; RT-qPCR
E_04077	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322357	128323157	GATA2	MECOM	Enhancer	Active	Disease	MECOM-rearranged acute myeloid leukemia	NA	NA	bone marrow	UBERON:0002371	HNT-34	CVCL_2071	malignant cell	CL:0001064	TF-complex dissection at a hijacked enhancer; Enhancer-promoter interaction; functional TF perturbation	CEBPA ChIP-seq; RUNX1/CEBPA ChIP-SICAP; RNA-seq; 4C-seq	Luciferase assay; TF-site mutagenesis; TF knockdown/perturbation; RT-qPCR
E_04078	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322357	128323157	IKZF1	MECOM	Enhancer	Active	Disease	MECOM-rearranged acute myeloid leukemia	NA	NA	bone marrow	UBERON:0002371	MOLM-1	NA	malignant cell	CL:0001064	TF-complex dissection at a hijacked enhancer; Enhancer-promoter interaction; functional TF perturbation	CEBPA ChIP-seq; RUNX1/CEBPA ChIP-SICAP; RNA-seq; 4C-seq	Luciferase assay; TF-site mutagenesis; TF knockdown/perturbation; RT-qPCR
E_04079	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322357	128323157	IKZF1	MECOM	Enhancer	Active	Disease	MECOM-rearranged acute myeloid leukemia	NA	NA	bone marrow	UBERON:0002371	MUTZ-3	CVCL_1433	malignant cell	CL:0001064	TF-complex dissection at a hijacked enhancer; Enhancer-promoter interaction; functional TF perturbation	CEBPA ChIP-seq; RUNX1/CEBPA ChIP-SICAP; RNA-seq; 4C-seq	Luciferase assay; TF-site mutagenesis; TF knockdown/perturbation; RT-qPCR
E_04080	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322357	128323157	IKZF1	MECOM	Enhancer	Active	Disease	MECOM-rearranged acute myeloid leukemia	NA	NA	bone marrow	UBERON:0002371	HNT-34	CVCL_2071	malignant cell	CL:0001064	TF-complex dissection at a hijacked enhancer; Enhancer-promoter interaction; functional TF perturbation	CEBPA ChIP-seq; RUNX1/CEBPA ChIP-SICAP; RNA-seq; 4C-seq	Luciferase assay; TF-site mutagenesis; TF knockdown/perturbation; RT-qPCR
E_04081	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322357	128323157	MYB	MECOM	Enhancer	Active	Disease	MECOM-rearranged acute myeloid leukemia	NA	NA	bone marrow	UBERON:0002371	MOLM-1	NA	malignant cell	CL:0001064	TF-complex dissection at a hijacked enhancer; Enhancer-promoter interaction; functional TF perturbation	CEBPA ChIP-seq; RUNX1/CEBPA ChIP-SICAP; RNA-seq; 4C-seq	Luciferase assay; TF-site mutagenesis; TF knockdown/perturbation; RT-qPCR
E_04082	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322357	128323157	MYB	MECOM	Enhancer	Active	Disease	MECOM-rearranged acute myeloid leukemia	NA	NA	bone marrow	UBERON:0002371	MUTZ-3	CVCL_1433	malignant cell	CL:0001064	TF-complex dissection at a hijacked enhancer; Enhancer-promoter interaction; functional TF perturbation	CEBPA ChIP-seq; RUNX1/CEBPA ChIP-SICAP; RNA-seq; 4C-seq	Luciferase assay; TF-site mutagenesis; TF knockdown/perturbation; RT-qPCR
E_04083	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322357	128323157	MYB	MECOM	Enhancer	Active	Disease	MECOM-rearranged acute myeloid leukemia	NA	NA	bone marrow	UBERON:0002371	HNT-34	CVCL_2071	malignant cell	CL:0001064	TF-complex dissection at a hijacked enhancer; Enhancer-promoter interaction; functional TF perturbation	CEBPA ChIP-seq; RUNX1/CEBPA ChIP-SICAP; RNA-seq; 4C-seq	Luciferase assay; TF-site mutagenesis; TF knockdown/perturbation; RT-qPCR
E_04084	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322357	128323157	RUNX1	MECOM	Enhancer	Active	Disease	MECOM-rearranged acute myeloid leukemia	NA	NA	bone marrow	UBERON:0002371	MOLM-1	NA	malignant cell	CL:0001064	TF-complex dissection at a hijacked enhancer; Enhancer-promoter interaction; functional TF perturbation	CEBPA ChIP-seq; RUNX1/CEBPA ChIP-SICAP; RNA-seq; 4C-seq	Luciferase assay; TF-site mutagenesis; TF knockdown/perturbation; RT-qPCR
E_04085	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322357	128323157	RUNX1	MECOM	Enhancer	Active	Disease	MECOM-rearranged acute myeloid leukemia	NA	NA	bone marrow	UBERON:0002371	MUTZ-3	CVCL_1433	malignant cell	CL:0001064	TF-complex dissection at a hijacked enhancer; Enhancer-promoter interaction; functional TF perturbation	CEBPA ChIP-seq; RUNX1/CEBPA ChIP-SICAP; RNA-seq; 4C-seq	Luciferase assay; TF-site mutagenesis; TF knockdown/perturbation; RT-qPCR
E_04086	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322357	128323157	RUNX1	MECOM	Enhancer	Active	Disease	MECOM-rearranged acute myeloid leukemia	NA	NA	bone marrow	UBERON:0002371	HNT-34	CVCL_2071	malignant cell	CL:0001064	TF-complex dissection at a hijacked enhancer; Enhancer-promoter interaction; functional TF perturbation	CEBPA ChIP-seq; RUNX1/CEBPA ChIP-SICAP; RNA-seq; 4C-seq	Luciferase assay; TF-site mutagenesis; TF knockdown/perturbation; RT-qPCR
E_04087	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322411	128323124	RUNX1	MECOM	Enhancer	Active	Disease	Acute myeloid leukemia with MECOM rearrangement [3q-AML]	NA	NA	bone marrow	UBERON:0002371	MUTZ-3	CVCL_1433	myeloid leukemia cell	NA	TF-site functional validation; enhancer complex characterization; Enhancer-promoter interaction	ChIP-seq; ChIP-SICAP quantitative mass spectrometry; RNA-seq; 4C-seq	Luciferase enhancer truncation; RUNX1-binding-site mutagenesis; RUNX1 knockdown; ChIP-qPCR; DNA pull-down; western blotting; co-immunoprecipitation; qPCR
E_04088	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322411	128323124	RUNX1	MECOM	Enhancer	Active	Disease	Acute myeloid leukemia with MECOM rearrangement [3q-AML]	NA	NA	bone marrow	UBERON:0002371	HNT-34	CVCL_2071	myeloid leukemia cell	NA	TF-site functional validation; enhancer complex characterization; Enhancer-promoter interaction	ChIP-seq; ChIP-SICAP quantitative mass spectrometry; RNA-seq; 4C-seq	Luciferase enhancer truncation; RUNX1-binding-site mutagenesis; RUNX1 knockdown; ChIP-qPCR; DNA pull-down; western blotting; co-immunoprecipitation; qPCR
E_04089	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322411	128323124	CEBPA	MECOM	Enhancer	Active	Disease	Acute myeloid leukemia with MECOM rearrangement [3q-AML]	NA	NA	bone marrow	UBERON:0002371	MUTZ-3	CVCL_1433	myeloid leukemia cell	NA	TF-site functional validation; enhancer complex characterization; Enhancer-promoter interaction	ChIP-seq; ChIP-SICAP quantitative mass spectrometry; RNA-seq; 4C-seq	Luciferase enhancer truncation; CEBPA-binding-site mutagenesis; CEBPA knockdown; ChIP-qPCR; DNA pull-down; western blotting; co-immunoprecipitation; qPCR
E_04090	2021	33911178	Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia	Homo sapiens	hg19	chr3	128322411	128323124	CEBPA	MECOM	Enhancer	Active	Disease	Acute myeloid leukemia with MECOM rearrangement [3q-AML]	NA	NA	bone marrow	UBERON:0002371	HNT-34	CVCL_2071	myeloid leukemia cell	NA	TF-site functional validation; enhancer complex characterization; Enhancer-promoter interaction	ChIP-seq; ChIP-SICAP quantitative mass spectrometry; RNA-seq; 4C-seq	Luciferase enhancer truncation; CEBPA-binding-site mutagenesis; CEBPA knockdown; ChIP-qPCR; DNA pull-down; western blotting; co-immunoprecipitation; qPCR
E_04091	2019	31519704	GATA3-Controlled Nucleosome Eviction Drives MYC Enhancer Activity in T-cell Development and Leukemia	Homo sapiens	hg19	chr8	130180217	130180629	GATA3	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	primary T-ALL	NA	T-lineage leukemia cell	NA	TF-dependent enhancer chromatin opening; Enhancer activity; leukemia initiation and maintenance	ATAC-seq; ChIP-seq; transcriptomic profiling; chromatin accessibility profiling	GATA3 genetic perturbation; N-Me functional assays; nucleosome occupancy analysis; leukemia transplantation/maintenance assays
E_04092	2019	31519704	GATA3-Controlled Nucleosome Eviction Drives MYC Enhancer Activity in T-cell Development and Leukemia	Homo sapiens	hg19	chr8	130180217	130180629	GATA3	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	primary T-ALL	NA	T-lineage leukemia cell	NA	TF-dependent enhancer chromatin opening; Enhancer activity; leukemia initiation and maintenance	ATAC-seq; ChIP-seq; transcriptomic profiling; chromatin accessibility profiling	GATA3 genetic perturbation; N-Me functional assays; nucleosome occupancy analysis; leukemia transplantation/maintenance assays
E_04093	2019	31519704	GATA3-Controlled Nucleosome Eviction Drives MYC Enhancer Activity in T-cell Development and Leukemia	Homo sapiens	hg19	chr8	130180065	130180972	GATA3	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	thymus	UBERON:0002370	human T-ALL and mouse T-ALL models	NA	T lymphoblast	NA	TF-dependent enhancer accessibility and leukemia functional validation	ATAC-seq; ChIP-seq; RNA-seq	GATA3 genetic perturbation; enhancer reporter; transplantation assay
E_04094	2019	31519704	GATA3-Controlled Nucleosome Eviction Drives MYC Enhancer Activity in T-cell Development and Leukemia	Homo sapiens	hg19	chr8	130180217	130180629	GATA3	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	human T-ALL cells	NA	T-lineage leukemia cell	NA	TF-dependent enhancer chromatin opening; Enhancer activity; leukemia initiation and maintenance	ATAC-seq; ChIP-seq; transcriptomic profiling; chromatin accessibility profiling	GATA3 genetic perturbation; N-Me functional assays; nucleosome occupancy analysis; leukemia transplantation/maintenance assays
E_04095	2019	31519704	GATA3-Controlled Nucleosome Eviction Drives MYC Enhancer Activity in T-cell Development and Leukemia	Homo sapiens	hg19	chr8	130180217	130180629	GATA3	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	mouse NOTCH1-driven T-ALL	NA	T-lineage leukemia cell	NA	TF-dependent enhancer chromatin opening; Enhancer activity; leukemia initiation and maintenance	ATAC-seq; ChIP-seq; transcriptomic profiling; chromatin accessibility profiling	GATA3 genetic perturbation; N-Me functional assays; nucleosome occupancy analysis; leukemia transplantation/maintenance assays
E_04096	2019	31519704	GATA3-Controlled Nucleosome Eviction Drives MYC Enhancer Activity in T-cell Development and Leukemia	Homo sapiens	hg19	chr8	130180217	130180629	GATA3	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	human T-ALL cells	NA	T-lineage leukemia cell	NA	TF-dependent enhancer chromatin opening; Enhancer activity; leukemia initiation and maintenance	ATAC-seq; ChIP-seq; transcriptomic profiling; chromatin accessibility profiling	GATA3 genetic perturbation; N-Me functional assays; nucleosome occupancy analysis; leukemia transplantation/maintenance assays
E_04097	2019	31519704	GATA3-Controlled Nucleosome Eviction Drives MYC Enhancer Activity in T-cell Development and Leukemia	Homo sapiens	hg19	chr8	130180217	130180629	GATA3	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	mouse NOTCH1-driven T-ALL	NA	T-lineage leukemia cell	NA	TF-dependent enhancer chromatin opening; Enhancer activity; leukemia initiation and maintenance	ATAC-seq; ChIP-seq; transcriptomic profiling; chromatin accessibility profiling	GATA3 genetic perturbation; N-Me functional assays; nucleosome occupancy analysis; leukemia transplantation/maintenance assays
E_04098	2025	40369080	A human-specific enhancer fine-tunes radial glia potency and corticogenesis	Homo sapiens	hg38	chr10	35949193	35950411	NA	FZD8	Enhancer	Active	Normal	NA	NA	NA	cerebral cortex	UBERON:0000956	NA	NA	radial glial cell	CL:0000681	Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation; In vivo reporter assay; genome editing	RNA-seq; scRNA-seq; ChIP-qPCR; CRISPRi; single-cell RNA-seq	Immunohistochemistry; Luciferase reporter assay; RT-qPCR; Mouse genetic deletion/knock-in; In vivo phenotyping
E_04099	2022	35390275	Promoter and enhancer RNAs regulate chromatin reorganization and activation of miR-10b/HOXD locus, and neoplastic transformation in glioma	Homo sapiens	hg19	chr2	177480000	177490000	CTCF	MIR10B	Enhancer	Active	Disease	glioma	MONDO:0021042	NA	brain	UBERON:0000955	normal human cortical astrocytes	NA	astrocyte	CL:0000127	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay; eRNA assay	RNA-seq; Hi-C; 4C-seq; ChIP-seq	LINC01116 knockdown; enhancer activation; ChIP-qPCR; RT-qPCR; glioma-cell viability and astrocyte-transformation assays
E_04100	2016	26751055	NANOG alone induces germ cells in primed epiblast in vitro by activation of enhancers	Mus musculus	mm10	chr1	13093655	13096290	Nanog	Prdm14	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	D2 epiblast-like cells (+Dox Nanog)	NA	epiblast cell	CL:0000352	Enhancer activity assay; Functional perturbation assay; TF binding assay; Germline specification assay	NANOG ChIP-seq; Expression microarray; H3K4me1/H3K27ac chromatin-data integration	Luciferase reporter assay; NANOG ChIP-qPCR; Doxycycline-inducible Nanog expression; RT-qPCR; PGCLC induction assay; Flow cytometry
E_04101	2016	26751055	NANOG alone induces germ cells in primed epiblast in vitro by activation of enhancers	Mus musculus	mm10	chr10	44390290	44390668	Nanog	Prdm1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	D2 epiblast-like cells (+Dox Nanog)	NA	epiblast cell	CL:0000352	Enhancer activity assay; Functional perturbation assay; TF binding assay; Germline specification assay	NANOG ChIP-seq; Expression microarray; H3K4me1/H3K27ac chromatin-data integration	Luciferase reporter assay; NANOG ChIP-qPCR; Doxycycline-inducible Nanog expression; RT-qPCR; PGCLC induction assay; Flow cytometry
E_04102	2011	21331042	Tbx6-dependent Sox2 regulation determines neural or mesodermal fate in axial stem cells	Mus musculus	mm10	chr3	34668443	34668497	NA	Sox2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Mouse embryonic tissue	NA	embryonic cell	NA	Enhancer activity assay	NA	Transgenic reporter assay; Site-directed Mutagenesis, in situ Hybridization
E_04103	2020	32342858	Disparate expression specificities coded by a shared Hox-C enhancer	Drosophila melanogaster	dm6	chr3R	7795000	7796400	exd	pb	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	embryonic cell	NA	embryonic cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	Transgenic reporter assay; CRISPR knockout; RT-qPCR; In situ hybridization
E_04104	2020	32342858	Disparate expression specificities coded by a shared Hox-C enhancer	Drosophila melanogaster	dm6	chr3R	7795000	7796400	exd	zen2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	embryonic cell	NA	embryonic cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	Transgenic reporter assay; CRISPR knockout; RT-qPCR; In situ hybridization
E_04105	2020	33057197	Dense and pleiotropic regulatory information in a developmental enhancer	Drosophila melanogaster	dm6	chr2R	10788877	10789168	hth	svb	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Drosophila embryo	NA	embryonic epithelial cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	Mutational scanning library; Automated microscopy imaging; RNA expression analysis	Transgenic reporter assay; lacZ staining; CRISPR knockout; ChIP-qPCR; EMSA; RT-qPCR; Western blot
E_04106	2019	31300060	CCAAT/enhancer-binding protein delta regulates the stemness of glioma stem-like cells through activating PDGFA expression upon inflammatory stimulation	Homo sapiens	hg38	chr7	5509938	5510616	CEBPD	PDGFA	Enhancer	Active	Disease	glioblastoma	MONDO:0018177	NA	brain	UBERON:0000955	glioma stem-like cells (GSCs)	NA	glioma stem cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	microarray; RNA-seq	Luciferase reporter assay; ChIP-qPCR, siRNA Knockdown, shRNA Knockdown; RT-qPCR; Western blot; Immunohistochemistry; Reporter assay
E_04107	2017	28777932	Long Noncoding RNAs CUPID1 and CUPID2 Mediate Breast Cancer Risk at 11q13 by Modulating the Response to DNA Damage	Homo sapiens	hg19	chr11	69329695	69333028	NA	LINC01488	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	pleural effusion	UBERON:0000175	MCF-7 DR-GFP	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	RNA CaptureSeq; RNA-seq	CRISPR interference (dCas9-KRAB); 3C-qPCR; Luciferase reporter assay; RT-qPCR
E_04108	2017	28777932	Long Noncoding RNAs CUPID1 and CUPID2 Mediate Breast Cancer Risk at 11q13 by Modulating the Response to DNA Damage	Homo sapiens	hg19	chr11	69329695	69333028	NA	LINC02747	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	pleural effusion	UBERON:0000175	MCF-7 DR-GFP	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	RNA CaptureSeq; RNA-seq	CRISPR interference (dCas9-KRAB); 3C-qPCR; Luciferase reporter assay; RT-qPCR
E_04109	2017	28777932	Long Noncoding RNAs CUPID1 and CUPID2 Mediate Breast Cancer Risk at 11q13 by Modulating the Response to DNA Damage	Homo sapiens	hg19	chr11	69329695	69333028	NA	CCND1	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	pleural effusion	UBERON:0000175	MCF-7 DR-GFP	NA	malignant cell	CL:0001064	Functional perturbation assay	RNA CaptureSeq; RNA-seq	CRISPR interference (dCas9-KRAB); RT-qPCR
E_04110	2019	31300060	CCAAT/enhancer-binding protein delta regulates the stemness of glioma stem-like cells through activating PDGFA expression upon inflammatory stimulation	Homo sapiens	hg38	chr7	5509938	5510616	CEBPD	PDGFA	Enhancer	Active	Disease	glioblastoma	MONDO:0018177	NA	brain	UBERON:0000955	U373MG/T98G-derived GSC model	NA	glioma stem-like cell	NA	CEBPD binds PDGFA promoter (~-538 to +70); this paper does not establish the supplied chr7 interval as an enhancer	microarray	PDGFA promoter luciferase assay; CEBPD ChIP; RT-qPCR; Western blot; stemness assays; Luciferase reporter assay; Reporter assay
E_04111	2013	23747203	Klf4 organizes long-range chromosomal interactions with the oct4 locus in reprogramming and pluripotency	Mus musculus	mm10	chr17	35643473	35645472	Klf4	Pou5f1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Embryonic stem cells (ESCs)	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; Functional perturbation assay; TF binding assay; Chromatin interaction assay	4C-seq; ChIP-seq; RNA-seq; 4C-seq	FISH; ChIP-qPCR, shRNA knockdown; Overexpression assay, Immunoprecipitation; RT-qPCR; Western blot; 4C
E_04112	2023	37945900	Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma	Homo sapiens	hg38	chr8	127329840	127331840	NA	MYC	Enhancer	Active	Disease	group 3 medulloblastoma	NA	DOID:0060104	cerebrospinal fluid	UBERON:0001359	D458 Med	CVCL_1161	medulloblastoma cell	NA	Functional perturbation assay; Chromatin interaction assay; ecDNA MYC super-enhancer CRISPRi target site	whole-genome sequencing; optical genome mapping; ATAC-seq; Hi-C; pooled CRISPRi screen; RNA-seq	individual CRISPRi validation; RT-qPCR; DNA-FISH; RNA-FISH
E_04113	2023	37945900	Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma	Homo sapiens	hg38	chr8	127329927	127331927	NA	MYC	Enhancer	Active	Disease	group 3 medulloblastoma	NA	DOID:0060104	cerebrospinal fluid	UBERON:0001359	D458 Med	CVCL_1161	medulloblastoma cell	NA	Functional perturbation assay; Chromatin interaction assay; ecDNA MYC super-enhancer CRISPRi target site	whole-genome sequencing; optical genome mapping; ATAC-seq; Hi-C; pooled CRISPRi screen; RNA-seq	individual CRISPRi validation; RT-qPCR; DNA-FISH; RNA-FISH
E_04114	2023	37945900	Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma	Homo sapiens	hg38	chr8	127330655	127330840	NA	MYC	Super-enhancer	Active	Disease	Medulloblastoma	NA	DOID:0050902	brain	UBERON:0000955	D-423MG	CVCL_1160	medulloblastoma cell	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	Hi-C; ATAC-seq; RNA-seq	CRISPRi, qRT-PCR; FISH
E_04115	2020	31591481	Oncogenic HOXB8 is driven by MYC-regulated super-enhancer and potentiates colorectal cancer invasiveness via BACH1	Homo sapiens	hg19	chr17	46682000	46685000	SP1	HOXB8	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	Functional perturbation assay	ChIP-seq; RNA-seq; ATAC-seq	CRISPRi; ChIP-qPCR; RT-qPCR; Western blot
E_04116	2020	31591481	Oncogenic HOXB8 is driven by MYC-regulated super-enhancer and potentiates colorectal cancer invasiveness via BACH1	Homo sapiens	hg19	chr17	46692000	46695000	MYC	HOXB8	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq; ATAC-seq	CRISPRi; ChIP-qPCR; RT-qPCR; Western blot
E_04117	2019	30649550	Histone demethylase KDM3A is required for enhancer activation of hippo target genes in colorectal cancer	Homo sapiens	hg19	chr1	85865000	85866500	TEAD1	CCN1	Enhancer	Active	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	CRISPR knockout; ChIP-qPCR; RT-qPCR; Western blot; Co-IP
E_04118	2019	30649550	Histone demethylase KDM3A is required for enhancer activation of hippo target genes in colorectal cancer	Homo sapiens	hg19	chr1	85868000	85869500	TEAD1	CCN1	Enhancer	Active	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	CRISPR knockout; ChIP-qPCR; RT-qPCR; Western blot; Co-IP
E_04119	2019	30649550	Histone demethylase KDM3A is required for enhancer activation of hippo target genes in colorectal cancer	Homo sapiens	hg19	chr1	85870000	85870500	TEAD1	CCN1	Enhancer	Active	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	CRISPR knockout; ChIP-qPCR; RT-qPCR; Western blot; Co-IP
E_04120	2019	30649550	Histone demethylase KDM3A is required for enhancer activation of hippo target genes in colorectal cancer	Homo sapiens	hg19	chr6	132265000	132266500	TEAD1	CCN2	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	CRISPR knockout; ChIP-qPCR; RT-qPCR; Western blot; Co-IP
E_04121	2019	30649550	Histone demethylase KDM3A is required for enhancer activation of hippo target genes in colorectal cancer	Homo sapiens	hg19	chr6	132270000	132270500	TEAD1	CCN2	Enhancer	Active	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	CRISPR knockout; ChIP-qPCR; RT-qPCR; Western blot; Co-IP
E_04122	2018	30038397	Dynamic interplay between enhancer-promoter topology and gene activity	Drosophila melanogaster	dm6	chr2R	9974054	9974699	NA	eve	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	blastoderm cell	NA	embryonic cell	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	NA	qRT-PCR; ChIP-qPCR
E_04123	2018	30038397	Dynamic interplay between enhancer-promoter topology and gene activity	Drosophila melanogaster	dm6	chr2R	9975013	9975699	NA	eve	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	blastoderm cell	NA	embryonic cell	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	NA	qRT-PCR; ChIP-qPCR
E_04124	2018	30038397	Dynamic interplay between enhancer-promoter topology and gene activity	Drosophila melanogaster	dm6	chr2R	9984101	9984849	NA	eve	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	blastoderm cell	NA	embryonic cell	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	NA	qRT-PCR; ChIP-qPCR
E_04125	2018	30038397	Dynamic interplay between enhancer-promoter topology and gene activity	Drosophila melanogaster	dm6	chr2R	9985221	9985886	NA	eve	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	blastoderm cell	NA	embryonic cell	NA	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	NA	qRT-PCR; ChIP-qPCR
E_04126	2009	19561607	The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer	Homo sapiens	hg19	chr8	128412536	128414073	TCF7L2	MYC	Enhancer	Active	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	colorectal cancer cell lines / primary colorectal tumor material	NA	malignant cell	CL:0001064	Risk-variant enhancer assay; allele-specific TF binding; long-range chromatin interaction	Genotype/allele-specific regulatory analysis	Luciferase reporter assay; TCF7L2 ChIP; 3C; allele-specific binding/expression analysis
E_04127	2020	31591481	Oncogenic HOXB8 is driven by MYC-regulated super-enhancer and potentiates colorectal cancer invasiveness via BACH1	Homo sapiens	hg19	chr17	46656000	46658000	NA	HOXB8	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay	ChIP-seq; RNA-seq	CRISPR knockout/CRISPRi; RT-qPCR
E_04128	2009	19561607	The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer	Homo sapiens	hg18	chr8	128482317	128483854	TCF7L2	MYC	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	COLO 205	CVCL_0218	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Disease-variant functional analysis; Allele-specific functional assay	NimbleGen 8q24 tiling array; TCF7L2 ChIP-chip (Affymetrix Human Tiling 2.0RF)	Luciferase reporter assay; ChIP-qPCR; 3C; Sequenom MALDI-TOF allele-specific assay
E_04129	2009	19561607	The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer	Homo sapiens	hg18	chr8	128482317	128483854	NA	MYC	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	ascitic fluid	UBERON:0007795	COLO 205	CVCL_0218	epithelial cell of colon	NA	Enhancer activity assay; Chromatin interaction assay; Allele-specific regulatory assay; Enhancer chromatin-state assay	NimbleGen 8q24 high-density tiling array	Luciferase reporter assay; Allele-specific reporter assay; p300 ChIP-qPCR; H3K4me1 ChIP-qPCR; H3K4me3 ChIP-qPCR; RNA polymerase II ChIP-qPCR; 3C; competitive PCR
E_04130	2009	19561607	The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer	Homo sapiens	hg18	chr8	128482317	128483854	TCF7L2	MYC	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	LS 174T	CVCL_1384	epithelial cell of colon	NA	Enhancer activity assay; TF binding assay; Chromatin interaction assay; Allele-specific regulatory assay	TCF7L2 ChIP-chip; Affymetrix Human Tiling 2.0R array	Luciferase reporter assay; Allele-specific reporter assay; TCF7L2 allele-specific ChIP; Sequenom MALDI-TOF allele quantification; 3C; competitive PCR
E_04131	2019	31594934	Transcriptional landscape and clinical utility of enhancer RNAs for eRNA-targeted therapy in cancer	Homo sapiens	hg38	chr10	5419501	5420500	NA	NET1	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	RNA-seq; ChIP-seq, Hi-C, ChIA-PET; GRO-seq	CRISPR Activation (CRISPRa), LNA-Mediated Knockdown; RT-qPCR, Cell Proliferation Assay
E_04132	2018	29358217	Homeostatic Response of Mouse renin Gene Transcription in a Hypertensive Environment Is Mediated by a Novel 5' Enhancer	Mus musculus	mm10	chr1	133347574	133364574	NA	Ren1	Enhancer	Active	Disease	Hypertension	NA	NA	NA	NA	As4.1,Tsukuba hypertensive mice	NA	NA	NA	Enhancer activity assay; Endogenous enhancer perturbation; In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_04133	2020	33193627	Functional Characterization of a Dual Enhancer/Promoter Regulatory Element Leading Human CD69 Expression	Homo sapiens	hg19	chr12	9916938	9918379	NA	CD69	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	Jurkat	CVCL_0065	T lymphoblast	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	RNA-seq; ChIP-seq	Luciferase reporter assay; CRISPR knockout; ChIP-qPCR; RT-qPCR; CRISPR-Cas9
E_04134	2023	37626123	MLL-AF4 cooperates with PAF1 and FACT to drive high-density enhancer interactions in leukemia	Homo sapiens	hg19	chr13	28843000	28843500	KMT2A::AFF1	FLT3	Enhancer	Active	Disease	KMT2A::AFF1-rearranged B-cell acute lymphoblastic leukemia	NA	NA	blood	UBERON:0000178	primary MLL-AF4 ALL	NA	B cell	CL:0000236	Chromatin interaction assay; Fusion-protein occupancy assay; Enhancer chromatin-state assay; Functional protein-degradation perturbation	MLL/AF4/H3K27ac ChIP-seq or TOPmentation; ATAC-seq; Micro-Capture-C; Capture-C; Micro-C	MLL-AF4 knockdown; PAF1/FACT degron perturbation; targeted Capture-C/MCC validation; RT-qPCR
E_04135	2020	32384149	13q12.2 deletions in acute lymphoblastic leukemia lead to upregulation of FLT3 through enhancer hijacking	Homo sapiens	hg19	chr13	28843000	28843500	RUNX1	FLT3	Enhancer	Active	Disease	B-cell acute lymphoblastic leukemia	MONDO:0004947	DOID:0080638	bone marrow	UBERON:0002371	Primary BCP ALL cells	NA	B-lymphoblast	CL:0017006	Enhancer activity assay; Chromatin interaction assay	ChIP-seq; RNA-seq, Hi-C; PLAC-seq; ATAC-seq; DNase-seq	RT-qPCR, FISH
E_04136	2023	37626123	MLL-AF4 cooperates with PAF1 and FACT to drive high-density enhancer interactions in leukemia	Homo sapiens	hg19	chr13	28843000	28843500	KMT2A::AFF1	FLT3	Enhancer	Active	Disease	KMT2A::AFF1-rearranged B-cell acute lymphoblastic leukemia	NA	NA	blood	UBERON:0000178	SEM/SEMK2 KMT2A::AFF1 B-ALL cells	CVCL_S906	B cell	CL:0000236	Chromatin interaction assay; Fusion-protein occupancy assay; Enhancer chromatin-state assay; Functional protein-degradation perturbation	MLL/AF4/H3K27ac ChIP-seq or TOPmentation; ATAC-seq; Micro-Capture-C; Capture-C; Micro-C	MLL-AF4 knockdown; PAF1/FACT degron perturbation; targeted Capture-C/MCC validation; RT-qPCR
E_04137	2023	37626123	MLL-AF4 cooperates with PAF1 and FACT to drive high-density enhancer interactions in leukemia	Homo sapiens	hg19	chr13	28843000	28843500	KMT2A::AFF1	FLT3	Enhancer	Active	Disease	KMT2A::AFF1-rearranged B-cell acute lymphoblastic leukemia	NA	NA	blood	UBERON:0000178	SEM	CVCL_0095	B cell	CL:0000236	Chromatin interaction assay; Fusion-protein occupancy assay; Enhancer chromatin-state assay; Functional protein-degradation perturbation	MLL/AF4/H3K27ac ChIP-seq or TOPmentation; ATAC-seq; Micro-Capture-C; Capture-C; Micro-C	MLL-AF4 knockdown; PAF1/FACT degron perturbation; targeted Capture-C/MCC validation; RT-qPCR
E_04138	2020	32384149	13q12.2 deletions in acute lymphoblastic leukemia lead to upregulation of FLT3 through enhancer hijacking	Homo sapiens	hg19	chr13	28843000	28843500	RUNX1	FLT3	Enhancer	Active	Disease	B-cell acute lymphoblastic leukemia	MONDO:0004947	DOID:0080638	bone marrow	UBERON:0002371	NALM-6	CVCL_0092	B-lymphoblast	CL:0017006	Enhancer activity assay; Chromatin interaction assay	ChIP-seq; RNA-seq, Hi-C; PLAC-seq; ATAC-seq; DNase-seq	RT-qPCR, FISH
E_04139	2020	32384149	13q12.2 deletions in acute lymphoblastic leukemia lead to upregulation of FLT3 through enhancer hijacking	Homo sapiens	hg19	chr13	28710000	28715000	RUNX1	FLT3	Enhancer	Active	Disease	B-cell acute lymphoblastic leukemia	MONDO:0004947	DOID:0080638	bone marrow	UBERON:0002371	NALM-6	CVCL_0092	B-lymphoblast	CL:0017006	Enhancer activity assay; Chromatin interaction assay	ChIP-seq; RNA-seq, Hi-C; PLAC-seq; ATAC-seq; DNase-seq	RT-qPCR, FISH
E_04140	2014	24905168	Reorganization of enhancer patterns in transition from naive to primed pluripotency	Mus musculus	mm10	chr4	101250000	101250600	Otx2	Pou3f1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Epiblast-like cells (EpiLC)	NA	epiblast-like cell	NA	Enhancer activity assay	ChIP-seq; RNA-seq	Transgenic reporter assay
E_04141	2014	24905168	Reorganization of enhancer patterns in transition from naive to primed pluripotency	Mus musculus	mm10	chr4	101250000	101250600	Pou5f1	Pou3f1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Epiblast-like cells (EpiLC)	NA	epiblast-like cell	NA	Enhancer activity assay	ChIP-seq; RNA-seq	Transgenic reporter assay
E_04142	2025	40966339	Functional maps of a genomic locus reveal confinement of an enhancer by its target gene	Mus musculus	mm10	chr3	34824938	34837938	Nanog	Sox2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	ES-R1	CVCL_2167	embryonic stem cell	CL:0002322	CRISPR deletion functional assay	ATAC-seq; ChIP-seq; Micro-C, transposon integration mapping; Micro-C	RT-qPCR, flow cytometry
E_04143	2025	40966339	Functional maps of a genomic locus reveal confinement of an enhancer by its target gene	Mus musculus	mm10	chr3	34824938	34837938	Pou5f1	Sox2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	ES-R1	CVCL_2167	embryonic stem cell	CL:0002322	CRISPR deletion functional assay	ATAC-seq; ChIP-seq; Micro-C, transposon integration mapping; Micro-C	RT-qPCR, flow cytometry
E_04144	2025	40966339	Functional maps of a genomic locus reveal confinement of an enhancer by its target gene	Mus musculus	mm10	chr3	34824938	34837938	Sox2	Sox2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	ES-R1	CVCL_2167	embryonic stem cell	CL:0002322	CRISPR deletion functional assay	ATAC-seq; ChIP-seq; Micro-C, transposon integration mapping; Micro-C	RT-qPCR, flow cytometry
E_04145	2019	30711920	H2AFY promoter deletion causes PITX1 endoactivation and Liebenberg syndrome	Mus musculus	mm10	chr13	69400000	69410000	NA	Pitx1	Enhancer	Active	Disease	brachydactyly-elbow wrist dysplasia syndrome	MONDO:0008520	NA	limb bud	NA	E11.5 mouse forelimb	NA	NA	NA	Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation; Structural-variant/promoter-insulator perturbation revealing enhancer retargeting	whole-genome sequencing; RNA-seq	CRISPR-Cas9 recreation of deletion in mice; RT-qPCR; whole-mount in situ hybridization; CRISPR-Cas9 endogenous deletion/editing; Mouse genetic deletion/knock-in
E_04146	2015	26163528	Id2 deletion attenuates Apc-deficient ileal tumor formation	Mus musculus	mm10	chr12	25090158	25096935	NA	Id2	Enhancer	Active	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	Apoptotic Cell	NA	NA	NA	Enhancer activity assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay
E_04147	2023	37567873	Spinal cord repair is modulated by the neurogenic factor Hb-egf under direction of a regeneration-associated enhancer	Danio rerio	danRer11	chr14	6760805	6761115	NA	hbegfa	Enhancer	Active	Normal	NA	NA	NA	spinal cord	UBERON:0002240	ependymo-radial glial cell	NA	radial glial cell	CL:0000681	Enhancer activity assay	ATAC-seq; RNA-seq; scRNA-seq	Transgenic reporter assay; CRISPR knockout; in situ hybridization; qRT-PCR
E_04148	2019	30620726	Single-nucleotide human disease mutation inactivates a blood-regenerative GATA2 enhancer	Homo sapiens	hg38	chr3	128191800	128192300	NA	GATA2	Enhancer	Repressed	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	bone marrow	UBERON:0002371	Hematopoietic stem/progenitor cells	NA	hematopoietic stem cell	CL:0000037	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation; In vivo functional validation	RNA-seq	Luciferase reporter assay, CRISPR knockout; RT-qPCR; Site-directed/motif mutagenesis; Mouse genetic deletion/knock-in
E_04149	2014	24703711	A single oncogenic enhancer rearrangement causes concomitant EVI1 and GATA2 deregulation in leukemia	Homo sapiens	hg38	chr3	128603821	128604120	NA	MECOM	Enhancer	Active	Disease	acute myeloid leukemia with inv(3)(q21.3q26.2)/t(3;3)(q21.3;q26.2)	NA	NA	bone marrow	UBERON:0002371	inv(3)/t(3;3) AML cells and primary AML samples	NA	myeloid leukemia cell	NA	Endogenous enhancer-hijacking functional validation	ChIP-seq; RNA-seq; chromatin-conformation analysis	Genomic enhancer excision; genome engineering; RT-qPCR; differentiation assay
E_04150	2014	25268989	Functional annotation of colon cancer risk SNPs	Homo sapiens	hg19	chr8	128140000	128145000	TCF7L2	MYC	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	Disease-variant functional analysis; Functional enhancer assay	ChIP-seq; GWAS	CRISPR deletion; expression profiling; Reporter assay
E_04151	2019	31046704	Functional characterization of two enhancers located downstream FOXP2	Homo sapiens	hg19	chr7	114541370	114543683	NA	FOXP2	Enhancer	Active	Disease	speech and language disorder / childhood apraxia-associated regulatory locus	NA	NA	brain	UBERON:0000955	SK-N-MC	CVCL_0530	neural cell model	NA	Endogenous enhancer deletion and target-gene functional characterization	ENCODE chromatin-state integration	CRISPR-Cas9 enhancer deletion; Reporter assay; gene-expression analysis; CRISPR-Cas9
E_04152	2019	31046704	Functional characterization of two enhancers located downstream FOXP2	Homo sapiens	hg19	chr7	114541370	114543683	NA	FOXP2	Enhancer	Active	Disease	speech and language disorder-associated FOXP2 regulatory locus	NA	NA	brain	UBERON:0000955	SK-N-MC	CVCL_0530	neural cell model	NA	Endogenous enhancer deletion and target-gene functional characterization	ENCODE chromatin-state integration	CRISPR-Cas9 enhancer deletion; Reporter assay; gene-expression analysis; CRISPR-Cas9
E_04153	2019	31046704	Functional characterization of two enhancers located downstream FOXP2	Homo sapiens	hg19	chr7	114456873	114463136	NA	FOXP2	Enhancer	Active	Disease	speech and language disorder / childhood apraxia-associated regulatory locus	NA	NA	brain	UBERON:0000955	SK-N-MC	CVCL_0530	neural cell model	NA	Endogenous enhancer deletion and target-gene functional characterization	ENCODE chromatin-state integration	CRISPR-Cas9 enhancer deletion; Reporter assay; gene-expression analysis; CRISPR-Cas9
E_04154	2019	31046704	Functional characterization of two enhancers located downstream FOXP2	Homo sapiens	hg19	chr7	114456873	114463136	NA	FOXP2	Enhancer	Active	Disease	speech and language disorder-associated FOXP2 regulatory locus	NA	NA	brain	UBERON:0000955	SK-N-MC	CVCL_0530	neural cell model	NA	Endogenous enhancer deletion and target-gene functional characterization	ENCODE chromatin-state integration	CRISPR-Cas9 enhancer deletion; Reporter assay; gene-expression analysis; CRISPR-Cas9
E_04155	2020	32352029	BCL9/STAT3 regulation of transcriptional enhancer networks promote DCIS progression	Homo sapiens	hg19	chr17	45414208	45414987	NA	ITGB3	Enhancer	Active	Normal	NA	NA	NA	breast	UBERON:0000310	293T cyno DLL3	CVCL_UE58	mammary epithelial cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-exo; RNA-seq; RPPA	ChIP-qPCR, shRNA Knockdown; RT-qPCR; Western blot; In vivo Invasion Assay
E_04156	2014	25321476	Identification and characterization of the novel Col10a1 regulatory mechanism during chondrocyte hypertrophic differentiation	Mus musculus	mm10	chr10	4147	4296	Runx2	Col10a1	Enhancer	Active	Normal	NA	NA	NA	limb bud	NA	Hypertrophic chondrocytes	NA	hypertrophic chondrocyte	CL:0000743	Enhancer activity assay; TF binding assay	NA	Transgenic reporter assay, EMSA; ChIP-qPCR; RT-qPCR; EMSA; ChIP; Reporter assay
E_04157	2014	25321476	Identification and characterization of the novel Col10a1 regulatory mechanism during chondrocyte hypertrophic differentiation	Mus musculus	mm10	chr10	128347441	128347590	Runx2	Col10a1	Enhancer	Active	Normal	NA	NA	NA	limb bud	NA	Hypertrophic chondrocytes	NA	hypertrophic chondrocyte	CL:0000743	Enhancer activity assay; TF binding assay	NA	Transgenic reporter assay, EMSA; ChIP-qPCR; RT-qPCR; EMSA; ChIP; Reporter assay
E_04158	2025	41028522	HSF1-DBC1 axis drives prostate cancer progression by activating a metastatic transcriptional program	Homo sapiens	hg38	chr22	24114000	24116000	HSF1	MMP11	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	SM1 (mCRPC cell line)	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay	ChIP-seq; RNA-seq	CRISPR knockout, qRT-PCR; Western blot, Transwell Migration Assay, Transwell Invasion Assay; ChIP
E_04159	2020	31773361	Genetic Predisposition to Glioma Mediated by a MAPKAP1 Enhancer Variant	Homo sapiens	hg19	chr9	128335472	128336978	NFIC	MAPKAP1	Enhancer	Active	Disease	glioma	MONDO:0021042	NA	blood	UBERON:0000178	Lymphoblastoid cell line	NA	lymphoblast	CL:0017005	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Luciferase reporter assay; EMSA; ChIP-qPCR; RT-qPCR
E_04160	2020	32679107	IL6/STAT3 Signaling Hijacks Estrogen Receptor α Enhancers to Drive Breast Cancer Metastasis	Homo sapiens	hg38	chr19	45409200	45410200	STAT3	BCL3	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Functional perturbation assay	ChIP-seq; RNA-seq	CRISPR knockout
E_04161	2019	30511964	Targeting FOXA1-mediated repression of TGF-β signaling suppresses castration-resistant prostate cancer progression	Homo sapiens	hg38	chr14	75664000	75664749	FOXA1	TGFB3	Enhancer	Repressed	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Functional perturbation assay; In vivo functional validation	ChIP-seq; RNA-seq	CRISPR knockout/CRISPRi; RT-qPCR; In vivo phenotyping; Xenograft/xenotransplant
E_04162	2019	30511964	Targeting FOXA1-mediated repression of TGF-β signaling suppresses castration-resistant prostate cancer progression	Homo sapiens	hg19	chr14	76419740	76421740	FOXA1	TGFB3	Enhancer	Repressed	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Endogenous enhancer perturbation; In vivo functional validation; TF-binding/chromatin assay; Disease-associated enhancer analysis	ChIP-seq	CRISPR-Cas9 targeted editing/deletion; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_04163	2018	29755131	KMT2C mediates the estrogen dependence of breast cancer through regulation of ERα enhancer function	Homo sapiens	hg19	chr11	100674936	100675904	ESR1	PGR	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	MCF-7	CVCL_0031	mammary epithelial cell	NA	Functional perturbation assay; TF binding assay; Enhancer chromatin-state assay	H3K4me1 ChIP-seq; H3K27ac ChIP-seq; ESR1 ChIP-seq; RNA-seq	ChIP-qPCR; KMT2C shRNA knockdown; RT-qPCR; Western blot; Cell proliferation assay
E_04164	2020	31773361	Genetic Predisposition to Glioma Mediated by a MAPKAP1 Enhancer Variant	Homo sapiens	hg19	chr9	128335472	128336978	NFIC	MAPKAP1	Enhancer	Active	Disease	glioma	MONDO:0021042	NA	brain	UBERON:0000955	U-251MG	CVCL_0021	glioma cell	NA	Enhancer activity assay; Functional perturbation assay; TF binding assay	NA	Luciferase reporter assay; EMSA; ChIP-qPCR; RT-qPCR
E_04165	2022	35864091	Etv2 regulates enhancer chromatin status to initiate Shh expression in the limb bud	Mus musculus	mm10	chr5	29314591	29316266	Etv2	Shh	Enhancer	Active	Normal	NA	NA	NA	limb bud	NA	Embryonic limb mesenchyme	NA	limb mesenchyme cell	NA	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ATAC-seq; ChIP-seq	Luciferase reporter assay; ChIP-qPCR; EMSA
E_04166	2026	41827844	MGMT Promoter and Enhancer Methylation in Melanoma Brain Metastases and Glioblastoma: Shared and Distinct Features	Homo sapiens	hg38	chr10	128906630	128909942	NA	MGMT	Enhancer	Active	Disease	glioblastoma	MONDO:0018177	NA	brain	UBERON:0000955	Primary tumor tissue	NA	glioblastoma cell	CL:0001063	Enhancer activity assay; Functional perturbation assay	DNA methylation profiling	Transgenic reporter assay; CRISPR knockout
E_04167	2016	26934861	4C-seq revealed long-range interactions of a functional enhancer at the 8q24 prostate cancer risk locus	Homo sapiens	hg19	chr8	128413136	128414674	TCF7L2	MYC	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	epithelial cell	CL:0000066	Enhancer activity assay; Chromatin interaction assay; Disease-variant functional analysis; Genetic risk regulatory analysis	4C-seq; Public ChIP-seq and epigenomic data integration; GWAS	Luciferase reporter assay; Transgenic reporter assay; 4C
E_04168	2003	12837695	A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly	Homo sapiens	hg19	chr7	156583796	156584568	NA	SHH	Enhancer	Active	Disease	preaxial polydactyly II	MONDO:0008270	NA	limb bud	NA	transgenic mouse embryos	NA	limb bud mesenchymal cell	NA	In vivo enhancer activity assay; disease variant analysis	NA	Transgenic mouse reporter assay; comparative sequence analysis; familial mutation and segregation analysis; mutant mouse analysis
E_04169	2025	40162972	Enhancer Hijacking Discovery in Acute Myeloid Leukemia by Pyjacker Identifies MNX1 Activation via Deletion 7q	Homo sapiens	hg19	chr7	92384001	92385000	NA	MNX1	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	NA	NA	ChiPSC22	CVCL_RN02	hematopoietic precursor cell	CL:0008001	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation; In vivo functional validation; Genomic engineering assay	WGS; RNA-seq	CRISPR/Cas9-mediated homology-directed enhancer insertion; PCR clone screening; hematopoietic stem/progenitor cell differentiation; Mouse genetic deletion/knock-in; Xenograft/xenotransplant
E_04170	2014	24256810	Identification and characterization of functional risk variants for colorectal cancer mapping to chromosome 11q23.1	Homo sapiens	hg19	chr11	111150916	111155431	NA	POU2AF2	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Regulatory variant functional assay	ChIP-seq; DNase-seq/ENCODE profiling; eQTL analysis	Luciferase reporter assay; Site-directed mutagenesis; EMSA
E_04171	2014	24256810	Identification and characterization of functional risk variants for colorectal cancer mapping to chromosome 11q23.1	Homo sapiens	hg19	chr11	111150916	111155431	NA	POU2AF2	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	SW480	CVCL_0546	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Regulatory variant functional assay	ChIP-seq; DNase-seq/ENCODE profiling; eQTL analysis	Luciferase reporter assay; Site-directed mutagenesis; EMSA
E_04172	2025	40162972	Enhancer Hijacking Discovery in Acute Myeloid Leukemia by Pyjacker Identifies MNX1 Activation via Deletion 7q	Homo sapiens	hg19	chr7	92384001	92385000	NA	MNX1	Enhancer	Active	Disease	acute myeloid leukemia with del(7)(q22q36)	NA	NA	NA	NA	ChiPSC22	CVCL_RN02	hematopoietic stem and progenitor cells (HSPCs)	NA	Enhancer activity assay; Functional perturbation assay	WGS; RNA-seq	CRISPR/Cas9-mediated enhancer insertion by homology-directed repair (HDR); integration PCR
E_04173	2025	40162972	Enhancer Hijacking Discovery in Acute Myeloid Leukemia by Pyjacker Identifies MNX1 Activation via Deletion 7q	Homo sapiens	hg19	chr7	92384001	92385000	NA	MNX1	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	blood	UBERON:0000178	Primary del(7q) AML cells (2KFQ)	NA	myeloid progenitor cell / leukemic blast	NA	Chromatin interaction assay; Enhancer chromatin-state assay; Enhancer hijacking analysis; Target-gene functional validation	WGS; RNA-seq; scRNA-seq; 4C-seq; ATAC-seq; ACT-seq (H3K27ac; H3K4me1)	qRT-PCR; genomic breakpoint PCR; MNX1 shRNA knockdown; Flow cytometry; PDX competitive fitness assay
E_04174	2025	40162972	Enhancer Hijacking Discovery in Acute Myeloid Leukemia by Pyjacker Identifies MNX1 Activation via Deletion 7q	Homo sapiens	hg19	chr7	92384001	92385000	NA	MNX1	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	bone marrow	UBERON:0002371	Primary del(7q) AML cells (2KFQ)	NA	myeloid progenitor cell / leukemic blast	NA	Chromatin interaction assay; Enhancer chromatin-state assay; Enhancer hijacking analysis; Target-gene functional validation	WGS; RNA-seq; scRNA-seq; 4C-seq; ATAC-seq; ACT-seq (H3K27ac; H3K4me1)	qRT-PCR; genomic breakpoint PCR; MNX1 shRNA knockdown; Flow cytometry; PDX competitive fitness assay
E_04175	2014	24256810	Identification and characterization of functional risk variants for colorectal cancer mapping to chromosome 11q23.1	Homo sapiens	hg19	chr11	111152290	111154290	NA	NA	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	HCT 116	CVCL_0291	epithelial cell	CL:0000066	Enhancer activity assay; TF binding assay; Chromatin-state profiling; Disease-variant functional analysis; Functional variant assay	ChIP-seq; eQTL analysis; GWAS	Luciferase reporter assay; EMSA; Site-directed mutagenesis; ChIP
E_04176	2014	24256810	Identification and characterization of functional risk variants for colorectal cancer mapping to chromosome 11q23.1	Homo sapiens	hg19	chr11	111152290	111154290	NA	NA	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	SW480	CVCL_0546	epithelial cell	CL:0000066	Enhancer activity assay; TF binding assay; Chromatin-state profiling; Disease-variant functional analysis; Functional variant assay	ChIP-seq; eQTL analysis; GWAS	Luciferase reporter assay; EMSA; Site-directed mutagenesis; ChIP
E_04177	2017	29326336	ARID5B as a critical downstream target of the TAL1 complex that activates the oncogenic transcriptional program and promotes T-cell leukemogenesis	Homo sapiens	hg19	chr10	63525013	63527013	TAL1	ARID5B	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Jurkat E6.1	CVCL_0367	T lymphoblast	NA	Oncogenic TF enhancer mapping; target-gene functional validation	TAL1-complex ChIP-seq; H3K27ac ChIP-seq; RNA-seq	ChIP-qPCR; Luciferase reporter assay; TAL1 perturbation; qRT-PCR; cell-growth assays
E_04178	2025	40162972	Enhancer Hijacking Discovery in Acute Myeloid Leukemia by Pyjacker Identifies MNX1 Activation via Deletion 7q	Homo sapiens	hg19	chr7	92384001	92385000	NA	MNX1	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	blood	UBERON:0000178	AML-661 PDX	NA	myeloid progenitor cell / leukemic blast	NA	Chromatin interaction assay; Enhancer chromatin-state assay; Enhancer hijacking analysis; Target-gene functional validation	WGS; RNA-seq; scRNA-seq; 4C-seq; ATAC-seq; ACT-seq (H3K27ac; H3K4me1)	qRT-PCR; genomic breakpoint PCR; MNX1 shRNA knockdown; Flow cytometry; PDX competitive fitness assay
E_04179	2025	40162972	Enhancer Hijacking Discovery in Acute Myeloid Leukemia by Pyjacker Identifies MNX1 Activation via Deletion 7q	Homo sapiens	hg19	chr7	92384001	92385000	NA	MNX1	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	bone marrow	UBERON:0002371	AML-661 PDX	NA	myeloid progenitor cell / leukemic blast	NA	Chromatin interaction assay; Enhancer chromatin-state assay; Enhancer hijacking analysis; Target-gene functional validation	WGS; RNA-seq; scRNA-seq; 4C-seq; ATAC-seq; ACT-seq (H3K27ac; H3K4me1)	qRT-PCR; genomic breakpoint PCR; MNX1 shRNA knockdown; Flow cytometry; PDX competitive fitness assay
E_04180	2025	40162972	Enhancer Hijacking Discovery in Acute Myeloid Leukemia by Pyjacker Identifies MNX1 Activation via Deletion 7q	Homo sapiens	hg19	chr7	92384001	92385000	NA	MNX1	Enhancer	Active	Disease	acute myeloid leukemia with del(7)(q22q36)	NA	NA	blood	UBERON:0000178	Primary del(7q) AML cells (2KFQ)	NA	myeloid progenitors and leukemic blasts	NA	Chromatin interaction assay; Chromatin accessibility assay; Enhancer identification assay	WGS; ATAC-seq; 4C-seq	3C
E_04181	2025	40162972	Enhancer Hijacking Discovery in Acute Myeloid Leukemia by Pyjacker Identifies MNX1 Activation via Deletion 7q	Homo sapiens	hg19	chr7	92384001	92385000	NA	MNX1	Enhancer	Active	Disease	acute myeloid leukemia with del(7)(q22q36)	NA	NA	bone marrow	UBERON:0002371	Primary del(7q) AML cells (2KFQ)	NA	myeloid progenitors and leukemic blasts	NA	Chromatin interaction assay; Chromatin accessibility assay; Enhancer identification assay	WGS; ATAC-seq; 4C-seq	3C
E_04182	2014	24256810	Identification and characterization of functional risk variants for colorectal cancer mapping to chromosome 11q23.1	Homo sapiens	hg19	chr11	111152290	111154290	NA	POU2AF2	Enhancer	Active	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	GWAS fine-mapping; allele-specific enhancer validation; candidate target association	H3K4me1 ChIP-seq; DNase-seq/ENCODE integration; genetic association; ChIP-seq; eQTL analysis	Luciferase reporter; EMSA; eQTL/expression analysis
E_04183	2014	24256810	Identification and characterization of functional risk variants for colorectal cancer mapping to chromosome 11q23.1	Homo sapiens	hg19	chr11	111152290	111154290	NA	POU2AF2	Enhancer	Active	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	SW480	CVCL_0546	malignant cell	CL:0001064	GWAS fine-mapping; allele-specific enhancer validation; candidate target association	H3K4me1 ChIP-seq; DNase-seq/ENCODE integration; genetic association; ChIP-seq; eQTL analysis	Luciferase reporter; EMSA; eQTL/expression analysis
E_04184	2014	24256810	Identification and characterization of functional risk variants for colorectal cancer mapping to chromosome 11q23.1	Homo sapiens	hg19	chr11	111152290	111154290	NA	COLCA1	Enhancer	Active	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	GWAS fine-mapping; allele-specific enhancer validation; candidate target association	H3K4me1 ChIP-seq; DNase-seq/ENCODE integration; genetic association; ChIP-seq; eQTL analysis	Luciferase reporter; EMSA; eQTL/expression analysis
E_04185	2014	24256810	Identification and characterization of functional risk variants for colorectal cancer mapping to chromosome 11q23.1	Homo sapiens	hg19	chr11	111152290	111154290	NA	COLCA1	Enhancer	Active	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	SW480	CVCL_0546	malignant cell	CL:0001064	GWAS fine-mapping; allele-specific enhancer validation; candidate target association	H3K4me1 ChIP-seq; DNase-seq/ENCODE integration; genetic association; ChIP-seq; eQTL analysis	Luciferase reporter; EMSA; eQTL/expression analysis
E_04186	2014	24256810	Identification and characterization of functional risk variants for colorectal cancer mapping to chromosome 11q23.1	Homo sapiens	hg19	chr11	111152290	111154290	NA	POU2AF3	Enhancer	Active	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	HCT 116	CVCL_0291	malignant cell	CL:0001064	GWAS fine-mapping; allele-specific enhancer validation; candidate target association	H3K4me1 ChIP-seq; DNase-seq/ENCODE integration; genetic association; ChIP-seq; eQTL analysis	Luciferase reporter; EMSA; eQTL/expression analysis
E_04187	2014	24256810	Identification and characterization of functional risk variants for colorectal cancer mapping to chromosome 11q23.1	Homo sapiens	hg19	chr11	111152290	111154290	NA	POU2AF3	Enhancer	Active	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	SW480	CVCL_0546	malignant cell	CL:0001064	GWAS fine-mapping; allele-specific enhancer validation; candidate target association	H3K4me1 ChIP-seq; DNase-seq/ENCODE integration; genetic association; ChIP-seq; eQTL analysis	Luciferase reporter; EMSA; eQTL/expression analysis
E_04188	2025	40162972	Enhancer Hijacking Discovery in Acute Myeloid Leukemia by Pyjacker Identifies MNX1 Activation via Deletion 7q	Homo sapiens	hg19	chr7	92384001	92385000	NA	MNX1	Enhancer	Active	Disease	acute myeloid leukemia with del(7)(q22q36)	NA	NA	blood	UBERON:0000178	Primary del(7q) AML cells (MTM9)	NA	myeloid progenitors and leukemic blasts	NA	Chromatin interaction assay; Chromatin accessibility assay; Enhancer identification assay	WGS; ATAC-seq; 4C-seq	3C
E_04189	2025	40162972	Enhancer Hijacking Discovery in Acute Myeloid Leukemia by Pyjacker Identifies MNX1 Activation via Deletion 7q	Homo sapiens	hg19	chr7	92384001	92385000	NA	MNX1	Enhancer	Active	Disease	acute myeloid leukemia with del(7)(q22q36)	NA	NA	bone marrow	UBERON:0002371	Primary del(7q) AML cells (MTM9)	NA	myeloid progenitors and leukemic blasts	NA	Chromatin interaction assay; Chromatin accessibility assay; Enhancer identification assay	WGS; ATAC-seq; 4C-seq	3C
E_04190	2019	31767869	LncRNA REG1CP promotes tumorigenesis through an enhancer complex to recruit FANCJ helicase for REG3A transcription	Homo sapiens	hg38	chr2	79165929	79165948	NA	REG3A	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	Primary colorectal-cancer tissues with paired normal colon mucosa	NA	malignant cell	CL:0001064	clinical-expression association; lncRNA enhancer-complex mechanism; functional perturbation	lncRNA expression microarray; TCGA/R2 transcriptomic analyses	qRT-PCR; ddPCR; in situ hybridization; REG1CP knockdown/rescue; FANCJ interaction/recruitment assays; xenograft
E_04191	2025	40162972	Enhancer Hijacking Discovery in Acute Myeloid Leukemia by Pyjacker Identifies MNX1 Activation via Deletion 7q	Homo sapiens	hg19	chr7	92384001	92385000	NA	MNX1	Enhancer	Active	Disease	acute myeloid leukemia with del(7q)	NA	NA	blood	UBERON:0000178	AML-661 PDX	NA	AML leukemic cells	NA	Chromatin interaction assay; Chromatin accessibility assay; Histone modification profiling	ATAC-seq; ACT-seq (H3K27ac; H3K4me1); 4C-seq; RNA-seq	3C
E_04192	2019	31767869	LncRNA REG1CP promotes tumorigenesis through an enhancer complex to recruit FANCJ helicase for REG3A transcription	Homo sapiens	hg38	chr2	79165929	79165948	NA	REG3A	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	HT-29/LIM1215 mechanistic validation	NA	malignant cell	CL:0001064	clinical-expression association; lncRNA enhancer-complex mechanism; functional perturbation	lncRNA expression microarray; TCGA/R2 transcriptomic analyses	qRT-PCR; ddPCR; in situ hybridization; REG1CP knockdown/rescue; FANCJ interaction/recruitment assays; xenograft
E_04193	2017	28378740	A CD47-associated super-enhancer links pro-inflammatory signalling to CD47 upregulation in breast cancer	Homo sapiens	hg19	chr3	107705500	107706800	NFKB1	CD47	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Jurkat	CVCL_0065	T lymphoblast	NA	Enhancer activity assay	ChIP-seq	Luciferase reporter assay
E_04194	2026	41827844	MGMT Promoter and Enhancer Methylation in Melanoma Brain Metastases and Glioblastoma: Shared and Distinct Features	Homo sapiens	hg38	chr10	128568604	128569741	NA	MGMT	Enhancer	Active	Disease	glioblastoma	MONDO:0018177	NA	brain	UBERON:0000955	Primary tumor tissue	NA	glioblastoma cell	CL:0001063	Enhancer activity assay	DNA methylation profiling	Transgenic reporter assay
E_04195	2026	41827844	MGMT Promoter and Enhancer Methylation in Melanoma Brain Metastases and Glioblastoma: Shared and Distinct Features	Homo sapiens	hg38	chr10	129033193	129034911	NA	MGMT	Enhancer	Active	Disease	glioblastoma	MONDO:0018177	NA	brain	UBERON:0000955	Primary tumor tissue	NA	glioblastoma cell	CL:0001063	Enhancer activity assay	DNA methylation profiling	Transgenic reporter assay
E_04196	2003	12837695	A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly	Homo sapiens	hg19	chr7	156583402	156585773	NA	SHH	Enhancer	Active	Disease	preaxial polydactyly II	MONDO:0008270	NA	limb bud	NA	developing limb bud	NA	limb bud mesenchymal cell	NA	Long-range developmental enhancer discovery; human disease-variant analysis; in vivo enhancer validation	Comparative genomics / sequence conservation analysis	Transgenic enhancer reporter; mutation segregation; ectopic SHH expression analysis; cross-species functional assays
E_04197	2003	12837695	A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly	Homo sapiens	hg19	chr7	156583796	156584568	NA	SHH	Enhancer	Active	Disease	preaxial polydactyly	NA	NA	limb	UBERON:0002101	affected families and vertebrate limb reporter models	NA	limb mesenchymal cell	NA	Human pathogenic regulatory-variant mapping; long-range developmental enhancer validation	Genetic linkage and mutation mapping	Transgenic enhancer reporter; comparative sequence analysis; developmental expression analysis
E_04198	2003	12837695	A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly	Homo sapiens	hg19	chr7	156583796	156584568	NA	SHH	Enhancer	Active	Disease	preaxial polydactyly	NA	NA	limb	UBERON:0002101	affected families	NA	limb mesenchymal cell	NA	Human pathogenic regulatory-variant mapping; long-range developmental enhancer validation	Genetic linkage/mutation mapping; comparative genomics	Transgenic enhancer reporter; developmental expression analysis
E_04199	2003	12837695	A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly	Homo sapiens	hg19	chr7	156583796	156584568	NA	SHH	Enhancer	Active	Disease	preaxial polydactyly	NA	NA	limb	UBERON:0002101	vertebrate limb transgenic models	NA	limb mesenchymal cell	NA	Human pathogenic regulatory-variant mapping; long-range developmental enhancer validation	Genetic linkage/mutation mapping; comparative genomics	Transgenic enhancer reporter; developmental expression analysis
E_04200	2003	12837695	A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly	Homo sapiens	hg19	chr7	156583402	156585773	NA	SHH	Enhancer	Active	Disease	preaxial polydactyly	NA	NA	limb bud	NA	transgenic mouse embryo	NA	limb bud mesenchymal cell	NA	In vivo enhancer activity assay; Regulatory variant functional assay	Comparative genomics; phylogenetic conservation analysis	Transgenic reporter assay; patient/mouse mutation mapping; mutation functional testing
E_04201	2023	36949154	Translocation t(6;7) in AML-M4 cell line GDM-1 results in MNX1 activation through enhancer-hijacking	Homo sapiens	hg19	chr6	135644579	135645062	NA	MNX1	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	DND-41	CVCL_2022	T lymphoblast	NA	Enhancer activity assay; Chromatin interaction assay	ChIP-seq; ATAC-seq; RNA-seq	Luciferase reporter assay; 4C-seq
E_04202	2017	29116202	Acetylated histone variant H2A.Z is involved in the activation of neo-enhancers in prostate cancer	Homo sapiens	hg19	chr2	11679389	11680097	AR	GREB1	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Disease-variant functional analysis	ChIP-seq; RNA-seq; NOMe-seq	ChIP-qPCR; RT-qPCR; Western blot
E_04203	2017	29116202	Acetylated histone variant H2A.Z is involved in the activation of neo-enhancers in prostate cancer	Homo sapiens	hg19	chr2	234861935	234862442	AR	TRPM8	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay; TF binding assay; Disease-variant functional analysis	ChIP-seq; RNA-seq; NOMe-seq	ChIP-qPCR; RT-qPCR; Western blot
E_04204	2019	31826955	FOXA1 upregulation promotes enhancer and transcriptional reprogramming in endocrine-resistant breast cancer	Homo sapiens	hg19	chr2	46523219	46568173	FOXA1	EPAS1	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	MCF7L-TamR	NA	malignant cell	CL:0001064	Enhancer activity assay; Functional perturbation assay	ChIP-seq; RNA-seq	CRISPR knockout; ChIP-qPCR; RT-qPCR; Western blot
E_04205	1990	2116990	Tandem AP-1-binding sites within the human beta-globin dominant control region function as an inducible enhancer in erythroid cells	Homo sapiens	hg19	chr11	5301983	5302001	FOS	HBG1	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	erythroid lineage cell	CL:0000764	Enhancer activity assay; TF-DNA binding assay; cis-regulatory mutational mapping	NA	Hemin induction; transient transfection by electroporation; Luciferase reporter assay; CAT internal-control assay; enhancer deletion/truncation mapping; synthetic oligonucleotide enhancer assay; enhancer scrambling/mutational analysis; DNase I footprinting; EMSA; competition EMSA; in vitro c-Jun/c-Fos DNA-binding assay; primer extension
E_04206	1990	2116990	Tandem AP-1-binding sites within the human beta-globin dominant control region function as an inducible enhancer in erythroid cells	Homo sapiens	hg19	chr11	5301983	5302001	JUN	HBG1	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	erythroid lineage cell	CL:0000764	Enhancer activity assay; TF-DNA binding assay; cis-regulatory mutational mapping	NA	Hemin induction; transient transfection by electroporation; Luciferase reporter assay; CAT internal-control assay; enhancer deletion/truncation mapping; synthetic oligonucleotide enhancer assay; enhancer scrambling/mutational analysis; DNase I footprinting; EMSA; competition EMSA; in vitro c-Jun/c-Fos DNA-binding assay; primer extension
E_04207	2012	23118011	Mice lacking a Myc enhancer that includes human SNP rs6983267 are resistant to intestinal tumors	Mus musculus	mm10	chr15	61449862	61451562	Tcf7l2	Myc	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	intestine	UBERON:0000160	ApcMin/+	NA	intestinal epithelial cell	CL:0002563	Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation; Endogenous enhancer deletion; in vivo tumor-susceptibility assay	GWAS	Homologous-recombination germline enhancer deletion; RT-qPCR; Tcf7l2 binding analysis; intestinal histology; ApcMin tumor-burden assay; Mouse genetic deletion/knock-in; In vivo phenotyping
E_04208	2012	23118011	Mice lacking a Myc enhancer that includes human SNP rs6983267 are resistant to intestinal tumors	Mus musculus	mm10	chr15	61449862	61451562	Tcf7l2	Myc	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	intestine	UBERON:0000160	Myc-335-null mouse intestinal epithelium	NA	intestinal epithelial cell	CL:0002563	Disease-variant functional analysis; Endogenous enhancer perturbation; In vivo functional validation; Endogenous enhancer deletion; in vivo tumor-susceptibility assay	GWAS	Homologous-recombination germline enhancer deletion; RT-qPCR; Tcf7l2 binding analysis; intestinal histology; ApcMin tumor-burden assay; Mouse genetic deletion/knock-in; In vivo phenotyping
E_04209	2014	24703906	A remote GATA2 hematopoietic enhancer drives leukemogenesis in inv(3)(q21;q26) by activating EVI1 expression	Homo sapiens	hg19	chr3	128124000	128125500	GATA2	MECOM	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	bone marrow	UBERON:0002371	AML blasts	NA	malignant cell	CL:0001064	Functional perturbation assay	ChIP-seq	RT-qPCR
E_04210	2014	24703906	A remote GATA2 hematopoietic enhancer drives leukemogenesis in inv(3)(q21;q26) by activating EVI1 expression	Homo sapiens	hg38	chr3	128603821	128604120	NA	MECOM	Enhancer	Active	Disease	acute myeloid leukemia with inv(3)(q21.3q26.2)/t(3;3)(q21.3;q26.2)	NA	NA	bone marrow	UBERON:0002371	inv(3) AML and G2DHE BAC-transgenic hematopoietic models	NA	hematopoietic stem/progenitor cell	NA	Genetic enhancer-hijacking validation	NA	BAC transgenesis; enhancer deletion; leukemia phenotyping; RT-qPCR
E_04211	2025	39695228	Nucleosome fibre topology guides transcription factor binding to enhancers	Mus musculus	mm9	chr6	122652222	122653558	Klf4	Nanog	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Primary MEFs from 129 and 129/C57BL/6 E12.5-E13.5 embryos	NA	fibroblast	CL:0000057	Enhancer activity assay; TF binding assay; Chromatin accessibility assay; Nucleosome positioning assay; Chromatin topology assay; Cellular reprogramming assay	ChIP-seq; ATAC-seq; RNA-seq; MNase-seq; Micro-C	PiggyBac dual fluorescent enhancer reporter assay; Flow cytometry; Fluorescence imaging; EMSA
E_04212	2025	39695228	Nucleosome fibre topology guides transcription factor binding to enhancers	Mus musculus	mm9	chr6	122652222	122653558	Pou5f1	Nanog	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Primary MEFs from 129 and 129/C57BL/6 E12.5-E13.5 embryos	NA	fibroblast	CL:0000057	Enhancer activity assay; TF binding assay; Chromatin accessibility assay; Nucleosome positioning assay; Chromatin topology assay; Cellular reprogramming assay	ChIP-seq; ATAC-seq; RNA-seq; MNase-seq; Micro-C	PiggyBac dual fluorescent enhancer reporter assay; Flow cytometry; Fluorescence imaging; EMSA
E_04213	2025	39695228	Nucleosome fibre topology guides transcription factor binding to enhancers	Mus musculus	mm9	chr6	122652222	122653558	Sox2	Nanog	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Primary MEFs from 129 and 129/C57BL/6 E12.5-E13.5 embryos	NA	fibroblast	CL:0000057	Enhancer activity assay; TF binding assay; Chromatin accessibility assay; Nucleosome positioning assay; Chromatin topology assay; Cellular reprogramming assay	ChIP-seq; ATAC-seq; RNA-seq; MNase-seq; Micro-C	PiggyBac dual fluorescent enhancer reporter assay; Flow cytometry; Fluorescence imaging; EMSA
E_04214	2025	39695228	Nucleosome fibre topology guides transcription factor binding to enhancers	Mus musculus	mm9	chr6	122652222	122653558	Klf4	Nanog	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	TF binding assay; Chromatin accessibility assay; Enhancer reporter assay; Nucleosome positioning assay; Chromatin topology assay	ChIP-seq; ATAC-seq; RNA-seq; MNase-seq; Micro-C	PiggyBac dual fluorescent enhancer reporter assay; Flow cytometry; Fluorescence imaging; Blastocyst chimera assay
E_04215	2025	39695228	Nucleosome fibre topology guides transcription factor binding to enhancers	Mus musculus	mm9	chr6	122652222	122653558	Pou5f1	Nanog	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	TF binding assay; Chromatin accessibility assay; Enhancer reporter assay; Nucleosome positioning assay; Chromatin topology assay	ChIP-seq; ATAC-seq; RNA-seq; MNase-seq; Micro-C	PiggyBac dual fluorescent enhancer reporter assay; Flow cytometry; Fluorescence imaging; Blastocyst chimera assay
E_04216	2025	39695228	Nucleosome fibre topology guides transcription factor binding to enhancers	Mus musculus	mm9	chr6	122652222	122653558	Sox2	Nanog	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	TF binding assay; Chromatin accessibility assay; Enhancer reporter assay; Nucleosome positioning assay; Chromatin topology assay	ChIP-seq; ATAC-seq; RNA-seq; MNase-seq; Micro-C	PiggyBac dual fluorescent enhancer reporter assay; Flow cytometry; Fluorescence imaging; Blastocyst chimera assay
E_04217	2018	29301908	Deletion of a Long-Range Dlx5 Enhancer Disrupts Inner Ear Development in Mice	Mus musculus	mm10	chr6	6058554	6059028	NA	Dlx5	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Embryonic whole mount	NA	embryonic cell	NA	Enhancer activity assay	NA	qRT-PCR, and ChIP-qPCR; CRISPR-Cas9
E_04218	2018	29301908	Deletion of a Long-Range Dlx5 Enhancer Disrupts Inner Ear Development in Mice	Mus musculus	mm10	chr6	6163229	6163674	NA	Dlx5	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Embryonic whole mount	NA	mouse embryo	NA	Enhancer activity assay	NA	qRT-PCR, and ChIP-qPCR; CRISPR-Cas9
E_04219	2016	26382291	Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development	Homo sapiens	hg19	chr6	1614904	1616335	NA	FOXC1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	E11.5 transgenic mouse embryo	NA	NA	NA	Enhancer activity assay; Motif perturbation assay	Computational enhancer prediction; public epigenomic data integration	Transient transgenic mouse Hsp68-lacZ reporter assay; X-gal staining; ZIC-motif deletion reporter assay
E_04220	2016	26382291	Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development	Homo sapiens	hg19	chr6	1614904	1616335	NA	GMDS	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	E11.5 transgenic mouse embryo	NA	NA	NA	Enhancer activity assay; Motif perturbation assay	Computational enhancer prediction; public epigenomic data integration	Transient transgenic mouse Hsp68-lacZ reporter assay; X-gal staining; ZIC-motif deletion reporter assay
E_04221	2016	26382291	Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development	Homo sapiens	hg19	chr6	1616341	1617336	NA	FOXC1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	E11.5 transgenic mouse embryo	NA	NA	NA	Enhancer activity assay; Motif perturbation assay	Computational enhancer prediction; public epigenomic data integration	Transient transgenic mouse Hsp68-lacZ reporter assay; X-gal staining; ZIC-motif deletion reporter assay
E_04222	2016	26382291	Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development	Homo sapiens	hg19	chr6	1616341	1617336	NA	GMDS	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	E11.5 transgenic mouse embryo	NA	NA	NA	Enhancer activity assay; Motif perturbation assay	Computational enhancer prediction; public epigenomic data integration	Transient transgenic mouse Hsp68-lacZ reporter assay; X-gal staining; ZIC-motif deletion reporter assay
E_04223	2016	26382291	Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development	Homo sapiens	hg19	chr6	1619847	1620844	NA	FOXC1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	E11.5 transgenic mouse embryo	NA	NA	NA	Enhancer activity assay; Motif perturbation assay	Computational enhancer prediction; public epigenomic data integration	Transient transgenic mouse Hsp68-lacZ reporter assay; X-gal staining; ZIC-motif deletion reporter assay
E_04224	2016	26382291	Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development	Homo sapiens	hg19	chr6	1619847	1620844	NA	GMDS	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	E11.5 transgenic mouse embryo	NA	NA	NA	Enhancer activity assay; Motif perturbation assay	Computational enhancer prediction; public epigenomic data integration	Transient transgenic mouse Hsp68-lacZ reporter assay; X-gal staining; ZIC-motif deletion reporter assay
E_04225	2016	26382291	Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development	Homo sapiens	hg19	chr6	1702408	1703763	NA	FOXC1	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	E11.5 transgenic mouse embryo	NA	NA	NA	Enhancer activity assay	Computational enhancer prediction; public epigenomic data integration	Transient transgenic mouse Hsp68-lacZ reporter assay; X-gal staining
E_04226	2016	26382291	Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development	Homo sapiens	hg19	chr6	1702408	1703763	NA	GMDS	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	E11.5 transgenic mouse embryo	NA	NA	NA	Enhancer activity assay	Computational enhancer prediction; public epigenomic data integration	Transient transgenic mouse Hsp68-lacZ reporter assay; X-gal staining
E_04227	2023	37542287	FACT regulates pluripotency through proximal and distal regulation of gene expression in murine embryonic stem cells	Mus musculus	mm10	chr3	34756748	34761748	NA	Sox2	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	murine embryonic stem cells (mESCs)	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; TF binding assay; Chromatin interaction assay	CUT&RUN	Luciferase reporter assay; ChIP-qPCR, qRT-PCR
E_04228	2023	37542287	FACT regulates pluripotency through proximal and distal regulation of gene expression in murine embryonic stem cells	Mus musculus	mm10	chr6	122612768	122617768	NA	Nanog	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	murine embryonic stem cells (mESCs)	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; TF binding assay; Chromatin interaction assay	CUT&RUN	Luciferase reporter assay; ChIP-qPCR, qRT-PCR
E_04229	2023	37542287	FACT regulates pluripotency through proximal and distal regulation of gene expression in murine embryonic stem cells	Mus musculus	mm10	chr6	122652768	122657768	NA	Nanog	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	murine embryonic stem cells (mESCs)	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; TF binding assay; Chromatin interaction assay	CUT&RUN	Luciferase reporter assay; ChIP-qPCR, qRT-PCR
E_04230	2023	37542287	FACT regulates pluripotency through proximal and distal regulation of gene expression in murine embryonic stem cells	Mus musculus	mm10	chr6	122717768	122722768	NA	Nanog	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	murine embryonic stem cells (mESCs)	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; TF binding assay; Chromatin interaction assay	CUT&RUN	Luciferase reporter assay; ChIP-qPCR, qRT-PCR
E_04231	2014	24920384	Functional analysis of limb transcriptional enhancers in the mouse	Mus musculus	mm9	chr1	165827290	165830012	NA	NA	Enhancer	Active	Normal	NA	NA	NA	limb bud	NA	E11.5 embryonic limb bud	NA	mesenchymal cell	CL:0008019	Enhancer activity assay; Endogenous enhancer perturbation; In vivo functional validation; In vivo enhancer deletion assay; Developmental enhancer assay; Candidate target expression analysis	NA	Transgenic LacZ reporter assay; X-gal staining; Salmon-gal staining; homologous recombination in embryonic stem cells; enhancer knockout mouse generation; Southern blot; PCR genotyping; qRT-PCR; whole-mount in situ hybridization; histological analysis; Mouse genetic deletion/knock-in
E_04232	2014	24920384	Functional analysis of limb transcriptional enhancers in the mouse	Mus musculus	mm9	chr1	165827290	165830012	NA	NA	Enhancer	Active	Normal	NA	NA	NA	limb bud	NA	E11.5 mouse limb bud	NA	mesenchymal cell	CL:0008019	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation; In vivo functional validation	NA	Transgenic lacZ Reporter Assay; Homologous recombination-mediated enhancer deletion; qRT-PCR; Whole-mount in situ hybridization; Skeletal analysis; Mouse genetic deletion/knock-in
E_04233	2014	24920384	Functional analysis of limb transcriptional enhancers in the mouse	Mus musculus	mm9	chr4	117063735	117065404	NA	NA	Enhancer	Active	Normal	NA	NA	NA	limb bud	NA	E11.5 embryonic limb bud	NA	mesenchymal cell	CL:0008019	Enhancer activity assay; Endogenous enhancer perturbation; In vivo functional validation; In vivo enhancer deletion assay; Developmental enhancer assay; Candidate target expression analysis	NA	Transgenic LacZ reporter assay; X-gal staining; Salmon-gal staining; homologous recombination in embryonic stem cells; enhancer knockout mouse generation; Southern blot; PCR genotyping; qRT-PCR; whole-mount in situ hybridization; histological analysis; Mouse genetic deletion/knock-in
E_04234	2014	24920384	Functional analysis of limb transcriptional enhancers in the mouse	Mus musculus	mm9	chr4	117063735	117065404	NA	NA	Enhancer	Active	Normal	NA	NA	NA	limb bud	NA	E11.5 mouse limb bud	NA	mesenchymal cell	CL:0008019	Enhancer activity assay; Functional perturbation assay; Endogenous enhancer perturbation; In vivo functional validation	NA	Transgenic lacZ Reporter Assay; Homologous recombination-mediated enhancer deletion; qRT-PCR; Whole-mount in situ hybridization; Skeletal analysis; Mouse genetic deletion/knock-in
E_04235	2002	12399963	Disruption of the RanBP17/Hox11L2 region by recombination with the TCRdelta locus in acute lymphoblastic leukemias with t(5;14)(q34;q11)	Homo sapiens	hg19	chr14	22420000	22422000	NA	TLX3	Enhancer	Active	Disease	B-cell acute lymphoblastic leukemia	MONDO:0004947	DOID:0080638	blood	UBERON:0000178	Leukemic B Lymphoblasts	NA	B-lymphoblast	CL:0017006	Enhancer activity assay; Functional perturbation assay; Chromatin interaction assay	NA	Southern Blot, PCR, Sequencing, FISH
E_04236	2017	28790107	RUNX1 is required for oncogenic Myb and Myc enhancer activity in T-cell acute lymphoblastic leukemia	Homo sapiens	hg19	chr8	130180217	130180629	RUNX1	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	human and mouse T-ALL models	NA	T-lineage leukemia cell	NA	TF requirement for oncogenic enhancer activity and accessibility	ChIP-seq; ATAC-based chromatin profiling; RNA expression profiling	RUNX1 deletion/perturbation; ChIP-qPCR; ATAC-qPCR; enhancer functional assays; leukemia growth assays
E_04237	2017	28790107	RUNX1 is required for oncogenic Myb and Myc enhancer activity in T-cell acute lymphoblastic leukemia	Homo sapiens	hg19	chr8	130180217	130180629	RUNX1	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	human and mouse T-ALL models	NA	T-lineage leukemia cell	NA	TF requirement for oncogenic enhancer activity and accessibility	ChIP-seq; ATAC-based chromatin profiling; RNA expression profiling	RUNX1 deletion/perturbation; ChIP-qPCR; ATAC-qPCR; enhancer functional assays; leukemia growth assays
E_04238	2017	28790107	RUNX1 is required for oncogenic Myb and Myc enhancer activity in T-cell acute lymphoblastic leukemia	Homo sapiens	hg19	chr8	130180065	130180972	RUNX1	MYC	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	T-ALL cell lines and primary T-ALL	NA	T lymphoblast	NA	TF dependency of oncogenic enhancer activity	ChIP-seq; RNA-seq	RUNX1 perturbation; enhancer reporter assay; leukemia growth assay
E_04239	2016	27768887	Progressive Loss of Function in a Limb Enhancer during Snake Evolution	Homo sapiens	hg38	chr7	156791087	156791875	ETS1	SHH	Enhancer	Active	Normal	NA	NA	NA	limb bud	NA	E11.5 transgenic and targeted-replacement mouse embryos carrying the human ZRS ortholog	NA	posterior limb-bud mesenchyme (zone of polarizing activity)	NA	In vivo enhancer sufficiency assay; ortholog replacement assay; TF-motif functional rescue; developmental phenotype assay	Comparative genomics; multi-species sequence alignment; evolutionary-rate analysis	Transgenic lacZ reporter assay; CRISPR/Cas9-mediated targeted genomic replacement; human/fish/snake ZRS ortholog replacement; synthetic 17-bp ETS-site restoration; skeletal preparation and limb phenotyping
E_04240	2011	21368045	The gonadotropin-releasing hormone cell-specific element is required for normal puberty and estrous cyclicity	Mus musculus	mm10	chr14	67742375	67743103	Gata4	Gnrh1	Enhancer	Repressed	Normal	NA	NA	NA	gonad	NA	Epithelial Cell,Granulosa Cells,GT1-7,GN11,Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation	NA	Luciferase reporter assay; Reporter assay
E_04241	2011	21368045	The gonadotropin-releasing hormone cell-specific element is required for normal puberty and estrous cyclicity	Mus musculus	mm10	chr14	67742375	67743103	Pou2f1	Gnrh1	Enhancer	Repressed	Normal	NA	NA	NA	gonad	NA	Epithelial Cell,Granulosa Cells,GT1-7,GN11,Embryonic Stem Cell	NA	NA	NA	Enhancer activity assay; In vivo functional validation	NA	Luciferase reporter assay; Reporter assay
E_04242	2022	36097291	Cohesin is required for long-range enhancer action at the Shh locus	Mus musculus	mm10	chr5	29314497	29315862	NA	Shh	Enhancer	Active	Normal	NA	NA	NA	limb bud	NA	ES-E14	CVCL_C320	embryonic stem cell	CL:0002322	Synthetic enhancer activation assay; Cohesin/CTCF functional perturbation assay; Chromatin conformation analysis	Hi-C data reanalysis; virtual 4C	TALE-VP64 synthetic enhancer activation; auxin-inducible SCC1/RAD21 degradation; auxin-inducible CTCF degradation; RNA FISH; DNA FISH; Immunofluorescence; Flow cytometry
E_04243	2009	19680443	Functional enhancers at the gene-poor 8q24 cancer-linked locus	Homo sapiens	hg19	chr8	128588859	128589357	AR	MYC	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Disease-variant functional analysis	ChIP-chip; GWAS	Luciferase reporter assay; ChIP-qPCR; Reporter assay
E_04244	2009	19680443	Functional enhancers at the gene-poor 8q24 cancer-linked locus	Homo sapiens	hg38	chr8	128600697	128601159	AR	MYC	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	uterine cervix	UBERON:0000002	HeLa	CVCL_0030	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Disease-variant functional analysis	ChIP-chip; GWAS	Luciferase reporter assay; ChIP-qPCR, EMSA; Reporter assay
E_04245	2009	19680443	Functional enhancers at the gene-poor 8q24 cancer-linked locus	Homo sapiens	hg38	chr8	128600697	128601159	FOXA1	MYC	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	uterine cervix	UBERON:0000002	HeLa	CVCL_0030	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Disease-variant functional analysis	ChIP-chip; GWAS	Luciferase reporter assay; ChIP-qPCR, EMSA; Reporter assay
E_04246	2009	19680443	Functional enhancers at the gene-poor 8q24 cancer-linked locus	Homo sapiens	hg18	chr8	128588859	128589357	AR	NA	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	left supraclavicular lymph node	UBERON:8480056	LNCaP	CVCL_0395	epithelial cell	CL:0000066	Enhancer activity assay; TF binding assay; Disease-variant functional analysis; Androgen-responsive enhancer assay	Custom 8q24 tiling array; AR ChIP-chip; GWAS	DHT stimulation; AR ChIP-qPCR; TK-luciferase reporter assay; resequencing; Reporter assay
E_04247	2009	19680443	Functional enhancers at the gene-poor 8q24 cancer-linked locus	Homo sapiens	hg18	chr8	128588859	128589357	AR	NA	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Disease-variant functional analysis; Epigenomic profiling	ChIP-chip (custom 8q24 tiling array); cDNA tiling array; GWAS	Luciferase reporter assay; AR ChIP-qPCR; Reporter assay
E_04248	2009	19680443	Functional enhancers at the gene-poor 8q24 cancer-linked locus	Homo sapiens	hg18	chr8	128600697	128601159	AR	NA	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	left supraclavicular lymph node	UBERON:8480056	LNCaP	CVCL_0395	epithelial cell	CL:0000066	Enhancer activity assay; TF binding assay; Disease-variant functional analysis; Androgen-responsive enhancer assay; Risk-variant functional assay	Custom 8q24 tiling array; AR ChIP-chip; GWAS	DHT stimulation; AR ChIP-qPCR; TK-luciferase reporter assay; Allele-specific reporter assay; resequencing; Reporter assay
E_04249	2009	19680443	Functional enhancers at the gene-poor 8q24 cancer-linked locus	Homo sapiens	hg18	chr8	128600697	128601159	FOXA1	NA	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	left supraclavicular lymph node	UBERON:8480056	LNCaP	CVCL_0395	epithelial cell	CL:0000066	Enhancer activity assay; TF binding assay; Disease-variant functional analysis; Risk-variant functional assay	Custom 8q24 tiling array; ChIP-chip; GWAS	DHT stimulation; TK-luciferase reporter assay; Allele-specific reporter assay; FOXA1 ChIP-qPCR; EMSA; competition EMSA; rs11986220 allelic-binding assay; resequencing; Reporter assay
E_04250	2022	35202564	Duplications disrupt chromatin architecture and rewire GPR101-enhancer communication in X-linked acrogigantism	Homo sapiens	hg19	chrX	135959959	135963959	NA	GPR101	Enhancer	Active	Disease	X-linked acrogigantism	MONDO:0010491	NA	pituitary gland	UBERON:0000007	GH3	CVCL_0273	malignant cell	CL:0001064	Enhancer activity assay; Chromatin interaction assay	4C-seq; H3K27ac regulatory annotation; Hi-C; 4C	Luciferase reporter assay
E_04251	2022	36284357	CRISPR-Cas9-mediated functional dissection of the foxc1 genomic region in zebrafish identifies critical conserved cis-regulatory elements	Danio rerio	danRer11	chr2	535659	535798	NA	foxc1a	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	embryonic cell	NA	embryonic cell	NA	Functional perturbation assay	NA	CRISPR knockout; qRT-PCR; Whole-mount in situ hybridization; CRISPR-Cas9
E_04252	2022	36284357	CRISPR-Cas9-mediated functional dissection of the foxc1 genomic region in zebrafish identifies critical conserved cis-regulatory elements	Danio rerio	danRer11	chr2	577491	577557	NA	foxc1a	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	embryonic cell	NA	embryonic cell	NA	Functional perturbation assay	NA	CRISPR knockout; qRT-PCR; Whole-mount in situ hybridization; CRISPR-Cas9
E_04253	2022	36284357	CRISPR-Cas9-mediated functional dissection of the foxc1 genomic region in zebrafish identifies critical conserved cis-regulatory elements	Danio rerio	danRer11	chr2	684320	684414	NA	foxc1a	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	embryonic cell	NA	embryonic cell	NA	Functional perturbation assay	NA	CRISPR knockout; qRT-PCR; Whole-mount in situ hybridization; CRISPR-Cas9
E_04254	2022	36284357	CRISPR-Cas9-mediated functional dissection of the foxc1 genomic region in zebrafish identifies critical conserved cis-regulatory elements	Danio rerio	danRer11	chr2	716946	717020	NA	foxq1a	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Whole zebrafish embryos	NA	NA	NA	Functional perturbation assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Gene expression analysis	NA	CRISPR-Cas9 genomic deletion; qRT-PCR; gross phenotypic analysis; CRISPR-Cas9 endogenous deletion/editing
E_04255	2022	36284357	CRISPR-Cas9-mediated functional dissection of the foxc1 genomic region in zebrafish identifies critical conserved cis-regulatory elements	Danio rerio	danRer11	chr2	716946	717020	NA	foxf2a	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	embryonic cell	NA	embryonic cell	NA	Functional perturbation assay	NA	CRISPR knockout; qRT-PCR; CRISPR-Cas9
E_04256	2022	36284357	CRISPR-Cas9-mediated functional dissection of the foxc1 genomic region in zebrafish identifies critical conserved cis-regulatory elements	Danio rerio	danRer11	chr20	26689284	26689441	NA	foxq1b	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Whole zebrafish embryos	NA	NA	NA	Functional perturbation assay; Disease-variant functional analysis; Endogenous enhancer perturbation; Gene expression analysis	NA	CRISPR-Cas9 genomic deletion; qRT-PCR; gross phenotypic analysis; CRISPR-Cas9 endogenous deletion/editing
E_04257	2022	36284357	CRISPR-Cas9-mediated functional dissection of the foxc1 genomic region in zebrafish identifies critical conserved cis-regulatory elements	Danio rerio	danRer11	chr20	26689284	26689441	NA	foxf2b	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	embryonic cell	NA	embryonic cell	NA	Functional perturbation assay	NA	CRISPR knockout; qRT-PCR; CRISPR-Cas9
E_04258	2012	21822303	Sox2 expression in breast tumours and activation in breast cancer stem cells	Homo sapiens	hg19	chr3	181433217	181434197	SOX2	SOX2	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	breast tumor mammosphere-forming cells	NA	breast cancer stem-like cell	NA	Enhancer activity assay; Functional perturbation assay	NA	SRR2 reporter assay; mammosphere assay; SOX2 knockdown; SOX2 overexpression; xenograft tumor-initiation assay
E_04259	2012	21822303	Sox2 expression in breast tumours and activation in breast cancer stem cells	Homo sapiens	hg19	chr3	181425707	181426096	NA	SOX2	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay	NA	Luciferase reporter assay
E_04260	2026	41759529	CRISPR-based functional genomics for dissecting therapeutic dependency in primary acute myeloid leukemia samples	Homo sapiens	hg38	chr6	135194929	135196024	NA	MYB	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	bone marrow	UBERON:0002371	PDX#2263	NA	malignant cell	CL:0001064	Enhancer essentiality screen; Functional cis-regulatory-element perturbation assay	Pooled CRISPRi dropout screen; in vivo CRISPR screen; ATAC-seq; single-cell ATAC/RNA profiling; Perturb-seq	Targeted MYB cis-regulatory-element CRISPRi; RT-qPCR; proliferation assay; Flow cytometry; in vivo competition validation
E_04261	2024	38224404	dCas9/CRISPR-based methylation of O-6-methylguanine-DNA methyltransferase enhances chemosensitivity to temozolomide in malignant glioma	Homo sapiens	hg19	chr10	131265950	131266000	NA	MGMT	Enhancer	Active	Disease	glioblastoma	MONDO:0018177	NA	brain	UBERON:0000955	KYSE-410	CVCL_1352	glioblastoma cell	CL:0001063	Enhancer activity assay; Functional perturbation assay	RNA-seq	CRISPR knockout; CRISPRi, qRT-PCR; Western blot
E_04262	2010	20453196	8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC	Homo sapiens	hg19	chr8	128173203	128174158	NA	MYC	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin interaction assay	NA	ChIP-qPCR, 3C
E_04263	2010	20453196	8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC	Homo sapiens	hg19	chr8	128423748	128424352	NA	MYC	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin interaction assay	NA	ChIP-qPCR, 3C
E_04264	2010	20453196	8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC	Homo sapiens	hg19	chr8	128482486	128483650	NA	MYC	Enhancer	Active	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	LS 174T	CVCL_1384	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin interaction assay	NA	ChIP-qPCR, 3C
E_04265	2010	20453196	8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC	Homo sapiens	hg19	chr8	128589642	128590670	NA	MYC	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin interaction assay	NA	ChIP-qPCR, 3C
E_04266	2010	20453196	8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC	Homo sapiens	hg18	chr8	128482317	128483854	NA	MYC	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Chromatin interaction assay; Enhancer-associated chromatin assay	NA	3C; p300 ChIP-qPCR; H3K4me2 ChIP-qPCR
E_04267	2021	34493733	Transcriptional network involving ERG and AR orchestrates Distal-less homeobox-1 mediated prostate cancer progression	Homo sapiens	hg19	chr2	172661000	172662500	AR	DLX1	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	VCaP	CVCL_2235	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin interaction assay	ChIP-seq; RNA-seq, ChIA-PET	ChIP-qPCR, qRT-PCR; Western blot, Re-ChIP
E_04268	2007	17671233	C/EBPalpha binds and activates the PU.1 distal enhancer to induce monocyte lineage commitment	Homo sapiens	hg38	chr11	47394824	47395023	CEBPA	SPI1	Enhancer	Active	Disease	acute myeloid leukemia-associated myeloid differentiation	NA	NA	bone marrow	UBERON:0002371	myeloid progenitor cells and leukemia-relevant myeloid models	NA	myeloid progenitor cell	NA	Direct TF-enhancer functional validation	NA	EMSA; ChIP; motif mutation; Luciferase reporter assay; differentiation assay
E_04269	2011	21051589	Mechanisms by which interleukin-6 regulates prostate-specific antigen gene expression in prostate LNCaP carcinoma cells	Homo sapiens	hg19	chr19	51353370	51354238	STAT3	KLK3	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Functional signaling perturbation assay	NA	5′ deletion luciferase reporter assay; immunoblot; ELISA; Reporter assay
E_04270	2010	19966852	PU.1 is regulated by NF-kappaB through a novel binding site in a 17 kb upstream enhancer element	Homo sapiens	hg38	chr11	47394824	47395023	RELA	SPI1	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	bone marrow	UBERON:0002371	primary AML samples and human myeloid cells	NA	myeloid leukemia cell	NA	TF-site and disease-variant enhancer validation	NA	Reporter assay; EMSA; ChIP; TF-site mutation; patient enhancer sequencing
E_04271	2014	24707046	Silencing of the EPHB3 tumor-suppressor gene in human colorectal cancer through decommissioning of a transcriptional enhancer	Homo sapiens	hg19	chr3	184276287	184278287	ASCL2	EPHB3	Enhancer	Inactive	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	colorectal tumor specimens	NA	malignant epithelial cell	NA	Enhancer activity assay; TF/chromatin occupancy; chromatin accessibility analysis; pathway-dependent enhancer reactivation; disease-associated enhancer decommissioning	NA	Luciferase reporter assay; ChIP; FAIRE; RT-qPCR; pathway perturbation; tumor-cell phenotyping
E_04272	2016	26795348	Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus	Homo sapiens	hg19	chr2	202204362	202205119	MYC	CASP8	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	T-47D	CVCL_0553	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay	RNA-seq; ChIP-seq	Luciferase reporter assay; RT-qPCR
E_04273	2024	39272130	Chromatin conformation capture in the clinic: 4C-seq/HiC distinguishes pathogenic from neutral duplications at the GPR101 locus	Homo sapiens	hg19	chrX	135632564	135633920	NA	GPR101	Enhancer	Active	Disease	X-linked acrogigantism	MONDO:0010491	NA	blood	UBERON:0000178	X-LAG patient-derived PBMCs	NA	peripheral blood mononuclear cell	CL:2000001	Chromatin interaction assay; Structural variant functional assessment	4C-seq; Hi-C; high-density aCGH; 4C	ddPCR; breakpoint-junction PCR; Sanger sequencing
E_04274	2016	27867070	The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances	Mus musculus	mm9	chr5	29641240	29642424	NA	Shh	Enhancer	Active	Normal	NA	NA	NA	limb bud	NA	E11.5 posterior limb bud/ZPA	NA	limb bud mesenchymal cell	NA	Enhancer activity assay; Chromatin interaction assay; Functional genomic rearrangement assay	4C-seq	LacZ enhancer-sensor/transgenic reporter assay; homologous recombination; Cre-loxP genomic rearrangements; RT-qPCR; whole-mount in situ hybridization; skeletal preparation
E_04275	2014	24707046	Silencing of the EPHB3 tumor-suppressor gene in human colorectal cancer through decommissioning of a transcriptional enhancer	Homo sapiens	hg19	chr3	184276287	184278287	ASCL2	EPHB3	Enhancer	Inactive	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	HT-29	CVCL_0320	malignant cell	CL:0001064	Enhancer activity assay; TF/chromatin occupancy; chromatin accessibility analysis; pathway-dependent enhancer reactivation; disease-associated enhancer decommissioning	NA	Luciferase reporter assay; ChIP; FAIRE; RT-qPCR; pathway perturbation; tumor-cell phenotyping
E_04276	2014	24707046	Silencing of the EPHB3 tumor-suppressor gene in human colorectal cancer through decommissioning of a transcriptional enhancer	Homo sapiens	hg19	chr3	184276287	184278287	ASCL2	EPHB3	Enhancer	Inactive	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	LS174T and other colorectal carcinoma cell lines	NA	malignant epithelial cell	NA	Enhancer activity assay; TF/chromatin occupancy; chromatin accessibility analysis; pathway-dependent enhancer reactivation; disease-associated enhancer decommissioning	NA	Luciferase reporter assay; ChIP; FAIRE; RT-qPCR; pathway perturbation; tumor-cell phenotyping
E_04277	2016	26795348	Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus	Homo sapiens	hg19	chr2	202122500	202124030	NA	CASP8	Enhancer	Active	Disease	breast cancer susceptibility	NA	NA	breast	UBERON:0000310	MCF-10A	CVCL_0598	mammary gland epithelial cell	NA	Enhancer activity assay; Functional variant assay; Genetic association study; eQTL analysis	Targeted discordant-haplotype sequencing; Strand-specific RNA-seq/eQTL analysis; ENCODE regulatory data integration	Dual-luciferase reporter assay; Genotyping; Sanger sequencing; RT-qPCR
E_04278	2016	26795348	Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus	Homo sapiens	hg19	chr2	202122500	202124030	NA	CASP8	Enhancer	Active	Disease	breast cancer susceptibility	NA	NA	breast	UBERON:0000310	T-47D	CVCL_0553	epithelial cell	CL:0000066	Enhancer activity assay; Functional variant assay; Genetic association study; eQTL analysis	Targeted discordant-haplotype sequencing; Strand-specific RNA-seq/eQTL analysis; ENCODE regulatory data integration	Dual-luciferase reporter assay; Genotyping; Sanger sequencing; RT-qPCR
E_04279	2016	27867070	The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances	Mus musculus	mm9	chr14	97485490	97486674	NA	Shh	Enhancer	Active	Normal	NA	NA	NA	limb bud	NA	E11.5 Z2D engineered embryonic limb bud	NA	limb bud mesenchymal cell	NA	Chromatin interaction assay; Heterologous enhancer replacement assay; Functional genomic rearrangement assay	4C-seq	Homologous recombination; LacZ reporter analysis; RT-qPCR; whole-mount in situ hybridization; skeletal preparation
E_04280	2011	21051589	Mechanisms by which interleukin-6 regulates prostate-specific antigen gene expression in prostate LNCaP carcinoma cells	Homo sapiens	hg19	chr19	50850114	50850982	STAT3	KLK3	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay
E_04281	2016	27867070	The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances	Mus musculus	mm9	chr14	97485490	97486674	NA	Shh	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	E14 mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Genome-engineering assay; Heterologous enhancer replacement construct generation	NA	Homologous recombination in E14 ESCs; targeted clone selection; generation of Z2D mice
E_04282	2016	27867070	The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances	Mus musculus	mm9	chr5	29641240	29642424	NA	Shh	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	E14 mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Genome-engineering assay for a known enhancer locus	NA	Homologous recombination in E14 ESCs; targeted clone selection; generation of engineered mouse alleles
E_04283	2020	32541043	Regulation of spatiotemporal limits of developmental gene expression via enhancer grammar	Drosophila melanogaster	dm6	chr2R	5208000	5208523	NA	T48	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	nc14 embryo	NA	embryonic cell	NA	Enhancer activity assay; Functional perturbation assay	RNA-seq	Transgenic reporter assay; RT-qPCR
E_04284	2020	32541043	Regulation of spatiotemporal limits of developmental gene expression via enhancer grammar	Drosophila melanogaster	dm6	chr3R	26880000	26880523	NA	CG5507	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Embryo	NA	embryonic cell	NA	Enhancer activity assay; Functional perturbation assay	NA	Transgenic reporter assay; RT-qPCR
E_04285	2023	38102337	Suppression of super-enhancer-driven TAL1 expression by KLF4 in T-cell acute lymphoblastic leukemia	Homo sapiens	hg19	chr1	47220000	47260000	NA	TAL1	Enhancer	Repressed	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Jurkat	CVCL_0065	T lymphoblast	NA	Enhancer activity assay; Functional perturbation assay	RNA-seq	Luciferase reporter assay, shRNA Knockdown; RT-qPCR; Western blot
E_04286	2023	38102337	Suppression of super-enhancer-driven TAL1 expression by KLF4 in T-cell acute lymphoblastic leukemia	Homo sapiens	hg19	chr1	47220000	47260000	NA	TAL1	Enhancer	Repressed	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	bone marrow	UBERON:0002371	MOLT-3	CVCL_0624	T lymphoblast	NA	Enhancer activity assay; Functional perturbation assay	RNA-seq	Luciferase reporter assay, shRNA Knockdown; RT-qPCR; Western blot
E_04287	2017	28881808	CXCL13 is androgen-responsive and involved in androgen induced prostate cancer cell migration and invasion	Homo sapiens	hg19	chr4	77558000	77558500	AR	CXCL13	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay; Chromatin-state profiling	ChIP-seq	Luciferase reporter assay; ChIP; Reporter assay
E_04288	1998	9878258	A long terminal repeat of the human endogenous retrovirus ERV-9 is located in the 5' boundary area of the human beta-globin locus control region	Homo sapiens	hg19	chr11	5314490	5316194	NA	HBE1	Enhancer	Active	Normal	NA	NA	NA	pleural effusion	UBERON:0000175	K-562	CVCL_0004	erythroid lineage cell	CL:0000764	Enhancer activity assay; LTR promoter/enhancer activity assay; Endogenous transcription assay	NA	DNA cloning and sequencing; restriction mapping; recombinant construct analysis; transient/stable transfection; CAT reporter assay; RT-PCR
E_04289	2016	26374622	Identification and functional analysis of acute myeloid leukemia susceptibility associated single nucleotide polymorphisms at non-protein coding regions of RUNX1	Homo sapiens	hg19	chr21	36180372	36181392	SPI1	RUNX1	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	bone marrow	UBERON:0002371	K-562	CVCL_0004	malignant cell	CL:0001064	Enhancer activity assay; Disease-variant functional analysis	NA	Luciferase reporter assay, EMSA; Luciferase reporter assay
E_04290	2016	26780995	Enhanced Identification of Transcriptional Enhancers Provides Mechanistic Insights into Diseases	Homo sapiens	hg19	chr19	33299481	33300688	EP300	CEP89	Enhancer	Inactive	Disease	colorectal cancer	MONDO:0005575	DOID:9256	breast	UBERON:0000310	Breast Cancer Cell	NA	malignant cell	CL:0001064	TF-binding/chromatin assay; Genetic-variant functional analysis; Disease-associated enhancer analysis	ChIP-seq; ATAC-seq; GWAS/genetic association	ChIP-qPCR/ChIP
E_04291	2022	34571027	An Enhancer-Driven Stem Cell-Like Program Mediated by SOX9 Blocks Intestinal Differentiation in Colorectal Cancer	Homo sapiens	hg19	chr15	56550000	56550573	TCF4	PROM1	Enhancer	Active	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	LS180	CVCL_0397	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay	ChIP-seq; RNA-seq	Luciferase reporter assay; RT-qPCR
E_04292	2010	20208536	Nucleosome dynamics define transcriptional enhancers	Homo sapiens	hg19	chr19	44905642	44906512	AR	KLK3	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	prostate gland	UBERON:0002367	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; TF binding assay	ChIP-seq; RNA-seq	Luciferase reporter assay; ChIP-qPCR
E_04293	2014	24667606	Targeted repression of AXIN2 and MYC gene expression using designer TALEs	Homo sapiens	hg19	chr17	60983452	60984775	NA	AXIN2	Enhancer	Repressed	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	HEK293FT,FLP-IN T-REX 293 CELLS	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_04294	2014	24667606	Targeted repression of AXIN2 and MYC gene expression using designer TALEs	Homo sapiens	hg19	chr17	60986269	60989232	NA	AXIN2	Enhancer	Repressed	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	HEK293FT,FLP-IN T-REX 293 CELLS	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_04295	2014	24667606	Targeted repression of AXIN2 and MYC gene expression using designer TALEs	Homo sapiens	hg19	chr8	128816178	128817335	NA	MYC	Enhancer	Repressed	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	HEK293FT,FLP-IN T-REX 293 CELLS	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_04296	2013	24086551	Identification of an enhancer that increases miR-200b~200a~429 gene expression in breast cancer cells	Homo sapiens	hg19	chr1	1092486	1093650	NA	MIR200B	Enhancer	Active	Normal	NA	NA	NA	breast	UBERON:0000310	HMLE	NA	mammary epithelial cell	NA	Enhancer activity assay; Chromatin state assay; eRNA analysis	ChIP-seq; DNA methylation profiling	Dual-luciferase reporter assay; ChIP-qPCR; DNA methylation analysis; qRT-PCR; RACE; Luciferase reporter assay; Reporter assay
E_04297	2013	24086551	Identification of an enhancer that increases miR-200b~200a~429 gene expression in breast cancer cells	Homo sapiens	hg19	chr1	1092486	1093650	NA	MIR200A	Enhancer	Active	Normal	NA	NA	NA	breast	UBERON:0000310	HMLE	NA	mammary epithelial cell	NA	Enhancer activity assay; Chromatin state assay; eRNA analysis	ChIP-seq; DNA methylation profiling	Dual-luciferase reporter assay; ChIP-qPCR; DNA methylation analysis; qRT-PCR; RACE; Luciferase reporter assay; Reporter assay
E_04298	2013	24086551	Identification of an enhancer that increases miR-200b~200a~429 gene expression in breast cancer cells	Homo sapiens	hg19	chr1	1092486	1093650	NA	MIR429	Enhancer	Active	Normal	NA	NA	NA	breast	UBERON:0000310	HMLE	NA	mammary epithelial cell	NA	Enhancer activity assay; Chromatin state assay; eRNA analysis	ChIP-seq; DNA methylation profiling	Dual-luciferase reporter assay; ChIP-qPCR; DNA methylation analysis; qRT-PCR; RACE; Luciferase reporter assay; Reporter assay
E_04299	2019	31744543	ETV2/ER71 regulates the generation of FLK1+ cells from mouse embryonic stem cells through miR-126-MAPK signaling	Mus musculus	mm10	chr8	47323116	47325387	Fos	Kdr	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; TF binding assay; developmental regulatory assay	miRNA-seq; RNA-seq	Luciferase reporter assay; ChIP-PCR; qRT-PCR; Western blot
E_04300	2019	31744543	ETV2/ER71 regulates the generation of FLK1+ cells from mouse embryonic stem cells through miR-126-MAPK signaling	Mus musculus	mm10	chr8	47323116	47325387	Jun	Kdr	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; TF binding assay; developmental regulatory assay	miRNA-seq; RNA-seq	Luciferase reporter assay; ChIP-PCR; qRT-PCR; Western blot
E_04301	2016	27376239	Hierarchy within the mammary STAT5-driven Wap super-enhancer	Mus musculus	mm10	chr11	103459000	103463000	Stat5a	Wap	Enhancer	Active	Normal	NA	NA	NA	mammary gland	UBERON:0001911	Mammary epithelial cell	NA	mammary epithelial cell	NA	Enhancer activity assay; TF binding assay	ChIP-seq; RNA-seq	Luciferase reporter assay; ChIP-qPCR
E_04302	2015	26071365	Lhx6 and Lhx8 promote palate development through negative regulation of a cell cycle inhibitor gene, p57Kip2	Mus musculus	mm10	chr7	143459000	143459700	Foxp1	Cdkn1c	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	E11.5 primary maxillary arch cells	NA	cranial neural crest-derived mesenchymal cell	NA	Enhancer activity assay; TF binding assay; developmental regulatory assay	LHX6 ChIP-seq; transcriptional profiling	p57Kip2 enh1 luciferase reporter assay; FOX motif analysis; FOXP1 overexpression; FOXD1 overexpression; ChIP-qPCR; Immunofluorescence; RNA in situ hybridization; Reporter assay
E_04303	2012	22429595	Characterization of the colorectal cancer-associated enhancer MYC-335 at 8q24: the role of rs67491583	Homo sapiens	hg19	chr8	128413174	128414429	GFI1	MYC	Enhancer	Repressed	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	colorectal cancer cell lines	NA	malignant cell	CL:0001064	Cancer-risk enhancer variant functional characterization; allele-specific TF binding	Genotyping / population variant analysis	ChIP; allele-specific binding; enhancer reporter; Wnt-response assay
E_04304	2012	22429595	Characterization of the colorectal cancer-associated enhancer MYC-335 at 8q24: the role of rs67491583	Homo sapiens	hg19	chr8	128413174	128414429	GFI1	MYC	Enhancer	Repressed	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	heterozygous enhancer models	NA	malignant cell	CL:0001064	Cancer-risk enhancer variant functional characterization; allele-specific TF binding	Genotyping / population variant analysis	ChIP; allele-specific binding; enhancer reporter; Wnt-response assay
E_04305	2012	22429595	Characterization of the colorectal cancer-associated enhancer MYC-335 at 8q24: the role of rs67491583	Homo sapiens	hg19	chr8	128413174	128414429	GFI1B	MYC	Enhancer	Repressed	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	colorectal cancer cell lines	NA	malignant cell	CL:0001064	Cancer-risk enhancer variant functional characterization; allele-specific TF binding	Genotyping / population variant analysis	ChIP; allele-specific binding; enhancer reporter; Wnt-response assay
E_04306	2012	22429595	Characterization of the colorectal cancer-associated enhancer MYC-335 at 8q24: the role of rs67491583	Homo sapiens	hg19	chr8	128413174	128414429	GFI1B	MYC	Enhancer	Repressed	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	heterozygous enhancer models	NA	malignant cell	CL:0001064	Cancer-risk enhancer variant functional characterization; allele-specific TF binding	Genotyping / population variant analysis	ChIP; allele-specific binding; enhancer reporter; Wnt-response assay
E_04307	2012	22429595	Characterization of the colorectal cancer-associated enhancer MYC-335 at 8q24: the role of rs67491583	Homo sapiens	hg19	chr8	128413174	128414429	TCF7L2	MYC	Enhancer	Repressed	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	colorectal cancer cell lines	NA	malignant cell	CL:0001064	Cancer-risk enhancer variant functional characterization; allele-specific TF binding	Genotyping / population variant analysis	ChIP; allele-specific binding; enhancer reporter; Wnt-response assay
E_04308	2012	22429595	Characterization of the colorectal cancer-associated enhancer MYC-335 at 8q24: the role of rs67491583	Homo sapiens	hg19	chr8	128413174	128414429	TCF7L2	MYC	Enhancer	Repressed	Disease	colorectal carcinoma	MONDO:0024331	DOID:0080199	colon	UBERON:0001155	heterozygous enhancer models	NA	malignant cell	CL:0001064	Cancer-risk enhancer variant functional characterization; allele-specific TF binding	Genotyping / population variant analysis	ChIP; allele-specific binding; enhancer reporter; Wnt-response assay
E_04309	2015	25529635	Fine-scale mapping of the 5q11.2 breast cancer locus reveals at least three independent risk variants regulating MAP3K1	Homo sapiens	hg19	chr5	56028968	56031097	NA	MAP3K1	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast epithelium	UBERON:0008367	Bre-80	CVCL_A283	mammary gland epithelial cell	NA	Enhancer activity assay; Chromatin interaction assay	NA	Luciferase reporter assay; 3C-qPCR
E_04310	2011	21056086	Mechanisms of bone morphogenetic protein 2 (BMP2) stimulated inhibitor of DNA binding 3 (Id3) transcription	Homo sapiens	hg19	chr1	23881789	23881796	BMP2	ID3	Enhancer	Active	Normal	NA	NA	NA	gonad	NA	Immortalized Murine Gonadotrope LβT2 Cell,Ovarian Cancer Cell	NA	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; RT-qPCR/qPCR
E_04311	2011	21056086	Mechanisms of bone morphogenetic protein 2 (BMP2) stimulated inhibitor of DNA binding 3 (Id3) transcription	Mus musculus	mm10	chr4	136140539	136140546	Smad1	Id3	Enhancer	Active	Normal	NA	NA	NA	gonad	NA	Immortalized Murine Gonadotrope L??T2 Cell,Ovarian Cancer Cell	NA	malignant cell	CL:0001064	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay
E_04312	2009	19773398	X-linked congenital adrenal hypoplasia with hypogonadotropic hypogonadism caused by an inversion disrupting a conserved noncoding element upstream of the NR0B1 (DAX1) gene	Homo sapiens	hg19	chrX	30331500	30332000	NR5A1	NR0B1	Enhancer	Active	Disease	X-linked adrenal hypoplasia congenita with hypogonadotropic hypogonadism	NA	NA	adrenal gland	UBERON:0002369	human congenital adrenal-hypoplasia family / reporter model	NA	steroidogenic/gonadal regulatory cell context	NA	Human structural-variant regulatory genetics; conserved-element reporter assay; TF-response assay	Comparative genomics / breakpoint mapping	Breakpoint PCR/sequencing; Luciferase reporter assay; NR5A1/SF1 cotransfection; expression analysis
E_04313	2009	19773398	X-linked congenital adrenal hypoplasia with hypogonadotropic hypogonadism caused by an inversion disrupting a conserved noncoding element upstream of the NR0B1 (DAX1) gene	Homo sapiens	hg19	chrX	30331500	30332000	NR5A1	NR0B1	Enhancer	Active	Disease	X-linked adrenal hypoplasia congenita with hypogonadotropic hypogonadism	NA	NA	testis	UBERON:0000473	human congenital adrenal-hypoplasia/hypogonadotropic-hypogonadism family / reporter model	NA	steroidogenic/gonadal regulatory cell context	NA	Human structural-variant regulatory genetics; conserved-element reporter assay; TF-response assay	Comparative genomics / breakpoint mapping	Breakpoint PCR/sequencing; Luciferase reporter assay; NR5A1/SF1 cotransfection; expression analysis
E_04314	2009	19773398	X-linked congenital adrenal hypoplasia with hypogonadotropic hypogonadism caused by an inversion disrupting a conserved noncoding element upstream of the NR0B1 (DAX1) gene	Homo sapiens	hg19	chrX	30331500	30332000	NR5A1	NR0B1	Enhancer	Active	Disease	X-linked adrenal hypoplasia congenita with hypogonadotropic hypogonadism	NA	NA	adrenal gland	UBERON:0002369	source duplicate retained: inversion-breakpoint regulatory context	NA	steroidogenic/gonadal regulatory cell context	NA	Human structural-variant regulatory genetics; conserved-element reporter assay; TF-response assay	Comparative genomics / breakpoint mapping	Breakpoint PCR/sequencing; Luciferase reporter assay; NR5A1/SF1 cotransfection; expression analysis
E_04315	2009	19773398	X-linked congenital adrenal hypoplasia with hypogonadotropic hypogonadism caused by an inversion disrupting a conserved noncoding element upstream of the NR0B1 (DAX1) gene	Homo sapiens	hg19	chrX	30317939	30318739	NR5A1	NR0B1	Enhancer	Active	Disease	X-Linked Congenital Adrenal Hypoplasia	NA	NA	kidney	UBERON:0002113	HEK293	CVCL_0045	NA	NA	Enhancer activity assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay
E_04316	2007	17094106	Mouse naked cuticle 2 (mNkd2) as a direct transcriptional target of Hoxc8 in vivo	Mus musculus	mm10	chr10	127874742	127875307	Hoxc8	Nkd2	Enhancer	Repressed	Normal	NA	NA	NA	embryo	NA	NIH 3T3	CVCL_0594	fibroblast	CL:0000057	Enhancer activity assay; TF binding assay; Gene expression assay	NA	ChIP; EMSA; Reporter assay; RT-PCR
E_04317	2015	25786345	p53-dependent expression of CXCR5 chemokine receptor in MCF-7 breast cancer cells	Homo sapiens	hg19	chr11	118813865	118815965	NA	CXCR5	Enhancer	Active	Disease	breast carcinoma	MONDO:0004989	DOID:3459	breast	UBERON:0000310	MCF-7	CVCL_0031	malignant cell	CL:0001064	Enhancer activity assay	NA	Luciferase reporter assay
E_04318	2012	22761896	Histone deacetylases regulate gonadotropin-releasing hormone I gene expression via modulating Otx2-driven transcriptional activity	Mus musculus	mm10	chr14	67741735	67744661	Otx2	Gnrh1	Enhancer	Active	Normal	NA	NA	NA	gonad	NA	GT1-7	CVCL_0281	NA	NA	Enhancer activity assay; TF-binding/chromatin assay	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; EMSA/gel-shift assay; Western blot; Histology/immunostaining
E_04319	2014	24498324	Epigenetic control of SPI1 gene by CTCF and ISWI ATPase SMARCA5	Homo sapiens	hg19	chr11	47363009	47364009	NA	SPI1	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	blood	UBERON:0000178	Human Myeloid Cells	NA	NA	NA	Enhancer activity assay; TF-binding/chromatin assay; Disease-associated enhancer analysis	NA	Luciferase reporter assay; Reporter assay; ChIP-qPCR/ChIP; Western blot
E_04320	2001	11263787	Activation of a fibroblast-specific enhancer of the proalpha2(I) collagen gene in tight-skin mice	Mus musculus	mm10	chr6	4488518	4490518	NA	Col1a2	Enhancer	Active	Disease	systemic sclerosis	NA	NA	skin	UBERON:0002097	Primary dermal fibroblasts from Tsk1/+ mice	NA	fibroblast of dermis	CL:0002551	Enhancer activity assay; Transgenic reporter assay; Disease-model enhancer activation assay; Cytokine-responsive enhancer assay	NA	Transgenic 2-kb Col1a2 enhancer-LacZ reporter assay; breeding into Tsk1/+ mice; beta-galactosidase reporter analysis; primary dermal fibroblast culture; transient reporter transfection; recombinant TGF-beta1 stimulation; Transgenic enhancer reporter assay
E_04321	2001	11263787	Activation of a fibroblast-specific enhancer of the proalpha2(I) collagen gene in tight-skin mice	Mus musculus	mm10	chr6	4486118	4492118	NA	Col1a2	Enhancer	Active	Disease	systemic sclerosis	NA	NA	skin	UBERON:0002097	Primary dermal fibroblasts from Tsk1/+ mice	NA	fibroblast of dermis	CL:0002551	Enhancer activity assay; Transgenic reporter assay; Disease-model enhancer activation assay; Fibroblast-lineage enhancer assay	NA	Transgenic 6-kb Col1a2 enhancer-LacZ reporter assay; breeding into Tsk1/+ mice; beta-galactosidase reporter analysis; primary dermal fibroblast culture; Transgenic enhancer reporter assay
E_04322	2001	11263787	Activation of a fibroblast-specific enhancer of the proalpha2(I) collagen gene in tight-skin mice	Mus musculus	mm10	chr6	4486118	4492118	NA	Col1a2	Enhancer	Active	Disease	systemic sclerosis-like fibrosis (tight-skin mouse model)	NA	NA	skin	UBERON:0002097	Tsk1/+ mouse dermal fibroblasts	NA	fibroblast	CL:0000057	In vivo fibroblast-specific enhancer assay; fibrosis-model comparison	NA	Col1a2 upstream-enhancer LacZ transgene; tissue staining; primary fibroblast analysis; TGF---1 stimulation
E_04323	2016	27822317	Narrowing the FOXF1 distant enhancer region on 16q24.1 critical for ACDMPV	Homo sapiens	hg19	chr16	86238601	86253509	NA	FOXF1	Enhancer	Active	Disease	alveolar capillary dysplasia with misalignment of pulmonary veins	MONDO:0009934	NA	lung	UBERON:0002048	ACDMPV patient genomic DNA/lung tissue	NA	lung fibroblast / pulmonary mesenchymal cell	NA	Pathogenic CNV overlap mapping; enhancer-core narrowing; lung chromatin-state integration; allele-specific methylation analysis	ENCODE DNase/TF/histone-mark data integration	Custom array-CGH; Sanger sequencing; bisulfite sequencing; patient genotype-phenotype analysis
E_04324	2016	27822317	Narrowing the FOXF1 distant enhancer region on 16q24.1 critical for ACDMPV	Homo sapiens	hg19	chr16	86238601	86253509	NA	FOXF1	Enhancer	Active	Disease	alveolar capillary dysplasia with misalignment of pulmonary veins	MONDO:0009934	NA	lung	UBERON:0002048	human lung fibroblast ENCODE regulatory context	NA	lung fibroblast / pulmonary mesenchymal cell	NA	Pathogenic CNV overlap mapping; enhancer-core narrowing; lung chromatin-state integration; allele-specific methylation analysis	ENCODE DNase/TF/histone-mark data integration	Custom array-CGH; Sanger sequencing; bisulfite sequencing; patient genotype-phenotype analysis
E_04325	2024	39362902	Developmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in Drosophila	Drosophila melanogaster	dm3	chr2R	212338	212586	NA	NA	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Schneider 2	CVCL_Z232	hemocyte-like cultured cell	NA	Enhancer activity assay; Enhancer-enhancer cooperativity assay; Housekeeping core-promoter activity assay	UMI-STARR-seq; paired-enhancer STARR-seq; STARR-seq	3C
E_04326	2024	39362902	Developmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in Drosophila	Drosophila melanogaster	dm3	chr2R	13743428	13743676	NA	NA	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Schneider 2	CVCL_Z232	hemocyte-like cultured cell	NA	Enhancer activity assay; Enhancer-enhancer cooperativity assay; Developmental core-promoter activity assay	UMI-STARR-seq; paired-enhancer STARR-seq; STARR-seq	3C
E_04327	2024	39362902	Developmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in Drosophila	Drosophila melanogaster	dm3	chr3R	18457294	18457542	NA	NA	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Schneider 2	CVCL_Z232	hemocyte-like cultured cell	NA	Enhancer activity assay; Enhancer-enhancer cooperativity assay; Developmental core-promoter activity assay	UMI-STARR-seq; paired-enhancer STARR-seq; STARR-seq	3C
E_04328	2024	39362902	Developmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in Drosophila	Drosophila melanogaster	dm3	chrX	1374546	1374794	NA	NA	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Schneider 2	CVCL_Z232	hemocyte-like cultured cell	NA	Enhancer activity assay; Enhancer-enhancer cooperativity assay; Developmental core-promoter activity assay	UMI-STARR-seq; paired-enhancer STARR-seq; STARR-seq	3C
E_04329	2024	39362902	Developmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in Drosophila	Drosophila melanogaster	dm3	chrX	18546964	18547212	NA	NA	Enhancer	Active	Normal	NA	NA	NA	embryo	NA	Schneider 2	CVCL_Z232	hemocyte-like cultured cell	NA	Enhancer activity assay; Enhancer-enhancer cooperativity assay; Housekeeping core-promoter activity assay	UMI-STARR-seq; paired-enhancer STARR-seq; STARR-seq	3C
E_04330	2021	33980539	Selective Requirement of MYB for Oncogenic Hyperactivation of a Translocated Enhancer in Leukemia	Homo sapiens	hg19	chr3	128322411	128323124	MYB	MECOM	Enhancer	Active	Disease	acute myeloid leukemia with MECOM rearrangement	NA	NA	blood	UBERON:0000178	MUTZ-3	CVCL_1433	hematopoietic progenitor/leukemia cell	NA	Endogenous enhancer dependency assay; CRISPR enhancer scan; TF-motif causality assay; enhancer-hijacking functional validation	H3K27ac ChIP-seq; ATAC-seq; pooled CRISPR-Cas9 tiling enhancer screen; deep amplicon sequencing	Individual sgRNA validation; MYB knockout; MYB-binding-motif mutagenesis; qRT-PCR; EVI1-GFP flow cytometry; immunoblotting; myeloid differentiation assay; cell-death assay
E_04331	2025	40162972	Enhancer Hijacking Discovery in Acute Myeloid Leukemia by Pyjacker Identifies MNX1 Activation via Deletion 7q	Homo sapiens	hg19	chr7	92384001	92385000	NA	MNX1	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	NA	NA	ChiPSC22-derived hematopoietic stem and progenitor cells	NA	hematopoietic stem and progenitor cell	NA	Chromatin interaction assay; Chromatin accessibility assay; Enhancer-hijacking assay; histone-modification profiling; functional enhancer insertion assay	WGS; RNA-seq; ATAC-seq; ACT-seq for H3K27ac and H3K4me1; 4C-seq; Pyjacker structural-variant analysis	CRISPR/Cas9-mediated 1-kb enhancer insertion by homology-directed repair; PCR clone validation; engineered HSPC differentiation; MNX1 expression validation
E_04332	2021	33980539	Selective Requirement of MYB for Oncogenic Hyperactivation of a Translocated Enhancer in Leukemia	Homo sapiens	hg19	chr3	128322411	128323124	MYB	MECOM	Enhancer	Active	Disease	acute myeloid leukemia with MECOM rearrangement	NA	NA	blood	UBERON:0000178	MUTZ-3	CVCL_1433	acute myeloid leukemia cell	NA	CRISPR enhancer dependency assay; TF-motif causality assay; enhancer-hijacking functional validation	H3K27ac ChIP-seq; ATAC-seq; pooled CRISPR-Cas9 enhancer scan; deep amplicon sequencing	Individual sgRNA validation; MYB knockout; MYB-binding-motif mutation; qRT-PCR; EVI1-GFP flow cytometry; immunoblotting; differentiation assay; cell-death assay
E_04333	2025	40162972	Enhancer Hijacking Discovery in Acute Myeloid Leukemia by Pyjacker Identifies MNX1 Activation via Deletion 7q	Homo sapiens	hg19	chr7	92384001	92385000	NA	MNX1	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	NA	NA	ChiPSC22-derived hematopoietic stem and progenitor cells	NA	hematopoietic stem and progenitor cell	NA	Chromatin interaction assay; Chromatin accessibility assay; Enhancer-hijacking assay; histone-modification profiling; functional enhancer insertion assay	WGS; RNA-seq; ATAC-seq; ACT-seq for H3K27ac and H3K4me1; 4C-seq; Pyjacker structural-variant analysis	CRISPR/Cas9-mediated enhancer insertion by homology-directed repair; PCR clone validation; engineered HSPC differentiation; MNX1 expression analysis
E_04334	2026	41771871	Nucleotide-resolution mapping of regulatory elements via allelic readout of tiled base editing	Homo sapiens	hg38	chr16	28930687	28931032	MYB	CD19	Enhancer	Active	Disease	B-cell acute lymphoblastic leukemia	MONDO:0004947	DOID:0080638	blood	UBERON:0000178	NALM-6	CVCL_0092	B-cell precursor	NA	Endogenous enhancer deletion; nucleotide-resolution enhancer mutagenesis; TF-binding-site functional validation; target-gene regulation; CAR-T resistance phenotype	ATAC-seq; H3K27ac ChIP-seq; high-throughput CRISPR base-editing screen; targeted amplicon sequencing	346-bp endogenous enhancer deletion; evoCDA base editing; ABE8e-SpRY base editing; single-gRNA validation; RT-qPCR; Flow cytometry; Sanger sequencing; CD19 CAR-T cytotoxicity assay
E_04335	2026	41771871	Nucleotide-resolution mapping of regulatory elements via allelic readout of tiled base editing	Homo sapiens	hg38	chr16	28930687	28931032	PAX5	CD19	Enhancer	Active	Disease	B-cell acute lymphoblastic leukemia	MONDO:0004947	DOID:0080638	blood	UBERON:0000178	NALM-6	CVCL_0092	B-cell precursor	NA	Endogenous enhancer deletion; nucleotide-resolution enhancer mutagenesis; TF-binding-site functional validation; target-gene regulation; CAR-T resistance phenotype	ATAC-seq; H3K27ac ChIP-seq; high-throughput CRISPR base-editing screen; targeted amplicon sequencing	346-bp endogenous enhancer deletion; evoCDA base editing; ABE8e-SpRY base editing; single-gRNA validation; RT-qPCR; Flow cytometry; Sanger sequencing; CD19 CAR-T cytotoxicity assay
E_04336	2026	41771871	Nucleotide-resolution mapping of regulatory elements via allelic readout of tiled base editing	Homo sapiens	hg38	chr16	28930687	28931032	EBF1	CD19	Enhancer	Active	Disease	B-cell acute lymphoblastic leukemia	MONDO:0004947	DOID:0080638	blood	UBERON:0000178	NALM-6	CVCL_0092	B-cell precursor	NA	Endogenous enhancer deletion; nucleotide-resolution enhancer mutagenesis; TF-binding-site functional validation; target-gene regulation	ATAC-seq; H3K27ac ChIP-seq; high-throughput CRISPR base-editing screen; targeted amplicon sequencing	346-bp endogenous enhancer deletion; evoCDA base editing; ABE8e-SpRY base editing; single-gRNA validation; RT-qPCR; Flow cytometry; Sanger sequencing
E_04337	2016	26979803	Chromatin interactions and candidate genes at ten prostate cancer risk loci.	Homo sapiens	hg19	chr10	51546800	51547317	HOXB13	AGAP7P	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	NA	NA	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Regulatory variant functional assay; TF binding assay; Chromatin interaction assay	Capture-based 3C-seq; ChIP-seq; RNA-seq/eQTL analysis	Luciferase reporter assay; site-directed mutagenesis
E_04338	2016	26979803	Chromatin interactions and candidate genes at ten prostate cancer risk loci.	Homo sapiens	hg19	chr10	51546800	51547317	AR	AGAP7P	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	NA	NA	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Regulatory variant functional assay; TF binding assay; Chromatin interaction assay	Capture-based 3C-seq; ChIP-seq; RNA-seq/eQTL analysis	Luciferase reporter assay; site-directed mutagenesis
E_04339	2016	26979803	Chromatin interactions and candidate genes at ten prostate cancer risk loci.	Homo sapiens	hg19	chr10	51546800	51547317	FOXA1	AGAP7P	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	NA	NA	LNCaP	CVCL_0395	malignant cell	CL:0001064	Enhancer activity assay; Regulatory variant functional assay; TF binding assay; Chromatin interaction assay	Capture-based 3C-seq; ChIP-seq; RNA-seq/eQTL analysis	Luciferase reporter assay; site-directed mutagenesis
E_04340	2018	29420474	Enhancer redundancy provides phenotypic robustness in mammalian development	Mus musculus	mm10	chr13	15342707	15344218	NA	Gli3	Enhancer	Active	Normal	NA	NA	NA	limb bud	UBERON:0004347	FVB mouse embryonic limb bud	NA	mesenchymal cell	CL:0008019	Enhancer activity assay; Endogenous enhancer deletion assay; Enhancer-target functional validation; Chromatin interaction assay; Chromatin-state profiling; Gene expression assay	H3K27ac ChIP-seq; RNA-seq; Capture-C; DNase-seq/DHS	CRISPR/Cas9 enhancer deletion; transgenic hsp68-LacZ reporter assay; fluorescent transgenic reporter assay; qRT-PCR; whole-mount RNA in situ hybridization; PCR genotyping; Sanger sequencing; skeletal phenotype analysis
E_04341	2018	29420474	Enhancer redundancy provides phenotypic robustness in mammalian development	Mus musculus	mm10	chr13	15548975	15550833	NA	Gli3	Enhancer	Active	Normal	NA	NA	NA	limb bud	UBERON:0004347	FVB mouse embryonic limb bud	NA	mesenchymal cell	CL:0008019	Enhancer activity assay; Endogenous enhancer deletion assay; Enhancer-target functional validation; Chromatin interaction assay; Chromatin-state profiling; Gene expression assay	H3K27ac ChIP-seq; RNA-seq; Capture-C; DNase-seq/DHS	CRISPR/Cas9 enhancer deletion; transgenic hsp68-LacZ reporter assay; fluorescent transgenic reporter assay; qRT-PCR; whole-mount RNA in situ hybridization; PCR genotyping; Sanger sequencing; skeletal phenotype analysis
E_04342	2018	29420474	Enhancer redundancy provides phenotypic robustness in mammalian development	Mus musculus	mm10	chr3	67070296	67071594	NA	Shox2	Enhancer	Active	Normal	NA	NA	NA	limb bud	UBERON:0004347	FVB mouse embryonic limb bud	NA	mesenchymal cell	CL:0008019	Enhancer activity assay; Endogenous enhancer deletion assay; Enhancer-target functional validation; Chromatin interaction assay; Chromatin-state profiling; Gene expression assay	H3K27ac ChIP-seq; RNA-seq; Capture-C; DNase-seq/DHS	CRISPR/Cas9 enhancer deletion; transgenic hsp68-LacZ reporter assay; fluorescent transgenic reporter assay; qRT-PCR; whole-mount RNA in situ hybridization; PCR genotyping; Sanger sequencing; skeletal phenotype analysis
E_04343	2018	29420474	Enhancer redundancy provides phenotypic robustness in mammalian development	Mus musculus	mm10	chr3	66938324	66940117	NA	Shox2	Enhancer	Active	Normal	NA	NA	NA	limb bud	UBERON:0004347	FVB mouse embryonic limb bud	NA	mesenchymal cell	CL:0008019	Enhancer activity assay; Endogenous enhancer deletion assay; Enhancer-target functional validation; Chromatin interaction assay; Chromatin-state profiling; Gene expression assay	H3K27ac ChIP-seq; RNA-seq; Capture-C; DNase-seq/DHS	CRISPR/Cas9 enhancer deletion; transgenic hsp68-LacZ reporter assay; fluorescent transgenic reporter assay; qRT-PCR; whole-mount RNA in situ hybridization; PCR genotyping; Sanger sequencing; skeletal phenotype analysis
E_04344	2018	29420474	Enhancer redundancy provides phenotypic robustness in mammalian development	Mus musculus	mm10	chr11	111827906	111829224	NA	Sox9	Enhancer	Active	Normal	NA	NA	NA	limb bud	UBERON:0004347	FVB mouse embryonic limb bud	NA	mesenchymal cell	CL:0008019	Enhancer activity assay; Endogenous enhancer deletion assay; Enhancer-target functional validation; Chromatin interaction assay; Chromatin-state profiling; Gene expression assay	H3K27ac ChIP-seq; RNA-seq; Capture-C; DNase-seq/DHS	CRISPR/Cas9 enhancer deletion; transgenic hsp68-LacZ reporter assay; qRT-PCR; whole-mount RNA in situ hybridization; PCR genotyping; Sanger sequencing; skeletal phenotype analysis
E_04345	2018	29420474	Enhancer redundancy provides phenotypic robustness in mammalian development	Mus musculus	mm10	chr11	113013634	113014961	NA	Sox9	Enhancer	Active	Normal	NA	NA	NA	limb bud	UBERON:0004347	FVB mouse embryonic limb bud	NA	mesenchymal cell	CL:0008019	Enhancer activity assay; Endogenous enhancer deletion assay; Enhancer-target functional validation; Chromatin interaction assay; Chromatin-state profiling; Gene expression assay	H3K27ac ChIP-seq; RNA-seq; Capture-C; DNase-seq/DHS	CRISPR/Cas9 enhancer deletion; transgenic hsp68-LacZ reporter assay; qRT-PCR; whole-mount RNA in situ hybridization; PCR genotyping; Sanger sequencing; skeletal phenotype analysis
E_04346	2018	29420474	Enhancer redundancy provides phenotypic robustness in mammalian development	Mus musculus	mm10	chr5	119610926	119613436	NA	Tbx3	Enhancer	Active	Normal	NA	NA	NA	limb bud	UBERON:0004347	FVB mouse embryonic limb bud	NA	mesenchymal cell	CL:0008019	Enhancer activity assay; Endogenous enhancer deletion assay; Enhancer-target functional validation; Chromatin interaction assay; Chromatin-state profiling; Gene expression assay	H3K27ac ChIP-seq; RNA-seq; Capture-C; DNase-seq/DHS	CRISPR/Cas9 enhancer deletion; transgenic hsp68-LacZ reporter assay; qRT-PCR; whole-mount RNA in situ hybridization; PCR genotyping; Sanger sequencing; skeletal phenotype analysis
E_04347	2018	29420474	Enhancer redundancy provides phenotypic robustness in mammalian development	Mus musculus	mm10	chr8	89454509	89455383	NA	Sall1	Enhancer	Active	Normal	NA	NA	NA	limb bud	UBERON:0004347	FVB mouse embryonic limb bud	NA	mesenchymal cell	CL:0008019	Enhancer activity assay; Endogenous enhancer deletion assay; Enhancer-target functional validation; Chromatin interaction assay; Chromatin-state profiling; Gene expression assay	H3K27ac ChIP-seq; RNA-seq; Capture-C; DNase-seq/DHS	CRISPR/Cas9 enhancer deletion; transgenic hsp68-LacZ reporter assay; qRT-PCR; whole-mount RNA in situ hybridization; PCR genotyping; Sanger sequencing; skeletal phenotype analysis
E_04348	2018	29420474	Enhancer redundancy provides phenotypic robustness in mammalian development	Mus musculus	mm10	chr13	118735525	118737413	NA	Fgf10	Enhancer	Active	Normal	NA	NA	NA	limb bud	UBERON:0004347	FVB mouse embryonic limb bud	NA	mesenchymal cell	CL:0008019	Enhancer activity assay; Endogenous enhancer deletion assay; Enhancer-target functional validation; Chromatin interaction assay; Chromatin-state profiling; Gene expression assay	H3K27ac ChIP-seq; RNA-seq; Capture-C; DNase-seq/DHS	CRISPR/Cas9 enhancer deletion; transgenic hsp68-LacZ reporter assay; qRT-PCR; whole-mount RNA in situ hybridization; PCR genotyping; Sanger sequencing; skeletal phenotype analysis
E_04349	2018	29420474	Enhancer redundancy provides phenotypic robustness in mammalian development	Mus musculus	mm10	chr6	143497299	143500849	NA	Sox5	Enhancer	Active	Normal	NA	NA	NA	limb bud	UBERON:0004347	FVB mouse embryonic limb bud	NA	mesenchymal cell	CL:0008019	Enhancer activity assay; Endogenous enhancer deletion assay; Enhancer-target functional validation; Chromatin interaction assay; Chromatin-state profiling; Gene expression assay	H3K27ac ChIP-seq; RNA-seq; Capture-C; DNase-seq/DHS	CRISPR/Cas9 enhancer deletion; transgenic hsp68-LacZ reporter assay; qRT-PCR; whole-mount RNA in situ hybridization; PCR genotyping; Sanger sequencing; skeletal phenotype analysis
E_04350	2018	29342133	A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies	Mus musculus	mm9	chr15	63291835	63550550	NA	Myc	Super-enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary mouse bone marrow	NA	hematopoietic stem cell	CL:0000037	Enhancer activity assay; Endogenous enhancer-cluster deletion assay; Enhancer-target functional validation; Chromatin interaction assay; Chromatin-state profiling; Gene expression assay	ATAC-seq; H3K27ac ChIP-seq; TF ChIP-seq; promoter capture Hi-C	LacZ/FDG enhancer reporter assay; TAMERE/Cre-mediated enhancer-cluster deletion; RT-qPCR; flow cytometry; competitive transplantation; colony-forming assay; DNA FISH
E_04351	2018	29342133	A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies	Mus musculus	mm9	chr15	63291835	63550550	NA	Myc	Super-enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	blood	UBERON:0000178	MLL-AF9-GFP+ CD45.2+ leukemic cells	NA	myeloid leukemic blast	NA	Endogenous enhancer-cluster deletion assay; Enhancer-target functional validation; Leukemia maintenance assay; Gene expression assay; Chromatin-state profiling	ATAC-seq; H3K27ac ChIP-seq	Mx1-Cre-mediated BENC deletion; MLL-AF9 leukemia transplantation; RT-qPCR; flow cytometry; peripheral-blood leukemia monitoring; survival analysis
E_04352	2018	29342133	A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies	Mus musculus	mm9	chr15	63479414	63480336	NA	Myc	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary mouse bone marrow	NA	hematopoietic stem cell	CL:0000037	Endogenous enhancer deletion assay; Enhancer-target functional validation; Chromatin accessibility assay; Chromatin-state profiling; Gene expression assay	ATAC-seq; H3K27ac ChIP-seq; TF ChIP-seq	CRISPR/Cas9 enhancer deletion; RT-qPCR; flow cytometry
E_04353	2018	29342133	A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies	Mus musculus	mm9	chr15	63489427	63490405	NA	Myc	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary mouse bone marrow	NA	hematopoietic stem cell	CL:0000037	Endogenous enhancer deletion assay; Enhancer-target functional validation; Chromatin accessibility assay; Chromatin-state profiling; Gene expression assay	ATAC-seq; H3K27ac ChIP-seq; TF ChIP-seq	CRISPR/Cas9 enhancer deletion; RT-qPCR; flow cytometry
E_04354	2019	31761532	Functional enhancers shape extrachromosomal oncogene amplifications	Homo sapiens	hg19	chr7	54955869	54956669	SOX2	EGFR	Enhancer	Active	Disease	glioblastoma	MONDO:0018177	DOID:3068	NA	NA	G361 patient-derived glioblastoma cell model	NA	glioblastoma cell	NA	Enhancer activity; TF binding; chromatin accessibility; enhancer-promoter interaction; cis-regulatory perturbation; target-gene expression; cellular fitness	H3K27ac ChIP-seq; ATAC-seq; POLR2A ChIP-seq; SOX2 ChIP-seq; RNA-seq; 4C-seq; pooled CRISPRi proliferation dropout screening	dCas9-KRAB CRISPR interference; enhancer-targeting sgRNA perturbation; RT-qPCR; Alamar Blue cell viability assay
E_04355	2019	31761532	Functional enhancers shape extrachromosomal oncogene amplifications	Homo sapiens	hg19	chr7	55000801	55001300	SOX2	EGFR	Enhancer	Active	Disease	glioblastoma	MONDO:0018177	DOID:3068	NA	NA	G361 patient-derived glioblastoma cell model	NA	glioblastoma cell	NA	Enhancer activity; TF binding; chromatin accessibility; enhancer-promoter interaction; cis-regulatory perturbation; target-gene expression; cellular fitness	H3K27ac ChIP-seq; ATAC-seq; POLR2A ChIP-seq; SOX2 ChIP-seq; RNA-seq; 4C-seq; pooled CRISPRi proliferation dropout screening	dCas9-KRAB CRISPR interference; enhancer-targeting sgRNA perturbation; RT-qPCR; Alamar Blue cell viability assay
E_04356	2019	31761532	Functional enhancers shape extrachromosomal oncogene amplifications	Homo sapiens	hg19	chr7	54955869	54956669	SOX2	EGFR	Enhancer	Active	Disease	glioblastoma	MONDO:0018177	DOID:3068	NA	NA	G361 patient-derived glioblastoma cell model	NA	glioblastoma cell	NA	Enhancer activity assay; TF binding assay; chromatin accessibility assay; enhancer-promoter interaction assay; functional cis-regulatory perturbation assay; target-gene expression assay; cellular fitness assay	H3K27ac ChIP-seq; ATAC-seq; POLR2A ChIP-seq; SOX2 ChIP-seq; RNA-seq; pooled CRISPRi proliferation dropout screening; 4C-seq	dCas9-KRAB CRISPR interference using multiple enhancer-targeting sgRNAs; RT-qPCR; Alamar Blue cell viability assay
E_04357	2019	31761532	Functional enhancers shape extrachromosomal oncogene amplifications	Homo sapiens	hg19	chr7	55000801	55001300	SOX2	EGFR	Enhancer	Active	Disease	glioblastoma	MONDO:0018177	DOID:3068	NA	NA	G361 patient-derived glioblastoma cell model	NA	glioblastoma cell	NA	Enhancer activity assay; TF binding assay; chromatin accessibility assay; enhancer-promoter interaction assay; functional cis-regulatory perturbation assay; target-gene expression assay; cellular fitness assay	H3K27ac ChIP-seq; ATAC-seq; POLR2A ChIP-seq; SOX2 ChIP-seq; RNA-seq; pooled CRISPRi proliferation dropout screening; 4C-seq	dCas9-KRAB CRISPR interference using multiple enhancer-targeting sgRNAs; RT-qPCR; Alamar Blue cell viability assay
E_04358	2018	29420474	Enhancer redundancy provides phenotypic robustness in mammalian development	Mus musculus	mm10	chr13	15342707	15344218	NA	Gli3	Enhancer	Active	Normal	NA	NA	NA	limb bud	UBERON:0004347	mouse embryonic limb bud	NA	NA	NA	Enhancer activity assay; endogenous cis-regulatory perturbation; target-gene expression assay; developmental phenotype assay	H3K27ac ChIP-seq; RNA-seq; Capture-C	CRISPR/Cas9 endogenous enhancer deletion; transgenic reporter assay; RNA in situ hybridization; qRT-PCR; skeletal phenotyping
E_04359	2018	29420474	Enhancer redundancy provides phenotypic robustness in mammalian development	Mus musculus	mm10	chr13	15548975	15550833	NA	Gli3	Enhancer	Active	Normal	NA	NA	NA	limb bud	UBERON:0004347	mouse embryonic limb bud	NA	NA	NA	Enhancer activity assay; endogenous cis-regulatory perturbation; target-gene expression assay; developmental phenotype assay	H3K27ac ChIP-seq; RNA-seq; Capture-C	CRISPR/Cas9 endogenous enhancer deletion; transgenic reporter assay; RNA in situ hybridization; qRT-PCR; skeletal phenotyping
E_04360	2018	29420474	Enhancer redundancy provides phenotypic robustness in mammalian development	Mus musculus	mm10	chr3	67070296	67071594	NA	Shox2	Enhancer	Active	Normal	NA	NA	NA	limb bud	UBERON:0004347	mouse embryonic limb bud	NA	NA	NA	Enhancer activity assay; endogenous cis-regulatory perturbation; target-gene expression assay; developmental phenotype assay	H3K27ac ChIP-seq; RNA-seq; Capture-C	CRISPR/Cas9 endogenous enhancer deletion; transgenic reporter assay; RNA in situ hybridization; qRT-PCR; skeletal phenotyping
E_04361	2018	29420474	Enhancer redundancy provides phenotypic robustness in mammalian development	Mus musculus	mm10	chr3	66938324	66940117	NA	Shox2	Enhancer	Active	Normal	NA	NA	NA	limb bud	UBERON:0004347	mouse embryonic limb bud	NA	NA	NA	Enhancer activity assay; endogenous cis-regulatory perturbation; target-gene expression assay; developmental phenotype assay	H3K27ac ChIP-seq; RNA-seq; Capture-C	CRISPR/Cas9 endogenous enhancer deletion; transgenic reporter assay; RNA in situ hybridization; qRT-PCR; skeletal phenotyping
E_04362	2018	29420474	Enhancer redundancy provides phenotypic robustness in mammalian development	Mus musculus	mm10	chr11	111827906	111829224	NA	Sox9	Enhancer	Active	Normal	NA	NA	NA	limb bud	UBERON:0004347	mouse embryonic limb bud	NA	NA	NA	Enhancer activity assay; endogenous cis-regulatory perturbation; target-gene expression assay; developmental phenotype assay	H3K27ac ChIP-seq; RNA-seq; Capture-C	CRISPR/Cas9 endogenous enhancer deletion; transgenic reporter assay; RNA in situ hybridization; qRT-PCR; skeletal phenotyping
E_04363	2018	29420474	Enhancer redundancy provides phenotypic robustness in mammalian development	Mus musculus	mm10	chr11	113013634	113014961	NA	Sox9	Enhancer	Active	Normal	NA	NA	NA	limb bud	UBERON:0004347	mouse embryonic limb bud	NA	NA	NA	Enhancer activity assay; endogenous cis-regulatory perturbation; target-gene expression assay; developmental phenotype assay	H3K27ac ChIP-seq; RNA-seq; Capture-C	CRISPR/Cas9 endogenous enhancer deletion; transgenic reporter assay; RNA in situ hybridization; qRT-PCR; skeletal phenotyping
E_04364	2018	29420474	Enhancer redundancy provides phenotypic robustness in mammalian development	Mus musculus	mm10	chr5	119610926	119613436	NA	Tbx3	Enhancer	Active	Normal	NA	NA	NA	limb bud	UBERON:0004347	mouse embryonic limb bud	NA	NA	NA	Enhancer activity assay; endogenous cis-regulatory perturbation; target-gene expression assay; developmental phenotype assay	H3K27ac ChIP-seq; RNA-seq; Capture-C	CRISPR/Cas9 endogenous enhancer deletion; transgenic reporter assay; RNA in situ hybridization; qRT-PCR; skeletal phenotyping
E_04365	2018	29420474	Enhancer redundancy provides phenotypic robustness in mammalian development	Mus musculus	mm10	chr8	89454509	89455383	NA	Sall1	Enhancer	Active	Normal	NA	NA	NA	limb bud	UBERON:0004347	mouse embryonic limb bud	NA	NA	NA	Enhancer activity assay; endogenous cis-regulatory perturbation; target-gene expression assay; developmental phenotype assay	H3K27ac ChIP-seq; RNA-seq; Capture-C	CRISPR/Cas9 endogenous enhancer deletion; transgenic reporter assay; RNA in situ hybridization; qRT-PCR; skeletal phenotyping
E_04366	2018	29420474	Enhancer redundancy provides phenotypic robustness in mammalian development	Mus musculus	mm10	chr13	118735525	118737413	NA	Fgf10	Enhancer	Active	Normal	NA	NA	NA	limb bud	UBERON:0004347	mouse embryonic limb bud	NA	NA	NA	Enhancer activity assay; endogenous cis-regulatory perturbation; target-gene expression assay; developmental phenotype assay	H3K27ac ChIP-seq; RNA-seq; Capture-C	CRISPR/Cas9 endogenous enhancer deletion; transgenic reporter assay; RNA in situ hybridization; qRT-PCR; skeletal phenotyping
E_04367	2018	29420474	Enhancer redundancy provides phenotypic robustness in mammalian development	Mus musculus	mm10	chr6	143497299	143500849	NA	Sox5	Enhancer	Active	Normal	NA	NA	NA	limb bud	UBERON:0004347	mouse embryonic limb bud	NA	NA	NA	Enhancer activity assay; endogenous cis-regulatory perturbation; target-gene expression assay; developmental phenotype assay	H3K27ac ChIP-seq; RNA-seq; Capture-C	CRISPR/Cas9 endogenous enhancer deletion; transgenic reporter assay; RNA in situ hybridization; qRT-PCR; skeletal phenotyping
E_04368	2018	29342133	A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies	Mus musculus	mm9	chr15	63291835	63550550	NA	Myc	Super-enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary mouse bone marrow	NA	hematopoietic stem cell	CL:0000037	Enhancer-cluster activity; endogenous cis-regulatory perturbation; target-gene expression; hematopoietic phenotype	ATAC-seq; H3K27ac ChIP-seq; RNA-seq	CRISPR/Cas9-mediated enhancer-cluster deletion; RT-qPCR; flow cytometry; transplantation; hematopoietic phenotyping
E_04369	2018	29342133	A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies	Mus musculus	mm9	chr15	63291835	63550550	NA	Myc	Super-enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	bone marrow	UBERON:0002371	MLL-AF9-induced mouse leukemic cells	NA	leukemic stem/progenitor cell	NA	Enhancer-cluster activity; endogenous cis-regulatory perturbation; target-gene expression; leukemia-maintenance phenotype	ATAC-seq; H3K27ac ChIP-seq; RNA-seq	conditional endogenous BENC deletion; RT-qPCR; flow cytometry; transplantation; leukemia maintenance assay
E_04370	2018	29342133	A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies	Mus musculus	mm9	chr15	63479414	63480336	NA	Myc	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary mouse bone marrow hematopoietic cells	NA	hematopoietic stem/progenitor cell	NA	Enhancer activity; endogenous enhancer-module perturbation; target-gene expression	ATAC-seq; H3K27ac ChIP-seq	CRISPR/Cas9-mediated enhancer module deletion; RT-qPCR; flow cytometry
E_04371	2025	40162972	Enhancer Hijacking Discovery in Acute Myeloid Leukemia by Pyjacker Identifies MNX1 Activation via Deletion 7q	Homo sapiens	hg19	chr7	92384001	92385000	NA	MNX1	Enhancer	Active	Disease	acute myeloid leukemia	MONDO:0018874	DOID:9119	NA	NA	ChiPSC22-derived hematopoietic stem and progenitor cells with engineered CDK6 enhancer insertion near MNX1	NA	hematopoietic stem and progenitor cell	NA	Enhancer hijacking assay; endogenous cis-regulatory engineering; target-gene activation assay	WGS; RNA-seq; ATAC-seq; H3K27ac chromatin profiling	CRISPR/Cas9 homology-directed enhancer insertion; hematopoietic differentiation; MNX1 expression validation
E_04372	2024	38849954	An oncogenic enhancer promotes melanoma progression via regulating ETV4 expression	Homo sapiens	hg38	chr17	59785798	59787315	STAT3	ETV4	Enhancer	Active	Disease	melanoma	MONDO:0005105	DOID:1909	NA	NA	A375	CVCL_0132	melanoma cell	NA	Enhancer activity assay; TF binding assay; chromatin interaction assay; endogenous cis-regulatory perturbation assay; target-gene expression assay; rescue assay; cellular and in vivo tumor phenotype assay	RNA-seq; ChIP-seq; Hi-C; CUT&Tag	CRISPR/Cas9 endogenous enhancer deletion; LNA-mediated enhancer inhibition; luciferase reporter assay; RT-qPCR; Western blot; ETV4 knockdown; ETV4 rescue/overexpression; CCK-8 assay; EdU assay; wound-healing assay; Transwell assay; xenograft tumor-growth assay
E_04373	2022	36351387	Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation	Homo sapiens	hg38	chr6	135053011	135056967	NA	MYB	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	leukemia cell	NA	Functional cis-regulatory perturbation assay; target-gene expression assay; enhancer-promoter interaction assay; cellular fitness assay	tiling paired-gRNA CRISPRi proliferation screen; H3K27ac ChIP-seq; DNase-seq; H3K4me3 PLAC-seq	individual KRAB-dCas9 CRISPRi; qRT-PCR; cell proliferation assay
E_04374	2022	36351387	Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation	Homo sapiens	hg38	chr6	135317799	135330892	NA	MYB	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	leukemia cell	NA	Functional cis-regulatory perturbation assay; target-gene expression assay; enhancer-promoter interaction assay; cellular fitness assay	tiling paired-gRNA CRISPRi proliferation screen; H3K27ac ChIP-seq; DNase-seq; H3K4me3 PLAC-seq	individual KRAB-dCas9 CRISPRi; qRT-PCR; cell proliferation assay
E_04375	2022	36351387	Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation	Homo sapiens	hg38	chr8	127898669	127900067	NA	MYC	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	leukemia cell	NA	Functional cis-regulatory perturbation assay; target-gene expression assay; enhancer-promoter interaction assay; cellular fitness assay	tiling paired-gRNA CRISPRi proliferation screen; H3K27ac ChIP-seq; DNase-seq; H3K4me3 PLAC-seq	individual KRAB-dCas9 CRISPRi; qRT-PCR; cell proliferation assay
E_04376	2022	36351387	Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation	Homo sapiens	hg38	chr8	127958446	127963236	NA	MYC	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	leukemia cell	NA	Functional cis-regulatory perturbation assay; target-gene expression assay; enhancer-promoter interaction assay; cellular fitness assay	tiling paired-gRNA CRISPRi proliferation screen; H3K27ac ChIP-seq; DNase-seq; H3K4me3 PLAC-seq	individual KRAB-dCas9 CRISPRi; qRT-PCR; cell proliferation assay
E_04377	2022	36351387	Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation	Homo sapiens	hg38	chr8	129689364	129691007	NA	MYC	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	leukemia cell	NA	Functional cis-regulatory perturbation assay; target-gene expression assay; enhancer-promoter interaction assay; cellular fitness assay	tiling paired-gRNA CRISPRi proliferation screen; H3K27ac ChIP-seq; DNase-seq; H3K4me3 PLAC-seq	individual KRAB-dCas9 CRISPRi; qRT-PCR; cell proliferation assay
E_04378	2022	36351387	Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation	Homo sapiens	hg38	chr8	128552785	128560796	NA	MYC	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	NA	NA	Hep-G2	CVCL_0027	hepatocellular carcinoma cell	NA	Functional cis-regulatory perturbation assay; target-gene expression assay; enhancer-promoter interaction assay; cellular fitness assay	tiling paired-gRNA CRISPRi proliferation screen; H3K27ac ChIP-seq; DNase-seq; H3K4me3 PLAC-seq	individual KRAB-dCas9 CRISPRi; qRT-PCR; cell proliferation assay
E_04379	2022	36351387	Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation	Homo sapiens	hg38	chr8	128653951	128654391	NA	MYC	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	NA	NA	Hep-G2	CVCL_0027	hepatocellular carcinoma cell	NA	Functional cis-regulatory perturbation assay; target-gene expression assay; enhancer-promoter interaction assay; cellular fitness assay	tiling paired-gRNA CRISPRi proliferation screen; H3K27ac ChIP-seq; DNase-seq; H3K4me3 PLAC-seq	individual KRAB-dCas9 CRISPRi; qRT-PCR; cell proliferation assay
E_04380	2022	36351387	Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation	Homo sapiens	hg38	chr6	135054002	135055805	NA	MYB	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	NA	NA	HCT 116	CVCL_0291	colorectal cancer cell	NA	Functional cis-regulatory perturbation assay; target-gene expression assay; enhancer-promoter interaction assay; cellular fitness assay	tiling paired-gRNA CRISPRi proliferation screen; H3K27ac ChIP-seq; DNase-seq; H3K4me3 PLAC-seq	individual KRAB-dCas9 CRISPRi; qRT-PCR; cell proliferation assay
E_04381	2022	36351387	Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation	Homo sapiens	hg38	chr8	127215031	127229803	NA	MYC	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	NA	NA	HCT 116	CVCL_0291	colorectal cancer cell	NA	Functional cis-regulatory perturbation assay; target-gene expression assay; enhancer-promoter interaction assay; cellular fitness assay	tiling paired-gRNA CRISPRi proliferation screen; H3K27ac ChIP-seq; DNase-seq; H3K4me3 PLAC-seq	individual KRAB-dCas9 CRISPRi; qRT-PCR; cell proliferation assay
E_04382	2022	36351387	Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation	Homo sapiens	hg38	chr8	129707012	129713257	NA	MYC	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	NA	NA	HCT 116	CVCL_0291	colorectal cancer cell	NA	Functional cis-regulatory perturbation assay; target-gene expression assay; enhancer-promoter interaction assay; cellular fitness assay	tiling paired-gRNA CRISPRi proliferation screen; H3K27ac ChIP-seq; DNase-seq; H3K4me3 PLAC-seq	individual KRAB-dCas9 CRISPRi; qRT-PCR; cell proliferation assay
E_04383	2022	36351387	Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation	Homo sapiens	hg38	chr6	135053202	135057983	NA	MYB	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	NA	NA	SW620	CVCL_0547	colorectal cancer cell	NA	Functional cis-regulatory perturbation assay; target-gene expression assay; enhancer-promoter interaction assay; cellular fitness assay	tiling paired-gRNA CRISPRi proliferation screen; H3K27ac ChIP-seq; DNase-seq; H3K4me3 PLAC-seq	individual KRAB-dCas9 CRISPRi; qRT-PCR; cell proliferation assay
E_04384	2022	36351387	Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation	Homo sapiens	hg38	chr6	135264692	135270087	NA	MYB	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	NA	NA	SW620	CVCL_0547	colorectal cancer cell	NA	Functional cis-regulatory perturbation assay; target-gene expression assay; enhancer-promoter interaction assay; cellular fitness assay	tiling paired-gRNA CRISPRi proliferation screen; H3K27ac ChIP-seq; DNase-seq; H3K4me3 PLAC-seq	individual KRAB-dCas9 CRISPRi; qRT-PCR; cell proliferation assay
E_04385	2022	36351387	Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation	Homo sapiens	hg38	chr8	128551455	128561408	NA	MYC	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	NA	NA	SW620	CVCL_0547	colorectal cancer cell	NA	Functional cis-regulatory perturbation assay; target-gene expression assay; enhancer-promoter interaction assay; cellular fitness assay	tiling paired-gRNA CRISPRi proliferation screen; H3K27ac ChIP-seq; DNase-seq; H3K4me3 PLAC-seq	individual KRAB-dCas9 CRISPRi; qRT-PCR; cell proliferation assay
E_04386	2022	36351387	Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation	Homo sapiens	hg38	chr6	135053543	135055818	NA	MYB	Enhancer	Active	Disease	lung adenocarcinoma	MONDO:0005061	DOID:3910	NA	NA	A-549	CVCL_0023	lung adenocarcinoma cell	NA	Functional cis-regulatory perturbation assay; target-gene expression assay; enhancer-promoter interaction assay; cellular fitness assay	tiling paired-gRNA CRISPRi proliferation screen; H3K27ac ChIP-seq; DNase-seq; H3K4me3 PLAC-seq	individual KRAB-dCas9 CRISPRi; qRT-PCR; cell proliferation assay
E_04387	2022	36351387	Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation	Homo sapiens	hg38	chr8	127217807	127227986	NA	MYC	Enhancer	Active	Disease	lung adenocarcinoma	MONDO:0005061	DOID:3910	NA	NA	A-549	CVCL_0023	lung adenocarcinoma cell	NA	Functional cis-regulatory perturbation assay; target-gene expression assay; enhancer-promoter interaction assay; cellular fitness assay	tiling paired-gRNA CRISPRi proliferation screen; H3K27ac ChIP-seq; DNase-seq; H3K4me3 PLAC-seq	individual KRAB-dCas9 CRISPRi; qRT-PCR; cell proliferation assay
E_04388	2022	36351387	Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation	Homo sapiens	hg38	chr8	127850678	127855822	NA	MYC	Enhancer	Active	Disease	lung adenocarcinoma	MONDO:0005061	DOID:3910	NA	NA	A-549	CVCL_0023	lung adenocarcinoma cell	NA	Functional cis-regulatory perturbation assay; target-gene expression assay; enhancer-promoter interaction assay; cellular fitness assay	tiling paired-gRNA CRISPRi proliferation screen; H3K27ac ChIP-seq; DNase-seq; H3K4me3 PLAC-seq	individual KRAB-dCas9 CRISPRi; qRT-PCR; cell proliferation assay
E_04389	2022	36351387	Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation	Homo sapiens	hg38	chr8	128551556	128560975	NA	MYC	Enhancer	Active	Disease	lung adenocarcinoma	MONDO:0005061	DOID:3910	NA	NA	A-549	CVCL_0023	lung adenocarcinoma cell	NA	Functional cis-regulatory perturbation assay; target-gene expression assay; enhancer-promoter interaction assay; cellular fitness assay	tiling paired-gRNA CRISPRi proliferation screen; H3K27ac ChIP-seq; DNase-seq; H3K4me3 PLAC-seq	individual KRAB-dCas9 CRISPRi; qRT-PCR; cell proliferation assay
E_04390	2022	36351387	Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation	Homo sapiens	hg38	chr8	128551556	128562132	NA	MYC	Enhancer	Active	Disease	non-small cell lung carcinoma	MONDO:0005233	DOID:3908	NA	NA	NCI-H460	CVCL_0459	non-small cell lung carcinoma cell	NA	Functional cis-regulatory perturbation assay; target-gene expression assay; enhancer-promoter interaction assay; cellular fitness assay	tiling paired-gRNA CRISPRi proliferation screen; DNase-seq; H3K4me3 PLAC-seq	individual KRAB-dCas9 CRISPRi; qRT-PCR; cell proliferation assay
E_04391	2022	36351387	Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation	Homo sapiens	hg38	chr6	135053211	135054964	NA	MYB	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	NA	NA	MCF-7	CVCL_0031	breast cancer cell	NA	Functional cis-regulatory perturbation assay; target-gene expression assay; enhancer-promoter interaction assay; cellular fitness assay	tiling paired-gRNA CRISPRi proliferation screen; H3K27ac ChIP-seq; DNase-seq; H3K4me3 PLAC-seq	individual KRAB-dCas9 CRISPRi; qRT-PCR; cell proliferation assay
E_04392	2022	36351387	Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation	Homo sapiens	hg38	chr8	127864966	127875151	NA	MYC	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	NA	NA	MCF-7	CVCL_0031	breast cancer cell	NA	Functional cis-regulatory perturbation assay; target-gene expression assay; enhancer-promoter interaction assay; cellular fitness assay	tiling paired-gRNA CRISPRi proliferation screen; H3K27ac ChIP-seq; DNase-seq; H3K4me3 PLAC-seq	individual KRAB-dCas9 CRISPRi; qRT-PCR; cell proliferation assay
E_04393	2022	36351387	Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation	Homo sapiens	hg38	chr8	128136925	128146306	NA	MYC	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	NA	NA	MCF-7	CVCL_0031	breast cancer cell	NA	Functional cis-regulatory perturbation assay; target-gene expression assay; enhancer-promoter interaction assay; cellular fitness assay	tiling paired-gRNA CRISPRi proliferation screen; H3K27ac ChIP-seq; DNase-seq; H3K4me3 PLAC-seq	individual KRAB-dCas9 CRISPRi; qRT-PCR; cell proliferation assay
E_04394	2022	36351387	Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation	Homo sapiens	hg38	chr6	135052392	135057872	NA	MYB	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	NA	NA	MDA-MB-231	CVCL_0062	breast cancer cell	NA	Functional cis-regulatory perturbation assay; target-gene expression assay; enhancer-promoter interaction assay; cellular fitness assay	tiling paired-gRNA CRISPRi proliferation screen; H3K27ac ChIP-seq; DNase-seq; H3K4me3 PLAC-seq	individual KRAB-dCas9 CRISPRi; qRT-PCR; cell proliferation assay
E_04395	2022	36351387	Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation	Homo sapiens	hg38	chr6	135360375	135361636	NA	MYB	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	NA	NA	DU145	NA	prostate cancer cell	NA	Functional cis-regulatory perturbation assay; target-gene expression assay; enhancer-promoter interaction assay; cellular fitness assay	tiling paired-gRNA CRISPRi proliferation screen; H3K27ac ChIP-seq; DNase-seq; H3K4me3 PLAC-seq	individual KRAB-dCas9 CRISPRi; qRT-PCR; cell proliferation assay
E_04396	2022	36351387	Systematic discovery and functional dissection of enhancers needed for cancer cell fitness and proliferation	Homo sapiens	hg38	chr6	135053624	135057983	NA	MYB	Enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	NA	NA	PC-3	CVCL_0035	prostate cancer cell	NA	Functional cis-regulatory perturbation assay; target-gene expression assay; enhancer-promoter interaction assay; cellular fitness assay	tiling paired-gRNA CRISPRi proliferation screen; H3K27ac ChIP-seq; DNase-seq; H3K4me3 PLAC-seq	individual KRAB-dCas9 CRISPRi; qRT-PCR; cell proliferation assay
E_04397	2024	38849954	An oncogenic enhancer promotes melanoma progression via regulating ETV4 expression	Homo sapiens	hg38	chr17	59785798	59787315	STAT3	ETV4	Enhancer	Active	Disease	melanoma	MONDO:0005105	DOID:1909	NA	NA	A-375	CVCL_0132	melanoma cell	NA	Enhancer activity assay; TF binding assay; chromatin interaction assay; endogenous cis-regulatory perturbation assay; target-gene expression assay; rescue assay; cellular phenotype assay; in vivo tumorigenicity assay	RNA-seq; ChIP-seq; Hi-C; CUT&Tag; scRNA-seq	CRISPR/Cas9 endogenous enhancer deletion; Sanger sequencing; LNA-mediated enhancer inhibition; luciferase reporter assay; qPCR; Western blot; STAT3 siRNA knockdown; ETV4 siRNA knockdown; ETV4 rescue/overexpression; CCK-8 assay; EdU assay; colony formation assay; wound-healing assay; Transwell migration assay; xenograft tumor-growth assay
E_04398	2025	39954255	CRISPR screening identifies regulators of enhancer-mediated androgen receptor transcription in advanced prostate cancer	Homo sapiens	hg19	chrX	66117800	66128800	HOXB13	AR	Enhancer	Active	Disease	castration-resistant prostate cancer	MONDO:0850353	DOID:0080909	NA	NA	LNCaP	CVCL_0395	prostate cancer cell	NA	TF binding assay; enhancer activity regulation assay; enhancer-promoter interaction assay; target-gene expression assay; functional trans-regulatory perturbation assay	CRISPR-Cas9 transcription-factor screen; H3K27ac ChIP-seq; HOXB13 ChIP-seq; ATAC-seq; 4C-seq; RNA-seq	siRNA-mediated HOXB13 knockdown; CRISPRi of HOXB13; HOXB13 rescue; RT-qPCR; immunoblotting; ChIP-qPCR
E_04399	2025	39954255	CRISPR screening identifies regulators of enhancer-mediated androgen receptor transcription in advanced prostate cancer	Homo sapiens	hg19	chrX	66117800	66128800	GATA2	AR	Enhancer	Active	Disease	castration-resistant prostate cancer	MONDO:0850353	DOID:0080909	NA	NA	LNCaP	CVCL_0395	prostate cancer cell	NA	TF binding assay; enhancer activity regulation assay; enhancer-promoter interaction assay; target-gene expression assay; functional trans-regulatory perturbation assay	CRISPR-Cas9 transcription-factor screen; H3K27ac ChIP-seq; GATA2 ChIP-seq; ATAC-seq; 4C-seq; RNA-seq	siRNA-mediated GATA2 knockdown; shRNA-mediated GATA2 knockdown; RT-qPCR; immunoblotting; ChIP-qPCR
E_04400	2025	39954255	CRISPR screening identifies regulators of enhancer-mediated androgen receptor transcription in advanced prostate cancer	Homo sapiens	hg19	chrX	66117800	66128800	TFAP2C	AR	Enhancer	Active	Disease	castration-resistant prostate cancer	MONDO:0850353	DOID:0080909	NA	NA	LNCaP	CVCL_0395	prostate cancer cell	NA	TF binding assay; enhancer activity regulation assay; enhancer-promoter interaction assay; target-gene expression assay; functional trans-regulatory perturbation assay	CRISPR-Cas9 transcription-factor screen; H3K27ac ChIP-seq; TFAP2C ChIP-seq; ATAC-seq; 4C-seq; RNA-seq	siRNA-mediated TFAP2C knockdown; CRISPRi of TFAP2C; TFAP2C rescue; RT-qPCR; immunoblotting; ChIP-qPCR
E_04401	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr4	56595633	56597129	NA	NMU	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	chronic myeloid leukemia cell	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; single-cell transcriptional response assay	multiplexed dCas9-KRAB CRISPRi enhancer screen; single-cell RNA-seq	ChIP-qPCR
E_04402	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chrX	12974924	12975424	NA	TMSB4X	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	chronic myeloid leukemia cell	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; single-cell transcriptional response assay	multiplexed dCas9-KRAB CRISPRi enhancer screen; single-cell RNA-seq	ChIP-qPCR
E_04403	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr11	33966283	33966783	NA	LMO2	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	chronic myeloid leukemia cell	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; single-cell transcriptional response assay	multiplexed dCas9-KRAB CRISPRi enhancer screen; single-cell RNA-seq	ChIP-qPCR
E_04404	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr11	5301716	5302216	NA	HBG1	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	chronic myeloid leukemia cell	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; single-cell transcriptional response assay	multiplexed dCas9-KRAB CRISPRi enhancer screen; single-cell RNA-seq	ChIP-qPCR
E_04405	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr17	39686364	39687253	NA	KRT19	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	chronic myeloid leukemia cell	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; single-cell transcriptional response assay	multiplexed dCas9-KRAB CRISPRi enhancer screen; single-cell RNA-seq	ChIP-qPCR
E_04406	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr16	23832970	23833701	NA	PRKCB	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	chronic myeloid leukemia cell	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; single-cell transcriptional response assay	multiplexed dCas9-KRAB CRISPRi enhancer screen; single-cell RNA-seq	ChIP-qPCR
E_04407	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr11	61738881	61739765	NA	FTH1	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	chronic myeloid leukemia cell	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; single-cell transcriptional response assay	multiplexed dCas9-KRAB CRISPRi enhancer screen; single-cell RNA-seq	ChIP-qPCR
E_04408	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr2	127402807	127403307	NA	GYPC	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	chronic myeloid leukemia cell	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; single-cell transcriptional response assay	multiplexed dCas9-KRAB CRISPRi enhancer screen; single-cell RNA-seq	ChIP-qPCR
E_04409	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chrX	48641226	48641726	NA	GATA1	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	chronic myeloid leukemia cell	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; single-cell transcriptional response assay	multiplexed dCas9-KRAB CRISPRi enhancer screen; single-cell RNA-seq	ChIP-qPCR
E_04410	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr6	49613633	49614484	NA	RHAG	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	chronic myeloid leukemia cell	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; single-cell transcriptional response assay	multiplexed dCas9-KRAB CRISPRi enhancer screen; single-cell RNA-seq	ChIP-qPCR
E_04411	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr20	30198365	30198865	NA	ID1	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	chronic myeloid leukemia cell	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; single-cell transcriptional response assay	multiplexed dCas9-KRAB CRISPRi enhancer screen; single-cell RNA-seq	ChIP-qPCR
E_04412	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr7	12762308	12762808	NA	ARL4A	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	chronic myeloid leukemia cell	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; single-cell transcriptional response assay	multiplexed dCas9-KRAB CRISPRi enhancer screen; single-cell RNA-seq	ChIP-qPCR
E_04413	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chrX	102488101	102488601	NA	BEX4	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	chronic myeloid leukemia cell	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; single-cell transcriptional response assay	multiplexed dCas9-KRAB CRISPRi enhancer screen; single-cell RNA-seq	ChIP-qPCR
E_04414	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr2	55367486	55368618	NA	RTN4	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	chronic myeloid leukemia cell	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; single-cell transcriptional response assay	multiplexed dCas9-KRAB CRISPRi enhancer screen; single-cell RNA-seq	ChIP-qPCR
E_04415	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr6	125628090	125628962	NA	HDDC2	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	chronic myeloid leukemia cell	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; single-cell transcriptional response assay	multiplexed dCas9-KRAB CRISPRi enhancer screen; single-cell RNA-seq	ChIP-qPCR
E_04416	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr1	29210277	29210777	NA	EPB41	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	chronic myeloid leukemia cell	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; single-cell transcriptional response assay	multiplexed dCas9-KRAB CRISPRi enhancer screen; single-cell RNA-seq	ChIP-qPCR
E_04417	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr9	75763292	75764854	NA	ANXA1	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	chronic myeloid leukemia cell	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; single-cell transcriptional response assay	multiplexed dCas9-KRAB CRISPRi enhancer screen; single-cell RNA-seq	ChIP-qPCR
E_04418	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr12	4262393	4263146	NA	CCND2	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	chronic myeloid leukemia cell	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; single-cell transcriptional response assay	multiplexed dCas9-KRAB CRISPRi enhancer screen; single-cell RNA-seq	ChIP-qPCR
E_04419	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr1	231182426	231182926	NA	FAM89A	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	chronic myeloid leukemia cell	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; single-cell transcriptional response assay	multiplexed dCas9-KRAB CRISPRi enhancer screen; single-cell RNA-seq	ChIP-qPCR
E_04420	2019	30612741	A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens	Homo sapiens	hg19	chr1	95550891	95551391	NA	TMEM56	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	chronic myeloid leukemia cell	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; single-cell transcriptional response assay	multiplexed dCas9-KRAB CRISPRi enhancer screen; single-cell RNA-seq	ChIP-qPCR
E_04421	2021	34326544	Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR-FlowFISH	Homo sapiens	hg38	chr11	5275847	5276247	NA	HBG1	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; endogenous CRE activity assay	CRISPRi HCR-FlowFISH screen; pooled sgRNA tiling; flow-cytometry-based transcript quantification	individual sgRNA perturbation; RT-qPCR validation
E_04422	2021	34326544	Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR-FlowFISH	Homo sapiens	hg38	chr11	61841500	61842900	NA	FADS3	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; endogenous CRE activity assay; reporter validation	CRISPRi HCR-FlowFISH screen; pooled sgRNA tiling; MPRA	individual sgRNA perturbation; RT-qPCR validation
E_04423	2021	34326544	Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR-FlowFISH	Homo sapiens	hg38	chr12	111994126	111994726	NA	ERP29	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; endogenous CRE activity assay	CRISPRi HCR-FlowFISH screen; pooled sgRNA tiling; flow-cytometry-based transcript quantification	individual sgRNA perturbation; RT-qPCR validation
E_04424	2021	34326544	Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR-FlowFISH	Homo sapiens	hg38	chr12	111995026	111995626	NA	ERP29	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; endogenous CRE activity assay	CRISPRi HCR-FlowFISH screen; pooled sgRNA tiling; flow-cytometry-based transcript quantification	individual sgRNA perturbation; RT-qPCR validation
E_04425	2021	34326544	Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR-FlowFISH	Homo sapiens	hg38	chr4	55670441	55671441	NA	NMU	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; endogenous CRE activity assay	CRISPRi HCR-FlowFISH screen; pooled sgRNA tiling; flow-cytometry-based transcript quantification	individual sgRNA perturbation; RT-qPCR validation
E_04426	2021	34326544	Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR-FlowFISH	Homo sapiens	hg38	chr5	89054814	89055614	NA	MEF2C	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; endogenous CRE activity assay	CRISPRi HCR-FlowFISH screen; pooled sgRNA tiling; flow-cytometry-based transcript quantification	individual sgRNA perturbation; RT-qPCR validation
E_04427	2023	37141313	Discovery of target genes and pathways at GWAS loci by pooled single-cell CRISPR screens	Homo sapiens	hg38	chr1	206671959	206673955	NA	MAPKAPK2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; chromatin interaction assay; GWAS regulatory-element functional assay	STING-seq pooled KRAB-dCas9-MeCP2 CRISPRi; single-cell RNA-seq; single-cell proteomic profiling; ATAC-seq; DNase-seq; H3K27ac ChIP-seq; H3K27ac HiChIP	ChIP-qPCR
E_04428	2023	37141313	Discovery of target genes and pathways at GWAS loci by pooled single-cell CRISPR screens	Homo sapiens	hg38	chr1	26321184	26321972	NA	CD52	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; target-protein expression assay; GWAS regulatory-element functional assay	STING-seq pooled KRAB-dCas9-MeCP2 CRISPRi; single-cell RNA-seq; oligo-tagged single-cell proteomics; ATAC-seq; DNase-seq; H3K27ac ChIP-seq; H3K27ac HiChIP	ChIP-qPCR
E_04429	2023	37141313	Discovery of target genes and pathways at GWAS loci by pooled single-cell CRISPR screens	Homo sapiens	hg38	chr9	132998625	132999653	NA	GFI1B	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; trans-regulatory network assay; GWAS regulatory-element functional assay	STING-seq pooled KRAB-dCas9-MeCP2 CRISPRi; single-cell RNA-seq; single-cell proteomics; ATAC-seq; DNase-seq; H3K27ac ChIP-seq	ChIP-qPCR
E_04430	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr8	102209982	102210471	NA	ZNF706	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04431	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr8	102210474	102211148	NA	ZNF706	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04432	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr8	124178948	124180157	NA	FAM83A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04433	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr8	124193563	124193945	NA	FAM83A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04434	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr8	124193998	124194195	NA	FAM83A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04435	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr8	97288536	97288894	NA	PTDSS1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04436	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr8	98789673	98790725	NA	LAPTM4B	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04437	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr8	98790775	98790901	NA	LAPTM4B	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04438	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr8	98790908	98791090	NA	LAPTM4B	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04439	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr11	5301792	5302144	NA	HBE1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04440	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr11	17374297	17375700	NA	NCR3LG1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04441	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr11	1783608	1784126	NA	CTSD	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04442	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr11	18414412	18414793	NA	LDHA	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04443	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr11	20388955	20389476	NA	HTATIP2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04444	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr11	2988913	2989223	NA	NAP1L4	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04445	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr11	316245	316608	NA	IFITM1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04446	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr11	326862	327696	NA	IFITM1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04447	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr11	329320	329921	NA	IFITM1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04448	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr11	350705	351232	NA	IFITM1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04449	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr11	353335	354301	NA	IFITM1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04450	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr11	355351	355535	NA	IFITM1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04451	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr11	356035	356520	NA	IFITM1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04452	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr11	3852741	3853403	NA	RHOG	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04453	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr11	3854684	3855091	NA	RHOG	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04454	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr11	3855557	3856826	NA	RHOG	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04455	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr11	3859821	3860019	NA	RHOG	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04456	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr11	407323	407640	NA	SIGIRR	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04457	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr11	503417	503684	NA	RNH1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04458	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr11	5293980	5294173	NA	HBE1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04459	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr11	5705493	5705627	NA	TRIM5	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04460	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr11	5705628	5706756	NA	TRIM5	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04461	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr11	6627979	6628950	NA	ILK	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04462	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr11	6639261	6640007	NA	TPP1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04463	2020	32483332	Targeted Perturb-seq enables genome-scale genetic screens in single cells	Homo sapiens	hg19	chr11	8935492	8935987	NA	AKIP1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; enhancer activity assay	TAP-seq; pooled dCas9-KRAB CRISPRi enhancer screen; targeted single-cell RNA-seq; DNase-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; Hi-C	ChIP-qPCR
E_04464	2025	40533554	In vivo mapping of mutagenesis sensitivity of human enhancers	Homo sapiens	hg38	chr8	48582383	48582610	NA	SNAI2	Enhancer	Active	Normal	NA	NA	NA	craniofacial region; limb bud	NA	NA	NA	NA	NA	In vivo enhancer activity assay; systematic enhancer mutagenesis assay; enhancer sequence-function assay; enhancer-promoter interaction-supported target assignment	ATAC-seq; scATAC-seq; DNase-seq; ChromBPNet sequence-to-accessibility modeling; DeepLIFT saturation mutagenesis prediction	CRISPR-mediated safe-harbor transgenic mouse enhancer reporter assay; LacZ staining; 12-bp block mutagenesis; single-block mutagenesis; targeted single-/double-nucleotide mutagenesis
E_04465	2025	40533554	In vivo mapping of mutagenesis sensitivity of human enhancers	Homo sapiens	hg38	chr12	113932853	113933123	NA	LHX5	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	NA	NA	NA	NA	In vivo enhancer activity assay; systematic enhancer mutagenesis assay; enhancer sequence-function assay; enhancer-promoter interaction-supported target assignment	ATAC-seq; scATAC-seq; DNase-seq; ChromBPNet sequence-to-accessibility modeling; DeepLIFT saturation mutagenesis prediction	CRISPR-mediated safe-harbor transgenic mouse enhancer reporter assay; LacZ staining; 12-bp block mutagenesis; single-block mutagenesis; targeted nucleotide mutagenesis
E_04466	2025	40533554	In vivo mapping of mutagenesis sensitivity of human enhancers	Homo sapiens	hg38	chr20	57157319	57157541	NA	BMP7	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	NA	NA	NA	NA	In vivo enhancer activity assay; systematic enhancer mutagenesis assay; enhancer sequence-function assay; enhancer-promoter interaction-supported target assignment	ATAC-seq; scATAC-seq; DNase-seq; ChromBPNet sequence-to-accessibility modeling; DeepLIFT saturation mutagenesis prediction	CRISPR-mediated safe-harbor transgenic mouse enhancer reporter assay; LacZ staining; 12-bp block mutagenesis; single-block mutagenesis; targeted single-/double-nucleotide mutagenesis
E_04467	2025	40533554	In vivo mapping of mutagenesis sensitivity of human enhancers	Homo sapiens	hg38	chr17	29667963	29668260	NA	EFCAB5	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	NA	NA	NA	NA	In vivo enhancer activity assay; systematic enhancer mutagenesis assay; enhancer sequence-function assay; enhancer-promoter interaction-supported target assignment	ATAC-seq; scATAC-seq; DNase-seq; ChromBPNet sequence-to-accessibility modeling; DeepLIFT saturation mutagenesis prediction	CRISPR-mediated safe-harbor transgenic mouse enhancer reporter assay; LacZ staining; 12-bp block mutagenesis; single-block mutagenesis; targeted nucleotide mutagenesis
E_04468	2025	40533554	In vivo mapping of mutagenesis sensitivity of human enhancers	Homo sapiens	hg38	chr7	150964528	150964958	NA	AGAP3	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	NA	NA	NA	NA	In vivo enhancer activity assay; systematic enhancer mutagenesis assay; enhancer sequence-function assay; enhancer-promoter interaction-supported target assignment	ATAC-seq; scATAC-seq; DNase-seq; ChromBPNet sequence-to-accessibility modeling; DeepLIFT saturation mutagenesis prediction	CRISPR-mediated safe-harbor transgenic mouse enhancer reporter assay; LacZ staining; 12-bp block mutagenesis; single-block mutagenesis; targeted nucleotide mutagenesis
E_04469	2016	27681417	Super-Enhancers at the Nanog Locus Differentially Regulate Neighboring Pluripotency-Associated Genes	Mus musculus	mm9	chr6	122612514	122614260	NA	Nanog	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Endogenous super-enhancer deletion assay; target-gene expression assay; enhancer-promoter interaction assay; cellular pluripotency regulatory assay	RNA-seq; chromatin interaction profiling	CRISPR/Cas9 endogenous super-enhancer deletion; RT-qPCR; eRNA depletion; chromatin-loop validation
E_04470	2016	27681417	Super-Enhancers at the Nanog Locus Differentially Regulate Neighboring Pluripotency-Associated Genes	Mus musculus	mm9	chr6	122612514	122614260	NA	Dppa3	Super-enhancer	Active	Normal	NA	NA	NA	NA	NA	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Endogenous super-enhancer deletion assay; target-gene expression assay; enhancer-promoter interaction assay; eRNA functional assay	RNA-seq; chromatin interaction profiling	CRISPR/Cas9 endogenous super-enhancer deletion; RT-qPCR; enhancer-RNA depletion; chromatin-loop validation
E_04471	2026	41413662	CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer's disease	Homo sapiens	hg38	chr11	61971767	61972148	NA	FTH1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	normal human astrocytes (NHA; Lonza CC-2565)	NA	astrocyte	CL:0000127	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; disease-relevant enhancer validation	Pooled dCas9-KRAB CRISPRi screen; single-cell RNA-seq; ATAC-seq; bulk RNA-seq; TT-seq	Individual CRISPRi; NanoString nCounter; western blot
E_04472	2026	41413662	CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer's disease	Homo sapiens	hg38	chr7	76291557	76291943	NA	HSPB1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	normal human astrocytes (NHA; Lonza CC-2565)	NA	astrocyte	CL:0000127	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; disease-relevant enhancer validation	Pooled dCas9-KRAB CRISPRi screen; single-cell RNA-seq; ATAC-seq; bulk RNA-seq; TT-seq	Individual CRISPRi; NanoString nCounter
E_04473	2026	41413662	CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer's disease	Homo sapiens	hg38	chr14	55102181	55102519	NA	LGALS3	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	normal human astrocytes (NHA; Lonza CC-2565)	NA	astrocyte	CL:0000127	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; disease-relevant enhancer validation	Pooled dCas9-KRAB CRISPRi screen; single-cell RNA-seq; ATAC-seq; bulk RNA-seq; TT-seq	Individual CRISPRi; NanoString nCounter
E_04474	2026	41413662	CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer's disease	Homo sapiens	hg38	chr7	76294322	76294561	NA	HSPB1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	normal human astrocytes (NHA; Lonza CC-2565)	NA	astrocyte	CL:0000127	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; disease-relevant enhancer validation	Pooled dCas9-KRAB CRISPRi screen; single-cell RNA-seq; ATAC-seq; bulk RNA-seq; TT-seq	Individual CRISPRi; NanoString nCounter
E_04475	2026	41413662	CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer's disease	Homo sapiens	hg38	chr1	23554524	23555279	NA	ID3	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	normal human astrocytes (NHA; Lonza CC-2565)	NA	astrocyte	CL:0000127	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; disease-relevant enhancer validation	Pooled dCas9-KRAB CRISPRi screen; single-cell RNA-seq; ATAC-seq; bulk RNA-seq; TT-seq	Individual CRISPRi; NanoString nCounter; qRT-PCR in an independent NHA donor line
E_04476	2026	41413662	CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer's disease	Homo sapiens	hg38	chr14	55103223	55103547	NA	LGALS3	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	normal human astrocytes (NHA; Lonza CC-2565)	NA	astrocyte	CL:0000127	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; disease-relevant enhancer validation	Pooled dCas9-KRAB CRISPRi screen; single-cell RNA-seq; ATAC-seq; bulk RNA-seq; TT-seq	Individual CRISPRi; NanoString nCounter
E_04477	2026	41413662	CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer's disease	Homo sapiens	hg38	chr7	76306789	76306923	NA	HSPB1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	normal human astrocytes (NHA; Lonza CC-2565)	NA	astrocyte	CL:0000127	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; disease-relevant enhancer validation	Pooled dCas9-KRAB CRISPRi screen; single-cell RNA-seq; ATAC-seq; bulk RNA-seq; TT-seq	Individual CRISPRi; NanoString nCounter
E_04478	2026	41413662	CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer's disease	Homo sapiens	hg38	chr14	55107890	55108603	NA	LGALS3	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	normal human astrocytes (NHA; Lonza CC-2565)	NA	astrocyte	CL:0000127	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; disease-relevant enhancer validation	Pooled dCas9-KRAB CRISPRi screen; single-cell RNA-seq; ATAC-seq; bulk RNA-seq; TT-seq	Individual CRISPRi; NanoString nCounter
E_04479	2026	41413662	CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer's disease	Homo sapiens	hg38	chr11	65418681	65419290	NA	NEAT1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	normal human astrocytes (NHA; Lonza CC-2565)	NA	astrocyte	CL:0000127	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; disease-relevant enhancer validation	Pooled dCas9-KRAB CRISPRi screen; single-cell RNA-seq; ATAC-seq; bulk RNA-seq; TT-seq	Individual CRISPRi; NanoString nCounter
E_04480	2026	41413662	CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer's disease	Homo sapiens	hg38	chr2	231611831	231612337	NA	PTMA	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	normal human astrocytes (NHA; Lonza CC-2565)	NA	astrocyte	CL:0000127	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; disease-relevant enhancer validation	Pooled dCas9-KRAB CRISPRi screen; single-cell RNA-seq; ATAC-seq; bulk RNA-seq; TT-seq	Individual CRISPRi; NanoString nCounter
E_04481	2026	41413662	CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer's disease	Homo sapiens	hg38	chr10	71860268	71860879	NA	PSAP	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	normal human astrocytes (NHA; Lonza CC-2565)	NA	astrocyte	CL:0000127	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; disease-relevant enhancer validation	Pooled dCas9-KRAB CRISPRi screen; single-cell RNA-seq; ATAC-seq; bulk RNA-seq; TT-seq	Individual CRISPRi; NanoString nCounter
E_04482	2026	41413662	CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer's disease	Homo sapiens	hg38	chr2	231666365	231666792	NA	PTMA	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	normal human astrocytes (NHA; Lonza CC-2565)	NA	astrocyte	CL:0000127	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; disease-relevant enhancer validation	Pooled dCas9-KRAB CRISPRi screen; single-cell RNA-seq; ATAC-seq; bulk RNA-seq; TT-seq	Individual CRISPRi; NanoString nCounter
E_04483	2026	41413662	CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer's disease	Homo sapiens	hg38	chr11	65420025	65420260	NA	NEAT1	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	normal human astrocytes (NHA; Lonza CC-2565)	NA	astrocyte	CL:0000127	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; disease-relevant enhancer validation	Pooled dCas9-KRAB CRISPRi screen; single-cell RNA-seq; ATAC-seq; bulk RNA-seq; TT-seq	Individual CRISPRi; NanoString nCounter
E_04484	2026	41413662	CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer's disease	Homo sapiens	hg38	chr2	231662113	231662589	NA	PTMA	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	normal human astrocytes (NHA; Lonza CC-2565)	NA	astrocyte	CL:0000127	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; disease-relevant enhancer validation	Pooled dCas9-KRAB CRISPRi screen; single-cell RNA-seq; ATAC-seq; bulk RNA-seq; TT-seq	Individual CRISPRi; NanoString nCounter
E_04485	2026	41413662	CRISPRi screening in cultured human astrocytes uncovers distal enhancers controlling genes dysregulated in Alzheimer's disease	Homo sapiens	hg38	chr10	90931002	90931592	NA	PCGF5	Enhancer	Active	Disease	Alzheimer disease	MONDO:0004975	DOID:10652	brain	UBERON:0000955	normal human astrocytes (NHA; Lonza CC-2565)	NA	astrocyte	CL:0000127	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; disease-relevant enhancer validation	Pooled dCas9-KRAB CRISPRi screen; single-cell RNA-seq; ATAC-seq; bulk RNA-seq; TT-seq	Individual CRISPRi; NanoString nCounter
E_04486	2022	35406623	Enhancer RNA Transcription Is Essential for a Novel CSF1 Enhancer in Triple-Negative Breast Cancer	Homo sapiens	hg38	chr1	110419306	110420815	NA	CSF1	Enhancer	Active	Disease	triple-negative breast carcinoma	MONDO:0005494	DOID:0060081	NA	NA	MDA-MB-436	CVCL_0623	NA	NA	Endogenous enhancer deletion assay; epigenetic enhancer perturbation assay; enhancer-target gene expression assay; eRNA functional assay; cancer phenotype assay	GRO-seq; H3K27ac ChIP-seq; ATAC-seq; RNA-seq; TCGA ATAC-seq; METABRIC transcriptomic analysis	CRISPR-Cas9 enhancer deletion; deletion genotyping PCR; Sanger sequencing; dCas9-KRAB CRISPRi; qRT-PCR; PspCas13b eRNA degradation; RfxCas13d eRNA degradation; siRNA eRNA knockdown; proliferation assay; Transwell migration assay; colony formation assay; Annexin V/PI apoptosis assay
E_04487	2022	35406623	Enhancer RNA Transcription Is Essential for a Novel CSF1 Enhancer in Triple-Negative Breast Cancer	Homo sapiens	hg38	chr1	110419306	110420815	NA	CSF1	Enhancer	Active	Disease	triple-negative breast carcinoma	MONDO:0005494	DOID:0060081	NA	NA	MDA-MB-468	CVCL_0419	NA	NA	Endogenous enhancer deletion assay; enhancer-target gene expression assay; independent TNBC cell-model validation	GRO-seq; H3K27ac ChIP-seq; ATAC-seq	CRISPR-Cas9 enhancer deletion; deletion genotyping; qRT-PCR
E_04488	2022	35406623	Enhancer RNA Transcription Is Essential for a Novel CSF1 Enhancer in Triple-Negative Breast Cancer	Homo sapiens	hg38	chr1	110419306	110420815	NA	CSF1	Enhancer	Active	Disease	ovarian serous adenocarcinoma	MONDO:0005211	DOID:5744	NA	NA	OVCAR-3	CVCL_0465	NA	NA	Epigenetic enhancer perturbation assay; enhancer-target gene expression assay; eRNA functional assay; cross-cancer enhancer validation	H3K27ac ChIP-seq; BRD4 ChIP-seq; TCGA pan-cancer expression analysis	dCas9-KRAB CRISPRi; qRT-PCR; PspCas13b eRNA degradation; Western blot
E_04489	2025	39948336	Comprehensive dissection of cis-regulatory elements in a 2.8 Mb topologically associated domain in six human cancers	Homo sapiens	hg19	chr8	128918899	128922009	NA	MYC	Enhancer	Active	Disease	melanoma	MONDO:0005105	DOID:1909	NA	NA	A-375	CVCL_0132	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; cancer cell growth assay; enhancer-promoter chromatin interaction assay	Pooled saturation CRISPRi tiling screen; sgRNA abundance sequencing; H3K27ac HiChIP; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; DNase-seq; NET-CAGE	Individual CRISPRi with three independent sgRNAs; MYC qPCR; CellTiter-Glo proliferation assay
E_04490	2025	39948336	Comprehensive dissection of cis-regulatory elements in a 2.8 Mb topologically associated domain in six human cancers	Homo sapiens	hg19	chr8	128971508	128973955	NA	MYC	Enhancer	Active	Disease	chronic myeloid leukemia	MONDO:0011996	DOID:8552	NA	NA	K-562	CVCL_0004	NA	NA	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; cancer cell growth assay; enhancer-promoter chromatin interaction assay	Pooled saturation CRISPRi tiling screen; sgRNA abundance sequencing; H3K27ac HiChIP; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; DNase-seq; NET-CAGE	Individual CRISPRi with three independent sgRNAs; MYC digital PCR; CellTiter-Glo proliferation assay
E_04491	2020	33113365	Defining Essential Enhancers for Pluripotent Stem Cells Using a Features-Oriented CRISPR-Cas9 Screen	Mus musculus	mm9	chr3	30622815	30624315	4-Oct	Lrrc31	Enhancer	Active	Normal	NA	NA	NA	NA	NA	ES-E14	CVCL_C320	embryonic stem cell	CL:0002322	Functional cis-regulatory perturbation assay; enhancer activity assay; enhancer-target gene interaction assay; enhancer-target gene expression assay; rescue assay; pluripotency phenotype assay	FOCUS CRISPR-Cas9 screen; ATAC-seq; OCT4 ChIP-seq; histone ChIP-seq; RNA-seq; 4C-seq; Hi-C integration; STAT3 ChIP-seq; proteomics	Independent sgRNA CRISPR validation; OCT4-motif mutation; SURVEYOR assay; targeted mutation sequencing; qRT-PCR; luciferase reporter assay; 3C; OCT4 ChIP-qPCR; alkaline phosphatase colony assay; embryoid body assay; somatic cell reprogramming assay; Lrrc31 siRNA/shRNA/CRISPR knockout; Lrrc31 overexpression rescue; Western blot
E_04492	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr21	25860076	25860781	NA	APP	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04493	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr21	25877281	25879361	NA	APP	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04494	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr21	25885332	25887393	NA	APP	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	Individual paired-sgRNA CRISPR deletion; flow cytometry; genotyping PCR; RT-qPCR
E_04495	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr21	25915500	25916543	NA	APP	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04496	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr21	26029930	26033014	NA	APP	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04497	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr21	26075785	26077283	NA	APP	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04498	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr21	26168392	26169982	NA	APP	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04499	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chrX	147913308	147914958	NA	FMR1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	Individual paired-sgRNA CRISPR deletion; flow cytometry; genotyping PCR
E_04500	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chrX	154019379	154020754	NA	MECP2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04501	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chrX	154022250	154023504	NA	MECP2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04502	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chrX	154024507	154026006	NA	MECP2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	Individual paired-sgRNA CRISPR deletion; independent deletion clones; flow cytometry; RT-qPCR; genotyping PCR
E_04503	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chrX	154027372	154028921	NA	MECP2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04504	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chrX	154035030	154038261	NA	MECP2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04505	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chrX	154040709	154041748	NA	MECP2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	Individual paired-sgRNA CRISPR deletion; flow cytometry; genotyping PCR
E_04506	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chrX	154045056	154047131	NA	MECP2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04507	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chrX	154049781	154050862	NA	MECP2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	Individual paired-sgRNA CRISPR deletion; independent deletion clones; flow cytometry; RT-qPCR; genotyping PCR
E_04508	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chrX	154055960	154057569	NA	MECP2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04509	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chrX	154060475	154061957	NA	MECP2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	Individual paired-sgRNA CRISPR deletion; independent deletion clones; flow cytometry; RT-qPCR; genotyping PCR
E_04510	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chrX	154077906	154081716	NA	MECP2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04511	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chrX	154100107	154105497	NA	MECP2	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04512	1995	7720572	Embryonic activation of the myoD gene is regulated by a highly conserved distal control element	Mus musculus	mm39	chr7	46002074	46003486	NA	Myod1	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	transgenic mouse embryo	NA	myogenic cell	CL:0000187	In vivo enhancer reporter assay; developmental enhancer mapping assay	Comparative sequence analysis	Transgenic LacZ reporter assay; deletion mapping; embryonic skeletal muscle expression analysis
E_04513	1999	10101129	Fine-scale transgenic mapping of the MyoD core enhancer: MyoD is regulated by distinct but overlapping mechanisms in myotomal and non-myotomal muscle lineages	Mus musculus	mm39	chr7	46002074	46003486	NA	Myod1	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	transgenic mouse embryo	NA	myogenic cell	CL:0000187	In vivo enhancer reporter assay; enhancer fine-mapping assay; enhancer mutagenesis assay	NA	Transgenic LacZ reporter assay; linker-scanning mutagenesis; developmental expression analysis; enhancer deletion-series analysis
E_04514	2004	14732408	The core enhancer is essential for proper timing of MyoD activation in limb buds and branchial arches	Mus musculus	mm39	chr7	46002074	46003486	NA	Myod1	Enhancer	Active	Normal	NA	NA	NA	skeletal muscle tissue	UBERON:0001134	mouse embryo	NA	myogenic cell	CL:0000187	Endogenous enhancer deletion assay; developmental gene-expression assay	NA	Targeted deletion of the MyoD core enhancer; RNA expression analysis; embryonic skeletal-muscle developmental analysis
E_04515	1987	3678824	An albumin enhancer located 10 kb upstream functions along with its promoter to direct efficient, liver-specific expression in transgenic mice	Mus musculus	mm39	chr5	90598256	90600256	NA	Alb	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	transgenic mouse liver	NA	hepatocyte	CL:0000182	In vivo enhancer reporter assay; tissue-specific enhancer assay	NA	Transgenic mouse reporter assay; orientation-independent enhancer assay; deletion analysis; tissue-specific expression analysis
E_04516	1989	2922398	Positive and negative regulatory elements in the mouse albumin enhancer	Mus musculus	mm39	chr5	90598256	90600256	Cebpa	Alb	Enhancer	Active	Normal	NA	NA	NA	liver	UBERON:0002107	mouse liver	NA	hepatocyte	CL:0000182	Enhancer functional dissection assay; TF-binding assay; positive/negative cis-element assay	NA	Reporter assay; enhancer deletion analysis; DNA-binding assay; C/EBP-binding analysis
E_04517	2016	27707736	Strict in vivo specificity of the Bcl11a erythroid enhancer	Mus musculus	mm10	chr11	24044043	24197927	NA	Bcl11a	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	fetal liver erythroid cells	NA	erythroblast	CL:0000765	Endogenous enhancer deletion assay; lineage-specific enhancer requirement assay; developmental globin regulation assay	NA	Germline deletion of the Bcl11a intronic enhancer; flow cytometry; qRT-PCR; fetal globin expression analysis; bone-marrow transplantation
E_04518	2008	18687876	A novel mode of enhancer evolution: the Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity	Mus musculus	mm10	chr4	115758000	115763500	Gata2	Tal1	Enhancer	Active	Normal	NA	NA	NA	hematopoietic system	UBERON:0002390	hematopoietic stem/progenitor cells	NA	hematopoietic stem cell	CL:0000037	Enhancer activity assay; enhancer-booster functional assay; TF-site functional assay	Comparative genomics; chromatin profiling	Transgenic LacZ reporter assay; stable reporter assay; single-copy Hprt reporter integration; GATA/ETS-site analysis; MIR-element deletion
E_04519	2009	19171877	Expression of the leukemia oncogene Lmo2 is controlled by an array of tissue-specific elements dispersed over 100 kb and bound by Tal1/Lmo2, Ets, and Gata factors	Mus musculus	mm39	chr2	103731755	103732196	Tal1	Lmo2	Enhancer	Active	Normal	NA	NA	NA	hematopoietic system	UBERON:0002390	primary mouse hematopoietic cells	NA	hematopoietic cell	CL:0000988	Enhancer activity assay; TF-binding assay; tissue-specific enhancer assay; in vivo developmental reporter assay	ChIP-chip; comparative genomics	Transgenic mouse reporter assay; luciferase reporter assay; TF transactivation assay; EMSA; mutational analysis
E_04520	2009	19171877	Expression of the leukemia oncogene Lmo2 is controlled by an array of tissue-specific elements dispersed over 100 kb and bound by Tal1/Lmo2, Ets, and Gata factors	Mus musculus	mm39	chr2	103731755	103732196	Gata2	Lmo2	Enhancer	Active	Normal	NA	NA	NA	hematopoietic system	UBERON:0002390	primary mouse hematopoietic cells	NA	hematopoietic cell	CL:0000988	Enhancer activity assay; TF-binding assay; tissue-specific enhancer assay; in vivo developmental reporter assay	ChIP-chip; comparative genomics	Transgenic mouse reporter assay; luciferase reporter assay; TF transactivation assay; EMSA; mutational analysis
E_04521	2009	19171877	Expression of the leukemia oncogene Lmo2 is controlled by an array of tissue-specific elements dispersed over 100 kb and bound by Tal1/Lmo2, Ets, and Gata factors	Mus musculus	mm39	chr2	103731755	103732196	Fli1	Lmo2	Enhancer	Active	Normal	NA	NA	NA	hematopoietic system	UBERON:0002390	primary mouse hematopoietic cells	NA	hematopoietic cell	CL:0000988	Enhancer activity assay; TF-binding assay; tissue-specific enhancer assay; in vivo developmental reporter assay	ChIP-chip; comparative genomics	Transgenic mouse reporter assay; luciferase reporter assay; TF transactivation assay; EMSA; mutational analysis
E_04522	2009	19171877	Expression of the leukemia oncogene Lmo2 is controlled by an array of tissue-specific elements dispersed over 100 kb and bound by Tal1/Lmo2, Ets, and Gata factors	Mus musculus	mm39	chr2	103731755	103732196	Sfpi1	Lmo2	Enhancer	Active	Normal	NA	NA	NA	hematopoietic system	UBERON:0002390	primary mouse hematopoietic cells	NA	hematopoietic cell	CL:0000988	Enhancer activity assay; TF-binding assay; tissue-specific enhancer assay; in vivo developmental reporter assay	ChIP-chip; comparative genomics	Transgenic mouse reporter assay; luciferase reporter assay; TF transactivation assay; EMSA; mutational analysis
E_04523	2009	19171877	Expression of the leukemia oncogene Lmo2 is controlled by an array of tissue-specific elements dispersed over 100 kb and bound by Tal1/Lmo2, Ets, and Gata factors	Mus musculus	mm39	chr2	103731755	103732196	Lmo2	Lmo2	Enhancer	Active	Normal	NA	NA	NA	hematopoietic system	UBERON:0002390	primary mouse hematopoietic cells	NA	hematopoietic cell	CL:0000988	Enhancer activity assay; TF-binding assay; tissue-specific enhancer assay; in vivo developmental reporter assay	ChIP-chip; comparative genomics	Transgenic mouse reporter assay; luciferase reporter assay; TF transactivation assay; EMSA; mutational analysis
E_04524	2011	21321362	An embryonic stage-specific enhancer within the murine beta-globin locus mediates domain-wide histone hyperacetylation	Mus musculus	mm39	chr7	103496069	103496784	NA	Hbb-y	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primitive erythroid cells	NA	erythroblast	CL:0000765	Endogenous enhancer deletion assay; developmental-stage-specific enhancer assay; chromatin-state assay; target-gene expression assay	DNase I hypersensitivity profiling; histone ChIP profiling	Luciferase reporter assay; targeted HS-E1 deletion; RT-qPCR; embryonic blood analysis
E_04525	2011	21321362	An embryonic stage-specific enhancer within the murine beta-globin locus mediates domain-wide histone hyperacetylation	Mus musculus	mm39	chr7	103496069	103496784	NA	Hbb-bh1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primitive erythroid cells	NA	erythroblast	CL:0000765	Endogenous enhancer deletion assay; developmental-stage-specific enhancer assay; chromatin-state assay; target-gene expression assay	DNase I hypersensitivity profiling; histone ChIP profiling	Luciferase reporter assay; targeted HS-E1 deletion; RT-qPCR; embryonic blood analysis
E_04526	2017	27993987	The mammal-specific Pdx1 Area II enhancer has multiple essential functions in early endocrine cell specification and postnatal β-cell maturation	Mus musculus	mm39	chr5	147208900	147209155	NA	Pdx1	Enhancer	Active	Normal	NA	NA	NA	pancreas	UBERON:0001264	primary mouse pancreatic endocrine cells	NA	pancreatic endocrine cell	CL:0008024	Endogenous enhancer deletion assay; developmental lineage assay; target-gene expression assay; cell-fate phenotype assay	NA	Targeted Area II deletion; immunofluorescence; flow cytometry; qRT-PCR; histone ChIP-qPCR; pancreatic developmental phenotype analysis
E_04527	1991	2000371	Human beta-globin locus control region: analysis of the 5' DNase I hypersensitive site HS 2 in transgenic mice	Homo sapiens	hg19	chr11	5280000	5281900	AP1	HBB	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	K-562	CVCL_0004	erythroid cell	CL:0000232	In vivo enhancer reporter assay; enhancer deletion-mapping assay; TF-footprinting assay	NA	Transgenic mouse beta-globin reporter assay; serial deletion analysis; DNase I footprinting; AP-1-site deletion analysis
E_04528	1992	1570310	Dissection of the enhancer activity of beta-globin 5' DNase I-hypersensitive site 2 in transgenic mice	Homo sapiens	hg19	chr11	5280500	5281232	NFE2	HBB	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	transgenic mouse erythroid tissue	NA	erythroid cell	CL:0000232	In vivo enhancer reporter assay; enhancer mutagenesis assay; TF-site functional assay	NA	Transgenic mouse reporter assay; 5'HS2 deletion-series analysis; NFE2/AP1-site deletion; beta-globin expression analysis
E_04529	1992	1570310	Dissection of the enhancer activity of beta-globin 5' DNase I-hypersensitive site 2 in transgenic mice	Homo sapiens	hg19	chr11	5280500	5281232	AP1	HBB	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	transgenic mouse erythroid tissue	NA	erythroid cell	CL:0000232	In vivo enhancer reporter assay; enhancer mutagenesis assay; TF-site functional assay	NA	Transgenic mouse reporter assay; 5'HS2 deletion-series analysis; NFE2/AP1-site deletion; beta-globin expression analysis
E_04530	1995	7557375	Targeted deletion of 5'HS2 of the murine beta-globin LCR reveals that it is not essential for proper regulation of the beta-globin locus	Mus musculus	mm10	chr7	110997000	110999000	Nfe2	Hbb-b1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary mouse erythroid cells	NA	erythroid cell	CL:0000232	Endogenous enhancer deletion assay; locus-expression assay; developmental hematopoietic phenotype assay	NA	Homologous-recombination deletion of 5'HS2; selectable-marker excision; beta-globin expression analysis; embryonic/fetal-liver phenotype analysis
E_04531	2002	12052878	Conserved sequences in a tissue-specific regulatory region of the pdx-1 gene mediate transcription in Pancreatic beta cells: role for hepatocyte nuclear factor 3 beta and Pax6	Mus musculus	mm10	chr5	147293900	147294130	Foxa2	Pdx1	Enhancer	Active	Normal	NA	NA	NA	pancreas	UBERON:0001264	primary pancreatic islet cells	NA	pancreatic beta cell	CL:0000169	Enhancer activity assay; TF-binding assay; enhancer mutagenesis assay; tissue-specific reporter assay	NA	Transgenic reporter assay; conserved-block mutagenesis; HNF3/Foxa2 binding assay; Pax6 binding assay; ChIP; reporter transactivation assay
E_04532	2002	12052878	Conserved sequences in a tissue-specific regulatory region of the pdx-1 gene mediate transcription in Pancreatic beta cells: role for hepatocyte nuclear factor 3 beta and Pax6	Mus musculus	mm10	chr5	147293900	147294130	Pax6	Pdx1	Enhancer	Active	Normal	NA	NA	NA	pancreas	UBERON:0001264	primary pancreatic islet cells	NA	pancreatic beta cell	CL:0000169	Enhancer activity assay; TF-binding assay; enhancer mutagenesis assay; tissue-specific reporter assay	NA	Transgenic reporter assay; conserved-block mutagenesis; Pax6 DNA-binding assay; ChIP; reporter transactivation assay
E_04533	2005	16147997	Interactions between areas I and II direct pdx-1 expression specifically to islet cell types of the mature and developing pancreas	Mus musculus	mm10	chr5	147293900	147294130	Nkx2-2	Pdx1	Enhancer	Active	Normal	NA	NA	NA	pancreas	UBERON:0001264	primary pancreatic islet cells	NA	pancreatic endocrine cell	CL:0008024	Enhancer interaction assay; tissue-specific reporter assay; TF-site functional assay	NA	Area I/Area II transgenic reporter assay; Nkx2-2 binding-site mutagenesis; developmental pancreas reporter analysis
E_04534	2005	16147997	Interactions between areas I and II direct pdx-1 expression specifically to islet cell types of the mature and developing pancreas	Mus musculus	mm10	chr5	147293900	147294130	NA	Pdx1	Enhancer	Active	Normal	NA	NA	NA	pancreas	UBERON:0001264	primary pancreatic islet cells	NA	pancreatic endocrine cell	CL:0008024	Enhancer interaction assay; tissue-specific reporter assay	NA	Area I/Area II transgenic reporter assay; developmental and adult islet expression analysis
E_04535	2019	31666694	Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs	Homo sapiens	hg19	chr11	69000000	69150000	NA	FGF4	Super-enhancer	Active	Disease	succinate dehydrogenase-deficient gastrointestinal stromal tumor	MONDO:0011719	DOID:9253	stomach	UBERON:0000945	GIST-T1	CVCL_4976	gastrointestinal stromal tumor cell	NA	Super-enhancer hijacking assay; insulator-disruption assay; enhancer-promoter interaction assay; oncogene activation assay	H3K27ac ChIP-seq; CTCF ChIP-seq; Hi-C; HiChIP; DNA methylation profiling	CRISPR/Cas9 deletion of CTCF boundary motifs; qRT-PCR; 5C/3D contact validation; xenograft drug-response assay
E_04536	2021	34315876	Super enhancer regulation of cytokine-induced chemokine production in alcoholic hepatitis	Homo sapiens	hg19	chr4	74600000	74850000	RELA	CXCL1	Super-enhancer	Active	Disease	alcoholic hepatitis	MONDO:0002050	DOID:8749	liver	UBERON:0002107	primary human liver sinusoidal endothelial cells	NA	endothelial cell	CL:0000115	Super-enhancer activity assay; endogenous epigenome-editing assay; cytokine-response assay; target-gene expression assay	RNA-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq	dCas9-KRAB repression of CXCL super-enhancer; TNF-alpha stimulation; qRT-PCR; BET inhibition; chemokine secretion assay
E_04537	2021	34315876	Super enhancer regulation of cytokine-induced chemokine production in alcoholic hepatitis	Homo sapiens	hg19	chr4	74600000	74850000	RELA	CXCL2	Super-enhancer	Active	Disease	alcoholic hepatitis	MONDO:0002050	DOID:8749	liver	UBERON:0002107	primary human liver sinusoidal endothelial cells	NA	endothelial cell	CL:0000115	Super-enhancer activity assay; endogenous epigenome-editing assay; cytokine-response assay; target-gene expression assay	RNA-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq	dCas9-KRAB repression of CXCL super-enhancer; TNF-alpha stimulation; qRT-PCR; BET inhibition; chemokine secretion assay
E_04538	2021	34315876	Super enhancer regulation of cytokine-induced chemokine production in alcoholic hepatitis	Homo sapiens	hg19	chr4	74600000	74850000	RELA	CXCL3	Super-enhancer	Active	Disease	alcoholic hepatitis	MONDO:0002050	DOID:8749	liver	UBERON:0002107	primary human liver sinusoidal endothelial cells	NA	endothelial cell	CL:0000115	Super-enhancer activity assay; endogenous epigenome-editing assay; cytokine-response assay; target-gene expression assay	RNA-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq	dCas9-KRAB repression of CXCL super-enhancer; TNF-alpha stimulation; qRT-PCR; BET inhibition; chemokine secretion assay
E_04539	2021	34315876	Super enhancer regulation of cytokine-induced chemokine production in alcoholic hepatitis	Homo sapiens	hg19	chr4	74600000	74850000	RELA	CXCL8	Super-enhancer	Active	Disease	alcoholic hepatitis	MONDO:0002050	DOID:8749	liver	UBERON:0002107	primary human liver sinusoidal endothelial cells	NA	endothelial cell	CL:0000115	Super-enhancer activity assay; endogenous epigenome-editing assay; cytokine-response assay; target-gene expression assay	RNA-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq	dCas9-KRAB repression of CXCL super-enhancer; TNF-alpha stimulation; qRT-PCR; BET inhibition; chemokine secretion assay
E_04540	2025	40405227	HBV sequence integrated to enhancer acting as oncogenic driver epigenetically promotes hepatocellular carcinoma development	Homo sapiens	hg38	chr5	1295000	1299000	NA	TERT	Enhancer	Active	Disease	hepatocellular carcinoma	MONDO:0007256	DOID:684	liver	UBERON:0002107	HepG2	CVCL_0027	hepatocyte	CL:0000182	Viral-integrated enhancer activity assay; enhancer perturbation assay; target-gene activation assay; cellular phenotype assay	RNA-seq; ChIP-seq	Luciferase enhancer assay; HBV-SITE-1 sequence comparison; HBV-miR-2 inhibition; qRT-PCR; proliferation assay; migration assay; xenograft assay
E_04541	2023	38101409	Super-enhancers include classical enhancers and facilitators to fully activate gene expression	Mus musculus	mm9	chr11	32145028	32146147	NA	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	fetal liver	UBERON:0002107	primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Endogenous enhancer reconstruction assay; enhancer sufficiency assay; enhancer cooperation assay; target-gene expression assay	ATAC-seq; RNA-seq; ChIPmentation; Tiled-C	RMGR synthetic locus reconstruction; CRISPR/Cas9 genome editing; RT-qPCR; enhancer reinsertion; PCR; Sanger sequencing
E_04542	2023	38101409	Super-enhancers include classical enhancers and facilitators to fully activate gene expression	Mus musculus	mm9	chr11	32150550	32151858	NA	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	fetal liver	UBERON:0002107	primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Endogenous enhancer reconstruction assay; enhancer sufficiency assay; enhancer cooperation assay; target-gene expression assay	ATAC-seq; RNA-seq; ChIPmentation; Tiled-C	RMGR synthetic locus reconstruction; CRISPR/Cas9 genome editing; RT-qPCR; enhancer reinsertion; PCR; Sanger sequencing
E_04543	2023	38101409	Super-enhancers include classical enhancers and facilitators to fully activate gene expression	Mus musculus	mm9	chr11	32145028	32146147	NA	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	fetal liver	UBERON:0002107	primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Endogenous enhancer reconstruction assay; enhancer sufficiency assay; enhancer cooperation assay; target-gene expression assay	ATAC-seq; RNA-seq; ChIPmentation; Tiled-C	RMGR synthetic locus reconstruction; CRISPR/Cas9 genome editing; RT-qPCR; enhancer reinsertion; PCR; Sanger sequencing
E_04544	2023	38101409	Super-enhancers include classical enhancers and facilitators to fully activate gene expression	Mus musculus	mm9	chr11	32150550	32151858	NA	Hba-a2	Enhancer	Active	Normal	NA	NA	NA	fetal liver	UBERON:0002107	primary mouse fetal liver erythroid cells	NA	erythroblast	CL:0000765	Endogenous enhancer reconstruction assay; enhancer sufficiency assay; enhancer cooperation assay; target-gene expression assay	ATAC-seq; RNA-seq; ChIPmentation; Tiled-C	RMGR synthetic locus reconstruction; CRISPR/Cas9 genome editing; RT-qPCR; enhancer reinsertion; PCR; Sanger sequencing
E_04545	2025	40592854	Klf5-adjacent super-enhancer functions as a 3D genome structure-dependent transcriptional driver to safeguard ESC identity	Mus musculus	mm10	chr14	99260419	99393893	NA	Klf5	Super-enhancer	Active	Normal	NA	NA	NA	embryo	UBERON:0000922	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Endogenous super-enhancer deletion assay; enhancer-target interaction assay; target-gene expression assay; rescue assay; differentiation phenotype assay	H3K27ac ChIP-seq; Hi-C; 4C-seq; scRNA-seq; RNA-seq	CRISPR/Cas9 K5aSE deletion; 3C-PCR; RT-qPCR; KLF5 rescue; CRISPRa target-gene rescue; embryoid-body differentiation assay
E_04546	2025	40592854	Klf5-adjacent super-enhancer functions as a 3D genome structure-dependent transcriptional driver to safeguard ESC identity	Mus musculus	mm10	chr14	99260419	99393893	NA	Tbc1d4	Super-enhancer	Active	Normal	NA	NA	NA	embryo	UBERON:0000922	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Endogenous super-enhancer deletion assay; long-range enhancer-target interaction assay; target-gene expression assay; rescue assay	H3K27ac ChIP-seq; Hi-C; 4C-seq; scRNA-seq; RNA-seq	CRISPR/Cas9 K5aSE deletion; 3C-PCR; RT-qPCR; CRISPRa target-gene rescue; CTCF-depletion assay
E_04547	2021	34739481	The Nestin neural enhancer is essential for normal levels of endogenous Nestin in neuroprogenitors but is not required for embryo development	Mus musculus	mm39	chr3	87881638	87881892	Sox3	Nes	Enhancer	Active	Normal	NA	NA	NA	central nervous system	UBERON:0001017	primary mouse embryonic neural progenitor cells	NA	neural progenitor cell	CL:0011020	Endogenous enhancer deletion assay; TF-binding assay; developmental target-gene expression assay	SOX3 ChIP-seq	CRISPR/Cas9 deletion of the 255-bp Nes intron-2 neural enhancer; independent 208-bp enhancer deletion; qRT-PCR; RNA in situ hybridization; immunofluorescence; embryonic CNS phenotype analysis
E_04548	2025	39882239	A conserved element in the first intron of Cd4 has a lineage specific, TCR signal-responsive, canonical enhancer function that matches the timing of cell surface CD4 upregulation required to prevent lineage choice error	Mus musculus	mm39	chr6	124862196	124862560	NA	Cd4	Enhancer	Active	Normal	NA	NA	NA	thymus	UBERON:0002370	primary mouse thymocytes	NA	T cell	CL:0000084	Enhancer activity assay; endogenous enhancer deletion assay; developmental-stage-specific enhancer assay; TCR-responsive enhancer assay; in vivo lineage reporter assay	NA	CRISPR/Cas9 deletion of coreNCE/E4m; transient enhancer reporter assay; TCR stimulation assay; CD4 surface-expression analysis; BAC-transgenic EGFP reporter assay; RT-qPCR; flow cytometry
E_04549	2015	26073540	Hematopoietic Signaling Mechanism Revealed from a Stem/Progenitor Cell Cistrome	Mus musculus	mm39	chr6	88180138	88180212	Gata2	Gata2	Enhancer	Active	Normal	NA	NA	NA	hematopoietic system	UBERON:0002390	primary mouse hematopoietic stem/progenitor cells	NA	hematopoietic precursor cell	CL:0008001	Endogenous enhancer perturbation assay; TF-binding assay; hematopoietic developmental assay; target-gene expression assay	GATA2 ChIP-seq; chromatin profiling	Targeted disruption of the Gata2 +9.5 enhancer; qRT-PCR; flow cytometry; hematopoietic progenitor assays; embryonic hematopoiesis analysis
E_04550	2021	34516632	Gata2 +9.5 enhancer regulates adult hematopoietic stem cell self-renewal and T-cell development	Mus musculus	mm39	chr6	88180138	88180212	Gata2	Gata2	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary mouse hematopoietic stem cells	NA	hematopoietic stem cell	CL:0000037	Endogenous enhancer mutation assay; hematopoietic stem-cell self-renewal assay; T-cell developmental assay; target-gene expression assay	NA	CRISPR-mediated Gata2 +9.5 enhancer mutation; competitive transplantation; flow cytometry; qRT-PCR; hematopoietic stem/progenitor-cell analysis; T-cell developmental analysis
E_04551	1995	7557375	Targeted deletion of 5'HS2 of the murine beta-globin LCR reveals that it is not essential for proper regulation of the beta-globin locus	Mus musculus	mm39	chr7	103501973	103526752	Nfe2	Hbb	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary mouse erythroid cells	NA	erythroid cell	CL:0000232	Endogenous locus-control-region perturbation assay; enhancer deletion assay; globin-expression assay	NA	Targeted deletion of 5'HS2; embryonic and adult beta-globin expression analysis; Southern blotting; hematologic phenotype analysis
E_04552	2015	26601269	Cis-regulatory mechanisms governing stem and progenitor cell transitions	Mus musculus	mm39	chr6	88093936	88094192	Gata2	Gata2	Enhancer	Active	Normal	NA	NA	NA	fetal liver	UBERON:0002107	primary mouse hematopoietic progenitor cells	NA	myeloid progenitor cell	CL:0008001	Endogenous enhancer deletion assay; hematopoietic differentiation assay; target-gene expression assay; developmental phenotype assay	RNA-seq	Targeted deletion of the Gata2 -77 enhancer; flow cytometry; colony-forming assay; qRT-PCR; fetal-liver hematopoietic analysis
E_04553	2017	28930689	Integrating Enhancer Mechanisms to Establish a Hierarchical Blood Development Program	Mus musculus	mm39	chr6	88093936	88094192	Gata2	Gata2	Enhancer	Active	Normal	NA	NA	NA	fetal liver	UBERON:0002107	primary mouse hematopoietic progenitor cells	NA	myeloid progenitor cell	CL:0008001	Endogenous enhancer perturbation assay; compound-enhancer genetic interaction assay; hematopoietic differentiation assay; target-gene expression assay	NA	Gata2 -77/+9.5 compound-heterozygous mouse analysis; flow cytometry; colony-forming assay; qRT-PCR; fetal-liver progenitor analysis
E_04554	2021	32594099	Gata2 -77 enhancer regulates adult hematopoietic stem cell survival	Mus musculus	mm39	chr6	88093936	88094192	Gata2	Gata2	Enhancer	Active	Normal	NA	NA	NA	bone marrow	UBERON:0002371	primary mouse hematopoietic stem/progenitor cells	NA	hematopoietic stem cell	CL:0000037	Endogenous enhancer deletion assay; hematopoietic stem-cell survival assay; transplantation assay; target-gene expression assay	NA	Gata2 -77 enhancer-mutant mouse analysis; competitive transplantation; flow cytometry; apoptosis analysis; qRT-PCR
E_04555	2017	27993987	The mammal-specific Pdx1 Area II enhancer has multiple essential functions in early endocrine cell specification and postnatal β-cell maturation	Mus musculus	mm39	chr5	147210505	147210760	NA	Pdx1	Enhancer	Active	Normal	NA	NA	NA	pancreas	UBERON:0001264	primary mouse pancreatic endocrine cells	NA	pancreatic endocrine cell	CL:0008024	Endogenous enhancer deletion assay; developmental lineage assay; target-gene expression assay; beta-cell maturation phenotype assay	NA	Targeted deletion of the 256-bp Pdx1 Area II enhancer; immunofluorescence; flow cytometry; qRT-PCR; glucose-tolerance analysis; pancreatic developmental phenotype analysis
E_04556	2005	16147997	Interactions between areas I and II direct pdx-1 expression specifically to islet cell types of the mature and developing pancreas	Mus musculus	mm39	chr5	147210505	147210760	NA	Pdx1	Enhancer	Active	Normal	NA	NA	NA	pancreas	UBERON:0001264	primary mouse pancreatic islet cells	NA	pancreatic endocrine cell	CL:0008024	In vivo enhancer reporter assay; enhancer interaction assay; tissue-specific enhancer assay	NA	Area II transgenic reporter assay; Area I plus Area II combinatorial reporter assay; developmental pancreas expression analysis
E_04557	2025	40588505	Enhancer hijacking drives FAM20C expression to promote papillary thyroid cancer progression	Homo sapiens	hg38	chr7	19050000	19056000	KLF12	FAM20C	Enhancer	Active	Disease	papillary thyroid carcinoma	MONDO:0005075	DOID:3969	thyroid gland	UBERON:0002046	K1	CVCL_2537	thyroid epithelial cell	CL:0002075	Cancer-specific enhancer activity assay; TF-binding assay; enhancer-target regulation assay; cellular phenotype assay	RNA-seq; H3K27ac ChIP-seq; chromatin profiling	Luciferase reporter assay; KLF12 perturbation; enhancer functional validation; qRT-PCR; Western blotting; proliferation assay; invasion assay; xenograft assay
E_04558	2025	40588505	Enhancer hijacking drives FAM20C expression to promote papillary thyroid cancer progression	Homo sapiens	hg38	chr7	19050000	19056000	KLF12	FAM20C	Enhancer	Active	Disease	papillary thyroid carcinoma	MONDO:0005075	DOID:3969	thyroid gland	UBERON:0002046	TPC-1	CVCL_6298	thyroid epithelial cell	CL:0002075	Cancer-specific enhancer activity assay; TF-binding assay; enhancer-target regulation assay; cellular phenotype assay	RNA-seq; H3K27ac ChIP-seq; chromatin profiling	Luciferase reporter assay; KLF12 perturbation; enhancer functional validation; qRT-PCR; Western blotting; proliferation assay; invasion assay
E_04559	2024	39033128	3D genomic analysis reveals novel enhancer-hijacking caused by complex structural alterations that drive oncogene overexpression	Homo sapiens	hg38	chr8	127730000	127850000	NA	ERBB2	Super-enhancer	Active	Disease	breast carcinoma	MONDO:0007254	DOID:1612	breast	UBERON:0000310	SK-BR-3	CVCL_0033	breast epithelial cell	CL:0002327	Enhancer-hijacking assay; enhancer-promoter interaction assay; promoter-competition assay; oncogene activation assay	H3K27ac HiChIP; Hi-C; RNA-seq; copy-number profiling	CRISPRi of MYC promoter; 3D interaction validation; ERBB2 expression analysis; ecDNA structural reconstruction
E_04560	2020	33199677	Enhancer hijacking determines extrachromosomal circular MYCN amplicon architecture in neuroblastoma	Homo sapiens	hg19	chr2	12600000	12800000	PHOX2B	MYCN	Super-enhancer	Active	Disease	neuroblastoma	MONDO:0005072	DOID:769	autonomic nervous system	UBERON:0002410	CHP-212	CVCL_1126	neuroblastoma cell	NA	Enhancer-hijacking assay; enhancer-promoter interaction assay; ecDNA structural analysis; target-gene regulatory assay	Whole-genome sequencing; Nanopore sequencing; H3K27ac ChIP-seq; ATAC-seq; Hi-C	4C-seq; enhancer-promoter interaction validation; ecDNA reconstruction; MYCN expression analysis
E_04561	2023	36650172	A genome-wide relay of signalling-responsive enhancers drives hematopoietic specification	Mus musculus	mm10	chr16	92822182	92822601	NA	Runx1	Enhancer	Active	Normal	NA	NA	NA	hematopoietic system	UBERON:0002390	mouse embryonic stem-cell-derived hemogenic endothelium	NA	hemogenic endothelial cell	CL:0002543	Enhancer activity assay; developmental-stage-specific enhancer assay; cytokine-responsive enhancer assay	ATAC-seq; RNA-seq; ChIP-seq; single-cell RNA-seq	Stable chromatin-integrated enhancer reporter assay; YFP flow-cytometry assay; developmental differentiation assay
E_04562	2023	36650172	A genome-wide relay of signalling-responsive enhancers drives hematopoietic specification	Mus musculus	mm10	chr12	109437601	109438085	TEAD4	Dlk1	Enhancer	Active	Normal	NA	NA	NA	hematopoietic system	UBERON:0002390	mouse embryonic stem-cell-derived hemogenic endothelium	NA	hemogenic endothelial cell	CL:0002543	Cytokine-responsive enhancer assay; TF-regulated enhancer assay; developmental-stage-specific enhancer assay	ATAC-seq; RNA-seq; ChIP-seq; single-cell RNA-seq	Stable chromatin-integrated enhancer reporter assay; VEGF withdrawal/stimulation assay; YFP flow cytometry
E_04563	2023	36650172	A genome-wide relay of signalling-responsive enhancers drives hematopoietic specification	Mus musculus	mm10	chr12	109437601	109438085	RUNX1	Dlk1	Enhancer	Active	Normal	NA	NA	NA	hematopoietic system	UBERON:0002390	mouse embryonic stem-cell-derived hematopoietic progenitor cells	NA	hematopoietic precursor cell	CL:0008001	Cytokine-responsive enhancer assay; TF-binding assay; developmental-stage-specific enhancer assay	ATAC-seq; RNA-seq; ChIP-seq; single-cell RNA-seq	Stable chromatin-integrated enhancer reporter assay; VEGF-response assay; YFP flow cytometry
E_04564	2023	36650172	A genome-wide relay of signalling-responsive enhancers drives hematopoietic specification	Mus musculus	mm10	chr12	109437601	109438085	NA	Dlk1	Enhancer	Active	Normal	NA	NA	NA	hematopoietic system	UBERON:0002390	mouse embryonic stem-cell-derived hemogenic endothelium	NA	hemogenic endothelial cell	CL:0002543	Enhancer activity assay; cytokine-responsive enhancer assay; developmental-stage-specific enhancer assay	ATAC-seq; RNA-seq; single-cell RNA-seq	Stable chromatin-integrated enhancer reporter assay; VEGF-response assay; YFP flow cytometry
E_04565	2006	16537902	Transcriptional link between blood and bone: the stem cell leukemia gene and its +19 stem cell enhancer are active in bone cells	Mus musculus	mm39	chr4	115758000	115763500	NA	Tal1	Enhancer	Active	Normal	NA	NA	NA	bone	UBERON:0002481	primary mouse osteogenic and hematopoietic cells	NA	NA	NA	In vivo enhancer reporter assay; tissue-specific enhancer activity assay	NA	Transgenic enhancer-reporter assay; in situ hybridization; immunohistochemistry; developmental expression analysis
E_04566	2016	27707736	Strict in vivo specificity of the Bcl11a erythroid enhancer	Mus musculus	mm10	chr11	24044043	24197927	NA	Bcl11a	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	fetal liver erythroid cells	NA	erythroblast	CL:0000765	Endogenous enhancer deletion assay; lineage-specific enhancer requirement assay; developmental globin-regulation assay	NA	Deletion of the Bcl11a erythroid enhancer; qRT-PCR; flow cytometry; fetal-liver erythroid analysis; bone-marrow transplantation; fetal-globin expression analysis
E_04567	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32145028	32146147	NA	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	fetal liver	UBERON:0002107	primary mouse erythroid cells	NA	erythroblast	CL:0000765	Endogenous enhancer deletion assay; super-enhancer constituent dissection assay; target-gene expression assay	Chromatin profiling; chromosome-conformation analysis	Targeted deletion of R1 enhancer; allele-specific α-globin expression analysis; qRT-PCR; hematologic phenotype analysis
E_04568	2016	27376235	Genetic dissection of the α-globin super-enhancer in vivo	Mus musculus	mm9	chr11	32150550	32151858	NA	Hba-a1	Enhancer	Active	Normal	NA	NA	NA	fetal liver	UBERON:0002107	primary mouse erythroid cells	NA	erythroblast	CL:0000765	Endogenous enhancer deletion assay; super-enhancer constituent dissection assay; target-gene expression assay	Chromatin profiling; chromosome-conformation analysis	Targeted deletion of R2 enhancer; allele-specific α-globin expression analysis; qRT-PCR; hematologic phenotype analysis
E_04569	2009	19561604	The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling	Homo sapiens	hg19	chr8	128413000	128414000	TCF7L2	MYC	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	colorectal cancer cells	NA	colon epithelial cell	CL:0000066	Enhancer reporter assay; TF-binding assay; allele-specific enhancer activity assay; in vivo developmental enhancer assay	TCF7L2 ChIP-chip; comparative genomics	Luciferase reporter assay; EMSA; allele-specific TF-binding assay; transgenic mouse enhancer reporter assay
E_04570	2009	19561607	The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer	Homo sapiens	hg19	chr8	128413000	128414000	TCF7L2	MYC	Enhancer	Active	Disease	colorectal cancer	MONDO:0005575	DOID:9256	colon	UBERON:0001155	Colo205	CVCL_0218	colon epithelial cell	CL:0000066	Enhancer activity assay; allele-specific TF-binding assay; enhancer-promoter interaction assay	ChIP profiling	ChIP; luciferase reporter assay; allele-specific binding analysis; chromosome-conformation capture assay
E_04571	2015	26287746	FTO Obesity Variant Circuitry and Adipocyte Browning in Humans	Homo sapiens	hg19	chr16	53800400	53801500	ARID5B	IRX3	Enhancer	Active	Disease	obesity	MONDO:0011122	DOID:9970	adipose tissue	UBERON:0001013	primary human adipocyte progenitor cells	NA	adipocyte progenitor cell	CL:0002332	Endogenous enhancer variant editing assay; TF-motif perturbation assay; enhancer-target regulation assay; adipocyte differentiation phenotype assay	Chromatin-state profiling; RNA-seq; epigenomic integration	CRISPR/Cas9 editing of rs1421085; ARID5B motif rescue; qRT-PCR; adipocyte differentiation assay; oxygen-consumption assay; mitochondrial thermogenesis assay
E_04572	2015	26287746	FTO Obesity Variant Circuitry and Adipocyte Browning in Humans	Homo sapiens	hg19	chr16	53800400	53801500	ARID5B	IRX5	Enhancer	Active	Disease	obesity	MONDO:0011122	DOID:9970	adipose tissue	UBERON:0001013	primary human adipocyte progenitor cells	NA	adipocyte progenitor cell	CL:0002332	Endogenous enhancer variant editing assay; TF-motif perturbation assay; enhancer-target regulation assay; adipocyte differentiation phenotype assay	Chromatin-state profiling; RNA-seq; epigenomic integration	CRISPR/Cas9 editing of rs1421085; ARID5B motif rescue; qRT-PCR; adipocyte differentiation assay; oxygen-consumption assay; mitochondrial thermogenesis assay
E_04573	2013	24290376	Disruption of autoregulatory feedback by a mutation in a remote, ultraconserved PAX6 enhancer causes aniridia	Homo sapiens	hg19	chr11	31685500	31686400	PAX6	PAX6	Enhancer	Active	Disease	aniridia	MONDO:0007119	DOID:0050536	eye	UBERON:0000970	primary ocular developmental tissue	NA	ocular cell	NA	Enhancer reporter assay; TF-binding-site mutagenesis assay; disease-associated enhancer variant assay; developmental enhancer assay	Comparative genomics	Luciferase reporter assay; transgenic enhancer assay; PAX6 binding assay; site-directed mutagenesis; developmental ocular reporter analysis
E_04574	2013	24290376	Disruption of autoregulatory feedback by a mutation in a remote, ultraconserved PAX6 enhancer causes aniridia	Homo sapiens	hg19	chr11	31685500	31686400	PAX6	PAX6	Enhancer	Inactive	Disease	aniridia	MONDO:0007119	DOID:0050536	eye	UBERON:0000970	patient-derived mutant enhancer context	NA	ocular cell	NA	Disease-associated enhancer loss-of-function assay; TF-binding-site disruption assay	Comparative genomics	Mutant-versus-wild-type enhancer reporter assay; PAX6 binding-site disruption analysis; developmental reporter assay
E_04575	2010	21478907	From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus	Homo sapiens	hg19	chr1	109816874	109818905	CEBPA	SORT1	Enhancer	Active	Disease	coronary artery disease	MONDO:0005010	DOID:3393	liver	UBERON:0002107	Hep3B	CVCL_0326	hepatocyte	CL:0000182	Allele-specific enhancer activity assay; TF-binding assay; enhancer variant functional assay; target-gene regulation assay	Expression quantitative trait locus analysis; population genetic fine-mapping	Luciferase reporter assay; EMSA; CEBPA binding analysis; allele-specific regulatory assay; SORT1 expression analysis
E_04576	2010	21478907	From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus	Homo sapiens	hg19	chr1	109816874	109818905	CEBPA	PSRC1	Enhancer	Active	Disease	coronary artery disease	MONDO:0005010	DOID:3393	liver	UBERON:0002107	Hep3B	CVCL_0326	hepatocyte	CL:0000182	Allele-specific enhancer activity assay; TF-binding assay; enhancer variant functional assay; target-gene regulation assay	Expression quantitative trait locus analysis; population genetic fine-mapping	Luciferase reporter assay; EMSA; CEBPA binding analysis; allele-specific regulatory assay; PSRC1 expression analysis
E_04577	2018	29367380	Interrogation of the Atherosclerosis-associated SORT1 Locus with Primary Human Hepatocytes, iPSC-hepatocytes, and Locus-humanized Mice	Homo sapiens	hg19	chr1	109816874	109818905	CEBPA	SORT1	Enhancer	Active	Disease	atherosclerosis	MONDO:0005311	DOID:2349	liver	UBERON:0002107	primary human hepatocytes	NA	hepatocyte	CL:0000182	Endogenous enhancer perturbation assay; allele-specific regulatory assay; target-gene expression assay	RNA-seq; genotype-expression analysis	CRISPR/Cas9 disruption of the rs12740374 minor-allele enhancer sequence; qRT-PCR; primary-hepatocyte analysis; locus-humanized mouse analysis
E_04578	2018	29367380	Interrogation of the Atherosclerosis-associated SORT1 Locus with Primary Human Hepatocytes, iPSC-hepatocytes, and Locus-humanized Mice	Homo sapiens	hg19	chr1	109816874	109818905	CEBPA	PSRC1	Enhancer	Active	Disease	atherosclerosis	MONDO:0005311	DOID:2349	liver	UBERON:0002107	primary human hepatocytes	NA	hepatocyte	CL:0000182	Endogenous enhancer perturbation assay; allele-specific regulatory assay; target-gene expression assay	RNA-seq; genotype-expression analysis	CRISPR/Cas9 disruption of the rs12740374 minor-allele enhancer sequence; qRT-PCR; primary-hepatocyte analysis; locus-humanized mouse analysis
E_04579	2011	21185279	The Pou5f1/Pou3f-dependent but SoxB-independent regulation of conserved enhancer N2 initiates Sox2 expression during epiblast to neural plate stages in vertebrates	Mus musculus	mm39	chr3	34700326	34700717	Pou5f1	Sox2	Enhancer	Active	Normal	NA	NA	NA	epiblast	UBERON:0006269	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Endogenous enhancer deletion assay; developmental enhancer activity assay; TF-dependent enhancer assay; target-gene expression assay	NA	Targeted deletion of Sox2 N2 enhancer; transgenic reporter assay; POU-factor knockdown; qRT-PCR; enhancer mutagenesis; developmental expression analysis
E_04580	2011	21185279	The Pou5f1/Pou3f-dependent but SoxB-independent regulation of conserved enhancer N2 initiates Sox2 expression during epiblast to neural plate stages in vertebrates	Mus musculus	mm39	chr3	34700326	34700717	Pou3f1	Sox2	Enhancer	Active	Normal	NA	NA	NA	neural plate	UBERON:0003075	neural progenitor cells	NA	neural progenitor cell	CL:0011020	Endogenous enhancer deletion assay; developmental enhancer activity assay; TF-dependent enhancer assay; target-gene expression assay	NA	Targeted deletion of Sox2 N2 enhancer; POU-factor knockdown; transgenic reporter assay; qRT-PCR; enhancer mutagenesis; neural-plate expression analysis
E_04581	2011	21185279	The Pou5f1/Pou3f-dependent but SoxB-independent regulation of conserved enhancer N2 initiates Sox2 expression during epiblast to neural plate stages in vertebrates	Mus musculus	mm39	chr3	34700326	34700717	Pou3f2	Sox2	Enhancer	Active	Normal	NA	NA	NA	neural plate	UBERON:0003075	neural progenitor cells	NA	neural progenitor cell	CL:0011020	Endogenous enhancer deletion assay; developmental enhancer activity assay; TF-dependent enhancer assay; target-gene expression assay	NA	Targeted deletion of Sox2 N2 enhancer; POU-factor knockdown; transgenic reporter assay; qRT-PCR; enhancer mutagenesis; neural-plate expression analysis
E_04582	2002	12136102	Identification of Sox-2 regulatory region which is under the control of Oct-3/4-Sox-2 complex	Mus musculus	mm39	chr3	34708174	34708233	Pou5f1	Sox2	Enhancer	Active	Normal	NA	NA	NA	embryo	UBERON:0000922	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; TF-binding assay; TF-site mutagenesis assay; pluripotency-specific enhancer assay	NA	Luciferase reporter assay; EMSA; Oct-Sox motif mutagenesis; cotransfection assay; deletion mapping
E_04583	2002	12136102	Identification of Sox-2 regulatory region which is under the control of Oct-3/4-Sox-2 complex	Mus musculus	mm39	chr3	34708174	34708233	Sox2	Sox2	Enhancer	Active	Normal	NA	NA	NA	embryo	UBERON:0000922	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; TF-binding assay; TF-site mutagenesis assay; autoregulatory enhancer assay	NA	Luciferase reporter assay; EMSA; Sox-binding-site mutagenesis; Oct-Sox cooperative-binding assay; cotransfection assay
E_04584	2002	12136102	Identification of Sox-2 regulatory region which is under the control of Oct-3/4-Sox-2 complex	Mus musculus	mm39	chr3	34708174	34708233	Pou3f1	Sox2	Enhancer	Active	Normal	NA	NA	NA	embryo	UBERON:0000922	mouse embryonal carcinoma/embryonic stem cells	NA	embryonic stem cell	CL:0002322	Enhancer activity assay; TF-dependent enhancer assay; pluripotency-associated enhancer assay	NA	Luciferase reporter assay; Oct6-Sox2 cotransfection assay; EMSA; enhancer mutagenesis
E_04585	2012	22914741	Functional characterization of tissue-specific enhancers in the DLX5/6 locus	Homo sapiens	hg18	chr7	95962912	95963295	NA	DLX5;DLX6	Enhancer	Active	Normal	NA	NA	NA	pharyngeal arch	UBERON:0002539	NA	NA	NA	NA	Transgenic enhancer activity assay	NA	E1b-GFP transgenic zebrafish reporter assay; Hsp68-LacZ transgenic mouse reporter assay
E_04586	2012	22914741	Functional characterization of tissue-specific enhancers in the DLX5/6 locus	Homo sapiens	hg18	chr7	95913505	95913684	NA	DLX5;DLX6	Enhancer	Active	Normal	NA	NA	NA	pharyngeal arch	UBERON:0002539	NA	NA	NA	NA	Transgenic enhancer activity assay	NA	E1b-GFP transgenic zebrafish reporter assay; Hsp68-LacZ transgenic mouse reporter assay
E_04587	2012	22914741	Functional characterization of tissue-specific enhancers in the DLX5/6 locus	Homo sapiens	hg18	chr7	95603887	95604377	NA	DLX5;DLX6	Enhancer	Active	Normal	NA	NA	NA	ear vesicle	UBERON:0003051	NA	NA	NA	NA	Transgenic enhancer activity assay	NA	E1b-GFP transgenic zebrafish reporter assay; Hsp68-LacZ transgenic mouse reporter assay
E_04588	2012	22914741	Functional characterization of tissue-specific enhancers in the DLX5/6 locus	Homo sapiens	hg18	chr7	95564858	95565640	NA	DLX5;DLX6	Enhancer	Active	Normal	NA	NA	NA	limb bud	UBERON:0004347	NA	NA	NA	NA	Transgenic enhancer activity assay	NA	Hsp68-LacZ transgenic mouse reporter assay
E_04589	2012	22914741	Functional characterization of tissue-specific enhancers in the DLX5/6 locus	Homo sapiens	hg18	chr7	95543084	95543539	NA	DLX5;DLX6	Enhancer	Active	Normal	NA	NA	NA	limb bud	UBERON:0004347	NA	NA	NA	NA	Transgenic enhancer activity assay	NA	E1b-GFP transgenic zebrafish reporter assay; Hsp68-LacZ transgenic mouse reporter assay
E_04590	2012	22914741	Functional characterization of tissue-specific enhancers in the DLX5/6 locus	Homo sapiens	hg18	chr7	96401902	96407985	NA	DLX5;DLX6	Enhancer	Active	Normal	NA	NA	NA	internal ear	UBERON:0001846	NA	NA	NA	NA	Transgenic enhancer activity assay	NA	Hsp68-LacZ transgenic mouse reporter assay
E_04591	2026	42057421	Functional and computational interrogation of juvenile idiopathic arthritis risk loci in CD4+ T cells	Homo sapiens	hg38	chr5	132496614	132497319	NA	IRF1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary CD4+ T cells	NA	activated CD4-positive, alpha-beta T cell, human	CL:0001043	Enhancer activity assay; allele-specific enhancer perturbation	PRO-seq; Micro-C; H3K27ac CUT&RUN	Dual-luciferase reporter assay; site-directed mutagenesis
E_04592	2022	35388006	Lupus enhancer risk variant causes dysregulation of IRF8 through cooperative lncRNA and DNA methylation machinery	Homo sapiens	hg38	chr16	85984914	85985132	SPI1	IRF8	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary CD14+ monocytes	NA	monocyte	CL:0000576	Enhancer activity assay; endogenous enhancer perturbation; enhancer-promoter interaction assay	ATAC-seq; H3K27ac ChIP-seq; RNA-seq; 4C-seq	CRISPR/Cas9 deletion; CRISPRa; CRISPRi; Cas9 RNP editing; dual-luciferase reporter assay; ChIP-qPCR; FAIRE-qPCR; DAPA; allele-specific binding analysis
E_04593	2023	36869052	An autoimmune pleiotropic SNP modulates IRF5 alternative promoter usage through ZBTB3-mediated chromatin looping	Homo sapiens	hg19	chr7	128573036	128573717	ZBTB3	IRF5	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	SC monocyte-derived cells	NA	monocyte	CL:0000576	Enhancer activity assay; endogenous enhancer perturbation; enhancer-promoter looping assay	ATAC-seq; ChIP-seq; RNA-seq; 4C-seq	CRISPRa; CRISPRi; CRISPR/Cas9 perturbation; luciferase reporter assay; 3C; allele-specific ChIP-qPCR
E_04594	2015	25259561	Oxidative stress regulates CFTR gene expression in human airway epithelial cells through a distal antioxidant response element	Homo sapiens	hg19	chr7	117075400	117076000	NFE2L2	CFTR	Enhancer	Active	Normal	NA	NA	NA	bronchus	UBERON:0002185	16HBE14o-	NA	bronchial epithelial cell	CL:0002328	Enhancer activity assay; TF-binding assay	DNase-seq; H3K27ac profiling	Dual-luciferase reporter assay; site-directed mutagenesis; EMSA; sulforaphane stimulation; TF occupancy analysis
E_04595	2015	25259561	Oxidative stress regulates CFTR gene expression in human airway epithelial cells through a distal antioxidant response element	Homo sapiens	hg19	chr7	117075400	117076000	NFKB1	CFTR	Enhancer	Active	Normal	NA	NA	NA	bronchus	UBERON:0002185	16HBE14o-	NA	bronchial epithelial cell	CL:0002328	Enhancer activity assay; TF-site perturbation	DNase-seq; H3K27ac profiling	Dual-luciferase reporter assay; site-directed mutagenesis; EMSA
E_04596	2015	25259561	Oxidative stress regulates CFTR gene expression in human airway epithelial cells through a distal antioxidant response element	Homo sapiens	hg19	chr7	117075400	117076000	BACH1	CFTR	Enhancer	Repressed	Normal	NA	NA	NA	bronchus	UBERON:0002185	16HBE14o-	NA	bronchial epithelial cell	CL:0002328	Enhancer regulatory-state assay; TF-binding assay	DNase-seq; H3K27ac profiling	EMSA; TF occupancy analysis; sulforaphane displacement assay
E_04597	2022	35017532	Identification of a modular super-enhancer in murine retinal development	Mus musculus	mm39	chr12	84570408	84611689	NA	Vsx2	Super-enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	retina	NA	retinal progenitor cell	CL:0002672	Endogenous super-enhancer perturbation; developmental phenotype assay	ATAC-seq; H3K27ac ChIP-seq; chromatin conformation profiling	CRISPR/Cas9 super-enhancer deletion; histological analysis; immunofluorescence; visual function phenotyping
E_04598	2022	35017532	Identification of a modular super-enhancer in murine retinal development	Mus musculus	mm39	chr12	84578818	84579815	NA	Vsx2	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	retina	NA	retinal progenitor cell	CL:0002672	Endogenous enhancer perturbation; developmental phenotype assay	ATAC-seq; H3K27ac ChIP-seq	CRISPR/Cas9 998-bp enhancer deletion; retinal histology; immunofluorescence; visual acuity assay
E_04599	2022	35017532	Identification of a modular super-enhancer in murine retinal development	Mus musculus	mm39	chr12	84586536	84590457	NA	Vsx2	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	retina	NA	retinal progenitor cell	CL:0002672	Endogenous enhancer perturbation; TF-site perturbation	ATAC-seq; H3K27ac ChIP-seq	CRISPR/Cas9 enhancer deletion; CRISPR-mediated Vsx2 consensus-binding-site deletion; retinal histology; visual acuity assay
E_04600	2022	35017532	Identification of a modular super-enhancer in murine retinal development	Mus musculus	mm39	chr12	84596238	84601716	NA	Vsx2	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	retina	NA	retinal bipolar neuron	CL:0000748	Endogenous enhancer perturbation; developmental cell-fate assay	ATAC-seq; H3K27ac ChIP-seq	CRISPR/Cas9 enhancer deletion; immunofluorescence; bipolar-cell quantification; visual function assay
E_04601	2020	32541005	Simultaneous deletion of Prdm1 and Vsx2 enhancers in the retina alters photoreceptor and bipolar cell fate specification, yet differs from deleting both genes	Mus musculus	mm39	chr10	44340801	44341000	Otx2	Prdm1	Enhancer	Active	Normal	NA	NA	NA	retina	UBERON:0000966	retina	NA	retinal progenitor cell	CL:0002672	Endogenous enhancer perturbation; cell-fate assay	NA	CRISPR/Cas9 in vivo retinal enhancer targeting; retinal electroporation; immunofluorescence; cell-fate quantification
E_04602	2019	31053643	Targeted genomic deletions identify diverse enhancer functions and generate a kidney-specific, endocrine-deficient Cyp27b1 pseudo-null mouse	Mus musculus	mm39	chr10	126879163	126879516	NA	Cyp27b1	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	kidney	NA	epithelial cell of proximal tubule	CL:0002306	Endogenous enhancer perturbation; endocrine-response assay	VDR ChIP-seq; pCREB ChIP-seq; H3K4me1 ChIP-seq; H3K27ac ChIP-seq	CRISPR/Cas9 targeted enhancer deletion; qRT-PCR; serum biochemical analysis; skeletal phenotyping
E_04603	2019	31053643	Targeted genomic deletions identify diverse enhancer functions and generate a kidney-specific, endocrine-deficient Cyp27b1 pseudo-null mouse	Mus musculus	mm39	chr10	126869870	126874496	NA	Cyp27b1	Enhancer	Active	Normal	NA	NA	NA	kidney	UBERON:0002113	kidney	NA	epithelial cell of proximal tubule	CL:0002306	Endogenous enhancer perturbation; endocrine-response assay	VDR ChIP-seq; pCREB ChIP-seq; H3K4me1 ChIP-seq; H3K27ac ChIP-seq	CRISPR/Cas9 targeted enhancer deletion; qRT-PCR; serum biochemical analysis; skeletal phenotyping
E_04604	2021	33869166	A Highly Conserved Shh Enhancer Coordinates Hypothalamic and Craniofacial Development	Mus musculus	mm39	chr5	29080378	29081677	Sox2	Shh	Enhancer	Active	Normal	NA	NA	NA	diencephalon	UBERON:0001894	embryonic diencephalon	NA	NA	NA	Endogenous enhancer perturbation; developmental phenotype assay	NA	CRISPR/Cas9 SBE2 deletion; RNA in situ hybridization; histological analysis; skeletal staining; genetic sensitization with Shh null allele
E_04605	2025	41081394	Generation and characterization of a knockout mouse of an enhancer of EBF3	Mus musculus	mm39	chr7	135684934	135686078	NA	Ebf3	Enhancer	Active	Normal	NA	NA	NA	brain	UBERON:0000955	embryonic forebrain/midbrain/hindbrain	NA	NA	NA	Endogenous enhancer perturbation; transcriptional and behavioral phenotype assay	RNA-seq	CRISPR/Cas9 enhancer deletion; qRT-PCR; behavioral phenotyping; body-composition phenotyping
E_04606	2020	32866060	Assigning Distal Genomic Enhancers to Cardiac Disease-Causing Genes	Homo sapiens	hg19	chr15	35012859	35016282	NA	ACTC1	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	hESC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Functional cis-regulatory element perturbation	ATAC-seq; H3K27ac ChIP-seq; H3K27ac HiChIP; ABC enhancer-gene modeling	CRISPR/Cas9 enhancer excision; RT-qPCR
E_04607	2020	32866060	Assigning Distal Genomic Enhancers to Cardiac Disease-Causing Genes	Homo sapiens	hg19	chr12	111364206	111368031	NA	MYL2	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	hESC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Functional cis-regulatory element perturbation	ATAC-seq; H3K27ac ChIP-seq; H3K27ac HiChIP; ABC enhancer-gene modeling	CRISPR/Cas9 enhancer excision; RT-qPCR
E_04608	2020	32866060	Assigning Distal Genomic Enhancers to Cardiac Disease-Causing Genes	Homo sapiens	hg19	chr8	125859000	125862000	NA	MTSS1	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	hESC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Functional cis-regulatory element perturbation	ATAC-seq; H3K27ac ChIP-seq; H3K27ac HiChIP; ABC enhancer-gene modeling	CRISPR/Cas9 enhancer excision; RT-qPCR
E_04609	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23912000	23912961	NA	MYH7	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	iPSC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; endogenous enhancer deletion; engineered heart tissue functional assay	H3K27ac ChIP-seq; promoter-capture Hi-C	CRISPR/Cas9 enhancer deletion; luciferase reporter assay; RT-qPCR; SDS-PAGE; engineered heart tissue contraction assay
E_04610	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr1	156095724	156096574	NA	LMNA	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	iPSC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay	H3K27ac ChIP-seq; promoter-capture Hi-C	Luciferase reporter assay
E_04611	2024	38231044	Mechanosensitive super-enhancers regulate genes linked to atherosclerosis in endothelial cells	Homo sapiens	hg19	chr16	69412415	69482923	NA	NQO1	Super-enhancer	Active	Normal	NA	NA	NA	aorta	UBERON:0000947	primary human aortic endothelial cells	NA	endothelial cell	CL:0000115	Super-enhancer perturbation; flow-responsive enhancer assay	H3K27ac ChIP-seq; ATAC-seq; RNA-seq; promoter capture Hi-C	CRISPRi; CRISPRa; qRT-PCR; protein expression assay
E_04612	2024	38231044	Mechanosensitive super-enhancers regulate genes linked to atherosclerosis in endothelial cells	Homo sapiens	hg19	chr16	69412415	69482923	NA	CYB5B	Super-enhancer	Active	Normal	NA	NA	NA	aorta	UBERON:0000947	primary human aortic endothelial cells	NA	endothelial cell	CL:0000115	Super-enhancer perturbation; flow-responsive enhancer assay	H3K27ac ChIP-seq; ATAC-seq; RNA-seq; promoter capture Hi-C	CRISPRi; CRISPRa; qRT-PCR
E_04613	2024	38231044	Mechanosensitive super-enhancers regulate genes linked to atherosclerosis in endothelial cells	Homo sapiens	hg19	chr16	69412415	69482923	NA	WWP2	Super-enhancer	Active	Normal	NA	NA	NA	aorta	UBERON:0000947	primary human aortic endothelial cells	NA	endothelial cell	CL:0000115	Super-enhancer perturbation; flow-responsive enhancer assay	H3K27ac ChIP-seq; ATAC-seq; RNA-seq; promoter capture Hi-C	CRISPRi; CRISPRa; qRT-PCR; protein expression assay
E_04614	2024	38231044	Mechanosensitive super-enhancers regulate genes linked to atherosclerosis in endothelial cells	Homo sapiens	hg19	chr6	11605189	11618730	NA	EDN1	Super-enhancer	Active	Normal	NA	NA	NA	aorta	UBERON:0000947	primary human aortic endothelial cells	NA	endothelial cell	CL:0000115	Super-enhancer perturbation; disturbed-flow response assay	H3K27ac ChIP-seq; ATAC-seq; RNA-seq; promoter capture Hi-C	CRISPRi; CRISPRa; qRT-PCR; protein expression assay
E_04615	2024	38231044	Mechanosensitive super-enhancers regulate genes linked to atherosclerosis in endothelial cells	Homo sapiens	hg19	chr6	11605189	11618730	NA	HIVEP1	Super-enhancer	Active	Normal	NA	NA	NA	aorta	UBERON:0000947	primary human aortic endothelial cells	NA	endothelial cell	CL:0000115	Super-enhancer perturbation; disturbed-flow response assay	H3K27ac ChIP-seq; ATAC-seq; RNA-seq; promoter capture Hi-C	CRISPRi; CRISPRa; qRT-PCR
E_04616	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23912000	23912961	NA	MYH7	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	iPSC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; endogenous enhancer deletion; cardiac functional phenotype assay	H3K27ac ChIP-seq; ATAC-seq; promoter-capture Hi-C	CRISPR/Cas9 enhancer deletion; luciferase reporter assay; RT-qPCR; SDS-PAGE; engineered heart tissue contraction assay
E_04617	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23913940	23915344	NA	MYH7	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	iPSC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; endogenous enhancer perturbation	H3K27ac ChIP-seq; ATAC-seq; promoter-capture Hi-C	Luciferase reporter assay; CRISPR/Cas9 deletion; RT-qPCR
E_04618	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr1	156095724	156096574	NA	LMNA	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	iPSC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay	H3K27ac ChIP-seq; ATAC-seq; promoter-capture Hi-C	Luciferase reporter assay
E_04619	2016	26966274	Functional Analysis of a Novel Genome-Wide Association Study Signal in SMAD3 That Confers Protection From Coronary Artery Disease	Homo sapiens	hg19	chr15	67442412	67442758	AP-1	SMAD3	Enhancer	Active	Normal	NA	NA	NA	artery	UBERON:0001637	primary human arterial smooth muscle cells	NA	smooth muscle cell	CL:0000192	Allele-specific enhancer activity assay; TF-binding assay	ChIP-seq; DNase-seq	Dual-luciferase reporter assay; AP-1 inhibition; ChIP-qPCR; siRNA knockdown
E_04620	2023	36792607	Molecular mechanisms of coronary artery disease risk at the PDGFD locus	Homo sapiens	hg19	chr11	103668888	103669037	FOXC1	PDGFD	Enhancer	Active	Normal	NA	NA	NA	coronary artery	UBERON:0001621	primary human coronary artery smooth muscle cells	NA	vascular associated smooth muscle cell	CL:0000359	Enhancer activity assay; endogenous cis-regulatory perturbation; allele-specific TF regulation	ATAC-seq; H3K27ac ChIP-seq; SMAD3 ChIP-seq; TCF21 ChIP-seq	Dual-luciferase reporter assay; CRISPRi; FOXC1 overexpression; qRT-PCR
E_04621	2023	36792607	Molecular mechanisms of coronary artery disease risk at the PDGFD locus	Homo sapiens	hg19	chr11	103668888	103669037	FOXC2	PDGFD	Enhancer	Active	Normal	NA	NA	NA	coronary artery	UBERON:0001621	primary human coronary artery smooth muscle cells	NA	vascular associated smooth muscle cell	CL:0000359	Enhancer activity assay; endogenous cis-regulatory perturbation; allele-specific TF regulation	ATAC-seq; H3K27ac ChIP-seq; SMAD3 ChIP-seq; TCF21 ChIP-seq	Dual-luciferase reporter assay; CRISPRi; FOXC2 overexpression; qRT-PCR
E_04622	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23876121	23878188	NKX2-5	MYH7	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	iPSC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; enhancer-modifying variant assay	H3K27ac ChIP-seq; ATAC-seq; promoter-capture Hi-C; cardiac TF ChIP-seq	Luciferase reporter assay; allele-specific reporter assay
E_04623	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23912000	23912961	NKX2-5	MYH7	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	iPSC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; endogenous enhancer deletion; cardiac functional phenotype assay	H3K27ac ChIP-seq; ATAC-seq; promoter-capture Hi-C; cardiac TF ChIP-seq	CRISPR/Cas9 enhancer deletion; luciferase reporter assay; RT-qPCR; SDS-PAGE; engineered heart tissue contraction assay
E_04624	2021	33478249	Genetic Variation in Enhancers Modifies Cardiomyopathy Gene Expression and Progression	Homo sapiens	hg19	chr14	23912000	23912961	TCF21	MYH7	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	iPSC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; endogenous enhancer deletion; enhancer-modifying variant assay	H3K27ac ChIP-seq; ATAC-seq; promoter-capture Hi-C; cardiac TF ChIP-seq	CRISPR/Cas9 enhancer deletion; luciferase reporter assay; allele-specific reporter assay; RT-qPCR
E_04625	2018	30429326	Genetic variant at coronary artery disease and ischemic stroke locus 1p32.2 regulates endothelial responses to hemodynamics	Homo sapiens	hg19	chr1	56962213	56963412	KLF2	PLPP3	Enhancer	Active	Normal	NA	NA	NA	aorta	UBERON:0000947	primary human aortic endothelial cells	NA	endothelial cell	CL:0000115	Enhancer activity assay; endogenous enhancer deletion; CRISPR interference; allele-specific enhancer assay	ATAC-seq; H3K27ac ChIP-seq; H3K4me2 ChIP-seq; RNA-seq	Luciferase reporter assay; CRISPR/Cas9 66-bp deletion; CRISPRi; ChIP-PCR; allele-specific reporter assay; shear-stress assay
E_04626	2015	25838425	Myocardial Infarction-Associated SNP at 6p24 Interferes With MEF2 Binding and Associates With PHACTR1 Expression Levels in Human Coronary Arteries	Homo sapiens	hg19	chr6	12903940	12903973	MEF2	PHACTR1	Enhancer	Active	Normal	NA	NA	NA	coronary artery	UBERON:0001621	hESC-derived endothelial cells	NA	endothelial cell	CL:0000115	Endogenous cis-regulatory deletion; TF-binding assay; allele-specific regulatory assay	eQTL analysis	CRISPR/Cas9 34-bp deletion; EMSA; MEF2 supershift assay; RT-qPCR
E_04627	2017	28753427	A Genetic Variant Associated with Five Vascular Diseases Is a Distal Regulator of Endothelin-1 Gene Expression	Homo sapiens	hg19	chr6	12903893	12903980	NA	EDN1	Enhancer	Active	Normal	NA	NA	NA	aorta	UBERON:0000947	iPSC-derived endothelial cells	NA	endothelial cell	CL:0000115	Endogenous enhancer deletion; allele-specific genome editing; distal regulatory assay	H3K27ac ChIP-seq; RNA-seq; 4C-seq	CRISPR/Cas9 88-bp enhancer deletion; CRISPR allele replacement; RT-qPCR; Big ET-1 protein assay
E_04628	2017	28753427	A Genetic Variant Associated with Five Vascular Diseases Is a Distal Regulator of Endothelin-1 Gene Expression	Homo sapiens	hg19	chr6	12903893	12903980	NA	EDN1	Enhancer	Active	Normal	NA	NA	NA	aorta	UBERON:0000947	iPSC-derived vascular smooth muscle cells	NA	vascular associated smooth muscle cell	CL:0000359	Endogenous enhancer deletion; distal regulatory assay	H3K27ac ChIP-seq; RNA-seq	CRISPR/Cas9 88-bp enhancer deletion; RT-qPCR
E_04629	2025	41125440	A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress	Homo sapiens	hg38	chr14	23379863	23380961	NA	MYH6	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	iPSC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Endogenous enhancer perturbation; enhancer-promoter interaction assay; cardiac stress-response assay	ATAC-seq; RNA-seq; HiCAR	CRISPRi; CRISPRa; RT-qPCR; ET-1 hypertrophic stress assay; calcium imaging; DNA-content/polyploidization assay; spontaneous contraction analysis
E_04630	2025	41125440	A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress	Homo sapiens	hg38	chr14	23379863	23380961	NA	CMTM5	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	iPSC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Endogenous enhancer perturbation	ATAC-seq; RNA-seq; HiCAR	CRISPRi; RT-qPCR
E_04631	2025	41125440	A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress	Homo sapiens	hg38	chr14	23378863	23379551	NA	CMTM5	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	iPSC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Endogenous enhancer perturbation	ATAC-seq; RNA-seq	CRISPRi; RT-qPCR
E_04632	2019	31287004	Integrative analysis of vascular endothelial cell genomic features identifies AIDA as a coronary artery disease candidate gene	Homo sapiens	hg19	chr1	222827855	222828970	NA	AIDA	Enhancer	Active	Normal	NA	NA	NA	aorta	UBERON:0000947	teloHAEC	NA	endothelial cell	CL:0000115	Endogenous cis-regulatory deletion; enhancer-promoter interaction assay; inflammatory-response assay	RNA-seq; ATAC-seq; Hi-C	CRISPR/Cas9 enhancer deletion; RT-qPCR; TNF-alpha stimulation
E_04633	2025	41057608	Coronary artery disease-associated variants regulate vascular smooth muscle cell gene expression	Homo sapiens	hg38	chr22	19983114	19983313	NA	ARVCF	Enhancer	Active	Normal	NA	NA	NA	aorta	UBERON:0000947	primary human aortic smooth muscle cells	NA	vascular associated smooth muscle cell	CL:0000359	Allele-specific enhancer activity assay; endogenous cis-regulatory perturbation	lentiMPRA; H3K27ac CUT&RUN; H3K4me3 CUT&RUN; H2BK20ac CUT&RUN; eQTL colocalization	CRISPRi; RT-qPCR
E_04634	2025	41057608	Coronary artery disease-associated variants regulate vascular smooth muscle cell gene expression	Homo sapiens	hg38	chr22	19983114	19983313	NA	COMT	Enhancer	Active	Normal	NA	NA	NA	aorta	UBERON:0000947	primary human aortic smooth muscle cells	NA	vascular associated smooth muscle cell	CL:0000359	Allele-specific enhancer activity assay; endogenous cis-regulatory perturbation	lentiMPRA; H3K27ac CUT&RUN; H3K4me3 CUT&RUN; H2BK20ac CUT&RUN	CRISPRi; RT-qPCR
E_04635	2022	35288587	Whole genome sequencing delineates regulatory, copy number, and cryptic splice variants in early onset cardiomyopathy	Homo sapiens	hg38	chr14	76289119	76289318	NA	TGFB3	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart	UBERON:0000948	iPSC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Allele-specific enhancer activity assay; disease-associated regulatory variant assay	Whole-genome sequencing; RNA-seq; MPRA	Luciferase reporter assay; RT-qPCR; Western blot
E_04636	2022	35288587	Whole genome sequencing delineates regulatory, copy number, and cryptic splice variants in early onset cardiomyopathy	Homo sapiens	hg38	chr7	151392082	151392281	NA	PRKAG2	Enhancer	Active	Disease	cardiomyopathy	MONDO:0004994	DOID:0050700	heart	UBERON:0000948	left ventricular myocardium	NA	cardiac muscle cell	CL:0000746	Allele-specific enhancer activity assay; disease-associated regulatory variant assay	Whole-genome sequencing; RNA-seq; MPRA	Luciferase reporter assay; RT-qPCR; Western blot
E_04637	2025	41057608	Coronary artery disease-associated variants regulate vascular smooth muscle cell gene expression	Homo sapiens	hg19	chr5	9547842	9548041	NA	SNHG18	Enhancer	Active	Normal	NA	NA	NA	aorta	UBERON:0000947	primary human aortic smooth muscle cells	NA	vascular associated smooth muscle cell	CL:0000359	Allele-specific enhancer activity assay; endogenous cis-regulatory perturbation	lentiMPRA; H3K27ac CUT&RUN; H3K4me3 CUT&RUN; H2BK20ac CUT&RUN; eQTL colocalization	CRISPRi; RT-qPCR
E_04638	2025	41057608	Coronary artery disease-associated variants regulate vascular smooth muscle cell gene expression	Homo sapiens	hg19	chr11	9292826	9293025	NA	NRIP3	Enhancer	Active	Normal	NA	NA	NA	aorta	UBERON:0000947	primary human aortic smooth muscle cells	NA	vascular associated smooth muscle cell	CL:0000359	Allele-specific enhancer activity assay; endogenous cis-regulatory perturbation	lentiMPRA; H3K27ac CUT&RUN; H3K4me3 CUT&RUN; H2BK20ac CUT&RUN; eQTL colocalization	CRISPRi; RT-qPCR
E_04639	2025	41125440	A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress	Homo sapiens	hg38	chr14	23377559	23378416	NA	MYH6	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	iPSC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Endogenous cis-regulatory element perturbation; cardiac stress-response assay	ATAC-seq; RNA-seq; HiCAR	CRISPRi; RT-qPCR; endothelin-1 hypertrophic stress assay
E_04640	2025	41125440	A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress	Homo sapiens	hg38	chr14	23379863	23380961	NA	MYH6	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	iPSC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Endogenous enhancer perturbation; enhancer-promoter interaction assay; cardiac functional phenotype assay	ATAC-seq; RNA-seq; HiCAR	CRISPRi; CRISPRa; RT-qPCR; endothelin-1 hypertrophic stress assay; calcium imaging; spontaneous contraction analysis; DNA-content assay
E_04641	2025	41057608	Coronary artery disease-associated variants regulate vascular smooth muscle cell gene expression	Homo sapiens	hg19	chr19	17832649	17832848	NA	MAP1S	Enhancer	Active	Normal	NA	NA	NA	aorta	UBERON:0000947	primary human aortic smooth muscle cells	NA	vascular associated smooth muscle cell	CL:0000359	Allele-specific enhancer activity assay; endogenous cis-regulatory perturbation	lentiMPRA; H3K27ac CUT&RUN; H3K4me3 CUT&RUN; H2BK20ac CUT&RUN; SMC eQTL colocalization	CRISPRi; RT-qPCR
E_04642	2025	41057608	Coronary artery disease-associated variants regulate vascular smooth muscle cell gene expression	Homo sapiens	hg19	chr1	38461722	38461921	NA	INPP5B	Enhancer	Active	Normal	NA	NA	NA	aorta	UBERON:0000947	primary human aortic smooth muscle cells	NA	vascular associated smooth muscle cell	CL:0000359	Allele-specific enhancer activity assay; endogenous cis-regulatory perturbation	lentiMPRA; H3K27ac CUT&RUN; H3K4me3 CUT&RUN; H2BK20ac CUT&RUN; SMC eQTL colocalization	CRISPRi; RT-qPCR
E_04643	2025	41057608	Coronary artery disease-associated variants regulate vascular smooth muscle cell gene expression	Homo sapiens	hg19	chr1	38461722	38461921	NA	FHL3	Enhancer	Active	Normal	NA	NA	NA	aorta	UBERON:0000947	primary human aortic smooth muscle cells	NA	vascular associated smooth muscle cell	CL:0000359	Allele-specific enhancer activity assay; endogenous cis-regulatory perturbation	lentiMPRA; H3K27ac CUT&RUN; H3K4me3 CUT&RUN; H2BK20ac CUT&RUN; SMC eQTL colocalization	CRISPRi; RT-qPCR
E_04644	2025	41057608	Coronary artery disease-associated variants regulate vascular smooth muscle cell gene expression	Homo sapiens	hg38	chr22	19983114	19983313	NA	ARVCF	Enhancer	Active	Normal	NA	NA	NA	aorta	UBERON:0000947	primary human aortic smooth muscle cells	NA	vascular associated smooth muscle cell	CL:0000359	Allele-specific enhancer activity assay; endogenous cis-regulatory perturbation	lentiMPRA; H3K27ac CUT&RUN; H3K4me3 CUT&RUN; H2BK20ac CUT&RUN; SMC eQTL colocalization	CRISPRi; RT-qPCR
E_04645	2025	41125440	A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress	Homo sapiens	hg38	chr14	23377559	23378416	NA	MYH6	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	iPSC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Endogenous cis-regulatory perturbation; cardiac stress-response assay	ATAC-seq; RNA-seq; HiCAR	CRISPRi; RT-qPCR; endothelin-1 hypertrophic stress assay
E_04646	2025	41125440	A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress	Homo sapiens	hg38	chr14	23378863	23379551	NA	CMTM5	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	iPSC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Endogenous cis-regulatory perturbation	ATAC-seq; RNA-seq; HiCAR	CRISPRi; RT-qPCR
E_04647	2025	41125440	A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress	Homo sapiens	hg38	chr14	23379863	23380961	NA	MYH6	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	iPSC-derived cardiomyocytes	NA	cardiac muscle cell	CL:0000746	Endogenous enhancer perturbation; enhancer-promoter interaction assay; cardiac stress-response assay	ATAC-seq; RNA-seq; HiCAR	CRISPRi; CRISPRa; RT-qPCR; endothelin-1 hypertrophic stress assay; calcium imaging; spontaneous contraction analysis; DNA-content assay
E_04648	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr15	74638179	74639054	NA	SIN3A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay; allelic cis-regulation assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04649	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr15	74724384	74724924	NA	SIN3A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay; allelic cis-regulation assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	Individual paired-sgRNA enhancer deletion; clonal validation; flow cytometry; RT-qPCR; allelic expression analysis
E_04650	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr15	74751789	74752496	NA	SIN3A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay; allelic cis-regulation assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	Individual paired-sgRNA enhancer deletion; clonal validation; flow cytometry; RT-qPCR; allelic expression analysis
E_04651	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr15	74768848	74769811	CTCF	SIN3A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay; allelic cis-regulation assay; transcriptional compensation assay; TF-motif perturbation assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	Individual paired-sgRNA enhancer deletion; clonal validation; flow cytometry; RT-qPCR; allelic expression analysis; CTCF-motif CRISPR editing
E_04652	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr15	74776955	74778648	NA	SIN3A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay; allelic cis-regulation assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	Individual paired-sgRNA enhancer deletion; clonal validation; flow cytometry; RT-qPCR; allelic expression analysis
E_04653	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr15	74798988	74800051	NA	SIN3A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay; allelic cis-regulation assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04654	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr15	74828806	74829796	NA	SIN3A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay; allelic cis-regulation assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04655	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr15	74900584	74901270	NA	SIN3A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay; allelic cis-regulation assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04656	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr15	74920508	74922951	NA	SIN3A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay; allelic cis-regulation assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04657	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr15	74929460	74932091	NA	SIN3A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay; allelic cis-regulation assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04658	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr15	74955769	74956062	NA	SIN3A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay; allelic cis-regulation assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04659	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr15	74958381	74958732	NA	SIN3A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay; allelic cis-regulation assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04660	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr15	74996439	74997608	NA	SIN3A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay; allelic cis-regulation assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04661	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr15	75039579	75041846	NA	SIN3A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay; allelic cis-regulation assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04662	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr15	75367117	75367526	NA	SIN3A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay; allelic cis-regulation assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04663	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr15	75639596	75640467	NA	SIN3A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay; allelic cis-regulation assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04664	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr15	75807885	75808824	NA	SIN3A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay; allelic cis-regulation assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04665	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr15	76101504	76101823	NA	SIN3A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay; allelic cis-regulation assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04666	2026	41881989	CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription	Homo sapiens	hg38	chr15	76152919	76153578	NA	SIN3A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	WTC11	CVCL_Y803	excitatory neuron	NA	Functional cis-regulatory deletion screen; enhancer-target gene expression assay; neuronal regulatory assay; allelic cis-regulation assay	CREST-seq paired-guide CRISPR tiling deletion screen; FACS-based reporter sorting; deep sequencing; RELICS functional-element calling; ATAC-seq; histone/CTCF/RNA polymerase II ChIP-seq; H3K4me3 PLAC-seq	ChIP-qPCR
E_04667	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54268115	54268740	NA	SOX17	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES8	CVCL_B207	endodermal cell	CL:0000223	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; cell-state transition assay	Genome-scale CRISPRi enhancer screen; ATAC-seq; H3K27ac ChIP-seq; EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; scRNA-seq; bulk RNA-seq	Individual dCas9-KRAB CRISPRi; SOX17-GFP flow cytometry; RT-qPCR
E_04668	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr3	27728339	27729090	NA	EOMES	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES8	CVCL_B207	endodermal cell	CL:0000223	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; cell-state transition assay	Genome-scale CRISPRi enhancer screen; ATAC-seq; H3K27ac ChIP-seq; EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; scRNA-seq; bulk RNA-seq	Individual dCas9-KRAB CRISPRi; SOX17-GFP flow cytometry; RT-qPCR
E_04669	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54300591	54300987	NA	SOX17	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES8	CVCL_B207	endodermal cell	CL:0000223	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; cell-state transition assay	Genome-scale CRISPRi enhancer screen; ATAC-seq; H3K27ac ChIP-seq; EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; scRNA-seq; bulk RNA-seq	Individual dCas9-KRAB CRISPRi; SOX17-GFP flow cytometry; RT-qPCR
E_04670	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr18	22026154	22027330	NA	GATA6	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES8	CVCL_B207	endodermal cell	CL:0000223	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; endogenous enhancer deletion assay; enhancer synergy assay	Genome-scale CRISPRi enhancer screen; ATAC-seq; H3K27ac ChIP-seq; EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; scRNA-seq; bulk RNA-seq	Individual dCas9-KRAB CRISPRi; CRISPR-Cas9 enhancer deletion; double-enhancer deletion; SOX17-GFP flow cytometry; RT-qPCR; genotyping
E_04671	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54454106	54455036	NA	SOX17	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES8	CVCL_B207	endodermal cell	CL:0000223	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; cell-state transition assay	Genome-scale CRISPRi enhancer screen; ATAC-seq; H3K27ac ChIP-seq; EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; scRNA-seq; bulk RNA-seq	Individual dCas9-KRAB CRISPRi; SOX17-GFP flow cytometry; RT-qPCR
E_04672	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54301978	54302426	NA	SOX17	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES8	CVCL_B207	endodermal cell	CL:0000223	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; cell-state transition assay	Genome-scale CRISPRi enhancer screen; ATAC-seq; H3K27ac ChIP-seq; EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; scRNA-seq; bulk RNA-seq	Individual dCas9-KRAB CRISPRi; SOX17-GFP flow cytometry; RT-qPCR
E_04673	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr3	27713390	27715985	NA	EOMES	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES8	CVCL_B207	endodermal cell	CL:0000223	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; cell-state transition assay	Genome-scale CRISPRi enhancer screen; ATAC-seq; H3K27ac ChIP-seq; EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; scRNA-seq; bulk RNA-seq	Individual dCas9-KRAB CRISPRi; SOX17-GFP flow cytometry; RT-qPCR
E_04674	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr1	226210507	226211585	NA	MIXL1	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES8	CVCL_B207	endodermal cell	CL:0000223	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; cell-state transition assay	Genome-scale CRISPRi enhancer screen; ATAC-seq; H3K27ac ChIP-seq; EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; scRNA-seq; bulk RNA-seq	Individual dCas9-KRAB CRISPRi; SOX17-GFP flow cytometry; RT-qPCR
E_04675	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr1	226215164	226215656	NA	MIXL1	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES8	CVCL_B207	endodermal cell	CL:0000223	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; cell-state transition assay	Genome-scale CRISPRi enhancer screen; ATAC-seq; H3K27ac ChIP-seq; EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; scRNA-seq; bulk RNA-seq	Individual dCas9-KRAB CRISPRi; SOX17-GFP flow cytometry; RT-qPCR
E_04676	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr18	22194123	22194455	NA	GATA6	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES8	CVCL_B207	endodermal cell	CL:0000223	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; cell-state transition assay	Genome-scale CRISPRi enhancer screen; ATAC-seq; H3K27ac ChIP-seq; EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; scRNA-seq; bulk RNA-seq	Individual dCas9-KRAB CRISPRi; SOX17-GFP flow cytometry; RT-qPCR
E_04677	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54259816	54260322	NA	SOX17	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES8	CVCL_B207	endodermal cell	CL:0000223	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; cell-state transition assay	Genome-scale CRISPRi enhancer screen; ATAC-seq; H3K27ac ChIP-seq; EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; scRNA-seq; bulk RNA-seq	Individual dCas9-KRAB CRISPRi; SOX17-GFP flow cytometry; RT-qPCR
E_04678	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr18	21933810	21935298	NA	GATA6	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES8	CVCL_B207	endodermal cell	CL:0000223	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; endogenous enhancer deletion assay; enhancer synergy assay	Genome-scale CRISPRi enhancer screen; ATAC-seq; H3K27ac ChIP-seq; EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; scRNA-seq; bulk RNA-seq	Individual dCas9-KRAB CRISPRi; CRISPR-Cas9 enhancer deletion; double-enhancer deletion; SOX17-GFP flow cytometry; RT-qPCR; genotyping
E_04679	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54224560	54225711	NA	SOX17	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES8	CVCL_B207	endodermal cell	CL:0000223	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; cell-state transition assay	Genome-scale CRISPRi enhancer screen; ATAC-seq; H3K27ac ChIP-seq; EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; scRNA-seq; bulk RNA-seq	Individual dCas9-KRAB CRISPRi; SOX17-GFP flow cytometry; RT-qPCR
E_04680	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr3	27712007	27712923	NA	EOMES	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES8	CVCL_B207	endodermal cell	CL:0000223	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; cell-state transition assay	Genome-scale CRISPRi enhancer screen; ATAC-seq; H3K27ac ChIP-seq; EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; scRNA-seq; bulk RNA-seq	Individual dCas9-KRAB CRISPRi; SOX17-GFP flow cytometry; RT-qPCR
E_04681	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr3	27730029	27730667	NA	EOMES	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES8	CVCL_B207	endodermal cell	CL:0000223	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; cell-state transition assay	Genome-scale CRISPRi enhancer screen; ATAC-seq; H3K27ac ChIP-seq; EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; scRNA-seq; bulk RNA-seq	Individual dCas9-KRAB CRISPRi; SOX17-GFP flow cytometry; RT-qPCR
E_04682	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54273053	54273554	NA	SOX17	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES8	CVCL_B207	endodermal cell	CL:0000223	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; cell-state transition assay	Genome-scale CRISPRi enhancer screen; ATAC-seq; H3K27ac ChIP-seq; EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; scRNA-seq; bulk RNA-seq	Individual dCas9-KRAB CRISPRi; SOX17-GFP flow cytometry; RT-qPCR
E_04683	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr1	226228164	226228831	NA	MIXL1	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES8	CVCL_B207	endodermal cell	CL:0000223	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; cell-state transition assay	Genome-scale CRISPRi enhancer screen; ATAC-seq; H3K27ac ChIP-seq; EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; scRNA-seq; bulk RNA-seq	Individual dCas9-KRAB CRISPRi; SOX17-GFP flow cytometry; RT-qPCR
E_04684	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr18	47853130	47853488	NA	SMAD2	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES8	CVCL_B207	endodermal cell	CL:0000223	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; cell-state transition assay	Genome-scale CRISPRi enhancer screen; ATAC-seq; H3K27ac ChIP-seq; Hi-C; CTCF ChIP-seq; scRNA-seq; bulk RNA-seq	Individual dCas9-KRAB CRISPRi; SOX17-GFP flow cytometry; RT-qPCR
E_04685	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr8	54443606	54444178	NA	SOX17	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES8	CVCL_B207	endodermal cell	CL:0000223	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; cell-state transition assay	Genome-scale CRISPRi enhancer screen; ATAC-seq; H3K27ac ChIP-seq; EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; scRNA-seq; bulk RNA-seq	Individual dCas9-KRAB CRISPRi; SOX17-GFP flow cytometry; RT-qPCR
E_04686	2023	37488417	Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions	Homo sapiens	hg38	chr1	226203745	226204150	NA	MIXL1	Enhancer	Active	Normal	NA	NA	NA	definitive endoderm	UBERON:0005439	HUES8	CVCL_B207	endodermal cell	CL:0000223	Functional cis-regulatory perturbation assay; enhancer-target gene expression assay; cell-state transition assay	Genome-scale CRISPRi enhancer screen; ATAC-seq; H3K27ac ChIP-seq; EOMES/GATA6/SOX17 ChIP-seq; Hi-C; CTCF ChIP-seq; scRNA-seq; bulk RNA-seq	Individual dCas9-KRAB CRISPRi; SOX17-GFP flow cytometry; RT-qPCR
E_04687	2025	41278953	Large-scale discovery of neural enhancers for cis-regulation therapies	Homo sapiens	hg38	chr2	165017467	165018951	NA	SCN2A	Enhancer	Active	Disease	autism spectrum disorder	MONDO:0005258	DOID:0060041	NA	NA	Pre-i3Neuron NGN2 iPSC clone 1	CVCL_C7XJ	excitatory neuron	NA	Enhancer activity assay; endogenous enhancer activation assay; enhancer-target gene expression assay; target-specificity assay; in vivo developmental enhancer assay; cerebral organoid validation	Lentiviral MPRA; multiplex single-cell CRISPRa screen; single-cell RNA-seq with direct gRNA capture; ATAC-seq; H3K27ac profiling	Individual enhancer-targeting CRISPRa; qRT-PCR; viral gRNA delivery; E12.5 mouse CNS enhancer reporter assay; human cerebral organoid validation
E_04688	2025	41278953	Large-scale discovery of neural enhancers for cis-regulation therapies	Homo sapiens	hg38	chr5	12016287	12016787	NA	CTNND2	Enhancer	Active	Disease	Cri-du-chat syndrome	MONDO:0007404	DOID:12580	NA	NA	Pre-i3Neuron NGN2 iPSC clone 1	CVCL_C7XJ	excitatory neuron	NA	Enhancer activity assay; endogenous enhancer activation assay; enhancer-target gene expression assay; disease-model validation	Lentiviral MPRA; multiplex single-cell CRISPRa screen; single-cell RNA-seq with direct gRNA capture; ATAC-seq; H3K27ac profiling	Individual enhancer-targeting CRISPRa; lentiviral gRNA delivery; qRT-PCR in two Cri-du-chat syndrome patient-derived iPSC lines
E_04689	2025	41278953	Large-scale discovery of neural enhancers for cis-regulation therapies	Homo sapiens	hg38	chr18	55483221	55483721	NA	TCF4	Enhancer	Active	Disease	Pitt-Hopkins syndrome	MONDO:0012589	DOID:0060488	NA	NA	Pre-i3Neuron NGN2 iPSC clone 1	CVCL_C7XJ	excitatory neuron	NA	Enhancer activity assay; endogenous enhancer activation assay; enhancer-target gene expression assay; disease-model validation	Lentiviral MPRA; multiplex single-cell CRISPRa screen; single-cell RNA-seq with direct gRNA capture; ATAC-seq; H3K27ac profiling	Individual enhancer-targeting CRISPRa; lentiviral gRNA delivery; qRT-PCR in two Pitt-Hopkins syndrome patient-derived iPSC lines
E_04690	2024	38889007	An enhancer RNA recruits KMT2A to regulate transcription of Myb	Mus musculus	mm9	chr10	20961000	20962500	Klf1	Myb	Enhancer	Active	Normal	NA	NA	NA	NA	NA	MEL-745A cl. DS19	CVCL_2111	erythroid cell	NA	Functional enhancer perturbation assay; enhancer RNA functional assay; enhancer-target gene expression assay; enhancer-promoter chromatin interaction assay; transcription elongation mechanism assay	RNA-seq; GATA1/LDB1/TAL1/RNA polymerase II ChIP-seq; RNA polymerase II Ser5P/Ser2P CUT&Tag	CRISPR-Cas9 Myrlin TSS deletion; dCas9-KRAB CRISPRi; Myrlin shRNA knockdown; RT-qPCR; 5-prime and 3-prime RACE; 3C; KLF1/GATA1/TAL1/LDB1/H3K27ac/KMT2A/WDR5/CDK9/RNA polymerase II ChIP-qPCR; Myrlin RNA-ChIP; biotinylated Myrlin RNA pull-down; ChIRP
E_04691	2025	41330917	Super-enhancers mediates SLC7A11 via FOXA1 to regulate disulfidptosis in prostate cancer	Homo sapiens	hg38	chr14	37583488	37589585	NA	FOXA1	Super-enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	NA	NA	PC-3	CVCL_0035	NA	NA	Super-enhancer functional perturbation assay; enhancer-target gene expression assay; enhancer activity assay; combinatorial enhancer perturbation assay; cancer metabolic phenotype assay	H3K27ac ChIP-seq; H3K27ac CUT&Tag-seq; ROSE super-enhancer calling; transcriptome sequencing; single-cell RNA-seq; spatial transcriptomic analysis	CRISPR-Cas9 perturbation of SE1/SE2/SE3; combinatorial 3xSE perturbation; FOXA1 qRT-PCR; FOXA1 Western blot; SE-FOXA1 promoter dual-luciferase reporter assay
E_04692	2025	41330917	Super-enhancers mediates SLC7A11 via FOXA1 to regulate disulfidptosis in prostate cancer	Homo sapiens	hg38	chr14	37583488	37589585	NA	FOXA1	Super-enhancer	Active	Disease	prostate cancer	MONDO:0008315	DOID:10283	NA	NA	DU145	CVCL_0105	NA	NA	Super-enhancer functional perturbation assay; enhancer-target gene expression assay; enhancer activity assay; combinatorial enhancer perturbation assay; cancer metabolic phenotype assay	H3K27ac ChIP-seq; H3K27ac CUT&Tag-seq; ROSE super-enhancer calling; transcriptome sequencing; single-cell RNA-seq; spatial transcriptomic analysis	CRISPR-Cas9 perturbation of SE1/SE2/SE3; combinatorial 3xSE perturbation; FOXA1 qRT-PCR; FOXA1 Western blot; SE-FOXA1 promoter dual-luciferase reporter assay
E_04693	2025	39731339	Super-enhancer Activates Master Transcription Factor NR3C1 Expression and Promotes 5-FU Resistance in Gastric Cancer	Homo sapiens	hg38	chr5	143233723	143262337	NR3C1	NR3C1	Super-enhancer	Active	Disease	gastric cancer	MONDO:0001056	DOID:10534	NA	NA	Hs 746.T	CVCL_0333	NA	NA	Super-enhancer identification; transcription-factor occupancy assay; drug-resistance regulatory assay; autoregulatory transcriptional circuitry analysis	H3K27ac ChIP-seq; ROSE super-enhancer calling; RNA-seq; NR3C1 CUT&Tag-seq; CRCmapper analysis; HOMER motif analysis	NR3C1/BRD4/MED1 ChIP-PCR and ChIP-qPCR; DNA-FISH and NR3C1 immunofluorescence; NR3C1 shRNA knockdown; JQ1 treatment; 5-FU sensitivity assay
E_04694	2025	39731339	Super-enhancer Activates Master Transcription Factor NR3C1 Expression and Promotes 5-FU Resistance in Gastric Cancer	Homo sapiens	hg38	chr5	143275273	143391380	NR3C1	NR3C1	Super-enhancer	Active	Disease	gastric cancer	MONDO:0001056	DOID:10534	NA	NA	Hs 746.T	CVCL_0333	NA	NA	Super-enhancer identification; transcription-factor occupancy assay; drug-resistance regulatory assay; autoregulatory transcriptional circuitry analysis	H3K27ac ChIP-seq; ROSE super-enhancer calling; RNA-seq; NR3C1 CUT&Tag-seq; CRCmapper analysis; HOMER motif analysis	NR3C1/BRD4/MED1 ChIP-PCR and ChIP-qPCR; DNA-FISH and NR3C1 immunofluorescence; NR3C1 shRNA knockdown; JQ1 treatment; 5-FU sensitivity assay
E_04695	2025	39731339	Super-enhancer Activates Master Transcription Factor NR3C1 Expression and Promotes 5-FU Resistance in Gastric Cancer	Homo sapiens	hg38	chr5	143486735	143509814	NR3C1	NR3C1	Super-enhancer	Active	Disease	gastric cancer	MONDO:0001056	DOID:10534	NA	NA	Hs 746.T	CVCL_0333	NA	NA	Super-enhancer identification; transcription-factor occupancy assay; drug-resistance regulatory assay; autoregulatory transcriptional circuitry analysis	H3K27ac ChIP-seq; ROSE super-enhancer calling; RNA-seq; NR3C1 CUT&Tag-seq; CRCmapper analysis; HOMER motif analysis	NR3C1/BRD4/MED1 ChIP-PCR and ChIP-qPCR; DNA-FISH and NR3C1 immunofluorescence; NR3C1 shRNA knockdown; JQ1 treatment; 5-FU sensitivity assay
E_04696	2025	41057395	Evidence for enhancer activity in intron 1 of TNFRSF1A using CRISPR/Cas9 in human induced pluripotent stem cell-derived macrophages	Homo sapiens	hg19	chr12	6444399	6447744	NA	TNFRSF1A	Enhancer	Active	Normal	NA	NA	NA	NA	NA	iPSC-derived macrophage	NA	macrophage	CL:0000235	Functional cis-regulatory deletion assay; enhancer activity assay; enhancer-target gene expression assay	ATAC-seq; H3K27ac ChIP-seq; RNA-seq	CRISPR-Cas9 homozygous enhancer deletion; luciferase reporter assay; deletion genotyping PCR; Sanger sequencing
E_04697	2022	35869079	A multi-omic dissection of super-enhancer driven oncogenic gene expression programs in ovarian cancer	Homo sapiens	hg19	chr20	52352051	52368920	NA	RAE1	Super-enhancer	Active	Disease	ovarian serous adenocarcinoma	MONDO:0005211	DOID:5744	NA	NA	OVCAR-3	CVCL_0465	NA	NA	Super-enhancer functional perturbation assay; enhancer-target gene expression assay; enhancer-promoter chromatin interaction assay; cancer proliferation and migration assay	High-throughput CRISPRi super-enhancer screen; RNA-seq; Hi-C; H3K27ac ChIP-seq; BRD4 ChIP-seq; single-cell RNA-seq; single-cell ATAC-seq	CRISPR-Cas9 super-enhancer deletion; genotyping PCR; proliferation assay; migration assay
E_04698	2022	35869079	A multi-omic dissection of super-enhancer driven oncogenic gene expression programs in ovarian cancer	Homo sapiens	hg19	chr1	16493671	16516686	NA	EPHA2	Super-enhancer	Active	Disease	ovarian serous adenocarcinoma	MONDO:0005211	DOID:5744	NA	NA	OVCAR-3	CVCL_0465	NA	NA	Super-enhancer functional perturbation assay; enhancer-target gene expression assay; enhancer-promoter chromatin interaction assay; cancer proliferation and migration assay	High-throughput CRISPRi super-enhancer screen; RNA-seq; Hi-C; H3K27ac ChIP-seq; BRD4 ChIP-seq; single-cell RNA-seq; single-cell ATAC-seq	CRISPR-Cas9 super-enhancer deletion; genotyping PCR; proliferation assay; migration assay
E_04699	2025	40588505	Enhancer hijacking drives FAM20C expression to promote papillary thyroid cancer progression	Homo sapiens	hg38	chr7	191383	191462	KLF12	FAM20C	Enhancer	Active	Disease	papillary thyroid carcinoma	MONDO:0005075	DOID:3969	thyroid gland	UBERON:0002046	TPC-1	CVCL_6298	NA	NA	Functional enhancer perturbation assay; enhancer-target gene expression assay; enhancer-promoter chromatin interaction assay; transcription-factor binding assay; cancer phenotype assay	H3K27ac ChIP-seq; RNA-seq; tumor-normal enhancer landscape profiling; TCGA transcriptomic and clinical analysis	H3K27ac ChIP-qPCR; BRD4 ChIP-qPCR; chromosome conformation capture assay; dCas9-KRAB CRISPRi; KLF12 ChIP/knockdown; RT-qPCR; Western blot; CCK-8 proliferation assay; Transwell migration and invasion assay
E_04700	2025	40588505	Enhancer hijacking drives FAM20C expression to promote papillary thyroid cancer progression	Homo sapiens	hg38	chr7	191383	191462	KLF12	FAM20C	Enhancer	Active	Disease	papillary thyroid carcinoma	MONDO:0005075	DOID:3969	thyroid gland	UBERON:0002046	KTC-1	CVCL_6300	NA	NA	Functional enhancer perturbation assay; enhancer-target gene expression assay; enhancer-promoter chromatin interaction assay; transcription-factor binding assay; cancer phenotype assay	H3K27ac ChIP-seq; RNA-seq; tumor-normal enhancer landscape profiling; TCGA transcriptomic and clinical analysis	H3K27ac ChIP-qPCR; BRD4 ChIP-qPCR; chromosome conformation capture assay; dCas9-KRAB CRISPRi; KLF12 ChIP/knockdown; RT-qPCR; Western blot; CCK-8 proliferation assay; Transwell migration and invasion assay
E_04701	2025	40588505	Enhancer hijacking drives FAM20C expression to promote papillary thyroid cancer progression	Homo sapiens	hg38	chr7	191828	191919	KLF12	FAM20C	Enhancer	Active	Disease	papillary thyroid carcinoma	MONDO:0005075	DOID:3969	thyroid gland	UBERON:0002046	TPC-1	CVCL_6298	NA	NA	Functional enhancer perturbation assay; enhancer-target gene expression assay; enhancer-promoter chromatin interaction assay; transcription-factor binding assay; cancer phenotype assay	H3K27ac ChIP-seq; RNA-seq; tumor-normal enhancer landscape profiling; TCGA transcriptomic and clinical analysis	H3K27ac ChIP-qPCR; BRD4 ChIP-qPCR; chromosome conformation capture assay; dCas9-KRAB CRISPRi; KLF12 ChIP/knockdown; RT-qPCR; Western blot; CCK-8 proliferation assay; Transwell migration and invasion assay
E_04702	2025	40588505	Enhancer hijacking drives FAM20C expression to promote papillary thyroid cancer progression	Homo sapiens	hg38	chr7	191828	191919	KLF12	FAM20C	Enhancer	Active	Disease	papillary thyroid carcinoma	MONDO:0005075	DOID:3969	thyroid gland	UBERON:0002046	KTC-1	CVCL_6300	NA	NA	Functional enhancer perturbation assay; enhancer-target gene expression assay; enhancer-promoter chromatin interaction assay; transcription-factor binding assay; cancer phenotype assay	H3K27ac ChIP-seq; RNA-seq; tumor-normal enhancer landscape profiling; TCGA transcriptomic and clinical analysis	H3K27ac ChIP-qPCR; BRD4 ChIP-qPCR; chromosome conformation capture assay; dCas9-KRAB CRISPRi; KLF12 ChIP/knockdown; RT-qPCR; Western blot; CCK-8 proliferation assay; Transwell migration and invasion assay
E_04703	2025	40588505	Enhancer hijacking drives FAM20C expression to promote papillary thyroid cancer progression	Homo sapiens	hg38	chr7	192516	192615	KLF12	FAM20C	Enhancer	Active	Disease	papillary thyroid carcinoma	MONDO:0005075	DOID:3969	thyroid gland	UBERON:0002046	TPC-1	CVCL_6298	NA	NA	Functional enhancer perturbation assay; enhancer-target gene expression assay; enhancer-promoter chromatin interaction assay; transcription-factor binding assay; cancer phenotype assay	H3K27ac ChIP-seq; RNA-seq; tumor-normal enhancer landscape profiling; TCGA transcriptomic and clinical analysis	H3K27ac ChIP-qPCR; BRD4 ChIP-qPCR; chromosome conformation capture assay; dCas9-KRAB CRISPRi; KLF12 ChIP/knockdown; RT-qPCR; Western blot; CCK-8 proliferation assay; Transwell migration and invasion assay
E_04704	2025	40588505	Enhancer hijacking drives FAM20C expression to promote papillary thyroid cancer progression	Homo sapiens	hg38	chr7	192516	192615	KLF12	FAM20C	Enhancer	Active	Disease	papillary thyroid carcinoma	MONDO:0005075	DOID:3969	thyroid gland	UBERON:0002046	KTC-1	CVCL_6300	NA	NA	Functional enhancer perturbation assay; enhancer-target gene expression assay; enhancer-promoter chromatin interaction assay; transcription-factor binding assay; cancer phenotype assay	H3K27ac ChIP-seq; RNA-seq; tumor-normal enhancer landscape profiling; TCGA transcriptomic and clinical analysis	H3K27ac ChIP-qPCR; BRD4 ChIP-qPCR; chromosome conformation capture assay; dCas9-KRAB CRISPRi; KLF12 ChIP/knockdown; RT-qPCR; Western blot; CCK-8 proliferation assay; Transwell migration and invasion assay
E_04705	2020	32771023	Disruption of super-enhancer-driven tumor suppressor gene RCAN1.4 expression promotes the malignancy of breast carcinoma	Homo sapiens	hg19	chr21	36167153	36169051	NA	RCAN1	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	NA	NA	MDA-MB-231	CVCL_0062	NA	NA	Enhancer activity assay; super-enhancer constituent validation; enhancer-target gene regulation assay	H3K27ac ChIP-seq; H3K4me1 ChIP-seq; H3K4me3 ChIP-seq; RNA-seq; ENCODE TF ChIP-seq integration; HMEC Hi-C	Dual-luciferase reporter assay; qRT-PCR; Western blot; JQ1 treatment; BRD4 knockdown
E_04706	2020	32771023	Disruption of super-enhancer-driven tumor suppressor gene RCAN1.4 expression promotes the malignancy of breast carcinoma	Homo sapiens	hg19	chr21	36167153	36169051	NA	RCAN1	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	NA	NA	BT-549	CVCL_1092	NA	NA	Enhancer activity assay; super-enhancer constituent validation; enhancer-target gene regulation assay	H3K27ac ChIP-seq; H3K4me1 ChIP-seq; H3K4me3 ChIP-seq; RNA-seq; ENCODE TF ChIP-seq integration; HMEC Hi-C	Dual-luciferase reporter assay; qRT-PCR; Western blot; JQ1 treatment; BRD4 knockdown
E_04707	2020	32771023	Disruption of super-enhancer-driven tumor suppressor gene RCAN1.4 expression promotes the malignancy of breast carcinoma	Homo sapiens	hg19	chr21	36173677	36175514	NA	RCAN1	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	NA	NA	MDA-MB-231	CVCL_0062	NA	NA	Enhancer activity assay; endogenous composite super-enhancer deletion assay; enhancer-target gene expression assay; cancer phenotype assay	H3K27ac ChIP-seq; H3K4me1 ChIP-seq; H3K4me3 ChIP-seq; RNA-seq; ENCODE TF ChIP-seq integration; HMEC Hi-C	Dual-luciferase reporter assay; double-CRISPR deletion of RCAN1.4-SEdistal containing E2-E4; qRT-PCR; Western blot; migration and invasion assay
E_04708	2020	32771023	Disruption of super-enhancer-driven tumor suppressor gene RCAN1.4 expression promotes the malignancy of breast carcinoma	Homo sapiens	hg19	chr21	36173677	36175514	NA	RCAN1	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	NA	NA	BT-549	CVCL_1092	NA	NA	Enhancer activity assay; endogenous composite super-enhancer deletion assay; enhancer-target gene expression assay; cancer phenotype assay	H3K27ac ChIP-seq; H3K4me1 ChIP-seq; H3K4me3 ChIP-seq; RNA-seq; ENCODE TF ChIP-seq integration; HMEC Hi-C	Dual-luciferase reporter assay; double-CRISPR deletion of RCAN1.4-SEdistal containing E2-E4; qRT-PCR; Western blot; migration and invasion assay
E_04709	2020	32771023	Disruption of super-enhancer-driven tumor suppressor gene RCAN1.4 expression promotes the malignancy of breast carcinoma	Homo sapiens	hg19	chr21	36179691	36181223	RUNX3	RCAN1	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	NA	NA	MDA-MB-231	CVCL_0062	NA	NA	Enhancer activity assay; endogenous composite super-enhancer deletion assay; transcription-factor binding assay; TF-motif perturbation assay; enhancer-target gene expression assay	H3K27ac ChIP-seq; H3K4me1 ChIP-seq; H3K4me3 ChIP-seq; RNA-seq; ENCODE TF ChIP-seq integration; HMEC Hi-C	Dual-luciferase reporter assay; RUNX3 ChIP-qPCR; RUNX3 knockdown; H3K27ac ChIP-qPCR after RUNX3 knockdown; RUNX3-motif site-directed mutagenesis; double-CRISPR deletion of RCAN1.4-SEdistal containing E2-E4; qRT-PCR; Western blot
E_04710	2020	32771023	Disruption of super-enhancer-driven tumor suppressor gene RCAN1.4 expression promotes the malignancy of breast carcinoma	Homo sapiens	hg19	chr21	36179691	36181223	RUNX3	RCAN1	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	NA	NA	BT-549	CVCL_1092	NA	NA	Enhancer activity assay; endogenous composite super-enhancer deletion assay; transcription-factor binding assay; TF-motif perturbation assay; enhancer-target gene expression assay	H3K27ac ChIP-seq; H3K4me1 ChIP-seq; H3K4me3 ChIP-seq; RNA-seq; ENCODE TF ChIP-seq integration; HMEC Hi-C	Dual-luciferase reporter assay; RUNX3 ChIP-qPCR; RUNX3 knockdown; H3K27ac ChIP-qPCR after RUNX3 knockdown; RUNX3-motif site-directed mutagenesis; double-CRISPR deletion of RCAN1.4-SEdistal containing E2-E4; qRT-PCR; Western blot
E_04711	2020	32771023	Disruption of super-enhancer-driven tumor suppressor gene RCAN1.4 expression promotes the malignancy of breast carcinoma	Homo sapiens	hg19	chr21	36185229	36187227	NA	RCAN1	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	NA	NA	MDA-MB-231	CVCL_0062	NA	NA	Enhancer activity assay; endogenous composite super-enhancer deletion assay; enhancer-target gene expression assay; cancer phenotype assay	H3K27ac ChIP-seq; H3K4me1 ChIP-seq; H3K4me3 ChIP-seq; RNA-seq; ENCODE TF ChIP-seq integration; HMEC Hi-C	Dual-luciferase reporter assay; double-CRISPR deletion of RCAN1.4-SEdistal containing E2-E4; qRT-PCR; Western blot; migration and invasion assay
E_04712	2020	32771023	Disruption of super-enhancer-driven tumor suppressor gene RCAN1.4 expression promotes the malignancy of breast carcinoma	Homo sapiens	hg19	chr21	36185229	36187227	NA	RCAN1	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	NA	NA	BT-549	CVCL_1092	NA	NA	Enhancer activity assay; endogenous composite super-enhancer deletion assay; enhancer-target gene expression assay; cancer phenotype assay	H3K27ac ChIP-seq; H3K4me1 ChIP-seq; H3K4me3 ChIP-seq; RNA-seq; ENCODE TF ChIP-seq integration; HMEC Hi-C	Dual-luciferase reporter assay; double-CRISPR deletion of RCAN1.4-SEdistal containing E2-E4; qRT-PCR; Western blot; migration and invasion assay
E_04713	2021	33107387	Genetic Dissection of a Super Enhancer Controlling the Nppa-Nppb Cluster in the Heart	Mus musculus	mm10	chr4	147959864	147970328	NA	Nppa	Super-enhancer	Active	Normal	NA	NA	NA	left ventricle	UBERON:0002084	NA	NA	cardiomyocyte	CL:0000746	In vivo super-enhancer deletion assay; enhancer-target gene expression assay; enhancer-promoter chromatin interaction assay; cardiac developmental and physiological phenotype assay	H3K27ac ChIP-seq/CUT&RUN; RNA-seq; cardiomyocyte epigenomic profiling; Hi-C/promoter-capture Hi-C integration; 4C-seq; EMERGE enhancer prediction	CRISPR-Cas9 germline RE1 deletion; RE1a/RE1b deletion analysis; qRT-PCR; RNA in situ hybridization; cardiac histology; heart-weight phenotyping; myocardial infarction model; transverse aortic constriction
E_04714	2021	33107387	Genetic Dissection of a Super Enhancer Controlling the Nppa-Nppb Cluster in the Heart	Mus musculus	mm10	chr4	147959864	147970328	NA	Nppb	Super-enhancer	Active	Normal	NA	NA	NA	left ventricle	UBERON:0002084	NA	NA	cardiomyocyte	CL:0000746	In vivo super-enhancer deletion assay; enhancer-target gene expression assay; enhancer-promoter chromatin interaction assay; cardiac developmental and physiological phenotype assay	H3K27ac ChIP-seq/CUT&RUN; RNA-seq; cardiomyocyte epigenomic profiling; Hi-C/promoter-capture Hi-C integration; 4C-seq; EMERGE enhancer prediction	CRISPR-Cas9 germline RE1 deletion; RE1a/RE1b deletion analysis; qRT-PCR; RNA in situ hybridization; cardiac histology; heart-weight phenotyping; myocardial infarction model; transverse aortic constriction
E_04715	2022	35794478	Super-enhancer hypermutation alters oncogene expression in B-cell lymphoma	Homo sapiens	hg19	chr3	187437535	187470559	PRDM1	BCL6	Super-enhancer	Active	Disease	diffuse large B-cell lymphoma	MONDO:0018905	DOID:0050745	NA	NA	HLY-1	CVCL_H207	NA	NA	Super-enhancer mutation functional assay; transcription-factor binding assay; enhancer-target gene expression assay; allele-specific regulatory assay; lymphoma fitness assay	H3K27ac ChIP-seq; H3K4me1 ChIP-seq; H3K4me3 ChIP-seq; H3K27me3 ChIP-seq; whole-genome sequencing; RNA-seq; ROSE super-enhancer calling; Hi-C/TAD integration; FishHook recurrent mutation analysis; mutational signature analysis	CRISPR-Cas9 correction of BCL6-iSE hotspot mutation; HDR donor editing; PCR and Sanger genotyping; RT-qPCR; Western blot; allele-specific RT-PCR; PRDM1/BLIMP1 ChIP-qPCR; EMSA; supershift assay; clonal survival and counter-selection assay
E_04716	2022	35794478	Super-enhancer hypermutation alters oncogene expression in B-cell lymphoma	Homo sapiens	hg19	chr3	187437535	187470559	PRDM1	BCL6	Super-enhancer	Active	Disease	diffuse large B-cell lymphoma	MONDO:0018905	DOID:0050745	NA	NA	OCI-Ly18	CVCL_1880	NA	NA	Super-enhancer mutation functional assay; transcription-factor binding assay; enhancer-target gene expression assay; allele-specific regulatory assay; lymphoma fitness assay	H3K27ac ChIP-seq; H3K4me1 ChIP-seq; H3K4me3 ChIP-seq; H3K27me3 ChIP-seq; whole-genome sequencing; RNA-seq; ROSE super-enhancer calling; Hi-C/TAD integration; FishHook recurrent mutation analysis; mutational signature analysis	CRISPR-Cas9 correction of BCL6-iSE hotspot mutation; HDR donor editing; PCR and Sanger genotyping; RT-qPCR; Western blot; allele-specific RT-PCR; PRDM1/BLIMP1 ChIP-qPCR; EMSA; supershift assay; clonal survival and counter-selection assay
E_04717	2022	35794478	Super-enhancer hypermutation alters oncogene expression in B-cell lymphoma	Homo sapiens	hg19	chr3	187437535	187470559	PRDM1	BCL6	Super-enhancer	Active	Disease	diffuse large B-cell lymphoma	MONDO:0018905	DOID:0050745	NA	NA	KARPAS-422	CVCL_1325	NA	NA	Super-enhancer mutation functional assay; transcription-factor binding assay; enhancer-target gene expression assay; lymphoma fitness assay	H3K27ac ChIP-seq; H3K4me1 ChIP-seq; H3K4me3 ChIP-seq; H3K27me3 ChIP-seq; whole-genome sequencing; RNA-seq; ROSE super-enhancer calling; Hi-C/TAD integration; FishHook recurrent mutation analysis; mutational signature analysis	CRISPR-Cas9 correction of BCL6-iSE hotspot mutation; HDR donor editing; PCR and Sanger genotyping; RT-qPCR; Western blot; PRDM1/BLIMP1 binding validation; clonal survival and counter-selection assay
E_04718	2022	35794478	Super-enhancer hypermutation alters oncogene expression in B-cell lymphoma	Homo sapiens	hg19	chr18	60938975	60991118	NR3C1	BCL2	Super-enhancer	Active	Disease	diffuse large B-cell lymphoma	MONDO:0018905	DOID:0050745	NA	NA	OCI-Ly10	CVCL_8795	NA	NA	Super-enhancer mutation functional assay; transcription-factor binding assay; enhancer-target gene expression assay; allele-specific regulatory assay; lymphoma fitness assay	H3K27ac ChIP-seq; H3K4me1 ChIP-seq; H3K4me3 ChIP-seq; H3K27me3 ChIP-seq; whole-genome sequencing; RNA-seq; ROSE super-enhancer calling; Hi-C/TAD integration; FishHook recurrent mutation analysis; mutational signature analysis	CRISPR-Cas9 correction of BCL2-SE NR3C1-binding-site mutation; HDR donor editing; PCR/Sanger genotyping; NR3C1 ChIP-qPCR; allelic ChIP sequencing; allele-specific expression analysis; RT-qPCR; clonal survival and counter-selection assay
E_04719	2022	35794478	Super-enhancer hypermutation alters oncogene expression in B-cell lymphoma	Homo sapiens	hg19	chr2	136863629	136919192	NR3C1	CXCR4	Super-enhancer	Active	Disease	diffuse large B-cell lymphoma	MONDO:0018905	DOID:0050745	NA	NA	RCK8	CVCL_1883	NA	NA	Super-enhancer mutation functional assay; transcription-factor binding assay; enhancer-target gene expression assay; allele-specific regulatory assay; lymphoma fitness assay	H3K27ac ChIP-seq; H3K4me1 ChIP-seq; H3K4me3 ChIP-seq; H3K27me3 ChIP-seq; whole-genome sequencing; RNA-seq; ROSE super-enhancer calling; Hi-C/TAD integration; FishHook recurrent mutation analysis; mutational signature analysis	CRISPR-Cas9 correction of CXCR4-SE NR3C1-binding-site mutation; HDR donor editing; PCR/Sanger genotyping; NR3C1 ChIP-qPCR; allelic ChIP sequencing; allele-specific expression analysis; RT-qPCR; clonal survival and counter-selection assay
E_04720	2022	35794478	Super-enhancer hypermutation alters oncogene expression in B-cell lymphoma	Homo sapiens	hg19	chr2	136863629	136919192	NR3C1	CXCR4	Super-enhancer	Active	Disease	diffuse large B-cell lymphoma	MONDO:0018905	DOID:0050745	NA	NA	HLY-1	CVCL_H207	NA	NA	Super-enhancer mutation functional assay; transcription-factor binding assay; enhancer-target gene expression assay; allele-specific regulatory assay; lymphoma fitness assay	H3K27ac ChIP-seq; H3K4me1 ChIP-seq; H3K4me3 ChIP-seq; H3K27me3 ChIP-seq; whole-genome sequencing; RNA-seq; ROSE super-enhancer calling; Hi-C/TAD integration; FishHook recurrent mutation analysis; mutational signature analysis	CRISPR-Cas9 correction of CXCR4-SE NR3C1-binding-site mutation; HDR donor editing; PCR/Sanger genotyping; NR3C1 ChIP-qPCR; allele-specific expression analysis; RT-qPCR; clonal survival and counter-selection assay
E_04721	2023	37738673	Epigenetic reprogramming of a distal developmental enhancer cluster drives SOX2 overexpression in breast and lung adenocarcinoma	Homo sapiens	hg38	chr3	181838600	181840100	FOXA1	SOX2	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	NA	NA	MCF-7	CVCL_0031	NA	NA	Functional enhancer perturbation assay; enhancer activity assay; enhancer-target gene expression assay; transcription-factor regulation assay; enhancer-promoter chromatin interaction assay; cancer colony-forming phenotype assay	ATAC-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; RNAPII ChIA-PET; RNA-seq; TCGA ATAC-seq; TCGA RNA-seq; transcription-factor ChIP-seq integration; TOBIAS footprint analysis; HOMER motif analysis	CRISPR-Cas9 SRR124-SRR134 cluster deletion; SRR124 dual-luciferase reporter assay; FOXA1 overexpression; NFIB overexpression; RT-qPCR; SOX2 Western blot; enhancer eRNA qRT-PCR; PCR and sequencing validation; colony formation assay
E_04722	2023	37738673	Epigenetic reprogramming of a distal developmental enhancer cluster drives SOX2 overexpression in breast and lung adenocarcinoma	Homo sapiens	hg38	chr3	181850500	181852000	FOXA1	SOX2	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	NA	NA	MCF-7	CVCL_0031	NA	NA	Functional enhancer perturbation assay; enhancer activity assay; enhancer-target gene expression assay; transcription-factor motif perturbation assay; enhancer-promoter chromatin interaction assay; cancer colony-forming phenotype assay	ATAC-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; RNAPII ChIA-PET; RNA-seq; TCGA ATAC-seq; TCGA RNA-seq; transcription-factor ChIP-seq integration; TOBIAS footprint analysis; HOMER motif analysis	CRISPR-Cas9 SRR124-SRR134 cluster deletion; SRR134 dual-luciferase reporter assay; FOXA1 overexpression; FOXA1-motif site-directed mutagenesis; NFIB overexpression; NFIB-motif mutagenesis; RT-qPCR; SOX2 Western blot; enhancer eRNA qRT-PCR; PCR and sequencing validation; colony formation assay
E_04723	2023	37738673	Epigenetic reprogramming of a distal developmental enhancer cluster drives SOX2 overexpression in breast and lung adenocarcinoma	Homo sapiens	hg38	chr3	181838600	181840100	FOXA1	SOX2	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	NA	NA	T-47D	CVCL_0553	NA	NA	Functional enhancer perturbation assay; enhancer activity assay; enhancer-target gene expression assay; transcription-factor regulation assay	ATAC-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; transcription-factor ChIP-seq integration; TCGA ATAC-seq; TCGA RNA-seq	SRR124 dual-luciferase reporter assay; heterozygous CRISPR-Cas9 SRR124-SRR134 cluster deletion; FOXA1 overexpression; NFIB overexpression; RT-qPCR; PCR and sequencing validation
E_04724	2023	37738673	Epigenetic reprogramming of a distal developmental enhancer cluster drives SOX2 overexpression in breast and lung adenocarcinoma	Homo sapiens	hg38	chr3	181850500	181852000	FOXA1	SOX2	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	NA	NA	T-47D	CVCL_0553	NA	NA	Functional enhancer perturbation assay; enhancer activity assay; enhancer-target gene expression assay; transcription-factor motif perturbation assay	ATAC-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; transcription-factor ChIP-seq integration; TCGA ATAC-seq; TCGA RNA-seq	SRR134 dual-luciferase reporter assay; heterozygous CRISPR-Cas9 SRR124-SRR134 cluster deletion; FOXA1 overexpression; FOXA1-motif site-directed mutagenesis; NFIB overexpression; RT-qPCR; PCR and sequencing validation
E_04725	2023	37738673	Epigenetic reprogramming of a distal developmental enhancer cluster drives SOX2 overexpression in breast and lung adenocarcinoma	Homo sapiens	hg38	chr3	181838600	181840100	FOXA1	SOX2	Enhancer	Active	Disease	lung adenocarcinoma	MONDO:0005061	DOID:3910	NA	NA	PC-9	CVCL_B260	NA	NA	Functional enhancer perturbation assay; enhancer activity assay; enhancer-target gene expression assay; transcription-factor regulation assay; cancer colony-forming phenotype assay	ATAC-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; transcription-factor ChIP-seq integration; TCGA ATAC-seq; TCGA RNA-seq	SRR124 dual-luciferase reporter assay; CRISPR-Cas9 SRR124-SRR134 cluster deletion; FOXA1 overexpression; RT-qPCR; PCR and sequencing validation; colony formation assay
E_04726	2023	37738673	Epigenetic reprogramming of a distal developmental enhancer cluster drives SOX2 overexpression in breast and lung adenocarcinoma	Homo sapiens	hg38	chr3	181850500	181852000	FOXA1	SOX2	Enhancer	Active	Disease	lung adenocarcinoma	MONDO:0005061	DOID:3910	NA	NA	PC-9	CVCL_B260	NA	NA	Functional enhancer perturbation assay; enhancer activity assay; enhancer-target gene expression assay; transcription-factor motif perturbation assay; cancer colony-forming phenotype assay	ATAC-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; transcription-factor ChIP-seq integration; TCGA ATAC-seq; TCGA RNA-seq	SRR134 dual-luciferase reporter assay; CRISPR-Cas9 SRR124-SRR134 cluster deletion; FOXA1 overexpression; FOXA1-motif site-directed mutagenesis; RT-qPCR; PCR and sequencing validation; colony formation assay
E_04727	2021	34789735	Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors	Homo sapiens	hg19	chr4	85354717	85355054	FOXA1	NKX6-1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	H1 hESC-derived PP2 pancreatic progenitors	CVCL_9771	pancreatic progenitor cell	CL:0011026	Functional cis-regulatory motif perturbation assay; transcription-factor binding assay; enhancer chromatin-state assay; enhancer-target gene expression assay; pancreatic cell-fate assay	FOXA1/FOXA2 ChIP-seq; PDX1/HNF6/SOX9 ChIP-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; ATAC-seq; RNA-seq; single-cell RNA-seq; Hi-C; motif enrichment analysis; ATAC-seq footprinting	CRISPR-Cas9 HDR optimization of endogenous FOXA-binding motifs; ssODN-mediated six-base substitution; PCR genotyping; Sanger sequencing; FOXA1 ChIP-qPCR; H3K4me1/H3K27ac ChIP-qPCR; PDX1 shRNA perturbation; qRT-PCR; immunofluorescence; flow cytometry
E_04728	2021	34789735	Sequence logic at enhancers governs a dual mechanism of endodermal organ fate induction by FOXA pioneer factors	Homo sapiens	hg19	chr4	85354717	85355054	FOXA2	NKX6-1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	H1 hESC-derived PP2 pancreatic progenitors	CVCL_9771	pancreatic progenitor cell	CL:0011026	Functional cis-regulatory motif perturbation assay; transcription-factor binding assay; enhancer chromatin-state assay; enhancer-target gene expression assay; pancreatic cell-fate assay	FOXA1/FOXA2 ChIP-seq; PDX1/HNF6/SOX9 ChIP-seq; H3K27ac ChIP-seq; H3K4me1 ChIP-seq; ATAC-seq; RNA-seq; single-cell RNA-seq; Hi-C; motif enrichment analysis; ATAC-seq footprinting	CRISPR-Cas9 HDR optimization of endogenous FOXA-binding motifs; ssODN-mediated six-base substitution; PCR genotyping; Sanger sequencing; FOXA2 ChIP-qPCR; H3K4me1/H3K27ac ChIP-qPCR; PDX1 shRNA perturbation; qRT-PCR; immunofluorescence; flow cytometry
E_04729	2025	39825430	Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes	Homo sapiens	hg38	chr1	40919322	40919917	NA	CITED4	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	NA	NA	MDA-MB-361	CVCL_0620	NA	NA	Functional enhancer CRISPRi assay; enhancer-target gene expression assay; breast-cancer-associated regulatory variant analysis	Omni-ATAC-seq; H3K27ac ChIP-seq integration; pooled dCas9-KRAB CRISPRi; single-cell Perturb-seq; 10x single-cell RNA-seq; PCAWG somatic mutation integration; pySpade enhancer-target analysis	Individual dCas9-KRAB enhancer CRISPRi; independent sgRNA validation; RT-qPCR
E_04730	2025	39825430	Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes	Homo sapiens	hg38	chr3	172516679	172517179	NA	TNFSF10	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	NA	NA	MDA-MB-361	CVCL_0620	NA	NA	Functional enhancer CRISPRi assay; enhancer-target gene expression assay; breast-cancer-associated regulatory-element screen	Omni-ATAC-seq; H3K27ac ChIP-seq integration; pooled dCas9-KRAB CRISPRi; single-cell Perturb-seq; 10x single-cell RNA-seq; pySpade enhancer-target analysis	Individual dCas9-KRAB enhancer CRISPRi; independent sgRNA validation; RT-qPCR
E_04731	2025	39825430	Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes	Homo sapiens	hg38	chr1	46183100	46183600	NA	TSPAN1	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	NA	NA	MDA-MB-361	CVCL_0620	NA	NA	Functional enhancer CRISPRi assay; enhancer-target gene expression assay; subtype-comparative enhancer assay	Omni-ATAC-seq; H3K27ac ChIP-seq integration; pooled dCas9-KRAB CRISPRi; single-cell Perturb-seq; 10x single-cell RNA-seq; pySpade enhancer-target analysis	Individual dCas9-KRAB enhancer CRISPRi; independent sgRNA validation; RT-qPCR
E_04732	2025	39825430	Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes	Homo sapiens	hg38	chr6	28921980	28922480	NA	TRIM27	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	NA	NA	MDA-MB-361	CVCL_0620	NA	NA	Functional enhancer CRISPRi assay; enhancer-target gene expression assay; somatic-mutation-associated enhancer analysis	Omni-ATAC-seq; H3K27ac ChIP-seq integration; pooled dCas9-KRAB CRISPRi; single-cell Perturb-seq; 10x single-cell RNA-seq; PCAWG somatic mutation integration; pySpade enhancer-target analysis	Individual dCas9-KRAB enhancer CRISPRi; independent sgRNA validation; RT-qPCR
E_04733	2025	39825430	Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes	Homo sapiens	hg38	chr11	65540483	65540983	NA	LTBP3	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	NA	NA	MDA-MB-361	CVCL_0620	NA	NA	Functional enhancer CRISPRi assay; enhancer-target gene expression assay; breast-cancer-associated regulatory-element screen	Omni-ATAC-seq; H3K27ac ChIP-seq integration; pooled dCas9-KRAB CRISPRi; single-cell Perturb-seq; 10x single-cell RNA-seq; pySpade enhancer-target analysis	Individual dCas9-KRAB enhancer CRISPRi; independent sgRNA validation; RT-qPCR
E_04734	2025	39825430	Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes	Homo sapiens	hg38	chr1	201461067	201461567	NA	PHLDA3	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	NA	NA	MDA-MB-361	CVCL_0620	NA	NA	Functional enhancer CRISPRi assay; enhancer-target gene expression assay; breast-cancer-associated regulatory-element screen	Omni-ATAC-seq; H3K27ac ChIP-seq integration; pooled dCas9-KRAB CRISPRi; single-cell Perturb-seq; 10x single-cell RNA-seq; pySpade enhancer-target analysis	Individual dCas9-KRAB enhancer CRISPRi; independent sgRNA validation; RT-qPCR
E_04735	2025	39825430	Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes	Homo sapiens	hg38	chr11	65915632	65916132	NA	FOSL1	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	NA	NA	MDA-MB-231	CVCL_0062	NA	NA	Functional enhancer CRISPRi assay; enhancer-target gene expression assay; ER-negative breast-cancer enhancer assay	Omni-ATAC-seq; H3K27ac ChIP-seq integration; pooled dCas9-KRAB CRISPRi; single-cell Perturb-seq; 10x single-cell RNA-seq; pySpade enhancer-target analysis	Individual dCas9-KRAB enhancer CRISPRi; independent sgRNA validation; RT-qPCR
E_04736	2025	39825430	Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes	Homo sapiens	hg38	chr6	32195448	32196078	NA	TAP2	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	NA	NA	MDA-MB-231	CVCL_0062	NA	NA	Functional enhancer CRISPRi assay; enhancer-target gene expression assay; somatic-mutation-associated enhancer analysis	Omni-ATAC-seq; H3K27ac ChIP-seq integration; pooled dCas9-KRAB CRISPRi; single-cell Perturb-seq; 10x single-cell RNA-seq; PCAWG somatic mutation integration; pySpade enhancer-target analysis	Individual dCas9-KRAB enhancer CRISPRi; independent sgRNA validation; RT-qPCR
E_04737	2025	39825430	Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes	Homo sapiens	hg38	chr6	16130859	16131359	NA	MYLIP	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	NA	NA	MDA-MB-231	CVCL_0062	NA	NA	Functional enhancer CRISPRi assay; enhancer-target gene expression assay; cancer proliferation phenotype assay	Omni-ATAC-seq; H3K27ac ChIP-seq integration; pooled dCas9-KRAB CRISPRi; single-cell Perturb-seq; 10x single-cell RNA-seq; pySpade enhancer-target analysis	Individual dCas9-KRAB enhancer CRISPRi; RT-qPCR for MYLIP and downstream SCD; flow-cytometry proliferation assay
E_04738	2025	39825430	Enhancer regulatory networks globally connect non-coding breast cancer loci to cancer genes	Homo sapiens	hg38	chr1	46183100	46183600	NA	TSPAN1	Enhancer	Active	Disease	breast cancer	MONDO:0007254	DOID:1612	NA	NA	MDA-MB-231	CVCL_0062	NA	NA	Functional enhancer CRISPRi assay; enhancer-target gene expression assay; subtype-comparative enhancer assay	Omni-ATAC-seq; H3K27ac ChIP-seq integration; pooled dCas9-KRAB CRISPRi; single-cell Perturb-seq; 10x single-cell RNA-seq; pySpade enhancer-target analysis	Individual dCas9-KRAB enhancer CRISPRi; independent sgRNA validation; RT-qPCR
E_04739	2024	38271204	Massively parallel disruption of enhancers active in human neural stem cells	Homo sapiens	hg19	chr14	33819160	33819187	NA	NPAS3	Enhancer	Active	Normal	NA	NA	NA	NA	NA	H9-derived human neural stem cells	NA	neural stem cell	CL:0000047	Functional cis-regulatory element perturbation; enhancer activity-associated proliferation assay; enhancer-target association	H3K27ac ChIP-seq; pooled sgRNA-Cas9 screen with high-throughput sequencing; PsychENCODE Hi-C	Individual sgRNA-Cas9 perturbation; targeted CRISPR indel validation by amplicon sequencing
E_04740	2024	38271204	Massively parallel disruption of enhancers active in human neural stem cells	Homo sapiens	hg19	chr14	33819218	33819245	NA	NPAS3	Enhancer	Active	Normal	NA	NA	NA	NA	NA	H9-derived human neural stem cells	NA	neural stem cell	CL:0000047	Functional cis-regulatory element perturbation; enhancer activity-associated proliferation assay; enhancer-target association	H3K27ac ChIP-seq; pooled sgRNA-Cas9 screen with high-throughput sequencing; targeted amplicon sequencing; PsychENCODE Hi-C	Individual sgRNA-Cas9 perturbation; targeted CRISPR indel validation
E_04741	2024	38271204	Massively parallel disruption of enhancers active in human neural stem cells	Homo sapiens	hg19	chr4	57166536	57169340	NA	CEP135	Enhancer	Active	Normal	NA	NA	NA	NA	NA	H9-derived human neural stem cells	NA	neural stem cell	CL:0000047	Functional enhancer perturbation; enhancer-target chromatin interaction; proliferation phenotype	H3K27ac ChIP-seq; pooled sgRNA-Cas9 screen with high-throughput sequencing; PsychENCODE Hi-C	NA
E_04742	2024	38271204	Massively parallel disruption of enhancers active in human neural stem cells	Homo sapiens	hg19	chr13	34115011	34118665	NA	STARD13	Enhancer	Active	Normal	NA	NA	NA	NA	NA	H9-derived human neural stem cells	NA	neural stem cell	CL:0000047	Functional enhancer perturbation; enhancer-target chromatin interaction; proliferation phenotype	H3K27ac ChIP-seq; pooled sgRNA-Cas9 screen with high-throughput sequencing; PsychENCODE Hi-C	NA
E_04743	2024	38271204	Massively parallel disruption of enhancers active in human neural stem cells	Homo sapiens	hg19	chr13	34115011	34118665	NA	PDS5B	Enhancer	Active	Normal	NA	NA	NA	NA	NA	H9-derived human neural stem cells	NA	neural stem cell	CL:0000047	Functional enhancer perturbation; enhancer-target chromatin interaction; proliferation phenotype	H3K27ac ChIP-seq; pooled sgRNA-Cas9 screen with high-throughput sequencing; PsychENCODE Hi-C	NA
E_04744	2024	38271204	Massively parallel disruption of enhancers active in human neural stem cells	Homo sapiens	hg19	chr1	212659361	212664765	NA	NSL1	Enhancer	Active	Normal	NA	NA	NA	NA	NA	H9-derived human neural stem cells	NA	neural stem cell	CL:0000047	Functional enhancer perturbation; enhancer-target chromatin interaction; proliferation phenotype	H3K27ac ChIP-seq; pooled sgRNA-Cas9 screen with high-throughput sequencing; PsychENCODE Hi-C	Individual enhancer-targeting sgRNA-Cas9 lentiviral perturbation; GFP competition proliferation assay; flow cytometry
E_04745	2021	33854062	Defining super-enhancer landscape in triple-negative breast cancer by multiomic profiling	Homo sapiens	hg19	chr6	1476600	1488400	NA	FOXC1	Super-enhancer	Active	Disease	triple-negative breast cancer	MONDO:0005494	DOID:0060081	NA	NA	BT-549	CVCL_1092	Breast cancer cell	NA	SSE245 constituent e1/e2 deletion; target-gene expression and tumor-cell phenotype validation	H3K27ac ChIP-seq; transcriptomic integration	CRISPR/Cas9-mediated e1/e2 deletion; deletion PCR; Western blot; clonogenic assay; 3D spheroid assay; dual-luciferase reporter assay; H3K27ac/BRD4/p300 ChIP-qPCR
E_04746	2021	33854062	Defining super-enhancer landscape in triple-negative breast cancer by multiomic profiling	Homo sapiens	hg19	chr6	1476600	1488400	NA	FOXC1	Super-enhancer	Active	Disease	triple-negative breast cancer	MONDO:0005494	DOID:0060081	NA	NA	MDA-MB-231	CVCL_0062	Breast cancer cell	NA	SSE245 constituent e1/e2 deletion; target-gene expression; phenotypic rescue and xenograft validation	H3K27ac ChIP-seq; DNase-seq; transcriptomic integration	CRISPR/Cas9-mediated e1/e2 deletion; deletion PCR; Western blot; clonogenic assay; 3D spheroid growth and invasion assay; FOXC1 overexpression rescue; mouse xenograft assay
E_04747	2021	33854062	Defining super-enhancer landscape in triple-negative breast cancer by multiomic profiling	Homo sapiens	hg19	chr6	1476600	1488400	NA	FOXC1	Super-enhancer	Active	Disease	triple-negative breast cancer	MONDO:0005494	DOID:0060081	NA	NA	MCF10DCIS.com	CVCL_5552	Breast carcinoma model cell	NA	SSE245 constituent e1/e2 deletion in a DCIS model used for TNBC-related functional analysis	H3K27ac ChIP-seq; transcriptomic integration	CRISPR/Cas9-mediated e1/e2 deletion; deletion PCR; Western blot; clonogenic assay; 3D spheroid assay
E_04748	2021	33854062	Defining super-enhancer landscape in triple-negative breast cancer by multiomic profiling	Homo sapiens	hg19	chr7	116208200	116224400	NA	MET	Super-enhancer	Active	Disease	triple-negative breast cancer	MONDO:0005494	DOID:0060081	NA	NA	BT-549	CVCL_1092	Breast cancer cell	NA	SSE185 constituent e2 deletion; target-gene expression and tumor-cell phenotype validation	H3K27ac ChIP-seq; transcriptomic integration	CRISPR/Cas9-mediated e2 deletion; deletion PCR; Western blot; clonogenic assay; 3D spheroid growth and invasion assay; H3K27ac/BRD4/p300 ChIP-qPCR
E_04749	2021	33854062	Defining super-enhancer landscape in triple-negative breast cancer by multiomic profiling	Homo sapiens	hg19	chr7	116208200	116224400	NA	MET	Super-enhancer	Active	Disease	triple-negative breast cancer	MONDO:0005494	DOID:0060081	NA	NA	MDA-MB-231	CVCL_0062	Breast cancer cell	NA	SSE185 constituent e2 deletion; target-gene expression and tumor-cell phenotype validation	H3K27ac ChIP-seq; transcriptomic integration	CRISPR/Cas9-mediated e2 deletion; deletion PCR; Western blot; clonogenic assay; 3D spheroid growth and invasion assay; H3K27ac/BRD4/p300 ChIP-qPCR
E_04750	2021	33854062	Defining super-enhancer landscape in triple-negative breast cancer by multiomic profiling	Homo sapiens	hg19	chr7	116208200	116224400	NA	MET	Super-enhancer	Active	Disease	triple-negative breast cancer	MONDO:0005494	DOID:0060081	NA	NA	MCF10DCIS.com	CVCL_5552	Breast carcinoma model cell	NA	SSE185 constituent e1 repression in a DCIS model used for TNBC-related functional analysis	H3K27ac ChIP-seq; transcriptomic integration	KRAB-dCas9-mediated e1 repression; MET expression analysis; clonogenic assay
E_04751	2021	33854062	Defining super-enhancer landscape in triple-negative breast cancer by multiomic profiling	Homo sapiens	hg19	chr7	36154800	36160600	NA	ANLN	Super-enhancer	Active	Disease	triple-negative breast cancer	MONDO:0005494	DOID:0060081	NA	NA	BT-549	CVCL_1092	Breast cancer cell	NA	SSE256 constituent e1 deletion; target-gene expression and clonogenicity validation	H3K27ac ChIP-seq; transcriptomic integration	CRISPR/Cas9-mediated e1 deletion; deletion PCR; Western blot; clonogenic assay
E_04752	2021	33854062	Defining super-enhancer landscape in triple-negative breast cancer by multiomic profiling	Homo sapiens	hg19	chr7	36154800	36160600	NA	ANLN	Super-enhancer	Active	Disease	triple-negative breast cancer	MONDO:0005494	DOID:0060081	NA	NA	Hs 578T	CVCL_0332	Breast cancer cell	NA	SSE256 constituent e1 deletion; target-gene expression and clonogenicity validation	H3K27ac ChIP-seq; transcriptomic integration	CRISPR/Cas9-mediated e1 deletion; deletion PCR; Western blot; clonogenic assay
E_04753	2011	21185279	The Pou5f1/Pou3f-dependent but SoxB-independent regulation of conserved enhancer N2 initiates Sox2 expression during epiblast to neural plate stages in vertebrates	Mus musculus	mm9	chr3	34545031	34545378	Pou5f1	Sox2	Enhancer	Active	Normal	NA	NA	NA	epiblast	UBERON:0003255	mouse embryo	NA	epiblast cell	NA	Endogenous enhancer deletion; enhancer reporter assay; TF perturbation assay; TF-binding assay	NA	N2/SRR1 functional subregion; 538-bp N2 targeted deletion; transgenic LacZ reporter assay; qRT-PCR; in situ hybridization; Pou5f1 knockdown; luciferase reporter assay; site-directed mutagenesis; EMSA
E_04754	2021	34103329	Enhancer Hijacking Drives Oncogenic BCL11B Expression in Lineage-Ambiguous Stem Cell Leukemia	Homo sapiens	hg19	chr6	156057468	156215697	NA	BCL11B	Super-enhancer	Active	Disease	acute leukemia of ambiguous lineage	MONDO:0019460	NA	bone marrow	UBERON:0002371	primary diagnostic bone-marrow leukemia cells	NA	lineage-ambiguous hematopoietic leukemic blast	NA	Supporting interval: ARID1B enhancer-containing FISH probe region	WGS;RNA-seq;H3K27ac ChIP-seq;H3K27ac HiChIP	patient-specific breakpoint PCR;Sanger sequencing;sequential RNA-FISH/DNA-FISH
E_04755	2021	34103329	Enhancer Hijacking Drives Oncogenic BCL11B Expression in Lineage-Ambiguous Stem Cell Leukemia	Homo sapiens	hg19	chr6	156458627	156620361	NA	BCL11B	Super-enhancer	Active	Disease	acute leukemia of ambiguous lineage	MONDO:0019460	NA	bone marrow	UBERON:0002371	primary diagnostic bone-marrow leukemia cells	NA	lineage-ambiguous hematopoietic leukemic blast	NA	Supporting interval: ARID1B enhancer-containing FISH probe region	WGS;RNA-seq;H3K27ac ChIP-seq;H3K27ac HiChIP	patient-specific breakpoint PCR;Sanger sequencing;sequential RNA-FISH/DNA-FISH
E_04756	2021	34103329	Enhancer Hijacking Drives Oncogenic BCL11B Expression in Lineage-Ambiguous Stem Cell Leukemia	Homo sapiens	hg19	chr8	130493286	130632903	NA	BCL11B	Super-enhancer	Active	Disease	acute leukemia of ambiguous lineage	MONDO:0019460	NA	bone marrow	UBERON:0002371	primary diagnostic bone-marrow leukemia cells	NA	lineage-ambiguous hematopoietic leukemic blast	NA	Supporting interval: BENC enhancer-containing FISH probe region	WGS;RNA-seq;H3K27ac ChIP-seq;H3K27ac HiChIP	patient-specific breakpoint PCR;Sanger sequencing;sequential RNA-FISH/DNA-FISH
E_04757	2021	34103329	Enhancer Hijacking Drives Oncogenic BCL11B Expression in Lineage-Ambiguous Stem Cell Leukemia	Homo sapiens	hg19	chr7	92117011	92306530	NA	BCL11B	Super-enhancer	Active	Disease	acute leukemia of ambiguous lineage	MONDO:0019460	NA	bone marrow	UBERON:0002371	primary diagnostic bone-marrow leukemia cells	NA	lineage-ambiguous hematopoietic leukemic blast	NA	Supporting interval: CDK6 enhancer-containing FISH probe region	WGS;RNA-seq;H3K27ac ChIP-seq;H3K27ac HiChIP	patient-specific breakpoint PCR;Sanger sequencing;sequential RNA-FISH/DNA-FISH
E_04758	2021	34103329	Enhancer Hijacking Drives Oncogenic BCL11B Expression in Lineage-Ambiguous Stem Cell Leukemia	Homo sapiens	hg19	chr7	92302711	92463709	NA	BCL11B	Super-enhancer	Active	Disease	acute leukemia of ambiguous lineage	MONDO:0019460	NA	bone marrow	UBERON:0002371	primary diagnostic bone-marrow leukemia cells	NA	lineage-ambiguous hematopoietic leukemic blast	NA	Supporting interval: CDK6 enhancer-containing FISH probe region	WGS;RNA-seq;H3K27ac ChIP-seq;H3K27ac HiChIP	patient-specific breakpoint PCR;Sanger sequencing;sequential RNA-FISH/DNA-FISH
E_04759	2023	37032358	Super-enhancer-driven TOX2 mediates oncogenesis in Natural Killer/T Cell Lymphoma	Homo sapiens	hg19	chr20	42567767	42593591	RUNX3	TOX2	Super-enhancer	Active	Disease	nasal type extranodal NK/T-cell lymphoma	MONDO:0019472	DOID:0080797	blood	UBERON:0000178	NK-YS	CVCL_8461	NK T-cell	CL:0000814	Super-enhancer activity assay; endogenous super-enhancer perturbation assay; TF-binding assay; TF-site mutagenesis assay; target-gene expression assay; cellular phenotype assay	H3K27ac NanoChIP-seq; H3K27ac ChIP-seq; RNA-seq	TOX2-e1/e2/e3 dual-luciferase reporter assay; CRISPR/dCas9-KRAB interference of TOX2-SE; RUNX3 ChIP-qPCR; RUNX3 binding-site-directed mutagenesis; RUNX3 shRNA knockdown; TOX2 shRNA knockdown; qRT-PCR; Western blotting; cell viability assay; cell-cycle analysis; colony-formation assay; TOX2 rescue assay; xenograft tumor-formation assay
E_04760	2012	23232398	T-bet and GATA3 orchestrate Th1 and Th2 differentiation through lineage-specific targeting of distal regulatory elements	Homo sapiens	hg18	chr1	67542131	67542929	TBX21	IL12RB2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human CD4+ T cells	NA	CD4-positive, alpha-beta T cell	CL:0000624	Enhancer activity assay; TF-binding assay; TF-dependent regulatory assay	TBX21 ChIP-seq; GATA3 ChIP-seq; DNase-seq; histone modification profiling	Luciferase reporter assay in activated human CD4+ T cells; TF-dependent reporter assay
E_04761	2012	23232398	T-bet and GATA3 orchestrate Th1 and Th2 differentiation through lineage-specific targeting of distal regulatory elements	Homo sapiens	hg18	chr18	65728245	65728831	TBX21	CD226	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human CD4+ T cells	NA	CD4-positive, alpha-beta T cell	CL:0000624	Enhancer activity assay; TF-binding assay; TF-dependent regulatory assay	TBX21 ChIP-seq; GATA3 ChIP-seq; DNase-seq; histone modification profiling	Luciferase reporter assay in activated human CD4+ T cells; TF-dependent reporter assay
E_04762	2012	23232398	T-bet and GATA3 orchestrate Th1 and Th2 differentiation through lineage-specific targeting of distal regulatory elements	Homo sapiens	hg18	chr4	81175402	81175943	TBX21	ANTXR2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human CD4+ T cells	NA	CD4-positive, alpha-beta T cell	CL:0000624	Enhancer activity assay; TF-binding assay; TF-dependent regulatory assay	TBX21 ChIP-seq; GATA3 ChIP-seq; DNase-seq; histone modification profiling	Luciferase reporter assay in activated human CD4+ T cells; TF-dependent reporter assay
E_04763	2012	23232398	T-bet and GATA3 orchestrate Th1 and Th2 differentiation through lineage-specific targeting of distal regulatory elements	Homo sapiens	hg18	chr6	160323919	160324583	TBX21	IGF2R	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human CD4+ T cells	NA	CD4-positive, alpha-beta T cell	CL:0000624	Enhancer activity assay; TF-binding assay; TF-dependent regulatory assay	TBX21 ChIP-seq; GATA3 ChIP-seq; DNase-seq; histone modification profiling	Luciferase reporter assay in activated human CD4+ T cells; TF-dependent reporter assay
E_04764	2012	23232398	T-bet and GATA3 orchestrate Th1 and Th2 differentiation through lineage-specific targeting of distal regulatory elements	Homo sapiens	hg18	chr18	40471400	40472121	TBX21	SETBP1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human CD4+ T cells	NA	CD4-positive, alpha-beta T cell	CL:0000624	Enhancer activity assay; TF-binding assay; TF-dependent regulatory assay	TBX21 ChIP-seq; GATA3 ChIP-seq; DNase-seq; histone modification profiling	Luciferase reporter assay in activated human CD4+ T cells; TF-dependent reporter assay
E_04765	2012	23232398	T-bet and GATA3 orchestrate Th1 and Th2 differentiation through lineage-specific targeting of distal regulatory elements	Homo sapiens	hg18	chr18	40592792	40593656	TBX21	SETBP1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human CD4+ T cells	NA	CD4-positive, alpha-beta T cell	CL:0000624	Enhancer activity assay; TF-binding assay; TF-dependent regulatory assay	TBX21 ChIP-seq; GATA3 ChIP-seq; DNase-seq; histone modification profiling	Luciferase reporter assay in activated human CD4+ T cells; TF-dependent reporter assay
E_04766	2023	36947815	Structural variation cooperates with permissive chromatin to control enhancer hijacking-mediated oncogenic transcription	Homo sapiens	hg19	chr14	98634158	98634265	NA	TLX3	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	NA	NA	DND-41	CVCL_2022	T-cell acute lymphoblastic leukemia cell	NA	Enhancer hijacking; BCL11B enhancer-1 component; pooled CRISPRi functional validation	WGS;optical genome mapping;Hi-C;4C-seq;RNA-seq;ATAC-seq;H3K27ac ChIP-seq;RRBS	pooled CRISPRi using dCas9-KRAB;RT-qPCR;breakpoint PCR;Sanger sequencing;DNA-FISH
E_04767	2023	36947815	Structural variation cooperates with permissive chromatin to control enhancer hijacking-mediated oncogenic transcription	Homo sapiens	hg19	chr14	98639829	98639880	NA	TLX3	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	NA	NA	DND-41	CVCL_2022	T-cell acute lymphoblastic leukemia cell	NA	Enhancer hijacking; BCL11B enhancer-2 component; pooled CRISPRi functional validation	WGS;optical genome mapping;Hi-C;4C-seq;RNA-seq;ATAC-seq;H3K27ac ChIP-seq;RRBS	pooled CRISPRi using dCas9-KRAB;RT-qPCR;breakpoint PCR;Sanger sequencing;DNA-FISH
E_04768	2023	36947815	Structural variation cooperates with permissive chromatin to control enhancer hijacking-mediated oncogenic transcription	Homo sapiens	hg19	chr14	98641914	98641973	NA	TLX3	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	NA	NA	DND-41	CVCL_2022	T-cell acute lymphoblastic leukemia cell	NA	Enhancer hijacking; BCL11B enhancer-3 component; pooled CRISPRi functional validation	WGS;optical genome mapping;Hi-C;4C-seq;RNA-seq;ATAC-seq;H3K27ac ChIP-seq;RRBS	pooled CRISPRi using dCas9-KRAB;RT-qPCR;breakpoint PCR;Sanger sequencing;DNA-FISH
E_04769	2023	36947815	Structural variation cooperates with permissive chromatin to control enhancer hijacking-mediated oncogenic transcription	Homo sapiens	hg19	chr14	98656016	98656142	NA	TLX3	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	NA	NA	DND-41	CVCL_2022	T-cell acute lymphoblastic leukemia cell	NA	Enhancer hijacking; BCL11B enhancer-4 component; pooled CRISPRi functional validation	WGS;optical genome mapping;Hi-C;4C-seq;RNA-seq;ATAC-seq;H3K27ac ChIP-seq;RRBS	pooled CRISPRi using dCas9-KRAB;RT-qPCR;breakpoint PCR;Sanger sequencing;DNA-FISH
E_04770	2023	36947815	Structural variation cooperates with permissive chromatin to control enhancer hijacking-mediated oncogenic transcription	Homo sapiens	hg19	chr14	98665002	98665025	NA	TLX3	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	NA	NA	DND-41	CVCL_2022	T-cell acute lymphoblastic leukemia cell	NA	Enhancer hijacking; BCL11B enhancer-5 component; pooled CRISPRi functional validation	WGS;optical genome mapping;Hi-C;4C-seq;RNA-seq;ATAC-seq;H3K27ac ChIP-seq;RRBS	pooled CRISPRi using dCas9-KRAB;RT-qPCR;breakpoint PCR;Sanger sequencing;DNA-FISH
E_04771	2023	36947815	Structural variation cooperates with permissive chromatin to control enhancer hijacking-mediated oncogenic transcription	Homo sapiens	hg19	chr14	98676720	98676777	NA	TLX3	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	NA	NA	DND-41	CVCL_2022	T-cell acute lymphoblastic leukemia cell	NA	Enhancer hijacking; BCL11B enhancer-6 component; pooled CRISPRi functional validation	WGS;optical genome mapping;Hi-C;4C-seq;RNA-seq;ATAC-seq;H3K27ac ChIP-seq;RRBS	pooled CRISPRi using dCas9-KRAB;RT-qPCR;breakpoint PCR;Sanger sequencing;DNA-FISH
E_04772	2023	36947815	Structural variation cooperates with permissive chromatin to control enhancer hijacking-mediated oncogenic transcription	Homo sapiens	hg19	chr14	98634158	98634265	NA	TLX3	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	peripheral blood	UBERON:0000178	DND-41	CVCL_2022	T-cell	CL:0000084	t(5;14)-mediated enhancer hijacking; BCL11B enhancer-1 component; pooled CRISPRi functional validation	WGS;optical genome mapping;Hi-C;4C-seq;RNA-seq;ATAC-seq;H3K27ac ChIP-seq;RRBS;allele-specific expression analysis	pooled dCas9-KRAB CRISPRi;RT-qPCR;CRISPR/Cas9 translocation engineering;breakpoint PCR;Sanger sequencing;DNA-FISH;5-azaD treatment
E_04773	2023	36947815	Structural variation cooperates with permissive chromatin to control enhancer hijacking-mediated oncogenic transcription	Homo sapiens	hg19	chr14	98639829	98639880	NA	TLX3	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	peripheral blood	UBERON:0000178	DND-41	CVCL_2022	T-cell	CL:0000084	t(5;14)-mediated enhancer hijacking; BCL11B enhancer-2 component; pooled CRISPRi functional validation	WGS;optical genome mapping;Hi-C;4C-seq;RNA-seq;ATAC-seq;H3K27ac ChIP-seq;RRBS;allele-specific expression analysis	pooled dCas9-KRAB CRISPRi;RT-qPCR;CRISPR/Cas9 translocation engineering;breakpoint PCR;Sanger sequencing;DNA-FISH;5-azaD treatment
E_04774	2023	36947815	Structural variation cooperates with permissive chromatin to control enhancer hijacking-mediated oncogenic transcription	Homo sapiens	hg19	chr14	98641914	98641973	NA	TLX3	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	peripheral blood	UBERON:0000178	DND-41	CVCL_2022	T-cell	CL:0000084	t(5;14)-mediated enhancer hijacking; BCL11B enhancer-3 component; pooled CRISPRi functional validation	WGS;optical genome mapping;Hi-C;4C-seq;RNA-seq;ATAC-seq;H3K27ac ChIP-seq;RRBS;allele-specific expression analysis	pooled dCas9-KRAB CRISPRi;RT-qPCR;CRISPR/Cas9 translocation engineering;breakpoint PCR;Sanger sequencing;DNA-FISH;5-azaD treatment
E_04775	2023	36947815	Structural variation cooperates with permissive chromatin to control enhancer hijacking-mediated oncogenic transcription	Homo sapiens	hg19	chr14	98656016	98656142	NA	TLX3	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	peripheral blood	UBERON:0000178	DND-41	CVCL_2022	T-cell	CL:0000084	t(5;14)-mediated enhancer hijacking; BCL11B enhancer-4 component; pooled CRISPRi functional validation	WGS;optical genome mapping;Hi-C;4C-seq;RNA-seq;ATAC-seq;H3K27ac ChIP-seq;RRBS;allele-specific expression analysis	pooled dCas9-KRAB CRISPRi;RT-qPCR;CRISPR/Cas9 translocation engineering;breakpoint PCR;Sanger sequencing;DNA-FISH;5-azaD treatment
E_04776	2023	36947815	Structural variation cooperates with permissive chromatin to control enhancer hijacking-mediated oncogenic transcription	Homo sapiens	hg19	chr14	98665002	98665025	NA	TLX3	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	peripheral blood	UBERON:0000178	DND-41	CVCL_2022	T-cell	CL:0000084	t(5;14)-mediated enhancer hijacking; BCL11B enhancer-5 component; pooled CRISPRi functional validation	WGS;optical genome mapping;Hi-C;4C-seq;RNA-seq;ATAC-seq;H3K27ac ChIP-seq;RRBS;allele-specific expression analysis	pooled dCas9-KRAB CRISPRi;RT-qPCR;CRISPR/Cas9 translocation engineering;breakpoint PCR;Sanger sequencing;DNA-FISH;5-azaD treatment
E_04777	2023	36947815	Structural variation cooperates with permissive chromatin to control enhancer hijacking-mediated oncogenic transcription	Homo sapiens	hg19	chr14	98676720	98676777	NA	TLX3	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	peripheral blood	UBERON:0000178	DND-41	CVCL_2022	T-cell	CL:0000084	t(5;14)-mediated enhancer hijacking; BCL11B enhancer-6 component; pooled CRISPRi functional validation	WGS;optical genome mapping;Hi-C;4C-seq;RNA-seq;ATAC-seq;H3K27ac ChIP-seq;RRBS;allele-specific expression analysis	pooled dCas9-KRAB CRISPRi;RT-qPCR;CRISPR/Cas9 translocation engineering;breakpoint PCR;Sanger sequencing;DNA-FISH;5-azaD treatment
E_04778	2007	17308084	Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU.1 and HMGA1	Homo sapiens	hg18	chr14	97280412	97280437	NA	NKX2-5	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	peripheral blood	UBERON:0000178	PEER	CVCL_1913	T-cell	CL:0000084	DSO.3 sequence-specific enhancer-core inhibition	MPSS DNase-seq;454 DNase-seq;DNase-I hypersensitivity mapping	26-mer double-stranded DNA inhibitory oligonucleotide treatment;RT-qPCR;FISH;fiber-FISH;nuclear-matrix attachment assay
E_04779	2007	17308084	Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU.1 and HMGA1	Homo sapiens	hg18	chr14	97734681	97734706	NA	NKX2-5	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	peripheral blood	UBERON:0000178	PEER	CVCL_1913	T-cell	CL:0000084	DSO.6 enhancer-core inhibition within hyperacetylated DNase-I hypersensitive cluster	MPSS DNase-seq;454 DNase-seq;DNase-I hypersensitivity mapping	26-mer double-stranded DNA inhibitory oligonucleotide treatment;histone-acetylation ChIP;RT-qPCR;sequence-mutation assay;FISH;fiber-FISH
E_04780	2007	17308084	Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU.1 and HMGA1	Homo sapiens	hg18	chr14	97734779	97734804	NA	NKX2-5	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	peripheral blood	UBERON:0000178	PEER	CVCL_1913	T-cell	CL:0000084	DSO.7 enhancer-core inhibition within hyperacetylated DNase-I hypersensitive cluster	MPSS DNase-seq;454 DNase-seq;DNase-I hypersensitivity mapping	26-mer double-stranded DNA inhibitory oligonucleotide treatment;histone-acetylation ChIP;RT-qPCR;FISH;fiber-FISH
E_04781	2007	17308084	Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU.1 and HMGA1	Homo sapiens	hg18	chr14	97745902	97745927	NA	NKX2-5	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	peripheral blood	UBERON:0000178	PEER	CVCL_1913	T-cell	CL:0000084	DSO.8 enhancer-core inhibition within hyperacetylated DNase-I hypersensitive cluster	MPSS DNase-seq;454 DNase-seq;DNase-I hypersensitivity mapping	26-mer double-stranded DNA inhibitory oligonucleotide treatment;histone-acetylation ChIP;RT-qPCR;FISH;fiber-FISH
E_04782	2007	17308084	Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU.1 and HMGA1	Homo sapiens	hg18	chr14	97746132	97746157	NA	NKX2-5	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	peripheral blood	UBERON:0000178	PEER	CVCL_1913	T-cell	CL:0000084	DSO.9 enhancer-core inhibition within hyperacetylated DNase-I hypersensitive cluster	MPSS DNase-seq;454 DNase-seq;DNase-I hypersensitivity mapping	26-mer double-stranded DNA inhibitory oligonucleotide treatment;histone-acetylation ChIP;RT-qPCR;FISH;fiber-FISH
E_04783	2007	17308084	Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU.1 and HMGA1	Homo sapiens	hg18	chr14	97864528	97864553	NA	NKX2-5	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	peripheral blood	UBERON:0000178	PEER	CVCL_1913	T-cell	CL:0000084	DSO.10 sequence-specific enhancer-core inhibition	MPSS DNase-seq;454 DNase-seq;DNase-I hypersensitivity mapping	26-mer double-stranded DNA inhibitory oligonucleotide treatment;RT-qPCR;FISH;fiber-FISH;nuclear-matrix attachment assay
E_04784	2007	17308084	Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU.1 and HMGA1	Homo sapiens	hg18	chr14	98130412	98130437	NA	NKX2-5	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	peripheral blood	UBERON:0000178	PEER	CVCL_1913	T-cell	CL:0000084	DSO.12 sequence-specific enhancer-core inhibition	MPSS DNase-seq;454 DNase-seq;DNase-I hypersensitivity mapping	26-mer double-stranded DNA inhibitory oligonucleotide treatment;RT-qPCR;FISH;fiber-FISH;nuclear-matrix attachment assay
E_04785	2007	17308084	Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU.1 and HMGA1	Homo sapiens	hg18	chr14	98180494	98180519	NA	NKX2-5	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	peripheral blood	UBERON:0000178	PEER	CVCL_1913	T-cell	CL:0000084	DSO.13 sequence-specific enhancer-core inhibition	MPSS DNase-seq;454 DNase-seq;DNase-I hypersensitivity mapping	26-mer double-stranded DNA inhibitory oligonucleotide treatment;RT-qPCR;FISH;fiber-FISH;nuclear-matrix attachment assay
E_04786	2007	17308084	Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU.1 and HMGA1	Homo sapiens	hg18	chr14	98330912	98330937	NA	NKX2-5	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	peripheral blood	UBERON:0000178	PEER	CVCL_1913	T-cell	CL:0000084	DSO.14 sequence-specific enhancer-core inhibition	MPSS DNase-seq;454 DNase-seq;DNase-I hypersensitivity mapping	26-mer double-stranded DNA inhibitory oligonucleotide treatment;RT-qPCR;FISH;fiber-FISH;nuclear-matrix attachment assay
E_04787	2007	17308084	Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU.1 and HMGA1	Homo sapiens	hg18	chr14	98670324	98670349	NA	BCL11B	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	peripheral blood	UBERON:0000178	PEER	CVCL_1913	T-cell	CL:0000084	DSO.15 sequence-specific BCL11B enhancer-core inhibition	MPSS DNase-seq;454 DNase-seq;DNase-I hypersensitivity mapping	26-mer double-stranded DNA inhibitory oligonucleotide treatment;RT-qPCR;FISH;fiber-FISH;nuclear-matrix attachment assay
E_04788	2007	17308084	Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU.1 and HMGA1	Homo sapiens	hg18	chr14	98722026	98722051	NA	BCL11B	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	peripheral blood	UBERON:0000178	PEER	CVCL_1913	T-cell	CL:0000084	DSO.16 sequence-specific BCL11B enhancer-core inhibition	MPSS DNase-seq;454 DNase-seq;DNase-I hypersensitivity mapping	26-mer double-stranded DNA inhibitory oligonucleotide treatment;RT-qPCR;FISH;fiber-FISH;nuclear-matrix attachment assay
E_04789	2013	23741008	A far downstream enhancer for murine Bcl11b controls its T-cell specific expression	Mus musculus	mm9	chr12	108396825	108398672	TCF7	Bcl11b	Enhancer	Active	Normal	NA	NA	NA	thymus	UBERON:0002370	primary mouse thymocytes and P2C2	NA	DN2 thymocyte	CL:0000806	Long-range Major Peak enhancer controlling normal T-lineage-specific Bcl11b activation	TCF-1 ChIP-seq;RNA-seq;histone-modification profiling	3C;stable luciferase reporter assay;TCF-1 binding-site deletion;conserved-region deletion;BAC recombineering reporter assay;bisulfite sequencing
E_04790	2016	26883634	RUNX super-enhancer control through the Notch pathway by Epstein-Barr virus transcription factors regulates B cell growth	Homo sapiens	hg19	chr1	25344250	25363078	EBNA2	RUNX3	Super-enhancer	Active	Disease	Burkitt lymphoma	MONDO:0007243	DOID:8584	lymphoid tissue	UBERON:0001744	Mutu III	NA	B cell	CL:0000236	Super-enhancer activity assay; TF-binding assay; enhancer deletion assay; enhancer-promoter interaction assay	EBNA2 ChIP-seq; H3K27ac ChIP-seq; chromatin interaction profiling	EBNA2 ChIP-qPCR; RBPJ ChIP-qPCR; RUNX3 enhancer-promoter reporter assay; enhancer-2 deletion analysis; RBPJ-dependent reporter assay
E_04791	2016	26883634	RUNX super-enhancer control through the Notch pathway by Epstein-Barr virus transcription factors regulates B cell growth	Homo sapiens	hg19	chr1	25344250	25363078	RBPJ	RUNX3	Super-enhancer	Active	Disease	Burkitt lymphoma	MONDO:0007243	DOID:8584	lymphoid tissue	UBERON:0001744	Mutu III	NA	B cell	CL:0000236	Super-enhancer activity assay; TF-binding assay; enhancer deletion assay; enhancer-promoter interaction assay	EBNA2 ChIP-seq; H3K27ac ChIP-seq; chromatin interaction profiling	RBPJ ChIP-qPCR; RUNX3 enhancer-promoter reporter assay; enhancer-2 deletion analysis
E_04792	2012	23232398	T-bet and GATA3 orchestrate Th1 and Th2 differentiation through lineage-specific targeting of distal regulatory elements	Homo sapiens	hg18	chr1	67542131	67542929	TBX21	IL12RB2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human CD4-positive T cells	NA	CD4-positive, alpha-beta T cell	CL:0000624	Enhancer activity assay; TF-binding assay; TF-dependent regulatory assay	TBX21 ChIP-seq; GATA3 ChIP-seq; DNase-seq; H3K4me1 profiling	Luciferase reporter assay in activated primary human CD4-positive T cells
E_04793	2012	23232398	T-bet and GATA3 orchestrate Th1 and Th2 differentiation through lineage-specific targeting of distal regulatory elements	Homo sapiens	hg18	chr18	65728245	65728831	TBX21	CD226	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human CD4-positive T cells	NA	CD4-positive, alpha-beta T cell	CL:0000624	Enhancer activity assay; TF-binding assay; TF-dependent regulatory assay	TBX21 ChIP-seq; GATA3 ChIP-seq; DNase-seq; H3K4me1 profiling	Luciferase reporter assay in activated primary human CD4-positive T cells
E_04794	2012	23232398	T-bet and GATA3 orchestrate Th1 and Th2 differentiation through lineage-specific targeting of distal regulatory elements	Homo sapiens	hg18	chr4	81175402	81175943	TBX21	ANTXR2	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human CD4-positive T cells	NA	CD4-positive, alpha-beta T cell	CL:0000624	Enhancer activity assay; TF-binding assay; TF-dependent regulatory assay	TBX21 ChIP-seq; GATA3 ChIP-seq; DNase-seq; H3K4me1 profiling	Luciferase reporter assay in activated primary human CD4-positive T cells
E_04795	2012	23232398	T-bet and GATA3 orchestrate Th1 and Th2 differentiation through lineage-specific targeting of distal regulatory elements	Homo sapiens	hg18	chr6	160323919	160324583	TBX21	IGF2R	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human CD4-positive T cells	NA	CD4-positive, alpha-beta T cell	CL:0000624	Enhancer activity assay; TF-binding assay; TF-dependent regulatory assay	TBX21 ChIP-seq; GATA3 ChIP-seq; DNase-seq; H3K4me1 profiling	Luciferase reporter assay in activated primary human CD4-positive T cells
E_04796	2012	23232398	T-bet and GATA3 orchestrate Th1 and Th2 differentiation through lineage-specific targeting of distal regulatory elements	Homo sapiens	hg18	chr18	40471400	40472121	TBX21	SETBP1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human CD4-positive T cells	NA	CD4-positive, alpha-beta T cell	CL:0000624	Enhancer activity assay; TF-binding assay; TF-dependent regulatory assay	TBX21 ChIP-seq; GATA3 ChIP-seq; DNase-seq; H3K4me1 profiling	Luciferase reporter assay in activated primary human CD4-positive T cells
E_04797	2012	23232398	T-bet and GATA3 orchestrate Th1 and Th2 differentiation through lineage-specific targeting of distal regulatory elements	Homo sapiens	hg18	chr18	40592792	40593656	TBX21	SETBP1	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human CD4-positive T cells	NA	CD4-positive, alpha-beta T cell	CL:0000624	Enhancer activity assay; TF-binding assay; TF-dependent regulatory assay	TBX21 ChIP-seq; GATA3 ChIP-seq; DNase-seq; H3K4me1 profiling	Luciferase reporter assay in activated primary human CD4-positive T cells
E_04798	2023	37032358	Super-enhancer-driven TOX2 mediates oncogenesis in Natural Killer/T Cell Lymphoma	Homo sapiens	hg19	chr20	42567767	42593591	RUNX3	TOX2	Super-enhancer	Active	Disease	nasal type extranodal NK/T-cell lymphoma	MONDO:0019472	DOID:0080797	blood	UBERON:0000178	NK-YS	CVCL_8461	NK T-cell	CL:0000814	Super-enhancer activity assay; endogenous super-enhancer perturbation assay; TF-binding assay; TF-site mutagenesis assay; target-gene expression assay; cellular phenotype assay	H3K27ac NanoChIP-seq; H3K27ac ChIP-seq; RNA-seq	TOX2-e1/e2/e3 dual-luciferase reporter assay; CRISPR/dCas9-KRAB interference of TOX2-SE; RUNX3 ChIP-qPCR; RUNX3 binding-site-directed mutagenesis; RUNX3 shRNA knockdown; TOX2 shRNA knockdown; qRT-PCR; Western blotting; proliferation assay; colony-formation assay; TOX2 rescue assay; xenograft tumor-formation assay
E_04799	2021	33444684	Super-enhancers for RUNX3 are required for cell proliferation in EBV-infected B cell lines	Homo sapiens	hg19	chr1	25344250	25363078	NA	RUNX3	Super-enhancer	Active	Disease	Burkitt lymphoma	MONDO:0007243	DOID:8584	lymphoid tissue	UBERON:0001744	Raji	CVCL_0511	B cell	CL:0000236	Endogenous super-enhancer deletion assay; target-gene expression assay; cellular phenotype assay	H3K27ac ChIP-seq; EBNA2 ChIP-seq integration	CRISPR/Cas9 genomic excision of seR3-59h and seR3-70h; genomic deletion PCR; qRT-PCR; JQ1 treatment; cell proliferation assay; colony-formation assay
E_04800	2022	35069677	Disruption of c-MYC Binding and Chromosomal Looping Involving Genetic Variants Associated With Ankylosing Spondylitis Upstream of the RUNX3 Promoter	Homo sapiens	hg19	chr1	25303971	25306641	MYC	RUNX3	Enhancer	Active	Disease	ankylosing spondylitis	MONDO:0005306	DOID:7147	blood	UBERON:0000178	primary human CD14-positive monocytes	NA	monocyte	CL:0000576	TF-binding assay; regulatory-variant functional assay; chromatin interaction assay	ENCODE H3K4me1/H3K27ac/DNase integration	MYC EMSA; Western blot-EMSA; allele-specific DNA-binding assay; 3C-qPCR; qRT-PCR
E_04801	2017	28793263	The Conserved Sonic Hedgehog Limb Enhancer Consists of Discrete Functional Elements that Regulate Precise Spatial Expression	Mus musculus	mm39	chr5	29519495	29520860	NA	Shh	Enhancer	Active	Normal	NA	NA	NA	limb bud	UBERON:0004347	mouse embryo	NA	limb bud mesenchymal cell	CL:0000134	Endogenous enhancer editing assay; enhancer functional dissection assay; developmental phenotype assay	NA	CRISPR/Cas9 genome editing of endogenous Zrs1; reporter analysis; enhancer deletion/substitution analysis; Shh expression analysis; embryonic limb phenotype analysis
E_04802	2005	16269442	Evaluation of the RET regulatory landscape reveals the biological relevance of a HSCR-implicated enhancer	Homo sapiens	hg19	chr10	43581812	43582711	NA	RET	Enhancer	Active	Disease	Hirschsprung disease	MONDO:0018300	DOID:10487	enteric nervous system	UBERON:0002005	NA	NA	neural crest cell	CL:0000333	Enhancer activity assay; developmental reporter assay	Comparative genomics	Reporter assay of conserved RET regulatory elements; transgenic developmental enhancer assay; enhancer activity analysis
E_04803	2010	20598273	Differential contributions of rare and common, coding and noncoding Ret mutations to multifactorial Hirschsprung disease liability	Homo sapiens	hg19	chr10	43581812	43582711	SOX10	RET	Enhancer	Active	Disease	Hirschsprung disease	MONDO:0018300	DOID:10487	enteric nervous system	UBERON:0002005	NA	NA	neural crest cell	CL:0000333	TF-binding assay; enhancer variant functional assay; target-gene transactivation assay	NA	SOX10 DNA-binding assay; allele-specific enhancer assay; RET transactivation assay; functional analysis of rs2435357
E_04804	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60725424	60725688	NA	BCL11A	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; enhancer-genotype association assay; erythroid-specific regulatory assay	Chromatin profiling; DNase hypersensitivity profiling	Enhancer reporter assay; erythroid differentiation analysis; BCL11A expression analysis; fetal hemoglobin analysis
E_04805	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60722238	60722466	NA	BCL11A	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; enhancer-genotype association assay; erythroid-specific regulatory assay	Chromatin profiling; DNase hypersensitivity profiling	Enhancer reporter assay; erythroid differentiation analysis; BCL11A expression analysis; fetal hemoglobin analysis
E_04806	2013	24115442	An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level	Homo sapiens	hg19	chr2	60718042	60718186	NA	BCL11A	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human erythroid cells	NA	erythroblast	CL:0000765	Enhancer activity assay; enhancer-genotype association assay; erythroid-specific regulatory assay	Chromatin profiling; DNase hypersensitivity profiling	Enhancer reporter assay; erythroid differentiation analysis; BCL11A expression analysis; fetal hemoglobin analysis
E_04807	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60725424	60725688	NA	BCL11A	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human erythroid progenitor cells	NA	erythroblast	CL:0000765	Endogenous enhancer perturbation assay; saturating mutagenesis assay; target-gene expression assay	CRISPR-Cas9 pooled saturating mutagenesis	CRISPR/Cas9 enhancer mutagenesis; primary human progenitor editing; erythroid differentiation assay; BCL11A expression analysis; fetal hemoglobin analysis; mouse transgenic validation
E_04808	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60722238	60722466	NA	BCL11A	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human erythroid progenitor cells	NA	erythroblast	CL:0000765	Endogenous enhancer perturbation assay; saturating mutagenesis assay; target-gene expression assay	CRISPR-Cas9 pooled saturating mutagenesis	CRISPR/Cas9 enhancer mutagenesis; primary human progenitor editing; erythroid differentiation assay; BCL11A expression analysis; fetal hemoglobin analysis; mouse transgenic validation
E_04809	2015	26375006	BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis	Homo sapiens	hg19	chr2	60718042	60718186	NA	BCL11A	Enhancer	Active	Normal	NA	NA	NA	blood	UBERON:0000178	primary human erythroid progenitor cells	NA	erythroblast	CL:0000765	Endogenous enhancer perturbation assay; saturating mutagenesis assay; target-gene expression assay	CRISPR-Cas9 pooled saturating mutagenesis	CRISPR/Cas9 enhancer mutagenesis; primary human progenitor editing; erythroid differentiation assay; BCL11A expression analysis; fetal hemoglobin analysis; mouse transgenic validation
E_04810	2015	26073540	Hematopoietic Signaling Mechanism Revealed from a Stem/Progenitor Cell Cistrome	Mus musculus	mm39	chr6	88180138	88180212	Gata2	Gata2	Enhancer	Active	Normal	NA	NA	NA	hematopoietic system	UBERON:0002390	primary mouse hematopoietic stem/progenitor cells	NA	hematopoietic progenitor cell	CL:0008001	Endogenous enhancer perturbation assay; TF-binding assay; target-gene expression assay	GATA2 ChIP-seq; comparative genomic profiling	Gene editing of Gata2 +9.5 enhancer; qRT-PCR; chromatin accessibility analysis; hematopoietic progenitor functional assays
E_04811	2008	18772437	Human-specific gain of function in a developmental enhancer	Homo sapiens	hg19	chr2	236773664	236774216	NA	NA	Enhancer	Active	Normal	NA	NA	NA	limb bud	UBERON:0004347	transgenic mouse embryo	NA	limb bud mesenchymal cell	CL:0000134	In vivo enhancer reporter assay; enhancer sequence mutagenesis assay	Comparative genomics	Transgenic LacZ reporter assay; human/chimpanzee/rhesus enhancer comparison; synthetic enhancer assay; site substitution analysis
E_04812	2021	34103329	Enhancer Hijacking Drives Oncogenic BCL11B Expression in Lineage-Ambiguous Stem Cell Leukemia	Homo sapiens	hg38	chr14	98541905	98544383	NA	BCL11B	Super-enhancer	Active	Disease	lineage-ambiguous acute leukemia	NA	NA	bone marrow	UBERON:0002371	primary BCL11B-deregulated leukemia cells	NA	hematopoietic progenitor-like leukemia cell	NA	Super-enhancer generation assay; enhancer-promoter interaction assay; allele-specific target-gene activation assay; genomic amplification assay	WGS; RNA-seq; H3K27ac ChIP-seq; H3K27ac HiChIP; long-read sequencing	DNA FISH; RNA-DNA FISH; genomic qPCR; BETA copy-number analysis; breakpoint mapping
E_04813	2007	17308084	Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU.1 and HMGA1	Homo sapiens	hg18	chr14	97720000	97780000	NA	NKX2-5	Enhancer	Active	Disease	T-cell acute lymphoblastic leukemia	MONDO:0004963	DOID:5603	blood	UBERON:0000178	Peer	CVCL_1913	T cell	CL:0000084	Enhancer inhibition assay; enhancer activity assay; chromatin-state assay; target-gene expression assay	DNase I hypersensitivity profiling; comparative genomic analysis	DSO.6-9 double-stranded oligonucleotide enhancer inhibition; RT-PCR; qRT-PCR; histone H3 acetylation ChIP; nuclear matrix attachment assay; sequence-specific inhibition controls
E_04814	2013	23741008	A far downstream enhancer for murine Bcl11b controls its T-cell specific expression	Mus musculus	mm9	chr12	108396825	108398672	Tcf7	Bcl11b	Enhancer	Active	Normal	NA	NA	NA	thymus	UBERON:0002370	primary mouse T-lineage progenitor cells	NA	T-lineage progenitor cell	NA	Enhancer activity assay; enhancer-promoter interaction assay; TF-site functional dissection assay; lineage-specific reporter assay	TCF-1 ChIP-seq; histone modification profiling	Stable reporter assay; BAC reporter recombineering; 3C assay; TCF-1-site mutagenesis; conserved-element deletion; bisulfite sequencing
E_04815	2014	25486255	CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells	Mus musculus	mm39	chr3	34806891	34820933	NA	Sox2	Super-enhancer	Active	Normal	NA	NA	NA	embryo	UBERON:0000922	F123 mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Endogenous super-enhancer deletion assay; enhancer-promoter interaction assay; target-gene expression assay	H3K27ac ChIP-seq; pluripotency-factor ChIP-seq integration; Hi-C; RNA-seq	Double-CRISPR/Cas9 deletion of Sox2 distal super-enhancer; deletion-spanning PCR; qPCR copy-number assay; Sanger sequencing; Sox2 expression analysis
E_04816	2016	27681417	Super-Enhancers at the Nanog Locus Differentially Regulate Neighboring Pluripotency-Associated Genes	Mus musculus	mm9	chr6	122611603	122614453	NA	Nanog	Super-enhancer	Active	Normal	NA	NA	NA	embryo	UBERON:0000922	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Endogenous super-enhancer deletion assay; enhancer reporter assay; enhancer-promoter interaction assay; eRNA functional assay	ChIP-seq integration; RNA-seq	CRISPR/Cas9 deletion of Nanog -45 super-enhancer; luciferase reporter assay; qRT-PCR; eRNA depletion; chromatin-looping analysis
E_04817	2016	27681417	Super-Enhancers at the Nanog Locus Differentially Regulate Neighboring Pluripotency-Associated Genes	Mus musculus	mm9	chr6	122611603	122614453	NA	Dppa3	Super-enhancer	Active	Normal	NA	NA	NA	embryo	UBERON:0000922	mouse embryonic stem cells	NA	embryonic stem cell	CL:0002322	Endogenous super-enhancer deletion assay; enhancer reporter assay; enhancer-promoter interaction assay; eRNA functional assay	ChIP-seq integration; RNA-seq	CRISPR/Cas9 deletion of Nanog -45 super-enhancer; luciferase reporter assay; qRT-PCR; eRNA depletion; chromatin-looping analysis
E_04818	2021	34320216	Characterization of a functional endothelial super-enhancer that regulates ADAMTS18 and angiogenesis	Homo sapiens	hg19	chr16	77627867	77630464	HIF1A	ADAMTS18	Enhancer	Active	Normal	NA	NA	NA	umbilical vein	UBERON:0002066	HUVEC	NA	endothelial cell	CL:0000115	Endogenous enhancer deletion assay; enhancer reporter assay; target-gene expression assay; angiogenesis phenotype assay	H3K27ac ChIP-seq; H3K4me1 ChIP-seq; GRO-seq; RNA-seq; Hi-C	CRISPR/Cas9 deletion of E2; enhancer-reporter assay; ADAMTS18 promoter reporter assay; qRT-PCR; endothelial proliferation assay; tube-formation assay; 3D sprouting assay
E_04819	2021	34320216	Characterization of a functional endothelial super-enhancer that regulates ADAMTS18 and angiogenesis	Homo sapiens	hg19	chr16	77602270	77604988	NA	ADAMTS18	Enhancer	Active	Normal	NA	NA	NA	umbilical vein	UBERON:0002066	EA.hy926	CVCL_3901	endothelial cell	CL:0000115	Endogenous enhancer deletion assay; enhancer-target interaction assay; target-gene expression assay; angiogenesis phenotype assay	H3K27ac ChIP-seq; H3K4me1 ChIP-seq; GRO-seq; RNA-seq; Hi-C	CRISPR/Cas9 deletion of SE12313-b; qRT-PCR; cell-proliferation assay; tube-formation assay
E_04820	2008	18772437	Human-specific gain of function in a developmental enhancer	Homo sapiens	hg19	chr2	236773664	236774216	NA	NA	Enhancer	Active	Normal	NA	NA	NA	limb bud	UBERON:0004347	transgenic mouse embryo	NA	limb bud mesenchymal cell	CL:0000134	In vivo enhancer reporter assay; comparative enhancer activity assay; enhancer sequence mutagenesis assay	Comparative genomics	Transgenic LacZ reporter assay; human/chimpanzee/rhesus enhancer comparison; synthetic sequence substitution analysis
E_04821	2005	16269442	Evaluation of the RET regulatory landscape reveals the biological relevance of a HSCR-implicated enhancer	Homo sapiens	hg19	chr10	43581812	43582711	NA	RET	Enhancer	Active	Disease	Hirschsprung disease	MONDO:0018300	DOID:10487	enteric nervous system	UBERON:0002005	primary enteric neural crest-derived cells	NA	neural crest cell	CL:0000333	Enhancer activity assay; developmental reporter assay; disease-associated enhancer analysis	Comparative genomics	Reporter assay of conserved RET regulatory elements; developmental enhancer assay; allele-specific enhancer analysis
E_04822	2015	26073540	Hematopoietic Signaling Mechanism Revealed from a Stem/Progenitor Cell Cistrome	Mus musculus	mm39	chr6	88180138	88180212	Gata2	Gata2	Enhancer	Active	Normal	NA	NA	NA	hematopoietic system	UBERON:0002390	primary mouse hematopoietic stem/progenitor cells	NA	hematopoietic progenitor cell	CL:0008001	Endogenous enhancer perturbation assay; TF-binding assay; target-gene expression assay	GATA2 ChIP-seq; chromatin profiling	Gata2 +9.5 enhancer editing/deletion; qRT-PCR; hematopoietic progenitor functional assays
E_04823	2023	37032358	Super-enhancer-driven TOX2 mediates oncogenesis in Natural Killer/T Cell Lymphoma	Homo sapiens	hg19	chr20	42567767	42593591	RUNX3	TOX2	Super-enhancer	Active	Disease	nasal type extranodal NK/T-cell lymphoma	MONDO:0019472	DOID:0080797	blood	UBERON:0000178	NK-YS	CVCL_8461	NK T-cell	CL:0000814	Super-enhancer activity assay; endogenous super-enhancer perturbation assay; TF-binding assay; TF-site mutagenesis assay; target-gene expression assay; cellular phenotype assay	H3K27ac NanoChIP-seq; H3K27ac ChIP-seq; RNA-seq	TOX2-e1/e2/e3 dual-luciferase reporter assay; CRISPR/dCas9-KRAB interference of TOX2-SE; RUNX3 ChIP-qPCR; RUNX3 binding-site-directed mutagenesis; RUNX3 shRNA knockdown; TOX2 shRNA knockdown; qRT-PCR; Western blotting; proliferation assay; colony-formation assay; xenograft tumor-formation assay
E_04824	2017	28793263	The Conserved Sonic Hedgehog Limb Enhancer Consists of Discrete Functional Elements that Regulate Precise Spatial Expression	Mus musculus	mm39	chr5	29519495	29520860	NA	Shh	Enhancer	Active	Normal	NA	NA	NA	limb bud	UBERON:0004347	mouse embryo	NA	mesenchymal cell	CL:0008019	Endogenous enhancer editing assay; enhancer functional dissection assay; developmental phenotype assay	NA	CRISPR/Cas9 genome editing of endogenous Zrs1; reporter analysis; enhancer deletion/substitution analysis; Shh expression analysis; embryonic limb phenotype analysis
E_04825	2005	16269442	Evaluation of the RET regulatory landscape reveals the biological relevance of a HSCR-implicated enhancer	Homo sapiens	hg19	chr10	43581812	43582711	NA	RET	Enhancer	Active	Disease	Hirschsprung disease	MONDO:0018300	DOID:10487	enteric nervous system	UBERON:0002005	NA	NA	neural crest cell	CL:0011012	Enhancer activity assay; developmental reporter assay; disease-associated enhancer analysis	Comparative genomics	Reporter assay of conserved RET regulatory elements; transgenic developmental enhancer assay; enhancer activity analysis; developmental enhancer assay; allele-specific enhancer analysis
E_04826	2010	20598273	Differential contributions of rare and common, coding and noncoding Ret mutations to multifactorial Hirschsprung disease liability	Homo sapiens	hg19	chr10	43581812	43582711	SOX10	RET	Enhancer	Active	Disease	Hirschsprung disease	MONDO:0018300	DOID:10487	enteric nervous system	UBERON:0002005	HeLa	CVCL_0030	epithelial cell	CL:0000066	TF-binding assay; enhancer variant functional assay; target-gene transactivation assay	NA	SOX10 transactivation assay; luciferase reporter assay; SOX10-binding-site deletion assay; SOX10 ChIP; functional analysis of rs2435357
E_04827	2015	26073540	Hematopoietic Signaling Mechanism Revealed from a Stem/Progenitor Cell Cistrome	Mus musculus	mm39	chr6	88180138	88180212	Gata2	Gata2	Enhancer	Active	Normal	NA	NA	NA	hematopoietic system	UBERON:0002390	primary mouse hematopoietic stem/progenitor cells	NA	hematopoietic precursor cell	CL:0008001	Endogenous enhancer perturbation assay; TF-binding assay; target-gene expression assay	GATA2 ChIP-seq; comparative genomic profiling; chromatin profiling	Gene editing of Gata2 +9.5 enhancer; qRT-PCR; chromatin accessibility analysis; hematopoietic progenitor functional assays; Gata2 +9.5 enhancer editing/deletion
E_04828	2008	18772437	Human-specific gain of function in a developmental enhancer	Homo sapiens	hg19	chr2	236773664	236774216	NA	NA	Enhancer	Active	Normal	NA	NA	NA	limb bud	UBERON:0004347	transgenic mouse embryo	NA	mesenchymal cell	CL:0008019	In vivo enhancer reporter assay; enhancer sequence mutagenesis assay; comparative enhancer activity assay	Comparative genomics	Transgenic LacZ reporter assay; human/chimpanzee/rhesus enhancer comparison; synthetic enhancer assay; site substitution analysis; synthetic sequence substitution analysis
E_04829	2016	27703156	Genome-wide compendium and functional assessment of in vivo heart enhancers	Mus musculus	mm10	chr5	122092252	122094768	NA	Myl2	Enhancer	Active	Disease	dilated cardiomyopathy	MONDO:0005021	DOID:12930	heart	UBERON:0000948	embryonic and adult mouse heart	NA	cardiac muscle cell	CL:0000746	Endogenous enhancer deletion; transgenic enhancer activity assay; cardiac phenotype assay	H3K27ac ChIP-seq; p300 ChIP-seq; RNA-seq	Homologous-recombination enhancer knockout; Hsp68-LacZ transgenic reporter assay; RT-qPCR; western blot; cardiac histology; echocardiography
E_04830	2016	27703156	Genome-wide compendium and functional assessment of in vivo heart enhancers	Mus musculus	mm10	chr14	54996893	54997224	NA	Myh7	Enhancer	Active	Disease	dilated cardiomyopathy	MONDO:0005021	DOID:12930	heart	UBERON:0000948	embryonic and adult mouse heart	NA	cardiac muscle cell	CL:0000746	Endogenous enhancer deletion; transgenic enhancer activity assay; cardiac phenotype assay	H3K27ac ChIP-seq; p300 ChIP-seq; RNA-seq	Homologous-recombination enhancer knockout; Hsp68-LacZ transgenic reporter assay; RT-qPCR; western blot; cardiac histology; echocardiography
E_04831	2019	31070942	Cardioprotective Effects of MTSS1 Enhancer Variants	Homo sapiens	hg38	chr8	124845017	124845217	NA	MTSS1	Enhancer	Active	Normal	NA	NA	NA	heart	UBERON:0000948	human left ventricular myocardium	NA	cardiac muscle cell	CL:0000746	Enhancer activity assay; endogenous enhancer deletion; CRISPR interference; allele-specific enhancer assay	GTEx eQTL analysis; cardiac GWAS integration	Transgenic zebrafish fluorescent reporter assay; CRISPR/Cas9 enhancer deletion; CRISPRi; luciferase reporter assay