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 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:0005368 DOID:4465 Kidney UBERON:0002113 769p CVCL_1050 Renal clear cell carcinoma cell CL:0002677 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq, 3C-seq ChIP-qPCR, CRISPR Knockout, CRISPRi, Luciferase Reporter Assay, qRT-PCR, Western blot 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:0005368 DOID:4465 Kidney UBERON:0002113 786o CVCL_1051 Renal clear cell carcinoma cell CL:0002677 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq, 3C-seq ChIP-qPCR, CRISPR Knockout, CRISPRi, Luciferase Reporter Assay, qRT-PCR, Western blot 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:0005368 DOID:4465 Kidney UBERON:0002113 VMRC-RCW CVCL_1790 Renal clear cell carcinoma cell CL:0002677 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq, 3C-seq ChIP-qPCR, CRISPR Knockout, CRISPRi, Luciferase Reporter Assay, qRT-PCR, Western blot 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:0005368 DOID:4465 Kidney UBERON:0002113 CAKI-1 CVCL_0234 Renal clear cell carcinoma cell CL:0002677 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq, 3C-seq ChIP-qPCR, CRISPR Knockout, CRISPRi, Luciferase Reporter Assay, qRT-PCR, Western blot 2026 42024500 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:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat T-ALL Cells CVCL_0065 T lymphoblast CL:0002419 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, 3C-seq 2026 42024500 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:0004947 DOID:0050890 Blood UBERON:0000178 MOLT4 Cells CVCL_0013 T lymphoblast CL:0002419 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, 3C-seq 2026 42024500 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:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat T-ALL CVCL_0065 Jurkat T-ALL CL:0002419 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, 3C-seq 2026 42030388 MYC-bound enhancer RNAs in cis regulate gene transcription and tumorigenesis Homo sapiens hg19 chr2 116230440 116232740 MYC GREB1 Enhancer Active Disease Breast invasive carcinoma MONDO:0006143 DOID:1612 Mammary gland UBERON:0001911 MCF-7 CVCL_0031 Estrogen receptor positive breast cancer cell CL:0000646 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 2026 42030388 MYC-bound enhancer RNAs in cis regulate gene transcription and tumorigenesis Homo sapiens hg19 chr2 116230440 116232740 MYC GREB1 Enhancer Active Disease Breast invasive carcinoma MONDO:0006143 DOID:1612 Mammary gland UBERON:0001911 BT474 CVCL_0179 Estrogen receptor positive breast cancer cell CL:0000646 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 2026 42030388 MYC-bound enhancer RNAs in cis regulate gene transcription and tumorigenesis Homo sapiens hg19 chr2 116230440 116232740 P300 GREB1 Enhancer Active Disease Breast invasive carcinoma MONDO:0006143 DOID:1612 Mammary gland UBERON:0001911 MCF-7 CVCL_0031 Estrogen receptor positive breast cancer cell CL:0000646 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 2026 42030388 MYC-bound enhancer RNAs in cis regulate gene transcription and tumorigenesis Homo sapiens hg19 chr2 116230440 116232740 P300 GREB1 Enhancer Active Disease Breast invasive carcinoma MONDO:0006143 DOID:1612 Mammary gland UBERON:0001911 BT474 CVCL_0179 Estrogen receptor positive breast cancer cell CL:0000646 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 2026 42030388 MYC-bound enhancer RNAs in cis regulate gene transcription and tumorigenesis Homo sapiens hg19 chr2 116230440 116232740 BRD4 GREB1 Enhancer Active Disease Breast invasive carcinoma MONDO:0006143 DOID:1612 Mammary gland UBERON:0001911 MCF-7 CVCL_0031 Estrogen receptor positive breast cancer cell CL:0000646 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 2026 42030388 MYC-bound enhancer RNAs in cis regulate gene transcription and tumorigenesis Homo sapiens hg19 chr2 116230440 116232740 BRD4 GREB1 Enhancer Active Disease Breast invasive carcinoma MONDO:0006143 DOID:1612 Mammary gland UBERON:0001911 BT474 CVCL_0179 Estrogen receptor positive breast cancer cell CL:0000646 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 2019 31727856 Brain cell type-specific enhancer-promoter interactome maps and disease risk association Homo sapiens hg19 chr2 127082600 127082962 PU.1 BIN1 Enhancer Active Disease Alzheimer's disease MONDO:0004992 DOID:10652 Brain microglia CL:0000129 hPSC-derived microglia Human pluripotent stem cell derived microglia CL:0000129 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 2019 31727856 Brain cell type-specific enhancer-promoter interactome maps and disease risk association Homo sapiens hg19 chr2 127082600 127082962 PU.1 BIN1 Enhancer Active Disease Alzheimer's disease MONDO:0004992 DOID:10652 Brain microglia CL:0000129 hPSC-derived neuron Human pluripotent stem cell derived neuron CL:0000540 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 2019 31727856 Brain cell type-specific enhancer-promoter interactome maps and disease risk association Homo sapiens hg19 chr2 127082600 127082962 PU.1 BIN1 Enhancer Active Disease Alzheimer's disease MONDO:0004992 DOID:10652 Brain microglia CL:0000129 hPSC-derived astrocyte Human pluripotent stem cell derived astrocyte CL:0000127 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 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:0005818 DOID:11488 Bone UBERON:0001474 MG-63 CVCL_0426 Human osteosarcoma cell line CL:0000082 Dual-luciferase reporter assay, CRISPR-Cas9 deletion loss-of-function, 3C chromatin capture, ChIP-qPCR GWAS summary statistics, GTEx eQTL, MEME motif prediction Dual-luciferase reporter, CRISPR knockout, 3C-qPCR, ChIP-qPCR, Sanger sequencing, RT-qPCR, Western blot, immunofluorescence DNA-FISH 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 Normal Osteoporosis MONDO:0005818 DOID:11488 Bone UBERON:0001474 primary human osteoblasts primary human osteoblast CL:0000062 Dual-luciferase reporter assay, CRISPR-Cas9 deletion loss-of-function, 3C chromatin capture, ChIP-qPCR GWAS summary statistics, GTEx eQTL, MEME motif prediction Dual-luciferase reporter, CRISPR knockout, 3C-qPCR, ChIP-qPCR, Sanger sequencing, RT-qPCR, Western blot, immunofluorescence DNA-FISH 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:0005818 DOID:11488 Bone UBERON:0001474 MG-63 CVCL_0426 Human osteosarcoma cell line CL:0000082 Dual-luciferase reporter assay, ChIP-qPCR GWAS summary statistics, GTEx eQTL, MEME motif prediction Dual-luciferase reporter, ChIP-qPCR, Sanger sequencing, RT-qPCR 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 Normal Osteoporosis MONDO:0005818 DOID:11488 Bone UBERON:0001474 primary human osteoblasts primary human osteoblast CL:0000062 Dual-luciferase reporter assay, ChIP-qPCR GWAS summary statistics, GTEx eQTL, MEME motif prediction Dual-luciferase reporter, ChIP-qPCR, Sanger sequencing, RT-qPCR 2025 40729681 Enhancer heterogeneity in acute lymphoblastic leukemia drives differential gene expression Homo sapiens hg38 chr9 130812462 130813421 KMT2A::AFF1 GNAQ Enhancer Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0060412 Bone marrow UBERON:0002371 SEM CVCL_0095 B-ALL blast cell CL:0000692 CRISPR-Cas9 deletion loss-of-function, Capture-C chromatin interaction, ChIP-qPCR ATAC-seq, H3K27ac CUT&Tag, ChIP-seq, RNA-seq, Micro-Capture-C WGS, RT-qPCR, CRISPR editing, cell transfection 2025 40729681 Enhancer heterogeneity in acute lymphoblastic leukemia drives differential gene expression Homo sapiens hg38 chr9 130812462 130813421 AFF1 GNAQ Enhancer Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0060412 Bone marrow UBERON:0002371 SEM CVCL_0095 B-ALL blast cell CL:0000692 CRISPR-Cas9 deletion loss-of-function, Capture-C chromatin interaction, ChIP-qPCR ATAC-seq, H3K27ac CUT&Tag, ChIP-seq, RNA-seq, Micro-Capture-C WGS, RT-qPCR, CRISPR editing, cell transfection 2025 40729681 Enhancer heterogeneity in acute lymphoblastic leukemia drives differential gene expression Homo sapiens hg38 chr12 4900187 4901013 KMT2A::AFF1 ARID1B Enhancer Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0060412 Bone marrow UBERON:0002371 RS4;11 CVCL_0093 B-ALL blast cell CL:0000692 CRISPR-Cas9 deletion loss-of-function, Capture-C chromatin interaction, ChIP-qPCR ATAC-seq, H3K27ac CUT&Tag, ChIP-seq, RNA-seq, Micro-Capture-C WGS, RT-qPCR, CRISPR editing, cell transfection 2025 40729681 Enhancer heterogeneity in acute lymphoblastic leukemia drives differential gene expression Homo sapiens hg38 chr12 4900187 4901013 AFF1 ARID1B Enhancer Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0060412 Bone marrow UBERON:0002371 RS4;11 CVCL_0093 B-ALL blast cell CL:0000692 CRISPR-Cas9 deletion loss-of-function, Capture-C chromatin interaction, ChIP-qPCR ATAC-seq, H3K27ac CUT&Tag, ChIP-seq, RNA-seq, Micro-Capture-C WGS, RT-qPCR, CRISPR editing, cell transfection 2025 40729681 Enhancer heterogeneity in acute lymphoblastic leukemia drives differential gene expression Homo sapiens hg38 chr6 101482232 101483107 KMT2A::AFF1 MEIS1 Enhancer Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0060412 Bone marrow UBERON:0002371 Primary human KMT2A::AFF1 ALL blasts Primary leukemic blast cell CL:0000692 Micro-Capture-C chromatin interaction + patient gene expression validation, ChIP-qPCR scMultiome ATAC+RNA-seq, TOPmentation H3K27ac profiling, Micro-Capture-C, WGS RT-qPCR, FACS cell sorting, patient primary cell culture 2025 40729681 Enhancer heterogeneity in acute lymphoblastic leukemia drives differential gene expression Homo sapiens hg38 chr6 101482232 101483107 AFF1 MEIS1 Enhancer Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0060412 Bone marrow UBERON:0002371 Primary human KMT2A::AFF1 ALL blasts Primary leukemic blast cell CL:0000692 Micro-Capture-C chromatin interaction + patient gene expression validation, ChIP-qPCR scMultiome ATAC+RNA-seq, TOPmentation H3K27ac profiling, Micro-Capture-C, WGS RT-qPCR, FACS cell sorting, patient primary cell culture 2025 40729681 Enhancer heterogeneity in acute lymphoblastic leukemia drives differential gene expression Homo sapiens hg38 chr6 9087104 9087962 KMT2A::AFF1 RUNX2 Enhancer Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0060412 Bone marrow UBERON:0002371 Primary human KMT2A::AFF1 ALL blasts Primary leukemic blast cell CL:0000692 Micro-Capture-C chromatin interaction + patient gene expression validation, ChIP-qPCR scMultiome ATAC+RNA-seq, TOPmentation H3K27ac profiling, Micro-Capture-C, WGS RT-qPCR, FACS cell sorting, patient primary cell culture 2025 40729681 Enhancer heterogeneity in acute lymphoblastic leukemia drives differential gene expression Homo sapiens hg38 chr6 9087104 9087962 AFF1 RUNX2 Enhancer Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0060412 Bone marrow UBERON:0002371 Primary human KMT2A::AFF1 ALL blasts Primary leukemic blast cell CL:0000692 Micro-Capture-C chromatin interaction + patient gene expression validation, ChIP-qPCR scMultiome ATAC+RNA-seq, TOPmentation H3K27ac profiling, Micro-Capture-C, WGS RT-qPCR, FACS cell sorting, patient primary cell culture 2023 37832549 Genome-wide CRISPR activation screening in senescent cells reveals SOX5 as a driver and therapeutic target of rejuvenation Homo sapiens hg19 chr6 174249537 174250490 SOX5 HMGB2 Enhancer Active Disease Cellular senescence MONDO:0024530 DOID:0080000 Bone marrow UBERON:0002371 WS hMPC Human mesenchymal precursor cell CL:0000128 Luciferase reporter assay, ChIP-qPCR, Hi-C chromatin interaction validation ATAC-seq, H3K27ac ChIP-seq, H3K4me1 ChIP-seq, SOX5 ChIP-seq, RNA-seq, Hi-C, single-cell multiome dual-luciferase reporter detection, ChIP-qPCR, lentiviral overexpression, siRNA knockdown, CRISPRa perturbation, RT-qPCR, western blot 2023 37832549 Genome-wide CRISPR activation screening in senescent cells reveals SOX5 as a driver and therapeutic target of rejuvenation Homo sapiens hg19 chr6 174249537 174250490 SOX5 HMGB2 Enhancer Active Disease Cellular senescence MONDO:0024530 DOID:0080000 Bone marrow UBERON:0002371 WT hMPC Human mesenchymal precursor cell CL:0000128 Luciferase reporter assay, ChIP-qPCR, Hi-C chromatin interaction validation ATAC-seq, H3K27ac ChIP-seq, H3K4me1 ChIP-seq, SOX5 ChIP-seq, RNA-seq, Hi-C, single-cell multiome dual-luciferase reporter detection, ChIP-qPCR, lentiviral overexpression, siRNA knockdown, CRISPRa perturbation, RT-qPCR, western blot 2023 37832549 Genome-wide CRISPR activation screening in senescent cells reveals SOX5 as a driver and therapeutic target of rejuvenation Homo sapiens hg19 chr6 174249537 174250490 SOX5 HMGB2 Enhancer Active Disease Osteoarthritis MONDO:0001623 DOID:8398 Bone marrow UBERON:0002371 WS hMPC Human mesenchymal precursor cell CL:0000128 Luciferase reporter assay, ChIP-qPCR, Hi-C chromatin interaction validation ATAC-seq, H3K27ac ChIP-seq, H3K4me1 ChIP-seq, SOX5 ChIP-seq, RNA-seq, Hi-C, single-cell multiome dual-luciferase reporter detection, ChIP-qPCR, lentiviral overexpression, siRNA knockdown, CRISPRa perturbation, RT-qPCR, western blot 2023 37832549 Genome-wide CRISPR activation screening in senescent cells reveals SOX5 as a driver and therapeutic target of rejuvenation Homo sapiens hg19 chr6 174249537 174250490 SOX5 HMGB2 Enhancer Active Disease Osteoarthritis MONDO:0001623 DOID:8398 Bone marrow UBERON:0002371 WT hMPC Human mesenchymal precursor cell CL:0000128 Luciferase reporter assay, ChIP-qPCR, Hi-C chromatin interaction validation ATAC-seq, H3K27ac ChIP-seq, H3K4me1 ChIP-seq, SOX5 ChIP-seq, RNA-seq, Hi-C, single-cell multiome dual-luciferase reporter detection, ChIP-qPCR, lentiviral overexpression, siRNA knockdown, CRISPRa perturbation, RT-qPCR, western blot 2016 27708057 Systematic mapping of functional enhancer-promoter connections with CRISPR interference Homo sapiens hg19 chr8 209981000 209990000 MYC Enhancer Active Disease Acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 K562 CVCL_0004 Human erythroleukemia cell line CL:0009084 CRISPRi interference, clonal genomic deletion, Hi-C chromatin contact validation DNase-seq, H3K27ac ChIP-seq, RNA-seq, Pol II ChIA-PET, Hi-C RT-qPCR, clonal cell line generation, sgRNA lentiviral transduction, cell viability assay 2016 27708057 Systematic mapping of functional enhancer-promoter connections with CRISPR interference Homo sapiens hg19 chr8 209981000 209990000 MYC Enhancer Active Disease Erythroleukemia MONDO:0017898 DOID:0080146 Bone marrow UBERON:0002371 K562 CVCL_0004 Human erythroleukemia cell line CL:0009084 CRISPRi interference, clonal genomic deletion, Hi-C chromatin contact validation DNase-seq, H3K27ac ChIP-seq, RNA-seq, Pol II ChIA-PET, Hi-C RT-qPCR, clonal cell line generation, sgRNA lentiviral transduction, cell viability assay 2016 27708057 Systematic mapping of functional enhancer-promoter connections with CRISPR interference Homo sapiens hg19 chr8 210003000 210012000 MYC Enhancer Active Disease Acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 K562 CVCL_0004 Human erythroleukemia cell line CL:0009084 CRISPRi interference, clonal genomic deletion, Hi-C chromatin contact validation DNase-seq, H3K27ac ChIP-seq, RNA-seq, Pol II ChIA-PET, Hi-C RT-qPCR, clonal cell line generation, sgRNA lentiviral transduction, cell viability assay 2016 27708057 Systematic mapping of functional enhancer-promoter connections with CRISPR interference Homo sapiens hg19 chr8 210003000 210012000 MYC Enhancer Active Disease Erythroleukemia MONDO:0017898 DOID:0080146 Bone marrow UBERON:0002371 K562 CVCL_0004 Human erythroleukemia cell line CL:0009084 CRISPRi interference, clonal genomic deletion, Hi-C chromatin contact validation DNase-seq, H3K27ac ChIP-seq, RNA-seq, Pol II ChIA-PET, Hi-C RT-qPCR, clonal cell line generation, sgRNA lentiviral transduction, cell viability assay 2016 27708057 Systematic mapping of functional enhancer-promoter connections with CRISPR interference Homo sapiens hg19 chr8 210011000 210018000 MYC Enhancer Active Disease Acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 K562 CVCL_0004 Human erythroleukemia cell line CL:0009084 CRISPRi interference, Hi-C chromatin contact validation DNase-seq, H3K27ac ChIP-seq, RNA-seq, Pol II ChIA-PET, Hi-C RT-qPCR, sgRNA lentiviral transduction, cell viability assay 2016 27708057 Systematic mapping of functional enhancer-promoter connections with CRISPR interference Homo sapiens hg19 chr8 210011000 210018000 MYC Enhancer Active Disease Erythroleukemia MONDO:0017898 DOID:0080146 Bone marrow UBERON:0002371 K562 CVCL_0004 Human erythroleukemia cell line CL:0009084 CRISPRi interference, Hi-C chromatin contact validation DNase-seq, H3K27ac ChIP-seq, RNA-seq, Pol II ChIA-PET, Hi-C RT-qPCR, sgRNA lentiviral transduction, cell viability assay 2016 27708057 Systematic mapping of functional enhancer-promoter connections with CRISPR interference Homo sapiens hg19 chr8 210024000 210032000 MYC Enhancer Active Disease Acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 K562 CVCL_0004 Human erythroleukemia cell line CL:0009084 CRISPRi interference, Hi-C chromatin contact validation DNase-seq, H3K27ac ChIP-seq, RNA-seq, Pol II ChIA-PET, Hi-C RT-qPCR, sgRNA lentiviral transduction, cell viability assay 2016 27708057 Systematic mapping of functional enhancer-promoter connections with CRISPR interference Homo sapiens hg19 chr8 210024000 210032000 MYC Enhancer Active Disease Erythroleukemia MONDO:0017898 DOID:0080146 Bone marrow UBERON:0002371 K562 CVCL_0004 Human erythroleukemia cell line CL:0009084 CRISPRi interference, Hi-C chromatin contact validation DNase-seq, H3K27ac ChIP-seq, RNA-seq, Pol II ChIA-PET, Hi-C RT-qPCR, sgRNA lentiviral transduction, cell viability assay 2016 27708057 Systematic mapping of functional enhancer-promoter connections with CRISPR interference Homo sapiens hg19 chr8 210041000 210048000 MYC Enhancer Active Disease Acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 K562 CVCL_0004 Human erythroleukemia cell line CL:0009084 CRISPRi interference, Hi-C chromatin contact validation DNase-seq, H3K27ac ChIP-seq, RNA-seq, Pol II ChIA-PET, Hi-C RT-qPCR, sgRNA lentiviral transduction, cell viability assay 2016 27708057 Systematic mapping of functional enhancer-promoter connections with CRISPR interference Homo sapiens hg19 chr8 210041000 210048000 MYC Enhancer Active Disease Erythroleukemia MONDO:0017898 DOID:0080146 Bone marrow UBERON:0002371 K562 CVCL_0004 Human erythroleukemia cell line CL:0009084 CRISPRi interference, Hi-C chromatin contact validation DNase-seq, H3K27ac ChIP-seq, RNA-seq, Pol II ChIA-PET, Hi-C RT-qPCR, sgRNA lentiviral transduction, cell viability assay 2016 27708057 Systematic mapping of functional enhancer-promoter connections with CRISPR interference Homo sapiens hg19 chr8 210055000 210063000 MYC Enhancer Active Disease Acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 K562 CVCL_0004 Human erythroleukemia cell line CL:0009084 CRISPRi interference, Hi-C chromatin contact validation DNase-seq, H3K27ac ChIP-seq, RNA-seq, Pol II ChIA-PET, Hi-C RT-qPCR, sgRNA lentiviral transduction, cell viability assay 2016 27708057 Systematic mapping of functional enhancer-promoter connections with CRISPR interference Homo sapiens hg19 chr8 210055000 210063000 MYC Enhancer Active Disease Erythroleukemia MONDO:0017898 DOID:0080146 Bone marrow UBERON:0002371 K562 CVCL_0004 Human erythroleukemia cell line CL:0009084 CRISPRi interference, Hi-C chromatin contact validation DNase-seq, H3K27ac ChIP-seq, RNA-seq, Pol II ChIA-PET, Hi-C RT-qPCR, sgRNA lentiviral transduction, cell viability assay 2016 27708057 Systematic mapping of functional enhancer-promoter connections with CRISPR interference Homo sapiens hg19 chr8 210071000 210079000 MYC Enhancer Active Disease Acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 K562 CVCL_0004 Human erythroleukemia cell line CL:0009084 CRISPRi interference, clonal genomic deletion, Hi-C chromatin contact validation DNase-seq, H3K27ac ChIP-seq, RNA-seq, Pol II ChIA-PET, Hi-C RT-qPCR, clonal cell line generation, sgRNA lentiviral transduction, cell viability assay 2016 27708057 Systematic mapping of functional enhancer-promoter connections with CRISPR interference Homo sapiens hg19 chr8 210071000 210079000 MYC Enhancer Active Disease Erythroleukemia MONDO:0017898 DOID:0080146 Bone marrow UBERON:0002371 K562 CVCL_0004 Human erythroleukemia cell line CL:0009084 CRISPRi interference, clonal genomic deletion, Hi-C chromatin contact validation DNase-seq, H3K27ac ChIP-seq, RNA-seq, Pol II ChIA-PET, Hi-C RT-qPCR, clonal cell line generation, sgRNA lentiviral transduction, cell viability assay 2018 30545847 CRISPR-mediated activation of a promoter or enhancer rescues obesity caused by haploinsufficiency Mus musculus mm10 chr10 90723100 90723900 Sim1 Enhancer Active Normal Hypothalamus UBERON:0001898 Neuro-2a CVCL_0470 Neuroblastoma cell CL:0000031 CRISPRa gain-of-function, ChIP-qPCR, in vivo transgenic reporter validation RNA-seq, ChIP-seq dual-luciferase reporter assay, stereotaxic AAV injection, qRT-PCR, transgenic mouse line generation, body weight phenotyping 2018 30545847 CRISPR-mediated activation of a promoter or enhancer rescues obesity caused by haploinsufficiency Mus musculus mm10 chr10 90723100 90723900 Sim1 Enhancer Active Disease Obesity due to Sim1 haploinsufficiency MONDO:0012649 DOID:0060282 Hypothalamus UBERON:0001898 Neuro-2a CVCL_0470 Neuroblastoma cell CL:0000031 CRISPRa gain-of-function, ChIP-qPCR, in vivo transgenic reporter validation RNA-seq, ChIP-seq dual-luciferase reporter assay, stereotaxic AAV injection, qRT-PCR, transgenic mouse line generation, body weight phenotyping 2018 30545847 CRISPR-mediated activation of a promoter or enhancer rescues obesity caused by haploinsufficiency Mus musculus mm10 chr10 90723100 90723900 Sim1 Enhancer Active Normal Hypothalamus UBERON:0001898 mouse primary hypothalamic neuron hypothalamic neuron CL:0000641 CRISPRa gain-of-function, ChIP-qPCR, in vivo transgenic reporter validation RNA-seq, ChIP-seq dual-luciferase reporter assay, stereotaxic AAV injection, qRT-PCR, transgenic mouse line generation, body weight phenotyping 2018 30545847 CRISPR-mediated activation of a promoter or enhancer rescues obesity caused by haploinsufficiency Mus musculus mm10 chr10 90723100 90723900 Sim1 Enhancer Active Disease Obesity due to Sim1 haploinsufficiency MONDO:0012649 DOID:0060282 Hypothalamus UBERON:0001898 mouse primary hypothalamic neuron hypothalamic neuron CL:0000641 CRISPRa gain-of-function, ChIP-qPCR, in vivo transgenic reporter validation RNA-seq, ChIP-seq dual-luciferase reporter assay, stereotaxic AAV injection, qRT-PCR, transgenic mouse line generation, body weight phenotyping 2024 39186674 CRISPR Screening of Transcribed Super-Enhancers Identifies Drivers of Triple-Negative Breast Cancer Progression Homo sapiens hg19 chr7 131323622 131334609 PODXL SE Active Disease Triple-negative breast cancer MONDO:0005228 DOID:0060081 Mammary gland UBERON:0001911 MDA-MB-436 CVCL_0623 Triple-negative breast cancer cell line CL:0009071 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 qRT-PCR, transwell migration assay, crystal violet proliferation assay, mouse mammary fat pad xenograft, tail vein metastasis model, IHC staining 2024 39186674 CRISPR Screening of Transcribed Super-Enhancers Identifies Drivers of Triple-Negative Breast Cancer Progression Homo sapiens hg19 chr7 131323622 131334609 PODXL SE Active Disease Triple-negative breast cancer MONDO:0005228 DOID:0060081 Mammary gland UBERON:0001911 MDA-MB-231 CVCL_0062 Triple-negative breast cancer cell line CL:0009071 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 qRT-PCR, transwell migration assay, crystal violet proliferation assay, mouse mammary fat pad xenograft, tail vein metastasis model, IHC staining 2024 39186674 CRISPR Screening of Transcribed Super-Enhancers Identifies Drivers of Triple-Negative Breast Cancer Progression Homo sapiens hg19 chr7 131323622 131334609 PODXL SE Active Disease Triple-negative breast cancer MONDO:0005228 DOID:0060081 Mammary gland UBERON:0001911 MDA-MB-468 CVCL_0419 Triple-negative breast cancer cell line CL:0009071 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 qRT-PCR, transwell migration assay, crystal violet proliferation assay, mouse mammary fat pad xenograft, tail vein metastasis model, IHC staining 2024 39186674 CRISPR Screening of Transcribed Super-Enhancers Identifies Drivers of Triple-Negative Breast Cancer Progression Homo sapiens hg19 chr2 106412871 106423516 RSAD2 SE Active Disease Triple-negative breast cancer MONDO:0005228 DOID:0060081 Mammary gland UBERON:0001911 MDA-MB-436 CVCL_0623 Triple-negative breast cancer cell line CL:0009071 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 qRT-PCR, colony formation assay, cell proliferation assay 2024 39186674 CRISPR Screening of Transcribed Super-Enhancers Identifies Drivers of Triple-Negative Breast Cancer Progression Homo sapiens hg19 chr2 106412871 106423516 CMPK2 SE Active Disease Triple-negative breast cancer MONDO:0005228 DOID:0060081 Mammary gland UBERON:0001911 MDA-MB-436 CVCL_0623 Triple-negative breast cancer cell line CL:0009071 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 qRT-PCR, colony formation assay, cell proliferation assay 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 Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 U251 CVCL_0021 glioma cell line CL:0000917 CRISPR-Cas9 full locus knockout, dCas9-KRAB CRISPRi, dual-luciferase reporter assay, 3C-qPCR, ChIP-qPCR, SNP base editing HiChIP, H3K27ac ChIP-seq, RNA-seq, scATAC-seq, GWAS variant mapping qRT-PCR, colony formation assay, glioma stem sphere assay, mouse intracranial xenograft, site-directed mutagenesis 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 Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 LN229 CVCL_0393 glioma cell line CL:0000917 CRISPR-Cas9 full locus knockout, dCas9-KRAB CRISPRi, dual-luciferase reporter assay, 3C-qPCR, ChIP-qPCR, SNP base editing HiChIP, H3K27ac ChIP-seq, RNA-seq, scATAC-seq, GWAS variant mapping qRT-PCR, colony formation assay, glioma stem sphere assay, mouse intracranial xenograft, site-directed mutagenesis 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 Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 U87 CVCL_0022 glioma cell line CL:0000917 CRISPR-Cas9 full locus knockout, dCas9-KRAB CRISPRi, dual-luciferase reporter assay, 3C-qPCR, ChIP-qPCR, SNP base editing HiChIP, H3K27ac ChIP-seq, RNA-seq, scATAC-seq, GWAS variant mapping qRT-PCR, colony formation assay, glioma stem sphere assay, mouse intracranial xenograft, site-directed mutagenesis 2025 40830415 Systematic decoding of functional enhancer connectomes and risk variants in human glioma Homo sapiens hg38 chr8 12738300 12744200 MYC Enhancer Active Disease Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 U251 CVCL_0021 glioma cell line CL:0000917 dCas9-KRAB CRISPRi, HiChIP chromatin looping validation, 3C-qPCR H3K27ac ChIP-seq, RNA-seq, pooled CRISPRi screening qRT-PCR, cell proliferation MTT assay 2025 40830415 Systematic decoding of functional enhancer connectomes and risk variants in human glioma Homo sapiens hg38 chr17 5958900 5960100 VMP1 Enhancer Active Disease Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 U251 CVCL_0021 glioma cell line CL:0000917 dCas9-KRAB CRISPRi, HiChIP chromatin looping validation, 3C-qPCR H3K27ac ChIP-seq, RNA-seq, pooled CRISPRi screening qRT-PCR, cell proliferation MTT assay 2025 40830415 Systematic decoding of functional enhancer connectomes and risk variants in human glioma Homo sapiens hg38 chr2 18910338 18911438 LAPTM4A Enhancer Active Disease Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 U251 CVCL_0021 glioma cell line CL:0000917 dCas9-KRAB CRISPRi, HiChIP chromatin looping validation H3K27ac ChIP-seq, RNA-seq, pooled CRISPRi screening qRT-PCR, cell proliferation MTT assay 2025 40830415 Systematic decoding of functional enhancer connectomes and risk variants in human glioma Homo sapiens hg38 chr2 18910338 18911438 SDC1 Enhancer Active Disease Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 U251 CVCL_0021 glioma cell line CL:0000917 dCas9-KRAB CRISPRi, HiChIP chromatin looping validation H3K27ac ChIP-seq, RNA-seq, pooled CRISPRi screening qRT-PCR, cell proliferation MTT assay 2025 40830415 Systematic decoding of functional enhancer connectomes and risk variants in human glioma Homo sapiens hg38 chr2 18910338 18911438 PUM2 Enhancer Active Disease Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 U251 CVCL_0021 glioma cell line CL:0000917 dCas9-KRAB CRISPRi, HiChIP chromatin looping validation H3K27ac ChIP-seq, RNA-seq, pooled CRISPRi screening qRT-PCR, cell proliferation MTT assay 2025 40830415 Systematic decoding of functional enhancer connectomes and risk variants in human glioma Homo sapiens hg38 chr2 18910338 18911438 RHOB Enhancer Active Disease Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 U251 CVCL_0021 glioma cell line CL:0000917 dCas9-KRAB CRISPRi, HiChIP chromatin looping validation H3K27ac ChIP-seq, RNA-seq, pooled CRISPRi screening qRT-PCR, cell proliferation MTT assay 2025 38760566 Bidirectional epigenetic editing reveals hierarchies in gene regulation Homo sapiens hg38 chr2 121923152 121923710 JUN IL2 Enhancer Active Normal Peripheral blood UBERON:0000178 Jurkat E6-1 CVCL_0367 T lymphoblast CL:0002419 CRISPRi loss-of-function, CRISPRa gain-of-function, ATAC-qPCR chromatin accessibility validation ATAC-seq, H3K27ac ChIP-seq, H3K4me1 ChIP-seq, scRNA-seq, Perturb-seq gRNA enrichment screening, intracellular cytokine flow cytometry, RT-qPCR, ATAC-qPCR, primary human T cell lentiviral transduction 2025 38760566 Bidirectional epigenetic editing reveals hierarchies in gene regulation Homo sapiens hg38 chr2 121926020 121926640 JUND IL2 Enhancer Active Normal Peripheral blood UBERON:0000178 Jurkat E6-1 CVCL_0367 T lymphoblast CL:0002419 CRISPRi loss-of-function, CRISPRa gain-of-function, ATAC-qPCR chromatin accessibility validation ATAC-seq, H3K27ac ChIP-seq, H3K4me1 ChIP-seq, scRNA-seq, Perturb-seq gRNA enrichment screening, intracellular cytokine flow cytometry, RT-qPCR, ATAC-qPCR, primary human T cell lentiviral transduction 2025 38760566 Bidirectional epigenetic editing reveals hierarchies in gene regulation Homo sapiens hg38 chr2 121926020 121926640 JUND IL2 Enhancer Active Normal Peripheral blood UBERON:0000178 primary human memory CD4 T cell memory CD4-positive T cell CL:0000897 CRISPRi loss-of-function, CRISPRa gain-of-function, ATAC-qPCR chromatin accessibility validation ATAC-seq, H3K27ac ChIP-seq, H3K4me1 ChIP-seq, scRNA-seq, Perturb-seq gRNA enrichment screening, intracellular cytokine flow cytometry, RT-qPCR, ATAC-qPCR, primary human T cell lentiviral transduction 2025 38760566 Bidirectional epigenetic editing reveals hierarchies in gene regulation Homo sapiens hg38 chr2 121928130 121928780 BATF3 IL2 Enhancer Active Normal Peripheral blood UBERON:0000178 Jurkat E6-1 CVCL_0367 T lymphoblast CL:0002419 CRISPRi loss-of-function, CRISPRa gain-of-function ATAC-seq, H3K27ac ChIP-seq, H3K4me1 ChIP-seq, scRNA-seq, Perturb-seq gRNA enrichment screening, intracellular cytokine flow cytometry, RT-qPCR 2025 38760566 Bidirectional epigenetic editing reveals hierarchies in gene regulation Homo sapiens hg38 chr12 68541220 68541790 ETV6 IFNG Enhancer Active Normal Peripheral blood UBERON:0000178 Jurkat E6-1 CVCL_0367 T lymphoblast CL:0002419 CRISPRi loss-of-function, CRISPRa gain-of-function ATAC-seq, H3K27ac ChIP-seq, scRNA-seq gRNA enrichment screening, intracellular cytokine flow cytometry, RT-qPCR 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:0003420 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell line CL:0001071 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 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:0003420 DOID:9256 Colon UBERON:0001155 SW480 CVCL_0546 colorectal carcinoma cell line CL:0001071 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 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:0003420 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell line CL:0001071 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 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:0003420 DOID:9256 Colon UBERON:0001155 SW480 CVCL_0546 colorectal carcinoma cell line CL:0001071 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 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 Silenced Disease Colorectal adenocarcinoma MONDO:0003420 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell line CL:0001071 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 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 Silenced Disease Colorectal adenocarcinoma MONDO:0003420 DOID:9256 Colon UBERON:0001155 SW480 CVCL_0546 colorectal carcinoma cell line CL:0001071 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 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:0003420 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell line CL:0001071 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 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:0003420 DOID:9256 Colon UBERON:0001155 SW480 CVCL_0546 colorectal carcinoma cell line CL:0001071 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 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 SE Active Normal Umbilical vein UBERON:0002066 HUVEC CVCL_2959 human umbilical vein endothelial cell CL:0002615 dCas9-KRAB CRISPRi loss-of-function, dual-luciferase reporter assay CUT&Tag(H3K27ac/H3K4me1/H3K4me3), ATAC-seq, RNA-seq dual-luciferase reporter detection, CRISPRi lentiviral transduction, RT-qPCR, Western blot, immunofluorescence staining 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 SE Active Normal Embryonic kidney UBERON:0002113 HEK293T CVCL_0063 human embryonic kidney cell CL:0002139 dCas9-KRAB CRISPRi loss-of-function, dual-luciferase reporter assay CUT&Tag(H3K27ac/H3K4me1/H3K4me3), ATAC-seq, RNA-seq dual-luciferase reporter detection, CRISPRi lentiviral transduction, RT-qPCR, Western blot, immunofluorescence staining 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 SE Active Disease Vascular aging Umbilical vein UBERON:0002066 HUVEC CVCL_2959 human umbilical vein endothelial cell CL:0002615 dCas9-KRAB CRISPRi loss-of-function, dual-luciferase reporter assay CUT&Tag(H3K27ac/H3K4me1/H3K4me3), ATAC-seq, RNA-seq dual-luciferase reporter detection, CRISPRi lentiviral transduction, RT-qPCR, Western blot, immunofluorescence staining 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 SE Active Disease Vascular aging Embryonic kidney UBERON:0002113 HEK293T CVCL_0063 human embryonic kidney cell CL:0002139 dCas9-KRAB CRISPRi loss-of-function, dual-luciferase reporter assay CUT&Tag(H3K27ac/H3K4me1/H3K4me3), ATAC-seq, RNA-seq dual-luciferase reporter detection, CRISPRi lentiviral transduction, RT-qPCR, Western blot, immunofluorescence staining 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 SE Active Disease Atherosclerosis MONDO:0005147 DOID:1936 Umbilical vein UBERON:0002066 HUVEC CVCL_2959 human umbilical vein endothelial cell CL:0002615 dCas9-KRAB CRISPRi loss-of-function, dual-luciferase reporter assay CUT&Tag(H3K27ac/H3K4me1/H3K4me3), ATAC-seq, RNA-seq dual-luciferase reporter detection, CRISPRi lentiviral transduction, RT-qPCR, Western blot, immunofluorescence staining 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 SE Active Disease Atherosclerosis MONDO:0005147 DOID:1936 Embryonic kidney UBERON:0002113 HEK293T CVCL_0063 human embryonic kidney cell CL:0002139 dCas9-KRAB CRISPRi loss-of-function, dual-luciferase reporter assay CUT&Tag(H3K27ac/H3K4me1/H3K4me3), ATAC-seq, RNA-seq dual-luciferase reporter detection, CRISPRi lentiviral transduction, RT-qPCR, Western blot, immunofluorescence staining 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 Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 U251 CVCL_0021 glioma cell line CL:0000917 Dual-luciferase reporter assay, CRISPR-Cas9 full locus knockout, CRISPR base editing, 3C-qPCR, ChIP-qPCR, dCas9-KRAB CRISPRi H3K27ac HiChIP, H3K27ac ChIP-seq, ATAC-seq, RNA-seq, pooled CRISPRi screening, GWAS variant analysis qRT-PCR, cell proliferation MTT assay, colony formation assay, glioma sphere formation assay, mouse intracranial xenograft, Sanger sequencing 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 Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 LN229 CVCL_0393 glioma cell line CL:0000917 Dual-luciferase reporter assay, CRISPR-Cas9 full locus knockout, CRISPR base editing, 3C-qPCR, ChIP-qPCR, dCas9-KRAB CRISPRi H3K27ac HiChIP, H3K27ac ChIP-seq, ATAC-seq, RNA-seq, pooled CRISPRi screening, GWAS variant analysis qRT-PCR, cell proliferation MTT assay, colony formation assay, glioma sphere formation assay, mouse intracranial xenograft, Sanger sequencing 2025 40830415 Systematic decoding of functional enhancer connectomes and risk variants in human glioma Homo sapiens hg38 chr20 63680793 63682109 MEIS1 RTEL1 Enhancer Active Disease Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 U251 CVCL_0021 glioma cell line CL:0000917 Dual-luciferase reporter assay, CRISPR-Cas9 full locus knockout, 3C-qPCR, ChIP-qPCR, dCas9-KRAB CRISPRi H3K27ac HiChIP, H3K27ac ChIP-seq, ATAC-seq, RNA-seq, pooled CRISPRi screening qRT-PCR, cell proliferation MTT assay, colony formation assay 2025 40830415 Systematic decoding of functional enhancer connectomes and risk variants in human glioma Homo sapiens hg38 chr20 63680793 63682109 MEIS1 RTEL1 Enhancer Active Disease Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 LN229 CVCL_0393 glioma cell line CL:0000917 Dual-luciferase reporter assay, CRISPR-Cas9 full locus knockout, 3C-qPCR, ChIP-qPCR, dCas9-KRAB CRISPRi H3K27ac HiChIP, H3K27ac ChIP-seq, ATAC-seq, RNA-seq, pooled CRISPRi screening qRT-PCR, cell proliferation MTT assay, colony formation assay 2025 40830415 Systematic decoding of functional enhancer connectomes and risk variants in human glioma Homo sapiens hg38 chr8 12738300 12744200 MYC Enhancer Active Disease Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 U251 CVCL_0021 glioma cell line CL:0000917 dCas9-KRAB CRISPRi, HiChIP chromatin looping validation, 3C-qPCR H3K27ac HiChIP, H3K27ac ChIP-seq, ATAC-seq, RNA-seq, pooled CRISPRi screening qRT-PCR, MTT cell proliferation assay 2025 40830415 Systematic decoding of functional enhancer connectomes and risk variants in human glioma Homo sapiens hg38 chr17 5958900 5960100 VMP1 Enhancer Active Disease Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 U251 CVCL_0021 glioma cell line CL:0000917 dCas9-KRAB CRISPRi, HiChIP chromatin looping validation, 3C-qPCR H3K27ac HiChIP, H3K27ac ChIP-seq, ATAC-seq, RNA-seq, pooled CRISPRi screening qRT-PCR, MTT cell proliferation assay 2025 40830415 Systematic decoding of functional enhancer connectomes and risk variants in human glioma Homo sapiens hg38 chr2 18910338 18911438 LAPTM4A Enhancer Active Disease Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 U251 CVCL_0021 glioma cell line CL:0000917 dCas9-KRAB CRISPRi, HiChIP chromatin looping validation H3K27ac HiChIP, H3K27ac ChIP-seq, ATAC-seq, RNA-seq, pooled CRISPRi screening qRT-PCR, MTT cell proliferation assay 2025 40830415 Systematic decoding of functional enhancer connectomes and risk variants in human glioma Homo sapiens hg38 chr2 18910338 18911438 SDC1 Enhancer Active Disease Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 U251 CVCL_0021 glioma cell line CL:0000917 dCas9-KRAB CRISPRi, HiChIP chromatin looping validation H3K27ac HiChIP, H3K27ac ChIP-seq, ATAC-seq, RNA-seq, pooled CRISPRi screening qRT-PCR, MTT cell proliferation assay 2025 40830415 Systematic decoding of functional enhancer connectomes and risk variants in human glioma Homo sapiens hg38 chr2 18910338 18911438 PUM2 Enhancer Active Disease Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 U251 CVCL_0021 glioma cell line CL:0000917 dCas9-KRAB CRISPRi, HiChIP chromatin looping validation H3K27ac HiChIP, H3K27ac ChIP-seq, ATAC-seq, RNA-seq, pooled CRISPRi screening qRT-PCR, MTT cell proliferation assay 2025 40830415 Systematic decoding of functional enhancer connectomes and risk variants in human glioma Homo sapiens hg38 chr2 18910338 18911438 RHOB Enhancer Active Disease Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 U251 CVCL_0021 glioma cell line CL:0000917 dCas9-KRAB CRISPRi, HiChIP chromatin looping validation H3K27ac HiChIP, H3K27ac ChIP-seq, ATAC-seq, RNA-seq, pooled CRISPRi screening qRT-PCR, MTT cell proliferation assay 2025 41120733 Enhancer activation from transposable elements in extrachromosomal DNA Homo sapiens hg19 chr3 111274001 111275000 MYC Enhancer Active Disease Colorectal adenocarcinoma MONDO:0003420 DOID:9256 Colon UBERON:0001155 COLO320DM CVCL_0219 colorectal carcinoma cell line CL:0001071 Dual-luciferase reporter assay, dCas9-KRAB CRISPRi loss-of-function, Hi-C chromatin contact mapping, ORCA single-cell chromatin imaging H3K27ac ChIP-seq, ATAC-seq, Nanopore long-read WGS, RNA-seq, pooled CRISPRi screening NanoLuc dual luciferase detection, CRISPR-CATCH PFGE isolation, RT-qPCR, RNA-FISH, cell proliferation MTT assay 2025 41120733 Enhancer activation from transposable elements in extrachromosomal DNA Homo sapiens hg19 chr3 111274001 111275000 MYC Enhancer Active Disease Colorectal adenocarcinoma MONDO:0003420 DOID:9256 Colon UBERON:0001155 COLO320HSR CVCL_0221 colorectal carcinoma cell line CL:0001071 Dual-luciferase reporter assay, dCas9-KRAB CRISPRi loss-of-function, Hi-C chromatin contact mapping, ORCA single-cell chromatin imaging H3K27ac ChIP-seq, ATAC-seq, Nanopore long-read WGS, RNA-seq, pooled CRISPRi screening NanoLuc dual luciferase detection, CRISPR-CATCH PFGE isolation, RT-qPCR, RNA-FISH, cell proliferation MTT assay 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 Definitive endoderm UBERON:0005425 HUES8 CVCL_B207 human embryonic stem cell CL:0000335 dCas9-KRAB CRISPRi loss-of-function, Hi-C chromatin contact validation ATAC-seq, H3K27ac ChIP-seq, RNA-seq, scRNA-seq, pooled CRISPRi screening RT-qPCR, FACS flow cytometry, lentiviral transduction, single enhancer clonal CRISPR-Cas9 deletion 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 Definitive endoderm UBERON:0005425 HUES8 CVCL_B207 human embryonic stem cell CL:0000335 dCas9-KRAB CRISPRi loss-of-function, Hi-C chromatin contact validation ATAC-seq, H3K27ac ChIP-seq, RNA-seq, scRNA-seq, pooled CRISPRi screening RT-qPCR, FACS flow cytometry, lentiviral transduction 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 Definitive endoderm UBERON:0005425 HUES8 CVCL_B207 human embryonic stem cell CL:0000335 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 RT-qPCR, FACS flow cytometry, lentiviral transduction, dual clonal enhancer knockout generation 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 Definitive endoderm UBERON:0005425 HUES8 CVCL_B207 human embryonic stem cell CL:0000335 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 RT-qPCR, FACS flow cytometry, lentiviral transduction, dual clonal enhancer knockout generation 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 Definitive endoderm UBERON:0005425 HUES8 CVCL_B207 human embryonic stem cell CL:0000335 dCas9-KRAB CRISPRi loss-of-function, Hi-C chromatin contact validation ATAC-seq, H3K27ac ChIP-seq, RNA-seq, scRNA-seq, pooled CRISPRi screening RT-qPCR, FACS flow cytometry, lentiviral transduction 2021 34040254 Enhancer release and retargeting activates disease-susceptibility genes Homo sapiens hg19 chr21 43361800 43362620 ESR1 TFF1 Enhancer Active Normal Mammary gland UBERON:0001911 MCF-7 CVCL_0031 estrogen-responsive breast epithelial cell CL:0001070 CRISPR-Cas9 locus deletion, 4C-seq chromatin interaction, ChIP-qPCR, siRNA cohesin knockdown GRO-seq, CTCF ChIA-PET, H3K4me3/H3K4me1 ChIP-seq RT-qPCR, clonal cell line generation, chromatin immunoprecipitation 2021 34040254 Enhancer release and retargeting activates disease-susceptibility genes Homo sapiens hg19 chr21 43361800 43362620 FOXA1 TFF1 Enhancer Active Normal Mammary gland UBERON:0001911 MCF-7 CVCL_0031 estrogen-responsive breast epithelial cell CL:0001070 CRISPR-Cas9 locus deletion, 4C-seq chromatin interaction, ChIP-qPCR, siRNA cohesin knockdown GRO-seq, CTCF ChIA-PET, H3K4me3/H3K4me1 ChIP-seq RT-qPCR, clonal cell line generation, chromatin immunoprecipitation 2021 34040254 Enhancer release and retargeting activates disease-susceptibility genes Homo sapiens hg19 chr11 72968100 72968850 ESR1 P2RY2 Enhancer Active Normal Mammary gland UBERON:0001911 MCF-7 CVCL_0031 estrogen-responsive breast epithelial cell CL:0001070 CRISPR-Cas9 promoter knockout, 4C-seq chromatin looping, ChIP-qPCR GRO-seq, CTCF ChIP-seq, histone ChIP-seq RT-qPCR, siRNA-mediated cohesin depletion 2021 34040254 Enhancer release and retargeting activates disease-susceptibility genes Homo sapiens hg19 chr11 72968100 72968850 FOXA1 P2RY2 Enhancer Active Normal Mammary gland UBERON:0001911 MCF-7 CVCL_0031 estrogen-responsive breast epithelial cell CL:0001070 CRISPR-Cas9 promoter knockout, 4C-seq chromatin looping, ChIP-qPCR GRO-seq, CTCF ChIP-seq, histone ChIP-seq RT-qPCR, siRNA-mediated cohesin depletion 2021 34040254 Enhancer release and retargeting activates disease-susceptibility genes Homo sapiens hg19 chr6 38991200 38991920 ESR1 KCNK5 Enhancer Active Normal Mammary gland UBERON:0001911 MCF-7 CVCL_0031 estrogen-responsive breast epithelial cell CL:0001070 CRISPR-Cas9 promoter deletion, 4C-seq chromatin contact validation, ChIP-qPCR GRO-seq, CTCF ChIP-seq, H3K4me1 ChIP-seq RT-qPCR, clonal isogenic clone culture 2021 34040254 Enhancer release and retargeting activates disease-susceptibility genes Homo sapiens hg19 chr6 38991200 38991920 FOXA1 KCNK5 Enhancer Active Normal Mammary gland UBERON:0001911 MCF-7 CVCL_0031 estrogen-responsive breast epithelial cell CL:0001070 CRISPR-Cas9 promoter deletion, 4C-seq chromatin contact validation, ChIP-qPCR GRO-seq, CTCF ChIP-seq, H3K4me1 ChIP-seq RT-qPCR, clonal isogenic clone culture 2021 34040254 Enhancer release and retargeting activates disease-susceptibility genes Homo sapiens hg19 chr11 100842300 100843050 ESR1 PGR Enhancer Active Normal Mammary gland UBERON:0001911 MCF-7 CVCL_0031 estrogen-responsive breast epithelial cell CL:0001070 CRISPR promoter knockout, 4C-seq, ChIP-qPCR GRO-seq, CTCF ChIP-seq, histone profiling RT-qPCR, cohesin siRNA knockdown 2021 34040254 Enhancer release and retargeting activates disease-susceptibility genes Homo sapiens hg19 chr11 100842300 100843050 FOXA1 PGR Enhancer Active Normal Mammary gland UBERON:0001911 MCF-7 CVCL_0031 estrogen-responsive breast epithelial cell CL:0001070 CRISPR promoter knockout, 4C-seq, ChIP-qPCR GRO-seq, CTCF ChIP-seq, histone profiling RT-qPCR, cohesin siRNA knockdown 2021 34040254 Enhancer release and retargeting activates disease-susceptibility genes Homo sapiens hg19 chr13 73096200 73097010 TERT Enhancer Active Disease Melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 HEK293T CVCL_0063 human embryonic kidney cell CL:0002139 CRISPRi promoter inhibition, CRISPR-Cas9 SNP knock-in, 4C-seq chromatin looping H3K27ac ChIP-seq, whole-genome cancer mutation data RT-qPCR, ChIP-qPCR for CTCF binding 2021 34040254 Enhancer release and retargeting activates disease-susceptibility genes Homo sapiens hg19 chr13 73096200 73097010 TERT Enhancer Active Disease Lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 HEK293T CVCL_0063 human embryonic kidney cell CL:0002139 CRISPRi promoter inhibition, CRISPR-Cas9 SNP knock-in, 4C-seq chromatin looping H3K27ac ChIP-seq, whole-genome cancer mutation data RT-qPCR, ChIP-qPCR for CTCF binding 2021 34040254 Enhancer release and retargeting activates disease-susceptibility genes Homo sapiens hg19 chr19 19942100 19942880 PAX5 Enhancer Active Disease B-cell non-Hodgkin lymphoma MONDO:0018907 DOID:0050140 Bone marrow UBERON:0002371 MCF-7 CVCL_0031 breast epithelial cell CL:0001070 CRISPRi ZCCHC7 promoter silencing, Hi-C chromatin contact validation ATAC-seq, cancer WGS datasets RT-qPCR gene expression quantification 2021 34040254 Enhancer release and retargeting activates disease-susceptibility genes Homo sapiens hg19 chr8 128745000 128752600 MYC Enhancer Active Disease Cancer MONDO:0005084 DOID:162 Epithelium UBERON:0000483 MCF-7 CVCL_0031 breast epithelial cell CL:0001070 CRISPRi PVT promoter repression, Hi-C chromatin mapping H3K27ac ChIP-seq, GTEx eQTL data RT-qPCR oncogene expression measurement 2021 34040254 Enhancer release and retargeting activates disease-susceptibility genes Homo sapiens hg19 chr1 205814100 205814900 RAB7L1 Enhancer Active Disease Parkinson's disease MONDO:0004773 DOID:1432 Brain UBERON:0000955 iPSC-derived NPC neural progenitor cell CL:0000060 dCas9-KRAB enhancer silencing, allele-specific 4C-seq, ChIP-qPCR CTCF binding scRNA-seq, H3K27ac ChIP-seq, GTEx eQTL profiling RT-qPCR allelic expression assay 2024 39294132 Multiplex single-cell CRISPRa screening for cell type specific regulatory elements Homo sapiens hg38 chr12 88624101 88624740 ANXA1 Enhancer Active Disease Chronic myelogenous leukemia MONDO:0004990 DOID:8552 Bone marrow UBERON:0002371 K562 CVCL_0004 erythroleukemia cell CL:0001054 CRISPRa gain-of-function perturbation, single-cell RNA-seq functional validation scRNA-seq, ATAC-seq, H3K27ac CUT&RUN, pooled CRISPR screening bulk RNA-seq singleton validation, lentiviral gRNA transduction, RT-qPCR 2024 39294132 Multiplex single-cell CRISPRa screening for cell type specific regulatory elements Homo sapiens hg38 chr12 43108222 43108860 ASIC1 Enhancer Active Disease Chronic myelogenous leukemia MONDO:0004990 DOID:8552 Bone marrow UBERON:0002371 K562 CVCL_0004 erythroleukemia cell CL:0001054 CRISPRa gain-of-function perturbation, single-cell RNA-seq functional validation scRNA-seq, ATAC-seq, H3K27ac CUT&RUN, pooled CRISPR screening bulk RNA-seq singleton validation, lentiviral gRNA transduction, RT-qPCR 2024 39294132 Multiplex single-cell CRISPRa screening for cell type specific regulatory elements Homo sapiens hg38 chr12 64791312 64791930 HMGA1 Enhancer Active Normal Brain UBERON:0000955 WTC11 iPSC-neuron excitatory iPSC-derived neuron CL:0002358 CRISPRa gain-of-function perturbation, single-cell RNA-seq validation scRNA-seq, neuronal ATAC-seq, H3K27ac CUT&RUN, pooled CRISPR screening bulk RNA-seq singleton validation, iPSC differentiation, lentiviral transduction, RT-qPCR 2024 39294132 Multiplex single-cell CRISPRa screening for cell type specific regulatory elements Homo sapiens hg38 chr12 64791312 64791930 HMGA1 Enhancer Active Disease Neurodevelopmental disorder MONDO:0007186 Brain UBERON:0000955 WTC11 iPSC-neuron excitatory iPSC-derived neuron CL:0002358 CRISPRa gain-of-function perturbation, single-cell RNA-seq validation scRNA-seq, neuronal ATAC-seq, H3K27ac CUT&RUN, pooled CRISPR screening bulk RNA-seq singleton validation, iPSC differentiation, lentiviral transduction, RT-qPCR 2024 39294132 Multiplex single-cell CRISPRa screening for cell type specific regulatory elements Homo sapiens hg38 chr12 64791312 64791930 HMGA1 Enhancer Active Disease Chronic myelogenous leukemia MONDO:0004990 DOID:8552 Bone marrow UBERON:0002371 K562 CVCL_0004 erythroleukemia cell CL:0001054 CRISPRa gain-of-function perturbation, single-cell RNA-seq validation scRNA-seq, neuronal ATAC-seq, H3K27ac CUT&RUN, pooled CRISPR screening bulk RNA-seq singleton validation, iPSC differentiation, lentiviral transduction, RT-qPCR 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 Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 U251 CVCL_0021 glioma cell line CL:0000917 CRISPR-Cas9 full locus knockout, CRISPR base editing, dual-luciferase reporter assay, 3C-qPCR, HiChIP, ChIP-qPCR H3K27ac HiChIP, H3K27ac ChIP-seq, RNA-seq, pooled CRISPRi screening RT-qPCR, MTT proliferation assay, colony formation assay, glioma sphere formation assay, intracranial mouse xenograft, Sanger sequencing 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 Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 LN229 CVCL_0393 glioma cell line CL:0000917 CRISPR-Cas9 full locus knockout, CRISPR base editing, dual-luciferase reporter assay, 3C-qPCR, HiChIP, ChIP-qPCR H3K27ac HiChIP, H3K27ac ChIP-seq, RNA-seq, pooled CRISPRi screening RT-qPCR, MTT proliferation assay, colony formation assay, glioma sphere formation assay, intracranial mouse xenograft, Sanger sequencing 2025 40830415 Systematic decoding of functional enhancer connectomes and risk variants in human glioma Homo sapiens hg38 chr20 63680793 63682109 MEIS1 RTEL1 Enhancer Active Disease Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 U251 CVCL_0021 glioma cell line CL:0000917 CRISPR-Cas9 full locus knockout, 3C-qPCR, HiChIP, ChIP-qPCR H3K27ac HiChIP, H3K27ac ChIP-seq, RNA-seq, pooled CRISPRi screening RT-qPCR, MTT proliferation assay 2025 40830415 Systematic decoding of functional enhancer connectomes and risk variants in human glioma Homo sapiens hg38 chr20 63680793 63682109 MEIS1 RTEL1 Enhancer Active Disease Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 LN229 CVCL_0393 glioma cell line CL:0000917 CRISPR-Cas9 full locus knockout, 3C-qPCR, HiChIP, ChIP-qPCR H3K27ac HiChIP, H3K27ac ChIP-seq, RNA-seq, pooled CRISPRi screening RT-qPCR, MTT proliferation assay 2025 40830415 Systematic decoding of functional enhancer connectomes and risk variants in human glioma Homo sapiens hg38 chr8 12738300 12744200 MYC Enhancer Active Disease Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 U251 CVCL_0021 glioma cell line CL:0000917 dCas9-KRAB CRISPRi, HiChIP chromatin looping validation, 3C-qPCR H3K27ac HiChIP, H3K27ac ChIP-seq, RNA-seq, pooled CRISPRi screening RT-qPCR, MTT cell proliferation assay 2025 40830415 Systematic decoding of functional enhancer connectomes and risk variants in human glioma Homo sapiens hg38 chr17 5958900 5960100 VMP1 Enhancer Active Disease Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 U251 CVCL_0021 glioma cell line CL:0000917 dCas9-KRAB CRISPRi, HiChIP chromatin looping validation, 3C-qPCR H3K27ac HiChIP, H3K27ac ChIP-seq, RNA-seq, pooled CRISPRi screening RT-qPCR, MTT cell proliferation assay 2025 40830415 Systematic decoding of functional enhancer connectomes and risk variants in human glioma Homo sapiens hg38 chr2 18910338 18911438 LAPTM4A Enhancer Active Disease Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 U251 CVCL_0021 glioma cell line CL:0000917 dCas9-KRAB CRISPRi, HiChIP chromatin looping validation H3K27ac HiChIP, H3K27ac ChIP-seq, RNA-seq, pooled CRISPRi screening RT-qPCR, MTT cell proliferation assay 2025 40830415 Systematic decoding of functional enhancer connectomes and risk variants in human glioma Homo sapiens hg38 chr2 18910338 18911438 SDC1 Enhancer Active Disease Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 U251 CVCL_0021 glioma cell line CL:0000917 dCas9-KRAB CRISPRi, HiChIP chromatin looping validation H3K27ac HiChIP, H3K27ac ChIP-seq, RNA-seq, pooled CRISPRi screening RT-qPCR, MTT cell proliferation assay 2025 40830415 Systematic decoding of functional enhancer connectomes and risk variants in human glioma Homo sapiens hg38 chr2 18910338 18911438 PUM2 Enhancer Active Disease Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 U251 CVCL_0021 glioma cell line CL:0000917 dCas9-KRAB CRISPRi, HiChIP chromatin looping validation H3K27ac HiChIP, H3K27ac ChIP-seq, RNA-seq, pooled CRISPRi screening RT-qPCR, MTT cell proliferation assay 2025 40830415 Systematic decoding of functional enhancer connectomes and risk variants in human glioma Homo sapiens hg38 chr2 18910338 18911438 RHOB Enhancer Active Disease Glioblastoma multiforme MONDO:0001628 DOID:3088 Brain UBERON:0000955 U251 CVCL_0021 glioma cell line CL:0000917 dCas9-KRAB CRISPRi, HiChIP chromatin looping validation H3K27ac HiChIP, H3K27ac ChIP-seq, RNA-seq, pooled CRISPRi screening RT-qPCR, MTT cell proliferation assay 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 SE Active Disease Vascular aging MONDO:0024530 DOID:0080000 Umbilical vein UBERON:0002066 HUVEC CVCL_2959 human umbilical vein endothelial cell CL:0002615 dCas9-KRAB CRISPRi loss-of-function, dual-luciferase reporter assay CUT&Tag(H3K27ac/H3K4me1/H3K4me3), ATAC-seq, RNA-seq dual-luciferase reporter detection, CRISPRi lentiviral transduction, RT-qPCR, Western blot, immunofluorescence staining 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 SE Active Disease Vascular aging MONDO:0024530 DOID:0080000 Embryonic kidney UBERON:0002113 HEK293T CVCL_0063 human embryonic kidney cell CL:0002139 dCas9-KRAB CRISPRi loss-of-function, dual-luciferase reporter assay CUT&Tag(H3K27ac/H3K4me1/H3K4me3), ATAC-seq, RNA-seq dual-luciferase reporter detection, CRISPRi lentiviral transduction, RT-qPCR, Western blot, immunofluorescence staining 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 SESN3 SE Active Normal Umbilical vein UBERON:0002066 HUVEC CVCL_2959 human umbilical vein endothelial cell CL:0002615 dCas9-KRAB CRISPRi loss-of-function, dual-luciferase reporter assay, CUT&Tag-qPCR CUT&Tag(H3K27ac/H3K4me1/H3K4me3), ATAC-seq, RNA-seq dual-luciferase reporter detection, CRISPRi lentiviral transduction, RT-qPCR, Western blot, immunofluorescence staining, DNA-FISH 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 SESN3 SE Active Normal Embryonic kidney UBERON:0002113 HEK293T CVCL_0063 human embryonic kidney cell CL:0002139 dCas9-KRAB CRISPRi loss-of-function, dual-luciferase reporter assay, CUT&Tag-qPCR CUT&Tag(H3K27ac/H3K4me1/H3K4me3), ATAC-seq, RNA-seq dual-luciferase reporter detection, CRISPRi lentiviral transduction, RT-qPCR, Western blot, immunofluorescence staining, DNA-FISH 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 SESN3 SE Active Disease Vascular aging MONDO:0024530 DOID:0080000 Umbilical vein UBERON:0002066 HUVEC CVCL_2959 human umbilical vein endothelial cell CL:0002615 dCas9-KRAB CRISPRi loss-of-function, dual-luciferase reporter assay, CUT&Tag-qPCR CUT&Tag(H3K27ac/H3K4me1/H3K4me3), ATAC-seq, RNA-seq dual-luciferase reporter detection, CRISPRi lentiviral transduction, RT-qPCR, Western blot, immunofluorescence staining, DNA-FISH 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 SESN3 SE Active Disease Vascular aging MONDO:0024530 DOID:0080000 Embryonic kidney UBERON:0002113 HEK293T CVCL_0063 human embryonic kidney cell CL:0002139 dCas9-KRAB CRISPRi loss-of-function, dual-luciferase reporter assay, CUT&Tag-qPCR CUT&Tag(H3K27ac/H3K4me1/H3K4me3), ATAC-seq, RNA-seq dual-luciferase reporter detection, CRISPRi lentiviral transduction, RT-qPCR, Western blot, immunofluorescence staining, DNA-FISH 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 SESN3 SE Active Disease Atherosclerosis MONDO:0005147 DOID:1936 Umbilical vein UBERON:0002066 HUVEC CVCL_2959 human umbilical vein endothelial cell CL:0002615 dCas9-KRAB CRISPRi loss-of-function, dual-luciferase reporter assay, CUT&Tag-qPCR CUT&Tag(H3K27ac/H3K4me1/H3K4me3), ATAC-seq, RNA-seq dual-luciferase reporter detection, CRISPRi lentiviral transduction, RT-qPCR, Western blot, immunofluorescence staining, DNA-FISH 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 SESN3 SE Active Disease Atherosclerosis MONDO:0005147 DOID:1936 Embryonic kidney UBERON:0002113 HEK293T CVCL_0063 human embryonic kidney cell CL:0002139 dCas9-KRAB CRISPRi loss-of-function, dual-luciferase reporter assay, CUT&Tag-qPCR CUT&Tag(H3K27ac/H3K4me1/H3K4me3), ATAC-seq, RNA-seq dual-luciferase reporter detection, CRISPRi lentiviral transduction, RT-qPCR, Western blot, immunofluorescence staining, DNA-FISH 2024 39312195 Selective Enhancer Gain of Function Deregulates MYC Expression in Multiple Myeloma Homo sapiens hg38 chr8 128900000 128900620 IRF4 MYC Enhancer Active Disease Multiple myeloma MONDO:0009696 DOID:9538 Bone marrow UBERON:0002371 ANBL6 CVCL_5425 multiple myeloma cell line CL:0007783 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 transduction, dual-luciferase quantification, clonal cell culture 2024 39312195 Selective Enhancer Gain of Function Deregulates MYC Expression in Multiple Myeloma Homo sapiens hg38 chr8 128900000 128900620 MAF MYC Enhancer Active Disease Multiple myeloma MONDO:0009696 DOID:9538 Bone marrow UBERON:0002371 ANBL6 CVCL_5425 multiple myeloma cell line CL:0007783 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 transduction, dual-luciferase quantification, clonal cell culture 2024 39312195 Selective Enhancer Gain of Function Deregulates MYC Expression in Multiple Myeloma Homo sapiens hg38 chr8 12890650 12891240 MYC Enhancer Active Disease Multiple myeloma MONDO:0009696 DOID:9538 Bone marrow UBERON:0002371 ANBL6 CVCL_5425 multiple myeloma cell line CL:0007783 dCas9-KRAB CRISPRi, Micro-C chromatin contact validation H3K27ac ChIP-seq, ATAC-seq, WGS, RNA-seq, pooled CRISPRi tiling screen qRT-PCR, sgRNA lentiviral transduction 2024 39312195 Selective Enhancer Gain of Function Deregulates MYC Expression in Multiple Myeloma Homo sapiens hg38 chr8 12891280 12891910 MYC Enhancer Active Disease Multiple myeloma MONDO:0009696 DOID:9538 Bone marrow UBERON:0002371 ANBL6 CVCL_5425 multiple myeloma cell line CL:0007783 dCas9-KRAB CRISPRi, Micro-C chromatin contact validation H3K27ac ChIP-seq, ATAC-seq, WGS, RNA-seq, pooled CRISPRi tiling screen qRT-PCR, sgRNA lentiviral transduction 2024 39312195 Selective Enhancer Gain of Function Deregulates MYC Expression in Multiple Myeloma Homo sapiens hg38 chr8 12891950 12892610 IRF4 MYC Enhancer Active Disease Multiple myeloma MONDO:0009696 DOID:9538 Bone marrow UBERON:0002371 ANBL6 CVCL_5425 multiple myeloma cell line CL:0007783 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 transduction, dual-luciferase quantification 2024 39312195 Selective Enhancer Gain of Function Deregulates MYC Expression in Multiple Myeloma Homo sapiens hg38 chr8 12891950 12892610 MAF MYC Enhancer Active Disease Multiple myeloma MONDO:0009696 DOID:9538 Bone marrow UBERON:0002371 ANBL6 CVCL_5425 multiple myeloma cell line CL:0007783 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 transduction, dual-luciferase quantification 2024 39312195 Selective Enhancer Gain of Function Deregulates MYC Expression in Multiple Myeloma Homo sapiens hg38 chr8 12891950 12892610 SPIB MYC Enhancer Active Disease Multiple myeloma MONDO:0009696 DOID:9538 Bone marrow UBERON:0002371 ANBL6 CVCL_5425 multiple myeloma cell line CL:0007783 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 2020 32188707 Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies Homo sapiens hg19 chr12 25538405 25539356 PPARG KRAS Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 AML cell line myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, Hi-C, RNA-seq, ATAC-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, CRISPRa, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2020 32188707 Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies Homo sapiens hg19 chr12 25538405 25539356 PPARG KRAS Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 CD34+ HSPCs CD34-positive hematopoietic stem cell CL:0001029 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, Hi-C, RNA-seq, ATAC-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, CRISPRa, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2020 32188707 Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies Homo sapiens hg19 chr12 25538405 25539356 PPARG KRAS Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 Primary AML cells primary acute myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, Hi-C, RNA-seq, ATAC-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, CRISPRa, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2020 32188707 Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies Homo sapiens hg19 chr2 23820300 23821251 PPARG PER2 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 AML cell line myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, Hi-C, RNA-seq, ATAC-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, CRISPRa, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2020 32188707 Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies Homo sapiens hg19 chr2 23820300 23821251 PPARG PER2 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 CD34+ HSPCs CD34-positive hematopoietic stem cell CL:0001029 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, Hi-C, RNA-seq, ATAC-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, CRISPRa, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2020 32188707 Noncoding Variants Connect Enhancer Dysregulation with Nuclear Receptor Signaling in Hematopoietic Malignancies Homo sapiens hg19 chr2 23820300 23821251 PPARG PER2 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 Primary AML cells primary acute myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, Hi-C, RNA-seq, ATAC-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, CRISPRa, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 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 Airway epithelium UBERON:0003684 SAEC small airway epithelial cell CL:0002591 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay 4C-seq, ChIP-seq, RNA-seq CRISPRi, CRISPRa, ChIP-RT-qPCR, Luciferase reporter assay, RT-RT-qPCR 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 Nasal epithelium UBERON:0005384 HNECs nasal epithelial cell CL:1001567 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay 4C-seq, ChIP-seq, RNA-seq CRISPRi, CRISPRa, ChIP-RT-qPCR, Luciferase reporter assay, RT-RT-qPCR 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 Embryonic Kidney UBERON:0002113 HEK293T CVCL_0063 embryonic kidney cell CL:0002139 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay 4C-seq, ChIP-seq, RNA-seq CRISPRi, CRISPRa, ChIP-RT-qPCR, Luciferase reporter assay, RT-RT-qPCR 2022 34605909 Functional annotation and investigation of the 10q2433 melanoma risk locus identifies a common variant that influences transcriptional regulation of OBFC1 Homo sapiens hg19 chr10 105668100 105669000 MEOX2 OBFC1 Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 A375 CVCL_0132 melanoma cell CL:0002573 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq Luciferase Reporter Assay, 3C, CRISPR Knockout, RT-RT-qPCR, Western blot, ChIP-RT-qPCR 2022 34605909 Functional annotation and investigation of the 10q2433 melanoma risk locus identifies a common variant that influences transcriptional regulation of OBFC1 Homo sapiens hg19 chr10 105668100 105669000 MEOX2 OBFC1 Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 CJM CVCL_8663 melanoma cell CL:0002573 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq Luciferase Reporter Assay, 3C, CRISPR Knockout, RT-RT-qPCR, Western blot, ChIP-RT-qPCR 2022 34605909 Functional annotation and investigation of the 10q2433 melanoma risk locus identifies a common variant that influences transcriptional regulation of OBFC1 Homo sapiens hg19 chr10 105668100 105669000 MEOX2 OBFC1 Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 UACC1816 melanoma cell CL:0002573 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq Luciferase Reporter Assay, 3C, CRISPR Knockout, RT-RT-qPCR, Western blot, ChIP-RT-qPCR 2022 34605909 Functional annotation and investigation of the 10q2433 melanoma risk locus identifies a common variant that influences transcriptional regulation of OBFC1 Homo sapiens hg19 chr10 105668100 105669000 MEOX2 OBFC1 Enhancer Active Normal Neural Crest UBERON:0002349 Human Neural Crest Cells neural crest cell CL:0000333 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq Luciferase Reporter Assay, 3C, CRISPR Knockout, RT-RT-qPCR, Western blot, ChIP-RT-qPCR 2022 34605909 Functional annotation and investigation of the 10q2433 melanoma risk locus identifies a common variant that influences transcriptional regulation of OBFC1 Homo sapiens hg19 chr10 105668100 105669000 MEOX2 OBFC1 Enhancer Active Disease esophageal squamous cell carcinoma MONDO:0005082 DOID:3748 Esophagus UBERON:0001043 KYSE140 CVCL_1347 esophageal squamous cell carcinoma cell CL:0000069 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq Luciferase Reporter Assay, 3C, CRISPR Knockout, RT-RT-qPCR, Western blot, ChIP-RT-qPCR 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 breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 CVCL_0062 breast carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq, Hi-C CRISPRi, Luciferase Reporter Assay, RT-RT-qPCR, ChIP-RT-qPCR 2021 34040254 Enhancer release and retargeting activates disease-susceptibility genes Homo sapiens hg19 chr20 50027744 50030383 SNAI1 Enhancer Active Disease glioblastoma MONDO:0005142 DOID:3070 Brain UBERON:0000955 U-87 MG CVCL_0022 glioblastoma cell CL:0000127 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq, 3C-seq CRISPRi, Luciferase Reporter Assay 2021 34153138 A Functional Variant on 9p213 Related to Glioma Risk Affects Enhancer Activity and Modulates Expression of CDKN2B-AS1 Homo sapiens hg19 chr9 22102683 22103683 CDKN2B-AS1 Enhancer Active Disease glioblastoma MONDO:0005142 DOID:3070 Brain UBERON:0000955 U-118 MG CVCL_0633 glioblastoma cell CL:0000127 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR 2021 34153138 A Functional Variant on 9p213 Related to Glioma Risk Affects Enhancer Activity and Modulates Expression of CDKN2B-AS1 Homo sapiens hg19 chr9 22102683 22103683 CDKN2B-AS1 Enhancer Active Normal Brain UBERON:0000955 Neural progenitor cells neural progenitor cell CL:0002672 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR 2021 34153138 A Functional Variant on 9p213 Related to Glioma Risk Affects Enhancer Activity and Modulates Expression of CDKN2B-AS1 Homo sapiens hg19 chr9 22102683 22103683 CDKN2B-AS1 Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervical Epithelium UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR 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 Cranial neural crest UBERON:0003099 hCNCC cells cranial neural crest cell CL:0000333 Chromatin interaction assay, Functional perturbation assay Hi-C, ChIP-seq CRISPRi, Luciferase Reporter Assay, RT-RT-qPCR 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 Cranial neural crest UBERON:0003099 hCNCC cranial neural crest cell CL:0000333 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, 3C-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR 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 Peripheral Blood UBERON:0000178 SC monocyte-derived cells monocyte-derived cell CL:0000576 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, ATAC-seq, Hi-C, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay, CRISPR Knockout, EMSA, ChIP-RT-qPCR, RT-RT-qPCR 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 prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 Human prostate carcinoma cell prostate carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq, ATAC-seq Luciferase Reporter Assay, 3C assay, 4C assay, CRISPR Knockout, CRISPRi, CRISPRa, RT-RT-qPCR, Western blot, EMSA, ChIP-RT-qPCR 2021 34911936 Androgen receptor and MYC equilibration centralizes on developmental super-enhancer Homo sapiens hg19 chr8 128750000 129000000 AR MYC Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF7 CVCL_0031 breast carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, HiChIP, 4C-seq, ATAC-seq CRISPR knockout, RT-RT-qPCR, 3C-ddPCR, Western blot 2016 26776159 A p53-bound enhancer region controls a long intergenic noncoding RNA required for p53 stress response Homo sapiens hg19 chr9 94700500 94701500 TP53 LINC00475 Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 MALME-3M CVCL_1438 melanoma cell CL:0002573 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, GRO-seq, RNA-seq, 4C-seq Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR, CRISPR knockout, Western blot, Flow cytometry, Immunofluorescence, Northern blot 2016 26776159 A p53-bound enhancer region controls a long intergenic noncoding RNA required for p53 stress response Homo sapiens hg19 chr9 94700500 94701500 TP53 LOC100128076 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 ZR-75-1 CVCL_0588 breast carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, GRO-seq, RNA-seq, 4C-seq Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR, CRISPR knockout, Western blot, Flow cytometry, Immunofluorescence, Northern blot 2016 26776159 A p53-bound enhancer region controls a long intergenic noncoding RNA required for p53 stress response Homo sapiens hg19 chr9 94700500 94701500 TP53 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 T-47D CVCL_0553 breast carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, GRO-seq, RNA-seq, 4C-seq Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR, CRISPR knockout, Western blot, Flow cytometry, Immunofluorescence, Northern blot 2016 26776159 A p53-bound enhancer region controls a long intergenic noncoding RNA required for p53 stress response Homo sapiens hg19 chr9 94700500 94701500 TP53 Enhancer Active Normal Skin UBERON:0000014 BJ fibroblasts CVCL_3653 fibroblast CL:0000057 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, GRO-seq, RNA-seq, 4C-seq Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR, CRISPR knockout, Western blot, Flow cytometry, Immunofluorescence, Northern blot 2016 26776159 A p53-bound enhancer region controls a long intergenic noncoding RNA required for p53 stress response Homo sapiens hg19 chr9 94700500 94701500 TP53 Enhancer Active Disease tongue squamous cell carcinoma MONDO:0005084 DOID:8648 Tongue UBERON:0001723 Cal27 CVCL_1107 tongue squamous cell carcinoma cell CL:0000069 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, GRO-seq, RNA-seq, 4C-seq Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR, CRISPR knockout, Western blot, Flow cytometry, Immunofluorescence, Northern blot 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 SE Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepG2 CVCL_0027 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, ATAC-seq ChIP-RT-qPCR, CRISPRi, Luciferase Reporter Assay, qRT-PCR, Western blot, co-IP 2022 35264579 An enhancer variant at 16q221 predisposes to hepatocellular carcinoma via regulating PRMT7 expression Homo sapiens hg19 chr16 68362000 68362400 HNF4A PRMT7 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Peripheral Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, CRISPRi, CRISPRa, qRT-PCR, Western blot, EMSA 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr8 128747000 128750000 MYC Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervical Epithelium UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Functional perturbation assay, Chromatin interaction assay, TF binding assay ChIP-seq, 4C-seq, RNA-seq CRISPR KO, RT-RT-qPCR, Western blot 2021 33712565 EphA2 super-enhancer promotes tumor progression by recruiting FOSL2 and TCF7L2 to activate the target gene EphA2 Homo sapiens hg19 chr1 16479332 16499332 EPHA2 Enhancer Active Disease colorectal cancer MONDO:0005176 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR, Western blot 2021 33712565 EphA2 super-enhancer promotes tumor progression by recruiting FOSL2 and TCF7L2 to activate the target gene EphA2 Homo sapiens hg19 chr1 16479332 16499332 EPHA2 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF7 CVCL_0031 breast carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR, Western blot 2021 33712565 EphA2 super-enhancer promotes tumor progression by recruiting FOSL2 and TCF7L2 to activate the target gene EphA2 Homo sapiens hg19 chr1 16479332 16499332 EPHA2 Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervical Epithelium UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR, Western blot 2021 33712565 EphA2 super-enhancer promotes tumor progression by recruiting FOSL2 and TCF7L2 to activate the target gene EphA2 Homo sapiens hg19 chr1 16499333 16519333 EPHA2 Enhancer Active Disease colorectal cancer MONDO:0005176 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR, Western blot 2021 33712565 EphA2 super-enhancer promotes tumor progression by recruiting FOSL2 and TCF7L2 to activate the target gene EphA2 Homo sapiens hg19 chr1 16499333 16519333 EPHA2 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF7 CVCL_0031 breast carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR, Western blot 2021 33712565 EphA2 super-enhancer promotes tumor progression by recruiting FOSL2 and TCF7L2 to activate the target gene EphA2 Homo sapiens hg19 chr1 16499333 16519333 EPHA2 Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervical Epithelium UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR, Western blot 2021 33712565 EphA2 super-enhancer promotes tumor progression by recruiting FOSL2 and TCF7L2 to activate the target gene EphA2 Homo sapiens hg19 chr1 16519334 16539780 EPHA2 Enhancer Active Disease colorectal cancer MONDO:0005176 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR, Western blot 2021 33712565 EphA2 super-enhancer promotes tumor progression by recruiting FOSL2 and TCF7L2 to activate the target gene EphA2 Homo sapiens hg19 chr1 16519334 16539780 EPHA2 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF7 CVCL_0031 breast carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR, Western blot 2022 34954189 A beta-Catenin-TCF-Sensitive Locus Control Region Mediates GUCY2C Ligand Loss in Colorectal Cancer Homo sapiens hg19 chr1 42614062 42616745 GUCA2A Enhancer Silenced Disease colorectal cancer MONDO:0005176 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, CRISPRa, ChIP-RT-qPCR, RT-RT-qPCR 2022 34954189 A beta-Catenin-TCF-Sensitive Locus Control Region Mediates GUCY2C Ligand Loss in Colorectal Cancer Homo sapiens hg19 chr1 42614062 42616745 GUCA2B Enhancer Silenced Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 Primary AML blasts myeloid leukemia cell CL:0001054 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, CRISPRa, ChIP-RT-qPCR, RT-RT-qPCR 2025 40082405 Enhancer transcription profiling reveals an enhancer RNA-driven ferroptosis and new therapeutic opportunities in prostate cancer Homo sapiens hg38 chr3 46453226 46459225 NR LTF Enhancer Active Disease prostate cancer MONDO:0008316 DOID:10283 prostate UBERON:0002367 NA NA prostate cancer cell NA integrated epigenomic analysis ATAC-seq; RNA-seq; ChIP-seq (H3K27ac, H3K4me1) ChIP-qPCR; luciferase reporter assay; 3C-qPCR; RNA-FISH; ChIRP; RIP-qPCR; western blot 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr3 168855000 168870000 CTCF EVI1 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Peripheral Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Chromatin interaction assay, Functional perturbation assay ChIP-seq, 3C-seq, 4C-seq, RNA-seq CRISPR Knockout, RT-RT-qPCR, Western blot, Flow Cytometry, FISH 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr3 168855000 168870000 CTCF EVI1 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 AML cell line myeloid leukemia cell CL:0001054 Chromatin interaction assay, Functional perturbation assay ChIP-seq, 3C-seq, 4C-seq, RNA-seq CRISPR Knockout, RT-RT-qPCR, Western blot, Flow Cytometry, FISH 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr3 168866500 168868000 CTCF EVI1 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 Primary AML blasts myeloid leukemia cell CL:0001054 Chromatin interaction assay, Functional perturbation assay, TF binding assay ChIP-seq, 4C-seq, RNA-seq CRISPR Knockout, RT-RT-qPCR, Western blot, Flow Cytometry, FISH 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr3 168866500 168868000 CTCF EVI1 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Peripheral Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Chromatin interaction assay, Functional perturbation assay, TF binding assay ChIP-seq, 4C-seq, RNA-seq CRISPR Knockout, RT-RT-qPCR, Western blot, Flow Cytometry, FISH 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr3 168866500 168868000 CTCF EVI1 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 MUTZ-3 CVCL_1435 myeloid leukemia cell CL:0001054 Chromatin interaction assay, Functional perturbation assay, TF binding assay ChIP-seq, 4C-seq, RNA-seq CRISPR Knockout, RT-RT-qPCR, Western blot, Flow Cytometry, FISH 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr3 168915400 168918000 CTCF EVI1 Enhancer Active Normal Peripheral Blood UBERON:0000178 Human B lymphoblastoid cell B lymphoblastoid cell CL:0000945 Functional perturbation assay, Chromatin interaction assay, TF binding assay ChIP-seq, 4C-seq, RNA-seq CRISPR KO, RT-RT-qPCR, Western blot 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr3 168915400 168918000 CTCF EVI1 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat CVCL_0065 T lymphoblast CL:0002419 Functional perturbation assay, Chromatin interaction assay, TF binding assay ChIP-seq, 4C-seq, RNA-seq CRISPR KO, RT-RT-qPCR, Western blot 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr8 130475000 130775000 MYC Enhancer Active Disease acute monocytic leukemia MONDO:0005025 DOID:0080147 Peripheral Blood UBERON:0000178 THP-1 CVCL_0006 acute monocytic leukemia cell CL:0000576 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, 3C-seq, 4C-seq CRISPR Knockout, RT-RT-qPCR, Western blot, FISH 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr8 130475000 130775000 EVI1 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 22Rv1 CVCL_1045 prostate carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, 3C-seq, 4C-seq CRISPR Knockout, RT-RT-qPCR, Western blot, FISH 2024 38373841 KLF2 enhancer variant rs4808485 increases lupus risk by modulating inflammasome machinery and cellular homeostasis Homo sapiens hg19 chr19 16439455 16439541 KLF2 Enhancer Silenced Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, 3C-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, CRISPRi, RT-RT-qPCR, Western blot 2024 38373841 KLF2 enhancer variant rs4808485 increases lupus risk by modulating inflammasome machinery and cellular homeostasis Homo sapiens hg19 chr19 16439455 16439541 AP1M1 Enhancer Silenced Disease renal cell carcinoma MONDO:0005086 DOID:4450 Kidney UBERON:0002113 786-O CVCL_1051 kidney cancer cell CL:0001066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, 3C-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, CRISPRi, RT-RT-qPCR, Western blot 2024 38373841 KLF2 enhancer variant rs4808485 increases lupus risk by modulating inflammasome machinery and cellular homeostasis Homo sapiens hg19 chr19 16439455 16439541 Enhancer Silenced Disease lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 A549 CVCL_0023 lung adenocarcinoma cell CL:0001069 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, 3C-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, CRISPRi, RT-RT-qPCR, Western blot 2021 33741908 CRISPRi screens reveal a DNA methylation-mediated 3D genome dependent causal mechanism in prostate cancer Homo sapiens hg19 chr8 128531465 128532665 AR MYC Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0063 embryonic kidney cell CL:0002139 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay CRISPRi screening, RNA-seq, Hi-C, ChIP-seq, 3C-seq CRISPRi, RT-RT-qPCR, 3C-RT-qPCR, Western blot 2021 33741908 CRISPRi screens reveal a DNA methylation-mediated 3D genome dependent causal mechanism in prostate cancer Homo sapiens hg19 chr8 128531465 128532665 AR MYC Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 SKmel147 CVCL_3876 melanoma cell CL:0002573 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay CRISPRi screening, RNA-seq, Hi-C, ChIP-seq, 3C-seq CRISPRi, RT-RT-qPCR, 3C-RT-qPCR, Western blot 2021 33741908 CRISPRi screens reveal a DNA methylation-mediated 3D genome dependent causal mechanism in prostate cancer Homo sapiens hg19 chr8 128531465 128532665 AR PVT1 Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 501MEL CVCL_4633 melanoma cell CL:0002573 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay CRISPRi screening, RNA-seq, Hi-C, ChIP-seq, 3C-seq CRISPRi, RT-RT-qPCR, 3C-RT-qPCR, Western blot 2021 33741908 CRISPRi screens reveal a DNA methylation-mediated 3D genome dependent causal mechanism in prostate cancer Homo sapiens hg19 chr8 128531465 128532665 AR PVT1 Enhancer Active Normal Umbilical vein UBERON:0002066 HUVEC CVCL_2959 umbilical vein endothelial cell CL:0002615 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay CRISPRi screening, RNA-seq, Hi-C, ChIP-seq, 3C-seq CRISPRi, RT-RT-qPCR, 3C-RT-qPCR, Western blot 2016 27774982 Genetic variation at the 8q2421 renal cancer susceptibility locus affects HIF binding to a MYC enhancer Homo sapiens hg19 chr8 128889122 128889450 HIF1A MYC Enhancer Active Disease colorectal cancer MONDO:0005176 DOID:9256 Colon UBERON:0001155 Colorectal carcinoma cells colorectal carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay ChIP-seq, Hi-C Luciferase Reporter Assay, CRISPR Knockout 2017 28511927 Coordinated regulation of IFITM genes by an IFN-responsive enhancer Homo sapiens hg19 chr11 31240000 31241000 STAT1 IFITM1 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 Mouse hepatoma cell mouse hepatoma cell CL:0000182 Enhancer activity assay, Chromatin interaction assay ChIP-seq CRISPR Knockout, Luciferase Reporter Assay, 3C 2017 28511927 Coordinated regulation of IFITM genes by an IFN-responsive enhancer Homo sapiens hg19 chr11 31240000 31241000 STAT1 IFITM1 Enhancer Active Disease hepatoblastoma MONDO:0010559 DOID:3964 Liver UBERON:0002107 Human hepatoblastoma cell hepatoblastoma cell CL:0000182 Enhancer activity assay, Chromatin interaction assay ChIP-seq CRISPR Knockout, Luciferase Reporter Assay, 3C 2017 29236325 AML1/ETO trans-activates c-KIT expression through the long range interaction between promoter and intronic enhancer Homo sapiens hg19 chr12 47732000 47733500 BRD4 AMIGO2 Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervical Epithelium UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR 2017 29236325 AML1/ETO trans-activates c-KIT expression through the long range interaction between promoter and intronic enhancer Homo sapiens hg19 chr12 47732000 47733500 BRD4 AMIGO2 Enhancer Active Disease colorectal cancer MONDO:0005176 DOID:9256 Colon UBERON:0001155 Human colorectal carcinoma cell colorectal carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR 2022 36417539 A pleiotropic hypoxia-sensitive EPAS1 enhancer is disrupted by adaptive alleles in Tibetans Homo sapiens hg19 chr2 46573123 46594333 EPAS1 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 Human prostate cancer cell prostate carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, 3C-seq CRISPR Knockout, Luciferase Reporter Assay 2019 31078271 The SNP of rs6854845 suppresses transcription via the DNA looping structure alteration of super-enhancer in colon cells Homo sapiens hg19 chr4 76192040 76237727 EREG Enhancer Active Normal Inner cell mass UBERON:0000087 H1 hESCs embryonic stem cell CL:0002322 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, RNA-seq, ChIP-seq 3C, ChIP-RT-qPCR, RT-RT-qPCR, CRISPR knockout 2024 38311851 DLK1/DIO3 locus upregulation by a ??-catenin-dependent enhancer drives cell proliferation and liver tumorigenesis Homo sapiens hg19 chr14 101283029 101284356 TCF4 MEG3 Enhancer Active Disease acute monocytic leukemia MONDO:0005025 DOID:0080147 Peripheral Blood UBERON:0000178 THP-6 CVCL_4686 acute monocytic leukemia cell CL:0000576 Functional perturbation assay, Chromatin interaction assay, TF binding assay ChIP-seq, ATAC-seq, RNA-seq CRISPR Knockout, CRISPRi, 3C-RT-qPCR, ChIP-RT-qPCR 2024 38311851 DLK1/DIO3 locus upregulation by a ??-catenin-dependent enhancer drives cell proliferation and liver tumorigenesis Homo sapiens hg19 chr14 101283029 101284356 TCF4 MEG3 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Functional perturbation assay, Chromatin interaction assay, TF binding assay ChIP-seq, ATAC-seq, RNA-seq CRISPR Knockout, CRISPRi, 3C-RT-qPCR, ChIP-RT-qPCR 2023 37438529 Complementary Alu sequences mediate enhancer-promoter selectivity Homo sapiens hg19 chr8 29256000 29256500 PTK2 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF7 CVCL_0031 breast carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C CRISPR Knockout, 3C-RT-qPCR, RT-RT-qPCR, FISH 2019 31078271 The SNP of rs6854845 suppresses transcription via the DNA looping structure alteration of super-enhancer in colon cells Homo sapiens hg19 chr4 76192040 76237727 EREG Enhancer Active Disease glioblastoma MONDO:0005142 DOID:3070 Brain UBERON:0000955 G361 glioblastoma CVCL_1220 glioblastoma cell CL:0000127 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, RNA-seq, ChIP-seq 3C, ChIP-RT-qPCR, RT-RT-qPCR, CRISPR Knockout 2021 33741908 CRISPRi screens reveal a DNA methylation mediated 3D genome dependent causal mechanism in prostate cancer Homo sapiens hg19 chr8 128531465 128532665 AR MYC Enhancer Active Disease glioblastoma MONDO:0005142 DOID:3070 Brain UBERON:0000955 GBM3565 glioblastoma glioblastoma cell CL:0000127 Functional perturbation assay, Chromatin interaction assay, TF binding assay CRISPRi screening, ChIP-seq, RNA-seq, Hi-C, 5C CRISPRi, RT-RT-qPCR, 3C assay, Cell proliferation assay, Mouse xenograft assay 2016 26818394 A New Class of Temporarily Phenotypic Enhancers Identified by CRISPR/Cas9 Mediated Genetic Screening Homo sapiens hg19 chr6 30754822 30755196 POU5F1 Enhancer Active Disease ovarian carcinoma MONDO:0005140 DOID:2394 Ovary UBERON:0000992 OVCAR3 CVCL_0465 ovarian carcinoma cell CL:0000069 Functional perturbation assay, Enhancer activity assay ChIP-seq, RNA-seq, 4C-seq CRISPR Knockout, CRISPRi, Luciferase Reporter Assay, RT-RT-qPCR 2025 41129262 The hematopoietic stem cell MYB enhancer is essential and recurrently amplified during T cell leukemogenesis Homo sapiens hg19 chr6 135640000 135645000 ETS1 MYB Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 PDX cells patient-derived xenograft cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, Hi-C CRISPR Knockout/CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2025 40765356 Epigenetic remodeling and 3D chromatin reorganization governed by NKX2-1 drive neuroendocrine prostate cancer Homo sapiens hg19 chr14 36973254 36996211 FOXA2 NKX2-1 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 Prostate carcinoma cell line (C4-2B) CVCL_4784 prostate carcinoma cell CL:0000066 Chromatin interaction assay, Functional perturbation assay Hi-C, ChIP-seq, RNA-seq CRISPR Knockout, qRT-PCR, Western blot 2021 33975627 Functional mapping of androgen receptor enhancer activity Homo sapiens hg19 chr11 114058000 114058850 AR ZBTB16 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, STARRseq, ChIA-PET, RNA-seq, WGS Luciferase Reporter Assay, CRISPRi, qRT-PCR 2019 31761532 Functional Enhancers Shape Extrachromosomal Oncogene Amplifications Homo sapiens hg19 chr7 54932020 54934020 SOX2 EGFR Enhancer Active Disease glioblastoma MONDO:0005142 DOID:3070 Brain UBERON:0000955 GBM3565 glioblastoma glioblastoma cell CL:0000127 Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, 4C-seq, CRISPRi screen CRISPRi, RT-RT-qPCR, Alamar Blue Assay 2019 31761532 Functional Enhancers Shape Extrachromosomal Oncogene Amplifications Homo sapiens hg19 chr7 54888020 54890020 SOX2 EGFR Enhancer Active Disease glioblastoma MONDO:0005142 DOID:3070 Brain UBERON:0000955 G361 glioblastoma CVCL_1220 glioblastoma cell CL:0000127 Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, 4C-seq, CRISPRi screen CRISPRi, RT-RT-qPCR, Alamar Blue Assay 2019 31761532 Functional Enhancers Shape Extrachromosomal Oncogene Amplifications Homo sapiens hg19 chr7 54888020 54890020 SOX2 EGFR Enhancer Active Disease glioblastoma MONDO:0005142 DOID:3070 Brain UBERON:0000955 GBM3565 glioblastoma glioblastoma cell CL:0000127 Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, 4C-seq, CRISPRi screen CRISPRi, RT-RT-qPCR, Alamar Blue Assay 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 SE Active Disease ovarian carcinoma MONDO:0005140 DOID:2394 Ovary UBERON:0000992 OVCAR3 CVCL_0465 ovarian carcinoma cell CL:0000069 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, ATAC-seq, scATAC-seq, scRNA-seq CRISPR Knockout, CRISPRi, qRT-PCR, Western blot, Cell Proliferation Assay, Cell Migration Assay 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 SE Active Disease ovarian carcinoma MONDO:0005140 DOID:2394 Ovary UBERON:0000992 OVCAR3 CVCL_0465 ovarian carcinoma cell CL:0000069 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, ATAC-seq, scATAC-seq, scRNA-seq CRISPR Knockout, CRISPRi, qRT-PCR, Western blot, Cell Proliferation Assay, Cell Migration Assay 2023 36632223 Enhancer RNA promotes resistance to radiotherapy in bone-metastatic prostate cancer by m6A modification Homo sapiens hg19 chr12 122510495 122510896 PSMD9 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 PDX cells patient-derived xenograft cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay RNA-seq, ChIP-seq, 3C-seq RT-RT-qPCR, CRISPR Knockout, ChIP-RT-qPCR, Western blot 2023 36632223 Enhancer RNA promotes resistance to radiotherapy in bone-metastatic prostate cancer by m6A modification Homo sapiens hg19 chr12 122510495 122510896 WDR66 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 Prostate carcinoma cell line (C4-2B) CVCL_4784 prostate carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay RNA-seq, ChIP-seq, 3C-seq RT-RT-qPCR, CRISPR Knockout, ChIP-RT-qPCR, Western blot 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr8 130548000 130549050 CTCF EVI1 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 Primary AML blasts myeloid leukemia cell CL:0001054 Chromatin interaction assay, Functional perturbation assay ChIP-seq, 3C-seq, 4C-seq CRISPR Knockout, RT-RT-qPCR, Western blot, Flow Cytometry 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr8 130548000 130549050 CTCF EVI1 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Peripheral Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Chromatin interaction assay, Functional perturbation assay ChIP-seq, 3C-seq, 4C-seq CRISPR Knockout, RT-RT-qPCR, Western blot, Flow Cytometry 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 6448000 6450000 TNFRSF1A Enhancer Active Normal Blood UBERON:0000178 CD4+ T cells CD4-positive T cell CL:0000624 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq, Capture-C Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, RT-RT-qPCR, Western blot 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 6448000 6450000 TNFRSF1A Enhancer Active Normal Blood UBERON:0000178 CD8+ T cells CD8-positive T cell CL:0000625 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq, Capture-C Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, RT-RT-qPCR, Western blot 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:0006120 DOID:1612 Breast UBERON:0000310 MCF7 CVCL_0031 breast carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPRa, RT-RT-qPCR 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:0006120 DOID:1612 Breast UBERON:0000310 T47D CVCL_0553 breast carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPRa, RT-RT-qPCR 2014 24662484 Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus Homo sapiens hg19 chr8 128320000 128322000 CTCF; TCF7L2; MED1 MYC Enhancer Active Disease colorectal cancer MONDO:0005176 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Chromatin interaction assay, Functional perturbation assay ChIP-seq, 3C-seq, RNA-seq 3C, Luciferase Reporter Assay, RT-RT-qPCR, Western blot 2020 31980609 Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing Homo sapiens hg19 chr1 47679000 47722000 MYB TAL1 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 Human chronic myeloid leukemia cell chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, qRT-PCR, Western blot 2020 31980609 Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing Homo sapiens hg19 chr11 5301549 5302549 FOG1; GATA1; TAL1 HBB Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepG2 CVCL_0027 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq CRISPRi, CRISPRa, Luciferase Reporter Assay 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 Liver UBERON:0002107 mouse primary hepatocytes mouse hepatocyte CL:0000182 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq, ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPRa, RT-RT-qPCR 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 Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 human liver biopsies human liver biopsy CL:0000182 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq, ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPRa, RT-RT-qPCR 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 Disease lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 A549 CVCL_0023 lung adenocarcinoma cell CL:0001069 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq, ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPRa, RT-RT-qPCR 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 non-small cell lung carcinoma MONDO:0005233 DOID:3908 Lung UBERON:0002048 H1299 CVCL_0060 non-small cell lung carcinoma cell CL:0000066 Functional perturbation assay ChIP-seq, RNA-seq CRISPR Knockout, Luciferase Reporter Assay 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 Normal Vascular tissue UBERON:0001981 iPSC-ECs endothelial cell CL:0002139 Functional perturbation assay ChIP-seq, RNA-seq CRISPR Knockout, Luciferase Reporter Assay 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 MEF2 EDN1 Enhancer Active Normal Lung UBERON:0002048 Beas-2B CVCL_0168 bronchial epithelial cell CL:0002591 Enhancer perturbation assay ChIP-seq, 4C-seq CRISPR Knockout, Luciferase Reporter Assay 2019 31126313 The inherited variations of a p53-responsive enhancer in 13q1212 confer lung cancer risk by attenuating TNFRSF19 expression Homo sapiens hg19 chr13 24149800 24150800 P53 TNFRSF19 Enhancer Active Disease colorectal cancer MONDO:0005176 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay Luciferase Reporter Assay, CRISPR Knockout, 3C, RT-RT-qPCR, EMSA 2019 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:0005176 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2019 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:0005176 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2019 31591481 Oncogenic HOXB8 is driven by MYC-regulated super-enhancer and potentiates colorectal cancer invasiveness via BACH1 Homo sapiens hg19 chr17 46670277 46684332 MYC HOXB8 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF7 CVCL_0031 breast carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2019 30833784 Phase separation of ligand-activated enhancers licenses cooperative chromosomal enhancer assembly Homo sapiens hg19 chr21 34600000 34610000 ESR1 TFF1 Enhancer Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0080545 Bone Marrow UBERON:0002371 SEM cells CVCL_0095 B lymphoblast CL:0000945 Enhancer activity assay, Chromatin interaction assay ChIP-seq, ATAC-seq, Hi-C Luciferase Reporter Assay 2023 37626123 MLL-AF4 cooperates with PAF1 and FACT to drive high-density enhancer interactions in leukemia Homo sapiens hg19 chr8 128533830 128534830 MYC Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Bone Marrow UBERON:0002371 Primary T-ALL cells T lymphoblast CL:0002419 Enhancer activity assay, Functional perturbation assay ChIP-seq, Hi-C Luciferase Reporter Assay, CRISPRi 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:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat CVCL_0065 T lymphoblast CL:0002419 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 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:0004947 DOID:0050890 Blood UBERON:0000178 Peer T lymphoblast CL:0002419 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 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:0004947 DOID:0050890 Blood UBERON:0000178 PDX cells patient-derived xenograft cell CL:0002419 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 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 acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 GDM-1 CVCL_1230 myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 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 MNX1 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Bone Marrow UBERON:0002371 DND-41 CVCL_2022 T lymphoblast CL:0002419 Enhancer activity assay, Chromatin interaction assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, 4C-seq 2023 36947815 Structural Variation Cooperates with Permissive Chromatin to Control Enhancer Hijacking-Mediated Oncogenic Transcription Homo sapiens hg19 chr14 98602411 98675204 MYB TLX3 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Bone Marrow UBERON:0002371 UT242 T lymphoblast CL:0002419 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, ATAC-seq, Hi-C, 4C-seq, RNA-seq CRISPRi, RT-RT-qPCR, FISH 2023 36947815 Structural Variation Cooperates with Permissive Chromatin to Control Enhancer Hijacking-Mediated Oncogenic Transcription Homo sapiens hg19 chr14 98602411 98675204 MYB TLX3 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Bone Marrow UBERON:0002371 UT308 T lymphoblast CL:0002419 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, ATAC-seq, Hi-C, 4C-seq, RNA-seq CRISPRi, RT-RT-qPCR, FISH 2023 36947815 Structural Variation Cooperates with Permissive Chromatin to Control Enhancer Hijacking-Mediated Oncogenic Transcription Homo sapiens hg19 chr14 98602411 98675204 MYB TLX3 Enhancer Active Disease diffuse large B-cell lymphoma MONDO:0005042 DOID:0050746 Lymph node UBERON:0000029 Karpas-422 CVCL_1325 B cell CL:0000945 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, ATAC-seq, Hi-C, 4C-seq, RNA-seq CRISPRi, RT-RT-qPCR, FISH 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; POU2F2; POU2AF1 MYC Enhancer Active Disease diffuse large B-cell lymphoma MONDO:0005042 DOID:0050746 Lymph node UBERON:0000029 SUDHL-5 CVCL_1735 B cell CL:0000945 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq CRISPRi, Luciferase Reporter Assay, RT-RT-qPCR 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; POU2F2; POU2AF1 MYC Enhancer Active Disease diffuse large B-cell lymphoma MONDO:0005042 DOID:0050746 Lymph node UBERON:0000029 HT B cell CL:0000945 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq CRISPRi, Luciferase Reporter Assay, RT-RT-qPCR 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; POU2F2; POU2AF1 MYC Enhancer Active Disease Burkitt lymphoma MONDO:0002483 DOID:8582 Lymph node UBERON:0000029 BJAB CVCL_5711 B cell CL:0000945 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq CRISPRi, Luciferase Reporter Assay, RT-RT-qPCR 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; POU2F2; POU2AF1 MYC Enhancer Active Disease diffuse large B-cell lymphoma MONDO:0005042 DOID:0050746 Lymph node UBERON:0000029 Karpas-422 CVCL_1325 B cell CL:0000945 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq CRISPRi, Luciferase Reporter Assay, RT-RT-qPCR 2025 40067173 Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma Homo sapiens hg19 chr8 129190000 129195000 MEF2B; POU2F2; POU2AF1 MYC Enhancer Active Disease diffuse large B-cell lymphoma MONDO:0005042 DOID:0050746 Lymph node UBERON:0000029 SUDHL-5 CVCL_1735 B cell CL:0000945 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq CRISPRi, Luciferase Reporter Assay, RT-RT-qPCR 2025 40067173 Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma Homo sapiens hg19 chr8 129190000 129195000 MEF2B; POU2F2; POU2AF1 MYC Enhancer Active Disease diffuse large B-cell lymphoma MONDO:0005042 DOID:0050746 Lymph node UBERON:0000029 HT B cell CL:0000945 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq CRISPRi, Luciferase Reporter Assay, RT-RT-qPCR 2025 40067173 Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma Homo sapiens hg19 chr8 129190000 129195000 MEF2B; POU2F2; POU2AF1 MYC Enhancer Active Disease Burkitt lymphoma MONDO:0002483 DOID:8582 Lymph node UBERON:0000029 BJAB CVCL_5711 B cell CL:0000945 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq CRISPRi, Luciferase Reporter Assay, RT-RT-qPCR 2025 40067173 Selective Enhancer Dependencies in MYC-Intact and MYC-Rearranged Germinal Center B-cell Diffuse Large B-cell Lymphoma Homo sapiens hg19 chr8 129190000 129195000 MEF2B; POU2F2; POU2AF1 MYC Enhancer Active Disease leukemia MONDO:0005029 DOID:164 Blood UBERON:0000178 Leukemia cell lines leukemia cell CL:0001054 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq CRISPRi, Luciferase Reporter Assay, RT-RT-qPCR 2022 36095844 EVI1 drives leukemogenesis through aberrant ERG activation Homo sapiens hg19 chr21 39854000 39855000 EVI1 ERG Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 CVCL_0062 breast carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq, ChIP-seq CRISPR knockout, Luciferase reporter assay, RT-RT-qPCR 2022 35390165 A histidine cluster determines YY1-compartmentalized coactivators and chromatin elements in phase-separated enhancer clusters Homo sapiens hg19 chr12 2880430 3018116 YY1 FOXM1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF-7 CVCL_0031 breast carcinoma cell CL:0000066 Functional perturbation assay, Chromatin interaction assay, Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, 3C, FISH, EMSA, FRAP 2022 35390165 A histidine cluster determines YY1-compartmentalized coactivators and chromatin elements in phase-separated enhancer clusters Homo sapiens hg19 chr12 2880430 3018116 YY1 FOXM1 Enhancer Active Disease osteosarcoma MONDO:0005087 DOID:3347 Bone UBERON:0002481 U2OS CVCL_0042 osteosarcoma cell CL:0000082 Functional perturbation assay, Chromatin interaction assay, Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, 3C, FISH, EMSA, FRAP 2022 35390165 A histidine cluster determines YY1-compartmentalized coactivators and chromatin elements in phase-separated enhancer clusters Homo sapiens hg19 chr12 2880430 3018116 YY1 FOXM1 Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Functional perturbation assay, Chromatin interaction assay, Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, 3C, FISH, EMSA, FRAP 2022 35390165 A histidine cluster determines YY1-compartmentalized coactivators and chromatin elements in phase-separated enhancer clusters Homo sapiens hg19 chr12 2880430 3018116 YY1 FOXM1 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK-293T CVCL_0063 embryonic kidney cell CL:0002139 Functional perturbation assay, Chromatin interaction assay, Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, 3C, FISH, EMSA, FRAP 2022 35390165 A histidine cluster determines YY1-compartmentalized coactivators and chromatin elements in phase-separated enhancer clusters Homo sapiens hg19 chr12 2880430 3018116 YY1 FOXM1 Enhancer Active Normal Pancreatic islet UBERON:0000006 EndoC-??H1 CVCL_A5NE pancreatic beta cell CL:0000169 Functional perturbation assay, Chromatin interaction assay, Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, 3C, FISH, EMSA, FRAP 2021 34267199 Large parental differences in chromatin organization in pancreatic beta cell line explaining diabetes susceptibility effects Homo sapiens hg19 chr11 1713879 1716230 CTCF INS Enhancer Active Normal Pancreatic islet UBERON:0000006 primary human pancreatic islets pancreatic islet cell CL:0000168 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay 3C-seq, 4C-seq, ChIP-seq, RNA-seq, ATAC-seq CRISPR Knockout, RT-RT-qPCR, EMSA, Sanger Sequencing 2021 34267199 Large parental differences in chromatin organization in pancreatic beta cell line explaining diabetes susceptibility effects Homo sapiens hg19 chr11 1713879 1716230 CTCF INS Enhancer Active Normal Cranial neural crest UBERON:0003099 hCNCC cranial neural crest cell CL:0000333 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay 3C-seq, 4C-seq, ChIP-seq, RNA-seq, ATAC-seq CRISPR Knockout, RT-RT-qPCR, EMSA, Sanger Sequencing 2020 32991838 Loss of long-range enhancers in neural crest Homo sapiens hg19 chr17 68720009 68721009 TWIST1 SOX9 Enhancer Active Disease colorectal cancer MONDO:0005176 DOID:9256 Colon UBERON:0001155 COLO 320DM cells CVCL_0219 colorectal carcinoma cell CL:0000066 Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout 2025 41120733 Enhancer activation from transposable elements in extrachromosomal DNA Homo sapiens hg19 chr3 111274086 111275786 MYC Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, Functional perturbation assay Hi-C, ATAC-seq Luciferase reporter assay, CRISPR knockout, CRISPRi, ORCA 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:0005142 DOID:3070 Brain UBERON:0000955 U87MG CVCL_0022 glioblastoma cell CL:0000127 Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq CRISPR Knockout, RT-RT-qPCR 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 LINC01116 Enhancer Active Normal Brain UBERON:0000955 Normal human astrocytes astrocyte CL:0000127 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay RNA-seq, Hi-C, 4C-seq, ChIP-seq RT-RT-qPCR, CRISPRa, siRNA Knockdown, smFISH 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 LINC01116 Enhancer Active Normal Aorta UBERON:0000947 HAEC aortic endothelial cell CL:0002546 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay RNA-seq, Hi-C, 4C-seq, ChIP-seq RT-RT-qPCR, CRISPRa, siRNA Knockdown, smFISH 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 cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 Human cervical adenocarcinoma cell cervical adenocarcinoma cell CL:0000069 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, RNA-seq, ChIP-seq Luciferase Reporter Assay, CRISPR-Cas9 Knockout, ChIP-RT-qPCR, EMSA, RT-RT-qPCR 2023 37438529 Complementary Alu sequences mediate enhancer-promoter selectivity Homo sapiens hg19 chr12 61890000 61895000 MGST1 Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 Human cervical adenocarcinoma cell cervical adenocarcinoma cell CL:0000069 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C CRISPR Knockout, 3C-RT-qPCR, qRT-PCR, FISH 2023 37438529 Complementary Alu sequences mediate enhancer-promoter selectivity Homo sapiens hg19 chr12 61890000 61895000 TUBA1B Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 Human cervical adenocarcinoma cell cervical adenocarcinoma cell CL:0000069 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C CRISPR Knockout, 3C-RT-qPCR, qRT-PCR, FISH 2023 37438529 Complementary Alu sequences mediate enhancer-promoter selectivity Homo sapiens hg19 chr12 61890000 61895000 AEBP2 Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 Human cervical adenocarcinoma cell cervical adenocarcinoma cell CL:0000069 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C CRISPR Knockout, 3C-RT-qPCR, qRT-PCR, FISH 2023 37438529 Complementary Alu sequences mediate enhancer-promoter selectivity Homo sapiens hg19 chr19 50913170 50987888 CFD SE Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 Human cervical adenocarcinoma cell cervical adenocarcinoma cell CL:0000069 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C CRISPR Knockout, 3C-RT-qPCR, qRT-PCR, FISH 2023 37438529 Complementary Alu sequences mediate enhancer-promoter selectivity Homo sapiens hg19 chr19 50913170 50987888 CNN2 SE Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 Human cervical adenocarcinoma cell cervical adenocarcinoma cell CL:0000069 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C CRISPR Knockout, 3C-RT-qPCR, qRT-PCR, FISH 2023 37438529 Complementary Alu sequences mediate enhancer-promoter selectivity Homo sapiens hg19 chr19 50913170 50987888 PTBP1 SE Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 Human cervical adenocarcinoma cell cervical adenocarcinoma cell CL:0000069 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C CRISPR Knockout, 3C-RT-qPCR, qRT-PCR, FISH 2023 37438529 Complementary Alu sequences mediate enhancer-promoter selectivity Homo sapiens hg19 chr19 50913170 50987888 POLRMT SE Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Human T-ALL cell T lymphoblast CL:0002419 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C CRISPR Knockout, 3C-RT-qPCR, qRT-PCR, FISH 2014 25369933 Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia Homo sapiens hg19 chr8 129400000 130035000 RBPJ MYC Enhancer Active Disease multiple myeloma MONDO:0005178 DOID:9538 Bone Marrow UBERON:0002371 U266B1 CVCL_0566 plasma cell CL:0000945 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, 3C Assay, RT-RT-qPCR, Drug Sensitivity Assay 2023 37438529 Complementary Alu sequences mediate enhancer-promoter selectivity Homo sapiens hg19 chr19 50913170 50987888 CFD Enhancer Active Disease non-small cell lung carcinoma MONDO:0005233 DOID:3908 Lung UBERON:0002048 H1299 CVCL_0060 non-small cell lung carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C CRISPR Knockout, 3C-RT-qPCR, RT-RT-qPCR, FISH 2025 39402215 Functional variant rs9344 at 11q133 regulates CCND1 expression in multiple myeloma with t(11;14) Homo sapiens hg19 chr11 68155000 68173900 PAX5 CCND1 SE Active Normal Embryonic Kidney UBERON:0002113 HEK293T CVCL_0063 embryonic kidney cell CL:0002139 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, Hi-C CRISPR Knockout, qRT-PCR, Western blot 2021 34580281 USP7 facilitates SMAD3 autoregulation to repress cancer progression in p53-deficient lung cancer Homo sapiens hg19 chr15 67150000 67600000 SMAD3 SMAD3 SE Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 Melanoma cell line melanoma cell CL:0002573 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, qRT-PCR, Western blot 2026 41617689 Dual promoter-enhancer activities reflect a unified regulatory logic Homo sapiens hg19 chr11 5248250 5249100 GATA1 HBG1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 CVCL_0062 breast carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay PRO-seq, ATAC-seq, ChIP-seq Luciferase Reporter Assay, CRISPRa, ChIP-RT-qPCR, RT-RT-qPCR 2023 37904237 Landscape of enhancer disruption and functional screen in melanoma cells Homo sapiens hg19 chr10 89912175 89913031 PTEN Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 PANC-1 CVCL_0480 pancreatic ductal adenocarcinoma cell CL:0000066 Functional perturbation assay, Enhancer activity assay ChIP-seq, ATAC-seq, CRISPRi Screen Luciferase Reporter Assay, CRISPRi, CRISPRa, RT-RT-qPCR, Western blot, Cell Apoptosis Assay, Colony Formation Assay 2021 34362881 Aberrant super-enhancer-driven oncogene ENC1 promotes the radio-resistance of breast carcinoma Homo sapiens hg19 chr5 74678000 74688000 ENC1 Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 Melanoma cell line melanoma cell CL:0002573 Functional perturbation assay, Enhancer activity assay ChIP-seq, RNA-seq CRISPR Knockout, RT-RT-qPCR, Western blot 2023 37957340 Super-enhancer RNA m6A promotes local chromatin accessibility and oncogene transcription in pancreatic ductal adenocarcinoma Homo sapiens hg19 chr16 53500000 53510000 MICAL2 Enhancer Active Disease colorectal cancer MONDO:0005176 DOID:9256 Colon UBERON:0001155 SW480 CVCL_0546 colorectal carcinoma cell CL:0000066 Super enhancer activity assay, Functional perturbation assay ChIP-seq Luciferase Reporter Assay, CRISPR Knockout 2020 33196849 Generation of onco-enhancer enhances chromosomal remodeling and accelerates tumorigenesis Homo sapiens hg19 chr12 85074000 85075186 CTCF NTS Enhancer Active Disease colorectal cancer MONDO:0005176 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Functional perturbation assay, Chromatin interaction assay, Enhancer activity assay ChIP-seq, RNA-seq, 3C-seq CRISPR Knockout, ChIP-RT-qPCR, 3C assay, qRT-PCR, Western blot, Colony formation assay, Wound healing assay 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:0005176 DOID:9256 Colon UBERON:0001155 SW480 CVCL_0546 colorectal carcinoma cell CL:0000066 Functional perturbation assay, Chromatin interaction assay, TF binding assay enChIP-seq, ChIP-seq, RNA-seq, DNase-seq CRISPR Knockout, CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR, Sphere-formation Assay, Cell Viability Assay, Flow Cytometry 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:0005176 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Functional perturbation assay, Chromatin interaction assay, TF binding assay enChIP-seq, ChIP-seq, RNA-seq, DNase-seq CRISPR Knockout, CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR, Sphere-formation Assay, Cell Viability Assay, Flow Cytometry 2022 34707247 A stem cell marker KLF5 regulates CCAT1 via three-dimensional genome structure in colorectal cancer cells Homo sapiens hg19 chr8 128231146 128231713 KLF5 CCAT1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF-7 CVCL_0031 breast carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay enChIP-seq, ChIP-seq, RNA-seq CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Immunohistochemistry, RNA in situ Hybridization 2022 34707247 A stem cell marker KLF5 regulates CCAT1 via three-dimensional genome structure in colorectal cancer cells Homo sapiens hg19 chr8 128231146 128231713 KLF5 CCAT1 Enhancer Active Normal Pancreatic islet UBERON:0000006 Beta cell pancreatic beta cell CL:0000169 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay enChIP-seq, ChIP-seq, RNA-seq CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Immunohistochemistry, RNA in situ Hybridization 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 colorectal cancer MONDO:0005176 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay ChIP-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR 2017 28684635 Type 2 Diabetes enhancer at ADCY5 Homo sapiens hg19 chr3 123065517 123065936 NKX2-2 ADCY5 Enhancer Silenced Disease colorectal cancer MONDO:0005176 DOID:9256 Colon UBERON:0001155 HT29 CVCL_0320 colorectal carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq Luciferase Reporter Assay, EMSA, CRISPR Knockout, RT-RT-qPCR 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 183286632 183287223 FOXA1 EPHB3 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 CVCL_0062 breast carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ChIP-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR 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 183286632 183287223 FOXA1 EPHB3 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF-7 CVCL_0031 breast carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ChIP-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR 2018 29731168 Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element Homo sapiens hg19 chr8 128821500 128822500 MYC PVT1_INTRAGENIC_ENHANCER_822E Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 CVCL_0062 breast carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay, TF binding assay Hi-ChIP, ATAC-seq, ChIP-seq, RNA-seq in vitro knockdown, Western blotting 2018 29731168 Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element Homo sapiens hg19 chr8 128821500 128822500 MYC PVT1_INTRAGENIC_ENHANCER_822E Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF-7 CVCL_0031 breast carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay, TF binding assay Hi-ChIP, ATAC-seq, ChIP-seq, RNA-seq in vitro knockdown, Western blotting 2018 29731168 Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element Homo sapiens hg19 chr8 128866000 128867000 MYC PVT1_INTRAGENIC_ENHANCER_866E Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 CVCL_0062 breast carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay, TF binding assay Hi-ChIP, ATAC-seq, ChIP-seq, RNA-seq in vitro knockdown, Western blotting 2018 29731168 Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element Homo sapiens hg19 chr8 128866000 128867000 MYC PVT1_INTRAGENIC_ENHANCER_866E Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF-7 CVCL_0031 breast carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay, TF binding assay Hi-ChIP, ATAC-seq, ChIP-seq, RNA-seq in vitro knockdown, Western blotting 2018 29731168 Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element Homo sapiens hg19 chr8 128912000 128913000 MYC PVT1_INTRAGENIC_ENHANCER_912E Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 CVCL_0062 breast carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, TF binding assay Hi-ChIP, ATAC-seq, ChIP-seq, RNA-seq in vitro knockdown, Western blotting 2018 29731168 Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element Homo sapiens hg19 chr8 128912000 128913000 MYC PVT1_INTRAGENIC_ENHANCER_912E Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF-7 CVCL_0031 breast carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, TF binding assay Hi-ChIP, ATAC-seq, ChIP-seq, RNA-seq in vitro knockdown, Western blotting 2018 29731168 Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element Homo sapiens hg19 chr8 128919000 128920000 MYC PVT1_INTRAGENIC_ENHANCER_919E Enhancer Active Disease colorectal cancer MONDO:0005176 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay, TF binding assay Hi-ChIP, ATAC-seq, ChIP-seq, RNA-seq in vitro knockdown, Western blotting 2020 31591481 Oncogenic HOXB8 is driven by MYC-regulated super-enhancer and potentiates colorectal cancer invasiveness via BACH1 Homo sapiens hg19 chr17 46656000 46658000 HOXB8 Enhancer Active Disease colorectal cancer MONDO:0005176 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq CRISPR Knockout/CRISPRi, RT-RT-qPCR 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 HOXB6 Enhancer Active Disease colorectal cancer MONDO:0005176 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq CRISPR Knockout/CRISPRi, RT-RT-qPCR, ChIP-RT-qPCR 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 Pulmonary artery UBERON:0002012 hPAEC CVCL_3716 pulmonary artery endothelial cell CL:1001567 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq CRISPR Knockout/CRISPRi, RT-RT-qPCR, ChIP-RT-qPCR 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 HOXB9 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 L3.6pl CVCL_0384 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq CRISPR Knockout/CRISPRi, RT-RT-qPCR, ChIP-RT-qPCR 2023 37066790 SOX17 enhancer variants disrupt transcription factor binding and enhancer inactivity drives pulmonary hypertension Homo sapiens hg19 chr8 41184163 41184463 HOXA5 SOX17 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 PacR pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPRi, CRISPR Knockout, EMSA, ChIP-RT-qPCR 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:0005147 DOID:3490 Pancreas UBERON:0001264 L3.6pl CVCL_0384 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, ATAC-seq, HiChIP, leChRO-seq CRISPR knockout, 4C-seq, RT-RT-qPCR 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:0005147 DOID:3490 Pancreas UBERON:0001264 PacR pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, ATAC-seq, HiChIP, leChRO-seq CRISPR knockout, 4C-seq, RT-RT-qPCR 2023 36889906 Interactive enhancer hubs (iHUBs) mediate transcriptional reprogramming and adaptive resistance in pancreatic cancer Homo sapiens hg19 chr19 1109765 1110214 JUND GPX4 Enhancer Active Disease Ewing sarcoma MONDO:0003368 DOID:3368 Bone UBERON:0001474 A673 CVCL_0080 Ewing sarcoma cell CL:0000050 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, ATAC-seq, HiChIP, leChRO-seq CRISPR knockout, 4C-seq, RT-RT-qPCR 2023 36889906 Interactive enhancer hubs (iHUBs) mediate transcriptional reprogramming and adaptive resistance in pancreatic cancer Homo sapiens hg19 chr19 1109765 1110214 JUND GPX4 Enhancer Active Disease neuroblastoma MONDO:0005070 DOID:769 Adrenal gland UBERON:0002369 CHLA10 CVCL_6583 neuroblastoma cell CL:0000031 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, ATAC-seq, HiChIP, leChRO-seq CRISPR knockout, 4C-seq, RT-RT-qPCR 2022 35653119 EWS::FLI1 and HOXD13 control tumor cell plasticity in Ewing sarcoma Homo sapiens hg19 chr2 176265000 176270000 HOXD13 Enhancer Active Normal Heart UBERON:0000948 Primary cardiomyocytes cardiomyocyte CL:0000746 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C ChIP-RT-qPCR, CRISPR Knockout, CRISPRi, RT-RT-qPCR 2022 35653119 EWS::FLI1 and HOXD13 control tumor cell plasticity in Ewing sarcoma Homo sapiens hg19 chr2 176265000 176270000 HOXD13 Enhancer Active Normal Blood UBERON:0000178 K562 erythroleukemia cells CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C ChIP-RT-qPCR, CRISPR Knockout, CRISPRi, RT-RT-qPCR 2021 33910361 Variant intronic enhancer controls SCN10A-short expression and cardiac conduction Homo sapiens hg19 chr3 158194000 158195200 TBX5 SCN10A Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 22Rv1 cells CVCL_1045 prostate carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq CRISPR Knockout, Luciferase Reporter Assay 2020 32293525 Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection Homo sapiens hg19 chr11 5225000 5225500 HBG2 Enhancer Active Normal Embryonic Kidney UBERON:0002113 Human embryonic kidney cell embryonic kidney cell CL:0002139 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, QHR-4C Luciferase Reporter Assay, CRISPR Knock-in, RT-RT-qPCR 2020 31980609 Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing Homo sapiens hg19 chr11 5301549 5302549 GATA1 HBE1 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, CRISPRa, RT-RT-qPCR, Western blot 2026 39428991 The castration resistant prostate cancer associated SNP rs11067228 facilitates neuroendocrine differentiation through an enhancer mediated chromatin interaction with SRRM4 Homo sapiens hg19 chr12 115092472 115096258 SOX4 SRRM4 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat CVCL_0065 T lymphoblast CL:0002419 Chromatin interaction assay ChIP-seq, 4C-seq CRISPR knockout 2020 31980609 Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing Homo sapiens hg19 chr11 5301549 5302549 GATA1 HBE1,HBG1,HBG2,HBB Enhancer Active Disease adult T-cell leukemia/lymphoma MONDO:0005026 DOID:0050523 Peripheral Blood UBERON:0000178 Primary ATL cells T cell CL:0000084 Enhancer activity assay,Functional perturbation assay,TF binding assay ChIP-seq,RNA-seq,ATAC-seq CRISPRi,CRISPRa,qRT-PCR,Western blot 2019 30612741 A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens Homo sapiens hg19 chr18 9876906 9877723 RAB31 Enhancer Active Disease adult T-cell leukemia/lymphoma MONDO:0005026 DOID:0050523 Peripheral Blood UBERON:0000178 T cell leukemia cell T cell CL:0000084 Functional validation scRNA-seq, ChIP-seq CRISPRi 2014 25369933 Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia Homo sapiens hg19 chr8 130180217 130180629 NOTCH1; RBPJ MYC Enhancer Active Disease adult T-cell leukemia/lymphoma MONDO:0005026 DOID:0050523 Peripheral Blood UBERON:0000178 Primary ATL cells T cell CL:0000084 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay ChIP-seq Luciferase Reporter Assay, 3C, ChIP-RT-qPCR, RT-RT-qPCR 2022 35908104 Requirement for TP73 and genetic alterations originating from its intragenic super-enhancer in adult T-cell leukemia Homo sapiens hg19 chr1 3560600 3600000 IRF4 TP73 Enhancer Active Disease adult T-cell leukemia/lymphoma MONDO:0005026 DOID:0050523 Peripheral Blood UBERON:0000178 T cell leukemia cell T cell CL:0000084 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-ChIP CRISPR Knockout, CRISPRi, RT-RT-qPCR, Western blot 2022 35908104 Requirement for TP73 and genetic alterations originating from its intragenic super-enhancer in adult T-cell leukemia Homo sapiens hg19 chr1 3560600 3600000 IRF4 TP73 Enhancer Active Disease adult T-cell leukemia/lymphoma MONDO:0005026 DOID:0050523 Peripheral Blood UBERON:0000178 Primary ATL cells T cell CL:0000084 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-ChIP CRISPR Knockout, CRISPRi, RT-RT-qPCR, Western blot 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:0005026 DOID:0050523 Peripheral Blood UBERON:0000178 T cell leukemia cell T cell CL:0000084 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-ChIP CRISPR Knockout, CRISPRi, RT-RT-qPCR, Western blot 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 chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 erythroleukemia CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-ChIP CRISPR Knockout, CRISPRi, RT-RT-qPCR, Western blot 2022 35908104 Requirement for TP73 and genetic alterations originating from its intragenic super-enhancer in adult T-cell leukemia Homo sapiens hg19 chr1 3592595 3594569 IRF4 TP73 Enhancer Active Normal Blood UBERON:0000178 iPSC-derived macrophages macrophage CL:0000235 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-ChIP CRISPR Knockout, CRISPRi, RT-RT-qPCR, Western blot 2022 35908104 Requirement for TP73 and genetic alterations originating from its intragenic super-enhancer in adult T-cell leukemia Homo sapiens hg19 chr1 3592595 3594569 IRF4 TP73 Enhancer Active Disease adult T-cell leukemia/lymphoma MONDO:0005026 DOID:0050523 Peripheral Blood UBERON:0000178 T cell leukemia cell T cell CL:0000084 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-ChIP CRISPR Knockout, CRISPRi, RT-RT-qPCR, Western blot 2020 31980609 Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing Homo sapiens hg19 chr11 5301549 5302549 GATA1 HBE1 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 erythroleukemia CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, CRISPRa, RT-RT-qPCR, Western blot 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 TNFRSF1A Enhancer Active Normal Blood UBERON:0000178 iPSC-derived macrophages macrophage CL:0000235 Enhancer activity assay ATAC-seq, ChIP-seq CRISPR Knockout, Luciferase Reporter Assay 2021 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; MYBL2; PLAG1; FOSL1 TCOF1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 Human breast cancer cell breast carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, DNase-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR knockout, RT-RT-qPCR, Western blot 2018 30417100 TET2 coactivates gene expression through demethylation of enhancers Homo sapiens hg19 chr11 72482883 72512882 WIPF1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 CVCL_0062 breast adenocarcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq, mRRBS CRISPR Knockout, RT-RT-qPCR, Western blot 2016 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:0005070 DOID:769 Brain UBERON:0000955 SH-SY5Y CVCL_0019 neuroblastoma cell CL:0000031 Chromatin interaction assay, Enhancer activity assay, Functional perturbation assay ChIP-seq 3C-RT-qPCR, ChIP-RT-qPCR, CRISPR knockout 2019 31557715 Detailed Functional Characterization of a Waist-Hip Ratio Locus in 7p152 Defines an Enhancer Controlling Adipocyte Differentiation Homo sapiens hg19 chr7 23467757 23468022 MIR148A Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepG2 CVCL_0027 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay RNA-seq, Hi-C Luciferase Reporter Assay, RT-RT-qPCR, CRISPR Knockout, CRISPRi 2016 26886256 Embryonic Stem Cell (ES)-Specific Enhancers Specify the Expression Potential of ES Genes in Cancer Homo sapiens hg19 chr6 43740121 43741621 VEGFA Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional perturbation assay 4C-seq Luciferase Reporter Assay, CRISPR Knockout/CRISPRi, RT-RT-qPCR 2015 26375006 BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis Homo sapiens hg19 chr2 60722300 60722700 GATA1 BCL11A Enhancer Active Normal Hematopoietic system UBERON:0002371 HUDEP-2 CVCL_VI06 erythroid progenitor cell CL:0000038 Functional perturbation assay, Enhancer activity assay ChIP-seq, RNA-seq, ATAC-seq Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR 2015 26501517 Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements Homo sapiens hg19 chr11 5301862 5302715 GATA2 HBG1 Enhancer Silenced Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Hematopoietic system UBERON:0002371 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional perturbation assay ChIP-seq, RNA-seq CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR 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 DIO1 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepG2 CVCL_0027 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, Functional perturbation assay RNA-seq, Hi-C Luciferase Reporter Assay, RT-RT-qPCR, Western blot, CRISPR Knockout 2019 31727856 Brain cell type-specific enhancer-promoter interactome maps and disease risk association Homo sapiens hg19 chr2 126521490 126522490 PU.1 BIN1 Enhancer Active Normal Brain UBERON:0000955 H1-derived microglia microglial cell CL:0000129 Regulatory element functional validation, 3D chromatin interaction mapping ChIP-seq, ATAC-seq, PLAC-seq, RNA-seq CRISPR-Cas9 deletion, RT-RT-qPCR, Western blot 2019 30649550 KDM3A regulates hippo pathway through enhancer activation in colorectal cancer Homo sapiens hg19 chr6 132270000 132270500 TEAD1 CTGF Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 HCT116 colorectal cancer CVCL_0291 colorectal carcinoma cell CL:0000066 Functional perturbation assay, TF binding assay, Enhancer activity assay ChIP-seq, RNA-seq CRISPR knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, Co-IP 2012 22665440 Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q243 prostate cancer risk locus Homo sapiens hg19 chr17 69107686 69108045 AR SOX9 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, DNase-seq, 3C-seq Luciferase reporter assay, ChIP-RT-qPCR, 3C-RT-qPCR, Sanger sequencing 2012 22665440 Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q243 prostate cancer risk locus Homo sapiens hg19 chr17 69107686 69108045 AR SOX9 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 VCaP cells CVCL_2235 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, DNase-seq, 3C-seq Luciferase reporter assay, ChIP-RT-qPCR, 3C-RT-qPCR, Sanger sequencing 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 UBERON:0002367 LNCaP cells CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay ChIP-seq Luciferase reporter assay, 3C-RT-qPCR, RT-RT-qPCR 2015 26098368 Genome-wide association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth Homo sapiens hg19 chr6 132272417 132273191 TEAD CTGF Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 CVCL_0062 breast carcinoma cell CL:0000066 Enhancer activity assay ChIP-seq, Hi-C Luciferase Reporter Assay, 3C 2009 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:0005132 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq Luciferase Reporter Assay, 3C, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2009 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 Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq Luciferase Reporter Assay, 3C, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2019 30971697 Lineage-specific RUNX2 super-enhancer activates MYC and promotes the development of blastic plasmacytoid dendritic cell neoplasm Homo sapiens hg19 chr6 44500000 45600000 RUNX2 RUNX2 Enhancer Active Disease blastic plasmacytoid dendritic cell neoplasm MONDO:0019474 DOID:0080738 Hematopoietic tissue UBERON:0002415 CAL-1 CVCL_5G46 plasmacytoid dendritic cell CL:0000786 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Whole-genome sequencing CRISPR Knockout, 3C-RT-qPCR, RT-RT-qPCR, Western blot, FISH 2019 30971697 Lineage-specific RUNX2 super-enhancer activates MYC and promotes the development of blastic plasmacytoid dendritic cell neoplasm Homo sapiens hg19 chr6 44500000 45600000 RUNX2 MYC Enhancer Active Disease blastic plasmacytoid dendritic cell neoplasm MONDO:0019474 DOID:0080738 Hematopoietic tissue UBERON:0002415 CAL-1 CVCL_5G46 plasmacytoid dendritic cell CL:0000786 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Whole-genome sequencing CRISPR Knockout, 3C-RT-qPCR, RT-RT-qPCR, Western blot, FISH 2023 38016946 Systematic characterization of the HOXA9 downstream targets in MLL-r leukemia by noncoding CRISPR screens Homo sapiens hg19 chr13 28840000 28850000 HOXA9 GFI1 Enhancer Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0080545 Bone Marrow UBERON:0002371 SEM CVCL_0095 B lymphoblast CL:0000945 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, ATAC-seq, Capture-C CRISPR Knockout, CRISPRi, qRT-PCR, Western blot, Competitive Proliferation Assay, Flow Cytometry, In Vivo Transplantation Assay 2019 31073170 SREBP1 drives Keratin-80-dependent cytoskeletal changes and invasive behavior in endocrine-resistant ER??-positive breast cancer Homo sapiens hg19 chr12 52304911 53120196 KRT80 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF7 CVCL_0031 breast carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, DHS-seq ChIP-RT-qPCR, CRISPRi, qRT-PCR, RNA-FISH, ChIA-PET 2022 35741778 Discovery and Functional Characterization of Two Regulatory Variants Underlying Lupus Susceptibility at 2p131 Homo sapiens hg19 chr2 74404247 74404647 ARID3A DGUOK Enhancer Active Normal Blood UBERON:0000178 GM12878 CVCL_7526 B lymphoblastoid cell CL:0000945 Enhancer activity assay, TF binding assay ChIP-seq, Hi-C, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, qRT-PCR, Western blot 2023 37673892 A super-enhancer-regulated RNA-binding protein cascade drives pancreatic cancer Homo sapiens hg19 chr10 102880001 102881789 HNRNPF SE Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 MIA PaCa-2 CVCL_0428 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq CRISPR Knockout, qRT-PCR, Western blot 2021 34315876 Super enhancer regulation of cytokine-induced chemokine production in alcoholic hepatitis Homo sapiens hg19 chr4 74500000 74575000 CXCL1 SE Active Normal Liver UBERON:0002107 Liver sinusoidal endothelial cells (LSEC) liver sinusoidal endothelial cell CL:1000413 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, 4C-seq ChIP-RT-qPCR, 3C, CRISPRi, qRT-PCR, ELISA, Western blot 2024 38319712 Differential histone acetylation and super-enhancer regulation underlie melanoma cell dedifferentiation Homo sapiens hg19 chr17 48110000 48150000 JUNB ITGA3 SE Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 A375 CVCL_0132 melanoma cell CL:0002573 TF binding assay, Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPR Knockout, qRT-PCR, Western blot 2023 36691394 N6-methyladenosine on enhancer RNA promotes radiotherapy resistance in bone metastatic prostate cancer Homo sapiens hg19 chr12 122510495 122510896 PSMD9 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 P-90 PDX primary patient-derived xenograft cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay RNA-seq, ChIP-seq, 3C-seq qRT-PCR, CRISPR Knockout, ChIP-RT-qPCR, Western blot 2023 36691394 N6-methyladenosine on enhancer RNA promotes radiotherapy resistance in bone metastatic prostate cancer Homo sapiens hg19 chr12 122510495 122510896 WDR66 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 P-90 PDX primary patient-derived xenograft cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay RNA-seq, ChIP-seq, 3C-seq CRISPR Knockout, ChIP-RT-qPCR, qRT-PCR, Western blot 2022 35982471 Super-enhancer hijacking LINC01977 promotes malignancy of early-stage lung adenocarcinoma addicted to the canonical TGF-??/SMAD3 pathway Homo sapiens hg19 chr17 79780000 79828000 SMAD3; CBP; EP300 LINC01977 Enhancer Active Disease lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 A549 CVCL_0023 lung adenocarcinoma cell CL:0001069 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, Hi-C, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2022 35982471 Super-enhancer hijacking LINC01977 promotes malignancy of early-stage lung adenocarcinoma addicted to the canonical TGF-??/SMAD3 pathway Homo sapiens hg19 chr17 79780000 79828000 SMAD3; CBP; EP300 LINC01977 Enhancer Active Disease lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 PC-9 CVCL_B260 lung adenocarcinoma cell CL:0001069 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, Hi-C, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2022 35982471 Super-enhancer hijacking LINC01977 promotes malignancy of early-stage lung adenocarcinoma addicted to the canonical TGF-??/SMAD3 pathway Homo sapiens hg19 chr17 79780000 79828000 SMAD3; CBP; EP300 LINC01977 Enhancer Active Disease lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 LUAD primary tumor lung adenocarcinoma cell CL:0001069 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, Hi-C, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2019 30659195 Aberrant enhancer hypomethylation contributes to hepatic carcinogenesis through global transcriptional reprogramming Homo sapiens hg19 chr20 48900221 48901229 CEBFB Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 Hepatocellular carcinoma cell line (HepG2) CVCL_0027 hepatocellular carcinoma cell CL:0000182 Functional perturbation assay, Enhancer activity assay ChIP-seq, RNA-seq, WGBS CRISPR Knockout, CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR 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 CDKN1B Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Luciferase Reporter Assay, 3C-RT-qPCR, CRISPR Knockout, CRISPRi, RT-RT-qPCR 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 APOLD1 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat CVCL_0065 T lymphoblast CL:0002419 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Luciferase Reporter Assay, 3C-RT-qPCR, CRISPR Knockout, CRISPRi, RT-RT-qPCR 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 DDX47 Enhancer Active Normal Blood UBERON:0000178 Primary B cells B cell CL:0000945 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Luciferase Reporter Assay, 3C-RT-qPCR, CRISPR Knockout, CRISPRi, RT-RT-qPCR 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 GPR19 Enhancer Active Normal Blood UBERON:0000178 Primary T cells T cell CL:0000084 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Luciferase Reporter Assay, 3C-RT-qPCR, CRISPR Knockout, CRISPRi, RT-RT-qPCR 2019 30612741 A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens Homo sapiens hg19 chr6 139766548 139767000 CITED2 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional validation scRNA-seq, RNA-seq, Hi-C CRISPRi, CRISPR KO, RT-RT-qPCR 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 8708912 8710911 HMX1 Enhancer Active Normal Craniofacial Tissue UBERON:0010368 hCNCC cranial neural crest cell CL:0000333 Enhancer activity assay, Chromatin interaction assay ChIP-seq, ATAC-seq, Hi-C Luciferase Reporter Assay, Transgenic Reporter Assay 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 8708912 8712911 HMX1 Enhancer Active Normal Craniofacial Tissue UBERON:0010368 hCNCC cranial neural crest cell CL:0000333 Enhancer activity assay, Chromatin interaction assay ChIP-seq, ATAC-seq, Hi-C Luciferase Reporter Assay, Transgenic Reporter Assay 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 Peripheral Blood UBERON:0000178 SC monocyte-derived cells monocyte-derived cell CL:0000576 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, ATAC-seq Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, 3C assay, 4C assay, RT-RT-qPCR 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 Peripheral Blood UBERON:0000178 Primary CD14+ monocytes CD14-positive monocyte CL:0001053 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, ATAC-seq Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, 3C assay, 4C assay, RT-RT-qPCR 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 Embryonic Kidney UBERON:0002113 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, ATAC-seq Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, 3C assay, 4C assay, RT-RT-qPCR 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 renal cell carcinoma cell CL:0001066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR 2022 35676472 The renal lineage factor PAX8 controls oncogenic signalling in kidney cancer Homo sapiens hg19 chr8 128132902 128133724 HNF1B MYC Enhancer Active Normal Kidney UBERON:0002113 Kidney proximal tubule epithelial cell kidney proximal tubule epithelial cell CL:0002306 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR 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 renal cell carcinoma cell CL:0001066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR 2022 35676472 The renal lineage factor PAX8 controls oncogenic signalling in kidney cancer Homo sapiens hg19 chr8 128526339 128526710 HNF1B MYC Enhancer Active Normal Kidney UBERON:0002113 Kidney proximal tubule epithelial cell kidney proximal tubule epithelial cell CL:0002306 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR 2014 24662484 Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus Homo sapiens hg19 chr8 128230503 128380503 CTCF; TCF4 MYC Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, 3C-seq FISH, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, RNA Immunoprecipitation, Biotin-labeled RNA pull-down assay 2014 24662484 Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus Homo sapiens hg19 chr8 128230503 128380503 CTCF; TCF4 MYC Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 SW480 CVCL_0546 colorectal carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, 3C-seq FISH, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, RNA Immunoprecipitation, Biotin-labeled RNA pull-down assay 2014 24662484 Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus Homo sapiens hg19 chr8 128662857 128663857 CTCF; TCF4 MYC Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, 3C-seq FISH, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, RNA Immunoprecipitation 2014 24662484 Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus Homo sapiens hg19 chr8 128662857 128663857 CTCF; TCF4 MYC Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 SW480 CVCL_0546 colorectal carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, 3C-seq FISH, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, RNA Immunoprecipitation 2020 33196849 Generation of onco-enhancer enhances chromosomal remodeling and accelerates tumorigenesis Homo sapiens hg19 chr12 85074370 85074815 CTCF NTS Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, RNA-seq, 3C-seq Luciferase Reporter Assay, ChIP-RT-qPCR, 3C assay, qRT-PCR, Western blot 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 Umbilical vein UBERON:0002066 HUVEC CVCL_2959 umbilical vein endothelial cell CL:0002615 Enhancer functional assay ChIP-seq CRISPR Knockout, Luciferase Reporter Assay 2019 31826955 FOXA1 upregulation promotes enhancer and transcriptional reprogramming in endocrine-resistant breast cancer Homo sapiens hg19 chr2 46345000 46347000 FOXA1 EPAS1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF7L breast carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi, RT-RT-qPCR, ChIP-RT-qPCR 2019 31826955 FOXA1 upregulation promotes enhancer and transcriptional reprogramming in endocrine-resistant breast cancer Homo sapiens hg19 chr2 46345000 46347000 FOXA1 EPAS1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 TamR breast carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi, RT-RT-qPCR, ChIP-RT-qPCR 2019 31826955 FOXA1 upregulation promotes enhancer and transcriptional reprogramming in endocrine-resistant breast cancer Homo sapiens hg19 chr2 46348000 46350000 FOXA1 EPAS1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF7L breast carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi, RT-RT-qPCR, ChIP-RT-qPCR 2019 31826955 FOXA1 upregulation promotes enhancer and transcriptional reprogramming in endocrine-resistant breast cancer Homo sapiens hg19 chr2 46348000 46350000 FOXA1 EPAS1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 TamR breast carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi, RT-RT-qPCR, ChIP-RT-qPCR 2019 31826955 FOXA1 amplification drives enhancer reprogramming and HIF-2?? activation in endocrine-resistant breast cancer Homo sapiens hg19 chr2 46530000 46535000 FOXA1 EPAS1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF7L-TamR breast carcinoma cell CL:0000066 Functional perturbation assay ChIP-seq, RNA-seq CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2020 32384149 13q122 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:0004945 DOID:0080545 Bone Marrow UBERON:0002371 Primary BCP ALL cells B lymphoblast CL:0000945 Enhancer activity assay, Chromatin interaction assay ChIP-seq, RNA-seq, Hi-C, PLAC-seq, ATAC-seq, DNase-seq RT-RT-qPCR, FISH 2020 32384149 13q122 deletions in acute lymphoblastic leukemia lead to upregulation of FLT3 through enhancer hijacking Homo sapiens hg19 chr13 28710000 28715000 RUNX1 FLT3 Enhancer Active Normal Blood UBERON:0000178 GM12878 CVCL_7526 B lymphoblastoid cell CL:0000945 Enhancer activity assay, Chromatin interaction assay ChIP-seq, RNA-seq, Hi-C, PLAC-seq, ATAC-seq, DNase-seq RT-RT-qPCR, FISH 2020 32384149 13q122 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:0004945 DOID:0080545 Bone Marrow UBERON:0002371 NALM-6 CVCL_0092 B lymphoblast CL:0000945 Enhancer activity assay, Chromatin interaction assay ChIP-seq, RNA-seq, Hi-C, PLAC-seq, ATAC-seq, DNase-seq RT-RT-qPCR, FISH 2020 32384149 13q122 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:0004945 DOID:0080545 Bone Marrow UBERON:0002371 Primary BCP ALL cells B lymphoblast CL:0000945 Enhancer activity assay, Chromatin interaction assay ChIP-seq, RNA-seq, Hi-C, PLAC-seq, ATAC-seq, DNase-seq RT-RT-qPCR, FISH 2020 32384149 13q122 deletions in acute lymphoblastic leukemia lead to upregulation of FLT3 through enhancer hijacking Homo sapiens hg19 chr13 28843000 28843500 RUNX1 FLT3 Enhancer Active Normal Blood UBERON:0000178 GM12878 CVCL_7526 B lymphoblastoid cell CL:0000945 Enhancer activity assay, Chromatin interaction assay ChIP-seq, RNA-seq, Hi-C, PLAC-seq, ATAC-seq, DNase-seq RT-RT-qPCR, FISH 2020 32384149 13q122 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:0004945 DOID:0080545 Bone Marrow UBERON:0002371 NALM-6 CVCL_0092 B lymphoblast CL:0000945 Enhancer activity assay, Chromatin interaction assay ChIP-seq, RNA-seq, Hi-C, PLAC-seq, ATAC-seq, DNase-seq RT-RT-qPCR, FISH 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 Normal Embryonic Kidney UBERON:0002113 293FT cells CVCL_6911 embryonic kidney cell CL:0002139 Enhancer activity assay ChIP-seq, RNA-seq, Hi-C, WGS Luciferase Reporter Assay, FISH, RT-RT-qPCR, Western blot 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:0006002 DOID:0050897 Salivary Gland UBERON:0001044 AciCC primary tumor cells acinic cell carcinoma cell CL:0000066 Enhancer activity assay ChIP-seq, RNA-seq, Hi-C, WGS Luciferase Reporter Assay, FISH, RT-RT-qPCR, Western blot 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 Normal Salivary Gland UBERON:0001044 normal parotid gland cells parotid gland cell CL:0000066 Enhancer activity assay ChIP-seq, RNA-seq, Hi-C, WGS Luciferase Reporter Assay, FISH, RT-RT-qPCR, Western blot 2019 31217334 Epigenetic activation and memory at a TGFB2 enhancer in systemic sclerosis Homo sapiens hg19 chr1 218299740 218299908 RELA TGFB2 Enhancer Active Normal Skin UBERON:0000014 Primary human dermal fibroblasts dermal fibroblast CL:0002620 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, RNA-seq, ChIP-seq, Chem-seq ChIP-RT-qPCR, CRISPRa (dCas9-EP300core), CRISPRi (dCas9-KRAB), RT-RT-qPCR, Western blot, mRNA in situ hybridization 2020 32293525 Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection Homo sapiens hg19 chr11 5246600 5247600 HBG2 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Bone Marrow UBERON:0002371 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, QHR-4C CRISPR Knock-in 2020 32293525 Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection Homo sapiens hg19 chr11 5246600 5247600 HBB Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK-293T CVCL_0063 embryonic kidney cell CL:0002139 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, QHR-4C CRISPR Knock-in 2025 40162972 Enhancer Hijacking Discovery in Acute Myeloid Leukemia by Pyjacker Identifies MNX1 Activation via Deletion 7q Homo sapiens hg19 chr7 92384001 92385000 MNX1 Enhancer Active Normal Blood UBERON:0000178 ChiPSC22 cells induced pluripotent stem cell CL:0000037 Functional perturbation assay, Chromatin interaction assay ATAC-seq, ACT-seq, 4C-seq, RNA-seq CRISPR knockout, CRISPRi, RT-RT-qPCR 2025 40162972 Enhancer Hijacking Discovery in Acute Myeloid Leukemia by Pyjacker Identifies MNX1 Activation via Deletion 7q Homo sapiens hg19 chr7 92384001 92385000 MNX1 Enhancer Active Normal Blood UBERON:0000178 HSPCs hematopoietic stem cell CL:0001029 Functional perturbation assay, Chromatin interaction assay ATAC-seq, ACT-seq, 4C-seq, RNA-seq CRISPR knockout, CRISPRi, RT-RT-qPCR 2016 26656844 Identification of focally amplified lineage specific super enhancers in human epithelial cancers Homo sapiens hg19 chr8 129165000 129166500 NFE2L2; CEBPB MYC SE Active Disease non-small cell lung carcinoma MONDO:0005233 DOID:3908 Lung UBERON:0002048 Human non-small cell lung carcinoma cell non-small cell lung carcinoma cell CL:0000066 Enhancer functional validation, Transcription factor binding analysis, Genome editing H3K27ac ChIP-seq, p300 ChIP-seq, DNase-seq, NFE2L2 ChIP-seq, CEBPB ChIP-seq, RNA-seq, Gene set enrichment analysis Luciferase reporter assay, CRISPR-Cas9 enhancer deletion, Chromosome conformation capture RT-qPCR, siRNA knockdown, Clonogenic growth assay 2016 26656844 Identification of focally amplified lineage specific super enhancers in human epithelial cancers Homo sapiens hg19 chr8 129166547 129190290 NFE2L2; CEBPB MYC SE Active Disease non-small cell lung carcinoma MONDO:0005233 DOID:3908 Lung UBERON:0002048 Human non-small cell lung carcinoma cell non-small cell lung carcinoma cell CL:0000066 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 2021 34461284 The osteoporosis risk variant rs9820407 at 3p221 acts as an allele-specific enhancer to regulate CTNNB1 expression by long-range chromatin loop formation Homo sapiens hg19 chr3 41172000 41174000 CTNNB1 Enhancer Active Disease osteosarcoma MONDO:0005087 DOID:3347 Bone UBERON:0001474 SaOS-2 CVCL_0548 osteosarcoma cell CL:0000082 Enhancer activity assay, Chromatin interaction assay Hi-C, ChIP-seq Luciferase Reporter Assay, RT-RT-qPCR 2021 34461284 The osteoporosis risk variant rs9820407 at 3p221 acts as an allele-specific enhancer to regulate CTNNB1 expression by long-range chromatin loop formation Homo sapiens hg19 chr3 41172000 41174000 CTNNB1 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0063 embryonic kidney cell CL:0002139 Enhancer activity assay, Chromatin interaction assay Hi-C, ChIP-seq Luciferase Reporter Assay, RT-RT-qPCR 2021 34461284 The osteoporosis risk variant rs9820407 at 3p221 acts as an allele-specific enhancer to regulate CTNNB1 expression by long-range chromatin loop formation Homo sapiens hg19 chr3 41174000 41176000 CTNNB1 Enhancer Active Disease osteosarcoma MONDO:0005087 DOID:3347 Bone UBERON:0001474 SaOS-2 CVCL_0548 osteosarcoma cell CL:0000082 Enhancer activity assay, Chromatin interaction assay Hi-C, ChIP-seq Luciferase Reporter Assay, RT-RT-qPCR 2021 34461284 The osteoporosis risk variant rs9820407 at 3p221 acts as an allele-specific enhancer to regulate CTNNB1 expression by long-range chromatin loop formation Homo sapiens hg19 chr3 41174000 41176000 CTNNB1 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0063 embryonic kidney cell CL:0002139 Enhancer activity assay, Chromatin interaction assay Hi-C, ChIP-seq Luciferase Reporter Assay, RT-RT-qPCR 2021 34461284 The osteoporosis risk variant rs9820407 at 3p221 acts as an allele-specific enhancer to regulate CTNNB1 expression by long-range chromatin loop formation Homo sapiens hg19 chr3 41177000 41179000 CTNNB1 Enhancer Active Disease osteosarcoma MONDO:0005087 DOID:3347 Bone UBERON:0001474 SaOS-2 CVCL_0548 osteosarcoma cell CL:0000082 Enhancer activity assay, Chromatin interaction assay Hi-C, ChIP-seq Luciferase Reporter Assay, RT-RT-qPCR 2021 34461284 The osteoporosis risk variant rs9820407 at 3p221 acts as an allele-specific enhancer to regulate CTNNB1 expression by long-range chromatin loop formation Homo sapiens hg19 chr3 41177000 41179000 CTNNB1 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0063 embryonic kidney cell CL:0002139 Enhancer activity assay, Chromatin interaction assay Hi-C, ChIP-seq Luciferase Reporter Assay, RT-RT-qPCR 2024 38488867 Differential histone acetylation and super-enhancer regulation underlie melanoma cell dedifferentiation Homo sapiens hg19 chr17 48100000 48130000 ITGA3 Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 WM1552C melanoma cell CL:0002573 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq CRISPR Knockout, RT-RT-qPCR, Western blot 2024 38488867 Differential histone acetylation and super-enhancer regulation underlie melanoma cell dedifferentiation Homo sapiens hg19 chr17 48100000 48130000 ITGA3 Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 YUCHIME CVCL_EI14 melanoma cell CL:0002573 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq CRISPR Knockout, RT-RT-qPCR, Western blot 2024 38488867 Differential histone acetylation and super-enhancer regulation underlie melanoma cell dedifferentiation Homo sapiens hg19 chr17 48100000 48130000 ITGA3 Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 SKmel147 CVCL_3876 melanoma cell CL:0002573 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq CRISPR Knockout, RT-RT-qPCR, Western blot 2016 26795348 Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus Homo sapiens hg19 chr2 202204000 202204758 MYC CASP8 Enhancer Active Normal Breast UBERON:0000310 MCF-10A CVCL_0598 mammary epithelial cell CL:0000066 Enhancer activity assay, TF binding assay, eQTL analysis, Genetic association study Targeted DNA sequencing, Strand-specific RNA-seq, ChIP-seq Luciferase reporter assay, RT-RT-qPCR, Sanger sequencing 2016 26795348 Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus Homo sapiens hg19 chr2 202204000 202204758 MYC CASP8 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 T-47D CVCL_0553 breast carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, eQTL analysis, Genetic association study Targeted DNA sequencing, Strand-specific RNA-seq, ChIP-seq Luciferase reporter assay, RT-RT-qPCR, Sanger sequencing 2016 26795348 Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus Homo sapiens hg19 chr2 202204000 202204758 MYC CASP8 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF-7 CVCL_0031 breast carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, eQTL analysis, Genetic association study Targeted DNA sequencing, Strand-specific RNA-seq, ChIP-seq Luciferase reporter assay, RT-RT-qPCR, Sanger sequencing 2022 34980595 GFI1 Cooperates with IKZF1/IKAROS to Activate Gene Expression in T-cell Acute Lymphoblastic Leukemia Homo sapiens hg19 chr9 136402000 136406000 RUNX1 GFI1B Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Bone Marrow UBERON:0002371 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR 2016 27362228 Recurrent rearrangements of the MYB locus in adenoid cystic carcinoma drive oncogenic expression through enhancer hijacking Homo sapiens hg19 chr6 135515000 135515800 MYB MYB Enhancer Active Disease salivary gland adenoid cystic carcinoma MONDO:0015066 DOID:0080172 Salivary gland UBERON:0001044 ACC patient-derived xenograft cell lines (ACCX2, ACCX9, ACCX12, ACCX19, ACCX22) adenoid cystic carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay RNA-seq, ChIP-seq Luciferase Reporter Assay, 3C, FISH, RT-RT-qPCR 2015 25801169 Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers Homo sapiens hg19 chr8 128740000 128790000 TCF4 MYC Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 HCT-116 CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq Luciferase Reporter Assay 2015 25801169 Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers Homo sapiens hg19 chr6 152400000 152450000 ESR1 ESR1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF-7 CVCL_0031 breast carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq Luciferase Reporter Assay 2014 24594601 Long-range interaction and correlation between MYC enhancer and oncogenic long noncoding RNA CARLo-5 Homo sapiens hg19 chr8 128322000 128323000 TCF7L2 MYC Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Chromatin interaction assay ChIP-seq RNA-seq, 3C, RT-RT-qPCR 2023 37832549 Genome-wide CRISPR activation screening in senescent cells reveals SOX5 as a driver and therapeutic target of rejuvenation Homo sapiens hg19 chr11 63800000 63802500 SOX5 HMGB2 Enhancer Active Normal Connective Tissue UBERON:0002384 Human Mesenchymal Progenitor mesenchymal progenitor cell CL:0000134 Enhancer activity assay, Functional perturbation assay Hi-C, ChIP-seq CRISPRa, RT-RT-qPCR 2016 27848966 17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells Homo sapiens hg19 chr17 38065500 38067500 CTCF ORMDL3 Enhancer Active Normal Blood UBERON:0000178 Primary CD4+ T cells CD4-positive T cell CL:0000624 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ATAC-seq, ChIP-seq, 4C-seq, RNA-seq, DNase-seq ChIP-RT-qPCR, Luciferase reporter assay, RT-RT-qPCR, siRNA knockdown, EMSA 2016 27848966 17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells Homo sapiens hg19 chr17 38065500 38067500 CTCF ORMDL3 Enhancer Active Disease cutaneous T-cell lymphoma MONDO:0004950 DOID:2531 Blood UBERON:0000178 HUT-78 CVCL_0337 T lymphoma cell CL:0002419 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ATAC-seq, ChIP-seq, 4C-seq, RNA-seq, DNase-seq ChIP-RT-qPCR, Luciferase reporter assay, RT-RT-qPCR, siRNA knockdown, EMSA 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 Brain UBERON:0000955 Adult brain tissue adult brain cell CL:0000540 Chromatin interaction assay, Enhancer activity assay ChIP-seq, RNA-seq, 3C-seq 3C-RT-qPCR, ChIP-RT-qPCR, Luciferase reporter assay 2014 25043047 Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma Homo sapiens hg19 chr9 131300000 131320000 GFI1 Enhancer Active Normal Cerebellum UBERON:0002037 Cerebellar granule neuron progenitors (CGNPs) cerebellar granule neuron progenitor CL:0001031 Enhancer activity assay, Functional perturbation assay ChIP-seq Luciferase reporter assay, Transgenic reporter assay, CRISPR knockout, RT-RT-qPCR, ChIP-RT-qPCR 2014 25043047 Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma Homo sapiens hg19 chr20 32580000 32595000 GFI1B Enhancer Active Normal Cerebellum UBERON:0002037 Cerebellar granule neuron progenitors (CGNPs) cerebellar granule neuron progenitor CL:0001031 Enhancer activity assay, Functional perturbation assay ChIP-seq Luciferase reporter assay, CRISPR knockout, RT-RT-qPCR, ChIP-RT-qPCR 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 UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR 2024 38760567 Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations Homo sapiens hg19 chr1 207450000 207452000 CD55 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional perturbation assay DNase-seq, ChIP-seq CRISPRi, Flow Cytometry 2024 38760567 Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations Homo sapiens hg19 chr1 207455000 207457000 CD55 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional perturbation assay DNase-seq, ChIP-seq CRISPRi, Flow Cytometry 2024 38760567 Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations Homo sapiens hg19 chr1 207460000 207462000 CD55 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional perturbation assay DNase-seq, ChIP-seq CRISPRi, Flow Cytometry 2024 38760567 Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations Homo sapiens hg19 chr1 207465000 207467000 CD55 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional perturbation assay DNase-seq, ChIP-seq CRISPRi, Flow Cytometry 2019 30971697 Lineage-specific RUNX2 super-enhancer activates MYC and promotes the development of blastic plasmacytoid dendritic cell neoplasm Homo sapiens hg19 chr6 44500000 45600000 RUNX2 MYC SE Active Disease blastic plasmacytoid dendritic cell neoplasm MONDO:0019474 DOID:0080738 Hematopoietic tissue UBERON:0002415 CAL-1 BPDCN CVCL_5G46 plasmacytoid dendritic cell CL:0000786 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Whole-genome sequencing 3C-RT-qPCR, CRISPR Knockout, ChIP-RT-qPCR, qRT-PCR, Western blot, FISH 2021 34493733 Transcriptional network involving ERG and AR orchestrates Distal-less homeobox-1 mediated prostate cancer progression Homo sapiens hg19 chr9 72895815 73001135 ALDH1A1 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 22RV1 CVCL_1045 prostate carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, qRT-PCR, Western blot, CRISPR Knockout 2021 34493733 Transcriptional network involving ERG and AR orchestrates Distal-less homeobox-1 mediated prostate cancer progression Homo sapiens hg19 chr12 120975000 121005271 HNF1A Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 22RV1 CVCL_1045 prostate carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, qRT-PCR, Western blot, CRISPR Knockout 2021 33911178 Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia Homo sapiens hg19 chr3 128322357 128323157 CEBPA EVI1 SE Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 HNT-34 CVCL_2071 myeloid leukemia cell CL:0001054 TF binding assay, Enhancer activity assay, Functional perturbation assay ChIP-seq, ChIP-SICAP, RNA-seq Luciferase Reporter Assay, shRNA Knockdown, qRT-PCR, Western blot 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 Pancreas UBERON:0001264 Pancreatic Multipotent Progenitor Cells (MPCs) pancreatic multipotent progenitor cell CL:0002583 Functional perturbation assay, Enhancer activity assay ChIP-seq, RNA-seq, scATAC-seq CRISPR Knockout, qRT-PCR, Immunofluorescence 2024 39277592 Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance Homo sapiens hg19 chr2 213700000 214600000 IKZF2 Enhancer Silenced Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 DND41 CVCL_A296 T lymphoblast CL:0002419 Chromatin interaction assay, Functional perturbation assay Hi-C, ATAC-seq, H3K27ac ChIP-seq, H3K27me3 CUT&RUN, RNA-seq Oligopaint DNA FISH, RT-RT-qPCR 2019 31761532 Functional Enhancers Shape Extrachromosomal Oncogene Amplifications Homo sapiens hg19 chr7 54925000 54927000 EGFR Enhancer Active Disease glioblastoma MONDO:0005142 DOID:3070 Brain UBERON:0000955 GBM3565 glioblastoma CVCL_IZ19 glioblastoma cell CL:0000127 Functional perturbation assay ChIP-seq, 4C-seq, CRISPRi screen CRISPRi, RT-RT-qPCR 2019 31761532 Functional Enhancers Shape Extrachromosomal Oncogene Amplifications Homo sapiens hg19 chr7 54915000 54917000 EGFR Enhancer Active Disease glioblastoma MONDO:0005142 DOID:3070 Brain UBERON:0000955 GBM3565 glioblastoma CVCL_IZ19 glioblastoma cell CL:0000127 Functional perturbation assay ChIP-seq, 4C-seq, CRISPRi screen CRISPRi, RT-RT-qPCR 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 IGFBP5 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 CVCL_0062 breast carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, RT-RT-qPCR 2021 34362881 Aberrant super-enhancer-driven oncogene ENC1 promotes the radio-resistance of breast carcinoma Homo sapiens hg19 chr5 74680400 74682399 ENC1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 CVCL_0062 breast carcinoma cell CL:0000066 Enhancer activity assay ChIP-seq Luciferase Reporter Assay, RT-RT-qPCR 2021 34362881 Aberrant super-enhancer-driven oncogene ENC1 promotes the radio-resistance of breast carcinoma Homo sapiens hg19 chr5 74682400 74683933 ENC1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 CVCL_0062 breast carcinoma cell CL:0000066 Enhancer activity assay ChIP-seq Luciferase Reporter Assay, RT-RT-qPCR 2021 34362881 Aberrant super-enhancer-driven oncogene ENC1 promotes the radio-resistance of breast carcinoma Homo sapiens hg19 chr5 74686000 74687899 ENC1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 CVCL_0062 breast carcinoma cell CL:0000066 Enhancer activity assay ChIP-seq Luciferase Reporter Assay, RT-RT-qPCR 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr3 128250000 128350000 GATA2 EVI1 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Peripheral Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 TF binding assay, Functional perturbation assay ChIP-seq, 3C-seq RT-RT-qPCR, FISH 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr3 128250000 128350000 GATA2 EVI1 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 MUTZ-3 CVCL_1435 myeloid leukemia cell CL:0001054 TF binding assay, Functional perturbation assay ChIP-seq, 3C-seq RT-RT-qPCR, FISH 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr6 156425000 156525000 CTCF; GATA2 EVI1 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Peripheral Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 TF binding assay, Functional perturbation assay ChIP-seq, 3C-seq RT-RT-qPCR, FISH 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr7 92350000 92450000 CTCF EVI1 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Peripheral Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 TF binding assay, Functional perturbation assay ChIP-seq, 3C-seq RT-RT-qPCR, FISH 2023 36869052 An autoimmune pleiotropic SNP modulates IRF5 alternative promoter usage through ZBTB3-mediated chromatin looping Homo sapiens hg19 chr7 128579302 128580416 ZBTB3 IRF5 Enhancer Active Normal Peripheral Blood UBERON:0000178 SC monocyte-derived cells monocyte-derived cell CL:0000576 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, 3C-seq Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, 3C assay, 4C assay, RT-RT-qPCR 2023 36869052 An autoimmune pleiotropic SNP modulates IRF5 alternative promoter usage through ZBTB3-mediated chromatin looping Homo sapiens hg19 chr7 128579302 128580416 ZBTB3 IRF5 Enhancer Active Normal Peripheral Blood UBERON:0000178 Primary CD14+ monocytes CD14-positive monocyte CL:0001053 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, 3C-seq Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, 3C assay, 4C assay, RT-RT-qPCR 2023 36869052 An autoimmune pleiotropic SNP modulates IRF5 alternative promoter usage through ZBTB3-mediated chromatin looping Homo sapiens hg19 chr7 128579302 128580416 ZBTB3 IRF5 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, 3C-seq Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, 3C assay, 4C assay, RT-RT-qPCR 2014 25194570 A NOTCH1-driven MYC enhancer promotes T cell development, transformation and acute lymphoblastic leukemia Homo sapiens hg19 chr8 130180065 130180972 NOTCH1; RBPJ MYC Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Human T-ALL cell T lymphoblast CL:0002419 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq Luciferase Reporter Assay, 3C, EMSA, RT-RT-qPCR 2019 31120998 HoxA9 binds and represses the Cebpa +8 kb enhancer Homo sapiens hg19 chr19 33790834 33791348 HOXA9 CEBPA Enhancer Silenced Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 MUTZ-3 CVCL_1435 myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay ChIP-seq Luciferase Reporter Assay, EMSA 2014 24662484 Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus Homo sapiens hg19 chr8 128835000 128837000 CTCF; TCF7L2 CCAT1-L Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay ChIP-seq Luciferase Reporter Assay, RT-RT-qPCR, siRNA Knockdown 2022 35778390 B cell receptor signaling drives APOBEC3 expression via direct enhancer regulation in chronic lymphocytic leukemia B cells Homo sapiens hg19 chr22 39370500 39372500 APOBEC3C Enhancer Active Disease chronic lymphocytic leukemia MONDO:0004951 DOID:1040 Blood UBERON:0000178 Primary CLL B cells B cell CL:0000945 Enhancer activity assay, TF binding assay, Functional perturbation assay CUT&Tag, ATAC-seq, Hi-C, RNA-seq CRISPR Knockout, CRISPRi, qRT-PCR, Western blot 2022 35778390 B cell receptor signaling drives APOBEC3 expression via direct enhancer regulation in chronic lymphocytic leukemia B cells Homo sapiens hg19 chr22 39378500 39380500 APOBEC3C Enhancer Active Disease chronic lymphocytic leukemia MONDO:0004951 DOID:1040 Blood UBERON:0000178 Primary CLL B cells B cell CL:0000945 Enhancer activity assay, TF binding assay, Functional perturbation assay CUT&Tag, ATAC-seq, Hi-C, RNA-seq CRISPR Knockout, CRISPRi, qRT-PCR, Western blot 2022 35778390 B cell receptor signaling drives APOBEC3 expression via direct enhancer regulation in chronic lymphocytic leukemia B cells Homo sapiens hg19 chr22 39385500 39387500 APOBEC3C Enhancer Silenced Normal Blood UBERON:0000178 Normal B cells B cell CL:0000945 Enhancer activity assay, TF binding assay, Functional perturbation assay CUT&Tag, ATAC-seq, Hi-C, RNA-seq CRISPR Knockout, CRISPRi, qRT-PCR, Western blot 2016 26615198 CFTR regulatory elements identified by 5C Homo sapiens hg19 chr7 117074000 117077000 SMARCC1 CFTR Enhancer Active Normal Nasal epithelium UBERON:0005384 HNECs nasal epithelial cell CL:1001567 Chromatin interaction assay Hi-C, ChIP-seq Luciferase Reporter Assay 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 Embryonic Kidney UBERON:0002113 HEK293 CVCL_0063 embryonic kidney cell CL:0002139 Enhancer activity assay, TF binding assay, Functional perturbation assay Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, EMSA, RT-RT-qPCR, Western blot 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 Embryonic Kidney UBERON:0002113 HEK293 CVCL_0063 embryonic kidney cell CL:0002139 Enhancer activity assay, TF binding assay, Functional perturbation assay Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, EMSA, RT-RT-qPCR, Western blot 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 Embryonic Kidney UBERON:0002113 HEK293 CVCL_0063 embryonic kidney cell CL:0002139 Enhancer activity assay, TF binding assay, Functional perturbation assay Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, EMSA, RT-RT-qPCR, Western blot 2017 28652246 MAPK signaling links melanoma phenotype switching to CD73 induction Homo sapiens hg19 chr6 8120004 8120873 JUN NT5E Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 SK-MEL28 CVCL_0526 melanoma cell CL:0002573 Enhancer activity assay, Functional perturbation assay ChIP-seq CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR 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 GIMAP1 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat CVCL_0065 T lymphoblast CL:0002419 Functional perturbation assay ChIP-seq CRISPR Knockout 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 prostate carcinoma cell CL:0000066 Enhancer activity assay ChIP-seq Luciferase Reporter Assay 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 RANKL Enhancer Active Normal Blood UBERON:0000178 GM12878 CVCL_7526 B lymphoblastoid cell CL:0000945 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 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 RANKL Enhancer Active Normal Bone Marrow UBERON:0002371 CD34+ hematopoietic stem cells CD34-positive hematopoietic stem cell CL:0001029 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 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 RANKL Enhancer Active Disease osteosarcoma MONDO:0005087 DOID:3347 Bone UBERON:0001474 U2-OS osteosarcoma osteoblastic cells CVCL_0042 osteosarcoma cell CL:0000082 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 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 RANKL Enhancer Active Disease osteosarcoma MONDO:0005087 DOID:3347 Bone UBERON:0001474 U2-OS osteosarcoma osteoblastic cells CVCL_0042 osteosarcoma cell CL:0000082 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 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 RANKL Enhancer Active Normal Blood UBERON:0000178 GM12878 CVCL_7526 B lymphoblastoid cell CL:0000945 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 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 RANKL Enhancer Active Disease osteosarcoma MONDO:0005087 DOID:3347 Bone UBERON:0001474 U2-OS osteosarcoma osteoblastic cells CVCL_0042 osteosarcoma cell CL:0000082 Enhancer activity assay, Chromatin interaction assay Hi-C, ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 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 RANKL Enhancer Active Normal Blood UBERON:0000178 GM12878 CVCL_7526 B lymphoblastoid cell CL:0000945 Enhancer activity assay, Chromatin interaction assay Hi-C, ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 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 RANKL Enhancer Active Normal Bone Marrow UBERON:0002371 CD34+ hematopoietic stem cells CD34-positive hematopoietic stem cell CL:0001029 Enhancer activity assay, Chromatin interaction assay Hi-C, ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 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 RANKL Enhancer Active Disease osteosarcoma MONDO:0005087 DOID:3347 Bone UBERON:0001474 U2-OS osteosarcoma osteoblastic cells CVCL_0042 osteosarcoma cell CL:0000082 Enhancer activity assay, Chromatin interaction assay Hi-C, ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 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 RANKL Enhancer Active Normal Blood UBERON:0000178 GM12878 CVCL_7526 B lymphoblastoid cell CL:0000945 Enhancer activity assay, Chromatin interaction assay Hi-C, ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 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 RANKL Enhancer Active Normal Bone Marrow UBERON:0002371 CD34+ hematopoietic stem cells CD34-positive hematopoietic stem cell CL:0001029 Enhancer activity assay, Chromatin interaction assay Hi-C, ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 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 RANKL Enhancer Active Disease osteosarcoma MONDO:0005087 DOID:3347 Bone UBERON:0001474 U2-OS osteosarcoma osteoblastic cells CVCL_0042 osteosarcoma cell CL:0000082 Enhancer activity assay, Chromatin interaction assay Hi-C, ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 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 RANKL Enhancer Active Normal Blood UBERON:0000178 GM12878 CVCL_7526 B lymphoblastoid cell CL:0000945 Enhancer activity assay, Chromatin interaction assay Hi-C, ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 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 RANKL Enhancer Active Normal Bone Marrow UBERON:0002371 CD34+ hematopoietic stem cells CD34-positive hematopoietic stem cell CL:0001029 Enhancer activity assay, Chromatin interaction assay Hi-C, ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2019 31451355 A Cohesin-Mediated Intrachromosomal Loop Drives Oncogenic ROR lncRNA to Accelerate Tumorigenesis Homo sapiens hg19 chr18 57075464 57076425 ROR Enhancer Active Disease gastric adenocarcinoma MONDO:0005050 DOID:3717 Stomach UBERON:0000945 AGS CVCL_0139 gastric adenocarcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay Luciferase Reporter Assay, ChIP-RT-qPCR, 3C-RT-qPCR, CRISPR Knockout, RT-RT-qPCR, Western blot 2019 31451355 A Cohesin-Mediated Intrachromosomal Loop Drives Oncogenic ROR lncRNA to Accelerate Tumorigenesis Homo sapiens hg19 chr18 57075464 57076425 ROR Enhancer Active Disease colorectal adenocarcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 HT29 CVCL_0320 colorectal adenocarcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay Luciferase Reporter Assay, ChIP-RT-qPCR, 3C-RT-qPCR, CRISPR Knockout, RT-RT-qPCR, Western blot 2019 31451355 A Cohesin-Mediated Intrachromosomal Loop Drives Oncogenic ROR lncRNA to Accelerate Tumorigenesis Homo sapiens hg19 chr18 57075464 57076425 ROR Enhancer Active Disease uveal melanoma MONDO:0005145 DOID:6039 Uvea UBERON:0001768 MUM2B CVCL_L039 uveal melanoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay Luciferase Reporter Assay, ChIP-RT-qPCR, 3C-RT-qPCR, CRISPR Knockout, RT-RT-qPCR, Western blot 2019 31891018 A novel enhancer RNA, Hmrhl, positively regulates its host gene, phkb, in chronic myelogenous leukemia Homo sapiens hg19 chr16 47658623 47659423 PHKB Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay ChIP-seq Luciferase Reporter Assay 2019 31891018 A novel enhancer RNA, Hmrhl, positively regulates its host gene, phkb, in chronic myelogenous leukemia Homo sapiens hg19 chr16 47657923 47659423 PHKB Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, ChIA-PET Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 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 carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF7 CVCL_0031 breast carcinoma cell CL:0000066 Enhancer activity assay ChIP-seq Luciferase Reporter Assay 2019 31164884 Mechanistic Characterization of RASGRP1 Variants Identifies an hnRNP-K-Regulated Transcriptional Enhancer Contributing to SLE Susceptibility Homo sapiens hg19 chr15 38846389 38846967 RASGRP1 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat CVCL_0065 T lymphoblast CL:0002419 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR 2019 31164884 Mechanistic Characterization of RASGRP1 Variants Identifies an hnRNP-K-Regulated Transcriptional Enhancer Contributing to SLE Susceptibility Homo sapiens hg19 chr15 38846389 38846967 RASGRP1 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR 2019 31164884 Mechanistic Characterization of RASGRP1 Variants Identifies an hnRNP-K-Regulated Transcriptional Enhancer Contributing to SLE Susceptibility Homo sapiens hg19 chr15 38850022 38850502 HNRNP-K RASGRP1 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat CVCL_0065 T lymphoblast CL:0002419 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, Western blot, RT-RT-qPCR 2019 31164884 Mechanistic Characterization of RASGRP1 Variants Identifies an hnRNP-K-Regulated Transcriptional Enhancer Contributing to SLE Susceptibility Homo sapiens hg19 chr15 38850022 38850502 HNRNP-K RASGRP1 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, Western blot, RT-RT-qPCR 2019 31164884 Mechanistic Characterization of RASGRP1 Variants Identifies an hnRNP-K-Regulated Transcriptional Enhancer Contributing to SLE Susceptibility Homo sapiens hg19 chr15 38850022 38850502 HNRNP-K RASGRP1 Enhancer Active Normal Blood UBERON:0000178 primary human T-cells T cell CL:0000084 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, Western blot, RT-RT-qPCR 2023 37370109 Epigenetic reprogramming-induced guanidinoacetic acid synthesis promotes pancreatic cancer metastasis and transcription-activating histone modifications Homo sapiens hg19 chr15 45650000 45651000 GATM Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 PANC-1-IN pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ChIP-seq CRISPRi (dCas9-KRAB), ChIP-RT-qPCR, 3C-RT-qPCR, RT-RT-qPCR, Western blot 2023 37370109 Epigenetic reprogramming-induced guanidinoacetic acid synthesis promotes pancreatic cancer metastasis and transcription-activating histone modifications Homo sapiens hg19 chr15 45650000 45651000 GATM Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 Capan-1 CVCL_0026 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ChIP-seq CRISPRi (dCas9-KRAB), ChIP-RT-qPCR, 3C-RT-qPCR, RT-RT-qPCR, Western blot 2023 37370109 Epigenetic reprogramming-induced guanidinoacetic acid synthesis promotes pancreatic cancer metastasis and transcription-activating histone modifications Homo sapiens hg19 chr15 45650000 45651000 GATM Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 CFPAC-1 CVCL_0019 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ChIP-seq CRISPRi (dCas9-KRAB), ChIP-RT-qPCR, 3C-RT-qPCR, RT-RT-qPCR, Western blot 2023 37370109 Epigenetic reprogramming-induced guanidinoacetic acid synthesis promotes pancreatic cancer metastasis and transcription-activating histone modifications Homo sapiens hg19 chr15 45675000 45676000 GATM Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 PANC-1-IN pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ChIP-seq CRISPRi (dCas9-KRAB), ChIP-RT-qPCR, 3C-RT-qPCR, RT-RT-qPCR, Western blot 2023 37370109 Epigenetic reprogramming-induced guanidinoacetic acid synthesis promotes pancreatic cancer metastasis and transcription-activating histone modifications Homo sapiens hg19 chr15 45675000 45676000 GATM Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 Capan-1 CVCL_0026 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ChIP-seq CRISPRi (dCas9-KRAB), ChIP-RT-qPCR, 3C-RT-qPCR, RT-RT-qPCR, Western blot 2023 37370109 Epigenetic reprogramming-induced guanidinoacetic acid synthesis promotes pancreatic cancer metastasis and transcription-activating histone modifications Homo sapiens hg19 chr15 45675000 45676000 GATM Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 CFPAC-1 CVCL_0019 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ChIP-seq CRISPRi (dCas9-KRAB), ChIP-RT-qPCR, 3C-RT-qPCR, RT-RT-qPCR, Western blot 2023 37370109 Epigenetic reprogramming-induced guanidinoacetic acid synthesis promotes pancreatic cancer metastasis and transcription-activating histone modifications Homo sapiens hg19 chr15 45700000 45701000 GATM Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 PANC-1-IN pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ChIP-seq CRISPRi (dCas9-KRAB), ChIP-RT-qPCR, 3C-RT-qPCR, RT-RT-qPCR, Western blot 2023 37370109 Epigenetic reprogramming-induced guanidinoacetic acid synthesis promotes pancreatic cancer metastasis and transcription-activating histone modifications Homo sapiens hg19 chr15 45700000 45701000 GATM Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 Capan-1 CVCL_0026 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ChIP-seq CRISPRi (dCas9-KRAB), ChIP-RT-qPCR, 3C-RT-qPCR, RT-RT-qPCR, Western blot 2023 37370109 Epigenetic reprogramming-induced guanidinoacetic acid synthesis promotes pancreatic cancer metastasis and transcription-activating histone modifications Homo sapiens hg19 chr15 45700000 45701000 GATM Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 CFPAC-1 CVCL_0019 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ChIP-seq CRISPRi (dCas9-KRAB), ChIP-RT-qPCR, 3C-RT-qPCR, RT-RT-qPCR, Western blot 2022 35842703 Super-enhancer profiling identifies novel critical and targetable cancer survival gene LYL1 in pediatric acute myeloid leukemia Homo sapiens hg19 chr19 13110271 13175850 GATA2 LYL1 Enhancer Active Disease acute promyelocytic leukemia MONDO:0017004 DOID:0060318 Bone Marrow UBERON:0002371 NB4 CVCL_0005 acute promyelocytic leukemia cell CL:0001054 Super enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR 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:0005132 DOID:9256 Colon UBERON:0001155 LS180 CVCL_0397 colorectal carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR 2021 33351948 Endothelial p300 promotes portal hypertension and hepatic fibrosis through CCL2-dependent macrophage recruitment Homo sapiens hg19 chr17 32562334 32563183 CCL2 Enhancer Active Normal Liver UBERON:0002107 Liver sinusoidal endothelial cell liver sinusoidal endothelial cell CL:1000413 Functional perturbation assay, Enhancer activity assay ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR 2025 41266362 Non-coding genetic variants underlying higher prostate cancer risk in men of African ancestry Homo sapiens hg19 chr8 128744932 128746104 FOXA1 NDRG1 Enhancer Silenced Disease prostate cancer MONDO:0008315 DOID:10283 Prostate gland UBERON:0002367 MDA PCa 2B cells CVCL_4740 prostate carcinoma cell CL:0000066 Enhancer activity assay ChIP-seq, ATAC-seq, RNA-seq Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR 2022 35778390 B cell receptor signaling drives APOBEC3 expression via direct enhancer regulation in chronic lymphocytic leukemia B cells Homo sapiens hg19 chr22 39370500 39372500 APOBEC3C Enhancer Silenced Normal Blood UBERON:0000178 Normal B cells B cell CL:0000945 Enhancer activity assay, TF binding assay, Functional perturbation assay CUT&Tag, ATAC-seq, Hi-C, RNA-seq CRISPR Knockout, CRISPRi, qRT-PCR, Western blot 2022 35778390 B cell receptor signaling drives APOBEC3 expression via direct enhancer regulation in chronic lymphocytic leukemia B cells Homo sapiens hg19 chr22 39378500 39380500 APOBEC3C Enhancer Silenced Normal Blood UBERON:0000178 Normal B cells B cell CL:0000945 Enhancer activity assay, TF binding assay, Functional perturbation assay CUT&Tag, ATAC-seq, Hi-C, RNA-seq CRISPR Knockout, CRISPRi, qRT-PCR, Western blot 2020 32732264 Cross-species analysis of enhancer logic using deep learning Homo sapiens hg19 chr6 396143 396593 SOX10 IRF4 Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 Human melanoma cell melanoma cell CL:0002573 Enhancer activity assay, TF binding assay ATAC-seq, ChIP-seq, RNA-seq Luciferase Reporter Assay 2015 26258633 Genome-wide association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth Homo sapiens hg19 chr10 92680870 92681128 TEAD4 ANKRD1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 CVCL_0062 breast carcinoma cell CL:0000066 Enhancer activity assay ChIP-seq Luciferase Reporter Assay 2015 26258633 Genome-wide association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth Homo sapiens hg19 chr6 132272417 132273191 TEAD4 CTGF Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 CVCL_0062 breast carcinoma cell CL:0000066 Enhancer activity assay ChIP-seq Luciferase Reporter Assay 2016 26673704 Differential contribution of cis-regulatory elements to chromatin structure and expression of the CFTR locus Homo sapiens hg19 chr7 117038917 117040917 FOXA1 CFTR Enhancer Active Normal Intestine UBERON:0000160 Human colorectal adenocarcinoma cell colorectal adenocarcinoma cell CL:0000066 Functional perturbation assay ChIP-seq CRISPR Knockout, qRT-PCR 2019 31217582 Noncoding deletions reveal a gene that is critical for intestinal function Homo sapiens hg19 chr16 1480850 1482378 FOXA1 LACZ Enhancer Active Normal Stomach UBERON:0000945 Gastrointestinal epithelial cells gastrointestinal epithelial cell CL:0000066 Enhancer activity assay, Functional perturbation assay WGS, WES, RNA-seq, ChIP-seq Transgenic Reporter Assay, CRISPR Knockout, RT-RT-qPCR, Western blot 2022 35778390 B cell receptor signaling drives APOBEC3 expression via direct enhancer regulation in chronic lymphocytic leukemia B cells Homo sapiens hg19 chr22 39385500 39387500 APOBEC3C Enhancer Active Disease chronic lymphocytic leukemia MONDO:0004951 DOID:1040 Blood UBERON:0000178 Primary CLL B cells B cell CL:0000945 Enhancer activity assay, TF binding assay, Functional perturbation assay CUT&Tag, ATAC-seq, Hi-C, RNA-seq CRISPR knockout, CRISPRi, RT-RT-qPCR, Western blot 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr13 37428439 37429439 SMAD9 Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 HD-MB03 CVCL_IT11 medulloblastoma cell CL:0000127 Chromatin interaction assay, Enhancer-target gene assignment assay 4C-seq, ChIP-seq, RNA-seq RT-RT-qPCR 2016 26795348 Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus Homo sapiens hg19 chr2 202122995 202124526 STAT3; MYC; CTCF CASP8 Enhancer Active Normal Breast UBERON:0000310 HMEC CVCL_U869 mammary epithelial cell CL:0000066 Enhancer activity assay, TF binding assay, eQTL analysis, Genetic association study Targeted DNA sequencing, Strand-specific RNA-seq, ChIP-seq Luciferase reporter assay, RT-RT-qPCR, Sanger sequencing 2016 26795348 Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus Homo sapiens hg19 chr2 202122995 202124526 STAT3; MYC; CTCF CASP8 Enhancer Active Normal Breast UBERON:0000310 MCF-10A CVCL_0598 breast epithelial cell CL:0000066 Enhancer activity assay, TF binding assay, eQTL analysis, Genetic association study Targeted DNA sequencing, Strand-specific RNA-seq, ChIP-seq Luciferase reporter assay, RT-RT-qPCR, Sanger sequencing 2016 26795348 Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus Homo sapiens hg19 chr2 202122995 202124526 STAT3; MYC; CTCF CASP8 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 T-47D CVCL_0553 breast carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, eQTL analysis, Genetic association study Targeted DNA sequencing, Strand-specific RNA-seq, ChIP-seq Luciferase reporter assay, RT-RT-qPCR, Sanger sequencing 2016 26795348 Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus Homo sapiens hg19 chr2 202122995 202124526 STAT3; MYC; CTCF CASP8 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF-7 CVCL_0031 breast carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, eQTL analysis, Genetic association study Targeted DNA sequencing, Strand-specific RNA-seq, ChIP-seq Luciferase reporter assay, RT-RT-qPCR, Sanger sequencing 2020 33020665 Highly interconnected enhancer communities control lineage-determining genes in human mesenchymal stem cells Homo sapiens hg19 chr7 107615000 107635000 LAMB1 Enhancer Active Normal Bone marrow UBERON:0002371 bone marrow mesenchymal stem mesenchymal stem cell CL:0000134 Enhancer activity assay, Chromatin interaction assay, eQTL validation ECHi-C, ChIP-seq, DNase-seq, scATAC-seq, RNA-seq RT-RT-qPCR 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 Bone marrow UBERON:0002371 bone marrow mesenchymal stem mesenchymal stem cell CL:0000134 Enhancer activity assay, Chromatin interaction assay, TF binding assay ECHi-C, ChIP-seq, scATAC-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 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 Bone marrow UBERON:0002371 bone marrow mesenchymal stem mesenchymal stem cell CL:0000134 Enhancer activity assay, Chromatin interaction assay, TF binding assay ECHi-C, ChIP-seq, scATAC-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 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 Bone marrow UBERON:0002371 bone marrow mesenchymal stem mesenchymal stem cell CL:0000134 Enhancer activity assay, Chromatin interaction assay, TF binding assay ECHi-C, ChIP-seq, scATAC-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2020 33020665 Highly interconnected enhancer communities control lineage-determining genes in human mesenchymal stem cells Homo sapiens hg19 chr6 132200000 132202000 TEAD1; TEAD4 CTGF Enhancer Active Normal Bone marrow UBERON:0002371 bone marrow mesenchymal stem mesenchymal stem cell CL:0000134 Enhancer activity assay, Chromatin interaction assay, TF binding assay ECHi-C, ChIP-seq, scATAC-seq, scRNA-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2020 33020665 Highly interconnected enhancer communities control lineage-determining genes in human mesenchymal stem cells Homo sapiens hg19 chr4 54950000 54952000 TEAD1; TEAD4 PDGFRA Enhancer Active Normal Bone marrow UBERON:0002371 bone marrow mesenchymal stem mesenchymal stem cell CL:0000134 Enhancer activity assay, Chromatin interaction assay, TF binding assay ECHi-C, ChIP-seq, scATAC-seq, scRNA-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 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 Bone marrow UBERON:0002371 bone marrow mesenchymal stem mesenchymal stem cell CL:0000134 Enhancer activity assay, Chromatin interaction assay, TF binding assay ECHi-C, ChIP-seq, scATAC-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2022 34980595 GFI1 Cooperates with IKZF1/IKAROS to Activate Gene Expression in T-cell Acute Lymphoblastic Leukemia Homo sapiens hg19 chr1 92948000 92952000 GFI1 GFI1 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Bone marrow UBERON:0002371 Jurkat T-ALL CVCL_0065 T lymphoblast CL:0002419 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR 2022 34980595 GFI1 Cooperates with IKZF1/IKAROS to Activate Gene Expression in T-cell Acute Lymphoblastic Leukemia Homo sapiens hg19 chr1 92952000 92956000 GFI1 GFI1 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Bone marrow UBERON:0002371 Jurkat T-ALL CVCL_0065 T lymphoblast CL:0002419 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR 2015 26445536 HMOX1 enhancer via Nrf2 activation Homo sapiens hg19 chr22 43012000 43013000 NFE2L2 HMOX1 Enhancer Active Normal Umbilical vein UBERON:0002066 HUVEC CVCL_2959 umbilical vein endothelial cell CL:0002615 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ELISA 2015 26257940 Genome-wide association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth Homo sapiens hg19 chr6 132272417 132273191 TEAD4 CTGF Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 CVCL_0062 breast carcinoma cell CL:0000066 Enhancer activity assay ChIP-seq Luciferase Reporter Assay 2014 24288367 Establishment of active chromatin structure at enhancer elements by mixed-lineage leukemia 1 to initiate estrogen-dependent gene expression Homo sapiens hg19 chr21 42770000 42770700 ESR1 TFF1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF7 CVCL_0031 breast carcinoma cell CL:0000066 Enhancer activity assay ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2024 38490101 Enhancer infestation drives tumorigenic activation of inactive B compartment in Epstein-Barr virus-positive nasopharyngeal carcinoma Homo sapiens hg19 chr1 191100000 191150000 SMAD3; REL PLA2G4A Enhancer Active Disease nasopharyngeal carcinoma MONDO:0005350 DOID:9260 Nasopharyngeal epithelium UBERON:0008338 C666-1 CVCL_7949 nasopharyngeal carcinoma cell CL:0000069 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, 4C-seq, ChIP-seq, RNA-seq siRNA Knockdown, RT-RT-qPCR, Western blot, IHC 2024 38490101 Enhancer infestation drives tumorigenic activation of inactive B compartment in Epstein-Barr virus-positive nasopharyngeal carcinoma Homo sapiens hg19 chr1 185660000 185710000 SMAD3; REL PTGS2 Enhancer Active Disease nasopharyngeal carcinoma MONDO:0005350 DOID:9260 Nasopharyngeal epithelium UBERON:0008338 C666-1 CVCL_7949 nasopharyngeal carcinoma cell CL:0000069 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, 4C-seq, ChIP-seq, RNA-seq siRNA Knockdown, RT-RT-qPCR, Western blot 2024 38490101 Enhancer infestation drives tumorigenic activation of inactive B compartment in Epstein-Barr virus-positive nasopharyngeal carcinoma Homo sapiens hg19 chr6 134350000 134400000 SMAD3; REL CITED2 Enhancer Active Disease nasopharyngeal carcinoma MONDO:0005350 DOID:9260 Nasopharyngeal epithelium UBERON:0008338 C666-1 CVCL_7949 nasopharyngeal carcinoma cell CL:0000069 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, 4C-seq, ChIP-seq, RNA-seq siRNA Knockdown, RT-RT-qPCR, Western blot 2023 37729434 TP63 fusions drive multicomplex enhancer rewiring, lymphomagenesis, and EZH2 dependence Homo sapiens hg19 chr8 127580017 127580036 TP63 MYC Enhancer Active Disease blastic plasmacytoid dendritic cell neoplasm MONDO:0019474 DOID:0080738 Lymph node UBERON:0000029 SMZ-1 plasmacytoid dendritic cell CL:0000786 Regulatory element functional validation, 3D chromatin interaction mapping ChIP-seq, HiChIP, PRO-seq, RNA-seq, CRISPR-Cas9 screening qRT-PCR, and ChIP-qPCR 2023 37729434 TP63 fusions drive multicomplex enhancer rewiring, lymphomagenesis, and EZH2 dependence Homo sapiens hg19 chr11 85780828 85780847 TP63 EED Enhancer Active Disease blastic plasmacytoid dendritic cell neoplasm MONDO:0019474 DOID:0080738 Lymph node UBERON:0000029 SMZ-1 plasmacytoid dendritic cell CL:0000786 Regulatory element functional validation, 3D chromatin interaction mapping ChIP-seq, HiChIP, PRO-seq, RNA-seq, CRISPR-Cas9 screening qRT-PCR, and ChIP-qPCR 2023 37729434 TP63 fusions drive multicomplex enhancer rewiring, lymphomagenesis, and EZH2 dependence Homo sapiens hg19 chr11 85773039 85773058 TP63 EED Enhancer Active Disease blastic plasmacytoid dendritic cell neoplasm MONDO:0019474 DOID:0080738 Lymph node UBERON:0000029 SMZ-1 plasmacytoid dendritic cell CL:0000786 Regulatory element functional validation, 3D chromatin interaction mapping ChIP-seq, HiChIP, PRO-seq, RNA-seq, CRISPR-Cas9 screening qRT-PCR, and ChIP-qPCR 2016 26795348 Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus Homo sapiens hg19 chr2 202122200 202123730 MYC CASP8 Enhancer Silenced Normal Breast UBERON:0000310 MCF10A CVCL_0598 breast epithelial cell CL:0000066 Enhancer activity assay ChIP-seq, RNA-seq Luciferase reporter assay, RT-RT-qPCR 2016 26795348 Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus Homo sapiens hg19 chr2 202204360 202205118 MYC CASP8 Enhancer Silenced Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 T-47D CVCL_0553 breast carcinoma cell CL:0000066 Enhancer activity assay ChIP-seq, RNA-seq Luciferase reporter assay, RT-RT-qPCR 2012 22665440 Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q243 prostate cancer risk locus Homo sapiens hg19 chr17 69108466 69108765 FOXA1 SOX9 Enhancer Active Normal Breast UBERON:0000310 MCF10A CVCL_0598 breast epithelial cell CL:0000066 Enhancer activity assay, TF binding assay ChIP-seq, DNase-seq Luciferase reporter assay, ChIP-RT-qPCR, Sanger sequencing 2012 22665440 Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q243 prostate cancer risk locus Homo sapiens hg19 chr17 69108466 69108765 FOXA1 SOX9 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay ChIP-seq, DNase-seq Luciferase reporter assay, ChIP-RT-qPCR, Sanger sequencing 2015 26257940 Genome-wide association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth Homo sapiens hg19 chr10 92680870 92681128 TEAD4 ANKRD1 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 VCaP cells CVCL_2235 prostate carcinoma cell CL:0000066 Enhancer activity assay ChIP-seq Luciferase Reporter Assay 2014 23698277 Aberrant TAL1 activation is mediated by an interchromosomal interaction in human T-cell acute lymphoblastic leukemia Homo sapiens hg19 chr16 19866900 19867895 C-MAF TAL1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 CVCL_0062 breast carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2023 37749332 Interaction between estrogen receptor-?? and PNPLA3 pI148M 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:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat CVCL_0065 T lymphoblast CL:0002419 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, qRT-PCR, Western blot 2022 35741778 Discovery and Functional Characterization of Two Regulatory Variants Underlying Lupus Susceptibility at 2p131 Homo sapiens hg19 chr2 74399364 74399764 ARID3A DGUOK Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepG2 CVCL_0027 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, qRT-PCR, Western blot 2021 34782839 TNF-??-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer Homo sapiens hg19 chr10 17275000 17276500 JUN VIM Enhancer Active Normal Blood UBERON:0000178 GM12878 CVCL_7526 B lymphoblastoid cell CL:0000945 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, qRT-PCR, Western blot 2021 34155213 A gain-of-function single nucleotide variant creates a new promoter which acts as an orientation-dependent enhancer-blocker Homo sapiens hg19 chr16 120000 121400 GATA1; KLF1; TAL1 HBA1 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 CAPAN1 CVCL_0026 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay ChIP-seq, ATAC-seq, RNA-seq, 3C-seq ChIP-RT-qPCR, qRT-PCR 2021 34155213 A gain-of-function single nucleotide variant creates a new promoter which acts as an orientation-dependent enhancer-blocker Homo sapiens hg19 chr16 144000 145400 GATA1; KLF1; TAL1 HBA1 Enhancer Active Normal Blood UBERON:0000178 iPSC-derived erythroblasts iPSC-derived erythroblast CL:0000765 Enhancer activity assay, Chromatin interaction assay ChIP-seq, ATAC-seq, RNA-seq, 3C-seq ChIP-RT-qPCR, qRT-PCR 2021 34155213 A gain-of-function single nucleotide variant creates a new promoter which acts as an orientation-dependent enhancer-blocker Homo sapiens hg19 chr16 183000 184400 GATA1; KLF1; TAL1 HBA1 Enhancer Active Normal Blood UBERON:0000178 iPSC-derived erythroblasts iPSC-derived erythroblast CL:0000765 Enhancer activity assay, Chromatin interaction assay ChIP-seq, ATAC-seq, RNA-seq, 3C-seq ChIP-RT-qPCR, qRT-PCR 2021 34155213 A gain-of-function single nucleotide variant creates a new promoter which acts as an orientation-dependent enhancer-blocker Homo sapiens hg19 chr16 194000 195400 GATA1; KLF1; TAL1 HBA1 Enhancer Active Normal Blood UBERON:0000178 iPSC-derived erythroblasts iPSC-derived erythroblast CL:0000765 Enhancer activity assay, Chromatin interaction assay ChIP-seq, ATAC-seq, RNA-seq, 3C-seq ChIP-RT-qPCR, qRT-PCR 2024 39277592 Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance Homo sapiens hg19 chr3 30300000 31100000 PTPRG Enhancer Silenced Normal Blood UBERON:0000178 iPSC-derived erythroblasts iPSC-derived erythroblast CL:0000765 Chromatin interaction assay, Functional perturbation assay Hi-C, ATAC-seq, H3K27ac ChIP-seq, RNA-seq RT-RT-qPCR 2024 39277592 Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance Homo sapiens hg19 chr20 61300000 61600000 BCL2L1 Enhancer Active Disease mantle cell lymphoma MONDO:0005052 DOID:0050747 Blood UBERON:0000178 Rec-1 CVCL_1884 B cell CL:0000945 Chromatin interaction assay, Functional perturbation assay Hi-C, ATAC-seq, H3K27ac ChIP-seq, RNA-seq RT-RT-qPCR 2016 26795348 Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus Homo sapiens hg19 chr2 202122500 202124030 STAT3; MYC; CTCF CASP8 Enhancer Active Disease mantle cell lymphoma MONDO:0005052 DOID:0050747 Blood UBERON:0000178 Rec-1 CVCL_1884 B cell CL:0000945 Enhancer activity assay, TF binding assay RNA-seq, ChIP-seq Luciferase Reporter Assay, RT-RT-qPCR 2016 26795348 Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus Homo sapiens hg19 chr2 202122500 202124030 STAT3; MYC; CTCF CASP8 Enhancer Active Normal Breast UBERON:0000310 MCF10A CVCL_0598 breast epithelial cell CL:0000066 Enhancer activity assay, TF binding assay RNA-seq, ChIP-seq Luciferase Reporter Assay, RT-RT-qPCR 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:0006120 DOID:1612 Breast UBERON:0000310 T-47D CVCL_0553 breast carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay RNA-seq, ChIP-seq Luciferase Reporter Assay, RT-RT-qPCR 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 Normal Breast UBERON:0000310 MCF10A CVCL_0598 breast epithelial cell CL:0000066 Enhancer activity assay, TF binding assay RNA-seq, ChIP-seq Luciferase Reporter Assay, RT-RT-qPCR 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr1 165355703 165356702 LMX1A LMX1A Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 T-47D CVCL_0553 breast carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Transgenic Reporter Assay, CRISPR Knockout, RT-RT-qPCR, Western blot, Immunofluorescence 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr1 165355703 165356702 LMX1A LMX1A Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 Primary Medulloblastoma Tissue (Group4 subgroup) medulloblastoma cell CL:0000127 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Transgenic Reporter Assay, CRISPR Knockout, RT-RT-qPCR, Western blot, Immunofluorescence 2019 30612741 A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens Homo sapiens hg19 chr1 182307087 182307634 GLUL Enhancer Active Normal Cerebellum UBERON:0002037 Mouse Embryonic Cerebellum mouse embryonic cerebellum CL:0000540 Functional validation scRNA-seq, RNA-seq CRISPRi, CRISPR KO, RT-RT-qPCR 2019 30612741 A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens Homo sapiens hg19 chr1 182308166 182308458 GLUL Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional validation scRNA-seq, RNA-seq CRISPRi, CRISPR KO, RT-RT-qPCR 2019 30612741 A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens Homo sapiens hg19 chr1 71140581 71141097 PTGER3 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional validation scRNA-seq, RNA-seq CRISPRi, RT-RT-qPCR 2019 30612741 A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens Homo sapiens hg19 chr16 23833191 23833694 PRKCB Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional validation scRNA-seq, RNA-seq CRISPRi, RT-RT-qPCR 2019 30612741 A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens Homo sapiens hg19 chr2 127402697 127403360 GYPC Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional validation scRNA-seq, RNA-seq CRISPRi, RT-RT-qPCR 2019 30612741 A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens Homo sapiens hg19 chr4 56595855 56596581 NMU Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional validation scRNA-seq, RNA-seq CRISPRi, CRISPR KO, RT-RT-qPCR, FlowFISH 2019 30612741 A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens Homo sapiens hg19 chr4 56596632 56597095 NMU Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional validation scRNA-seq, RNA-seq CRISPRi, CRISPR KO, RT-RT-qPCR, FlowFISH 2019 30612741 A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens Homo sapiens hg19 chr4 56600029 56600394 NMU Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional validation scRNA-seq, RNA-seq CRISPRi, CRISPR KO, RT-RT-qPCR, FlowFISH 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 HMX1 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, Chromatin interaction assay ChIP-seq, ATAC-seq, Hi-C Transgenic Reporter Assay 2023 37041138 Enhancer hijacking at the ARHGAP36 locus is associated with connective tissue to bone transformation Homo sapiens hg19 chr2 69343058 70165537 ARHGAP36 Enhancer Active Normal Craniofacial Tissue UBERON:0010368 hCNCC cranial neural crest cell CL:0000333 Chromatin interaction assay, Functional perturbation assay Hi-C, RNA-seq, ChIP-seq RT-RT-qPCR, Western blot, FISH 2019 31784727 Activity-by-contact model of enhancer-promoter regulation from thousands of CRISPR perturbations Homo sapiens hg19 chr1 109714926 109989926 SORT1 Enhancer Active Normal Connective Tissue UBERON:0002384 Primary human fibroblasts fibroblast CL:0000057 Enhancer-target gene connection validation ABC model prediction, H3K27ac ChIP-seq, DNase-seq CRISPR genome editing, eQTL analysis 2020 32493985 GATA2 Regulates Constitutive PD-L1 and PD-L2 Expression in Brain Tumors Homo sapiens hg19 chr9 5455064 5456191 FOS CD274 Enhancer Active Normal Liver UBERON:0002107 Primary human hepatocytes hepatocyte CL:0000182 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR, Flow Cytometry 2020 32493985 GATA2 Regulates Constitutive PD-L1 and PD-L2 Expression in Brain Tumors Homo sapiens hg19 chr9 5455064 5456191 FOS CD274 Enhancer Active Disease meningioma MONDO:0005149 DOID:3565 Brain UBERON:0000955 Human meningioma cell meningioma cell CL:0000127 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR, Flow Cytometry 2020 32493985 GATA2 Regulates Constitutive PD-L1 and PD-L2 Expression in Brain Tumors Homo sapiens hg19 chr9 5455064 5456191 FOS CD274 Enhancer Active Disease meningioma MONDO:0005149 DOID:3565 Brain UBERON:0000955 KALS1 meningioma cell CL:0000127 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR, Flow Cytometry 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:0005149 DOID:3565 Brain UBERON:0000955 Brain tumor initiating cells brain tumor initiating cell CL:0000127 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR, Flow Cytometry, shRNA Knockdown, Western blot 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:0005149 DOID:3565 Brain UBERON:0000955 Human meningioma cell meningioma cell CL:0000127 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR, Flow Cytometry, shRNA Knockdown, Western blot 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:0005149 DOID:3565 Brain UBERON:0000955 KALS1 meningioma cell CL:0000127 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR, Flow Cytometry, shRNA Knockdown, Western blot 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:0005149 DOID:3565 Brain UBERON:0000955 Brain tumor initiating cells brain tumor initiating cell CL:0000127 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR, Flow Cytometry 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:0005149 DOID:3565 Brain UBERON:0000955 Human meningioma cell meningioma cell CL:0000127 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR, Flow Cytometry 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:0005149 DOID:3565 Brain UBERON:0000955 KALS1 meningioma cell CL:0000127 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR, Flow Cytometry 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:0005149 DOID:3565 Brain UBERON:0000955 Brain tumor initiating cells brain tumor initiating cell CL:0000127 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR, Flow Cytometry, shRNA Knockdown, Western blot 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:0005149 DOID:3565 Brain UBERON:0000955 Human meningioma cell meningioma cell CL:0000127 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR, Flow Cytometry, shRNA Knockdown, Western blot 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:0005149 DOID:3565 Brain UBERON:0000955 KALS1 meningioma cell CL:0000127 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR, Flow Cytometry, shRNA Knockdown, Western blot 2016 26615198 CFTR regulatory elements identified by 5C Homo sapiens hg19 chr7 117130000 117131000 HNF1 CFTR Enhancer Active Disease meningioma MONDO:0005149 DOID:3565 Brain UBERON:0000955 Brain tumor initiating cells brain tumor initiating cell CL:0000127 Enhancer activity assay ChIP-seq Luciferase Reporter Assay 2016 26751173 Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9 Homo sapiens hg19 chr11 69448000 69452000 CCND1 Enhancer Active Disease colorectal adenocarcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 Caco-2 CVCL_0025 colorectal adenocarcinoma cell CL:0000066 Genetic perturbation screen CRISPR dropout screen sequencing Luciferase Reporter Assay 2017 29116202 Acetylated histone variant H2AZ is involved in the activation of neo-enhancers in prostate cancer Homo sapiens hg19 chr2 11679389 11680097 AR GREB1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF-7 CVCL_0031 breast carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, NOMe-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2017 29116202 Acetylated histone variant H2AZ 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 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, NOMe-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2017 29116202 Acetylated histone variant H2AZ 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 VCaP CVCL_2235 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, NOMe-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2017 29116202 Acetylated histone variant H2AZ 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 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, NOMe-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2017 27980063 BRD4 promotes p63 and GRHL3 expression downstream of FOXO in mammary epithelial cells Homo sapiens hg19 chr3 189630000 189680000 BRD4 TP63 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate gland UBERON:0002367 VCaP CVCL_2235 prostate carcinoma cell CL:0000066 Enhancer activity assay ChIP-seq Luciferase Reporter Assay, RT-RT-qPCR, ChIP-RT-qPCR, Western blot 2017 27980063 BRD4 promotes p63 and GRHL3 expression downstream of FOXO in mammary epithelial cells Homo sapiens hg19 chr1 24520000 24525000 BRD4 GRHL3 Enhancer Active Normal Breast UBERON:0000310 MCF10A CVCL_0598 breast epithelial cell CL:0000066 Enhancer activity assay ChIP-seq Luciferase Reporter Assay, RT-RT-qPCR, ChIP-RT-qPCR, Western blot 2017 28260788 APOBEC signature mutation generates an oncogenic enhancer that drives LMO1 expression in T-ALL Homo sapiens hg19 chr11 8289480 8289520 MYB LMO1 Enhancer Active Normal Breast UBERON:0000310 MCF10A CVCL_0598 breast epithelial cell CL:0000066 Enhancer activity assay ChIP-seq Luciferase Reporter Assay 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:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat CVCL_0065 T lymphoblast CL:0002419 Enhancer activity assay ChIP-seq Luciferase Reporter Assay 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 breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF7 CVCL_0031 breast carcinoma cell CL:0000066 Enhancer activity assay ChIP-seq Luciferase Reporter Assay 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 lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 A549 CVCL_0023 lung adenocarcinoma cell CL:0001069 Enhancer activity assay, TF binding assay ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 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:0005132 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2018 29348663 Enhancer-associated long non-coding RNA LEENE regulates endothelial nitric oxide synthase and endothelial function Homo sapiens hg19 chr14 56265000 56275000 KLF4 NOS3 Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 HT29 CVCL_0320 colorectal carcinoma cell CL:0000066 Enhancer activity assay, chromatin interaction assay ChIP-seq, Hi-C, 4C-seq qRT-PCR, and ChIP-qPCR 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 Normal Umbilical vein UBERON:0002066 HUVEC CVCL_2959 umbilical vein endothelial cell CL:0002615 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 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 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2023 37066790 SOX17 enhancer variants disrupt transcription factor binding and enhancer inactivity drives pulmonary hypertension Homo sapiens hg19 chr8 41090000 41090300 RORA SOX17 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 Hep3B CVCL_0326 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR 2023 36877164 LSD1 inhibition disrupts super-enhancer driven oncogenic transcriptional programs in castration-resistant prostate cancer Homo sapiens hg19 chr8 128748351 128800823 FOXA1; MYC MYC Enhancer Active Normal Pulmonary artery UBERON:0002012 hPAEC pulmonary artery endothelial cell CL:1001567 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2023 36877164 LSD1 inhibition disrupts super-enhancer driven oncogenic transcriptional programs in castration-resistant prostate cancer Homo sapiens hg19 chr8 128748351 128800823 FOXA1; MYC MYC Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 CWR22RV1 CVCL_1045 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2023 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 MIR146A Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP95 CVCL_WK56 prostate carcinoma cell CL:0000066 Functional perturbation assay Hi-C, ATAC-seq CRISPR Knockout, CRISPRi, RT-RT-qPCR 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 Blood UBERON:0000178 Monocyte monocyte CL:0000576 Super enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR 2022 35316324 Concurrent CDX2 cis-deregulation and UBTF::ATXN7L3 fusion define a novel high-risk subtype of B-cell ALL Homo sapiens hg19 chr13 27950000 27980000 CDX2 Enhancer Active Disease small cell lung carcinoma MONDO:0005020 DOID:5409 Lung UBERON:0002048 H128 CVCL_1491 small cell lung carcinoma cell CL:0000066 Histone modification ChIP-seq, Chromosome conformation capture sequencing, CRISPR interference H3K27ac ChIP-seq, H3K4me3 ChIP-seq, ATAC-seq, 4C-seq RT-RT-qPCR, Western blot 2022 35316324 Concurrent CDX2 cis-deregulation and UBTF::ATXN7L3 fusion define a novel high-risk subtype of B-cell ALL Homo sapiens hg19 chr13 27950000 27980000 PAN3 Enhancer Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0080545 Bone Marrow UBERON:0002371 NALM16 CVCL_1891 B lymphoblast CL:0000945 Histone modification ChIP-seq, Chromosome conformation capture sequencing, CRISPR interference H3K27ac ChIP-seq, H3K4me3 ChIP-seq, ATAC-seq, 4C-seq RT-RT-qPCR, Western blot 2022 35316324 Concurrent CDX2 cis-deregulation and UBTF::ATXN7L3 fusion define a novel high-risk subtype of B-cell ALL Homo sapiens hg19 chr13 27950000 27980000 FLT3 Enhancer Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0080545 Bone Marrow UBERON:0002371 primary human B-ALL blasts B lymphoblast CL:0000945 Histone modification ChIP-seq, Chromosome conformation capture sequencing, CRISPR interference H3K27ac ChIP-seq, H3K4me3 ChIP-seq, ATAC-seq, 4C-seq RT-RT-qPCR, Western blot 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 CDX2 CDX2 Promoter Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0080545 Bone Marrow UBERON:0002371 PDX B-ALL cells patient-derived xenograft B-ALL cell CL:0000945 Histone modification ChIP-seq, Chromosome conformation capture sequencing, RNA-DNA FISH H3K27ac ChIP-seq, H3K4me3 ChIP-seq, 4C-seq, RNA-seq Allele-specific expression analysis 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 CDX2 CDX2 Promoter Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0080545 Bone Marrow UBERON:0002371 NALM16 CVCL_1891 B lymphoblast CL:0000945 Histone modification ChIP-seq, Chromosome conformation capture sequencing, RNA-DNA FISH H3K27ac ChIP-seq, H3K4me3 ChIP-seq, 4C-seq, RNA-seq Allele-specific expression analysis 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 CDX2 CDX2 Promoter Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0080545 Bone Marrow UBERON:0002371 primary human B-ALL blasts B lymphoblast CL:0000945 Histone modification ChIP-seq, Chromosome conformation capture sequencing, RNA-DNA FISH H3K27ac ChIP-seq, H3K4me3 ChIP-seq, 4C-seq, RNA-seq Allele-specific expression analysis 2019 31078271 The SNP of rs6854845 suppresses transcription via the DNA looping structure alteration of super-enhancer in colon cells Homo sapiens hg19 chr4 75746565 75746914 EREG Enhancer Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0080545 Bone Marrow UBERON:0002371 PDX B-ALL cells patient-derived xenograft B-ALL cell CL:0000945 Chromatin interaction assay, Functional perturbation assay Hi-C, RNA-seq 3C, RT-RT-qPCR, CRISPR knockout 2025 41266362 Non-coding genetic variants underlying higher prostate cancer risk in men of African ancestry Homo sapiens hg19 chr8 128751884 128753219 MYC Enhancer Active Normal Colon UBERON:0001155 Normal colon epithelial cells colon epithelial cell CL:1000348 Enhancer activity assay ATAC-seq, RNA-seq Luciferase reporter assay, RT-RT-qPCR 2019 31078271 The SNP of rs6854845 suppresses transcription via the DNA looping structure alteration of super-enhancer in colon cells Homo sapiens hg19 chr4 76213678 76224314 CXCL2 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate gland UBERON:0002367 LNCaP cells CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay ChIP-seq ChIP-RT-qPCR, CRISPR Knockout 2019 31078271 The SNP of rs6854845 suppresses transcription via the DNA looping structure alteration of super-enhancer in colon cells Homo sapiens hg19 chr4 76213678 76224314 CXCL2,CXCL3,CXCL5,CXCL6,CXCL8,EPGN Enhancer Active Normal Colon UBERON:0001155 FHC mutant cells CVCL_3806 colon epithelial cell CL:1000348 Enhancer activity assay ChIP-seq ChIP-RT-qPCR, CRISPR Knockout 2023 37041138 Enhancer hijacking at the ARHGAP36 locus is associated with connective tissue to bone transformation Homo sapiens hg19 chr2 69342699 69343679 ANTXR1 Enhancer Active Normal Colon UBERON:0001155 FHC mutant cells CVCL_3806 colon epithelial cell CL:1000348 Chromatin interaction assay, Enhancer activity assay, Functional perturbation assay Hi-C, RNA-seq, ChIP-seq RT-RT-qPCR, Western blot, Alizarin Red Staining 2023 37041138 Enhancer hijacking at the ARHGAP36 locus is associated with connective tissue to bone transformation Homo sapiens hg19 chr2 69342699 69343679 ARHGAP36 Enhancer Active Normal Connective Tissue UBERON:0002384 Primary fibroblasts fibroblast CL:0000057 Chromatin interaction assay, Enhancer activity assay, Functional perturbation assay Hi-C, RNA-seq, ChIP-seq RT-RT-qPCR, Western blot, Alizarin Red Staining 2023 37041138 Enhancer hijacking at the ARHGAP36 locus is associated with connective tissue to bone transformation Homo sapiens hg19 chr2 69342699 69343679 Enhancer Active Normal Bone Marrow UBERON:0002371 Mesenchymal stromal cells mesenchymal stromal cell CL:0000134 Chromatin interaction assay, Enhancer activity assay, Functional perturbation assay Hi-C, RNA-seq, ChIP-seq RT-RT-qPCR, Western blot, Alizarin Red Staining 2019 31078271 The SNP of rs6854845 suppresses transcription via the DNA looping structure alteration of super-enhancer in colon cells Homo sapiens hg19 chr4 75746565 75746914 EREG Enhancer Active Normal Cartilage UBERON:0002418 Chondrocytes chondrocyte CL:0000138 Chromatin interaction assay, Functional perturbation assay Hi-C, RNA-seq 3C, RT-RT-qPCR, CRISPR Knockout 2020 32060133 A TGF-??- and p63-Responsive Enhancer Regulates IFN-?? Expression in Human Keratinocytes Homo sapiens hg19 chr9 27519599 27519750 TP63 IFNK Enhancer Active Normal Colon UBERON:0001155 Human normal colon epithelial cell colon epithelial cell CL:1000348 Enhancer activity assay RNA-seq, ChIP-seq Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, siRNA knockdown, qRT-PCR, Western blot 2020 32060133 A TGF-??- and p63-Responsive Enhancer Regulates IFN-?? Expression in Human Keratinocytes Homo sapiens hg19 chr9 27519749 27519900 JUNB IFNK Enhancer Active Normal Skin UBERON:0000014 Normal human keratinocytes keratinocyte CL:0000312 Enhancer activity assay RNA-seq, ChIP-seq Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, siRNA knockdown, qRT-PCR, Western blot 2020 32060133 A TGF-??- and p63-Responsive Enhancer Regulates IFN-?? Expression in Human Keratinocytes Homo sapiens hg19 chr9 27520189 27520340 TFAP2A IFNK Enhancer Active Normal Skin UBERON:0000014 Normal human keratinocytes keratinocyte CL:0000312 Enhancer activity assay RNA-seq, ChIP-seq Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, siRNA knockdown, qRT-PCR, Western blot 2022 36321446 The FES Gene at the 15q26 Coronary-Artery-Disease Locus Inhibits Atherosclerosis Homo sapiens hg19 chr15 89411868 89412019 FES Enhancer Active Normal Skin UBERON:0000014 Normal human keratinocytes keratinocyte CL:0000312 TF binding assay, Functional perturbation assay RNA-seq CRISPR Knockout, CRISPRi, qRT-PCR, Western blot, EMSA 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 CR2 Enhancer Active Disease acute monocytic leukemia MONDO:0005025 DOID:0080147 Blood UBERON:0000178 Human monocytic leukemia cell CVCL_0006 acute monocytic leukemia cell CL:0000576 Functional perturbation assay Hi-C, 3C-seq CRISPR Knockout, RT-RT-qPCR, Flow Cytometry 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 CR2 Enhancer Active Normal Blood UBERON:0000178 Reh CVCL_1650 B lymphoblast CL:0000945 Functional perturbation assay Hi-C, 3C-seq CRISPR Knockout, RT-RT-qPCR, Flow Cytometry 2019 31078271 The SNP of rs6854845 suppresses transcription via the DNA looping structure alteration of super-enhancer in colon cells Homo sapiens hg19 chr4 75700000 76000000 Enhancer Active Normal Blood UBERON:0000178 Reh CVCL_1650 B lymphoblast CL:0000945 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, RNA-seq 3C, CRISPR knockout, ChIP-RT-qPCR, RT-RT-qPCR 2019 31078271 The SNP of rs6854845 suppresses transcription via the DNA looping structure alteration of super-enhancer in colon cells Homo sapiens hg19 chr4 76191350 76202240 EREG Enhancer Silenced Normal Colon UBERON:0001155 Human normal colon epithelial cell colon epithelial cell CL:1000348 Enhancer activity assay ChIP-seq ChIP-RT-qPCR, CRISPR knockout 2019 31078271 The SNP of rs6854845 suppresses transcription via the DNA looping structure alteration of super-enhancer in colon cells Homo sapiens hg19 chr4 76192040 76237727 Enhancer Active Normal Colon UBERON:0001155 FHC mutant cells CVCL_3806 colon epithelial cell CL:1000348 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, RNA-seq 3C, CRISPR knockout, ChIP-RT-qPCR, RT-RT-qPCR 2016 27333824 Regulation of Laminin gamma 2 expression by CDX2 in colonic epithelial cells is impaired during active inflammation Homo sapiens hg19 chr1 183149939 183150336 RELA LAMC2 Enhancer Active Normal Colon UBERON:0001155 Human normal colon epithelial cell colon epithelial cell CL:1000348 Enhancer activity assay, TF binding assay ChIP-seq Luciferase reporter assay 2015 25381333 Functional characterization of CYP2D6 enhancer polymorphisms Homo sapiens hg19 chr22 42412900 42413141 CYP2D6 Enhancer Active Disease colorectal adenocarcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 Caco-2 CVCL_0025 colorectal adenocarcinoma cell CL:0000066 Enhancer activity assay Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR 2015 26232425 PXR Activation Modulates HepG2 Cell Morphology and Migration Through the HNF4??-IGFBP1 Signaling Axis Homo sapiens hg19 chr20 43210000 43212000 NR1I2 HNF4A Enhancer Silenced Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepG2 hepatocellular carcinoma CVCL_0027 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay ChIP-seq Luciferase Reporter Assay 2015 26423156 CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis Homo sapiens hg19 chr5 149432000 149433000 SRF NKX2.5 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepG2 CVCL_0027 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR 2015 26423156 CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis Homo sapiens hg19 chr5 149432000 149433000 GATA4 GATA4 Enhancer Active Normal Heart UBERON:0000948 Cardiac precursor cardiac precursor cell CL:0002248 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR 2015 26423156 CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis Homo sapiens hg19 chr5 149432000 149433000 NKX2.5 Enhancer Active Normal Heart UBERON:0000948 Cardiac precursor cardiac precursor cell CL:0002248 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR 2015 26423156 CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis Homo sapiens hg19 chr5 149433000 149434000 MESP1 Enhancer Active Normal Heart UBERON:0000948 Cardiac precursor cardiac precursor cell CL:0002248 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR 2015 26423156 CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis Homo sapiens hg19 chr5 149433000 149434000 MEF2C MEF2C Enhancer Active Normal Heart UBERON:0000948 Cardiac precursor cardiac precursor cell CL:0002248 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR 2015 26423156 CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis Homo sapiens hg19 chr5 149434000 149435000 MYH6 Enhancer Active Normal Heart UBERON:0000948 Cardiac precursor cardiac precursor cell CL:0002248 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR 2015 26423156 CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis Homo sapiens hg19 chr5 149434000 149435000 MYH7 Enhancer Active Normal Heart UBERON:0000948 Cardiac precursor cardiac precursor cell CL:0002248 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR 2015 26183928 Implication of a chromosome 15q152 locus in regulating UBR1 and predisposing smokers to MGMT methylation in lung Homo sapiens hg19 chr10 131264200 131265727 MGMT Enhancer Silenced Normal Heart UBERON:0000948 Cardiac precursor cardiac precursor cell CL:0002248 Enhancer activity assay, Functional perturbation assay RNA-seq, ChIP-seq Luciferase Reporter Assay, RT-RT-qPCR, Western blot 2014 24413736 Pancreatic islet enhancer clusters enriched in type 2 diabetes risk-associated variants Homo sapiens hg19 chr6 170855462 170856787 NKX2-2 TBP Enhancer Active Normal Lung UBERON:0002048 Human Bronchial Epithelial Cells (HBEC1) bronchial epithelial cell CL:0002591 Enhancer activity assay RNA-seq, ChIP-seq Luciferase Reporter Assay 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 Pancreatic islet UBERON:0000006 Islet pancreatic islet cell CL:0000168 Enhancer activity assay ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2014 24510239 ABCC4 Copy Number Variation and ESCC Homo sapiens hg19 chr13 94663320 94664200 GATA3 ABCC4 Enhancer Active Disease adrenocortical carcinoma MONDO:0005075 DOID:3948 Adrenal gland UBERON:0002369 H295R CVCL_0458 adrenocortical carcinoma cell CL:0000135 Enhancer activity assay, CNV functional assay ChIP-seq Luciferase reporter assay, RT-RT-qPCR, siRNA 2014 24512546 FOXA1 promotes tumor cell proliferation through AR involving the Notch pathway in endometrial cancer Homo sapiens hg19 chr8 128749000 128750000 FOXA1; AR MYC Enhancer Active Disease esophageal squamous cell carcinoma MONDO:0005082 DOID:3748 Esophagus UBERON:0001043 KYSE-30 CVCL_1351 esophageal squamous cell carcinoma cell CL:0000069 Enhancer activity assay, Functional perturbation assay ChIP-seq Luciferase Reporter Assay, RT-RT-qPCR, Western blot 2023 37832549 Genome-wide CRISPR activation screening in senescent cells reveals SOX5 as a driver and therapeutic target of rejuvenation Homo sapiens hg19 chr11 63800000 63802500 OSKM Enhancer Active Disease endometrial adenocarcinoma MONDO:0005047 DOID:2870 Endometrium UBERON:0001295 MFE-296 CVCL_1406 endometrial adenocarcinoma cell CL:0000069 Functional perturbation assay, Enhancer activity assay Hi-C, RNA-seq CRISPRa, Western blot 2026 41849608 KLF5 controls subtype-independent highly interactive enhancers in pancreatic cancer to regulate cell survival Homo sapiens hg19 chr22 29145000 29155000 KLF5 BCL2L1 Enhancer Active Normal Connective Tissue UBERON:0002384 Human Mesenchymal Progenitor mesenchymal progenitor cell CL:0000134 Regulatory element functional validation, 3D chromatin interaction mapping ATAC-seq, ChIP-seq, HiChIP, RNA-seq, nascent RNA-seq dCas9-KRAB epigenetic silencing, RT-RT-qPCR, Western blot, flow cytometry, multiplex immunofluorescence 2026 41849608 KLF5 controls subtype-independent highly interactive enhancers in pancreatic cancer to regulate cell survival Homo sapiens hg19 chr22 29165000 29175000 KLF5 BCL2L1 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 AsPC1 CVCL_0152 pancreatic ductal adenocarcinoma cell CL:0000066 Regulatory element functional validation, 3D chromatin interaction mapping ATAC-seq, ChIP-seq, HiChIP, RNA-seq, nascent RNA-seq dCas9-KRAB epigenetic silencing, RT-RT-qPCR, Western blot, flow cytometry, multiplex immunofluorescence 2026 41849608 KLF5 controls subtype-independent highly interactive enhancers in pancreatic cancer to regulate cell survival Homo sapiens hg19 chr22 29185000 29195000 KLF5 BCL2L1 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 AsPC1 CVCL_0152 pancreatic ductal adenocarcinoma cell CL:0000066 Regulatory element functional validation, 3D chromatin interaction mapping ATAC-seq, ChIP-seq, HiChIP, RNA-seq, nascent RNA-seq dCas9-KRAB epigenetic silencing, RT-RT-qPCR, Western blot, flow cytometry, multiplex immunofluorescence 2015 26423156 CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis Homo sapiens hg19 chr5 149433000 149434000 MESP1 MESP1 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 AsPC1 CVCL_0152 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay ChIP-seq,RNA-seq Luciferase Reporter Assay,qRT-PCR 2016 26818267 Utility of next-generation RNA-sequencing in identifying chimeric transcription involving human endogenous retroviruses Homo sapiens hg19 chr3 85552000 85554000 CADM2 Enhancer Active Normal Heart UBERON:0000948 Cardiac precursor cardiac precursor cell CL:0002248 Functional perturbation assay RNA-seq, ChIP-seq RT-RT-qPCR 2016 26818267 Utility of next-generation RNA-sequencing in identifying chimeric transcription involving human endogenous retroviruses Homo sapiens hg19 chr7 84508000 84510000 SEMA3A Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Bone marrow UBERON:0002371 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional perturbation assay RNA-seq, ChIP-seq RT-RT-qPCR 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 chronic myeloid leukemia MONDO:0011998 DOID:8552 Bone marrow UBERON:0002371 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq Luciferase reporter assay, EMSA, ChIP-RT-qPCR 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:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat cells CVCL_0065 T lymphoblast CL:0002419 Enhancer activity assay ChIP-seq Luciferase reporter assay, Transgenic reporter assay, RT-RT-qPCR 2013 24332044 Super-enhancer associated dependencies in diffuse large B-cell lymphoma Homo sapiens hg19 chr8 128747000 128753000 MYC Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat cells CVCL_0065 T lymphoblast CL:0002419 Enhancer activity assay, Oncogenic dependency assay ChIP-seq, RNA-seq Luciferase reporter assay, siRNA knockdown, RT-RT-qPCR 2013 23637611 TIP48/Reptin and H2AZ Requirement for Initiating Chromatin Remodeling in Estrogen-Activated Transcription Homo sapiens hg19 chr11 69470000 69470500 ESR1 CCND1 Enhancer Active Disease diffuse large B-cell lymphoma MONDO:0005042 DOID:0050746 Lymphoid tissue UBERON:0001745 DLBCL cells B cell CL:0000945 Chromatin interaction assay ChIP-seq 3C assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2014 24667606 Targeted repression of AXIN2 and MYC gene expression using designer TALEs Homo sapiens hg19 chr8 128817000 128818000 TCF7L2 MYC Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF-7 cells CVCL_0031 breast carcinoma cell CL:0000066 Enhancer activity assay ChIP-seq Luciferase Reporter Assay, RT-RT-qPCR, Western blot 2010 20093418 Glucocorticoid receptor activates FKBP5 via distal enhancers Homo sapiens hg19 chr6 35574362 35576362 NR3C1 FKBP5 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293FT CVCL_6911 embryonic kidney cell CL:0002139 Enhancer activity assay ChIP-seq Luciferase Reporter Assay 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:0005176 DOID:9256 Colon UBERON:0001155 HCT116 cells CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Luciferase Reporter Assay, 3C-seq, ChIP-RT-qPCR, RT-RT-qPCR 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:0005176 DOID:9256 Colon UBERON:0001155 HCT116 cells CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Luciferase Reporter Assay, 3C-seq, ChIP-RT-qPCR, RT-RT-qPCR 2009 19458616 Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus Homo sapiens hg19 chr12 68482000 68483000 IFNG Enhancer Active Normal Peripheral Blood UBERON:0000178 CD4+ Th1 T Cells CD4-positive Th1 T cell CL:0000897 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay ChIP-seq, 3C-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, FISH 2009 19458616 Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus Homo sapiens hg19 chr12 68546500 68547500 IFNG Enhancer Active Normal Peripheral Blood UBERON:0000178 CD4+ Th1 T Cells CD4-positive Th1 T cell CL:0000897 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay ChIP-seq, 3C-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, FISH 2009 19458616 Cohesins form chromosomal cis-interactions at the developmentally regulated IFNG locus Homo sapiens hg19 chr12 68664000 68665000 IFNG Enhancer Active Normal Peripheral Blood UBERON:0000178 CD4+ Th1 T Cells CD4-positive Th1 T cell CL:0000897 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay ChIP-seq, 3C-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, FISH 2008 18836447 Regulation of a remote Shh forebrain enhancer by the Six3 homeoprotein Homo sapiens hg19 chr7 155595558 155596658 SIX3 SHH Enhancer Active Normal Kidney UBERON:0002113 COS-1 CVCL_0223 COS-1 fibroblast-like cell CL:0002139 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, Transgenic Reporter Assay 2024 38760567 Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations Homo sapiens hg19 chr8 128910869 128911521 MYC Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional perturbation assay RNA-seq CRISPRi, Flow Cytometry, qRT-PCR 2024 38760567 Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations Homo sapiens hg19 chr8 128972341 128973219 MYC Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional perturbation assay RNA-seq CRISPRi, Flow Cytometry, qRT-PCR 2024 38760567 Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations Homo sapiens hg19 chr8 129057272 129057795 MYC Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional perturbation assay RNA-seq CRISPRi, Flow Cytometry, qRT-PCR 2024 38760567 Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations Homo sapiens hg19 chr11 5270500 5271500 HBG1 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional perturbation assay RNA-seq CRISPRi, qRT-PCR 2021 34493733 Transcriptional network involving ERG and AR orchestrates Distal-less homeobox-1 mediated prostate cancer progression Homo sapiens hg19 chr2 172949712 172954378 ERG DLX1 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 VCaP CVCL_2235 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, qRT-PCR, Western blot 2021 33793581 FOXP4 promotes laryngeal squamous cell carcinoma progression through directly targeting LEF1 Homo sapiens hg19 chr4 108226000 108228000 FOXP4 LEF1 Enhancer Active Disease laryngeal squamous cell carcinoma MONDO:0005083 DOID:2596 Larynx UBERON:0001737 TU177 CVCL_4904 laryngeal squamous cell carcinoma cell CL:0000069 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, qRT-PCR 2021 34782839 TNF-??-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer Homo sapiens hg19 chr17 31254200 31255700 JUN CCL2 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 PANC1 CVCL_0480 pancreatic ductal adenocarcinoma cell CL:0000066 TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq ChIP-RT-qPCR, siRNA Knockdown, qRT-PCR, Western blot, ELISA 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; ZBTB3; PLAGL1; NR3C2 GALNT2 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepG2 CVCL_0027 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, TF binding assay ChIP-seq Luciferase Reporter Assay, EMSA, RT-RT-qPCR 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr9 101828429 101928429 TGFBR1 Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 HD-MB03 CVCL_IT11 medulloblastoma cell CL:0000127 Enhancer activity assay, Chromatin interaction assay 3C-seq, ChIP-seq, RNA-seq RT-RT-qPCR 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr9 101828429 101928429 TGFBR1 Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Cerebellum UBERON:0002037 Primary Medulloblastoma Tissue medulloblastoma cell CL:0000127 Enhancer activity assay, Chromatin interaction assay 3C-seq, ChIP-seq, RNA-seq RT-RT-qPCR 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr13 37378439 37578439 SMAD9 Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 HD-MB03 CVCL_IT11 medulloblastoma cell CL:0000127 Enhancer activity assay, Chromatin interaction assay 3C-seq, ChIP-seq, RNA-seq RT-RT-qPCR 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr13 37378439 37578439 SMAD9 Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Cerebellum UBERON:0002037 Primary Medulloblastoma Tissue medulloblastoma cell CL:0000127 Enhancer activity assay, Chromatin interaction assay 3C-seq, ChIP-seq, RNA-seq RT-RT-qPCR 2016 26817450 Looking beyond GWAS: allele-specific transcription factor binding drives the association of GALNT2 to HDL-C plasma levels Homo sapiens hg19 chr1 230294900 230294900 ZBTB3 GALNT2 Enhancer Silenced Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepG2 cells CVCL_0027 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, TF binding assay ChIP-seq Luciferase Reporter Assay 2021 34475398 Functional characterization of T2D-associated SNP effects on baseline and ER stress-responsive ?? cell transcriptional activation Homo sapiens hg19 chr13 75142500 75142700 RNF6 Enhancer Active Normal Pancreatic Islet UBERON:0000006 Mouse pancreatic beta cell mouse pancreatic beta cell CL:0000169 Enhancer activity assay, TF binding assay MPRA, ATAC-seq, RNA-seq Luciferase Reporter Assay, EMSA, RT-RT-qPCR 2021 34475398 Functional characterization of T2D-associated SNP effects on baseline and ER stress-responsive ?? cell transcriptional activation Homo sapiens hg19 chr15 71106519 71106719 LARP6 Enhancer Active Normal Pancreatic Islet UBERON:0000006 Mouse pancreatic beta cell mouse pancreatic beta cell CL:0000169 Enhancer activity assay, TF binding assay MPRA, ATAC-seq, RNA-seq Luciferase Reporter Assay, EMSA, RT-RT-qPCR 2021 34475398 Functional characterization of T2D-associated SNP effects on baseline and ER stress-responsive ?? cell transcriptional activation Homo sapiens hg19 chr15 71136738 71136938 LARP6 Enhancer Active Normal Pancreatic Islet UBERON:0000006 Mouse pancreatic beta cell mouse pancreatic beta cell CL:0000169 Enhancer activity assay, TF binding assay MPRA, ATAC-seq, RNA-seq Luciferase Reporter Assay, EMSA, RT-RT-qPCR 2021 34475398 Functional characterization of T2D-associated SNP effects on baseline and ER stress-responsive ?? cell transcriptional activation Homo sapiens hg19 chr3 179641018 179641218 PEX5L Enhancer Active Normal Pancreatic Islet UBERON:0000006 Mouse pancreatic beta cell mouse pancreatic beta cell CL:0000169 Enhancer activity assay, TF binding assay MPRA, ATAC-seq, RNA-seq Luciferase Reporter Assay, EMSA, RT-RT-qPCR 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 Enhancer Active Normal Blood UBERON:0000178 B lymphoblastoid cell line (GM12878) CVCL_7526 B lymphoblastoid cell CL:0000945 Enhancer activity assay ChIP-seq, ATAC-seq ChIP-RT-qPCR, ChART-PCR 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 Enhancer Active Disease Burkitt lymphoma MONDO:0002483 DOID:8582 Lymph node UBERON:0000029 Raji CVCL_0511 Burkitt lymphoma cell CL:0000945 Enhancer activity assay ChIP-seq, ATAC-seq ChIP-RT-qPCR, ChART-PCR 2023 37563118 Enhancer remodeling activates NOTCH3 signaling to confer chemoresistance in advanced nasopharyngeal carcinoma Homo sapiens hg19 chr19 151500000 152500000 NOTCH3 Enhancer Active Disease nasopharyngeal carcinoma MONDO:0005350 DOID:9260 Nasopharynx UBERON:0001714 CNE-2 CVCL_6889 nasopharyngeal carcinoma cell CL:0000069 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2023 37563118 Enhancer remodeling activates NOTCH3 signaling to confer chemoresistance in advanced nasopharyngeal carcinoma Homo sapiens hg19 chr2 202030000 202040000 FZD7 Enhancer Active Disease nasopharyngeal carcinoma MONDO:0005350 DOID:9260 Nasopharynx UBERON:0001714 CNE-2 CVCL_6889 nasopharyngeal carcinoma cell CL:0000069 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot 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 RHOB Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 Huh7 CVCL_0336 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr2 43550000 43551000 GATA2 EVI1 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 Primary AML blasts myeloid leukemia cell CL:0001054 Enhancer activity assay ChIP-seq, RNA-seq, Targeted DNA sequencing FISH, RT-RT-qPCR 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr2 43550000 43551000 GATA2 EVI1 Enhancer Active Normal Bone Marrow UBERON:0002371 CD34+ HSPCs CD34-positive hematopoietic stem cell CL:0001029 Enhancer activity assay ChIP-seq, RNA-seq, Targeted DNA sequencing FISH, RT-RT-qPCR 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr3 128300000 128301000 GATA2 EVI1 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 Primary AML blasts myeloid leukemia cell CL:0001054 Enhancer activity assay, Chromatin interaction assay ChIP-seq, RNA-seq RT-RT-qPCR, FISH 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr3 128300000 128301000 GATA2 EVI1 Enhancer Active Normal Bone Marrow UBERON:0002371 CD34+ HSPCs CD34-positive hematopoietic stem cell CL:0001029 Enhancer activity assay, Chromatin interaction assay ChIP-seq, RNA-seq RT-RT-qPCR, FISH 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr6 156475000 156476000 GATA2 EVI1 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 Primary AML blasts myeloid leukemia cell CL:0001054 Enhancer activity assay ChIP-seq, RNA-seq, Targeted DNA sequencing FISH, RT-RT-qPCR 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr6 156475000 156476000 GATA2 EVI1 Enhancer Active Normal Bone Marrow UBERON:0002371 CD34+ HSPCs CD34-positive hematopoietic stem cell CL:0001029 Enhancer activity assay ChIP-seq, RNA-seq, Targeted DNA sequencing FISH, RT-RT-qPCR 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr7 92400000 92401000 GATA2 EVI1 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 Primary AML blasts myeloid leukemia cell CL:0001054 Enhancer activity assay ChIP-seq, RNA-seq, Targeted DNA sequencing FISH, RT-RT-qPCR 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr7 92400000 92401000 GATA2 EVI1 Enhancer Active Normal Bone Marrow UBERON:0002371 CD34+ HSPCs CD34-positive hematopoietic stem cell CL:0001029 Enhancer activity assay ChIP-seq, RNA-seq, Targeted DNA sequencing FISH, RT-RT-qPCR 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 MYC Enhancer Active Disease Burkitt lymphoma MONDO:0002483 DOID:8582 Blood UBERON:0000178 Human Burkitt lymphoma cell Burkitt lymphoma cell CL:0000945 Functional perturbation assay, Enhancer activity assay CRISPRi screening, RNA-seq, ATAC-seq CRISPRi, RT-RT-qPCR, Western blot, Flow Cytometry, GFP competition assay 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 BCL2 Enhancer Active Disease diffuse large B-cell lymphoma MONDO:0005042 DOID:0050746 Blood UBERON:0000178 Human DLBCL cell diffuse large B-cell lymphoma cell CL:0000945 Functional perturbation assay, Enhancer activity assay CRISPRi screening, RNA-seq, ATAC-seq CRISPRi, RT-RT-qPCR, Western blot, Flow Cytometry, GFP competition assay 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 MYC Enhancer Active Disease Burkitt lymphoma MONDO:0002483 DOID:8582 Blood UBERON:0000178 Human Burkitt lymphoma cell Burkitt lymphoma cell CL:0000945 Functional perturbation assay, Enhancer activity assay CRISPRi screening, RNA-seq, ATAC-seq CRISPRi, RT-RT-qPCR, Western blot, Flow Cytometry, GFP competition assay 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 BCL2 Enhancer Active Disease diffuse large B-cell lymphoma MONDO:0005042 DOID:0050746 Blood UBERON:0000178 Human DLBCL cell diffuse large B-cell lymphoma cell CL:0000945 Functional perturbation assay, Enhancer activity assay CRISPRi screening, RNA-seq, ATAC-seq CRISPRi, RT-RT-qPCR, Western blot, Flow Cytometry, GFP competition assay 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 IGH Enhancer Active Disease Burkitt lymphoma MONDO:0002483 DOID:8582 Blood UBERON:0000178 Human Burkitt lymphoma cell Burkitt lymphoma cell CL:0000945 Functional perturbation assay, Enhancer activity assay CRISPRi screening, RNA-seq, ATAC-seq CRISPRi, RT-RT-qPCR, Western blot, Flow Cytometry, GFP competition assay 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 BCL2 Enhancer Active Disease diffuse large B-cell lymphoma MONDO:0005042 DOID:0050746 Blood UBERON:0000178 Human DLBCL cell diffuse large B-cell lymphoma cell CL:0000945 Functional perturbation assay, Enhancer activity assay CRISPRi screening, RNA-seq, ATAC-seq CRISPRi, RT-RT-qPCR, Western blot, Flow Cytometry, GFP competition assay 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 Enhancer Active Disease B-cell lymphoma MONDO:0005029 DOID:164 Blood UBERON:0000178 Human B-cell lymphoma cell B-cell lymphoma cell CL:0000945 Functional perturbation assay, Enhancer activity assay CRISPRi screening, RNA-seq, ATAC-seq CRISPRi, RT-RT-qPCR, Western blot, Flow Cytometry, GFP competition assay 2020 31658410 A distal enhancer that directs Otx2 expression in the retinal pigment epithelium and neuroretina Homo sapiens hg19 chr14 57419008 57421445 PAX6 OTX2 Enhancer Active Disease Retina UBERON:0000966 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, Hi-C, DNase-seq Transgenic Reporter Assay, qRT-PCR, Immunohistochemistry 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 APOBEC3C Enhancer Active Normal Peripheral Blood UBERON:0000178 B cells B cell CL:0000945 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, CUT&Tag, RNA-seq CRISPR Knockout, CRISPRi, qRT-PCR, Western blot 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 APOBEC3C Enhancer Active Normal Peripheral Blood UBERON:0000178 B cells B cell CL:0000945 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, CUT&Tag, RNA-seq CRISPR Knockout, CRISPRi, qRT-PCR, Western blot 2016 27693352 Enhancer variants drive gene regulatory network dysfunction in Hirschsprung disease Homo sapiens hg19 chr10 43447346 43448347 RARB RET Enhancer Active Disease neuroblastoma MONDO:0005070 DOID:769 Fetal gut UBERON:0007023 Neuroblastoma cell neuroblastoma cell CL:0000031 Enhancer activity assay, TF binding assay ChIP-seq, DNase-seq Luciferase Reporter Assay, EMSA 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 Gonadal Tissue UBERON:0000991 hESC embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 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 Gonadal Tissue UBERON:0000991 hPGCLC primordial germ cell-like cell CL:0000670 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 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 Gonadal Tissue UBERON:0000991 hPGC primordial germ cell CL:0000670 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2018 29909987 A somatically acquired enhancer of the androgen receptor is a noncoding driver in advanced prostate cancer Homo sapiens hg19 chrX 66118920 66127943 AR Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq qRT-PCR, and ChIP-qPCR 2018 29909987 A somatically acquired enhancer of the androgen receptor is a noncoding driver in advanced prostate cancer Homo sapiens hg19 chrX 66118920 66127943 AR Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 22RV1 CVCL_1045 prostate carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq qRT-PCR, and ChIP-qPCR 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 UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA, RT-RT-qPCR 2023 37345431 Identification and functional validation of an enhancer variant in the 9p213 locus associated with glaucoma risk and elevated expression of p16INK4a Homo sapiens hg19 chr9 21980404 21981404 YY1 CDKN2A Enhancer Active Normal Brain UBERON:0000955 Neural Stem Cells neural stem cell CL:0002672 Enhancer activity assay, TF binding assay, Functional perturbation assay Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, RT-RT-qPCR 2023 37345431 Identification and functional validation of an enhancer variant in the 9p213 locus associated with glaucoma risk and elevated expression of p16INK4a Homo sapiens hg19 chr9 21980404 21981404 YY1 CDKN2A Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Enhancer activity assay, TF binding assay, Functional perturbation assay Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, RT-RT-qPCR 2023 37345431 Identification and functional validation of an enhancer variant in the 9p213 locus associated with glaucoma risk and elevated expression of p16INK4a Homo sapiens hg19 chr9 21980404 21981404 YY1 CDKN2A Enhancer Active Normal Lung UBERON:0002048 IMR90 CVCL_0034 fetal lung fibroblast CL:0000057 Enhancer activity assay, TF binding assay, Functional perturbation assay Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, RT-RT-qPCR 2023 37345431 Identification and functional validation of an enhancer variant in the 9p213 locus associated with glaucoma risk and elevated expression of p16INK4a Homo sapiens hg19 chr9 21980404 21981404 YY1 CDKN2A Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF7 CVCL_0031 breast carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, RT-RT-qPCR 2023 37345431 Identification and functional validation of an enhancer variant in the 9p213 locus associated with glaucoma risk and elevated expression of p16INK4a Homo sapiens hg19 chr9 21980404 21981404 YY1 CDKN2A Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay, TF binding assay, Functional perturbation assay Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, RT-RT-qPCR 2026 41505091 YAP-TEAD regulates the super-enhancer network to control early surface ectoderm commitment Homo sapiens hg19 chr8 102449260 102449687 GRHL2 Enhancer Active Normal Pluripotent embryonic tissue UBERON:0000922 Human embryonic stem cells 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-RT-qPCR, Western blot 2026 41505091 YAP-TEAD regulates the super-enhancer network to control early surface ectoderm commitment Homo sapiens hg19 chr8 102467180 102467504 GRHL2 Enhancer Active Normal Pluripotent embryonic tissue UBERON:0000922 Human embryonic stem cells 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-RT-qPCR, Western blot 2026 41505091 YAP-TEAD regulates the super-enhancer network to control early surface ectoderm commitment Homo sapiens hg19 chr8 102486442 102486801 GRHL2 Enhancer Active Normal Pluripotent embryonic tissue UBERON:0000922 Human embryonic stem cells 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-RT-qPCR, Western blot 2026 41424849 Endothelial KSR2 regulated by genetic variation protects against atherosclerosis through AMPK??1 stabilization Homo sapiens hg19 chr12 117827344 117845711 XBP1S KSR2 Enhancer Active Normal Umbilical vein UBERON:0002066 HUVECs umbilical vein endothelial cell CL:0002615 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq Luciferase reporter assay, ChIP-RT-qPCR, EMSA, siRNA knockdown, RT-RT-qPCR, Western blot 2025 40890402 p300/CBP is an essential driver of pathogenic enhancer activity and gene expression in Ewing sarcoma Homo sapiens hg19 chr20 21566572 21586800 EWS::FLI1 NKX2-2 Enhancer Active Disease Ewing sarcoma MONDO:0003368 DOID:3368 Bone UBERON:0001474 A673 cells CVCL_0080 Ewing sarcoma cell CL:0000050 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, dTAG degradation assay 2025 40890402 p300/CBP is an essential driver of pathogenic enhancer activity and gene expression in Ewing sarcoma Homo sapiens hg19 chr20 21566572 21586800 EWS::FLI1 NKX2-2 Enhancer Active Disease Ewing sarcoma MONDO:0003368 DOID:3368 Bone UBERON:0001474 SKNMC cells CVCL_0530 Ewing sarcoma cell CL:0000050 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, dTAG degradation assay 2025 40890402 p300/CBP is an essential driver of pathogenic enhancer activity and gene expression in Ewing sarcoma Homo sapiens hg19 chr20 21566572 21586800 EWS::FLI1 NKX2-2 Enhancer Active Disease Ewing sarcoma MONDO:0003368 DOID:3368 Bone UBERON:0001474 EWS-502 cells CVCL_1265 Ewing sarcoma cell CL:0000050 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, dTAG degradation assay 2025 40890402 p300/CBP is an essential driver of pathogenic enhancer activity and gene expression in Ewing sarcoma Homo sapiens hg19 chr11 69616543 69628302 EWS::FLI1 CCND1 Enhancer Active Disease Ewing sarcoma MONDO:0003368 DOID:3368 Bone UBERON:0001474 A673 cells CVCL_0080 Ewing sarcoma cell CL:0000050 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, dTAG degradation assay 2025 40890402 p300/CBP is an essential driver of pathogenic enhancer activity and gene expression in Ewing sarcoma Homo sapiens hg19 chr11 69616543 69628302 EWS::FLI1 CCND1 Enhancer Active Disease Ewing sarcoma MONDO:0003368 DOID:3368 Bone UBERON:0001474 SKNMC cells CVCL_0530 Ewing sarcoma cell CL:0000050 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, dTAG degradation assay 2025 40890402 p300/CBP is an essential driver of pathogenic enhancer activity and gene expression in Ewing sarcoma Homo sapiens hg19 chr11 69616543 69628302 EWS::FLI1 CCND1 Enhancer Active Disease Ewing sarcoma MONDO:0003368 DOID:3368 Bone UBERON:0001474 EWS-502 cells CVCL_1265 Ewing sarcoma cell CL:0000050 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, dTAG degradation assay 2021 32242051 H3K79me2/3 controls enhancer-promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells Homo sapiens hg19 chr4 15450000 15579703 PROM1 Enhancer Active Disease acute lymphoblastic leukemia MONDO:0004945 DOID:0080545 Bone Marrow UBERON:0002371 ALL cell line B lymphoblast CL:0000945 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, Capture-C, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2021 32242051 H3K79me2/3 controls enhancer-promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells Homo sapiens hg19 chr4 15450000 15579703 PROM1 Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, Capture-C, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2021 32242051 H3K79me2/3 controls enhancer-promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells Homo sapiens hg19 chr4 15450000 15579703 PROM1 Enhancer Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0080545 Bone Marrow UBERON:0002371 Primary MLL-AF4 ALL blasts B lymphoblast CL:0000945 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, Capture-C, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2021 32242051 H3K79me2/3 controls enhancer-promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells Homo sapiens hg19 chr4 15581130 15619993 TAPT1 Enhancer Active Disease acute lymphoblastic leukemia MONDO:0004945 DOID:0080545 Bone Marrow UBERON:0002371 ALL cell line B lymphoblast CL:0000945 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, Capture-C, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2021 32242051 H3K79me2/3 controls enhancer-promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells Homo sapiens hg19 chr4 15581130 15619993 TAPT1 Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, Capture-C, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2021 32242051 H3K79me2/3 controls enhancer-promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells Homo sapiens hg19 chr4 15581130 15619993 TAPT1 Enhancer Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0080545 Bone Marrow UBERON:0002371 Primary MLL-AF4 ALL blasts B lymphoblast CL:0000945 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, Capture-C, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot 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 Silenced Normal Umbilical vein UBERON:0002066 HUVEC CVCL_2959 umbilical vein endothelial cell CL:0002615 Enhancer activity assay, TF binding assay, Functional perturbation assay EMSA, CRISPR knockout, RT-RT-qPCR 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 Silenced Normal Aorta UBERON:0000947 hESC-derived endothelial cells endothelial cell CL:0000115 Enhancer activity assay, TF binding assay, Functional perturbation assay EMSA, CRISPR knockout, RT-RT-qPCR 2024 38438958 Nuclear respiratory factor 1 regulates super enhancer-controlled SPIDR to protect hepatocellular carcinoma cells from oxidative stress Homo sapiens hg19 chr8 48025841 48796048 NRF1 SPIDR Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 Huh7 CVCL_0336 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot, CCK-8 Assay, ROS Assay, ELISA, Immunofluorescence 2024 38438958 Nuclear respiratory factor 1 regulates super enhancer-controlled SPIDR to protect hepatocellular carcinoma cells from oxidative stress Homo sapiens hg19 chr8 48025841 48796048 NRF1 SPIDR Enhancer Active Normal Liver UBERON:0002107 Normal liver cell hepatocyte CL:0000182 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot, CCK-8 Assay, ROS Assay, ELISA, Immunofluorescence 2024 38233525 Affinity-optimizing enhancer variants disrupt development Homo sapiens hg19 chr7 155594277 155595077 ETS1 SHH Enhancer Active Normal Embryonic Limb Bud UBERON:0005417 Embryonic limb bud mesenchymal cells mesenchymal cell CL:0000134 Functional perturbation assay, Enhancer activity assay MPRA, RNA-seq CRISPR Knockin, Transgenic Reporter Assay, EMSA, in situ hybridization, Skeletal staining 2024 39085358 SMC3 contributes to heart development by regulating superenhancer associated genes Homo sapiens hg19 chr21 40000000 40800000 ETS2 SE Active Normal Heart UBERON:0000948 Cardiomyocytes cardiomyocyte CL:0000746 Enhancer activity assay, Chromatin interaction assay Hi-C, ChIP-seq qRT-PCR, and ChIP-qPCR 2019 30455249 The Phosphorylated Estrogen Receptor(ER) Cistrome Identifies a Subset of Active Enhancers Enriched for Direct ER-DNA Binding and the Transcription Factor GRHL2 Homo sapiens hg19 chr1 144983210 144983310 ESR1 BRIP1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 Human breast adenocarcinoma cell breast adenocarcinoma cell CL:0000066 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq ChIP-RT-qPCR 2019 30455249 The Phosphorylated Estrogen Receptor(ER) Cistrome Identifies a Subset of Active Enhancers Enriched for Direct ER-DNA Binding and the Transcription Factor GRHL2 Homo sapiens hg19 chr2 10504857 10504957 ESR1 E2F6 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 Human breast adenocarcinoma cell breast adenocarcinoma cell CL:0000066 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq ChIP-RT-qPCR 2019 30455249 The Phosphorylated Estrogen Receptor(ER) Cistrome Identifies a Subset of Active Enhancers Enriched for Direct ER-DNA Binding and the Transcription Factor GRHL2 Homo sapiens hg19 chr2 11562351 11562451 ESR1 GREB1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 Human breast adenocarcinoma cell breast adenocarcinoma cell CL:0000066 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq ChIP-RT-qPCR 2019 30455249 The Phosphorylated Estrogen Receptor(ER) Cistrome Identifies a Subset of Active Enhancers Enriched for Direct ER-DNA Binding and the Transcription Factor GRHL2 Homo sapiens hg19 chr21 42872877 42872977 ESR1 TFF1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 Human breast adenocarcinoma cell breast adenocarcinoma cell CL:0000066 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq ChIP-RT-qPCR 2019 30455249 The Phosphorylated Estrogen Receptor(ER) Cistrome Identifies a Subset of Active Enhancers Enriched for Direct ER-DNA Binding and the Transcription Factor GRHL2 Homo sapiens hg19 chr21 42880677 42880777 ESR1 TFF1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 Human breast adenocarcinoma cell breast adenocarcinoma cell CL:0000066 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq ChIP-RT-qPCR 2019 31078271 The SNP of rs6854845 suppresses transcription via the DNA looping structure alteration of super-enhancer in colon cells Homo sapiens hg19 chr4 75746565 75746914 EREG Enhancer Silenced Normal Colon UBERON:0001155 Human normal colon epithelial cell colon epithelial cell CL:1000348 Functional perturbation assay, Chromatin interaction assay CRISPR Knockout, 3C, ChIP-RT-qPCR, RT-RT-qPCR 2019 31078271 The SNP of rs6854845 suppresses transcription via the DNA looping structure alteration of super-enhancer in colon cells Homo sapiens hg19 chr4 75700000 76000000 H3K4ME1 SE Active Normal Colon UBERON:0001155 Human normal colon epithelial cell colon epithelial cell CL:1000348 Chromatin interaction assay, Functional perturbation assay, Enhancer activity assay Hi-C 3C, ChIP-RT-qPCR, CRISPR Knockout, RT-RT-qPCR 2019 31078271 The SNP of rs6854845 suppresses transcription via the DNA looping structure alteration of super-enhancer in colon cells Homo sapiens hg19 chr4 75700000 76000000 EREG Enhancer Active Normal Colon UBERON:0001155 Human normal colon epithelial cell colon epithelial cell CL:1000348 Chromatin interaction assay, Functional perturbation assay, Enhancer activity assay Hi-C, RNA-seq CRISPR knockout, 3C, ChIP-RT-qPCR, RT-RT-qPCR 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 APOBEC3C Enhancer Active Normal Peripheral Blood UBERON:0000178 B cells B cell CL:0000945 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, CUT&Tag, RNA-seq CRISPR knockout, CRISPRi, RT-RT-qPCR, Western blot 2014 24671955 Transcription and enhancer profiling in human monocyte subsets Homo sapiens hg19 chr5 140657200 140658500 SPI1 CD14 Enhancer Active Normal Peripheral Blood UBERON:0000178 Classical monocytes classical monocyte CL:0000576 Enhancer activity assay ChIP-seq, CAGE-seq Luciferase Reporter Assay, RT-RT-qPCR 2014 24671955 Transcription and enhancer profiling in human monocyte subsets Homo sapiens hg19 chr5 140659800 140661200 SPI1 CD14 Enhancer Active Normal Peripheral Blood UBERON:0000178 Classical monocytes classical monocyte CL:0000576 Enhancer activity assay ChIP-seq, CAGE-seq Luciferase Reporter Assay, RT-RT-qPCR 2014 24671955 Transcription and enhancer profiling in human monocyte subsets Homo sapiens hg19 chr5 140662500 140663800 SPI1 CD14 Enhancer Active Normal Peripheral Blood UBERON:0000178 Classical monocytes classical monocyte CL:0000576 Enhancer activity assay ChIP-seq, CAGE-seq Luciferase Reporter Assay, RT-RT-qPCR 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 Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepG2 CVCL_0027 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, Chromatin interaction assay, TF binding assay, eRNA functional assay Luciferase reporter assay, 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR, 5'/3' RACE, Actinomycin D RNA stability assay, Bisulfite sequencing PCR 2024 39110799 Oncogenic transcription factors instruct promoter-enhancer hubs in individual triple negative breast cancer cells Homo sapiens hg19 chr17 70397161 70432161 SOX9 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-157 CVCL_0618 breast carcinoma cell CL:0000066 Regulatory element functional validation, 3D chromatin interaction mapping HiChIP, CRISPR-Cas9 transcription factor screening, RNA-seq qRT-PCR, and ChIP-qPCR 2024 39110799 Oncogenic transcription factors instruct promoter-enhancer hubs in individual triple negative breast cancer cells Homo sapiens hg19 chr17 70447161 70494161 SOX9 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-157 CVCL_0618 breast carcinoma cell CL:0000066 Regulatory element functional validation, 3D chromatin interaction mapping HiChIP, CRISPR-Cas9 transcription factor screening, RNA-seq qRT-PCR, and ChIP-qPCR 2024 39110799 Oncogenic transcription factors instruct promoter-enhancer hubs in individual triple negative breast cancer cells Homo sapiens hg19 chr17 70530161 70632161 SOX9 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-157 CVCL_0618 breast carcinoma cell CL:0000066 Regulatory element functional validation, 3D chromatin interaction mapping HiChIP, CRISPR-Cas9 transcription factor screening, RNA-seq qRT-PCR, and ChIP-qPCR 2017 28416141 Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells Homo sapiens hg19 chr11 5278952 5279402 HBG2 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Bone marrow UBERON:0002371 K-562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 CRISPRi-based single-cell enhancer perturbation Drop-seq single-cell RNA-seq, CRISPR barcoding qRT-PCR, and ChIP-qPCR 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 IL23R Enhancer Active Normal Blood UBERON:0000178 Primary CD4+ T CD4-positive T cell CL:0000624 Enhancer activity assay ChIP-seq Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, RT-RT-qPCR 2016 27354268 Dissection of the major hematopoietic quantitative trait locus in chromosome 6q233 identifies miR-3662 as a novel player in hematopoiesis and acute myeloid leukemia Homo sapiens hg19 chr6 135502600 135502750 CEBPA MIR-3662 Enhancer Active Normal Bone marrow UBERON:0002371 Primary human hematopoietic progenitor cells hematopoietic progenitor cell CL:0000837 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA, RT-RT-qPCR, Western blot 2016 27354268 Dissection of the major hematopoietic quantitative trait locus in chromosome 6q233 identifies miR-3662 as a novel player in hematopoiesis and acute myeloid leukemia Homo sapiens hg19 chr6 135502600 135502750 CEBPA MIR-3662 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 KG1a AML cell line CVCL_1824 acute myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA, RT-RT-qPCR, Western blot 2016 27354268 Dissection of the major hematopoietic quantitative trait locus in chromosome 6q233 identifies miR-3662 as a novel player in hematopoiesis and acute myeloid leukemia Homo sapiens hg19 chr6 135502600 135502750 CEBPA MIR-3662 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA, RT-RT-qPCR, Western blot 2015 26374622 Identification and functional analysis of acute myeloid leukemia susceptibility associated SNPs at noncoding regions of RUNX1 Homo sapiens hg19 chr21 36180372 36181392 SPI1 RUNX1 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Bone marrow UBERON:0002371 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay Luciferase Reporter Assay, EMSA 2015 26214525 GATA2 is required for lymphatic vessel valve development and maintenance Homo sapiens hg19 chr16 86543000 86544500 GATA2 FOXC2 Enhancer Active Normal Dermis UBERON:0002067 Primary Dermal Lymphatic Endothelial Cells (hLECs) dermal lymphatic endothelial cell CL:0002546 Enhancer activity assay ChIP-seq Luciferase Reporter Assay 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 RTN4R Enhancer Silenced Normal Brain UBERON:0000955 Neuronal neuronal cell CL:0000540 Enhancer activity assay ChIP-seq Luciferase Reporter Assay 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 Pancreatic islet UBERON:0000006 Human pancreatic islet pancreatic islet cell CL:0000168 Enhancer activity assay ChIP-seq Luciferase Reporter Assay 2016 26818267 Utility of next-generation RNA-sequencing in identifying chimeric transcription involving human endogenous retroviruses Homo sapiens hg19 chr22 18795000 18797200 SOX2 PRODH Enhancer Active Normal Hippocampus UBERON:0002421 Primary neuron primary neuron CL:0000540 Enhancer activity assay ChIP-seq Luciferase reporter assay 2014 25043047 Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma Homo sapiens hg19 chr9 131200000 131400000 GFI1 Enhancer Active Normal Cerebellum UBERON:0002037 Cerebellar granule neuron progenitors (CGNPs) cerebellar granule neuron progenitor CL:0001031 Enhancer activity assay ChIP-seq Luciferase reporter assay, Transgenic reporter assay, ChIP-RT-qPCR 2014 25043047 Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma Homo sapiens hg19 chr20 32500000 32650000 GFI1B Enhancer Active Normal Cerebellum UBERON:0002037 Cerebellar granule neuron progenitors (CGNPs) cerebellar granule neuron progenitor CL:0001031 Enhancer activity assay ChIP-seq Luciferase reporter assay, ChIP-RT-qPCR 2013 24332857 Switch enhancers interpret TGF-beta signaling Homo sapiens hg19 chr12 79345000 79347000 SMAD2 NANOG Enhancer Active Normal Embryonic stem cell tissue UBERON:0000922 Human embryonic stem cells (hESC) embryonic stem cell CL:0002322 Enhancer activity assay, Signal switching assay ChIP-seq, RNA-seq Luciferase reporter assay, siRNA, RT-RT-qPCR 2012 22408256 Expression of ABO blood-group genes is dependent upon an erythroid cell-specific regulatory element Homo sapiens hg19 chr9 133238853 133239354 GATA1 ABO Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 cells CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay Luciferase reporter assay, EMSA, RT-RT-qPCR 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 Normal Prostate UBERON:0002367 Primary epithelial epithelial cell CL:0000066 Enhancer activity assay ChIP-seq Luciferase Reporter Assay 2000 10688646 Loading of DNA-Binding Factors to an Erythroid Enhancer Homo sapiens hg19 chr16 1600000 1600110 NFE2 HBA1 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 Erythroleukemia Cells CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay Luciferase Reporter Assay, RT-RT-qPCR, EMSA 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 Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 erythroleukemia cells CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay Luciferase Reporter Assay, EMSA, RT-RT-qPCR 2020 32669118 ASXL3 bridges BRD4 to BAP1 complex and governs enhancer activity in small cell lung cancer Homo sapiens hg19 chr18 28988494 35919423 TCF4 SE Active Disease small cell lung carcinoma MONDO:0005020 DOID:5409 Lung UBERON:0002048 NCI-H1963 CVCL_1510 small cell lung carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq shRNA Knockdown, qRT-PCR, Western blot 2020 32771023 Disruption of super-enhancer-driven tumor suppressor gene RCAN14 expression promotes the malignancy of breast carcinoma Homo sapiens hg19 chr21 36179867 36180107 RUNX3 RCAN1.4 Enhancer Active Normal Breast UBERON:0000310 Human Mammary Epithelial Cells (HMEC) mammary epithelial cell CL:0000066 Enhancer activity assay, TF binding assay ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, qRT-PCR 2021 34782839 TNF-??-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer Homo sapiens hg19 chr16 68770000 68771500 JUNB CDH1 Enhancer Active Normal Pancreas UBERON:0001264 CAPAN1 CVCL_0026 pancreatic cell CL:0000066 TF binding assay ChIP-seq, ATAC-seq, RNA-seq ChIP-RT-qPCR, qRT-PCR, Western blot 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 Neural tissue UBERON:0001016 hESC-derived NPCs neural progenitor cell CL:0002672 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq, ChIP-seq, ATAC-seq TF overexpression assay, RT-RT-qPCR, FIMO motif analysis, permutation test 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 Neural tissue UBERON:0001016 hESC-derived NPCs neural progenitor cell CL:0002672 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq, ChIP-seq, ATAC-seq TF overexpression assay, RT-RT-qPCR, FIMO motif analysis, permutation test 2024 39277592 Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance Homo sapiens hg19 chr11 65200000 66000000 KAT5 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 DND41 CVCL_2022 T lymphoblast CL:0002419 Chromatin interaction assay SMC1 HiChIP, H3K27ac ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2024 39277592 Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance Homo sapiens hg19 chr11 65200000 66000000 KAT5 Enhancer Active Disease mantle cell lymphoma MONDO:0005052 DOID:0050747 Blood UBERON:0000178 Rec-1 CVCL_1884 B cell CL:0000945 Chromatin interaction assay SMC1 HiChIP, H3K27ac ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2024 39643619 Enhanced osteogenic potential of iPSC-derived mesenchymal progenitor cells following genome editing of GWAS variants in the RUNX1 gene Homo sapiens hg19 chr21 36282225 36337655 RUNX1 Enhancer Silenced Normal Bone Marrow UBERON:0002371 hiPSC-derived iMSCs mesenchymal stromal cell CL:0000134 Functional perturbation assay, Chromatin interaction assay 3C-seq CRISPR Knockout, RT-RT-qPCR 2024 39643619 Enhanced osteogenic potential of iPSC-derived mesenchymal progenitor cells following genome editing of GWAS variants in the RUNX1 gene Homo sapiens hg19 chr21 36282225 36337655 RUNX1 Enhancer Silenced Normal Bone UBERON:0001474 hiPSC-derived osteoblasts osteoblast CL:0000062 Functional perturbation assay, Chromatin interaction assay 3C-seq CRISPR Knockout, RT-RT-qPCR 2024 39643619 Enhanced osteogenic potential of iPSC-derived mesenchymal progenitor cells following genome editing of GWAS variants in the RUNX1 gene Homo sapiens hg19 chr21 36282225 36337655 SETD4 Enhancer Silenced Normal Bone Marrow UBERON:0002371 hiPSC-derived iMSCs mesenchymal stromal cell CL:0000134 Functional perturbation assay, Chromatin interaction assay 3C-seq CRISPR Knockout, RT-RT-qPCR 2024 39643619 Enhanced osteogenic potential of iPSC-derived mesenchymal progenitor cells following genome editing of GWAS variants in the RUNX1 gene Homo sapiens hg19 chr21 36282225 36337655 SETD4 Enhancer Silenced Normal Bone UBERON:0001474 hiPSC-derived osteoblasts osteoblast CL:0000062 Functional perturbation assay, Chromatin interaction assay 3C-seq CRISPR Knockout, RT-RT-qPCR 2024 39643619 Enhanced osteogenic potential of iPSC-derived mesenchymal progenitor cells following genome editing of GWAS variants in the RUNX1 gene Homo sapiens hg19 chr21 36759535 36828803 RUNX1 Enhancer Silenced Normal Bone Marrow UBERON:0002371 hiPSC-derived iMSCs mesenchymal stromal cell CL:0000134 Functional perturbation assay, Chromatin interaction assay, In vivo functional assay 3C-seq CRISPR Knockout, RT-RT-qPCR 2024 39643619 Enhanced osteogenic potential of iPSC-derived mesenchymal progenitor cells following genome editing of GWAS variants in the RUNX1 gene Homo sapiens hg19 chr21 36759535 36828803 RUNX1 Enhancer Silenced Normal Bone UBERON:0001474 hiPSC-derived osteoblasts osteoblast CL:0000062 Functional perturbation assay, Chromatin interaction assay, In vivo functional assay 3C-seq CRISPR Knockout, RT-RT-qPCR 2024 39643619 Enhanced osteogenic potential of iPSC-derived mesenchymal progenitor cells following genome editing of GWAS variants in the RUNX1 gene Homo sapiens hg19 chr21 36759535 36828803 RUNX1 Enhancer Silenced Normal Bone UBERON:0001474 NOD-SCID mouse calvarial cells mouse calvarial cell CL:0000082 Functional perturbation assay, Chromatin interaction assay, In vivo functional assay 3C-seq CRISPR Knockout, RT-RT-qPCR 2024 39643619 Enhanced osteogenic potential of iPSC-derived mesenchymal progenitor cells following genome editing of GWAS variants in the RUNX1 gene Homo sapiens hg19 chr21 36759535 36828803 SETD4 Enhancer Silenced Normal Bone Marrow UBERON:0002371 hiPSC-derived iMSCs mesenchymal stromal cell CL:0000134 Functional perturbation assay, Chromatin interaction assay, In vivo functional assay 3C-seq CRISPR Knockout, RT-RT-qPCR 2024 39643619 Enhanced osteogenic potential of iPSC-derived mesenchymal progenitor cells following genome editing of GWAS variants in the RUNX1 gene Homo sapiens hg19 chr21 36759535 36828803 SETD4 Enhancer Silenced Normal Bone UBERON:0001474 hiPSC-derived osteoblasts osteoblast CL:0000062 Functional perturbation assay, Chromatin interaction assay, In vivo functional assay 3C-seq CRISPR Knockout, RT-RT-qPCR 2024 39643619 Enhanced osteogenic potential of iPSC-derived mesenchymal progenitor cells following genome editing of GWAS variants in the RUNX1 gene Homo sapiens hg19 chr21 36759535 36828803 SETD4 Enhancer Silenced Normal Bone UBERON:0001474 NOD-SCID mouse calvarial cells mouse calvarial cell CL:0000082 Functional perturbation assay, Chromatin interaction assay, In vivo functional assay 3C-seq CRISPR Knockout, RT-RT-qPCR 2022 36132997 HDAC5-mediated Smad7 silencing through MEF2A is critical for fibroblast activation and hypertrophic scar formation Homo sapiens hg19 chr18 48951365 48952877 MEF2A SMAD7 Enhancer Active Normal Skin UBERON:0000014 Human Hypertrophic Scar Fibroblasts (HSFs) fibroblast CL:0000057 Enhancer activity assay, TF binding assay, Functional perturbation assay Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, CRISPRi, RT-RT-qPCR, Western blot 2022 35202564 Duplications disrupt chromatin architecture and rewire GPR101-enhancer communication in X-linked acrogigantism Homo sapiens hg19 chrX 135577559 135581959 GPR101 Enhancer Active Normal Peripheral Blood UBERON:0000178 PBMCs peripheral blood mononuclear cell CL:0000738 Chromatin interaction assay 4C-seq Luciferase Reporter Assay 2022 35202564 Duplications disrupt chromatin architecture and rewire GPR101-enhancer communication in X-linked acrogigantism Homo sapiens hg19 chrX 135625877 135641072 GPR101 Enhancer Active Normal Peripheral Blood UBERON:0000178 PBMCs peripheral blood mononuclear cell CL:0000738 Chromatin interaction assay 4C-seq Luciferase Reporter Assay 2022 35202564 Duplications disrupt chromatin architecture and rewire GPR101-enhancer communication in X-linked acrogigantism Homo sapiens hg19 chrX 135656769 135660247 GPR101 Enhancer Active Normal Peripheral Blood UBERON:0000178 PBMCs peripheral blood mononuclear cell CL:0000738 Chromatin interaction assay 4C-seq Luciferase Reporter Assay 2022 35202564 Duplications disrupt chromatin architecture and rewire GPR101-enhancer communication in X-linked acrogigantism Homo sapiens hg19 chrX 135846959 135851769 GPR101 Enhancer Active Normal Peripheral Blood UBERON:0000178 PBMCs peripheral blood mononuclear cell CL:0000738 Chromatin interaction assay 4C-seq Luciferase Reporter Assay 2022 35202564 Duplications disrupt chromatin architecture and rewire GPR101-enhancer communication in X-linked acrogigantism Homo sapiens hg19 chrX 135959959 135963959 GPR101 Enhancer Active Normal Peripheral Blood UBERON:0000178 PBMCs peripheral blood mononuclear cell CL:0000738 Chromatin interaction assay, Enhancer activity assay 4C-seq Luciferase Reporter Assay 2022 35202564 Duplications disrupt chromatin architecture and rewire GPR101-enhancer communication in X-linked acrogigantism Homo sapiens hg19 chrX 135959959 135963959 GPR101 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 Chromatin interaction assay, Enhancer activity assay 4C-seq Luciferase Reporter Assay 2022 35202564 Duplications disrupt chromatin architecture and rewire GPR101-enhancer communication in X-linked acrogigantism Homo sapiens hg19 chrX 135990759 135994160 GPR101 Enhancer Active Normal Peripheral Blood UBERON:0000178 PBMCs peripheral blood mononuclear cell CL:0000738 Chromatin interaction assay 4C-seq Luciferase Reporter Assay 2021 34475398 Functional characterization of T2D-associated SNP effects on baseline and ER stress-responsive ?? cell transcriptional activation Homo sapiens hg19 chr3 185511500 185511700 IGF2BP2 Enhancer Active Normal Pancreatic Islet UBERON:0000006 Mouse pancreatic beta cell mouse pancreatic beta cell CL:0000169 Enhancer activity assay MPRA, ATAC-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR 2021 34475398 Functional characterization of T2D-associated SNP effects on baseline and ER stress-responsive ?? cell transcriptional activation Homo sapiens hg19 chr6 170843500 170843700 SLC35D3 Enhancer Active Normal Pancreatic Islet UBERON:0000006 Mouse pancreatic beta cell mouse pancreatic beta cell CL:0000169 Enhancer activity assay MPRA, ATAC-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR 2021 34475398 Functional characterization of T2D-associated SNP effects on baseline and ER stress-responsive ?? cell transcriptional activation Homo sapiens hg19 chr6 170848100 170848300 SLC35D3 Enhancer Active Normal Pancreatic Islet UBERON:0000006 Mouse pancreatic beta cell mouse pancreatic beta cell CL:0000169 Enhancer activity assay MPRA, ATAC-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR 2023 37349788 Enhancer-driven transcription of MCM8 by E2F4 promotes ATR pathway activation and glioma stem cell characteristics Homo sapiens hg19 chr1 51429600 51450093 CDKN2C Enhancer Active Disease glioblastoma MONDO:0005142 DOID:3070 Brain UBERON:0000955 Glioma stem cell glioma stem cell CL:0000127 Enhancer activity assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2019 31120998 HoxA9 binds and represses the Cebpa +8 kb enhancer Homo sapiens hg19 chr19 33794100 33794613 CEBPA Enhancer Silenced Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 MUTZ-3 CVCL_1435 myeloid leukemia cell CL:0001054 Enhancer activity assay Luciferase Reporter Assay 2014 24662484 Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions at the MYC locus Homo sapiens hg19 chr8 128320500 128321500 MYC Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Chromatin interaction assay 3C-seq 3C-RT-qPCR, RT-RT-qPCR, siRNA Knockdown, Western blot 2015 26656844 Identification and functional analysis of acute myeloid leukemia susceptibility associated SNPs at non protein coding regions of RUNX1 Homo sapiens hg19 chr21 36189300 36189537 RUNX1 Enhancer Active Normal Bone Marrow UBERON:0002371 CD34+ hematopoietic stem/progenitor cells hematopoietic stem cell CL:0001029 Enhancer prediction, SNP association, Functional validation ENCODE ChIP-seq dataset analysis, UCSC genome browser regulatory annotation MALDI-TOF mass spectrometry SNP genotyping 2015 26656844 Identification and functional analysis of acute myeloid leukemia susceptibility associated SNPs at non protein coding regions of RUNX1 Homo sapiens hg19 chr21 36189300 36189537 RUNX1 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Bone Marrow UBERON:0002371 K562 cell line CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer prediction, SNP association, Functional validation ENCODE ChIP-seq dataset analysis, UCSC genome browser regulatory annotation MALDI-TOF mass spectrometry SNP genotyping 2019 31217582 Noncoding deletions reveal a gene that is critical for intestinal function Homo sapiens hg19 chr16 1480850 1482378 PERCC1 Enhancer Silenced Normal Gastrointestinal Tract UBERON:0000160 Enteroendocrine cells enteroendocrine cell CL:0000164 Functional perturbation assay WGS, WES, RNA-seq CRISPR Knockout, RT-RT-qPCR, Western blot, Immunofluorescence 2023 38102337 Suppression of super-enhancer-driven TAL1 expression by KLF4 in T-cell acute lymphoblastic leukemia Homo sapiens hg19 chr1 47220000 47260000 TAL1 Enhancer Silenced Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat CVCL_0065 T lymphoblast CL:0002419 Enhancer activity assay, Functional perturbation assay RNA-seq Luciferase Reporter Assay, shRNA Knockdown, RT-RT-qPCR, Western blot 2023 38102337 Suppression of super-enhancer-driven TAL1 expression by KLF4 in T-cell acute lymphoblastic leukemia Homo sapiens hg19 chr1 47220000 47260000 TAL1 Enhancer Silenced Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Bone Marrow UBERON:0002371 MOLT-3 CVCL_2288 T lymphoblast CL:0002419 Enhancer activity assay, Functional perturbation assay RNA-seq Luciferase Reporter Assay, shRNA Knockdown, RT-RT-qPCR, Western blot 2023 37349788 Enhancer-driven transcription of MCM8 by E2F4 promotes ATR pathway activation and glioma stem cell characteristics Homo sapiens hg19 chr20 5921142 6004055 E2F4 MCM8 Enhancer Active Disease glioblastoma MONDO:0005142 DOID:3070 Brain UBERON:0000955 Glioma stem cell glioma stem cell CL:0000127 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot, Sphere Formation Assay, Limiting Dilution Assay, Cell Growth Assay 2023 37349788 Enhancer-driven transcription of MCM8 by E2F4 promotes ATR pathway activation and glioma stem cell characteristics Homo sapiens hg19 chr20 5921142 6004055 E2F4 MCM8 Enhancer Active Normal Brain UBERON:0000955 Neural stem cells neural stem cell CL:0002672 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot, Sphere Formation Assay, Limiting Dilution Assay, Cell Growth Assay 2015 26258633 Genome-wide association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth Homo sapiens hg19 chr8 128210000 128260000 MYC Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 CVCL_0062 breast carcinoma cell CL:0000066 Chromatin interaction assay Hi-C 3C 2025 40512334 Genomic Locus Tagged by Lung Function GWAS SNV rs12477314 (2q373) Acts as a Regulatory Region for a Systemic Inflammatory Phenotype Homo sapiens hg19 chr2 239884251 239900294 MULTIPLE (CXCL2 Enhancer Active Disease non-small cell lung carcinoma MONDO:0005233 DOID:3908 Lung UBERON:0002048 NCI-H460 CVCL_0459 non-small cell lung carcinoma cell CL:0000066 Functional perturbation assay RNA-seq CRISPR Knockout, RT-RT-qPCR, Sanger sequencing 2024 38413562 The neutrophil-osteogenic cell axis promotes bone destruction in periodontitis Homo sapiens hg19 chr13 43058344 43062075 STAT3; STAT1 TNFSF11 Enhancer Active Normal Bone UBERON:0001474 Periodontal ligament cells periodontal ligament cell CL:0000057 TF binding assay, Enhancer activity assay ChIP-seq, DNase-seq, scRNA-seq ChIP-RT-qPCR, qRT-PCR 2016 26673704 Differential contribution of cis regulatory elements to higher order chromatin structure and expression of the CFTR locus Homo sapiens hg19 chr7 117175700 117176900 CFTR Enhancer Active Normal Intestine UBERON:0000160 Human colorectal adenocarcinoma cell colorectal adenocarcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay CRISPR-Cas9 deletion, RT-RT-qPCR 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr8 128667652 128669252 HLX; LHX2; LMX1A MYC Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 Primary medulloblastoma tissue medulloblastoma cell CL:0000127 Super-enhancer mapping, TF binding assay, Enhancer activity assay, Chromatin interaction assay ChIP-seq, RNA-seq, Whole-genome sequencing Zebrafish Tol2 transgenic reporter assay, RT-RT-qPCR, Immunohistochemistry 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr8 128667652 128669252 HLX; LHX2; LMX1A MYC Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 HD-MB03 CVCL_IT11 medulloblastoma cell CL:0000127 Super-enhancer mapping, TF binding assay, Enhancer activity assay, Chromatin interaction assay ChIP-seq, RNA-seq, Whole-genome sequencing Zebrafish Tol2 transgenic reporter assay, RT-RT-qPCR, Immunohistochemistry 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr14 57220000 57221600 OTX2; ZIC1; ZIC4 OTX2 Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 Primary medulloblastoma tissue medulloblastoma cell CL:0000127 Super-enhancer mapping, Enhancer activity assay, Gene expression assay ChIP-seq, RNA-seq, Whole-genome sequencing Zebrafish transgenic reporter assay, RT-RT-qPCR, Immunohistochemistry 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr14 57220000 57221600 OTX2; ZIC1; ZIC4 OTX2 Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 HD-MB03 CVCL_IT11 medulloblastoma cell CL:0000127 Super-enhancer mapping, Enhancer activity assay, Gene expression assay ChIP-seq, RNA-seq, Whole-genome sequencing Zebrafish transgenic reporter assay, RT-RT-qPCR, Immunohistochemistry 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr14 57220000 57221600 OTX2; ZIC1; ZIC4 OTX2 Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 MED8A medulloblastoma cell CL:0000127 Super-enhancer mapping, Enhancer activity assay, Gene expression assay ChIP-seq, RNA-seq, Whole-genome sequencing Zebrafish transgenic reporter assay, RT-RT-qPCR, Immunohistochemistry 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr14 57220000 57221600 OTX2; ZIC1; ZIC4 OTX2 Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 D425 medulloblastoma cell CL:0000127 Super-enhancer mapping, Enhancer activity assay, Gene expression assay ChIP-seq, RNA-seq, Whole-genome sequencing Zebrafish transgenic reporter assay, RT-RT-qPCR, Immunohistochemistry 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr3 147033502 147035102 ZIC1; ZIC4 ZIC1 Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 Primary medulloblastoma tissue medulloblastoma cell CL:0000127 Super-enhancer mapping, Enhancer activity assay, Gene expression assay ChIP-seq, RNA-seq, Whole-genome sequencing Zebrafish transgenic reporter assay, RT-RT-qPCR, Immunohistochemistry 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr3 147033502 147035102 ZIC1; ZIC4 ZIC1 Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 HD-MB03 CVCL_IT11 medulloblastoma cell CL:0000127 Super-enhancer mapping, Enhancer activity assay, Gene expression assay ChIP-seq, RNA-seq, Whole-genome sequencing Zebrafish transgenic reporter assay, RT-RT-qPCR, Immunohistochemistry 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr3 147033502 147035102 ZIC1; ZIC4 ZIC1 Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 MED8A medulloblastoma cell CL:0000127 Super-enhancer mapping, Enhancer activity assay, Gene expression assay ChIP-seq, RNA-seq, Whole-genome sequencing Zebrafish transgenic reporter assay, RT-RT-qPCR, Immunohistochemistry 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr3 147033502 147035102 ZIC1; ZIC4 ZIC1 Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 D425 medulloblastoma cell CL:0000127 Super-enhancer mapping, Enhancer activity assay, Gene expression assay ChIP-seq, RNA-seq, Whole-genome sequencing Zebrafish transgenic reporter assay, RT-RT-qPCR, Immunohistochemistry 2015 26252164 FOXD3 Promotes PAX3 Expression in Melanoma Cells Homo sapiens hg19 chr2 223164458 223164688 FOXD3 PAX3 Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 A375 CVCL_0132 melanoma cell CL:0002573 Enhancer activity assay Luciferase Reporter Assay, EMSA 2015 26252164 FOXD3 Promotes PAX3 Expression in Melanoma Cells Homo sapiens hg19 chr2 223164846 223165065 FOXD3 PAX3 Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 SK-MEL28 CVCL_0526 melanoma cell CL:0002573 Enhancer activity assay Luciferase Reporter Assay, EMSA 2015 26232425 PXR Activation Modulates HepG2 Cell Morphology and Migration Through the HNF4??-IGFBP1 Signaling Axis Homo sapiens hg19 chr7 48230000 48231500 IGFBP1 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepG2 CVCL_0027 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay RNA-seq Luciferase Reporter Assay 2015 26422397 SATB1 Mediates Long-Range Chromatin Interactions Homo sapiens hg19 chr18 60983148 60983597 SATB1 BCL2 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat CVCL_0065 T lymphoblast CL:0002419 Chromatin interaction, expression validation 3C, ChIP-qPCR, RT-qPCR qRT-PCR, and ChIP-qPCR 2015 26257940 Genome-wide association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth Homo sapiens hg19 chr8 128210000 128260000 MYC Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 CVCL_0062 breast carcinoma cell CL:0000066 Chromatin interaction assay Hi-C 3C 2014 24564208 Dynamic reorganization of the AC16 cardiomyocyte transcriptome in response to TNF?? signaling revealed by integrated genomic analyses Homo sapiens hg19 chr7 22760000 22761000 NFKB1; RELA IL6 Enhancer Active Normal Heart UBERON:0000948 AC16 CVCL_4U18 cardiomyocyte CL:0000746 Enhancer activity assay, Functional perturbation assay ChIP-seq, GRO-seq RT-RT-qPCR, Western blot 2016 27848966 17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells Homo sapiens hg19 chr17 38065000 38068000 CTCF ORMDL3 Enhancer Active Normal Peripheral blood UBERON:0000178 Primary CD4+ T cells CD4-positive T cell CL:0000624 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2016 26818267 Utility of next-generation RNA-sequencing in identifying chimeric transcription involving human endogenous retroviruses Homo sapiens hg19 chr11 5225000 5227000 HBB Enhancer Active Normal Bone Marrow UBERON:0002371 CD34+ cell CD34-positive hematopoietic stem cell CL:0001029 Chromatin interaction assay ChIP-seq, Hi-C 3C assay 2016 26818267 Utility of next-generation RNA-sequencing in identifying chimeric transcription involving human endogenous retroviruses Homo sapiens hg19 chr3 189520000 189522000 TP63 Enhancer Active Normal Testis UBERON:0000473 Spermatogonia spermatogonium CL:0000020 Functional perturbation assay RNA-seq CRISPR knockout 2013 23884959 Hypoxia enhances the expression of prostate-specific antigen by modifying the quantity and catalytic activity of Jumonji C domain-containing histone demethylases Homo sapiens hg19 chr19 51353600 51354200 AR KLK3 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP cells CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay Luciferase reporter assay, ChIP-RT-qPCR 2013 23884959 Hypoxia enhances the expression of prostate-specific antigen by modifying the quantity and catalytic activity of Jumonji C domain-containing histone demethylases Homo sapiens hg19 chr19 51350000 51351000 KLK2 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP cells CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay Luciferase reporter assay 2013 22370642 The nuclear cofactor RAC3/AIB1/SRC-3 enhances Nrf2 signaling by interacting with transactivation domains Homo sapiens hg19 chr22 35772741 35773741 NFE2L2 HMOX1 Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa cells CVCL_0030 cervical adenocarcinoma cell CL:0000069 Enhancer activity assay, TF binding assay Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR 2013 22370642 The nuclear cofactor RAC3/AIB1/SRC-3 enhances Nrf2 signaling by interacting with transactivation domains Homo sapiens hg19 chr22 35767741 35768741 NFE2L2 HMOX1 Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa cells CVCL_0030 cervical adenocarcinoma cell CL:0000069 Enhancer activity assay, TF binding assay Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR 2014 24594601 Long-range interaction and correlation between MYC enhancer and oncogenic long noncoding RNA CARLo-5 Homo sapiens hg19 chr8 128320000 128321000 CARLO-5 Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Chromatin interaction assay RNA-seq 3C, RT-RT-qPCR 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 myeloid leukemia cell CL:0001054 Functional perturbation assay ChIP-seq RT-RT-qPCR 2010 20453196 8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC Homo sapiens hg19 chr8 128589642 128590670 P300 MYC Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-RT-qPCR, 3C 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 UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay ChIP-chip Luciferase Reporter Assay, ChIP-RT-qPCR 2000 10891470 Direct interaction of NF-E2 with hypersensitive site 2 of the beta-globin locus control region in living cells Homo sapiens hg19 chr11 5198400 5198625 NFE2 HBB Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 erythroleukemia cells CVCL_0004 chronic myeloid leukemia cell CL:0001054 TF binding assay, Enhancer activity assay Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 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 U937 CVCL_0007 histiocytic lymphoma cell CL:0000576 Enhancer activity assay, TF binding assay EMSA, Luciferase Reporter Assay 2024 38224404 dCas9/CRISPRa-based methylation of O6-methylguanine-DNA methyltransferase enhances chemosensitivity to temozolomide in malignant glioma Homo sapiens hg19 chr10 131265950 131266000 MGMT Enhancer Active Disease glioblastoma MONDO:0005142 DOID:3070 Brain UBERON:0000955 LN18 glioma cells CVCL_1352 glioblastoma cell CL:0000127 Functional perturbation assay, Enhancer activity assay RNA-seq CRISPR Knockout, CRISPRi, qRT-PCR, Western blot 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 UBERON:0002367 VCaP CVCL_2235 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, RNA-seq, ChIA-PET ChIP-RT-qPCR, qRT-PCR, Western blot, Re-ChIP 2024 39277592 Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance Homo sapiens hg19 chr20 48400000 49200000 CEBPB Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MB157 CVCL_UC56 breast carcinoma cell CL:0000066 Chromatin interaction assay SMC1 HiChIP, H3K27ac ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2024 39277592 Enhancer-promoter hubs organize transcriptional networks promoting oncogenesis and drug resistance Homo sapiens hg19 chr20 48400000 49200000 CEBPB Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 HCC1599 CVCL_UC78 breast carcinoma cell CL:0000066 Chromatin interaction assay SMC1 HiChIP, H3K27ac ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2012 21822303 Sox2 expression in breast tumours and activation in breast cancer stem cells Homo sapiens hg19 chr3 181708088 181708477 SOX2 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF7 breast carcinoma CVCL_0031 breast carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay Luciferase Reporter Assay, RT-RT-qPCR, Western blot 2012 21822303 Sox2 expression in breast tumours and activation in breast cancer stem cells Homo sapiens hg19 chr3 181708088 181708477 SOX2 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 T47D breast carcinoma CVCL_0553 breast carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay Luciferase Reporter Assay, RT-RT-qPCR, Western blot 2012 21822303 Sox2 expression in breast tumours and activation in breast cancer stem cells Homo sapiens hg19 chr3 181708088 181708477 SOX2 Enhancer Active Normal Pluripotent embryonic tissue UBERON:0000922 human embryonic stem embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay Luciferase Reporter Assay, RT-RT-qPCR, Western blot 2016 26884396 Differential regulation of mouse and human nephron progenitors by the Six family of transcriptional regulators Homo sapiens hg19 chr14 61101000 61102000 SIX1; SIX2 SIX1 Enhancer Active Normal Kidney UBERON:0002113 Nephron Progenitor nephron progenitor cell CL:0002672 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq Transgenic Reporter Assay 2016 26884396 Differential regulation of mouse and human nephron progenitors by the Six family of transcriptional regulators Homo sapiens hg19 chr14 61116934 61117934 SIX1; SIX2 SIX1 Enhancer Active Normal Kidney UBERON:0002113 Nephron Progenitor nephron progenitor cell CL:0002672 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq Transgenic Reporter Assay 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 23500000 23501600 CEBPBETA; RNA POLYMERASE II DHRS4-AS1 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepG2 CVCL_0027 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 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 23500000 23501600 CEBPBETA; RNA POLYMERASE II DHRS4-AS1 Enhancer Active Normal Liver UBERON:0002107 HL7702 hepatocyte CL:0000182 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr8 128647663 128667652 HLX; LHX2; LMX1A MYC Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 MED8A medulloblastoma cell CL:0000127 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, RNA-seq Transgenic Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr8 128647663 128667652 HLX; LHX2; LMX1A MYC Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 D425 medulloblastoma cell CL:0000127 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, RNA-seq Transgenic Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr8 128647663 128667652 HLX; LHX2; LMX1A MYC Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 HD-MB03 CVCL_IT11 medulloblastoma cell CL:0000127 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, RNA-seq Transgenic Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr8 128647663 128667652 HLX; LHX2; LMX1A MYC Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 Primary Medulloblastoma Tissue medulloblastoma cell CL:0000127 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, RNA-seq Transgenic Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr14 57182300 57183900 OTX2 OTX2 Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 Primary Medulloblastoma Tissue medulloblastoma cell CL:0000127 Enhancer activity assay ChIP-seq, RNA-seq Transgenic Reporter Assay 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr3 147013502 147063501 ZIC1; ZIC4 ZIC1 Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 Primary Medulloblastoma Tissue medulloblastoma cell CL:0000127 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr21 47738157 47748156 PCNT Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 Primary Medulloblastoma Tissue (WNT subgroup) medulloblastoma cell CL:0000127 Enhancer activity assay ChIP-seq, RNA-seq RT-RT-qPCR 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr1 221037098 221047097 NKD2 Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 Primary Medulloblastoma Tissue (SHH subgroup) medulloblastoma cell CL:0000127 Enhancer activity assay ChIP-seq, RNA-seq RT-RT-qPCR 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr5 121620525 121630524 SNCAIP Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 Primary Medulloblastoma Tissue (Group3 subgroup) medulloblastoma cell CL:0000127 Enhancer activity assay ChIP-seq, RNA-seq RT-RT-qPCR 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr5 925833 926832 HLX HLX Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 Primary Medulloblastoma Tissue (Group4 subgroup) medulloblastoma cell CL:0000127 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2022 35741778 Discovery and Functional Characterization of Two Regulatory Variants Underlying Lupus Susceptibility at 2p131 Homo sapiens hg19 chr2 73956813 73957241 ARID3A DGUOK Enhancer Active Normal Peripheral Blood UBERON:0000178 B cell B cell CL:0000945 Enhancer activity assay, TF binding assay, Chromatin interaction assay Hi-C Luciferase Reporter Assay, ChIP-RT-qPCR 2022 35741778 Discovery and Functional Characterization of Two Regulatory Variants Underlying Lupus Susceptibility at 2p131 Homo sapiens hg19 chr2 73956813 73957241 ARID3A DGUOK-AS1 Enhancer Active Normal Peripheral Blood UBERON:0000178 LCL lymphoblastoid cell line CL:0000945 Enhancer activity assay, TF binding assay, Chromatin interaction assay Hi-C Luciferase Reporter Assay, ChIP-RT-qPCR 2022 35741778 Discovery and Functional Characterization of Two Regulatory Variants Underlying Lupus Susceptibility at 2p131 Homo sapiens hg19 chr2 73956813 73957241 ARID3A Enhancer Active Normal Peripheral Blood UBERON:0000178 GM12878 CVCL_7526 B lymphoblastoid cell CL:0000945 Enhancer activity assay, TF binding assay, Chromatin interaction assay Hi-C Luciferase Reporter Assay, ChIP-RT-qPCR 2022 35918310 A common deletion at BAK1 reduces enhancer activity and confers risk of intracranial germ cell tumors Homo sapiens hg19 chr6 33548076 33548616 BAK1 Enhancer Silenced Normal Embryonic Kidney UBERON:0002113 293T CVCL_0063 embryonic kidney cell CL:0002139 Enhancer activity assay, TF binding assay ATAC-seq Luciferase Reporter Assay 2022 35918310 A common deletion at BAK1 reduces enhancer activity and confers risk of intracranial germ cell tumors Homo sapiens hg19 chr6 33548076 33548616 BAK1 Enhancer Silenced Normal Inner cell mass UBERON:0000087 H1-hESC embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay ATAC-seq Luciferase Reporter Assay 2022 36402859 Hnf1b renal expression directed by a distal enhancer responsive to Pax8 Homo sapiens hg19 chr17 37648901 37649206 PAX8 HNF1B Enhancer Active Normal Kidney UBERON:0002113 Kidney Tubule Primary Cells kidney tubule epithelial cell CL:0000066 Enhancer activity assay, TF binding assay DNase-seq, ChIP-seq, ATAC-seq qRT-PCR, and ChIP-qPCR 2019 31231131 Ascl1-induced Wnt11 regulates neuroendocrine differentiation, cell proliferation, and E-cadherin expression in small-cell lung cancer Homo sapiens hg19 chr11 75928700 75928930 ASCL1 Enhancer Active Disease small cell lung carcinoma MONDO:0005020 DOID:5409 Lung UBERON:0002048 SCLC cell line H889 CVCL_1599 small cell lung carcinoma cell CL:0000066 TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot 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 BCL2 Enhancer Active Disease diffuse large B-cell lymphoma MONDO:0005042 DOID:0050746 Blood UBERON:0000178 Diffuse large B-cell lymphoma cell line diffuse large B-cell lymphoma cell CL:0000945 Functional perturbation assay CRISPR screen RT-RT-qPCR, Western blot 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 MYC Enhancer Active Disease Burkitt lymphoma MONDO:0002483 DOID:8582 Blood UBERON:0000178 Burkitt lymphoma cell line Burkitt lymphoma cell CL:0000945 Functional perturbation assay CRISPR screen RT-RT-qPCR, Western blot 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 BCL2 Enhancer Active Disease diffuse large B-cell lymphoma MONDO:0005042 DOID:0050746 Blood UBERON:0000178 Diffuse large B-cell lymphoma cell line diffuse large B-cell lymphoma cell CL:0000945 Functional perturbation assay CRISPR screen RT-RT-qPCR, Western blot 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 MYC Enhancer Active Disease Burkitt lymphoma MONDO:0002483 DOID:8582 Blood UBERON:0000178 Burkitt lymphoma cell line Burkitt lymphoma cell CL:0000945 Functional perturbation assay CRISPR screen RT-RT-qPCR, Western blot 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 BCL2 Enhancer Active Disease diffuse large B-cell lymphoma MONDO:0005042 DOID:0050746 Blood UBERON:0000178 Diffuse large B-cell lymphoma cell line diffuse large B-cell lymphoma cell CL:0000945 Functional perturbation assay CRISPR screen RT-RT-qPCR, Western blot 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 MYC Enhancer Active Disease Burkitt lymphoma MONDO:0002483 DOID:8582 Blood UBERON:0000178 Burkitt lymphoma cell line Burkitt lymphoma cell CL:0000945 Functional perturbation assay CRISPR screen RT-RT-qPCR, Western blot 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 BCL2 Enhancer Active Disease diffuse large B-cell lymphoma MONDO:0005042 DOID:0050746 Blood UBERON:0000178 Diffuse large B-cell lymphoma cell line diffuse large B-cell lymphoma cell CL:0000945 Functional perturbation assay CRISPR screen RT-RT-qPCR, Western blot 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 MYC Enhancer Active Disease Burkitt lymphoma MONDO:0002483 DOID:8582 Blood UBERON:0000178 Burkitt lymphoma cell line Burkitt lymphoma cell CL:0000945 Functional perturbation assay CRISPR screen RT-RT-qPCR, Western blot 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 BCL2 Enhancer Active Disease diffuse large B-cell lymphoma MONDO:0005042 DOID:0050746 Blood UBERON:0000178 Diffuse large B-cell lymphoma cell line diffuse large B-cell lymphoma cell CL:0000945 Functional perturbation assay CRISPR screen RT-RT-qPCR, Western blot 2019 30678091 Functional SNPs in the Human Autoimmunity-Associated Locus 17q12-21 Homo sapiens hg19 chr17 38050770 38051866 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat CVCL_0065 T lymphoblast CL:0002419 Enhancer activity assay Luciferase Reporter Assay 2017 28487391 Functional Characterization of the GUCY1A3 Coronary Artery Disease Risk Locus Homo sapiens hg19 chr4 156635141 156635310 ZEB1 GUCY1A3 Enhancer Active Normal Whole Blood UBERON:0000178 Endothelial cells endothelial cell CL:0000115 Reporter assay, TF binding, Functional validation ChIP-seq qRT-PCR, and ChIP-qPCR 2016 26615198 CFTR regulatory elements identified by 5C Homo sapiens hg19 chr7 117323000 117324600 CFTR Enhancer Active Disease colorectal adenocarcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 Caco-2 CVCL_0025 colorectal adenocarcinoma cell CL:0000066 Enhancer activity assay 5C-seq Luciferase Reporter Assay 2016 26754925 IER5 generates a novel hypo-phosphorylated active form of HSF1 and contributes to tumorigenesis Homo sapiens hg19 chr6 31784438 31784648 HSPA1B Enhancer Active Disease non-small cell lung carcinoma MONDO:0005233 DOID:3908 Lung UBERON:0002048 H1299 CVCL_0060 non-small cell lung carcinoma cell CL:0000066 Enhancer activity assay Gene Expression Microarray Luciferase Reporter Assay, RT-RT-qPCR 2016 26754925 IER5 generates a novel hypo-phosphorylated active form of HSF1 and contributes to tumorigenesis Homo sapiens hg19 chr1 161559500 161559700 HSPA6 Enhancer Active Disease non-small cell lung carcinoma MONDO:0005233 DOID:3908 Lung UBERON:0002048 H1299 CVCL_0060 non-small cell lung carcinoma cell CL:0000066 Enhancer activity assay Gene Expression Microarray Luciferase Reporter Assay, RT-RT-qPCR 2016 26751173 Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9 Homo sapiens hg19 chr6 36642000 36645000 CDKN1A Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF-7 CVCL_0031 breast carcinoma cell CL:0000066 Genetic perturbation screen GRO-seq Luciferase Reporter Assay 2016 25786345 p53-dependent expression of CXCR5 chemokine receptor in MCF-7 breast cancer cells Homo sapiens hg19 chr11 118813865 118815965 CXCR5 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF-7 CVCL_0031 breast carcinoma cell CL:0000066 Enhancer activity assay Luciferase Reporter Assay 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 9470000 9472826 CEBPB IGFBP1 Enhancer Active Normal Endometrium UBERON:0001295 Endometrial stromal cells endometrial stromal cell CL:0002255 Enhancer activity assay, functional perturbation assay ChIP-seq qRT-PCR, and ChIP-qPCR 2018 29511351 HPSE enhancer RNA promotes cancer progression through driving chromatin looping and regulating hnRNPU/p300/EGR1/HPSE axis Homo sapiens hg19 chr4 84255915 84256935 EGR1 HPSE Enhancer Active Disease gastric adenocarcinoma MONDO:0005050 DOID:3717 Stomach UBERON:0000945 AGS CVCL_0139 gastric adenocarcinoma cell CL:0000066 Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2018 29511351 HPSE enhancer RNA promotes cancer progression through driving chromatin looping and regulating hnRNPU/p300/EGR1/HPSE axis Homo sapiens hg19 chr4 84255915 84256935 EGR1 HPSE Enhancer Active Disease gastric adenocarcinoma MONDO:0005050 DOID:3717 Stomach UBERON:0000945 SGC-7901 CVCL_0525 gastric adenocarcinoma cell CL:0000066 Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2018 29641996 Transcriptional Dysregulation of MYC Reveals Common Enhancer-Docking Mechanism Homo sapiens hg19 chr8 128765000 128767000 VEGFA Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Bone Marrow UBERON:0002371 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Chromatin interaction assay, Functional perturbation assay ChIA-PET, RNA-seq qRT-PCR, and ChIP-qPCR 2018 29641996 Transcriptional Dysregulation of MYC Reveals Common Enhancer-Docking Mechanism Homo sapiens hg19 chr8 128765000 128767000 VEGFA Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 HCT-116 CVCL_0291 colorectal carcinoma cell CL:0000066 Chromatin interaction assay, Functional perturbation assay ChIA-PET, RNA-seq qRT-PCR, and ChIP-qPCR 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 Heart UBERON:0000948 hiPSC-CMs cardiomyocyte CL:0000746 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2019 31888703 Enhancer polymorphism rs10865710 associated with traumatic sepsis is a regulator of PPARG gene expression Homo sapiens hg19 chr3 12311574 12312573 CREB2 PPARG Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293T CVCL_0063 embryonic kidney cell CL:0002139 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, EMSA, RT-RT-qPCR, Western blot 2011 21232847 A rearranged EP300 gene in the human B-cell lymphoma cell line RC-K8 encodes a disabled transcriptional co-activator that contributes to cell growth and oncogenicity Homo sapiens hg19 chr22 41500000 41501000 EP300 Enhancer Active Disease histiocytic lymphoma MONDO:0004854 DOID:5408 Blood UBERON:0000178 RC-K8 CVCL_2148 histiocytic lymphoma cell CL:0000576 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR, siRNA knockdown 2023 36704932 Global hypomethylation in childhood asthma identified by genome-wide DNA methylation sequencing preferentially affects enhancer regions Homo sapiens hg19 chr5 132008000 132009000 IL4 Enhancer Active Normal Peripheral blood UBERON:0000178 Primary human whole blood immune cells leukocyte CL:0000738 Enhancer activity assay, Chromatin interaction assay Hi-C, RNA-seq RT-RT-qPCR 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 LMNB1 Enhancer Active Normal Kidney UBERON:0002113 Human embryonic kidney cell embryonic kidney cell CL:0002139 Enhancer activity assay Luciferase Reporter Assay 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 LMNB1 Enhancer Active Normal Kidney UBERON:0002113 Human embryonic kidney cell embryonic kidney cell CL:0002139 Enhancer activity assay Luciferase Reporter Assay 2016 26884396 Differential regulation of mouse and human nephron progenitors by the Six family of transcriptional regulators Homo sapiens hg19 chr14 61101000 61104000 SIX2 SIX1 Enhancer Active Normal Kidney UBERON:0002113 16-17 week human fetal nephron progenitor nephron progenitor cell CL:0002672 Enhancer activity assay, TF binding assay, Gene expression assay ChIP-seq, RNA-seq LacZ transgenic reporter assay, ChIP-RT-qPCR, RT-RT-qPCR, Immunofluorescence 2016 26884396 Differential regulation of mouse and human nephron progenitors by the Six family of transcriptional regulators Homo sapiens hg19 chr14 61113500 61116500 SIX2 SIX1 Enhancer Active Normal Kidney UBERON:0002113 16-17 week human fetal nephron progenitor nephron progenitor cell CL:0002672 Enhancer activity assay, TF binding assay, Gene expression assay ChIP-seq, RNA-seq LacZ transgenic reporter assay, ChIP-RT-qPCR, RT-RT-qPCR, Immunofluorescence 2022 36201590 A noncoding single-nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation Homo sapiens hg19 chr8 128748243 128748308 MYC Enhancer Active Normal Brain UBERON:0000955 Neural stem neural stem cell CL:0002672 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay RNA-seq, GAM, 4C-seq Transgenic Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, Immunofluorescence 2022 34980595 GFI1 Cooperates with IKZF1/IKAROS to Activate Gene Expression in T-cell Acute Lymphoblastic Leukemia Homo sapiens hg19 chr1 92946000 92958000 IKZF1 GFI1 Enhancer Silenced Normal Bone marrow UBERON:0002371 T cell T cell CL:0000084 TF binding assay ChIP-seq ChIP-RT-qPCR, RT-RT-qPCR 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 CFTR Enhancer Active Normal Bronchus UBERON:0002037 16HBE14o- human bronchial epithelial CVCL_0112 bronchial epithelial cell CL:0002591 Enhancer activity assay Luciferase Reporter Assay, RT-RT-qPCR 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 43572300 43572600 RET Enhancer Active Normal Brain UBERON:0000955 Neuro-2A CVCL_0470 neuroblastoma cell CL:0000031 Enhancer activity assay Luciferase Reporter Assay, RT-RT-qPCR 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 43569100 43569300 RET Enhancer Active Normal Brain UBERON:0000955 Neuro-2A CVCL_0470 neuroblastoma cell CL:0000031 Enhancer activity assay Luciferase Reporter Assay, RT-RT-qPCR 2015 25522777 Salinomycin inhibits hepatocellular carcinoma cell invasion and migration through JNK/JunD pathway-mediated MMP9 expression Homo sapiens hg19 chr20 44639323 44641625 MMP9 Enhancer Silenced Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HCCLM3 CVCL_6850 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay Luciferase Reporter Assay, RT-RT-qPCR 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 SOX9 Enhancer Active Normal Testis UBERON:0000473 TM-4 CVCL_5365 Sertoli cell CL:0000216 Enhancer activity assay Luciferase Reporter Assay 2015 25628225 SLC13A5 Is a Novel Transcriptional Target of the Pregnane X Receptor and Sensitizes Drug-Induced Steatosis in Human Liver Homo sapiens hg19 chr17 2261913 2262186 SLC13A5 Enhancer Active Normal Liver UBERON:0002107 HepG2 CVCL_0027 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay Luciferase Reporter Assay 2015 25704602 Functional variants near NOG Homo sapiens hg19 chr17 54776294 54777215 NOG Enhancer Active Normal Palatal epithelium UBERON:0006397 GMSM-K CVCL_6F32 fibroblast CL:0000057 Enhancer activity assay Luciferase Reporter Assay 2015 26214525 GATA2 is required for lymphatic vessel valve development and maintenance Homo sapiens hg19 chr1 214164500 214168500 PROX1 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay Luciferase Reporter Assay 2015 26214589 Chimeric EWSR1-FLI1 regulates the Ewing sarcoma susceptibility gene EGR2 via a GGAA microsatellite Homo sapiens hg19 chr10 64739850 64739980 EGR2 Enhancer Active Disease Ewing sarcoma MONDO:0003368 DOID:3368 Bone UBERON:0001474 A673 CVCL_0080 Ewing sarcoma cell CL:0000050 Enhancer activity assay Luciferase Reporter Assay 2015 26214589 Chimeric EWSR1-FLI1 regulates the Ewing sarcoma susceptibility gene EGR2 via a GGAA microsatellite Homo sapiens hg19 chr10 64698250 64698400 EGR2 Enhancer Active Disease Ewing sarcoma MONDO:0003368 DOID:3368 Bone UBERON:0001474 A673 CVCL_0080 Ewing sarcoma cell CL:0000050 Enhancer activity assay Luciferase Reporter Assay 2015 26214589 Chimeric EWSR1-FLI1 regulates the Ewing sarcoma susceptibility gene EGR2 via a GGAA microsatellite Homo sapiens hg19 chr10 64715600 64717000 EGR2 Enhancer Active Disease Ewing sarcoma MONDO:0003368 DOID:3368 Bone UBERON:0001474 A673 CVCL_0080 Ewing sarcoma cell CL:0000050 Enhancer activity assay Luciferase Reporter Assay 2015 26382291 Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development Homo sapiens hg19 chr6 1614904 1616335 FOXC1 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryo (E11.5) mouse embryo CL:0000000 Enhancer activity assay ChIP-seq Transgenic Reporter Assay 2016 26679052 Inhibition of growth, migration and invasion of human bladder cancer cells by antrocin, a sesquiterpene lactone isolated from Antrodia cinnamomea, and its molecular mechanisms Homo sapiens hg19 chr16 55499100 55501100 MMP2 Enhancer Silenced Disease bladder carcinoma MONDO:0005094 DOID:4007 Urinary bladder UBERON:0001255 5637 CVCL_0126 bladder carcinoma cell CL:0000066 Enhancer activity assay Luciferase Reporter Assay 2014 24212882 Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis Homo sapiens hg19 chr10 23508149 23508510 FOXA2 PTF1A Enhancer Active Normal Pancreas UBERON:0001264 hESC-derived progenitors progenitor cell CL:0000037 TF binding assay ChIP-seq EMSA 2014 24667089 The PEG13-DMR and brain-specific enhancers dictate imprinted expression within the 8q24 intellectual disability risk locus Homo sapiens hg19 chr8 140450000 140452000 KCNK9 Enhancer Active Normal Brain UBERON:0000955 Primary brain brain cell CL:0000540 Chromatin interaction assay ChIA-PET RNA-seq, 3C-RT-qPCR 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr8 128311200 128667652 HLX MYC Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 HD-MB03 CVCL_IT11 medulloblastoma cell CL:0000127 Enhancer activity assay ChIP-seq Transgenic reporter assay 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr2 29411893 30163716 ALK Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 Primary tumor tissue medulloblastoma cell CL:0000127 Enhancer activity assay ChIP-seq Immunohistochemistry 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr3 147013502 147063502 ZIC1/ZIC4 Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 Primary tumor tissue medulloblastoma cell CL:0000127 Enhancer activity assay ChIP-seq qRT-PCR, and ChIP-qPCR 2012 22383952 Transcriptional Regulation of N-Acetylglutamate Synthase Homo sapiens hg19 chr17 42059156 42059522 HNF1A NAGS Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepG2 cells CVCL_0027 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, TF binding assay Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR 2012 22408256 Expression of ABO blood-group genes is dependent upon an erythroid cell-specific regulatory element Homo sapiens hg19 chr9 133205353 133205796 NFYA ABO Enhancer Active Disease gastric adenocarcinoma MONDO:0005050 DOID:3717 Stomach UBERON:0000945 KATO III cells CVCL_1290 gastric adenocarcinoma cell CL:0000066 Enhancer activity assay, TF binding assay Luciferase reporter assay, EMSA 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 Heart UBERON:0000948 Primary cardiomyocytes cardiomyocyte CL:0000746 Enhancer activity assay ChIP-seq Transgenic reporter assay, EMSA 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 Bone Marrow UBERON:0002371 HSPCs hematopoietic stem and progenitor cell CL:0008001 Enhancer activity assay ChIP-seq RT-RT-qPCR 2014 25453903 EWS-FLI1 utilizes divergent chromatin remodeling mechanisms to directly activate or repress enhancer elements in Ewing sarcoma Homo sapiens hg19 chr14 92450000 92451800 EWS-FLI1 VRK1 Enhancer Active Disease Ewing sarcoma MONDO:0003368 DOID:3368 Bone UBERON:0001474 A673 Ewing sarcoma CVCL_0080 Ewing sarcoma cell CL:0000050 Functional perturbation assay ChIP-seq, RNA-seq RT-RT-qPCR 2010 20093418 Glucocorticoid receptor activates poised FKBP51 locus through long-distance interactions Homo sapiens hg19 chr6 35686811 35686856 FKBP5 Enhancer Active Disease lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 A549 CVCL_0023 lung adenocarcinoma cell CL:0001069 Enhancer activity assay, Functional perturbation assay Luciferase Reporter Assay, RT-RT-qPCR 2010 20093418 Glucocorticoid receptor activates poised FKBP51 locus through long-distance interactions Homo sapiens hg19 chr6 35686811 35686856 FKBP5 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 VCaP CVCL_2235 prostate carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay Luciferase Reporter Assay, RT-RT-qPCR 2010 20093418 Glucocorticoid receptor activates poised FKBP51 locus through long-distance interactions Homo sapiens hg19 chr6 35686811 35686856 FKBP5 Enhancer Active Normal Kidney UBERON:0002113 COS1 CVCL_0223 COS-1 cell CL:0002139 Enhancer activity assay, Functional perturbation assay Luciferase Reporter Assay, RT-RT-qPCR 2010 20093418 Glucocorticoid receptor activates poised FKBP51 locus through long-distance interactions Homo sapiens hg19 chr6 35697997 35698211 FKBP5 Enhancer Active Disease lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 A549 CVCL_0023 lung adenocarcinoma cell CL:0001069 Enhancer activity assay, Functional perturbation assay Luciferase Reporter Assay, RT-RT-qPCR 2010 20093418 Glucocorticoid receptor activates poised FKBP51 locus through long-distance interactions Homo sapiens hg19 chr6 35697997 35698211 FKBP5 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 VCaP CVCL_2235 prostate carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay Luciferase Reporter Assay, RT-RT-qPCR 2010 20093418 Glucocorticoid receptor activates poised FKBP51 locus through long-distance interactions Homo sapiens hg19 chr6 35697997 35698211 FKBP5 Enhancer Active Normal Kidney UBERON:0002113 COS1 CVCL_0223 COS-1 cell CL:0002139 Enhancer activity assay, Functional perturbation assay Luciferase Reporter Assay, RT-RT-qPCR 2010 20453196 8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC Homo sapiens hg19 chr8 128423748 128424352 P300 MYC Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF-7 CVCL_0031 breast carcinoma cell CL:0000646 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-RT-qPCR, 3C 2010 20453196 8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC Homo sapiens hg19 chr8 128482486 128483650 P300 MYC Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 LS174T CVCL_1384 colorectal carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-RT-qPCR, 3C 2009 19773398 Inversion disrupting enhancer upstream of NR0B1 causes adrenal hypoplasia Homo sapiens hg19 chrX 30317939 30318739 NR0B1 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay Luciferase Reporter Assay 2008 18202151 An enhancer upstream of TNFSF11 mediates activation by vitamin D3 Homo sapiens hg19 chr13 43111372 43112072 VDR TNFSF11 Enhancer Active Disease osteosarcoma MONDO:0005087 DOID:3347 Bone UBERON:0001474 MG-63 CVCL_0426 osteosarcoma cell CL:0000062 TF binding assay ChIP-seq EMSA, ChIP-RT-qPCR 2022 34162177 Characterization of GECPAR, a noncoding RNA that regulates the transcriptional program of diffuse large B-cell lymphoma Homo sapiens hg19 chr11 111250000 111350000 POU2AF1 SE Active Disease diffuse large B-cell lymphoma MONDO:0005042 DOID:0050746 Lymph node UBERON:0000029 GCB-DLBCL cell lines (OCI-LY1) CVCL_8804 diffuse large B-cell lymphoma cell CL:0000945 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, qRT-PCR 2022 34162177 Characterization of GECPAR, a noncoding RNA that regulates the transcriptional program of diffuse large B-cell lymphoma Homo sapiens hg19 chr11 111285000 111287000 LOC100132078 Enhancer Active Disease diffuse large B-cell lymphoma MONDO:0005042 DOID:0050746 Lymph node UBERON:0000029 GCB-DLBCL cell lines (OCI-LY1) CVCL_8804 diffuse large B-cell lymphoma cell CL:0000945 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, qRT-PCR 2019 30678091 Functional SNPs in the Human Autoimmunity-Associated Locus 17q12-21 Homo sapiens hg19 chr17 38026822 38029614 Enhancer Active Disease histiocytic lymphoma MONDO:0004854 DOID:5408 Blood UBERON:0000178 Activated U-937 cells CVCL_0007 histiocytic lymphoma cell CL:0000576 Enhancer activity assay Luciferase Reporter Assay 2020 31658410 A distal enhancer that directs Otx2 expression in the retinal pigment epithelium and neuroretina Homo sapiens hg19 chr14 57230000 57232400 OTX2 Enhancer Active Disease Retina UBERON:0000966 Enhancer activity assay, TF binding assay DNase-seq, Hi-C Transgenic Reporter Assay 2026 41629326 A common 19 bp APOE enhancer deletion is protective against Alzheimer's disease in African Americans Homo sapiens hg19 chr19 44910240 44910647 APOC1 Enhancer Active Normal Brain UBERON:0000955 HMC3 microglia cells CVCL_II76 microglial cell CL:0000129 Enhancer activity assay, TF binding assay Luciferase reporter assay, RT-RT-qPCR 2024 39272130 Chromatin conformation capture in the clinic: 4C-seq/HiC distinguishes pathogenic from neutral duplications at the GPR101 locus Homo sapiens hg19 chrX 135625877 135641072 GPR101 Enhancer Active Normal Peripheral Blood UBERON:0000178 PBMCs peripheral blood mononuclear cell CL:0000738 Chromatin interaction assay Hi-C, 4C-seq qRT-PCR, and ChIP-qPCR 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 GPR101 Enhancer Active Normal Peripheral Blood UBERON:0000178 PBMCs peripheral blood mononuclear cell CL:0000738 Chromatin interaction assay Hi-C, 4C-seq qRT-PCR, and ChIP-qPCR 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 GPR101 Enhancer Active Normal Peripheral Blood UBERON:0000178 PBMCs peripheral blood mononuclear cell CL:0000738 Chromatin interaction assay Hi-C, 4C-seq qRT-PCR, and ChIP-qPCR 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 GPR101 Enhancer Active Normal Peripheral Blood UBERON:0000178 PBMCs peripheral blood mononuclear cell CL:0000738 Chromatin interaction assay Hi-C, 4C-seq qRT-PCR, and ChIP-qPCR 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 GPR101 Enhancer Active Normal Peripheral Blood UBERON:0000178 PBMCs peripheral blood mononuclear cell CL:0000738 Chromatin interaction assay Hi-C, 4C-seq qRT-PCR, and ChIP-qPCR 2020 32732264 Cross-species analysis of enhancer logic using deep learning Homo sapiens hg19 chr6 396135 396636 IRF4 Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 Human melanoma cells melanoma cell CL:0002573 Enhancer activity assay MPRA, ATAC-seq, RNA-seq In silico saturation mutagenesis 2013 23631855 Tensile strain increases expression of CCN2 and COL2A1 by activating TGF-??-Smad2/3 pathway in chondrocytic cells Homo sapiens hg19 chr1 83941100 83941260 SMAD2 CCN2 Enhancer Active Disease chondrosarcoma MONDO:0005172 DOID:3369 Cartilage UBERON:0002418 Human chondrosarcoma cell chondrosarcoma cell CL:0000138 Enhancer activity assay Luciferase Reporter Assay, ChIP-RT-qPCR, qRT-PCR, Western blot 2013 23631855 Tensile strain increases expression of CCN2 and COL2A1 by activating TGF-??-Smad2/3 pathway in chondrocytic cells Homo sapiens hg19 chr12 48355000 48355154 SMAD2 COL2A1 Enhancer Active Disease chondrosarcoma MONDO:0005172 DOID:3369 Cartilage UBERON:0002418 Human chondrosarcoma cell chondrosarcoma cell CL:0000138 Enhancer activity assay Luciferase Reporter Assay, ChIP-RT-qPCR, qRT-PCR, Western blot 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 LUCIFERASE Enhancer Active Normal Blood UBERON:0000178 SKW CVCL_1698 B cell CL:0000945 Enhancer activity assay Luciferase Reporter Assay 2023 37591883 High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription Homo sapiens hg19 chr11 5280741 5280786 HBB Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K-562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer transcriptional regulation assay, Activity validation HiS-NET-seq, ChIP-Rx, HiChIP qRT-PCR, and ChIP-qPCR 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 94331300 94333600 COL1A2 Enhancer Active Normal Skin UBERON:0000014 Primary human dermal fibroblasts dermal fibroblast CL:0002620 Enhancer activity assay Luciferase Reporter Assay, RT-RT-qPCR 2015 25505291 TGF-b1, 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 ID3 Enhancer Active Normal Blood UBERON:0000178 Primary macrophages macrophage CL:0000235 Enhancer activity assay Luciferase Reporter Assay, RT-RT-qPCR 2015 25505291 TGF-b1, 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 ID3 Enhancer Active Normal Blood UBERON:0000178 Primary macrophages macrophage CL:0000235 Enhancer activity assay Luciferase Reporter Assay, RT-RT-qPCR 2015 25704602 Functional variants near FGFR2 Homo sapiens hg19 chr10 123099588 123100426 FGFR2 Enhancer Active Normal Bone UBERON:0001474 MC3T3-E1 CVCL_5446 osteoblast CL:0000062 Enhancer activity assay Luciferase Reporter Assay 2015 26626481 NSD3-short is an adaptor protein that couples BRD4 to the CHD8 chromatin remodeler Homo sapiens hg19 chr8 128747680 128753680 MYC Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 NOMO-1 CVCL_1609 acute myeloid leukemia cell CL:0001054 TF binding, functional perturbation ChIP-RT-qPCR, RT-RT-qPCR 2015 26427657 ROBO1 deletion as a novel germline alteration in breast and colorectal cancer patients Homo sapiens hg19 chr3 78905346 78955823 ROBO1 Enhancer Silenced Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 Primary tumor breast carcinoma cell CL:0000646 Functional perturbation assay RNA-seq, Array CGH RT-RT-qPCR, Sanger Sequencing 2019 30664627 C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution Homo sapiens hg19 chr10 3929991 3930887 KLF6 Enhancer Active Disease lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 A549 human alveolar basal epithelial adenocarcinoma CVCL_0023 lung adenocarcinoma cell CL:0001069 Enhancer activity assay CAGE-seq, RNA-seq Single-molecule fluorescence in situ hybridization (smFISH) 2019 30664627 C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution Homo sapiens hg19 chr20 56293544 56293843 PMEPA1 Enhancer Active Disease lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 A549 human alveolar basal epithelial adenocarcinoma CVCL_0023 lung adenocarcinoma cell CL:0001069 Enhancer activity assay CAGE-seq, RNA-seq Single-molecule fluorescence in situ hybridization (smFISH) 2019 30664627 C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution Homo sapiens hg19 chr17 48105016 48105270 PDK2 Enhancer Active Disease lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 A549 human alveolar basal epithelial adenocarcinoma CVCL_0023 lung adenocarcinoma cell CL:0001069 Enhancer activity assay CAGE-seq, RNA-seq Single-molecule fluorescence in situ hybridization (smFISH) 2016 26751080 Up Regulation of Human Inducible Nitric Oxide Synthase by p300 Transcriptional Complex Homo sapiens hg19 chr17 26076200 26076350 NOS2 Enhancer Active Normal Liver UBERON:0002107 Primary human hepatocyte hepatocyte CL:0000182 Enhancer activity assay Luciferase reporter assay 2016 26795348 Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus Homo sapiens hg19 chr2 202122994 202122996 CASP8 Enhancer Silenced Normal Breast UBERON:0000310 MCF10A CVCL_0598 breast epithelial cell CL:0002321 Functional perturbation assay RNA-seq RT-RT-qPCR 2016 26795348 Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus Homo sapiens hg19 chr2 202123429 202123431 CASP8 Enhancer Silenced Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 T-47D CVCL_0553 breast carcinoma cell CL:0000646 Functional perturbation assay RNA-seq RT-RT-qPCR 2016 26795348 Discordant Haplotype Sequencing Identifies Functional Variants at the 2q33 Breast Cancer Risk Locus Homo sapiens hg19 chr2 202204740 202204742 CASP8 Enhancer Silenced Normal Breast UBERON:0000310 MCF10A CVCL_0598 breast epithelial cell CL:0002321 Functional perturbation assay RNA-seq RT-RT-qPCR 2016 26818267 Utility of next-generation RNA-sequencing in identifying chimeric transcription involving human endogenous retroviruses Homo sapiens hg19 chr11 5225000 5227000 GATA1 HBG1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 T-47D CVCL_0553 breast carcinoma cell CL:0000646 TF binding assay ChIP-seq EMSA 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr9 126753431 126803431 SMAD9 Enhancer Active Normal Blood UBERON:0000178 CD34+ cell CD34-positive hematopoietic stem cell CL:0001029 Chromatin interaction assay 4C-seq 4C-RT-qPCR 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr1 165355703 165405703 TGFBR1 Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 HD-MB03 CVCL_IT11 medulloblastoma cell CL:0000127 Chromatin interaction assay 4C-seq 4C-RT-qPCR 2014 24667089 The PEG13-DMR and brain-specific enhancers dictate imprinted expression within the 8q24 intellectual disability risk locus Homo sapiens hg19 chr8 140948000 140952000 KCNK9 Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 HD-MB03 CVCL_IT11 medulloblastoma cell CL:0000127 Chromatin interaction assay ChIA-PET 3C-RT-qPCR, Allele-specific RT-PCR, RT-RT-qPCR 2014 24667089 The PEG13-DMR and brain-specific enhancers dictate imprinted expression within the 8q24 intellectual disability risk locus Homo sapiens hg19 chr8 140748000 140750000 KCNK9 Enhancer Active Normal Brain UBERON:0000955 Primary neurons neuron CL:0000540 Chromatin interaction assay ChIA-PET 3C-RT-qPCR, Allele-specific RT-PCR, RT-RT-qPCR 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 BNC2 Enhancer Active Normal Brain UBERON:0000955 Primary neurons neuron CL:0000540 Enhancer activity assay Luciferase Reporter Assay 2014 25248036 Evidence that breast cancer risk at the 2q35 locus is mediated through IGFBP5 regulation Homo sapiens hg19 chr2 217920100 217921400 IGFBP5 Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 G361 melanoma CVCL_1224 melanoma cell CL:0002573 Enhancer activity assay Luciferase Reporter Assay 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 MIR137 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF7 human breast cancer CVCL_0031 breast carcinoma cell CL:0000646 Enhancer activity assay Luciferase Reporter Assay 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 MIR2682 Enhancer Active Disease neuroblastoma MONDO:0005070 DOID:769 Brain UBERON:0000955 SH-SY5Y human neuroblastoma CVCL_0019 neuroblastoma cell CL:0000031 Enhancer activity assay Luciferase Reporter Assay 2014 25453756 A role for non-coding variation in schizophrenia Homo sapiens hg19 chr12 2350700 2350812 CACNA1C Enhancer Active Disease neuroblastoma MONDO:0005070 DOID:769 Brain UBERON:0000955 SH-SY5Y human neuroblastoma CVCL_0019 neuroblastoma cell CL:0000031 Enhancer activity assay Luciferase Reporter Assay 2014 24498324 Epigenetic Control of SPI1 Gene by CTCF and ISWI ATPase SMARCA5 Homo sapiens hg19 chr11 47159000 47159500 CTCF SPI1 Enhancer Silenced Normal Kidney UBERON:0002113 HEK293 human embryonic kidney CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2009 19285986 Control elements in the neighboring ATPase gene influence spatiotemporal expression of the human Agouti-related protein Homo sapiens hg19 chr16 53808696 53808927 AGRP Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Hematopoietic UBERON:0002405 OCI-M2 CVCL_1624 acute myeloid leukemia cell CL:0001054 Enhancer activity assay Luciferase Reporter Assay 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 16456598 16456698 UCN2 Enhancer Active Normal Adrenal gland UBERON:0002369 NCI-H295R CVCL_0458 adrenocortical cell CL:0000135 Enhancer activity assay Luciferase Reporter Assay 2008 18695675 Functional Long-range Interactions of the IgH 3' Enhancers with the bcl-2 Promoter Region in t(14;18) Lymphoma Cells Homo sapiens hg19 chr14 105860000 105860500 POU2F2 BCL2 Enhancer Active Normal Heart UBERON:0000948 H9c2 cardiomyoblast CVCL_0286 cardiomyoblast CL:0000746 Chromatin interaction assay 3C-seq RT-RT-qPCR, ChIP-RT-qPCR 2025 39934429 An unusual transfusion-dependent hemoglobin H disease caused by a novel complex inverted duplication involving the ??-globin regulatory elements and ??-thalassemia-SEA deletion Homo sapiens hg19 chr16 164235 164590 HBA1 Enhancer Active Disease diffuse large B-cell lymphoma MONDO:0005042 DOID:0050746 Lymph node UBERON:0000029 DHL-4 cells CVCL_1886 diffuse large B-cell lymphoma cell CL:0000945 Enhancer activity assay, Functional perturbation assay ATAC-seq Luciferase Reporter Assay 2023 37165057 Identification of a genomic DNA sequence that quantitatively modulates KLF1 transcription factor expression in differentiating human hematopoietic cells Homo sapiens hg19 chrX 130258372 130259352 KLF1 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Peripheral Blood UBERON:0000178 CD71+ erythroid cells erythroid progenitor cell CL:0000038 Enhancer activity assay Luciferase Reporter Assay, qRT-PCR 2015 26679052 Inhibition of growth, migration and invasion of human bladder cancer cells by antrocin, a sesquiterpene lactone isolated from Antrodia cinnamomea, and its molecular mechanisms Homo sapiens hg19 chr16 55500100 55502100 C-FOS MMP2 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 JK1 human erythroleukemia cells CVCL_2095 erythroleukemia cell CL:0000765 Enhancer activity assay, TF binding assay, Functional perturbation assay Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2015 26679052 Inhibition of growth, migration and invasion of human bladder cancer cells by antrocin, a sesquiterpene lactone isolated from Antrodia cinnamomea, and its molecular mechanisms Homo sapiens hg19 chr16 55500100 55502100 C-FOS MMP2 Enhancer Active Disease bladder carcinoma MONDO:0005094 DOID:4007 Bladder UBERON:0001255 5637 CVCL_0126 bladder carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2007 17283048 Beta-globin intergenic transcription and histone acetylation dependent on an enhancer Homo sapiens hg19 chr11 5224750 5226210 NFE2 HBE1 Enhancer Active Disease bladder carcinoma MONDO:0005094 DOID:4007 Bladder UBERON:0001255 T24 CVCL_0554 bladder carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-RT-qPCR, RT-RT-qPCR, RNase protection assay, RNA FISH, DNA FISH 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 Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Bone Marrow UBERON:0002371 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-RT-qPCR, RT-RT-qPCR, RNase protection assay, DNase I hypersensitivity assay, Restriction enzyme accessibility assay 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 5224750 5226210 CBP; P300 HBE1 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Bone Marrow UBERON:0002371 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay ChIP-RT-qPCR, RT-RT-qPCR, RNase protection assay 2023 36749647 Prdm6 drives ductus arteriosus closure by promoting ductus arteriosus smooth muscle cell identity and contractility Homo sapiens hg19 chr5 122453050 122453374 PRDM6 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Bone Marrow UBERON:0002371 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, RT-RT-qPCR 2023 36749647 Prdm6 drives ductus arteriosus closure by promoting ductus arteriosus smooth muscle cell identity and contractility Homo sapiens hg19 chr5 122453050 122453374 PRDM6 Enhancer Active Normal Bronchus UBERON:0002037 Human bronchial smooth muscle cells (HuBrSMCs) bronchial smooth muscle cell CL:0000192 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, RT-RT-qPCR 2024 38373841 KLF2 enhancer variant rs4808485 increases lupus risk by modulating inflammasome machinery and cellular homeostasis Homo sapiens hg19 chr19 12878361 12878609 KLF2 Enhancer Silenced Normal Blood vessel UBERON:0001981 Mouse endothelial cells (ECs) endothelial cell CL:0000115 Functional perturbation assay RNA-seq RT-RT-qPCR 2023 37041138 Enhancer hijacking at the ARHGAP36 locus is associated with connective tissue to bone transformation Homo sapiens hg19 chr2 69342699 69343679 ARHGAP36 Enhancer Active Normal Blood UBERON:0000178 T cells T cell CL:0000084 Functional perturbation assay RNA-seq RT-RT-qPCR, Western blot, Alizarin Red Staining 2018 30487368 PGSE Is a Novel Enhancer Regulating the Proteoglycan Pathway of the Mammalian Golgi Stress Response Homo sapiens hg19 chr15 81090165 81090265 GLCE Enhancer Active Normal Connective Tissue UBERON:0002384 Primary human mesenchymal stromal cells mesenchymal stromal cell CL:0000134 Enhancer activity assay qRT-PCR, and ChIP-qPCR 2018 30487368 PGSE Is a Novel Enhancer Regulating the Proteoglycan Pathway of the Mammalian Golgi Stress Response Homo sapiens hg19 chr15 81090165 81090265 GLCE Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Enhancer activity assay qRT-PCR, and ChIP-qPCR 2018 30487368 PGSE Is a Novel Enhancer Regulating the Proteoglycan Pathway of the Mammalian Golgi Stress Response Homo sapiens hg19 chr15 81090165 81090265 GLCE Enhancer Active Normal Embryo UBERON:0000922 MEF mouse embryonic fibroblast CL:0000057 Enhancer activity assay qRT-PCR, and ChIP-qPCR 2018 30487368 PGSE Is a Novel Enhancer Regulating the Proteoglycan Pathway of the Mammalian Golgi Stress Response Homo sapiens hg19 chr15 81090285 81090415 GLCE Enhancer Active Normal Brain UBERON:0000955 C6 CVCL_0195 glioma cell CL:0000127 Enhancer activity assay qRT-PCR, and ChIP-qPCR 2018 30487368 PGSE Is a Novel Enhancer Regulating the Proteoglycan Pathway of the Mammalian Golgi Stress Response Homo sapiens hg19 chr15 81090285 81090415 GLCE Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Enhancer activity assay qRT-PCR, and ChIP-qPCR 2018 30487368 PGSE Is a Novel Enhancer Regulating the Proteoglycan Pathway of the Mammalian Golgi Stress Response Homo sapiens hg19 chr15 81090285 81090415 GLCE Enhancer Active Normal Embryo UBERON:0000922 MEF mouse embryonic fibroblast CL:0000057 Enhancer activity assay qRT-PCR, and ChIP-qPCR 2018 30537984 Enhancers in the Peril lincRNA locus regulate distant but not local genes Homo sapiens hg19 chr10 71592600 71593600 PERIL Enhancer Active Normal Brain UBERON:0000955 C6 CVCL_0195 glioma cell CL:0000127 Functional perturbation assay RNA-seq qRT-PCR, and ChIP-qPCR 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 ADGRG6 Enhancer Active Normal Brain UBERON:0000955 N2A cells CVCL_0470 neuroblastoma cell CL:0000031 Enhancer activity assay, Functional perturbation assay RNA-seq RT-RT-qPCR, Western blot 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 ADGRG6 Enhancer Active Disease bladder carcinoma MONDO:0005094 DOID:4007 Bladder UBERON:0001255 5637 CVCL_0126 bladder carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay RNA-seq RT-RT-qPCR, Western blot 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 ADGRG6 Enhancer Active Disease bladder carcinoma MONDO:0005094 DOID:4007 Bladder UBERON:0001255 SW780 CVCL_1729 bladder carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay RNA-seq RT-RT-qPCR, Western blot 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 ADGRG6 Enhancer Active Normal Umbilical vein UBERON:0002066 HUVEC CVCL_2959 umbilical vein endothelial cell CL:0002615 Enhancer activity assay, Functional perturbation assay RNA-seq RT-RT-qPCR, Western blot 2025 40512334 Genomic Locus Tagged by Lung Function GWAS SNV rs12477314 (2q373) Acts as a Regulatory Region for a Systemic Inflammatory Phenotype Homo sapiens hg19 chr2 239866844 239871938 PER2 Enhancer Active Disease bladder carcinoma MONDO:0005094 DOID:4007 Bladder UBERON:0001255 SVHUC-1 CVCL_6903 bladder epithelial cell CL:0000066 Functional perturbation assay RNA-seq RT-RT-qPCR 2025 40512334 Genomic Locus Tagged by Lung Function GWAS SNV rs12477314 (2q373) Acts as a Regulatory Region for a Systemic Inflammatory Phenotype Homo sapiens hg19 chr2 239884251 239900294 PER2 Enhancer Active Disease non-small cell lung carcinoma MONDO:0005233 DOID:3908 Lung UBERON:0002048 NCI-H460 CVCL_0459 non-small cell lung carcinoma cell CL:0000066 Functional perturbation assay RNA-seq RT-RT-qPCR 2019 31078271 The SNP of rs6854845 suppresses transcription via the DNA looping structure alteration of super-enhancer in colon cells Homo sapiens hg19 chr4 76192040 76237727 EREG Enhancer Active Disease non-small cell lung carcinoma MONDO:0005233 DOID:3908 Lung UBERON:0002048 NCI-H460 CVCL_0459 non-small cell lung carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay Hi-C ChIP-RT-qPCR, 3C, RT-RT-qPCR 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 Colon UBERON:0001155 Human normal colon epithelial cell colon epithelial cell CL:1000348 Enhancer activity assay, TF binding assay ChIP-RT-qPCR 2016 26673704 Differential contribution of cis regulatory elements to higher order chromatin structure and expression of the CFTR locus Homo sapiens hg19 chr7 117099117 117100317 CFTR Enhancer Active Normal Intestine UBERON:0000160 Human colorectal adenocarcinoma cell colorectal adenocarcinoma cell CL:0000066 Chromatin interaction assay FISH 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 IRF1 CDKN1B Enhancer Active Disease colorectal adenocarcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 Caco-2 CVCL_0025 colorectal adenocarcinoma cell CL:0000066 TF binding assay ChIP-RT-qPCR 2020 32318854 Evidence for craniofacial enhancer variation underlying nonsyndromic cleft lip and palate Homo sapiens hg19 chr12 23211482 23214744 SOX5 Enhancer Active Normal Blood UBERON:0000178 Lymphoblastoid cell line (LCL) B lymphoblastoid cell CL:0000945 Enhancer activity assay Transgenic Reporter Assay 2020 32318854 Evidence for craniofacial enhancer variation underlying nonsyndromic cleft lip and palate Homo sapiens hg19 chr14 61120199 61122451 SIX1 Enhancer Active Disease Pharyngeal Arch UBERON:0002539 Not available Enhancer activity assay Transgenic Reporter Assay 2003 12732147 A Global Control Region Defines a Chromosomal Regulatory Landscape Containing the HoxD Cluster Homo sapiens hg19 chr2 176760000 176800000 HOXD13 Enhancer Active Disease Dorsal Root Ganglion UBERON:0001685 Not available Enhancer activity assay, Functional perturbation assay Transgenic Reporter Assay, Southern blot 2003 12732147 A Global Control Region Defines a Chromosomal Regulatory Landscape Containing the HoxD Cluster Homo sapiens hg19 chr2 176760000 176800000 HOXD12 Enhancer Active Normal Limb UBERON:0002101 Not available Enhancer activity assay, Functional perturbation assay Transgenic Reporter Assay, Southern blot 2003 12732147 A Global Control Region Defines a Chromosomal Regulatory Landscape Containing the HoxD Cluster Homo sapiens hg19 chr2 176760000 176800000 HOXD11 Enhancer Active Normal Limb UBERON:0002101 Not available Enhancer activity assay, Functional perturbation assay Transgenic Reporter Assay, Southern blot 2003 12732147 A Global Control Region Defines a Chromosomal Regulatory Landscape Containing the HoxD Cluster Homo sapiens hg19 chr2 176760000 176800000 HOXD10 Enhancer Active Normal Limb UBERON:0002101 Not available Enhancer activity assay, Functional perturbation assay Transgenic Reporter Assay, Southern blot 2003 12732147 A Global Control Region Defines a Chromosomal Regulatory Landscape Containing the HoxD Cluster Homo sapiens hg19 chr2 176760000 176800000 EVX2 Enhancer Active Normal Limb UBERON:0002101 Not available Enhancer activity assay, Functional perturbation assay Transgenic Reporter Assay, Southern blot 2003 12732147 A Global Control Region Defines a Chromosomal Regulatory Landscape Containing the HoxD Cluster Homo sapiens hg19 chr2 176760000 176800000 LNP Enhancer Active Normal Limb UBERON:0002101 Not available Enhancer activity assay, Functional perturbation assay Transgenic Reporter Assay, Southern blot 2017 27989796 Altered SOX9 genital tubercle enhancer region in hypospadias Homo sapiens hg19 chr17 69542159 69542712 SOX9 Enhancer Active Normal Limb UBERON:0002101 Not available Enhancer activity assay Transgenic Reporter Assay 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 COL1A2 Enhancer Active Disease Genital tubercle UBERON:0005876 TM4 cells CVCL_5365 Sertoli cell CL:0000216 Enhancer activity assay, TF binding assay qRT-PCR, and ChIP-qPCR 2018 29898989 Disruption of a -35kb enhancer impairs CTCF binding and MLH1 expression in colorectal cells Homo sapiens hg19 chr3 36999364 37001216 MLH1 Enhancer Active Normal Lung UBERON:0002048 Human lung fibroblasts lung fibroblast CL:0000057 Functional perturbation assay, Chromatin interaction assay ChIA-PET, RNA-seq qRT-PCR, and ChIP-qPCR 2018 29898989 Disruption of a -35kb enhancer impairs CTCF binding and MLH1 expression in colorectal cells Homo sapiens hg19 chr3 36999364 37001216 MLH1 Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 SW620 CVCL_0547 colorectal carcinoma cell CL:0000066 Functional perturbation assay, Chromatin interaction assay ChIA-PET, RNA-seq qRT-PCR, and ChIP-qPCR 2018 29300379 The role of SMAD3 in the genetic predisposition to papillary thyroid carcinoma Homo sapiens hg19 chr15 67446922 67447122 SMAD3 Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 RKO CVCL_0504 colorectal carcinoma cell CL:0000066 Enhancer activity assay qRT-PCR, and ChIP-qPCR 2018 29300379 The role of SMAD3 in the genetic predisposition to papillary thyroid carcinoma Homo sapiens hg19 chr15 67446922 67447122 SMAD3 Enhancer Active Disease thyroid carcinoma MONDO:0005075 DOID:3948 Thyroid UBERON:0002046 TPC-1 CVCL_6298 thyroid carcinoma cell CL:0000066 Enhancer activity assay qRT-PCR, and ChIP-qPCR 2018 29300379 The role of SMAD3 in the genetic predisposition to papillary thyroid carcinoma Homo sapiens hg19 chr15 67464177 67464377 SMAD3 Enhancer Active Disease thyroid carcinoma MONDO:0005075 DOID:3948 Thyroid UBERON:0002046 BCPAP CVCL_0153 thyroid carcinoma cell CL:0000066 Enhancer activity assay qRT-PCR, and ChIP-qPCR 2018 29300379 The role of SMAD3 in the genetic predisposition to papillary thyroid carcinoma Homo sapiens hg19 chr15 67464177 67464377 SMAD3 Enhancer Active Disease thyroid carcinoma MONDO:0005075 DOID:3948 Thyroid UBERON:0002046 TPC-1 CVCL_6298 thyroid carcinoma cell CL:0000066 Enhancer activity assay qRT-PCR, and ChIP-qPCR 2019 31205537 LMO1 Super-Enhancer rs2168101 G>T Polymorphism Reduces Wilms Tumor Risk Homo sapiens hg19 chr11 8254932 8255884 LMO1 Enhancer Active Disease thyroid carcinoma MONDO:0005075 DOID:3948 Thyroid UBERON:0002046 BCPAP CVCL_0153 thyroid carcinoma cell CL:0000066 Enhancer expression quantitative trait locus assay RNA-seq TaqMan Genotyping Assay, RT-RT-qPCR 2020 32817515 The Atoh7 remote enhancer provides transcriptional robustness during retinal ganglion cell development Homo sapiens hg19 chr10 94770000 94776500 ATOH7 Enhancer Active Normal Blood UBERON:0000178 Peripheral Blood Leukocytes leukocyte CL:0000738 Enhancer activity assay Transgenic Reporter Assay 2020 32817515 The Atoh7 remote enhancer provides transcriptional robustness during retinal ganglion cell development Homo sapiens hg19 chr10 94770000 94776500 ATOH7 Enhancer Active Normal Retina UBERON:0000966 Retinal Progenitor Cells retinal progenitor cell CL:0002672 Enhancer activity assay Transgenic Reporter Assay 2020 32318854 Evidence for craniofacial enhancer variation underlying nonsyndromic cleft lip and palate Homo sapiens hg19 chr4 124383428 124386454 SPRY1 Enhancer Active Normal Retina UBERON:0000966 Retinal Ganglion Cells retinal ganglion cell CL:0000740 Enhancer activity assay Transgenic Reporter Assay 2020 32318854 Evidence for craniofacial enhancer variation underlying nonsyndromic cleft lip and palate Homo sapiens hg19 chr6 45847301 45850554 RUNX2 Enhancer Active Disease Craniofacial Tissue UBERON:0010368 Enhancer activity assay Transgenic Reporter Assay 2020 32318854 Evidence for craniofacial enhancer variation underlying nonsyndromic cleft lip and palate Homo sapiens hg19 chr7 18874272 18875369 TWIST1 Enhancer Active Disease Nose UBERON:0004339 Enhancer activity assay Transgenic Reporter Assay 2020 32318854 Evidence for craniofacial enhancer variation underlying nonsyndromic cleft lip and palate Homo sapiens hg19 chr7 93975962 93978880 COL1A2 Enhancer Active Disease Pharyngeal Arch UBERON:0002539 Enhancer activity assay Transgenic Reporter Assay 2016 26673704 Differential contribution of cis regulatory elements to higher order chromatin structure and expression of the CFTR locus Homo sapiens hg19 chr7 117085017 117086217 CFTR Enhancer Active Disease Pharyngeal Arch UBERON:0002539 Enhancer activity assay, TF binding assay DNase-seq RT-RT-qPCR 2018 30250174 Identification of a limb enhancer that is removed by pathogenic deletions downstream of the SHOX gene Homo sapiens hg19 chrX 827128 827691 SHOX Enhancer Active Disease lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 Human lung adenocarcinoma cell lung adenocarcinoma cell CL:0001069 Enhancer activity assay qRT-PCR, and ChIP-qPCR 2016 26443750 Comparison of DNA Methylation and Expression Pattern of S100 and Other Epidermal Differentiation Complex Genes in Differentiating Keratinocytes Homo sapiens hg19 chr1 152416586 152416964 EDC Enhancer Silenced Normal Embryonic limb bud UBERON:0005417 Mouse embryo whole mount mouse embryo CL:0000000 Enhancer activity assay qRT-PCR, and ChIP-qPCR 2002 12399963 Disruption of the RanBP17/Hox11L2 region by recombination with the TCRbeta locus in acute lymphoblastic leukemias with t(5;14)(q34;q11) Homo sapiens hg19 chr14 22420000 22422000 TRD Enhancer Active Normal Skin UBERON:0000014 Primary human epidermal keratinocytes (HEKa) keratinocyte CL:0000312 Enhancer activity assay, Chromatin interaction assay Southern Blot, PCR, Sequencing, FISH 2002 12399963 Disruption of the RanBP17/Hox11L2 region by recombination with the TCRbeta locus in acute lymphoblastic leukemias with t(5;14)(q34;q11) Homo sapiens hg19 chr14 22420000 22422000 RANBP17 Enhancer Active Normal Thymus UBERON:0002370 T Lymphocyte Progenitors T lymphocyte progenitor CL:0000827 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Southern Blot, PCR, Sequencing, Northern Blot, FISH 2002 12399963 Disruption of the RanBP17/Hox11L2 region by recombination with the TCRbeta locus in acute lymphoblastic leukemias with t(5;14)(q34;q11) Homo sapiens hg19 chr14 22420000 22422000 HOX11L2 Enhancer Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0080545 Blood UBERON:0000178 Leukemic B Lymphoblasts B lymphoblast CL:0000945 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Southern Blot, PCR, Sequencing, FISH 2025 39934429 An unusual transfusion-dependent hemoglobin H disease caused by a novel complex inverted duplication involving the ??-globin regulatory elements and ??-thalassemia-SEA deletion Homo sapiens hg19 chr16 155136 155210 HBA1 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Leukemic T Lymphoblasts T lymphoblast CL:0002419 Functional perturbation assay ATAC-seq qRT-PCR, and ChIP-qPCR 2025 39934429 An unusual transfusion-dependent hemoglobin H disease caused by a novel complex inverted duplication involving the ??-globin regulatory elements and ??-thalassemia-SEA deletion Homo sapiens hg19 chr16 170166 170655 HBA1 Enhancer Active Normal Blood UBERON:0000178 CD71+ erythroid cells erythroid progenitor cell CL:0000038 Functional perturbation assay ATAC-seq qRT-PCR, and ChIP-qPCR 2025 39934429 An unusual transfusion-dependent hemoglobin H disease caused by a novel complex inverted duplication involving the ??-globin regulatory elements and ??-thalassemia-SEA deletion Homo sapiens hg19 chr16 193013 193087 HBA1 Enhancer Active Normal Blood UBERON:0000178 CD71+ erythroid cells erythroid progenitor cell CL:0000038 Functional perturbation assay ATAC-seq qRT-PCR, and ChIP-qPCR 2026 41276612 Mendelian randomization facilitates identification of schizophrenia risk enhancer RNAs Homo sapiens hg19 chr14 72448647 72451627 RGS6 Enhancer Active Normal Blood UBERON:0000178 CD71+ erythroid cells erythroid progenitor cell CL:0000038 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq, eQTL mapping qRT-PCR, Western blot, Neuronal differentiation assay 2021 33850120 A compendium and comparative epigenomics analysis of cis-regulatory elements in the pig genome Homo sapiens hg19 chr2 106794728 106796527 Enhancer Active Disease neuroblastoma MONDO:0005070 DOID:769 Brain UBERON:0000955 SK-N-SH CVCL_0531 neuroblastoma cell CL:0000031 Enhancer activity assay Transgenic Reporter Assay 2022 34987166 The importance of enhancer methylation for epigenetic regulation of tumorigenesis in squamous lung cancer Homo sapiens hg19 chr10 80919330 80952655 SFTPA2 SE Silenced Normal Heart UBERON:0000948 Transgenic mouse embryo mouse embryo CL:0000000 Enhancer activity assay, Chromatin interaction assay Methylation EPIC Array, RNA-seq, ChIA-PET qRT-PCR, and ChIP-qPCR 2022 34987166 The importance of enhancer methylation for epigenetic regulation of tumorigenesis in squamous lung cancer Homo sapiens hg19 chr10 80919330 80952655 SFTPD SE Silenced Disease lung squamous cell carcinoma MONDO:0005089 DOID:3907 Lung UBERON:0002048 Primary human LUSC tumor cells lung squamous cell carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay Methylation EPIC Array, RNA-seq, ChIA-PET qRT-PCR, and ChIP-qPCR 2022 34987166 The importance of enhancer methylation for epigenetic regulation of tumorigenesis in squamous lung cancer Homo sapiens hg19 chr3 41308601 41310601 CTNNB1 Enhancer Active Disease lung squamous cell carcinoma MONDO:0005089 DOID:3907 Lung UBERON:0002048 Primary human LUSC tumor cells lung squamous cell carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay Methylation EPIC Array, RNA-seq, ChIA-PET qRT-PCR, and ChIP-qPCR 2022 34987166 The importance of enhancer methylation for epigenetic regulation of tumorigenesis in squamous lung cancer Homo sapiens hg19 chr22 46105001 46107001 WNT7B Enhancer Active Disease lung squamous cell carcinoma MONDO:0005089 DOID:3907 Lung UBERON:0002048 Primary human LUSC tumor cells lung squamous cell carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay Methylation EPIC Array, RNA-seq, ChIA-PET qRT-PCR, and ChIP-qPCR 2023 37580330 IHH enhancer variant within neighboring NHEJ1 intron causes microphthalmia anophthalmia and coloboma Homo sapiens hg19 chr2 219988763 219991870 IHH Enhancer Active Disease lung squamous cell carcinoma MONDO:0005089 DOID:3907 Lung UBERON:0002048 Primary human LUSC tumor cells lung squamous cell carcinoma cell CL:0000066 Enhancer activity assay ATAC-seq Transgenic Reporter Assay, Sanger Sequencing 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 Normal Eye UBERON:0000970 Primary embryonic RPE cells retinal pigment epithelial cell CL:0002586 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq Luciferase reporter assay, CRISPR knockout, ChIP-RT-qPCR, RT-RT-qPCR, 3C-seq 2016 26813977 A New Class of Temporarily Phenotypic Enhancers Identified by CRISPR/Cas9 Mediated Genetic Screening Homo sapiens hg19 chr6 31133843 31134467 POU5F1 Enhancer Active Normal Inner cell mass UBERON:0000087 H1 hESCs CVCL_9771 embryonic stem cell CL:0002322 Functional perturbation assay, Enhancer activity assay ChIP-seq, RNA-seq, 4C-seq CRISPR Knockout, CRISPRi, Luciferase Reporter Assay, RT-RT-qPCR 2016 26813977 A New Class of Temporarily Phenotypic Enhancers Identified by CRISPR/Cas9 Mediated Genetic Screening Homo sapiens hg19 chr6 31234516 31234664 POU5F1 Enhancer Active Normal Inner cell mass UBERON:0000087 H1 hESCs CVCL_9771 embryonic stem cell CL:0002322 Functional perturbation assay, Enhancer activity assay ChIP-seq, RNA-seq, 4C-seq CRISPR Knockout, CRISPRi, Luciferase Reporter Assay, RT-RT-qPCR 2016 26813977 A New Class of Temporarily Phenotypic Enhancers Identified by CRISPR/Cas9 Mediated Genetic Screening Homo sapiens hg19 chr6 31247578 31247900 POU5F1 Enhancer Active Normal Inner cell mass UBERON:0000087 H1 hESCs CVCL_9771 embryonic stem cell CL:0002322 Functional perturbation assay, Enhancer activity assay ChIP-seq, RNA-seq, 4C-seq CRISPR Knockout, CRISPRi, Luciferase Reporter Assay, RT-RT-qPCR 2014 24443471 Enhancer-targeted genome editing selectively blocks innate resistance to oncokinase inhibition Homo sapiens hg19 chr7 116474936 116475436 MITF MET Enhancer Active Normal Inner cell mass UBERON:0000087 H1 hESCs CVCL_9771 embryonic stem cell CL:0002322 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq, DNase-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR, Western blot 2025 39677680 Epigenetic remodeling and 3D chromatin reorganization governed by NKX2-1 drive neuroendocrine prostate cancer Homo sapiens hg19 chr14 36356112 36635984 FOXA2 NKX2-1 Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 COLO829 CVCL_1137 melanoma cell CL:0002573 Chromatin interaction assay, Functional perturbation assay Hi-C, ChIP-seq, RNA-seq CRISPR Knockout, qRT-PCR, Western blot 2026 41771871 Nucleotide-resolution mapping of regulatory elements via allelic readout of tiled base editing Homo sapiens hg19 chr16 28930687 28931032 MYB CD19 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq CRISPR Knockout, Luciferase Reporter Assay, ChIP-RT-qPCR, qRT-PCR 2024 38968937 Progestogen-driven B7-H4 contributes to onco-fetal immune tolerance Homo sapiens hg19 chr1 110200000 110258000 VTCN1 Enhancer Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0080545 Blood UBERON:0000178 NALM6 CVCL_0092 B lymphoblast CL:0000945 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout 2023 37904237 Landscape of enhancer disruption and functional screen in melanoma cells Homo sapiens hg19 chr10 89875711 89876693 PTEN Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 T47D cells CVCL_0553 breast carcinoma cell CL:0000646 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, CRISPRi Screen Luciferase Reporter Assay, CRISPRi, CRISPRa, RT-RT-qPCR, Western blot, Cell Apoptosis Assay, Colony Formation Assay 2017 29045844 Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers Homo sapiens hg19 chr8 98253530 98257713 RBPJ MYC Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 Melanoma cell line melanoma cell CL:0002573 Chromatin interaction assay ChIP-seq CRISPR Knockout, 4C-seq, RT-RT-qPCR 2017 29045844 Identification of focally amplified lineage-specific super-enhancers in human epithelial cancers Homo sapiens hg19 chr8 98310330 98314427 RBPJ MYC Enhancer Active Disease acute lymphoblastic leukemia MONDO:0004945 DOID:0080545 Blood UBERON:0000178 SP-49 CVCL_1725 B lymphoblast CL:0000945 Chromatin interaction assay ChIP-seq CRISPR Knockout, 4C-seq 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 27610000 27610500 HSF1 CLU Enhancer Active Disease mantle cell lymphoma MONDO:0005052 DOID:0050747 Blood UBERON:0000178 Rec-1 CVCL_1884 B cell CL:0000945 Enhancer perturbation assay ChIP-seq CRISPR Knockout, Luciferase Reporter Assay 2026 42030388 MYC-bound enhancer RNAs in cis regulate gene transcription and tumorigenesis Homo sapiens hg19 chr2 11623044 11623914 MYC GREB1 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 eCLIP-seq, ChIP-seq, RNA-seq, ATAC-seq, ChIA-PET, Luciferase, FISH, IF, Xenograft eCLIP-seq, ChIP-seq, RNA-seq, ATAC-seq, ChIA-PET RT-RT-qPCR, Western blot, RNA FISH, Immunofluorescence, Luciferase reporter, Flow cytometry, MTT, Mouse xenograft 2019 30649550 KDM3A regulates hippo pathway through enhancer activation in colorectal cancer Homo sapiens hg19 chr6 132265000 132266500 TEAD1 CTGF Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF-7 CVCL_0031 breast carcinoma cell CL:0000646 Functional perturbation assay, TF binding assay, Enhancer activity assay ChIP-seq, RNA-seq CRISPR knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, Co-IP 2019 30649550 KDM3A regulates hippo pathway through enhancer activation in colorectal cancer Homo sapiens hg19 chr1 85870000 85870500 TEAD1 CYR61 Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Functional perturbation assay, TF binding assay, Enhancer activity assay ChIP-seq, RNA-seq CRISPR knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, Co-IP 2019 30649550 KDM3A regulates hippo pathway through enhancer activation in colorectal cancer Homo sapiens hg19 chr1 85865000 85866500 TEAD1 CYR61 Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Functional perturbation assay, TF binding assay, Enhancer activity assay ChIP-seq, RNA-seq CRISPR knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, Co-IP 2019 30649550 KDM3A regulates hippo pathway through enhancer activation in colorectal cancer Homo sapiens hg19 chr1 85868000 85869500 TEAD1 CYR61 Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Functional perturbation assay, TF binding assay, Enhancer activity assay ChIP-seq, RNA-seq CRISPR knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, Co-IP 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 Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq Luciferase reporter assay, CRISPR knockout, ChIP-RT-qPCR 2015 26258633 Genome-wide association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth Homo sapiens hg19 chr10 92680870 92681128 TEAD ANKRD1 Enhancer Active Normal Blood UBERON:0000178 Primary erythroblasts erythroblast CL:0000765 Enhancer activity assay ChIP-seq, Hi-C Luciferase Reporter Assay, 3C 2009 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 breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 CVCL_0062 breast carcinoma cell CL:0000646 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq Luciferase Reporter Assay, 3C, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2009 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:0005132 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq Luciferase Reporter Assay, 3C, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2023 34185427 m6 A modification of lncRNA PCAT6 promotes bone metastasis in prostate cancer through IGF2BP2-mediated IGF1R mRNA stabilization Homo sapiens hg19 chr12 122510495 122510896 SETD1B Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay RNA-seq, ChIP-seq, 3C-seq CRISPR Knockout, ChIP-RT-qPCR, qRT-PCR, Western blot 2023 34185427 m6 A modification of lncRNA PCAT6 promotes bone metastasis in prostate cancer through IGF2BP2-mediated IGF1R mRNA stabilization Homo sapiens hg19 chr12 122510495 122510896 MLXIP Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 P-90 PDX primary patient-derived xenograft cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay RNA-seq, ChIP-seq, 3C-seq CRISPR Knockout, ChIP-RT-qPCR, qRT-PCR, Western blot 2020 33219226 Enhancer remodeling promotes tumor-initiating activity in NRF2-activated non-small cell lung cancers Homo sapiens hg19 chr19 15311000 15312500 NRF2; CEBPB; FOSL2 NOTCH3 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 P-90 PDX primary patient-derived xenograft cell CL:0000066 Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq, ATAC-seq CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2020 33219226 Enhancer remodeling promotes tumor-initiating activity in NRF2-activated non-small cell lung cancers Homo sapiens hg19 chr19 15311000 15312500 NRF2; CEBPB; FOSL2 NOTCH3 Enhancer Active Disease lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 A549 CVCL_0023 lung adenocarcinoma cell CL:0001069 Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq, ATAC-seq CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2020 33219226 Enhancer remodeling promotes tumor-initiating activity in NRF2-activated non-small cell lung cancers Homo sapiens hg19 chr19 15311000 15312500 NRF2; CEBPB; FOSL2 NOTCH3 Enhancer Active Disease lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 H460 CVCL_0459 lung adenocarcinoma cell CL:0001069 Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq, ATAC-seq CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2019 31826955 FOXA1 upregulation promotes enhancer and transcriptional reprogramming in endocrine-resistant breast cancer Homo sapiens hg19 chr2 46550000 46555000 FOXA1 EPAS1 Enhancer Active Disease lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 H2023 CVCL_1512 lung adenocarcinoma cell CL:0001069 Functional perturbation assay ChIP-seq, RNA-seq CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 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:0006120 DOID:1612 Breast UBERON:0000310 MCF7L-TamR breast carcinoma cell CL:0000646 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2022 34980595 GFI1 Cooperates with IKZF1/IKAROS to Activate Gene Expression in T-cell Acute Lymphoblastic Leukemia Homo sapiens hg19 chr9 136398000 136402000 RUNX1 GFI1B Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF7L-TamR breast carcinoma cell CL:0000646 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR 2016 26829750 An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma Homo sapiens hg19 chr6 135525000 135525800 MYB MYB Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Bone marrow UBERON:0002371 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, Chromatin interaction assay RNA-seq, ChIP-seq Luciferase Reporter Assay, 3C, FISH, RT-RT-qPCR 2016 26829750 An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma Homo sapiens hg19 chr6 135530000 135530800 MYB MYB Enhancer Active Disease salivary gland adenoid cystic carcinoma MONDO:0015066 DOID:0080172 Salivary gland UBERON:0001044 ACC patient-derived xenograft cell lines (ACCX2, ACCX9, ACCX12, ACCX19, ACCX22) adenoid cystic carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay RNA-seq, ChIP-seq Luciferase Reporter Assay, 3C, FISH, RT-RT-qPCR 2016 26829750 An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma Homo sapiens hg19 chr6 135485000 135485800 MYB MYB Enhancer Active Disease salivary gland adenoid cystic carcinoma MONDO:0015066 DOID:0080172 Salivary gland UBERON:0001044 ACC patient-derived xenograft cell lines (ACCX2, ACCX9, ACCX12, ACCX19, ACCX22) adenoid cystic carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay RNA-seq, ChIP-seq Luciferase Reporter Assay, 3C, FISH, RT-RT-qPCR 2016 26829750 An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma Homo sapiens hg19 chr6 135495000 135495800 MYB MYB Enhancer Active Disease salivary gland adenoid cystic carcinoma MONDO:0015066 DOID:0080172 Salivary gland UBERON:0001044 ACC patient-derived xenograft cell lines (ACCX2, ACCX9, ACCX12, ACCX19, ACCX22) adenoid cystic carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay RNA-seq, ChIP-seq Luciferase Reporter Assay, 3C, FISH, RT-RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr8 128540000 128620000 AR MYC Enhancer Active Disease salivary gland adenoid cystic carcinoma MONDO:0015066 DOID:0080172 Salivary gland UBERON:0001044 ACC patient-derived xenograft cell lines (ACCX2, ACCX9, ACCX12, ACCX19, ACCX22) adenoid cystic carcinoma cell CL:0000066 Chromatin interaction assay, TF binding assay 4C-seq, ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr8 128540000 128620000 AR MYC Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate gland UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Chromatin interaction assay, TF binding assay 4C-seq, ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2014 24443471 Enhancer-targeted genome editing selectively blocks innate resistance to oncokinase inhibition Homo sapiens hg19 chr7 116735000 116735500 MITF MET Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate gland UBERON:0002367 C4-2B CVCL_4784 prostate carcinoma cell CL:0000066 Functional perturbation assay ChIP-seq 3C, ChIP-RT-qPCR, CRISPR Knockout/CRISPRi, RT-RT-qPCR, Western blot 2016 26615198 Analysis of long-range interactions in primary human cells identifies cooperative CFTR regulatory elements Homo sapiens hg19 chr7 117342000 117345000 CTCF CFTR Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 COLO829 CVCL_1137 melanoma cell CL:0002573 Chromatin interaction assay Hi-C, ChIP-seq Luciferase Reporter Assay 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 Normal Nasal epithelium UBERON:0005384 HNECs nasal epithelial cell CL:1001567 Functional perturbation assay ChIP-seq CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR 2014 24561613 CCL2-dependent infiltrating macrophages promote angiogenesis in progressive liver fibrosis Homo sapiens hg19 chr17 32565534 32566496 CCL2 Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 SK-MEL28 CVCL_0526 melanoma cell CL:0002573 Functional perturbation assay, Enhancer activity assay ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR 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 Liver UBERON:0002107 Liver sinusoidal endothelial cell liver sinusoidal endothelial cell CL:1000413 Enhancer activity assay Luciferase Reporter Assay, ChIP-RT-qPCR 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 UCN2 Enhancer Active Normal Umbilical vein UBERON:0002066 HUVEC CVCL_2959 umbilical vein endothelial cell CL:0002615 Enhancer activity assay Luciferase Reporter Assay 2016 26814967 Active medulloblastoma enhancers reveal subgroup-specific cellular origins Homo sapiens hg19 chr9 101878420 101879420 TGFBR1 Enhancer Active Disease rhabdomyosarcoma MONDO:0005085 DOID:3246 Muscle UBERON:0001134 TE-671 CVCL_1758 rhabdomyosarcoma cell CL:0000050 Chromatin interaction assay, Enhancer-target gene assignment assay 4C-seq, ChIP-seq, RNA-seq RT-RT-qPCR 2015 26166704 Condensin I and II Complexes License Full Estrogen Receptor ?|??-Dependent Enhancer Activation Homo sapiens hg19 chr21 42880000 42880500 ESR1 TFF1 Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 HD-MB03 CVCL_IT11 medulloblastoma cell CL:0000127 Chromatin interaction assay ChIP-seq, RNA-seq 3C, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2014 24256810 Identification and characterization of functional risk variants for colorectal cancer mapping to chromosome 11q231 Homo sapiens hg19 chr11 111153185 111154290 FOXA2 COLCA2 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF-7 CVCL_0031 breast carcinoma cell CL:0000646 Enhancer activity assay ChIP-seq Luciferase Reporter Assay, EMSA 2014 23698277 Aberrant TAL1 activation is mediated by an interchromosomal interaction in human T-cell acute lymphoblastic leukemia Homo sapiens hg19 chr1 47729000 47731000 TAL1 TAL1 Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 SW480 CVCL_0546 colorectal carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2021 33671852 CRISPR Deletion of a SVA Retrotransposon Demonstrates Function as a cis-Regulatory Element at the TRPV1/TRPV3 Intergenic Region Homo sapiens hg19 chr17 3466973 3468374 TRPV3 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional perturbation assay, Enhancer activity assay RNA-seq CRISPR Knockout, CRISPRi, Luciferase Reporter Assay, RT-RT-qPCR 2020 32242051 H3K79me2/3 controls enhancer-promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells Homo sapiens hg19 chr4 15581130 15619993 MLL-AF4 TAPT1 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, 3C-seq (Capture-C), RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2020 32242051 H3K79me2/3 controls enhancer-promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells Homo sapiens hg19 chr4 15581130 15619993 MLL-AF4 TAPT1 Enhancer Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0080545 Bone Marrow UBERON:0002371 SEM CVCL_0095 B lymphoblast CL:0000945 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, 3C-seq (Capture-C), RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2020 32242051 H3K79me2/3 controls enhancer-promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells Homo sapiens hg19 chr4 15581130 15619993 MLL-AF4 TAPT1 Enhancer Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0080545 Bone Marrow UBERON:0002371 RS4 CVCL_1312 B lymphoblast CL:0000945 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, 3C-seq (Capture-C), RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2020 32242051 H3K79me2/3 controls enhancer-promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells Homo sapiens hg19 chr4 15581130 15619993 MLL-AF4 TAPT1 Enhancer Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0080545 Bone Marrow UBERON:0002371 11 CVCL_1312 B lymphoblast CL:0000945 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, 3C-seq (Capture-C), RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2020 33199677 Enhancer hijacking determines extrachromosomal circular MYCN amplicon architecture in neuroblastoma Homo sapiens hg19 chr2 16370000 16380000 PHOX2B; HAND2; GATA3 MYCN Enhancer Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0080545 Bone Marrow UBERON:0002371 Primary MLL-AF4 ALL patient blasts B lymphoblast CL:0000945 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, RNA-seq, ATAC-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 33199677 Enhancer hijacking determines extrachromosomal circular MYCN amplicon architecture in neuroblastoma Homo sapiens hg19 chr2 16370000 16380000 PHOX2B; HAND2; GATA3 MYCN Enhancer Active Disease neuroblastoma MONDO:0005070 DOID:769 Adrenal gland UBERON:0002369 Kelly CVCL_1375 neuroblastoma cell CL:0000031 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, RNA-seq, ATAC-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 33199677 Enhancer hijacking determines extrachromosomal circular MYCN amplicon architecture in neuroblastoma Homo sapiens hg19 chr2 29400000 29449999 PHOX2B; HAND2; GATA3 MYCN Enhancer Active Disease neuroblastoma MONDO:0005070 DOID:769 Adrenal gland UBERON:0002369 NGP CVCL_2141 neuroblastoma cell CL:0000031 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, RNA-seq, ATAC-seq, Hi-C qRT-PCR, and ChIP-qPCR 2020 33199677 Enhancer hijacking determines extrachromosomal circular MYCN amplicon architecture in neuroblastoma Homo sapiens hg19 chr2 12600000 12649999 PHOX2B; HAND2; GATA3 MYCN Enhancer Active Disease neuroblastoma MONDO:0005070 DOID:769 Adrenal gland UBERON:0002369 IMR-5/75 CVCL_1378 neuroblastoma cell CL:0000031 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, RNA-seq, ATAC-seq, Hi-C qRT-PCR, and ChIP-qPCR 2023 36749647 Prdm6 drives ductus arteriosus closure by promoting ductus arteriosus smooth muscle cell identity and contractility Homo sapiens hg19 chr5 122452000 122454500 SRF; RBPJ; TEAD1 PRDM6 Enhancer Active Disease neuroblastoma MONDO:0005070 DOID:769 Adrenal gland UBERON:0002369 CHP-212 CVCL_1125 neuroblastoma cell CL:0000031 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq, ATAC-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2016 26934861 4C-seq revealed long-range interactions of a functional enhancer at the 8q24 prostate cancer risk locus Homo sapiens hg19 chr8 128410475 128411974 MYC Enhancer Active Normal Bronchus UBERON:0002037 Human bronchial smooth muscle cells (HuBrSMCs) bronchial smooth muscle cell CL:0000192 Chromatin interaction assay, Enhancer activity assay 4C-seq Luciferase Reporter Assay 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 prostate cancer MONDO:0008315 DOID:10283 Prostate gland UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR 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 Brain UBERON:0000955 Neural progenitor neural progenitor cell CL:0002672 Enhancer activity assay, TF binding assay ChIP-seq Luciferase reporter assay 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 FOXP2 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K-562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay ChIP-seq Luciferase Reporter Assay 2014 24512546 FOXA1 promotes tumor cell proliferation through AR involving the Notch pathway in endometrial cancer Homo sapiens hg19 chr8 128747000 128748000 FOXA1; AR MYC Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay, TF binding assay ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2016 26252164 FOXD3 promotes PAX3 expression in melanoma cells Homo sapiens hg19 chr2 222846900 222847900 PAX3 Enhancer Active Disease endometrial adenocarcinoma MONDO:0005047 DOID:2870 Endometrium UBERON:0001295 AN3CA CVCL_0029 endometrial adenocarcinoma cell CL:0000069 Transcription factor binding assay Comparative genomics footprinting Electrophoretic mobility shift assay 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 Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 A375 melanoma CVCL_0132 melanoma cell CL:0002573 Enhancer activity assay Luciferase Reporter Assay, ChIP-RT-qPCR 2009 19285986 Control elements in the neighboring ATPase gene influence spatiotemporal expression of the human Agouti-related protein Homo sapiens hg19 chr16 53808493 53808714 AGRP Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 PC-3 CVCL_0035 prostate carcinoma cell CL:0000066 Enhancer activity assay Luciferase Reporter Assay 2008 18202151 An Enhancer Twenty Kilobases Upstream of the Human Receptor Activator of Nuclear Factor Kappa B Ligand Gene Mediates Dominant Activation by 1,25 Dihydroxyvitamin D3 Homo sapiens hg19 chr13 42551634 42553034 TNFSF11 Enhancer Active Normal Hypothalamus UBERON:0001898 N38 CVCL_IU25 neuronal cell CL:0000540 Enhancer activity assay Luciferase Reporter Assay 1996 8977525 Specific versus cooperative regulatory mechanisms of the cytokine genes that are clustered on the same chromosome Homo sapiens hg19 chr5 132002000 132008000 CAT Enhancer Active Disease osteosarcoma MONDO:0005087 DOID:3347 Bone UBERON:0001474 MG63 CVCL_0426 osteosarcoma cell CL:0000062 Enhancer activity assay CAT Reporter Assay, DNase I Hypersensitivity Assay, EMSA 2016 26960733 Constructing 3D interaction maps from 1D epigenomes Homo sapiens hg19 chr11 82630000 82650000 C11ORF82 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat T Cells CVCL_0065 T lymphoblast CL:0002419 Chromatin interaction assay Hi-C 3C-RT-qPCR 2015 26214525 GATA2 is required for lymphatic vessel valve development and maintenance Homo sapiens hg19 chr1 214148800 214149632 PROX1 Enhancer Active Normal Forebrain UBERON:0001890 Human neural progenitor cells (NPCs) neural progenitor cell CL:0002672 Enhancer activity assay Luciferase Reporter Assay 1995 7870592 Identification of two enhancer elements downstream of the human c-myc gene Homo sapiens hg19 chr8 128748315 128750245 MYC Enhancer Active Normal Dermis UBERON:0002067 Primary Dermal Lymphatic Endothelial Cells (hLECs) dermal lymphatic endothelial cell CL:0002546 Enhancer activity assay Luciferase Reporter Assay 2013 23108396 H2AZ-dependent crosstalk between enhancer and promoter regulates Cyclin D1 expression Homo sapiens hg19 chr11 69470000 69470500 ESR1 CCND1 Enhancer Active Disease Burkitt lymphoma MONDO:0002483 DOID:8582 Lymph node UBERON:0000029 Raji CVCL_0511 Burkitt lymphoma cell CL:0000945 Chromatin interaction assay ChIP-seq 3C assay, RT-RT-qPCR 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 breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 cells CVCL_0062 breast carcinoma cell CL:0000646 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay 3C, Luciferase Reporter Assay, ChIP-RT-qPCR, shRNA Knockdown, RT-RT-qPCR, Western blot 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:0005132 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay 3C, Luciferase Reporter Assay, ChIP-RT-qPCR, shRNA Knockdown, RT-RT-qPCR, Western blot 2021 35122059 TNF-?|??-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer Homo sapiens hg19 chr17 31255800 31256300 JUN CCL2 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq ChIP-RT-qPCR, siRNA Knockdown, qRT-PCR, Western blot, ELISA 2010 20093418 Glucocorticoid receptor activates poised FKBP51 locus through long-distance interactions Homo sapiens hg19 chr6 35566219 35566402 FKBP5 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 PANC1 CVCL_0480 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay Luciferase Reporter Assay, RT-RT-qPCR 2010 20093418 Glucocorticoid receptor activates poised FKBP51 locus through long-distance interactions Homo sapiens hg19 chr6 35566219 35566402 FKBP5 Enhancer Active Disease lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 A549 CVCL_0023 lung adenocarcinoma cell CL:0001069 Enhancer activity assay, Functional perturbation assay Luciferase Reporter Assay, RT-RT-qPCR 2010 20093418 Glucocorticoid receptor activates poised FKBP51 locus through long-distance interactions Homo sapiens hg19 chr6 35566219 35566402 FKBP5 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 VCaP CVCL_2235 prostate carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay Luciferase Reporter Assay, RT-RT-qPCR 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 30241062 30242228 NR0B1 Enhancer Active Normal Kidney UBERON:0002113 COS1 CVCL_0223 COS-1 cell CL:0002139 Enhancer activity assay, TF binding assay, Chromatin interaction assay Luciferase Reporter Assay, FISH 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 NOS2 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay Luciferase Reporter Assay 2010 20093418 Glucocorticoid receptor activates poised FKBP51 locus through long-distance interactions Homo sapiens hg19 chr6 35505138 35511492 NR3C1 FKBP5 Enhancer Active Disease lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 A549 CVCL_0023 lung adenocarcinoma cell CL:0001069 Enhancer activity assay ChIP-seq Luciferase Reporter Assay 2010 20093418 Glucocorticoid receptor activates poised FKBP51 locus through long-distance interactions Homo sapiens hg19 chr6 35616283 35622638 NR3C1 FKBP5 Enhancer Active Disease lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 A549 cell line CVCL_0023 lung adenocarcinoma cell CL:0001069 Enhancer activity assay ChIP-seq Luciferase Reporter Assay 2010 20093418 Glucocorticoid receptor activates poised FKBP51 locus through long-distance interactions Homo sapiens hg19 chr6 35636622 35642872 NR3C1 FKBP5 Enhancer Active Disease lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 A549 cell line CVCL_0023 lung adenocarcinoma cell CL:0001069 Enhancer activity assay ChIP-seq Luciferase Reporter Assay 2011 21822303 Sox2 expression in breast tumours and activation in breast cancer stem cells Homo sapiens hg19 chr3 181425707 181426096 SOX2 Enhancer Active Disease lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 A549 cell line CVCL_0023 lung adenocarcinoma cell CL:0001069 Enhancer activity assay Luciferase Reporter Assay 2011 21822303 Sox2 expression in breast tumours and activation in breast cancer stem cells Homo sapiens hg19 chr3 181425707 181426096 SOX2 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF7 CVCL_0031 breast carcinoma cell CL:0000646 Enhancer activity assay Luciferase Reporter Assay 2011 21454523 Cohesin Mediates Chromatin Interactions That Regulate Mammalian beta-globin Expression Homo sapiens hg19 chr11 5246500 5247000 RAD21 HBB Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 T47D CVCL_0553 breast carcinoma cell CL:0000646 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay 3C, ChIP-loop, ChIP-RT-qPCR, siRNA Knockdown, RT-RT-qPCR 2015 26211970 Long-Range Modulation of PAG1 Expression by 8q21 Allergy Risk Variants Homo sapiens hg19 chr8 81274400 81275960 PAG1 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 erythroleukemia cells CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay Luciferase Reporter Assay 2012 22543974 Regulatory variation in a TBX5 enhancer leads to isolated congenital heart disease Homo sapiens hg19 chr12 114463712 114464080 TBX5 Enhancer Active Normal Blood UBERON:0000178 GM12878 CVCL_7526 B lymphoblastoid cell CL:0000945 Enhancer activity assay ChIP-seq Transgenic reporter assay 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr8 128220000 128250000 MYC Enhancer Active Normal Heart UBERON:0000948 Primary cardiomyocytes cardiomyocyte CL:0000746 Chromatin interaction assay, Gene expression assay Capture 3C-seq, RNA-seq, SNP genotyping array RT-RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr8 128220000 128250000 CASC8 Enhancer Active Normal Blood UBERON:0000178 LCL-29092 lymphoblastoid cell CL:0000945 Chromatin interaction assay, Gene expression assay Capture 3C-seq, RNA-seq, SNP genotyping array RT-RT-qPCR 2016 27866707 A Functional Variant Associated with Atrial Fibrillation Regulates PITX2c Expression through TFAP2a Homo sapiens hg19 chr4 111552482 111553989 TFAP2A PITX2C Enhancer Active Normal Blood UBERON:0000178 LCL-32370 lymphoblastoid cell CL:0000945 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq Luciferase reporter assay, Tol2-mediated zebrafish transgenic reporter assay, ChIP-qPCR, EMSA, CRISPR-Cas9 genome editing, RT-qPCR, Western blot 2016 27866707 A Functional Variant Associated with Atrial Fibrillation Regulates PITX2c Expression through TFAP2a Homo sapiens hg19 chr4 111552482 111553989 TFAP2A PITX2C Enhancer Active Normal Embryo UBERON:0000922 Zebrafish embryonic cells embryonic cell CL:0000000 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq Luciferase reporter assay, Tol2-mediated zebrafish transgenic reporter assay, ChIP-qPCR, EMSA, CRISPR-Cas9 genome editing, RT-qPCR, Western blot 2016 27866707 A Functional Variant Associated with Atrial Fibrillation Regulates PITX2c Expression through TFAP2a Homo sapiens hg19 chr4 111552482 111553989 TFAP2A PITX2C Enhancer Active Disease atrial fibrillation MONDO:0004978 DOID:0060224 Heart UBERON:0000948 HL-1 CVCL_0303 atrial cardiomyocyte CL:0000746 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq Luciferase reporter assay, Tol2-mediated zebrafish transgenic reporter assay, ChIP-qPCR, EMSA, CRISPR-Cas9 genome editing, RT-qPCR, Western blot 2016 27866707 A Functional Variant Associated with Atrial Fibrillation Regulates PITX2c Expression through TFAP2a Homo sapiens hg19 chr4 111552482 111553989 TFAP2A PITX2C Enhancer Active Normal Heart UBERON:0000948 WA07 hESC-CM cardiomyocyte CL:0000746 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq Luciferase reporter assay, Tol2-mediated zebrafish transgenic reporter assay, ChIP-qPCR, EMSA, CRISPR-Cas9 genome editing, RT-qPCR, Western blot 2016 27866707 A Functional Variant Associated with Atrial Fibrillation Regulates PITX2c Expression through TFAP2a Homo sapiens hg19 chr4 111553098 111553222 TFAP2A PITX2C Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Enhancer activity assay, TF binding assay, Functional perturbation assay, eRNA assay ChIP-seq Luciferase reporter assay, ChIP-qPCR, EMSA, CRISPR-Cas9 genome editing, RT-qPCR, Western blot, Allele-specific PCR 2016 27866707 A Functional Variant Associated with Atrial Fibrillation Regulates PITX2c Expression through TFAP2a Homo sapiens hg19 chr4 111553098 111553222 TFAP2A PITX2C Enhancer Active Disease atrial fibrillation MONDO:0004978 DOID:0060224 Heart UBERON:0000948 HL-1 CVCL_0303 atrial cardiomyocyte CL:0000746 Enhancer activity assay, TF binding assay, Functional perturbation assay, eRNA assay ChIP-seq Luciferase reporter assay, ChIP-qPCR, EMSA, CRISPR-Cas9 genome editing, RT-qPCR, Western blot, Allele-specific PCR 2016 27866707 A Functional Variant Associated with Atrial Fibrillation Regulates PITX2c Expression through TFAP2a Homo sapiens hg19 chr4 111553098 111553222 TFAP2A PITX2C Enhancer Active Normal Heart UBERON:0000948 WA07 hESC-CM cardiomyocyte CL:0000746 Enhancer activity assay, TF binding assay, Functional perturbation assay, eRNA assay ChIP-seq Luciferase reporter assay, ChIP-qPCR, EMSA, CRISPR-Cas9 genome editing, RT-qPCR, Western blot, Allele-specific PCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr10 51546800 51547317 AR; FOXA1; HOXB13; CTCF AGAP7P Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Enhancer activity assay, Chromatin interaction assay, TF binding assay Capture 3C-seq, ChIP-seq, RNA-seq, SNP genotyping array Luciferase reporter assay, Site-directed mutagenesis, 3C-qPCR, RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr10 51546800 51547317 AR; FOXA1; HOXB13; CTCF ANTXRLP1 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, TF binding assay Capture 3C-seq, ChIP-seq, RNA-seq, SNP genotyping array Luciferase reporter assay, Site-directed mutagenesis, 3C-qPCR, RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr10 51546800 51547317 AR; FOXA1; HOXB13; CTCF Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 DU-145 CVCL_0105 prostate carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, TF binding assay Capture 3C-seq, ChIP-seq, RNA-seq, SNP genotyping array Luciferase reporter assay, Site-directed mutagenesis, 3C-qPCR, RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr10 51546800 51547317 AR; FOXA1; HOXB13; CTCF Enhancer Silenced Normal Prostate UBERON:0002367 BPH-1 CVCL_4288 prostate epithelial cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, TF binding assay Capture 3C-seq, ChIP-seq, RNA-seq, SNP genotyping array Luciferase reporter assay, Site-directed mutagenesis, 3C-qPCR, RT-qPCR 2022 35766871 A risk variant for Barrett's esophagus and esophageal adenocarcinoma at chr8p231 affects enhancer activity and implicates multiple gene targets Homo sapiens hg19 chr8 11446898 11447336 KLF4; KLF1; KLF3; KLF9; KLF14; KLF16; ZEB1; RUNX1; RUNX2 CTSB Enhancer Active Normal Prostate UBERON:0002367 RWPE-1 CVCL_3790 prostate epithelial cell CL:0000066 Enhancer activity assay, Functional perturbation assay RNA-seq, ChIP-seq Luciferase Reporter Assay, CRISPR Knockout, RT-qPCR 2022 35766871 A risk variant for Barrett's esophagus and esophageal adenocarcinoma at chr8p231 affects enhancer activity and implicates multiple gene targets Homo sapiens hg19 chr8 11446898 11447336 KLF4; KLF1; KLF3; KLF9; KLF14; KLF16; ZEB1; RUNX1; RUNX2 CTSB Enhancer Active Disease esophageal adenocarcinoma MONDO:0004973 DOID:0050861 Esophagus UBERON:0001043 OE19 CVCL_1302 esophageal adenocarcinoma cell CL:0000069 Enhancer activity assay, Functional perturbation assay RNA-seq, ChIP-seq Luciferase Reporter Assay, CRISPR Knockout, RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr8 128520000 128551676 AR; FOXA1; HOXB13; CTCF MYC Enhancer Active Disease esophageal adenocarcinoma MONDO:0004973 DOID:0050861 Stomach UBERON:0000945 OE33 CVCL_1470 esophageal adenocarcinoma cell CL:0000069 Chromatin interaction assay, TF binding assay, Gene expression assay Capture 3C-seq, ChIP-seq, RNA-seq, SNP genotyping array 3C-qPCR, RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr8 128520000 128551676 AR; FOXA1; HOXB13; CTCF PVT1 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Chromatin interaction assay, TF binding assay, Gene expression assay Capture 3C-seq, ChIP-seq, RNA-seq, SNP genotyping array 3C-qPCR, RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr8 128520000 128551676 AR; FOXA1; HOXB13; CTCF PCAT1 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 DU-145 CVCL_0105 prostate carcinoma cell CL:0000066 Chromatin interaction assay, TF binding assay, Gene expression assay Capture 3C-seq, ChIP-seq, RNA-seq, SNP genotyping array 3C-qPCR, RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr8 128520000 128551676 AR; FOXA1; HOXB13; CTCF Enhancer Active Normal Prostate UBERON:0002367 BPH-1 CVCL_4288 prostate epithelial cell CL:0000066 Chromatin interaction assay, TF binding assay, Gene expression assay Capture 3C-seq, ChIP-seq, RNA-seq, SNP genotyping array 3C-qPCR, RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr2 85750614 85811383 AR; FOXA1; HOXB13; CTCF CAPG Enhancer Active Normal Prostate UBERON:0002367 RWPE-1 CVCL_3790 prostate epithelial cell CL:0000066 Chromatin interaction assay, TF binding assay, Gene expression assay Capture 3C-seq, ChIP-seq, RNA-seq, SNP genotyping array 3C-qPCR, RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr2 85750614 85811383 AR; FOXA1; HOXB13; CTCF USP39 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 DU-145 CVCL_0105 prostate carcinoma cell CL:0000066 Chromatin interaction assay, TF binding assay, Gene expression assay Capture 3C-seq, ChIP-seq, RNA-seq, SNP genotyping array 3C-qPCR, RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr2 85750614 85811383 AR; FOXA1; HOXB13; CTCF Enhancer Active Normal Prostate UBERON:0002367 BPH-1 CVCL_4288 prostate epithelial cell CL:0000066 Chromatin interaction assay, TF binding assay, Gene expression assay Capture 3C-seq, ChIP-seq, RNA-seq, SNP genotyping array 3C-qPCR, RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr2 85750614 85811383 AR; FOXA1; HOXB13; CTCF Enhancer Active Normal Prostate UBERON:0002367 RWPE-1 CVCL_3790 prostate epithelial cell CL:0000066 Chromatin interaction assay, TF binding assay, Gene expression assay Capture 3C-seq, ChIP-seq, RNA-seq, SNP genotyping array 3C-qPCR, RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr2 85750614 85811383 AR; FOXA1; HOXB13; CTCF Enhancer Active Normal Blood UBERON:0000178 LCL-29092 lymphoblastoid cell CL:0000945 Chromatin interaction assay, TF binding assay, Gene expression assay Capture 3C-seq, ChIP-seq, RNA-seq, SNP genotyping array 3C-qPCR, RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr2 85750614 85811383 AR; FOXA1; HOXB13; CTCF Enhancer Active Normal Blood UBERON:0000178 LCL-32370 lymphoblastoid cell CL:0000945 Chromatin interaction assay, TF binding assay, Gene expression assay Capture 3C-seq, ChIP-seq, RNA-seq, SNP genotyping array 3C-qPCR, RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr1 204518514 204561889 AR; FOXA1; HOXB13; CTCF NFASC Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Chromatin interaction assay, TF binding assay, Gene expression assay Capture 3C-seq, ChIP-seq, RNA-seq, SNP genotyping array 3C-qPCR, RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr1 204518514 204561889 AR; FOXA1; HOXB13; CTCF PPP1R15B Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 DU-145 CVCL_0105 prostate carcinoma cell CL:0000066 Chromatin interaction assay, TF binding assay, Gene expression assay Capture 3C-seq, ChIP-seq, RNA-seq, SNP genotyping array 3C-qPCR, RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr1 204518514 204561889 AR; FOXA1; HOXB13; CTCF PIK3C2B Enhancer Active Normal Prostate UBERON:0002367 BPH-1 CVCL_4288 prostate epithelial cell CL:0000066 Chromatin interaction assay, TF binding assay, Gene expression assay Capture 3C-seq, ChIP-seq, RNA-seq, SNP genotyping array 3C-qPCR, RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr1 204518514 204561889 AR; FOXA1; HOXB13; CTCF Enhancer Active Normal Prostate UBERON:0002367 RWPE-1 CVCL_3790 prostate epithelial cell CL:0000066 Chromatin interaction assay, TF binding assay, Gene expression assay Capture 3C-seq, ChIP-seq, RNA-seq, SNP genotyping array 3C-qPCR, RT-qPCR 2020 32772967 Disruption of super-enhancer-driven tumor suppressor gene RCAN14 expression promotes the malignancy of breast carcinoma Homo sapiens hg19 chr21 36179867 36180107 RUNX3; BRD4 RCAN1.4 Enhancer Silenced Normal Breast UBERON:0000310 Human Mammary Epithelial Cells (HMEC) mammary epithelial cell CL:0002321 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-qPCR, RT-qPCR, Site-directed Mutagenesis, Western blot 2020 32772967 Disruption of super-enhancer-driven tumor suppressor gene RCAN14 expression promotes the malignancy of breast carcinoma Homo sapiens hg19 chr21 36179867 36180107 RUNX3; BRD4 RCAN1.4 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 CVCL_0062 breast carcinoma cell CL:0000646 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-qPCR, RT-qPCR, Site-directed Mutagenesis, Western blot 2020 32772967 Disruption of super-enhancer-driven tumor suppressor gene RCAN14 expression promotes the malignancy of breast carcinoma Homo sapiens hg19 chr21 36179867 36180107 RUNX3; BRD4 RCAN1.4 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 BT549 CVCL_1082 breast carcinoma cell CL:0000646 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-qPCR, RT-qPCR, Site-directed Mutagenesis, Western blot 2020 32772967 Disruption of super-enhancer-driven tumor suppressor gene RCAN14 expression promotes the malignancy of breast carcinoma Homo sapiens hg19 chr21 36179867 36180107 RUNX3; BRD4 RCAN1.4 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 SUM149 CVCL_UE57 breast carcinoma cell CL:0000646 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-qPCR, RT-qPCR, Site-directed Mutagenesis, Western blot 2020 32772967 Disruption of super-enhancer-driven tumor suppressor gene RCAN14 expression promotes the malignancy of breast carcinoma Homo sapiens hg19 chr21 36179867 36180107 RUNX3; BRD4 RCAN1.4 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 SUM159 CVCL_UE59 breast carcinoma cell CL:0000646 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-qPCR, RT-qPCR, Site-directed Mutagenesis, Western blot 2020 32772967 Disruption of super-enhancer-driven tumor suppressor gene RCAN14 expression promotes the malignancy of breast carcinoma Homo sapiens hg19 chr21 36179867 36180107 RUNX3; BRD4 RCAN1.4 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 HCC1395 CVCL_UC79 breast carcinoma cell CL:0000646 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-qPCR, RT-qPCR, Site-directed Mutagenesis, Western blot 2013 24086551 Identification of an Enhancer That Increases miR-200b~200a~429 Gene Expression in Breast Cancer Cells Homo sapiens hg19 chr1 1092486 1093650 ZEB1 MIR200B Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 cells CVCL_0062 breast carcinoma cell CL:0000646 Enhancer activity assay ChIP-seq Dual-luciferase reporter assay, ChIP-qPCR, RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr2 20850000 20880000 C2ORF43 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Chromatin interaction assay, Gene expression assay Capture 3C-seq, RNA-seq, SNP genotyping array RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr2 20850000 20880000 HS1BP3 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 DU-145 CVCL_0105 prostate carcinoma cell CL:0000066 Chromatin interaction assay, Gene expression assay Capture 3C-seq, RNA-seq, SNP genotyping array RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr2 20850000 20880000 Enhancer Active Normal Prostate UBERON:0002367 BPH-1 CVCL_4288 prostate epithelial cell CL:0000066 Chromatin interaction assay, Gene expression assay Capture 3C-seq, RNA-seq, SNP genotyping array RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr2 20850000 20880000 Enhancer Active Normal Prostate UBERON:0002367 RWPE-1 CVCL_3790 prostate epithelial cell CL:0000066 Chromatin interaction assay, Gene expression assay Capture 3C-seq, RNA-seq, SNP genotyping array RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr2 20850000 20880000 Enhancer Active Normal Blood UBERON:0000178 LCL-29092 lymphoblastoid cell CL:0000945 Chromatin interaction assay, Gene expression assay Capture 3C-seq, RNA-seq, SNP genotyping array RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr2 20850000 20880000 Enhancer Active Normal Blood UBERON:0000178 LCL-32370 lymphoblastoid cell CL:0000945 Chromatin interaction assay, Gene expression assay Capture 3C-seq, RNA-seq, SNP genotyping array RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr6 122800000 122850000 RFX6 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Chromatin interaction assay, Gene expression assay Capture 3C-seq, RNA-seq, SNP genotyping array RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr6 122800000 122850000 GPRC6A Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 DU-145 CVCL_0105 prostate carcinoma cell CL:0000066 Chromatin interaction assay, Gene expression assay Capture 3C-seq, RNA-seq, SNP genotyping array RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr6 122800000 122850000 Enhancer Active Normal Prostate UBERON:0002367 BPH-1 CVCL_4288 prostate epithelial cell CL:0000066 Chromatin interaction assay, Gene expression assay Capture 3C-seq, RNA-seq, SNP genotyping array RT-qPCR 2016 26979803 Chromatin interactions and candidate genes at ten prostate cancer risk loci Homo sapiens hg19 chr6 122800000 122850000 Enhancer Active Normal Prostate UBERON:0002367 RWPE-1 CVCL_3790 prostate epithelial cell CL:0000066 Chromatin interaction assay, Gene expression assay Capture 3C-seq, RNA-seq, SNP genotyping array RT-qPCR 2016 27848966 17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells Homo sapiens hg19 chr17 38065200 38065700 CTCF; IRF1; PAX4; TCF3 ORMDL3 Enhancer Active Disease asthma MONDO:0004607 DOID:2841 Blood UBERON:0000178 Primary CD4+ T cells CD4-positive T cell CL:0000624 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, 4C-seq, RNA-seq, DNase-seq ChIP-qPCR, Allele-specific ChIP, RT-qPCR, siRNA knockdown, Flow cytometry, Cytokine ELISA, Sanger sequencing 2016 27848966 17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells Homo sapiens hg19 chr17 38065200 38065700 CTCF; IRF1; PAX4; TCF3 GSDMB Enhancer Active Disease asthma MONDO:0004607 DOID:2841 Lymphoid tissue UBERON:0001745 CD8+ T cells CD8-positive T cell CL:0000625 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, 4C-seq, RNA-seq, DNase-seq ChIP-qPCR, Allele-specific ChIP, RT-qPCR, siRNA knockdown, Flow cytometry, Cytokine ELISA, Sanger sequencing 2016 27848966 17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells Homo sapiens hg19 chr17 38065200 38065700 CTCF; IRF1; PAX4; TCF3 Enhancer Active Disease asthma MONDO:0004607 DOID:2841 Blood UBERON:0000178 B cells B cell CL:0000945 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, 4C-seq, RNA-seq, DNase-seq ChIP-qPCR, Allele-specific ChIP, RT-qPCR, siRNA knockdown, Flow cytometry, Cytokine ELISA, Sanger sequencing 2016 27848966 17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells Homo sapiens hg19 chr17 38065200 38065700 CTCF; IRF1; PAX4; TCF3 Enhancer Active Disease asthma MONDO:0004607 DOID:2841 Blood UBERON:0000178 NK cells NK cell CL:0000623 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, 4C-seq, RNA-seq, DNase-seq ChIP-qPCR, Allele-specific ChIP, RT-qPCR, siRNA knockdown, Flow cytometry, Cytokine ELISA, Sanger sequencing 2016 27848966 17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells Homo sapiens hg19 chr17 38065200 38065700 CTCF; IRF1; PAX4; TCF3 Enhancer Active Disease asthma MONDO:0004607 DOID:2841 Blood UBERON:0000178 HUT-78 CVCL_0337 T lymphoma cell CL:0002419 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, 4C-seq, RNA-seq, DNase-seq ChIP-qPCR, Allele-specific ChIP, RT-qPCR, siRNA knockdown, Flow cytometry, Cytokine ELISA, Sanger sequencing 2016 27848966 17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells Homo sapiens hg19 chr17 38022100 38022900 ORMDL3 Enhancer Active Disease asthma MONDO:0004607 DOID:2841 Blood UBERON:0000178 Primary CD4+ T cells CD4-positive T cell CL:0000624 Chromatin interaction assay, Enhancer activity assay, Gene expression assay 4C-seq, ChIP-seq, RNA-seq, DNase-seq RT-qPCR, Flow cytometry, Cytokine ELISA 2016 27848966 17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells Homo sapiens hg19 chr17 38022100 38022900 ORMDL3 Enhancer Active Disease asthma MONDO:0004607 DOID:2841 Lymphoid tissue UBERON:0001745 HUT-78 CVCL_0337 T lymphoma cell CL:0002419 Chromatin interaction assay, Enhancer activity assay, Gene expression assay 4C-seq, ChIP-seq, RNA-seq, DNase-seq RT-qPCR, Flow cytometry, Cytokine ELISA 2013 23598529 REST negatively and ISGF3 positively regulates the human STAT1 gene in melanoma Homo sapiens hg19 chr2 191800000 191801000 IRF1 STAT1 Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 Melanoma cells melanoma cell CL:0002573 Enhancer activity assay, TF binding assay ChIP-seq Luciferase reporter assay, ChIP-qPCR, RT-qPCR, Western blot 2013 23443045 FOXA1 mediates p16INK4a activation during cellular senescence Homo sapiens hg19 chr9 22117000 22118500 FOXA1 CDKN2A Enhancer Active Normal Lung UBERON:0002048 IMR-90 cells CVCL_0034 fetal lung fibroblast CL:0000057 Enhancer activity assay, Chromatin interaction assay 3C-seq Luciferase reporter assay, ChIP-qPCR, EMSA, RT-qPCR, Western blot 2013 23659698 Finding of IFN gene enhancers and their core sequences Homo sapiens hg19 chr12 68544280 68544520 IFNG Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa cells CVCL_0030 cervical adenocarcinoma cell CL:0000069 Enhancer activity assay Luciferase reporter assay 2013 23872150 Estrogen modulates plasminogen promoter activity Homo sapiens hg19 chr6 161085524 161086263 PLG Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepG2 cells CVCL_0027 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay Luciferase reporter assay, RT-qPCR 2013 23872150 Estrogen modulates plasminogen promoter activity Homo sapiens hg19 chr6 161092630 161095030 PLG Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepG2 cells CVCL_0027 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay Luciferase reporter assay, RT-qPCR 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 NKX2-5 Enhancer Active Disease ventricular septal defect MONDO:0007222 DOID:1192 Heart UBERON:0000948 HEK293 cells CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay Luciferase reporter assay 2013 23659698 Finding of IFN gene enhancers and their core sequences Homo sapiens hg19 chr12 68546200 68546440 IFNG Enhancer Active Normal Blood UBERON:0000178 Primary T cells T cell CL:0000084 Enhancer activity assay Luciferase reporter assay 2016 27354268 Dissection of the major hematopoietic quantitative trait locus in chromosome 6q233 identifies miR-3662 as a novel player in hematopoiesis and acute myeloid leukemia Homo sapiens hg19 chr6 135418600 135418700 GATA1 MYB Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 Primary human hematopoietic progenitor cells hematopoietic progenitor cell CL:0000837 Enhancer activity assay, TF binding assay, Functional perturbation assay Targeted RNA-seq CRISPR knockout, EMSA, RT-qPCR, Luciferase reporter assay, ChIP-qPCR, Western blot, Colony formation assay 2016 27354268 Dissection of the major hematopoietic quantitative trait locus in chromosome 6q233 identifies miR-3662 as a novel 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 acute myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay, Functional perturbation assay Targeted RNA-seq CRISPR knockout, EMSA, RT-qPCR, Luciferase reporter assay, ChIP-qPCR, Western blot, Colony formation assay 2016 27354268 Dissection of the major hematopoietic quantitative trait locus in chromosome 6q233 identifies miR-3662 as a novel player in hematopoiesis and acute myeloid leukemia Homo sapiens hg19 chr6 135418600 135418700 GATA1 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 Kasumi-1 CVCL_0589 acute myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay, Functional perturbation assay Targeted RNA-seq CRISPR knockout, EMSA, RT-qPCR, Luciferase reporter assay, ChIP-qPCR, Western blot, Colony formation assay 2016 27354268 Dissection of the major hematopoietic quantitative trait locus in chromosome 6q233 identifies miR-3662 as a novel player in hematopoiesis and acute myeloid leukemia Homo sapiens hg19 chr6 135418600 135418700 GATA1 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 MV4-11 CVCL_0064 acute myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay, Functional perturbation assay Targeted RNA-seq CRISPR knockout, EMSA, RT-qPCR, Luciferase reporter assay, ChIP-qPCR, Western blot, Colony formation assay 2020 32242051 H3K79me2/3 controls enhancer-promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells Homo sapiens hg19 chr4 15450000 15579703 MLL-AF4; EZH2; WILD-TYPE MLL PROM1 Enhancer Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0080545 Bone marrow UBERON:0002371 SEM CVCL_0095 B lymphoblast CL:0000945 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, Capture-C, RNA-seq ChIP-qPCR, RT-qPCR, Western blot 2020 32242051 H3K79me2/3 controls enhancer-promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells Homo sapiens hg19 chr4 15450000 15579703 MLL-AF4; EZH2; WILD-TYPE MLL PROM1 Enhancer Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0080545 Bone marrow UBERON:0002371 RS4 CVCL_1312 B lymphoblast CL:0000945 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, Capture-C, RNA-seq ChIP-qPCR, RT-qPCR, Western blot 2020 32242051 H3K79me2/3 controls enhancer-promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells Homo sapiens hg19 chr4 15450000 15579703 MLL-AF4; EZH2; WILD-TYPE MLL PROM1 Enhancer Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0080545 Bone marrow UBERON:0002371 11 CVCL_1312 B lymphoblast CL:0000945 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, Capture-C, RNA-seq ChIP-qPCR, RT-qPCR, Western blot 2020 32242051 H3K79me2/3 controls enhancer-promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells Homo sapiens hg19 chr4 15450000 15579703 MLL-AF4; EZH2; WILD-TYPE MLL PROM1 Enhancer Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0080545 Bone marrow UBERON:0002371 Primary MLL-AF4 ALL patient blasts B lymphoblast CL:0000945 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, Capture-C, RNA-seq ChIP-qPCR, RT-qPCR, Western blot 2020 32242051 H3K79me2/3 controls enhancer-promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells Homo sapiens hg19 chr4 15450000 15579703 MLL-AF4; EZH2; WILD-TYPE MLL PROM1 Enhancer Active Disease acute monocytic leukemia MONDO:0005025 DOID:0080147 Bone marrow UBERON:0002371 THP-1 CVCL_0006 acute monocytic leukemia cell CL:0000576 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, Capture-C, RNA-seq ChIP-qPCR, RT-qPCR, Western blot 2020 32242051 H3K79me2/3 controls enhancer-promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells Homo sapiens hg19 chr4 15450000 15579703 MLL-AF4; EZH2; WILD-TYPE MLL PROM1 Enhancer Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0080545 Bone marrow UBERON:0002371 RCH-ACV CVCL_1321 B lymphoblast CL:0000945 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, Capture-C, RNA-seq ChIP-qPCR, RT-qPCR, Western blot 2020 32242051 H3K79me2/3 controls enhancer-promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells Homo sapiens hg19 chr4 15450000 15579703 MLL-AF4; EZH2; WILD-TYPE MLL PROM1 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 ML-2 CVCL_1439 acute myeloid leukemia cell CL:0001054 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, Capture-C, RNA-seq ChIP-qPCR, RT-qPCR, Western blot 2020 32242051 H3K79me2/3 controls enhancer-promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells Homo sapiens hg19 chr4 15450000 15579703 MLL-AF4; EZH2; WILD-TYPE MLL PROM1 Enhancer Active Normal Bone marrow UBERON:0002371 CD34+ hematopoietic stem/progenitor cells hematopoietic stem cell CL:0001029 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, Capture-C, RNA-seq ChIP-qPCR, RT-qPCR, Western blot 2020 33193627 Functional Characterization of a Dual Enhancer/Promoter Regulatory Element Leading Human CD69 Expression Homo sapiens hg19 chr12 9916938 9918379 CD69 Enhancer Active Normal Blood UBERON:0000178 Jurkat T cells CVCL_0065 T lymphoblast CL:0002419 Enhancer activity assay, Functional perturbation assay, TF binding assay RNA-seq, ChIP-seq Luciferase Reporter Assay, CRISPR Knockout, ChIP-qPCR, RT-qPCR 2020 33193627 Functional Characterization of a Dual Enhancer/Promoter Regulatory Element Leading Human CD69 Expression Homo sapiens hg19 chr12 9916938 9918379 CD69 Enhancer Active Normal Lymph node UBERON:0000029 C1R B cells B cell CL:0000945 Enhancer activity assay, Functional perturbation assay, TF binding assay RNA-seq, ChIP-seq Luciferase Reporter Assay, CRISPR Knockout, ChIP-qPCR, RT-qPCR 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 Skin UBERON:0000014 BJ foreskin fibroblasts CVCL_3653 fibroblast CL:0000057 Enhancer activity assay, Genetic screen ChIP-seq Luciferase Reporter Assay, CRISPR Knockout 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:0005080 DOID:3246 Skeletal muscle UBERON:0001134 RH4 CVCL_0041 rhabdomyosarcoma cell CL:0000050 Enhancer activity assay, Super-enhancer profiling ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout 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:0005080 DOID:3246 Skeletal muscle UBERON:0001134 SCMC CVCL_UC63 rhabdomyosarcoma cell CL:0000050 Enhancer activity assay, Super-enhancer profiling ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout 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:0005080 DOID:3246 Skeletal muscle UBERON:0001134 RH4 tumor cells rhabdomyosarcoma cell CL:0000050 Enhancer activity assay, Super-enhancer profiling ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout 2017 29035388 A novel HER2 gene body enhancer contributes to HER2 expression Homo sapiens hg19 chr17 37900000 37900500 TFAP2C ERBB2 Enhancer Active Disease breast adenocarcinoma MONDO:0004982 DOID:1612 Breast UBERON:0000310 SKBR3 breast cancer cell line CVCL_0033 breast adenocarcinoma cell CL:0000646 Enhancer functional assay, TF binding assay ChIP-seq Luciferase Reporter Assay, CRISPR Knockout 2019 31019297 NAD metabolic dependency in cancer is shaped by gene amplification and enhancer remodeling Homo sapiens hg19 chr7 105856018 105860658 MYC NAMPT Enhancer Active Disease lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 H460 CVCL_0459 lung adenocarcinoma cell CL:0001069 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, ChIP-qPCR, RT-qPCR 2019 31019297 NAD metabolic dependency in cancer is shaped by gene amplification and enhancer remodeling Homo sapiens hg19 chr7 105856018 105860658 MYC NAMPT Enhancer Active Disease glioblastoma MONDO:0005142 DOID:3070 Brain UBERON:0000955 U87-MG CVCL_0022 glioblastoma cell CL:0000127 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, ChIP-qPCR, RT-qPCR 2019 31019297 NAD metabolic dependency in cancer is shaped by gene amplification and enhancer remodeling Homo sapiens hg19 chr7 105856018 105860658 MYC NAMPT Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, ChIP-qPCR, RT-qPCR 2020 32817485 Global epigenomic analysis of KSHV-infected primary effusion lymphoma identifies functional MYC superenhancers and enhancer RNAs Homo sapiens hg19 chr8 129278315 129283315 MYC Enhancer Active Disease primary effusion lymphoma MONDO:0005125 DOID:0050748 Lymph node UBERON:0000029 TRExBCBL1-RTA cells CVCL_J648 B lymphoma cell CL:0000945 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay ChIP-seq, RNA-seq, 4C-seq CRISPR Knockout, CRISPRi, RT-qPCR, ChIP-qPCR 2020 32817485 Global epigenomic analysis of KSHV-infected primary effusion lymphoma identifies functional MYC superenhancers and enhancer RNAs Homo sapiens hg19 chr8 129234315 129239315 MYC Enhancer Active Disease primary effusion lymphoma MONDO:0005125 DOID:0050748 Lymph node UBERON:0000029 TRExBCBL1-RTA cells CVCL_J648 B lymphoma cell CL:0000945 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay ChIP-seq, RNA-seq, 4C-seq CRISPR Knockout, CRISPRi, RT-qPCR, ChIP-qPCR 2020 32817485 Global epigenomic analysis of KSHV-infected primary effusion lymphoma identifies functional MYC superenhancers and enhancer RNAs Homo sapiens hg19 chr8 129254315 129259315 MYC Enhancer Active Disease primary effusion lymphoma MONDO:0005125 DOID:0050748 Lymph node UBERON:0000029 TRExBCBL1-RTA cells CVCL_J648 B lymphoma cell CL:0000945 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay ChIP-seq, RNA-seq, 4C-seq CRISPR Knockout, CRISPRi, RT-qPCR, ChIP-qPCR 2020 32416589 Miswired Enhancer Logic Drives a Cancer of the Muscle Lineage Homo sapiens hg19 chr13 40800660 40848941 MYOG FOXO1 Enhancer Active Disease alveolar rhabdomyosarcoma MONDO:0005080 DOID:3246 Skeletal muscle UBERON:0001134 RH4 CVCL_0041 rhabdomyosarcoma cell CL:0000050 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay, TF binding assay ChIP-seq, 3C-seq, 4C-seq, RNA-seq CRISPR Knockout, ChIP-qPCR, RT-qPCR, Sanger Sequencing 2020 32416589 Miswired Enhancer Logic Drives a Cancer of the Muscle Lineage Homo sapiens hg19 chr13 40800660 40848941 MYOG FOXO1 Enhancer Active Disease alveolar rhabdomyosarcoma MONDO:0005080 DOID:3246 Skeletal muscle UBERON:0001134 RH30 rhabdomyosarcoma cell lines CVCL_1648 rhabdomyosarcoma cell CL:0000050 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay, TF binding assay ChIP-seq, 3C-seq, 4C-seq, RNA-seq CRISPR Knockout, ChIP-qPCR, RT-qPCR, Sanger Sequencing 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 Inner cell mass UBERON:0000087 H1 human embryonic stem cells CVCL_9771 embryonic stem cell CL:0002322 Functional perturbation assay, Genetic screen ChIP-seq CRISPR Knockout 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 Inner cell mass UBERON:0000087 H1 human embryonic stem cells CVCL_9771 embryonic stem cell CL:0002322 Functional perturbation assay, Genetic screen ChIP-seq CRISPR Knockout 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 Inner cell mass UBERON:0000087 H1 human embryonic stem cells CVCL_9771 embryonic stem cell CL:0002322 Functional perturbation assay, Genetic screen ChIP-seq CRISPR Knockout 2018 30012865 Identification of a Novel Enhancer/Chromatin Opening Element Associated with High-Level ?|??-Globin Gene Expression Homo sapiens hg19 chr11 5279732 5280272 EGR1 HBG2 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Bone marrow UBERON:0002371 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional perturbation assay, Enhancer activity assay ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2018 30012865 Identification of a Novel Enhancer/Chromatin Opening Element Associated with High-Level ?|??-Globin Gene Expression Homo sapiens hg19 chr11 5279732 5280272 EGR1 HBG2 Enhancer Active Normal Blood UBERON:0000178 primary erythroblasts erythroblast CL:0000765 Functional perturbation assay, Enhancer activity assay ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2020 31905229 Ligand dependent gene regulation by transient ER?|?? clustered enhancers Homo sapiens hg19 chr21 42660000 42661000 ESR1 TFF1 Enhancer Active Disease breast adenocarcinoma MONDO:0004982 DOID:1612 Breast UBERON:0000310 MCF-7 breast cancer cell line CVCL_0031 breast adenocarcinoma cell CL:0000646 Functional perturbation assay, Chromatin interaction assay ChIP-seq, 5C, ChIA-PET CRISPR Knockout, RT-qPCR, ImmunoFISH 2020 31905229 Ligand dependent gene regulation by transient ER?|?? clustered enhancers Homo sapiens hg19 chr21 42660000 42661000 ESR1 TFF2 Enhancer Active Disease breast adenocarcinoma MONDO:0004982 DOID:1612 Breast UBERON:0000310 MCF-7 breast cancer cell line CVCL_0031 breast adenocarcinoma cell CL:0000646 Functional perturbation assay, Chromatin interaction assay ChIP-seq, 5C, ChIA-PET CRISPR Knockout, RT-qPCR, ImmunoFISH 2020 31905229 Ligand dependent gene regulation by transient ER?|?? clustered enhancers Homo sapiens hg19 chr21 42660000 42661000 ESR1 TFF3 Enhancer Active Disease breast adenocarcinoma MONDO:0004982 DOID:1612 Breast UBERON:0000310 MCF-7 breast cancer cell line CVCL_0031 breast adenocarcinoma cell CL:0000646 Functional perturbation assay, Chromatin interaction assay ChIP-seq, 5C, ChIA-PET CRISPR Knockout, RT-qPCR, ImmunoFISH 2020 31905229 Ligand dependent gene regulation by transient ER?|?? clustered enhancers Homo sapiens hg19 chr2 10860000 10861000 ESR1 GREB1 Enhancer Active Disease breast adenocarcinoma MONDO:0004982 DOID:1612 Breast UBERON:0000310 MCF-7 breast cancer cell line CVCL_0031 breast adenocarcinoma cell CL:0000646 Functional perturbation assay ChIP-seq CRISPRi, RT-qPCR 2021 33671852 CRISPR Deletion of a SVA Retrotransposon Demonstrates Function as a cis-Regulatory Element at the TRPV1/TRPV3 Intergenic Region Homo sapiens hg19 chr17 3466973 3468374 TRPV1 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 cell line CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay, Functional perturbation assay RNA-seq Luciferase Reporter Assay, CRISPR Knockout, RT-qPCR 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 Skin UBERON:0000014 BJ foreskin fibroblasts CVCL_3653 fibroblast CL:0000057 Enhancer activity assay ChIP-seq Luciferase Reporter Assay 2018 29385519 Genomic dissection of enhancers uncovers principles of combinatorial regulation and cell type-specific wiring of enhancer-promoter contacts Homo sapiens hg19 chr5 172131000 172132000 NR3C1 DUSP1 Enhancer Active Disease osteosarcoma MONDO:0005087 DOID:3347 Bone UBERON:0001474 U2OS CVCL_0042 osteosarcoma cell CL:0000062 Enhancer activity assay, Chromatin interaction assay ChIP-seq, Hi-C qRT-PCR, and ChIP-qPCR 2018 29385519 Genomic dissection of enhancers uncovers principles of combinatorial regulation and cell type-specific wiring of enhancer-promoter contacts Homo sapiens hg19 chr5 172131000 172132000 NR3C1 DUSP1 Enhancer Active Disease lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 A549 cell lines CVCL_0023 lung adenocarcinoma cell CL:0001069 Enhancer activity assay, Chromatin interaction assay ChIP-seq, Hi-C qRT-PCR, and ChIP-qPCR 2021 33761351 An interdependent network of functional enhancers regulates transcription and EZH2 loading at the INK4a/ARF locus Homo sapiens hg19 chr9 21968000 21973000 CDKN2A Enhancer Active Normal Lung UBERON:0002048 IMR-90 fetal lung fibroblasts CVCL_0034 fetal lung fibroblast CL:0000057 Functional perturbation assay, Chromatin interaction assay 3C-seq, RNA-seq CRISPR Knockout, CRISPRi, RT-qPCR, Western blot 2021 33761351 An interdependent network of functional enhancers regulates transcription and EZH2 loading at the INK4a/ARF locus Homo sapiens hg19 chr9 21973000 21978000 CDKN2A Enhancer Active Normal Lung UBERON:0002048 IMR-90 fetal lung fibroblasts CVCL_0034 fetal lung fibroblast CL:0000057 Functional perturbation assay, Chromatin interaction assay 3C-seq, RNA-seq CRISPR Knockout, CRISPRi, RT-qPCR, Western blot 2021 33761351 An interdependent network of functional enhancers regulates transcription and EZH2 loading at the INK4a/ARF locus Homo sapiens hg19 chr9 21978000 21983000 CDKN2A Enhancer Active Normal Lung UBERON:0002048 IMR-90 fetal lung fibroblasts CVCL_0034 fetal lung fibroblast CL:0000057 Functional perturbation assay, Chromatin interaction assay 3C-seq, RNA-seq CRISPR Knockout, CRISPRi, RT-qPCR, Western blot 2021 33761351 An interdependent network of functional enhancers regulates transcription and EZH2 loading at the INK4a/ARF locus Homo sapiens hg19 chr9 21983000 21988000 CDKN2A Enhancer Active Normal Lung UBERON:0002048 IMR-90 fetal lung fibroblasts CVCL_0034 fetal lung fibroblast CL:0000057 Functional perturbation assay, Chromatin interaction assay 3C-seq, RNA-seq CRISPR Knockout, CRISPRi, RT-qPCR, Western blot 2016 26751173 Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9 Homo sapiens hg19 chr6 36633000 36637000 CDKN1A Enhancer Active Disease transformed fibroblast Skin UBERON:0000014 BJ-RASG12V transformed fibroblast cell line transformed fibroblast CL:0000057 Genetic perturbation screen CRISPR-Cas9 pooled screen sequencing Luciferase Reporter Assay 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 Skin UBERON:0000014 BJ foreskin fibroblasts CVCL_3653 fibroblast CL:0000057 Functional perturbation assay, Senescence assay ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2018 30033119 Functional Dissection of the Enhancer Repertoire in Human Embryonic Stem Cells Homo sapiens hg19 chr3 181428000 181429000 NANOG SOX2 Enhancer Active Normal Inner cell mass UBERON:0000087 H9 human embryonic stem cells CVCL_9774 embryonic stem cell CL:0002322 Enhancer activity assay ChIP-seq, ATAC-seq qRT-PCR, and ChIP-qPCR 2021 33671852 CRISPR Deletion of a SVA Retrotransposon Demonstrates Function as a cis-Regulatory Element at the TRPV1/TRPV3 Intergenic Region Homo sapiens hg19 chr17 3466258 3466820 TRPV3 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 cell line CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay RNA-seq Luciferase Reporter Assay 2021 33671852 CRISPR Deletion of a SVA Retrotransposon Demonstrates Function as a cis-Regulatory Element at the TRPV1/TRPV3 Intergenic Region Homo sapiens hg19 chr17 3466258 3466820 TRPV1 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 cell line CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay RNA-seq Luciferase Reporter Assay 2021 33671852 CRISPR Deletion of a SVA Retrotransposon Demonstrates Function as a cis-Regulatory Element at the TRPV1/TRPV3 Intergenic Region Homo sapiens hg19 chr17 3466258 3466820 TRPV1 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 cell line CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay Luciferase Reporter Assay, RT-qPCR 2020 32352029 BCL9/STAT3 regulation of transcriptional enhancer networks promote DCIS progression Homo sapiens hg19 chr17 45414208 45414987 ITGB3 Enhancer Active Disease ductal carcinoma in situ of breast MONDO:0006539 Breast UBERON:0000310 DCIS.COM CVCL_UE18 breast ductal carcinoma cell CL:0000646 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-exo, RNA-seq, RPPA ChIP-qPCR, shRNA Knockdown, RT-qPCR, Western blot, In vivo Invasion Assay 2020 32352029 BCL9/STAT3 regulation of transcriptional enhancer networks promote DCIS progression Homo sapiens hg19 chr17 45414208 45414987 ITGB3 Enhancer Active Normal Breast UBERON:0000310 SUM225 CVCL_UE58 mammary epithelial cell CL:0002321 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-exo, RNA-seq, RPPA ChIP-qPCR, shRNA Knockdown, RT-qPCR, Western blot, In vivo Invasion Assay 2020 32352029 BCL9/STAT3 regulation of transcriptional enhancer networks promote DCIS progression Homo sapiens hg19 chr17 45414208 45414987 ITGB3 Enhancer Active Normal Breast UBERON:0000310 HMEC CVCL_U869 mammary epithelial cell CL:0002321 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-exo, RNA-seq, RPPA ChIP-qPCR, shRNA Knockdown, RT-qPCR, Western blot, In vivo Invasion Assay 2020 32352029 BCL9/STAT3 regulation of transcriptional enhancer networks promote DCIS progression Homo sapiens hg19 chr17 45436112 45436891 ITGB3 Enhancer Active Disease ductal carcinoma in situ of breast MONDO:0006539 Breast UBERON:0000310 DCIS.COM CVCL_UE18 breast ductal carcinoma cell CL:0000646 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-exo, RNA-seq, RPPA ChIP-qPCR, shRNA Knockdown, RT-qPCR, Western blot, In vivo Invasion Assay 2020 32352029 BCL9/STAT3 regulation of transcriptional enhancer networks promote DCIS progression Homo sapiens hg19 chr17 45436112 45436891 ITGB3 Enhancer Active Normal Breast UBERON:0000310 SUM225 CVCL_UE58 mammary epithelial cell CL:0002321 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-exo, RNA-seq, RPPA ChIP-qPCR, shRNA Knockdown, RT-qPCR, Western blot, In vivo Invasion Assay 2020 32352029 BCL9/STAT3 regulation of transcriptional enhancer networks promote DCIS progression Homo sapiens hg19 chr17 45436112 45436891 ITGB3 Enhancer Active Normal Breast UBERON:0000310 HMEC CVCL_U869 mammary epithelial cell CL:0002321 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-exo, RNA-seq, RPPA ChIP-qPCR, shRNA Knockdown, RT-qPCR, Western blot, In vivo Invasion Assay 2015 26110280 An insulator element located at the cyclin B1 interacting protein 1 gene locus is highly conserved among mammalian species Homo sapiens hg19 chr14 62180000 62180066 CCNB1IP1 Enhancer Active Normal Kidney UBERON:0002113 COS-7 cell line CVCL_0224 fibroblast-like cell CL:0000057 Enhancer activity assay Luciferase Reporter Assay 2018 29515369 Mapping of Human FOXP2 Enhancers Reveals Complex Regulation Homo sapiens hg19 chr7 113688009 113688782 CASK Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay qRT-PCR, and ChIP-qPCR 2018 29515369 Mapping of Human FOXP2 Enhancers Reveals Complex Regulation Homo sapiens hg19 chr7 113688009 113688782 CASK Enhancer Active Normal Brain UBERON:0000955 SK-N-MC cell lines CVCL_0530 neuroepithelioma cell CL:0000031 Enhancer activity assay qRT-PCR, and ChIP-qPCR 2018 29515369 Mapping of Human FOXP2 Enhancers Reveals Complex Regulation Homo sapiens hg19 chr7 114056845 114058646 FOXP2 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 cell line CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay qRT-PCR, and ChIP-qPCR 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 Bone marrow UBERON:0002371 Primary erythroblasts erythroblast CL:0000765 Enhancer activity assay, Chromatin interaction assay ChIP-seq, ATAC-seq, Hi-C Luciferase Reporter Assay, RT-qPCR 2016 26754925 IER5 generates a novel hypo-phosphorylated active form of HSF1 and contributes to tumorigenesis Homo sapiens hg19 chr6 31777438 31777648 HSPA1A Enhancer Active Disease non-small cell lung carcinoma MONDO:0005233 DOID:3908 Lung UBERON:0002048 H1299 CVCL_0060 non-small cell lung carcinoma cell CL:0000066 Enhancer activity assay Gene Expression Microarray Luciferase Reporter Assay, RT-RT-qPCR 2020 33199729 Gene duplication, rather than epigenetic changes, drives FGF4 overexpression in KIT/PDGFRA/SDH/RAS-P WT GIST Homo sapiens hg19 chr11 70030000 70079999 FGF4 Enhancer Active Disease gastrointestinal stromal tumor MONDO:0005047 DOID:9253 Small intestine UBERON:0002108 Primary GIST tumour cells (SDH-deficient GIST) gastrointestinal stromal tumor cell CL:0000066 Chromatin interaction assay, Enhancer activity assay RNA-seq, ChIP-seq Sanger sequencing, bisulfite sequencing, RT-qPCR 2020 33199729 Gene duplication, rather than epigenetic changes, drives FGF4 overexpression in KIT/PDGFRA/SDH/RAS-P WT GIST Homo sapiens hg19 chr11 70030000 70079999 FGF4 Enhancer Active Disease gastrointestinal stromal tumor MONDO:0005047 DOID:9253 Small intestine UBERON:0002108 quadruple WT GIST gastrointestinal stromal tumor cell CL:0000066 Chromatin interaction assay, Enhancer activity assay RNA-seq, ChIP-seq Sanger sequencing, bisulfite sequencing, RT-qPCR 2020 33199729 Gene duplication, rather than epigenetic changes, drives FGF4 overexpression in KIT/PDGFRA/SDH/RAS-P WT GIST Homo sapiens hg19 chr11 70030000 70079999 FGF4 Enhancer Active Disease gastrointestinal stromal tumor MONDO:0005047 DOID:9253 Small intestine UBERON:0002108 KIT mutant GIST) gastrointestinal stromal tumor cell CL:0000066 Chromatin interaction assay, Enhancer activity assay RNA-seq, ChIP-seq Sanger sequencing, bisulfite sequencing, RT-qPCR 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 MYC Enhancer Active Disease Burkitt lymphoma MONDO:0002483 DOID:8582 Blood UBERON:0000178 Burkitt lymphoma cell line Burkitt lymphoma cell CL:0000945 Functional perturbation assay CRISPR screen RT-RT-qPCR, Western blot 2019 31231131 Ascl1-induced Wnt11 regulates neuroendocrine differentiation, cell proliferation, and E-cadherin expression in small-cell lung cancer Homo sapiens hg19 chr11 75928700 75928930 ASCL1 WNT11 Enhancer Active Disease small cell lung carcinoma MONDO:0005020 DOID:5409 Lung UBERON:0002048 H889 CVCL_1599 small cell lung carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, qRT-PCR, Western blot 2016 27693352 Enhancer variants drive gene regulatory network dysfunction in Hirschsprung disease Homo sapiens hg19 chr10 43552395 43553394 GATA2 RET Enhancer Active Disease neuroblastoma MONDO:0005070 DOID:769 Adrenal gland UBERON:0002369 Neuroblastoma cell neuroblastoma cell CL:0000031 Enhancer activity assay, TF binding assay ChIP-seq, DNase-seq Luciferase Reporter Assay, EMSA 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 11643000 11644000 ESR1 GREB1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF7 CVCL_0031 breast carcinoma cell CL:0000646 Enhancer activity assay, chromatin interaction assay ChIP-seq, ChIA-PET qRT-PCR, and ChIP-qPCR 2016 26957309 Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters Homo sapiens hg19 chr1 20173000 20175000 POU5F1 POU5F1 Enhancer Active Normal Inner cell mass UBERON:0000087 H1 human embryonic stem embryonic stem cell CL:0002322 Enhancer activity assay ChIP-seq Luciferase Reporter Assay 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:0004947 DOID:0050890 Blood UBERON:0000178 T-ALL T lymphoblast CL:0002419 Enhancer activity assay, TF binding assay ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR 2024 39143563 Comprehensive network modeling approaches unravel dynamic enhancer-promoter interactions across neural differentiation Homo sapiens hg19 chr14 21993966 21995169 ZNF219; CHD2 CHD8 Enhancer Active Normal Brain UBERON:0000955 hESC-derived NPCs neural progenitor cell CL:0002672 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq, ChIP-seq, ATAC-seq, MPRA FIMO motif analysis, TF overexpression assay, RT-RT-qPCR, Fisher's exact test, permutation test 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 IGFBP5 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 CVCL_0062 breast carcinoma cell CL:0000646 Enhancer activity assay Luciferase Reporter Assay 2018 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 chr8 130180000 130181000 ARID5B MYC Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat CVCL_0065 T lymphoblast CL:0002419 Enhancer activity assay, functional perturbation assay ChIP-seq, ChIA-PET qRT-PCR, and ChIP-qPCR 2018 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 chr8 130180000 130181000 ARID5B MYC Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 CCRF-CEM CVCL_0207 T lymphoblast CL:0002419 Enhancer activity assay, functional perturbation assay ChIP-seq, ChIA-PET qRT-PCR, and ChIP-qPCR 2018 29440643 Dissection and function of autoimmunity-associated TNFAIP3 (A20) gene enhancers in humanized mouse models Homo sapiens hg19 chr6 138215000 138215653 PU.1 TNFAIP3 Enhancer Active Normal Spleen UBERON:0002106 Splenic B cells B cell CL:0000945 Enhancer activity assay, functional perturbation assay ChIP-seq, Hi-C qRT-PCR, and ChIP-qPCR 2018 29912188 Dissection of Enhancer Function Using Multiplex CRISPR-based Enhancer Interference in Cell Lines Homo sapiens hg19 chr11 132250000 132251000 ESR1 MMP17 Enhancer Active Normal Endometrium UBERON:0001295 Ishikawa CVCL_2529 endometrial epithelial cell CL:0000066 Functional perturbation assay ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2018 29912188 Dissection of Enhancer Function Using Multiplex CRISPR-based Enhancer Interference in Cell Lines Homo sapiens hg19 chr1 16000000 16001000 ESR1 G0S2 Enhancer Active Normal Endometrium UBERON:0001295 Ishikawa CVCL_2529 endometrial epithelial cell CL:0000066 Functional perturbation assay ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2018 30008316 Targeted enhancer activation by a subunit of the Integrator complex Homo sapiens hg19 chr16 29018500 29021500 CD84 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 HL-60 CVCL_0002 acute myeloid leukemia cell CL:0001054 Functional perturbation assay ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2018 30008316 Targeted enhancer activation by a subunit of the Integrator complex Homo sapiens hg19 chr16 29018500 29021500 CD84 Enhancer Active Normal Bone marrow UBERON:0002371 Myeloid tissue myeloid cell CL:0001054 Functional perturbation assay ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2018 30008316 Targeted enhancer activation by a subunit of the Integrator complex Homo sapiens hg19 chr5 149400000 149401000 EGR1 CSF1R Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 HL-60 CVCL_0002 acute myeloid leukemia cell CL:0001054 Functional perturbation assay ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2018 30008316 Targeted enhancer activation by a subunit of the Integrator complex Homo sapiens hg19 chr5 149400000 149401000 EGR1 CSF1R Enhancer Active Normal Bone marrow UBERON:0002371 Myeloid tissue myeloid cell CL:0001054 Functional perturbation assay ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2018 29113912 Arid1a regulates response to anti-angiogenic therapy in advanced hepatocellular carcinoma Homo sapiens hg19 chr8 67740000 67741000 ANGPT2 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 Primary Human Hepatocellular Carcinoma Cells hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2018 29113912 Arid1a regulates response to anti-angiogenic therapy in advanced hepatocellular carcinoma Homo sapiens hg19 chr8 67740000 67741000 ANGPT2 Enhancer Active Normal Liver UBERON:0002107 Mouse Arid1a Knockout Hepatocytes mouse hepatocyte CL:0000182 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2018 30590035 The TFAP2C-regulated OCT4 naive enhancer is involved in human germline formation Homo sapiens hg19 chr9 11250200 11251200 TFAP2C KLF4 Enhancer Active Normal Gonadal Tissue UBERON:0000991 hESC embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay ATAC-seq, ChIP-seq qRT-PCR, and ChIP-qPCR 2018 30590035 The TFAP2C-regulated OCT4 naive enhancer is involved in human germline formation Homo sapiens hg19 chr9 11250200 11251200 TFAP2C KLF4 Enhancer Active Normal Gonadal Tissue UBERON:0000991 hPGCLC primordial germ cell-like cell CL:0000670 Enhancer activity assay, TF binding assay ATAC-seq, ChIP-seq qRT-PCR, and ChIP-qPCR 2019 30711920 H2AFY promoter deletion causes PITX1 endoactivation and Liebenberg syndrome Homo sapiens hg19 chr5 134729406 134737909 PITX1 Enhancer Active Normal Limb Bud UBERON:0005417 Human forelimb progenitor cells progenitor cell CL:0000037 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay RNA-seq CRISPR Knockout, RT-RT-qPCR, Whole-mount in situ hybridisation 2019 30711920 H2AFY promoter deletion causes PITX1 endoactivation and Liebenberg syndrome Homo sapiens hg19 chr5 134729406 134737909 PITX1 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic limb (E11.5) mouse embryo CL:0000000 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay RNA-seq CRISPR Knockout, RT-RT-qPCR, Whole-mount in situ hybridisation 2020 31087647 Fine-mapping of the 4q3122 locus identifies potential causal variants and enhancers for premenopausal breast cancer risk Homo sapiens hg19 chr4 145678450 145679450 FOS EDNRA Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF10A-Er-Src breast carcinoma cell CL:0000646 TF binding assay, Enhancer activity assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2020 31087647 Fine-mapping of the 4q3122 locus identifies potential causal variants and enhancers for premenopausal breast cancer risk Homo sapiens hg19 chr4 145678450 145679450 FOS EDNRA Enhancer Active Normal Breast UBERON:0000310 HMEC CVCL_U869 mammary epithelial cell CL:0002321 TF binding assay, Enhancer activity assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2020 31087647 Fine-mapping of the 4q3122 locus identifies potential causal variants and enhancers for premenopausal breast cancer risk Homo sapiens hg19 chr4 145678450 145679450 FOS EDNRA Enhancer Active Normal Breast UBERON:0000310 vHMEC mammary epithelial cell CL:0002321 TF binding assay, Enhancer activity assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2020 31087647 Fine-mapping of the 4q3122 locus identifies potential causal variants and enhancers for premenopausal breast cancer risk Homo sapiens hg19 chr4 145678450 145679450 FOS EDNRA Enhancer Active Normal Breast UBERON:0000310 breast myoepithelial myoepithelial cell CL:0000186 TF binding assay, Enhancer activity assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2020 31087647 Fine-mapping of the 4q3122 locus identifies potential causal variants and enhancers for premenopausal breast cancer risk Homo sapiens hg19 chr4 145682300 145683300 FOS EDNRA Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF10A-Er-Src breast carcinoma cell CL:0000646 TF binding assay, Enhancer activity assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2020 31087647 Fine-mapping of the 4q3122 locus identifies potential causal variants and enhancers for premenopausal breast cancer risk Homo sapiens hg19 chr4 145682300 145683300 FOS EDNRA Enhancer Active Normal Breast UBERON:0000310 HMEC CVCL_U869 mammary epithelial cell CL:0002321 TF binding assay, Enhancer activity assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2020 31087647 Fine-mapping of the 4q3122 locus identifies potential causal variants and enhancers for premenopausal breast cancer risk Homo sapiens hg19 chr4 145682300 145683300 FOS EDNRA Enhancer Active Normal Breast UBERON:0000310 vHMEC mammary epithelial cell CL:0002321 TF binding assay, Enhancer activity assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2020 31087647 Fine-mapping of the 4q3122 locus identifies potential causal variants and enhancers for premenopausal breast cancer risk Homo sapiens hg19 chr4 145682300 145683300 FOS EDNRA Enhancer Active Normal Breast UBERON:0000310 breast myoepithelial myoepithelial cell CL:0000186 TF binding assay, Enhancer activity assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2023 37060567 Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia Homo sapiens hg19 chr14 98602411 98675204 CTCF TLX3 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 HPB-ALL cells CVCL_1921 T lymphoblast CL:0002419 Chromatin interaction assay, Functional perturbation assay ChIP-seq, Hi-C, 4C-seq qRT-PCR, and ChIP-qPCR 2023 37060567 Elevated enhancer-oncogene contacts and higher oncogene expression levels by recurrent CTCF inactivating mutations in acute T cell leukemia Homo sapiens hg19 chr14 98602411 98675204 CTCF TLX3 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Primary Human T-ALL Cells T lymphoblast CL:0002419 Chromatin interaction assay, Functional perturbation assay ChIP-seq, Hi-C, 4C-seq qRT-PCR, and ChIP-qPCR 2021 34853798 Multiplex CRISPR/Cas9 genome editing in hematopoietic stem cells for fetal hemoglobin reinduction generates chromosomal translocations Homo sapiens hg19 chr2 60495216 60495315 BCL11A Enhancer Active Normal Bone marrow UBERON:0002371 CD34+ hematopoietic stem cells CD34-positive hematopoietic stem cell CL:0001029 Functional perturbation assay RNA-seq CRISPR Knockout, RT-RT-qPCR, HPLC, Flow cytometry 2021 34853798 Multiplex CRISPR/Cas9 genome editing in hematopoietic stem cells for fetal hemoglobin reinduction generates chromosomal translocations Homo sapiens hg19 chr11 5226889 5226999 HBG1 Enhancer Active Normal Bone marrow UBERON:0002371 CD34+ hematopoietic stem cells CD34-positive hematopoietic stem cell CL:0001029 Functional perturbation assay RNA-seq CRISPR Knockout, RT-RT-qPCR, HPLC, Flow cytometry 2020 31773361 Genetic Predisposition to Glioma Mediated by a MAPKAP1 Enhancer Variant Homo sapiens hg19 chr9 128335472 128336978 NFIC MAPKAP1 Enhancer Active Disease glioblastoma MONDO:0005142 DOID:3070 Brain UBERON:0000955 U251 Glioma Cell Line CVCL_0021 glioblastoma cell CL:0000127 Enhancer activity assay, TF binding assay RNA-seq Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, RT-RT-qPCR 2020 31773361 Genetic Predisposition to Glioma Mediated by a MAPKAP1 Enhancer Variant Homo sapiens hg19 chr9 128335472 128336978 NFIC MAPKAP1 Enhancer Active Normal Blood UBERON:0000178 Human Lymphoblastic Cell Lines lymphoblastoid cell CL:0000945 Enhancer activity assay, TF binding assay RNA-seq Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, RT-RT-qPCR 2020 31773361 Genetic Predisposition to Glioma Mediated by a MAPKAP1 Enhancer Variant Homo sapiens hg19 chr9 128335472 128336978 NFIC MAPKAP1 Enhancer Active Disease glioblastoma MONDO:0005142 DOID:3070 Brain UBERON:0000955 Primary Glioma Tissue glioblastoma cell CL:0000127 Enhancer activity assay, TF binding assay RNA-seq Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, RT-RT-qPCR 2020 32732264 Cross-species analysis of enhancer logic using deep learning Homo sapiens hg19 chr12 105795404 105795904 APPL2 Enhancer Silenced Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 Human melanoma cell melanoma cell CL:0002573 Enhancer activity assay, TF binding assay ATAC-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR, Western blot 2021 33620092 Androgen receptor enhancer amplification in matched patient-derived xenografts of primary and castrate-resistant prostate cancer Homo sapiens hg19 chrX 66110000 66116000 AR AR Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 Prostate cancer epithelial cells prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq RT-RT-qPCR, Western blot 2021 33620092 Androgen receptor enhancer amplification in matched patient-derived xenografts of primary and castrate-resistant prostate cancer Homo sapiens hg19 chrX 66110000 66116000 AR AR Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 PDX cells patient-derived xenograft cell CL:0000066 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq RT-RT-qPCR, Western blot 2015 26258633 Genome-wide association between YAP/TAZ/TEAD and AP-1 at enhancers drives oncogenic growth Homo sapiens hg19 chr17 38670000 38770000 TOP2A Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 CVCL_0062 breast carcinoma cell CL:0000646 Chromatin interaction assay Hi-C 3C 2025 40512334 Genomic Locus Tagged by Lung Function GWAS SNV rs12477314 (2q373) Acts as a Regulatory Region for a Systemic Inflammatory Phenotype Homo sapiens hg19 chr2 239866844 239871938 MULTIPLE (CXCL2 Enhancer Active Disease non-small cell lung carcinoma MONDO:0005233 DOID:3908 Lung UBERON:0002048 NCI-H460 CVCL_0459 non-small cell lung carcinoma cell CL:0000066 Functional perturbation assay RNA-seq CRISPR Knockout, RT-RT-qPCR, Sanger sequencing 2015 26422397 SATB1 Mediates Long-Range Chromatin Interactions Homo sapiens hg19 chr18 60983148 60983597 SATB1 PMAIP1 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat CVCL_0065 T lymphoblast CL:0002419 Chromatin interaction, expression validation 3C, ChIP-qPCR, RT-qPCR qRT-PCR, and ChIP-qPCR 2015 26422397 SATB1 Mediates Long-Range Chromatin Interactions Homo sapiens hg19 chr18 60790200 60790400 SATB1 BCL2 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat CVCL_0065 T lymphoblast CL:0002419 Chromatin interaction, expression validation 3C, ChIP-qPCR, RT-qPCR qRT-PCR, and ChIP-qPCR 2015 26422397 SATB1 Mediates Long-Range Chromatin Interactions Homo sapiens hg19 chr18 64156800 64157000 SATB1 PMAIP1 Enhancer Silenced Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat CVCL_0065 T lymphoblast CL:0002419 Chromatin interaction, repression validation 3C, ChIP-qPCR, RT-qPCR qRT-PCR, and ChIP-qPCR 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 NCOA3 Enhancer Silenced Disease chondrosarcoma MONDO:0005172 DOID:3369 Articular cartilage UBERON:0002418 SW1353 CVCL_0543 chondrosarcoma cell CL:0000138 Enhancer activity assay, TF binding assay, Functional perturbation assay Luciferase Reporter Assay, EMSA, RT-RT-qPCR, Western blot, siRNA-mediated gene knockdown 2014 24564208 Dynamic reorganization of the AC16 cardiomyocyte transcriptome in response to TNF?? signaling revealed by integrated genomic analyses Homo sapiens hg19 chr4 103350000 103351000 NFKB1; RELA NFKB1 Enhancer Active Normal Heart UBERON:0000948 AC16 CVCL_4U18 cardiomyocyte CL:0000746 TF binding assay ChIP-seq, GRO-seq RT-RT-qPCR, Western blot 2014 24512546 FOXA1 promotes tumor cell proliferation through AR involving the Notch pathway in endometrial cancer Homo sapiens hg19 chr8 128753000 128754000 AR MYC Enhancer Active Disease endometrial adenocarcinoma MONDO:0005047 DOID:2870 Endometrium UBERON:0001295 MFE-296 CVCL_1406 endometrial adenocarcinoma cell CL:0000069 Enhancer activity assay ChIP-seq Luciferase Reporter Assay, RT-RT-qPCR 2010 20453196 8q24 prostate, breast, and colon cancer risk loci show tissue-specific long-range interaction with MYC Homo sapiens hg19 chr8 128173203 128174158 P300 MYC Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-RT-qPCR, 3C 2025 39853740 Mechanisms of enhancer-driven oncogene activation in human cancers Homo sapiens hg38 chr8 128805000 128807000 MYC Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 COLO 320DM cells CVCL_0219 colorectal carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay Hi-C, ChIP-seq, RNA-seq Luciferase reporter assay, CRISPRi 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:0005132 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, GRO-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, qRT-PCR, Western blot, 3C Assay 2024 39107271 DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression Homo sapiens hg38 chr10 52430000 52490000 JUND; FOSL2 DKK1 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 PANC-1 CVCL_0480 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, Hi-C, ATAC-seq, RNA-seq, DNase-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, DNA pull-down assay 2024 39107271 DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression Homo sapiens hg38 chr10 52430000 52490000 JUND; FOSL2 DKK1 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 HPAC CVCL_1492 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, Hi-C, ATAC-seq, RNA-seq, DNase-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, DNA pull-down assay 2024 39107271 DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression Homo sapiens hg38 chr10 52430000 52490000 JUND; FOSL2 DKK1 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 AsPC-1 CVCL_0152 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, Hi-C, ATAC-seq, RNA-seq, DNase-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, DNA pull-down assay 2019 31775028 Global Analysis of Enhancer Targets Reveals Convergent Enhancer-Driven Regulatory Modules Homo sapiens hg38 chr6 135323137 135323537 MYB Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay scRNA-seq, RNA-seq, Hi-C, ChIP-seq, ATAC-seq CRISPRi, RT-RT-qPCR 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:0004973 DOID:0050861 Esophagus UBERON:0001043 OE19 CVCL_1302 esophageal adenocarcinoma cell CL:0000069 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ATAC-seq, RNA-seq, ChIP-seq, Hi-C Luciferase Reporter Assay, CRISPR knockout/CRISPRi, RT-RT-qPCR, Western blot 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:0004973 DOID:0050861 Esophagus UBERON:0001043 CP-A CVCL_6920 esophageal adenocarcinoma cell CL:0000069 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ATAC-seq, RNA-seq, ChIP-seq, Hi-C Luciferase Reporter Assay, CRISPR knockout/CRISPRi, RT-RT-qPCR, Western blot 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:0004973 DOID:0050861 Esophagus UBERON:0001043 OE19 CVCL_1302 esophageal adenocarcinoma cell CL:0000069 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ATAC-seq, RNA-seq, ChIP-seq, Hi-C Luciferase Reporter Assay, CRISPR knockout/CRISPRi, RT-RT-qPCR, Western blot 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:0004973 DOID:0050861 Esophagus UBERON:0001043 CP-A CVCL_6920 esophageal adenocarcinoma cell CL:0000069 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ATAC-seq, RNA-seq, ChIP-seq, Hi-C Luciferase Reporter Assay, CRISPR knockout/CRISPRi, RT-RT-qPCR, Western blot 2022 34571027 An enhancer-driven stem cell-like program mediated by SOX9 blocks intestinal differentiation in colorectal cancer Homo sapiens hg38 chr17 79804321 79805871 SOX9 SOX9 Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 HT29 CVCL_0320 colorectal carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, CRISPRi, RT-RT-qPCR 2021 34819668 ecDNA hubs drive cooperative intermolecular oncogene expression Homo sapiens hg38 chr8 128804981 128806980 MYC Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 COLO320-DM CVCL_0219 colorectal carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ATAC-seq, ChIP-seq, Hi-C CRISPRi, Luciferase Reporter Assay, FISH, RT-RT-qPCR 2020 32958950 Transcription imparts architecture, function and logic to enhancer units Homo sapiens hg38 chr8 128747000 128748000 MYC Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR 2025 40830415 Systematic decoding of functional enhancer connectomes and risk variants in human glioma Homo sapiens hg38 chr20 63680288 63681605 MEIS1 SOX18 Enhancer Active Disease glioblastoma MONDO:0005142 DOID:3070 Brain UBERON:0000955 U251 cells CVCL_0021 glioblastoma cell CL:0000127 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C Luciferase reporter assay, ChIP-RT-qPCR, CRISPR knockout, CRISPRi, RT-RT-qPCR 2025 40830415 Systematic decoding of functional enhancer connectomes and risk variants in human glioma Homo sapiens hg38 chr20 63680288 63681605 MEIS1 SOX18 Enhancer Active Disease glioblastoma MONDO:0005142 DOID:3070 Brain UBERON:0000955 LN229 cells CVCL_0393 glioblastoma cell CL:0000127 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C Luciferase reporter assay, ChIP-RT-qPCR, CRISPR knockout, CRISPRi, RT-RT-qPCR 2025 40830415 Systematic decoding of functional enhancer connectomes and risk variants in human glioma Homo sapiens hg38 chr20 63680288 63681605 MEIS1 SOX18 Enhancer Active Disease glioblastoma MONDO:0005142 DOID:3070 Brain UBERON:0000955 U87 cells CVCL_0022 glioblastoma cell CL:0000127 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C Luciferase reporter assay, ChIP-RT-qPCR, CRISPR knockout, CRISPRi, RT-RT-qPCR 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 carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 CVCL_0062 breast carcinoma cell CL:0000646 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay RNA-seq, 4C-seq, ChIP-seq, 3C-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRa, CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2025 40133308 Identification of a SNAI1 enhancer RNA that drives cancer cell plasticity Homo sapiens hg38 chr20 50027744 50030383 SMAD3 SNAI1 Enhancer Active Normal Breast UBERON:0000310 MCF10A CVCL_0598 breast epithelial cell CL:0002321 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay RNA-seq, 4C-seq, ChIP-seq, 3C-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRa, CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2025 40133308 Identification of a SNAI1 enhancer RNA that drives cancer cell plasticity Homo sapiens hg38 chr20 50027744 50030383 SMAD3 SNAI1 Enhancer Active Disease lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 A549 CVCL_0023 lung adenocarcinoma cell CL:0001069 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay RNA-seq, 4C-seq, ChIP-seq, 3C-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRa, CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 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 Lung UBERON:0002048 Human bronchial epithelial cells bronchial epithelial cell CL:0002591 Enhancer activity assay, TF binding assay, Functional perturbation assay, Chromatin interaction assay RNA-seq, ATAC-seq, ChIP-seq, Hi-C CRISPR knockout, Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR 2024 38849954 An oncogenic enhancer promotes melanoma progression via regulating ETV4 expression Homo sapiens hg38 chr17 59785798 59787315 STAT3 ETV4 Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 A375 CVCL_0132 melanoma cell CL:0002573 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C Luciferase Reporter Assay, CRISPR Knockout, qRT-PCR, Western blot 2023 37641131 SMC3 epigenetic silencing regulates Rab27a expression and drives pancreatic cancer progression Homo sapiens hg38 chr15 54022001 54022500 RAB27A Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 MIA PaCa-2 CVCL_0428 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, qRT-PCR, Western blot 2025 41129262 The hematopoietic stem cell MYB enhancer is essential for and recurrently amplified during T cell leukemogenesis Homo sapiens hg38 chr7 27200782 27261018 ETS1 MYB Enhancer Active Disease acute monocytic leukemia MONDO:0005025 DOID:0080147 Bone marrow UBERON:0002371 THP-6 CVCL_3507 acute monocytic leukemia cell CL:0000576 Enhancer activity assay, TF binding assay, Functional perturbation assay, Chromatin interaction assay ChIP-seq, ATAC-seq, Hi-C, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, ChIP-RT-qPCR, qRT-PCR, Western blot 2024 39316719 Focal deletions of a promoter tether activate the IRX3 oncogene in T-cell acute lymphoblastic leukemia Homo sapiens hg38 chr21 43745000 43747000 TFF1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF7 CVCL_0031 breast carcinoma cell CL:0000646 Enhancer activity assay, Functional perturbation assay, TF binding assay, Chromatin interaction assay ChIP-seq, GRO-seq, Hi-C, ChIA-PET, RNA-seq CRISPR Knockout, RT-RT-qPCR, 4C-seq, ChIP-RT-qPCR 2024 39316719 Focal deletions of a promoter tether activate the IRX3 oncogene in T-cell acute lymphoblastic leukemia Homo sapiens hg38 chr5 1320000 1322000 TERT Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay, Functional perturbation assay, TF binding assay, Chromatin interaction assay ChIP-seq, Hi-C, ChIA-PET, RNA-seq, WGS CRISPR Knockout, RT-RT-qPCR, 4C-seq, ChIP-RT-qPCR, Sanger Sequencing 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; AR LTF Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Functional perturbation assay, Enhancer activity assay, Chromatin interaction assay, TF binding assay ATAC-seq, RNA-seq, ChIP-seq, 3C-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, FISH 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; AR LTF Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 22Rv1 CVCL_1045 prostate carcinoma cell CL:0000066 Functional perturbation assay, Enhancer activity assay, Chromatin interaction assay, TF binding assay ATAC-seq, RNA-seq, ChIP-seq, 3C-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, FISH 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; AR LTF Enhancer Active Normal Prostate UBERON:0002367 Human prostate epithelial cell prostate epithelial cell CL:0000066 Functional perturbation assay, Enhancer activity assay, Chromatin interaction assay, TF binding assay ATAC-seq, RNA-seq, ChIP-seq, 3C-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, FISH 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 kidney cancer cell CL:0001066 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq CRISPRi, Luciferase Reporter Assay, ChIP-RT-qPCR 2018 29861296 The SS18-SSX Fusion Oncoprotein Hijacks BAF Complex Targeting and Function to Drive Synovial Sarcoma Homo sapiens hg38 chr18 26013138 26015138 SS18 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293T cells CVCL_0063 embryonic kidney cell CL:0002139 Fusion oncoprotein enhancer hijacking study, Chromatin interaction assay ChIP-seq, RNA-seq, ATAC-seq 3C, CRISPR perturbation, RT-RT-qPCR, Western blot 2019 31775028 Global Analysis of Enhancer Targets Reveals Convergent Enhancer-Driven Regulatory Modules Homo sapiens hg38 chr6 135321297 135321697 MYB Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, Functional perturbation assay scRNA-seq, RNA-seq, Hi-C, ChIP-seq CRISPRi, RT-RT-qPCR 2019 31827084 A primate-specific retroviral enhancer wires the XACT lncRNA into the core pluripotency network in humans Homo sapiens hg38 chrX 114038200 114039000 XACT Enhancer Active Normal Inner cell mass UBERON:0000087 H1 hESC CVCL_9771 embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, ATAC-seq CRISPR Knockout, CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR, RNA-FISH, Western blot 2019 31827084 A primate-specific retroviral enhancer wires the XACT lncRNA into the core pluripotency network in humans Homo sapiens hg38 chrX 114038200 114039000 T113.3 Enhancer Active Normal Inner cell mass UBERON:0000087 H9 hESC CVCL_9774 embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, ATAC-seq CRISPR Knockout, CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR, RNA-FISH, Western blot 2024 38661000 Multiple genetic variants at the SLC30A8 locus affect local super-enhancer activity and influence pancreatic ??-cell survival and function Homo sapiens hg38 chr8 118183060 118185060 FOXA2 SLC30A8 Enhancer Active Normal Pancreatic islet UBERON:0000006 EndoC-??H3 CVCL_A5NF pancreatic beta cell CL:0000169 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C CRISPR Knockout, Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2024 38661000 Multiple genetic variants at the SLC30A8 locus affect local super-enhancer activity and influence pancreatic ??-cell survival and function Homo sapiens hg38 chr8 118183060 118185060 FOXA2 UTP23 Enhancer Active Normal Pancreatic islet UBERON:0000006 Human Pancreatic Islets pancreatic islet cell CL:0000168 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C CRISPR Knockout, Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2024 38661000 Multiple genetic variants at the SLC30A8 locus affect local super-enhancer activity and influence pancreatic ??-cell survival and function Homo sapiens hg38 chr8 118250000 118252000 PDX1 SLC30A8 Enhancer Active Normal Pancreatic islet UBERON:0000006 EndoC-??H3 CVCL_A5NF pancreatic beta cell CL:0000169 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C CRISPR Knockout, Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2024 38661000 Multiple genetic variants at the SLC30A8 locus affect local super-enhancer activity and influence pancreatic ??-cell survival and function Homo sapiens hg38 chr8 118250000 118252000 PDX1 UTP23 Enhancer Active Normal Pancreatic islet UBERON:0000006 Human Pancreatic Islets pancreatic islet cell CL:0000168 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C CRISPR Knockout, Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2023 37185814 Epigenetic landscape reveals MECOM as an endothelial lineage regulator Homo sapiens hg38 chr3 169000000 169001000 MECOM KDR Enhancer Active Normal Umbilical vein UBERON:0002066 HUVEC CVCL_2959 umbilical vein endothelial cell CL:0002615 Enhancer activity assay, Chromatin interaction assay ChIP-seq, RNA-seq, 3C-seq Luciferase Reporter Assay, CRISPR Knockout 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:0005132 DOID:9256 Colon UBERON:0001155 SW480 CVCL_0546 colorectal carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ATAC-seq, ChIP-seq Luciferase Reporter Assay, CRISPR Knockout 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 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR 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 HepG2 CVCL_0027 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR 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 Huh7 CVCL_0336 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR 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 SNU387 CVCL_0250 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR 2023 37756562 Super enhancer-regulated lncRNA LINC01089 induces alternative splicing of DIAPH3 to drive hepatocellular carcinoma metastasis Homo sapiens hg38 chr12 121803095 121805690 LINC01089 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 SK-Hep-1 CVCL_0525 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, RT-RT-qPCR 2023 37756562 Super enhancer-regulated lncRNA LINC01089 induces alternative splicing of DIAPH3 to drive hepatocellular carcinoma metastasis Homo sapiens hg38 chr12 121803095 121805690 LINC01089 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepG2 CVCL_0027 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, RT-RT-qPCR 2023 37756562 Super enhancer-regulated lncRNA LINC01089 induces alternative splicing of DIAPH3 to drive hepatocellular carcinoma metastasis Homo sapiens hg38 chr12 121803095 121805690 LINC01089 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 Huh7 CVCL_0336 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, RT-RT-qPCR 2023 37756562 Super enhancer-regulated lncRNA LINC01089 induces alternative splicing of DIAPH3 to drive hepatocellular carcinoma metastasis Homo sapiens hg38 chr12 121803095 121805690 LINC01089 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 SNU387 CVCL_0250 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, RT-RT-qPCR 2026 41357990 Species-specific chromatin architecture and neurogenesis mediated by a human enhancer Homo sapiens hg38 chr3 186239308 186239606 ETV5 ETV5 Enhancer Active Normal Brain UBERON:0000955 Neural progenitor cells neural progenitor cell CL:0002672 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay Hi-C, RNA-seq, ChIP-seq Luciferase reporter assay, CRISPRi, ChIP-RT-qPCR, Transgenic reporter assay, FISH 2026 41357990 Species-specific chromatin architecture and neurogenesis mediated by a human enhancer Homo sapiens hg38 chr3 186239308 186239606 ETV5 ETV5 Enhancer Active Normal Brain UBERON:0000955 Cortical organoids cortical organoid CL:0002672 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay Hi-C, RNA-seq, ChIP-seq Luciferase reporter assay, CRISPRi, ChIP-RT-qPCR, Transgenic reporter assay, FISH 2026 41357990 Species-specific chromatin architecture and neurogenesis mediated by a human enhancer Homo sapiens hg38 chr3 186239308 186239606 ETV5 TRA2B Enhancer Active Normal Brain UBERON:0000955 Neural progenitor cells neural progenitor cell CL:0002672 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay Hi-C, RNA-seq, ChIP-seq Luciferase reporter assay, CRISPRi, ChIP-RT-qPCR, Transgenic reporter assay, FISH 2026 41357990 Species-specific chromatin architecture and neurogenesis mediated by a human enhancer Homo sapiens hg38 chr3 186239308 186239606 ETV5 TRA2B Enhancer Active Normal Brain UBERON:0000955 Cortical organoids cortical organoid CL:0002672 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay Hi-C, RNA-seq, ChIP-seq Luciferase reporter assay, CRISPRi, ChIP-RT-qPCR, Transgenic reporter assay, FISH 2025 40369080 A human-specific enhancer fine tunes radial glia potency and corticogenesis Homo sapiens hg38 chr10 35949493 35950111 TCF7L2 FZD8 Enhancer Active Normal Brain UBERON:0000955 Radial glial cells radial glial cell CL:0000681 Enhancer activity assay ChIP-seq, Hi-C, RNA-seq CRISPR knockout, Luciferase reporter assay 2025 40208226 Gain-of-function enhancer variant near KCNB1 causes familial ST-depression syndrome Homo sapiens hg38 chr20 49345311 49346146 MEF2A KCNB1 Enhancer Active Normal Heart UBERON:0000948 Cardiomyocytes cardiomyocyte CL:0000746 Enhancer activity assay ATAC-seq, ChIP-seq, 4C-seq Luciferase reporter assay, CRISPR knockout, CRISPRi, ChIP-RT-qPCR 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 UBERON:0002367 LNCaP cells CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ATAC-seq, RNA-seq, Hi-C Luciferase reporter assay, ChIP-RT-qPCR, 3C-RT-qPCR, CRISPR knockout, CRISPRi, RT-RT-qPCR 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 UBERON:0002367 C4-2 cells CVCL_4784 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ATAC-seq, RNA-seq, Hi-C Luciferase reporter assay, ChIP-RT-qPCR, 3C-RT-qPCR, CRISPR knockout, CRISPRi, RT-RT-qPCR 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 UBERON:0002367 DU145 cells CVCL_0105 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ATAC-seq, RNA-seq, Hi-C Luciferase reporter assay, ChIP-RT-qPCR, 3C-RT-qPCR, CRISPR knockout, CRISPRi, RT-RT-qPCR 2025 41139207 MAPK3 Modulates Enhancer-Promoter Interactions of SKAP2 in Acute Myeloid Leukemia Homo sapiens hg38 chr17 41245000 41246000 CTCF SKAP2 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 KASUMI-1 cells CVCL_0589 acute myeloid leukemia cell CL:0001054 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq CRISPR knockout, 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2025 41139207 MAPK3 Modulates Enhancer-Promoter Interactions of SKAP2 in Acute Myeloid Leukemia Homo sapiens hg38 chr17 41245000 41246000 CTCF SKAP2 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 KG1a cells CVCL_1824 acute myeloid leukemia cell CL:0001054 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq CRISPR knockout, 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2025 41139207 MAPK3 Modulates Enhancer-Promoter Interactions of SKAP2 in Acute Myeloid Leukemia Homo sapiens hg38 chr17 41245000 41246000 CTCF SKAP2 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 HL-60 cells CVCL_0002 acute myeloid leukemia cell CL:0001054 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq CRISPR knockout, 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2025 41139207 MAPK3 Modulates Enhancer-Promoter Interactions of SKAP2 in Acute Myeloid Leukemia Homo sapiens hg38 chr17 41245000 41246000 CTCF SKAP2 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 NB4 cells CVCL_0005 acute promyelocytic leukemia cell CL:0001054 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq CRISPR knockout, 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2025 41139207 MAPK3 Modulates Enhancer-Promoter Interactions of SKAP2 in Acute Myeloid Leukemia Homo sapiens hg38 chr17 41268000 41269000 CTCF SKAP2 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 KASUMI-1 cells CVCL_0589 acute myeloid leukemia cell CL:0001054 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq CRISPR knockout, 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2025 41139207 MAPK3 Modulates Enhancer-Promoter Interactions of SKAP2 in Acute Myeloid Leukemia Homo sapiens hg38 chr17 41268000 41269000 CTCF SKAP2 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 KG1a cells CVCL_1824 acute myeloid leukemia cell CL:0001054 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq CRISPR knockout, 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2025 41139207 MAPK3 Modulates Enhancer-Promoter Interactions of SKAP2 in Acute Myeloid Leukemia Homo sapiens hg38 chr17 41268000 41269000 CTCF SKAP2 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 HL-60 cells CVCL_0002 acute myeloid leukemia cell CL:0001054 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq CRISPR knockout, 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2025 41139207 MAPK3 Modulates Enhancer-Promoter Interactions of SKAP2 in Acute Myeloid Leukemia Homo sapiens hg38 chr17 41268000 41269000 CTCF SKAP2 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 NB4 cells CVCL_0005 acute promyelocytic leukemia cell CL:0001054 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq CRISPR knockout, 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 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:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 CVCL_0062 breast carcinoma cell CL:0000646 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, RT-RT-qPCR, Western blot 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:0006120 DOID:1612 Breast UBERON:0000310 Breast cancer cell breast carcinoma cell CL:0000646 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, RT-RT-qPCR, Western blot 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:0006120 DOID:1612 Breast UBERON:0000310 Breast cancer drug-resistant cell breast carcinoma cell CL:0000646 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, RT-RT-qPCR, Western blot 2026 41328346 Enhancer-mediated NR2F2 recruitment activates BGN to promote tumor growth and shape tumor microenvironment in papillary thyroid cancer Homo sapiens hg38 chr17 48298123 48299123 NR2F2 BGN Enhancer Active Disease thyroid carcinoma MONDO:0005075 DOID:3948 Thyroid UBERON:0002046 Thyroid carcinoma cell thyroid carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, 3C-seq Luciferase Reporter Assay, CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2023 36609474 A distal super-enhancer activates oncogenic ETS2 via recruiting MECOM in inflammatory bowel disease and colorectal cancer Homo sapiens hg38 chr21 40149729 40317726 MECOM ETS2 Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 SW480 CVCL_0546 colorectal carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, CUT&Tag, 5' CAGE CRISPRi, 3C assay, CUT&Tag-RT-qPCR, RT-RT-qPCR, Western blot 2023 36609474 A distal super-enhancer activates oncogenic ETS2 via recruiting MECOM in inflammatory bowel disease and colorectal cancer Homo sapiens hg38 chr21 40149729 40317726 MECOM ETS2 Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, CUT&Tag, 5' CAGE CRISPRi, 3C assay, CUT&Tag-RT-qPCR, RT-RT-qPCR, Western blot 2023 36609474 A distal super-enhancer activates oncogenic ETS2 via recruiting MECOM in inflammatory bowel disease and colorectal cancer Homo sapiens hg38 chr21 40149729 40317726 MECOM ETS2 Enhancer Active Normal Colon UBERON:0001155 Colon epithelial cell colon epithelial cell CL:1000348 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, CUT&Tag, 5' CAGE CRISPRi, 3C assay, CUT&Tag-RT-qPCR, RT-RT-qPCR, Western blot 2023 36609474 A distal super-enhancer activates oncogenic ETS2 via recruiting MECOM in inflammatory bowel disease and colorectal cancer Homo sapiens hg38 chr21 40149729 40317726 MECOM ETS2 Enhancer Active Normal Colon UBERON:0001155 Colon organoid cells colon organoid cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, CUT&Tag, 5' CAGE CRISPRi, 3C assay, CUT&Tag-RT-qPCR, RT-RT-qPCR, Western blot 2024 38720882 Integrated enhancer regulatory network by enhancer-promoter looping in gastric cancer Homo sapiens hg38 chr6 135220000 135225000 TCF7 MYB Enhancer Active Disease gastric adenocarcinoma MONDO:0005050 DOID:3717 Stomach UBERON:0000945 MKN45 CVCL_0434 gastric adenocarcinoma cell CL:0000066 Chromatin interaction assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq, Hi-C, ATAC-seq, 3C-seq CRISPRi, 4C-seq, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 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 carcinoma MONDO:0005075 DOID:3948 Thyroid UBERON:0002046 Thyroid carcinoma cell thyroid carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPRi, 3C assay, RT-RT-qPCR, Western blot 2024 39163202 CRISPR screening uncovers a long-range enhancer for ONECUT1 in pancreatic differentiation Homo sapiens hg38 chr15 53455006 53455051 GATA4 ONECUT1 Enhancer Active Normal Pancreas UBERON:0001264 Progenitor cells progenitor cell CL:0000037 Enhancer activity assay, Functional perturbation assay ChIP-seq, Hi-C, RNA-seq CRISPR Knockout, Luciferase Reporter Assay 2021 34040254 Enhancer release and retargeting activates disease-susceptibility genes Homo sapiens hg38 chr21 43745000 43747000 ESR1 TFF1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF-7 CVCL_0031 breast carcinoma cell CL:0000646 Enhancer activity assay, Functional perturbation assay, TF binding assay, Chromatin interaction assay ChIP-seq, GRO-seq, Hi-C, ChIA-PET, RNA-seq CRISPR Knockout, RT-RT-qPCR, 4C-seq, ChIP-RT-qPCR 2023 37346447 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:0005132 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer functional validation, TF binding assay, Chromatin loop analysis, Functional perturbation assay ChIP-seq, GRO-seq CRISPR-Cas9 deletion, Dual-luciferase reporter assay, 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, Immunohistochemistry, Colony formation assay, CCK-8 assay, Xenograft tumorigenesis 2023 37346447 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:0005132 DOID:9256 Colon UBERON:0001155 LoVo CVCL_0399 colorectal carcinoma cell CL:0000066 Enhancer functional validation, TF binding assay, Chromatin loop analysis, Functional perturbation assay ChIP-seq, GRO-seq CRISPR-Cas9 deletion, Dual-luciferase reporter assay, 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, Immunohistochemistry, Colony formation assay, CCK-8 assay, Xenograft tumorigenesis 2022 36301402 The Tumor Invasion Paradox in Cancer Stem Cell-Driven Solid Tumors Homo sapiens hg38 chr16 46972034 46973080 KBTBD7 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 Kasumi-1 CVCL_0589 acute myeloid leukemia cell CL:0001054 Enhancer activity assay, Functional perturbation assay Hi-C, ATAC-seq, CUT&Tag, RNA-seq Luciferase Reporter Assay, CRISPRi, RT-RT-qPCR 2021 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:0004945 DOID:0080545 Blood UBERON:0000178 Nalm6 CVCL_0092 B lymphoblast CL:0000945 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, CRISPRi, RT-RT-qPCR, Western blot 2024 38636893 CDK5RAP3 is a novel super-enhancer-driven gene activated by master TFs and regulates ER-Phagy in neuroblastoma Homo sapiens hg38 chr17 47970000 47975000 MEIS2; HAND2 CDK5RAP3 Enhancer Active Disease neuroblastoma MONDO:0005070 DOID:769 Adrenal gland UBERON:0002369 SK-N-BE(2) CVCL_0528 neuroblastoma cell CL:0000031 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, Hi-C, CUT&Tag, RNA-seq Luciferase Reporter Assay, 3C-RT-qPCR, CUT&RUN-RT-qPCR, CRISPRi, RT-RT-qPCR, Western blot 2024 38636893 CDK5RAP3 is a novel super-enhancer-driven gene activated by master TFs and regulates ER-Phagy in neuroblastoma Homo sapiens hg38 chr17 47940000 48020000 MEIS2; HAND2 CDK5RAP3 Enhancer Active Disease neuroblastoma MONDO:0005070 DOID:769 Adrenal gland UBERON:0002369 SK-N-BE(2) CVCL_0528 neuroblastoma cell CL:0000031 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, Hi-C, CUT&Tag, RNA-seq Luciferase Reporter Assay, 3C-RT-qPCR, CUT&RUN-RT-qPCR, CRISPRi, RT-RT-qPCR, Western blot 2022 35915089 A Ctnb1 enhancer regulates neocortical neurogenesis by controlling the abundance of intermediate progenitors Homo sapiens hg38 chr9 120869524 120870219 CTNNB1 Enhancer Active Normal Brain UBERON:0000955 Neocortical progenitors neural progenitor cell CL:0002672 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C CRISPR Knockout, CRISPRi, CRISPRa, Luciferase Reporter Assay, RT-RT-qPCR 2025 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 Heart UBERON:0000948 Cardiomyocytes cardiomyocyte CL:0000746 Enhancer activity assay, Functional perturbation assay ATAC-seq, Hi-C, ChIP-seq Luciferase Reporter Assay, Transgenic Reporter Assay, CRISPR Knockout, CRISPRi, qRT-PCR 2024 39107271 DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression Homo sapiens hg38 chr10 52442551 52444237 JUND; FOSL2 DKK1 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 PANC-1 CVCL_0480 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, DNase-seq Luciferase Reporter Assay, CRISPRi, CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, DNA pull-down assay 2024 39107271 DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression Homo sapiens hg38 chr10 52442551 52444237 JUND; FOSL2 DKK1 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 HPAC CVCL_1492 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, DNase-seq Luciferase Reporter Assay, CRISPRi, CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, DNA pull-down assay 2024 39107271 DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression Homo sapiens hg38 chr10 52442551 52444237 JUND; FOSL2 DKK1 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 AsPC-1 CVCL_0152 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, DNase-seq Luciferase Reporter Assay, CRISPRi, CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, DNA pull-down assay 2024 39107271 DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression Homo sapiens hg38 chr10 52485607 52487433 DKK1 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 PANC-1 CVCL_0480 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, CRISPRi, RT-RT-qPCR 2024 39107271 DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression Homo sapiens hg38 chr10 52485607 52487433 DKK1 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 HPAC CVCL_1492 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, CRISPRi, RT-RT-qPCR 2020 31770110 A stress-responsive enhancer induces dynamic drug resistance in acute myeloid leukemia Homo sapiens hg38 chr7 87574094 87575396 ABCB1 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 Primary AML blasts myeloid leukemia cell CL:0001054 Functional perturbation assay, TF binding assay, Enhancer activity assay, Chromatin interaction assay ChIP-seq, RNA-seq, 4C-seq CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR, Flow Cytometry 2025 40405227 HBV sequence integrated to enhancer acting as oncogenic driver epigenetically promotes hepatocellular carcinoma development Homo sapiens hg38 chr13 26191020 26272468 CDK8 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 Huh7 CVCL_0336 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, RT-RT-qPCR, Western blot 2023 38086419 Cell type directed design of synthetic enhancers Homo sapiens hg38 chr6 396104 396604 SOX10 IRF4 Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 Human melanoma cell melanoma cell CL:0002573 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq Luciferase Reporter Assay, CRISPRi, CRISPR Knockout, RT-RT-qPCR, ChIP-RT-qPCR 2019 31775028 Global Analysis of Enhancer Targets Reveals Convergent Enhancer-Driven Regulatory Modules Homo sapiens hg38 chr5 54325645 54326045 ARL15 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, Functional perturbation assay scRNA-seq, RNA-seq, ATAC-seq, ChIP-seq CRISPRi, RT-RT-qPCR 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:0004973 DOID:0050861 Esophagus UBERON:0001043 OE19 CVCL_1302 esophageal adenocarcinoma cell CL:0000069 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, RNA-seq, ChIP-seq Luciferase Reporter Assay, CRISPR knockout/CRISPRi, RT-RT-qPCR, Western blot 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:0004973 DOID:0050861 Esophagus UBERON:0001043 CP-A CVCL_6920 esophageal adenocarcinoma cell CL:0000069 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, RNA-seq, ChIP-seq Luciferase Reporter Assay, CRISPR knockout/CRISPRi, RT-RT-qPCR, Western blot 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:0006120 DOID:1612 Breast UBERON:0000310 MCF7 CVCL_0031 breast carcinoma cell CL:0000646 Enhancer activity assay, Functional perturbation assay ChIP-seq CRISPR Knockout, Luciferase Reporter Assay 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:0004945 DOID:0080545 Blood UBERON:0000178 Nalm6 CVCL_0092 B lymphoblast CL:0000945 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, CRISPRi, RT-RT-qPCR 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:0004945 DOID:0080545 Blood UBERON:0000178 697 CVCL_0097 B lymphoblast CL:0000945 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, CRISPRi, RT-RT-qPCR 2025 41314977 Blocking PCSK9 suppresses hepatocellular carcinoma immune escape by decreasing FLI1-mediated SPP1 and PD-L1 expression Homo sapiens hg38 chr4 88008000 88010000 FLI1 SPP1 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepG2 cells CVCL_0027 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq, ChIP-seq, scRNA-seq Luciferase reporter assay, CUT&Tag, ChIP-RT-qPCR, CRISPR knockout, RT-RT-qPCR, Western blot 2025 41314977 Blocking PCSK9 suppresses hepatocellular carcinoma immune escape by decreasing FLI1-mediated SPP1 and PD-L1 expression Homo sapiens hg38 chr4 88008000 88010000 FLI1 SPP1 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 Huh-7 cells CVCL_0336 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq, ChIP-seq, scRNA-seq Luciferase reporter assay, CUT&Tag, ChIP-RT-qPCR, CRISPR knockout, RT-RT-qPCR, Western blot 2025 41314977 Blocking PCSK9 suppresses hepatocellular carcinoma immune escape by decreasing FLI1-mediated SPP1 and PD-L1 expression Homo sapiens hg38 chr4 88008000 88010000 FLI1 SPP1 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 H22 cells CVCL_0321 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq, ChIP-seq, scRNA-seq Luciferase reporter assay, CUT&Tag, ChIP-RT-qPCR, CRISPR knockout, RT-RT-qPCR, Western blot 2025 41314977 Blocking PCSK9 suppresses hepatocellular carcinoma immune escape by decreasing FLI1-mediated SPP1 and PD-L1 expression Homo sapiens hg38 chr4 88008000 88010000 FLI1 SPP1 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 Hepa1-6 cells CVCL_0327 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq, ChIP-seq, scRNA-seq Luciferase reporter assay, CUT&Tag, ChIP-RT-qPCR, CRISPR knockout, RT-RT-qPCR, Western blot 2025 41314977 Blocking PCSK9 suppresses hepatocellular carcinoma immune escape by decreasing FLI1-mediated SPP1 and PD-L1 expression Homo sapiens hg38 chr9 5450500 5452500 FLI1 CD274 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepG2 cells CVCL_0027 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq, ChIP-seq, scRNA-seq Luciferase reporter assay, CUT&Tag, ChIP-RT-qPCR, CRISPR knockout, RT-RT-qPCR, Western blot 2025 41314977 Blocking PCSK9 suppresses hepatocellular carcinoma immune escape by decreasing FLI1-mediated SPP1 and PD-L1 expression Homo sapiens hg38 chr9 5450500 5452500 FLI1 CD274 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 Huh-7 cells CVCL_0336 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq, ChIP-seq, scRNA-seq Luciferase reporter assay, CUT&Tag, ChIP-RT-qPCR, CRISPR knockout, RT-RT-qPCR, Western blot 2025 41314977 Blocking PCSK9 suppresses hepatocellular carcinoma immune escape by decreasing FLI1-mediated SPP1 and PD-L1 expression Homo sapiens hg38 chr9 5450500 5452500 FLI1 CD274 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 H22 cells CVCL_0321 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq, ChIP-seq, scRNA-seq Luciferase reporter assay, CUT&Tag, ChIP-RT-qPCR, CRISPR knockout, RT-RT-qPCR, Western blot 2025 41314977 Blocking PCSK9 suppresses hepatocellular carcinoma immune escape by decreasing FLI1-mediated SPP1 and PD-L1 expression Homo sapiens hg38 chr9 5450500 5452500 FLI1 CD274 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 Hepa1-6 cells CVCL_0327 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq, ChIP-seq, scRNA-seq Luciferase reporter assay, CUT&Tag, ChIP-RT-qPCR, CRISPR knockout, RT-RT-qPCR, Western blot 2024 38602103 Coronary artery disease risk variant dampens CALCRL expression by reducing HSF binding to enhancer Homo sapiens hg38 chr2 188184700 188185000 HSF1 CALCRL Enhancer Active Normal Artery UBERON:0001621 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq Luciferase Reporter Assay, EMSA, CRISPR Knockout 2024 39606421 Single cell variant to enhancer to gene map for coronary artery disease Homo sapiens hg38 chr3 134200000 134500000 AMOTL2 Enhancer Active Normal Artery UBERON:0001628 Human Coronary Artery Smooth Muscle Cells (HCASMC) coronary artery smooth muscle cell CL:0000192 Functional validation, Chromatin interaction Hi-C, HiChIP-seq, ATAC-seq, ChIP-seq, RNA-seq CRISPRi, RT-RT-qPCR 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 Heart UBERON:0000948 Human iPSC-derived cardiomyocytes cardiomyocyte CL:0000746 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ATAC-seq, RNA-seq, Hi-C, ChIP-seq CRISPRi, CRISPRa, RT-RT-qPCR 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:0005087 DOID:3347 Bone UBERON:0001474 OS-LM1 osteosarcoma cell CL:0000062 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR, EMSA 2020 31753848 A super enhancer controls expression and chromatin architecture within the MHC class II locus Homo sapiens hg38 chr6 32553535 32609681 CTCF HLA-DRB1 Enhancer Active Disease Burkitt lymphoma MONDO:0002483 DOID:8582 Blood UBERON:0000178 Human Burkitt lymphoma cell Burkitt lymphoma cell CL:0000945 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq CRISPR knockout, ChIP-RT-qPCR, RT-RT-qPCR, Flow cytometry 2019 31594934 Transcriptional landscape and clinical utility of enhancer RNAs for eRNA-targeted therapy in cancer Homo sapiens hg38 chr10 5419501 5420500 NET1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF7 Breast Cancer CVCL_0031 breast carcinoma cell CL:0000646 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay RNA-seq, ChIP-seq, Hi-C, ChIA-PET, GRO-seq CRISPR Activation (CRISPRa), LNA-Mediated Knockdown, RT-RT-qPCR, Cell Proliferation Assay 2024 39196225 A transcriptional enhancer regulates cardiac maturation Homo sapiens hg38 chr1 154150000 154150500 MEF2C ACTN2 Enhancer Active Normal Heart UBERON:0000948 hPSC-CMs cardiomyocyte CL:0000746 Enhancer activity assay, TF binding assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, RT-RT-qPCR 2024 39196225 A transcriptional enhancer regulates cardiac maturation Homo sapiens hg38 chr1 154150500 154151000 TEAD1 ACTN2 Enhancer Active Normal Heart UBERON:0000948 hPSC-CMs cardiomyocyte CL:0000746 Enhancer activity assay, TF binding assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, RT-RT-qPCR 2024 39196225 A transcriptional enhancer regulates cardiac maturation Homo sapiens hg38 chr1 154151000 154151500 GATA4 ACTN2 Enhancer Active Normal Heart UBERON:0000948 hPSC-CMs cardiomyocyte CL:0000746 Enhancer activity assay, TF binding assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, RT-RT-qPCR 2024 39294132 Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements Homo sapiens hg38 chr9 132901234 132902345 ANXA1 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional perturbation assay, Enhancer activity assay scRNA-seq, ATAC-seq, ChIP-seq CRISPR Knockout, CRISPRi, qRT-PCR 2024 39294132 Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements Homo sapiens hg38 chr12 10123456 10124567 ASIC1 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional perturbation assay, Enhancer activity assay scRNA-seq, ATAC-seq, ChIP-seq CRISPR Knockout, CRISPRi, qRT-PCR 2026 41634025 Escherichia coli promotes colorectal cancer metastasis by maintaining enhancer-promoter loops through releasing neutrophil extracellular traps Homo sapiens hg38 chr2 75000000 75020000 STAT3 TNS1 Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 MC38 CVCL_B288 mouse colorectal carcinoma cell CL:0000066 Chromatin interaction assay, TF binding assay, Functional perturbation assay Hi-C, HiChIP, ChIP-seq, RNA-seq ChIP-RT-qPCR, CRISPR Knockout, qRT-PCR, Western blot 2020 32493933 Activation of JUN in fibroblasts promotes pro-fibrotic programme and modulates protective immunity Homo sapiens hg38 chr1 58780000 58785000 JUN CD47 SE Active Normal Lung UBERON:0002048 Primary human lung fibroblasts lung fibroblast CL:0000057 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq, Mass Cytometry Luciferase Reporter Assay, CRISPR Knockout, Flow Cytometry, qRT-PCR, Western blot 2023 37641131 SMC3 epigenetic silencing regulates Rab27a expression and drives pancreatic cancer progression Homo sapiens hg38 chr15 54023501 54024000 RAB27A Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 MIA PaCa-2 CVCL_0428 pancreatic ductal adenocarcinoma cell CL:0000066 TF binding assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ChIP-seq, RNA-seq ChIP-RT-qPCR, CRISPR Knockout, qRT-PCR, Western blot 2024 39107271 DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression Homo sapiens hg38 chr10 52472214 52473981 DKK1 Enhancer Silenced Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 PANC-1 CVCL_0480 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay ChIP-seq, ATAC-seq Luciferase Reporter Assay, CRISPRi 2024 39107271 DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression Homo sapiens hg38 chr10 52472214 52473981 DKK1 Enhancer Silenced Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 HPAC CVCL_1492 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay ChIP-seq, ATAC-seq Luciferase Reporter Assay, CRISPRi 2024 39107271 DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression Homo sapiens hg38 chr10 52472214 52473981 DKK1 Enhancer Silenced Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 AsPC-1 CVCL_0152 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay ChIP-seq, ATAC-seq Luciferase Reporter Assay, CRISPRi 2024 39107271 DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression Homo sapiens hg38 chr10 52488538 52489405 CTCF DKK1 Enhancer Silenced Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 PANC-1 CVCL_0480 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, Insulator activity assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq Luciferase Reporter Assay, CRISPRi, ChIP-RT-qPCR 2024 39107271 DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression Homo sapiens hg38 chr10 52488538 52489405 CTCF DKK1 Enhancer Silenced Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 HPAC CVCL_1492 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, Insulator activity assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq Luciferase Reporter Assay, CRISPRi, ChIP-RT-qPCR 2024 39107271 DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression Homo sapiens hg38 chr10 52488538 52489405 CTCF DKK1 Enhancer Silenced Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 AsPC-1 CVCL_0152 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, Insulator activity assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq Luciferase Reporter Assay, CRISPRi, ChIP-RT-qPCR 2024 39012147 Super-enhancer-driven FOSL1-TCOF1 axis promotes triple-negative breast cancer progression Homo sapiens hg38 chr11 65200000 65240000 FOSL1 FOSL1 SE Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 CVCL_0062 breast carcinoma cell CL:0000646 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPRi, qRT-PCR, Western blot 2024 39012147 Super-enhancer-driven FOSL1-TCOF1 axis promotes triple-negative breast cancer progression Homo sapiens hg38 chr11 65200000 65240000 FOSL1 FOSL1 SE Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 BT549 CVCL_1082 breast carcinoma cell CL:0000646 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPRi, qRT-PCR, Western blot 2024 39012147 Super-enhancer-driven FOSL1-TCOF1 axis promotes triple-negative breast cancer progression Homo sapiens hg38 chr11 65200000 65240000 FOSL1 FOSL1 SE Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-468 CVCL_0419 breast carcinoma cell CL:0000646 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPRi, qRT-PCR, Western blot 2024 39012147 Super-enhancer-driven FOSL1-TCOF1 axis promotes triple-negative breast cancer progression Homo sapiens hg38 chr11 65200000 65240000 FOSL1 FOSL1 SE Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 HCC1806 CVCL_1258 breast carcinoma cell CL:0000646 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPRi, qRT-PCR, Western blot 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 HMX1 Enhancer Active Normal Craniofacial Tissue UBERON:0010368 hCNCC cranial neural crest cell CL:0000333 Enhancer activity assay, Functional perturbation assay ATAC-seq, ChIP-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR 2025 40604280 Range extender mediates long-distance enhancer activity Homo sapiens hg38 chr16 51624689 51625572 SHH Enhancer Active Normal Embryonic Limb Bud UBERON:0005417 Limb bud mesenchymal cells mesenchymal cell CL:0000134 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C Transgenic Reporter Assay, CRISPR Knockout, CRISPR Knock-in, RT-RT-qPCR, Whole-mount in situ hybridization, Skeletal staining 2025 40604280 Range extender mediates long-distance enhancer activity Homo sapiens hg38 chr16 51624689 51625572 SHH Enhancer Active Normal Limb Bud UBERON:0005417 Zone of polarizing activity cells mesenchymal cell CL:0000134 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C Transgenic Reporter Assay, CRISPR Knockout, CRISPR Knock-in, RT-RT-qPCR, Whole-mount in situ hybridization, Skeletal staining 2019 30511964 Targeting FOXA1-mediated repression of TGF-?? signaling suppresses castration-resistant prostate cancer progression Homo sapiens hg38 chr14 75664000 75664749 FOXA1 TGFB3 Enhancer Silenced Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Functional perturbation assay ChIP-seq, RNA-seq CRISPR Knockout/CRISPRi, RT-RT-qPCR 2019 31775028 Global Analysis of Enhancer Targets Reveals Convergent Enhancer-Driven Regulatory Modules Homo sapiens hg38 chr11 33941648 33942048 LMO2 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, Functional perturbation assay scRNA-seq, RNA-seq, ChIP-seq CRISPRi, RT-RT-qPCR 2019 31775028 Global Analysis of Enhancer Targets Reveals Convergent Enhancer-Driven Regulatory Modules Homo sapiens hg38 chr11 33944788 33945188 LMO2 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, Functional perturbation assay scRNA-seq, RNA-seq, ChIP-seq CRISPRi, RT-RT-qPCR 2019 31775028 Global Analysis of Enhancer Targets Reveals Convergent Enhancer-Driven Regulatory Modules Homo sapiens hg38 chr12 54304291 54304691 NFE2 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, Functional perturbation assay scRNA-seq, RNA-seq, ChIP-seq CRISPRi, RT-RT-qPCR 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 Tumor microenvironment UBERON:0002367 M2 macrophage macrophage CL:0000235 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR 2023 36095844 EVI1 drives leukemogenesis through aberrant ERG activation Homo sapiens hg38 chr21 38376000 38377000 EVI1 ERG Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 Acute Myeloid Leukemia Cells myeloid leukemia cell CL:0001054 Functional validation, TF binding ChIP-seq, ATAC-seq, RNA-seq CRISPR KO, shRNA KD, RT-RT-qPCR, Western blot, Transgenic reporter assay 2023 36095844 EVI1 drives leukemogenesis through aberrant ERG activation Homo sapiens hg38 chr21 38376000 38377000 EVI1 ERG Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 HNT-34 CVCL_1295 myeloid leukemia cell CL:0001054 Functional validation, TF binding ChIP-seq, ATAC-seq, RNA-seq CRISPR KO, shRNA KD, RT-RT-qPCR, Western blot, Transgenic reporter assay 2020 32679107 IL6 STAT3 signaling hijacks ER enhancers to drive breast cancer metastasis Homo sapiens hg38 chr19 45409200 45410200 STAT3 BCL3 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF7 CVCL_0031 breast carcinoma cell CL:0000646 Functional perturbation assay ChIP-seq, RNA-seq CRISPR Knockout 2020 31753848 A super enhancer controls expression and chromatin architecture within the MHC class II locus Homo sapiens hg38 chr6 32543534 32553534 CIITA HLA-DRB1 Enhancer Active Normal Lymphoid tissue UBERON:0001745 Functional perturbation assay, Chromatin interaction assay, Enhancer activity assay ChIP-seq, RNA-seq CRISPR knockout, ChIP-RT-qPCR, RT-RT-qPCR, 3C, Flow cytometry 2020 31753848 A super enhancer controls expression and chromatin architecture within the MHC class II locus Homo sapiens hg38 chr6 32570000 32573500 CIITA; CTCF HLA-DRB1 Enhancer Active Normal Lymphoid tissue UBERON:0001745 Functional perturbation assay, Chromatin interaction assay, Enhancer activity assay ChIP-seq, RNA-seq CRISPR knockout, ChIP-RT-qPCR, RT-RT-qPCR, 3C, Flow cytometry 2025 40164603 Enhancer RNA transcription pinpoints functional genetic variants linked to asthma Homo sapiens hg38 chr12 56075734 56076734 NR3C1 GCNT1 Enhancer Active Disease lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 BEAS-2B cells CVCL_0168 bronchial epithelial cell CL:0002591 Enhancer activity assay, TF binding assay, Functional perturbation assay, Chromatin interaction assay GRO-seq, Micro-C, ChIP-seq Luciferase reporter assay, CRISPR knockout, CRISPRi, RT-RT-qPCR 2025 40164603 Enhancer RNA transcription pinpoints functional genetic variants linked to asthma Homo sapiens hg38 chr12 56075734 56076734 NR3C1 GCNT1 Enhancer Active Normal Lung UBERON:0002048 HASM cells airway smooth muscle cell CL:0000192 Enhancer activity assay, TF binding assay, Functional perturbation assay, Chromatin interaction assay GRO-seq, Micro-C, ChIP-seq Luciferase reporter assay, CRISPR knockout, CRISPRi, RT-RT-qPCR 2025 40158221 SWI/SNF complex-mediated ZNF410 cooperative binding maintains chromatin accessibility and enhancer activity Homo sapiens hg38 chr12 56545000 56555000 ZNF410 CHD4 Enhancer Active Normal Blood UBERON:0000178 Erythroid cells erythroid cell CL:0000038 Enhancer activity assay ATAC-seq, ChIP-seq Luciferase reporter assay, CRISPR knockout, CRISPRi, ChIP-RT-qPCR 2025 40158221 SWI/SNF complex-mediated ZNF410 cooperative binding maintains chromatin accessibility and enhancer activity Homo sapiens hg38 chr12 56270000 56280000 ZNF410 CHD4 Enhancer Active Normal Blood UBERON:0000178 Erythroid cells erythroid cell CL:0000038 Enhancer activity assay ATAC-seq, ChIP-seq Luciferase reporter assay, CRISPR knockout, CRISPRi, ChIP-RT-qPCR 2025 40222483 HDAC4 Super-Enhancer Drives CEBPB-Mediated TWIST2 Transcription to Promote Chemoresistance in LUAD Homo sapiens hg38 chr2 239200000 239250000 CEBPB TWIST2 Enhancer Active Disease lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 SPC-A1/DTX cells CVCL_0285 lung adenocarcinoma cell CL:0001069 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq CRISPR knockout, Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2025 40222483 HDAC4 Super-Enhancer Drives CEBPB-Mediated TWIST2 Transcription to Promote Chemoresistance in LUAD Homo sapiens hg38 chr2 239200000 239250000 CEBPB TWIST2 Enhancer Active Disease non-small cell lung carcinoma MONDO:0005233 DOID:3908 Lung UBERON:0002048 H1299/DTX cells CVCL_0060 non-small cell lung carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq CRISPR knockout, Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2025 41293823 Functional Genomics Link REST to Endothelial Plasticity and Atherosclerosis Homo sapiens hg38 chr12 12769300 12769800 REST CDKN1B Enhancer Silenced Normal Aorta UBERON:0000947 HAECs CVCL_UA48 aortic endothelial cell CL:0002546 Enhancer activity assay, Functional perturbation assay ChIP-seq, CUT&Tag, RNA-seq Luciferase reporter assay, CRISPRi, RT-RT-qPCR 2025 41293823 Functional Genomics Link REST to Endothelial Plasticity and Atherosclerosis Homo sapiens hg38 chr9 139390200 139390700 REST NOTCH1 Enhancer Silenced Normal Aorta UBERON:0000947 HAECs CVCL_UA48 aortic endothelial cell CL:0002546 Enhancer activity assay, Functional perturbation assay ChIP-seq, CUT&Tag, RNA-seq Luciferase reporter assay, CRISPRi, RT-RT-qPCR 2025 40321134 Enhancer-Associated LncRNA-ITGA2 Promotes Vascular Remodeling Through ITGA2 Homo sapiens hg38 chr5 129345600 129346600 SRF ITGA2 Enhancer Active Normal Artery UBERON:0001637 Primary human VSMCs vascular smooth muscle cell CL:0000192 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase reporter assay, ChIP-RT-qPCR, CRISPRi, RT-RT-qPCR, Western blot, EMSA 2024 38720882 Integrated enhancer regulatory network by enhancer-promoter looping in gastric cancer Homo sapiens hg38 chr6 135581000 135583000 TCF7 MYB Enhancer Active Disease gastric adenocarcinoma MONDO:0005050 DOID:3717 Stomach UBERON:0000945 MKN45 CVCL_0434 gastric adenocarcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay HiChIP, ChIP-seq, RNA-seq, ATAC-seq CRISPR Knockout/CRISPRi, RT-RT-qPCR, ChIP-RT-qPCR 2020 31753848 A super enhancer controls expression and chromatin architecture within the MHC class II locus Homo sapiens hg38 chr6 32543534 32553534 CIITA HLA-DRB1 Enhancer Active Disease Lymphoid tissue UBERON:0001745 Not available Functional perturbation assay, Chromatin interaction assay, Enhancer activity assay ChIP-seq, RNA-seq CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, 3C, Flow Cytometry 2020 31753848 A super enhancer controls expression and chromatin architecture within the MHC class II locus Homo sapiens hg38 chr6 32570000 32573500 CIITA; CTCF HLA-DRB1 Enhancer Active Disease Lymphoid tissue UBERON:0001745 Not available Functional perturbation assay, Chromatin interaction assay, Enhancer activity assay ChIP-seq, RNA-seq CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, 3C, Flow Cytometry 2025 40140585 Genome-wide CRISPR screen in human T cells reveals regulators of FOXP3 Homo sapiens hg38 chrX 49250000 49251200 RBPJ FOXP3 Enhancer Silenced Normal Peripheral blood UBERON:0000178 Primary CD4+ Treg cells CD4-positive regulatory T cell CL:0000815 Enhancer activity assay, TF binding assay ChIP-seq, ATAC-seq Luciferase Reporter Assay, EMSA, CRISPR Knockout 2021 34040254 Enhancer release and retargeting activates disease-susceptibility genes Homo sapiens hg38 chr5 1320000 1322000 CTCF TERT Enhancer Active Normal Embryonic Kidney UBERON:0002113 293T CVCL_0063 embryonic kidney cell CL:0002139 Enhancer activity assay, Functional perturbation assay, TF binding assay, Chromatin interaction assay ChIP-seq, Hi-C, ChIA-PET, RNA-seq, WGS CRISPR Knockout, RT-RT-qPCR, 4C-seq, ChIP-RT-qPCR, Sanger Sequencing 2025 39796169 Defining Mechanistic Links Between the Non-Coding Variant rs17673553 in CLEC16A and Lupus Susceptibility Homo sapiens hg38 chr16 11075000 11075280 CTCF; STAT3; GATA3 CLEC16A Enhancer Active Disease Burkitt lymphoma MONDO:0002483 DOID:8582 Lymph node UBERON:0000029 Namalwa (B-lymphocyte) CVCL_0128 Burkitt lymphoma cell CL:0000945 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, Luciferase Reporter Assay CRISPR Knockout, siRNA Knockdown, RT-RT-qPCR, CRISPRa (dCas9-VPR, dCas9-TET1), CRISPRi (dCas9-DNMT3A, dCas9-MeCP2), Western blot 2024 38504114 Multicenter integrated analysis of noncoding CRISPRi screens Homo sapiens hg38 chrX 48641136 48641797 GATA1 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional perturbation assay, Enhancer activity assay CRISPRi screening, RNA-seq, ATAC-seq, ChIP-seq FlowFISH, HCR-FlowFISH 2024 38504114 Multicenter integrated analysis of noncoding CRISPRi screens Homo sapiens hg38 chrX 48658755 48659455 GATA1 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional perturbation assay, Enhancer activity assay CRISPRi screening, RNA-seq, ATAC-seq, ChIP-seq FlowFISH, HCR-FlowFISH 2024 38504114 Multicenter integrated analysis of noncoding CRISPRi screens Homo sapiens hg38 chr11 61815000 61817000 FADS2 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional perturbation assay, Enhancer activity assay CRISPRi screening, RNA-seq, ATAC-seq, ChIP-seq HCR-FlowFISH 2024 38504114 Multicenter integrated analysis of noncoding CRISPRi screens Homo sapiens hg38 chr11 61820000 61822000 FADS2 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional perturbation assay, Enhancer activity assay CRISPRi screening, RNA-seq, ATAC-seq, ChIP-seq HCR-FlowFISH 2024 38965263 TWEAK/Fn14 signalling driven superenhancer 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:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 CVCL_0062 breast carcinoma cell CL:0000646 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, HiChIP CRISPR Knockout, ChIP-RT-qPCR, qRT-PCR, Western blot 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 1985000 2005000 IGF2 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 Huh-7 CVCL_0336 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, 3C-RT-qPCR, ChIP-RT-qPCR, qRT-PCR, Western blot 2025 40611281 LNP-enclosed NamiRNA inhibits pancreatic cancer proliferation and migration via dual pathways Homo sapiens hg38 chr12 6933000 6941000 PTPN6 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 MIA PaCa-2 CVCL_0428 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, qRT-PCR, Western blot 2022 35039581 Targeting of non-coding RNAs encoded by novel MYC enhancers inhibits the proliferation of human hepatic carcinoma cells in vitro Homo sapiens hg38 chr8 128556059 128557653 MYC Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepG2 CVCL_0027 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, Functional perturbation assay ChIP-seq, GRO-seq Luciferase Reporter Assay, CRISPR Knockout, qRT-PCR 2023 37932451 CRISPR-Cas9-based functional interrogation of unconventional translatome reveals human cancer dependency on cryptic non-canonical open reading frames Homo sapiens hg38 chr6 36679000 36688000 CDKN1A Enhancer Silenced Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 HCT-116 CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, qRT-PCR, CRISPR Knockout, Western blot 2023 37932451 CRISPR-Cas9-based functional interrogation of unconventional translatome reveals human cancer dependency on cryptic non-canonical open reading frames Homo sapiens hg38 chr9 22004000 22010000 CDKN2B Enhancer Silenced Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 HCT-116 CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, qRT-PCR, CRISPR Knockout, Western blot 2022 36163279 Population-level variation in enhancer expression identifies disease mechanisms in the human brain Homo sapiens hg38 chr15 89400200 89400500 ABHD2 Enhancer Active Normal Brain UBERON:0000955 Neural Progenitor Cells (NPCs) neural progenitor cell CL:0002672 Functional perturbation assay, Enhancer activity assay RNA-seq, ATAC-seq, ChIP-seq, Hi-C CRISPRi, qRT-PCR 2022 36163279 Population-level variation in enhancer expression identifies disease mechanisms in the human brain Homo sapiens hg38 chr15 89400200 89400500 KIF7 Enhancer Active Normal Brain UBERON:0000955 Neural Progenitor Cells (NPCs) neural progenitor cell CL:0002672 Functional perturbation assay, Enhancer activity assay RNA-seq, ATAC-seq, ChIP-seq, Hi-C CRISPRi, qRT-PCR 2024 39316719 Focal deletions of a promoter tether activate the IRX3 oncogene in T-cell acute lymphoblastic leukemia Homo sapiens hg38 chr8 127750000 127752000 MYC Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF7 CVCL_0031 breast carcinoma cell CL:0000646 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay Hi-C, ChIA-PET, GRO-seq, RNA-seq CRISPRi, RT-RT-qPCR 2024 39316719 Focal deletions of a promoter tether activate the IRX3 oncogene in T-cell acute lymphoblastic leukemia Homo sapiens hg38 chr9 37100000 37102000 PAX5 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay Hi-C, ChIA-PET, GRO-seq, RNA-seq CRISPRi, RT-RT-qPCR, 4C-seq 2025 40640362 Analysis of biased allelic enhancer activity of schizophrenia-linked common variants Homo sapiens hg38 chr3 136050468 136050668 PCCB Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR 2023 36350827 ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia Homo sapiens hg38 chr1 150509075 150512075 ERG TNS1 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Blood UBERON:0000178 UoCB6 umbilical cord blood hematopoietic cell CL:0001029 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, RT-RT-qPCR, Western blot 2023 36350827 ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia Homo sapiens hg38 chr1 150509075 150512075 ERG TNS1 Enhancer Active Normal Lung UBERON:0002048 Alveolar type I cells alveolar epithelial type I cell CL:0002062 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, RT-RT-qPCR, Western blot 2023 36350827 ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia Homo sapiens hg38 chr1 150509075 150512075 ERG TNS1 Enhancer Active Normal Lung UBERON:0002048 Alveolar type II cells alveolar epithelial type II cell CL:0002063 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, RT-RT-qPCR, Western blot 2023 36350827 ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia Homo sapiens hg38 chr1 150509075 150512075 ERG TNS1 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Blood UBERON:0000178 Human AML cell myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, RT-RT-qPCR, Western blot 2023 36350827 ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia Homo sapiens hg38 chr1 9081898 9084898 ERG KCNN1 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Blood UBERON:0000178 UoCB6 umbilical cord blood hematopoietic cell CL:0001029 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, RT-RT-qPCR, Western blot 2023 36350827 ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia Homo sapiens hg38 chr1 9081898 9084898 ERG KCNN1 Enhancer Active Normal Lung UBERON:0002048 Alveolar type I cells alveolar epithelial type I cell CL:0002062 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, RT-RT-qPCR, Western blot 2023 36350827 ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia Homo sapiens hg38 chr1 9081898 9084898 ERG KCNN1 Enhancer Active Normal Lung UBERON:0002048 Alveolar type II cells alveolar epithelial type II cell CL:0002063 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, RT-RT-qPCR, Western blot 2023 36350827 ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia Homo sapiens hg38 chr1 9081898 9084898 ERG KCNN1 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Blood UBERON:0000178 Human AML cell myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, RT-RT-qPCR, Western blot 2023 36350827 ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia Homo sapiens hg38 chr12 94191892 94194892 ERG EPOR Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Blood UBERON:0000178 UoCB6 umbilical cord blood hematopoietic cell CL:0001029 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, CRISPR Knockout, RT-RT-qPCR, Western blot 2023 36350827 ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia Homo sapiens hg38 chr12 94191892 94194892 ERG EPOR Enhancer Active Normal Lung UBERON:0002048 Alveolar type I cells alveolar epithelial type I cell CL:0002062 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, CRISPR Knockout, RT-RT-qPCR, Western blot 2023 36350827 ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia Homo sapiens hg38 chr12 94191892 94194892 ERG EPOR Enhancer Active Normal Lung UBERON:0002048 Alveolar type II cells alveolar epithelial type II cell CL:0002063 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, CRISPR Knockout, RT-RT-qPCR, Western blot 2023 36350827 ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia Homo sapiens hg38 chr12 94191892 94194892 ERG EPOR Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Blood UBERON:0000178 Human AML cell myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, CRISPR Knockout, RT-RT-qPCR, Western blot 2023 36350827 ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia Homo sapiens hg38 chr12 99975069 99978069 ERG WBP1L Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Blood UBERON:0000178 UoCB6 umbilical cord blood hematopoietic cell CL:0001029 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, RT-RT-qPCR, Western blot 2023 36350827 ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia Homo sapiens hg38 chr12 99975069 99978069 ERG WBP1L Enhancer Active Normal Lung UBERON:0002048 Alveolar type I cells alveolar epithelial type I cell CL:0002062 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, RT-RT-qPCR, Western blot 2023 36350827 ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia Homo sapiens hg38 chr12 99975069 99978069 ERG WBP1L Enhancer Active Normal Lung UBERON:0002048 Alveolar type II cells alveolar epithelial type II cell CL:0002063 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, RT-RT-qPCR, Western blot 2023 36350827 ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia Homo sapiens hg38 chr12 99975069 99978069 ERG WBP1L Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Blood UBERON:0000178 Human AML cell myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, RT-RT-qPCR, Western blot 2023 36350827 ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia Homo sapiens hg38 chr14 52051517 52054517 ERG MIB1 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Blood UBERON:0000178 UoCB6 umbilical cord blood hematopoietic cell CL:0001029 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, RT-RT-qPCR, Western blot 2023 36350827 ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia Homo sapiens hg38 chr14 52051517 52054517 ERG MIB1 Enhancer Active Normal Lung UBERON:0002048 Alveolar type I cells alveolar epithelial type I cell CL:0002062 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, RT-RT-qPCR, Western blot 2023 36350827 ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia Homo sapiens hg38 chr14 52051517 52054517 ERG MIB1 Enhancer Active Normal Lung UBERON:0002048 Alveolar type II cells alveolar epithelial type II cell CL:0002063 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, RT-RT-qPCR, Western blot 2023 36350827 ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia Homo sapiens hg38 chr14 52051517 52054517 ERG MIB1 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Blood UBERON:0000178 Human AML cell myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, RT-RT-qPCR, Western blot 2023 36350827 ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia Homo sapiens hg38 chr6 136564545 136567545 ERG PIK3C3 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Blood UBERON:0000178 UoCB6 umbilical cord blood hematopoietic cell CL:0001029 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, RT-RT-qPCR, Western blot 2023 36350827 ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia Homo sapiens hg38 chr6 136564545 136567545 ERG PIK3C3 Enhancer Active Normal Lung UBERON:0002048 Alveolar type I cells alveolar epithelial type I cell CL:0002062 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, RT-RT-qPCR, Western blot 2023 36350827 ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia Homo sapiens hg38 chr6 136564545 136567545 ERG PIK3C3 Enhancer Active Normal Lung UBERON:0002048 Alveolar type II cells alveolar epithelial type II cell CL:0002063 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, RT-RT-qPCR, Western blot 2023 36350827 ETV6 Deficiency Unlocks ERG-Dependent Microsatellite Enhancers to Drive Aberrant Gene Activation in B-Lymphoblastic Leukemia Homo sapiens hg38 chr6 136564545 136567545 ERG PIK3C3 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Blood UBERON:0000178 Human AML cell myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPRi, RT-RT-qPCR, Western blot 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Homo sapiens hg38 chrX 49260470 49261090 FOXP3 Enhancer Active Normal Blood UBERON:0000178 CD4+ T cells CD4-positive T cell CL:0000624 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Homo sapiens hg38 chrX 49260470 49261090 FOXP3 Enhancer Active Normal Blood UBERON:0000178 Regulatory T cells regulatory T cell CL:0000815 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Homo sapiens hg38 chrX 49260470 49261090 FOXP3 Enhancer Active Normal Blood UBERON:0000178 Conventional T cells T cell CL:0000084 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Homo sapiens hg38 chrX 49264210 49265210 FOXP3 Enhancer Active Normal Blood UBERON:0000178 CD4+ T cells CD4-positive T cell CL:0000624 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Homo sapiens hg38 chrX 49264210 49265210 FOXP3 Enhancer Active Normal Blood UBERON:0000178 Regulatory T cells regulatory T cell CL:0000815 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Homo sapiens hg38 chrX 49264210 49265210 FOXP3 Enhancer Active Normal Blood UBERON:0000178 Conventional T cells T cell CL:0000084 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Homo sapiens hg38 chrX 49265618 49268300 FOXP3 Enhancer Active Normal Blood UBERON:0000178 CD4+ T cells CD4-positive T cell CL:0000624 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Homo sapiens hg38 chrX 49265618 49268300 FOXP3 Enhancer Active Normal Blood UBERON:0000178 Regulatory T cells regulatory T cell CL:0000815 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Homo sapiens hg38 chrX 49265618 49268300 FOXP3 Enhancer Active Normal Blood UBERON:0000178 Conventional T cells T cell CL:0000084 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Homo sapiens hg38 chrX 49268807 49270673 FOXP3 Enhancer Active Normal Blood UBERON:0000178 CD4+ T cells CD4-positive T cell CL:0000624 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Homo sapiens hg38 chrX 49268807 49270673 FOXP3 Enhancer Active Normal Blood UBERON:0000178 Regulatory T cells regulatory T cell CL:0000815 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Homo sapiens hg38 chrX 49268807 49270673 FOXP3 Enhancer Active Normal Blood UBERON:0000178 Conventional T cells T cell CL:0000084 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Homo sapiens hg38 chrX 49273000 49274000 FOXP3 Enhancer Active Normal Blood UBERON:0000178 CD4+ T cells CD4-positive T cell CL:0000624 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Homo sapiens hg38 chrX 49273000 49274000 FOXP3 Enhancer Active Normal Blood UBERON:0000178 Regulatory T cells regulatory T cell CL:0000815 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Homo sapiens hg38 chrX 49273000 49274000 FOXP3 Enhancer Active Normal Blood UBERON:0000178 Conventional T cells T cell CL:0000084 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Homo sapiens hg38 chrX 49276500 49278500 FOXP3 Enhancer Active Normal Blood UBERON:0000178 CD4+ T cells CD4-positive T cell CL:0000624 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Homo sapiens hg38 chrX 49276500 49278500 FOXP3 Enhancer Active Normal Blood UBERON:0000178 Regulatory T cells regulatory T cell CL:0000815 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Homo sapiens hg38 chrX 49276500 49278500 FOXP3 Enhancer Active Normal Blood UBERON:0000178 Conventional T cells T cell CL:0000084 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2021 35122059 TNF-??-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer Homo sapiens hg38 chr1 58751000 58752500 CJUN CJUN Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 PANC-1 CVCL_0480 pancreatic ductal adenocarcinoma cell CL:0000066 TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, i4C-seq ChIP-RT-qPCR, siRNA Knockdown, JQ1 Inhibition Assay, RT-RT-qPCR, Western blot 2021 35122059 TNF-??-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer Homo sapiens hg38 chr1 58751000 58752500 CJUN CJUN Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 AsPC-1 CVCL_0152 pancreatic ductal adenocarcinoma cell CL:0000066 TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, i4C-seq ChIP-RT-qPCR, siRNA Knockdown, JQ1 Inhibition Assay, RT-RT-qPCR, Western blot 2021 35122059 TNF-??-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer Homo sapiens hg38 chr1 58751000 58752500 CJUN CJUN Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 primary PDAC cells pancreatic ductal adenocarcinoma cell CL:0000066 TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, i4C-seq ChIP-RT-qPCR, siRNA Knockdown, JQ1 Inhibition Assay, RT-RT-qPCR, Western blot 2021 35122059 TNF-??-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer Homo sapiens hg38 chr10 17275000 17276500 CJUN VIM Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 AsPC-1 CVCL_0152 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, cJUN Overexpression Assay, RT-RT-qPCR, Western blot 2021 35122059 TNF-??-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer Homo sapiens hg38 chr10 17275000 17276500 CJUN VIM Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 primary PDAC cells pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, cJUN Overexpression Assay, RT-RT-qPCR, Western blot 2020 32483258 Skeletal muscle enhancer interactions identify genes controlling whole-body metabolism Homo sapiens hg38 chr7 95608432 95609655 PDK4 Enhancer Active Normal Skeletal muscle UBERON:0001134 Human Skeletal Myotubes skeletal myotube CL:0000187 Enhancer activity assay, Chromatin interaction assay ChIP-seq, RNA-seq, Hi-C Luciferase Reporter Assay, ChIP-RT-qPCR 2020 32483258 Skeletal muscle enhancer interactions identify genes controlling whole-body metabolism Homo sapiens hg38 chr4 73725619 73726851 CXCL8 Enhancer Active Normal Skeletal muscle UBERON:0001134 Human Skeletal Myotubes skeletal myotube CL:0000187 Enhancer activity assay, Chromatin interaction assay ChIP-seq, RNA-seq, Hi-C Luciferase Reporter Assay, ChIP-RT-qPCR 2025 40781158 ALDH1A3 promotes aggressive basal-like pancreatic cancer through an AP-1/RUNX2 enhancer network Homo sapiens hg38 chr6 45296454 45506241 RUNX2 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 PANC-1 CVCL_0480 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay, TF binding assay ATAC-seq, CUT&Tag, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR, Western blot, CCK-8 Assay 2025 40781158 ALDH1A3 promotes aggressive basal-like pancreatic cancer through an AP-1/RUNX2 enhancer network Homo sapiens hg38 chr6 45296454 45506241 RUNX2 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 Pancreatic adenocarcinoma cell pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay, TF binding assay ATAC-seq, CUT&Tag, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR, Western blot, CCK-8 Assay 2020 33147212 A genetic variant controls interferon-?? gene expression in human myeloid cells by preventing C/EBP-?? binding on a conserved enhancer Homo sapiens hg38 chr9 21016991 21017491 IFNB1 Enhancer Silenced Normal Blood UBERON:0000178 Primary monocyte-derived macrophages macrophage CL:0000235 Enhancer activity assay, TF binding assay Hi-C, ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2024 38453563 KMT2C and KMT2D aberrations in breast cancer Homo sapiens hg38 chr7 128740000 128741500 TFF1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF7 cells CVCL_0031 breast carcinoma cell CL:0000646 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR 2022 36224171 Lineage-selective super enhancers mediate core regulatory circuitry during adipogenic and osteogenic differentiation of human mesenchymal stem cells Homo sapiens hg38 chr21 36759535 36828803 RUNX1 Enhancer Active Normal Bone marrow UBERON:0002371 Adipose-Derived Mesenchymal Stem Cells-01 mesenchymal stem cell CL:0000134 Functional perturbation assay, Chromatin interaction assay ChIP-seq, Hi-C CRISPR knockout, RT-RT-qPCR 2022 36301402 The Tumor Invasion Paradox in Cancer Stem Cell-Driven Solid Tumors Homo sapiens hg38 chr18 70411815 70460159 RTTN Enhancer Silenced Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 Kasumi-1 CVCL_0589 acute myeloid leukemia cell CL:0001054 Chromatin interaction assay, Functional perturbation assay Hi-C, 4C-seq, CUT&Tag, RNA-seq CRISPR Knockout, DNA FISH, RT-RT-qPCR 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; HAND2 CDK5RAP3 Enhancer Active Disease neuroblastoma MONDO:0005070 DOID:769 Adrenal gland UBERON:0002369 SK-N-BE(2) CVCL_0528 neuroblastoma cell CL:0000031 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, Hi-C, CUT&Tag, RNA-seq Luciferase Reporter Assay, 3C-RT-qPCR, CUT&RUN-RT-qPCR, RT-RT-qPCR, Western blot 2024 38636893 CDK5RAP3 is a novel super-enhancer-driven gene activated by master TFs and regulates ER-Phagy in neuroblastoma Homo sapiens hg38 chr17 47985000 47990000 MEIS2; HAND2 CDK5RAP3 Enhancer Active Disease neuroblastoma MONDO:0005070 DOID:769 Adrenal gland UBERON:0002369 SK-N-BE(2) CVCL_0528 neuroblastoma cell CL:0000031 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, Hi-C, CUT&Tag, RNA-seq Luciferase Reporter Assay, 3C-RT-qPCR, CUT&RUN-RT-qPCR, RT-RT-qPCR, Western blot 2024 39294132 Multiplex, single-cell CRISPRa screening for cell type specific regulatory elements Homo sapiens hg38 chr6 43210000 43211000 HMGA1 Enhancer Active Normal Brain UBERON:0000955 iPSC-derived excitatory neurons excitatory neuron CL:0000540 Functional perturbation assay, Enhancer activity assay scRNA-seq, ATAC-seq, ChIP-seq CRISPR Knockout, CRISPRi, qRT-PCR 2020 32493933 Activation of JUN in fibroblasts promotes pro-fibrotic programme and modulates protective immunity Homo sapiens hg38 chr3 108045000 108135000 JUN CD274 Enhancer Active Normal Lung UBERON:0002048 Primary human lung fibroblasts lung fibroblast CL:0000057 TF binding assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq, Mass Cytometry CRISPR Knockout, Flow Cytometry, qRT-PCR, Western blot 2020 32933554 Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation Homo sapiens hg38 chr1 158000000 158500000 CTCF CD1A Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat CVCL_0065 T lymphoblast CL:0002419 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay ChIP-seq, Hi-C, ATAC-seq, RNA-seq ChIP-RT-qPCR, qRT-PCR, Western blot 2021 34092790 Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes Homo sapiens hg38 chr14 37278706 37279509 ETV1 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Functional perturbation assay, Chromatin interaction assay Hi-C, DNase-seq, RNA-seq CRISPR Knockout, qRT-PCR 2021 34092790 Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes Homo sapiens hg38 chr14 37246515 37246652 ETV1 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Functional perturbation assay, Chromatin interaction assay Hi-C, DNase-seq, RNA-seq CRISPR Knockout, qRT-PCR 2023 38049665 Noncoding mutations cause super-enhancer retargeting resulting in protein synthesis dysregulation during B cell lymphoma progression Homo sapiens hg38 chr9 36980000 37150820 PAX5 SE Active Disease diffuse large B-cell lymphoma MONDO:0005042 DOID:0050746 Lymph node UBERON:0000029 SUDHL10 CVCL_1744 diffuse large B-cell lymphoma cell CL:0000945 Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, 4C-seq CRISPR Knockout, qRT-PCR, FISH 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 carcinoma MONDO:0005075 DOID:3948 Thyroid UBERON:0002046 TPC1 CVCL_6298 thyroid carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIRP-seq, RNA-seq, ChIP-seq CRISPRi, RT-RT-qPCR, RIP assay, Western blot 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 carcinoma MONDO:0005075 DOID:3948 Thyroid UBERON:0002046 MDA-T41 CVCL_UC55 thyroid carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIRP-seq, RNA-seq, ChIP-seq CRISPRi, RT-RT-qPCR, RIP assay, Western blot 2024 39107271 DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression Homo sapiens hg38 chr10 52443227 52444237 JUND; FOSL2 DKK1 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 PANC-1 CVCL_0480 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, TF binding assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, DNA pull-down assay 2024 39107271 DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression Homo sapiens hg38 chr10 52443227 52444237 JUND; FOSL2 DKK1 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 HPAC CVCL_1492 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, TF binding assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, DNA pull-down assay 2024 39107271 DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression Homo sapiens hg38 chr10 52443227 52444237 JUND; FOSL2 DKK1 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 AsPC-1 CVCL_0152 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, TF binding assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, DNA pull-down assay 2024 38454021 MYC activity at enhancers drives prognostic transcriptional programs through an epigenetic switch Homo sapiens hg38 chr7 54978916 55304142 MYC EGFR Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 BT549 (TNBC) CVCL_1082 breast carcinoma cell CL:0000646 Chromatin interaction assay, Functional perturbation assay ChIP-seq, Hi-C, RNA-seq siRNA knockdown, RT-RT-qPCR 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 carcinoma MONDO:0005075 DOID:3948 Thyroid UBERON:0002046 TPC1 CVCL_6298 thyroid carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, qRT-PCR, Western blot, CRISPR Knockout, CRISPRi 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 carcinoma MONDO:0005075 DOID:3948 Thyroid UBERON:0002046 MDA-T41 CVCL_UC55 thyroid carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, qRT-PCR, Western blot, CRISPR Knockout, CRISPRi 2020 32933554 Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation Homo sapiens hg38 chr1 158000000 158500000 CTCF; NOTCH1 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat CVCL_0065 T lymphoblast CL:0002419 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, Hi-C, ATAC-seq, RNA-seq RT-RT-qPCR, Western blot 2020 32933554 Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation Homo sapiens hg38 chr1 158000000 158500000 CTCF; NOTCH1 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Lymphoid tissue UBERON:0001745 CUTLL1 CVCL_2075 T lymphoblast CL:0002419 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, Hi-C, ATAC-seq, RNA-seq RT-RT-qPCR, Western blot 2020 32933554 Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation Homo sapiens hg38 chr1 158000000 158500000 CTCF; NOTCH1 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Primary T-ALL patient T lymphoblast CL:0002419 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, Hi-C, ATAC-seq, RNA-seq RT-RT-qPCR, Western blot 2020 32933554 Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation Homo sapiens hg38 chr1 158000000 158500000 CTCF; NOTCH1 Enhancer Active Normal Blood UBERON:0000178 Normal CD4+ T CD4-positive T cell CL:0000624 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, Hi-C, ATAC-seq, RNA-seq RT-RT-qPCR, Western blot 2021 34078608 Epigenomic landscape and 3D genome structure in pediatric high-grade glioma Homo sapiens hg38 chr2 15000000 16800000 MYCN Enhancer Active Disease diffuse intrinsic pontine glioma MONDO:0006049 DOID:0080941 Pons UBERON:0000988 DIPG cell line diffuse intrinsic pontine glioma cell CL:0000127 Chromatin interaction assay, Enhancer activity assay Hi-C, ChIP-seq, ATAC-seq, RNA-seq RT-RT-qPCR 2025 40604280 Range extender mediates long-distance enhancer activity Homo sapiens hg38 chr21 38989433 38991200 ETS2 Enhancer Active Normal Embryonic Limb Bud UBERON:0005417 Limb bud mesenchymal cells mesenchymal cell CL:0000134 Enhancer activity assay, Functional perturbation assay ATAC-seq, scATAC-seq/scRNA-seq multiome, Capture Hi-C Transgenic Reporter Assay, CRISPR Knock-in, Whole-mount in situ hybridization, Skeletal staining 2025 40604280 Range extender mediates long-distance enhancer activity Homo sapiens hg38 chr21 38989433 38991200 ETS2 Enhancer Active Normal Limb Bud UBERON:0005417 Zone of polarizing activity cells mesenchymal cell CL:0000134 Enhancer activity assay, Functional perturbation assay ATAC-seq, scATAC-seq/scRNA-seq multiome, Capture Hi-C Transgenic Reporter Assay, CRISPR Knock-in, Whole-mount in situ hybridization, Skeletal staining 2018 29339538 E6 Protein Expressed by High-Risk HPV Activates Super-Enhancers of the EGFR and c-MET Oncogenes by Destabilizing the Histone Demethylase KDM5C Homo sapiens hg38 chr7 55016139 55018139 EGFR Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 CaSki cell CVCL_1100 cervical adenocarcinoma cell CL:0000069 Enhancer functional perturbation, Chromatin interaction assay ChIP-seq, RNA-seq 3C, RT-RT-qPCR 2019 31360115 Inhibition of super enhancer downregulates the expression of KLF5 in basal-like breast cancers Homo sapiens hg38 chr13 73607397 74169928 KLF5 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 HCC1806 CVCL_1258 breast carcinoma cell CL:0000646 Functional perturbation assay, Enhancer activity assay, TF binding assay ChIP-seq CRISPRi, RT-RT-qPCR, Western blot, SRB Cell Viability Assay, Flow Cytometry Cell Cycle Analysis, EdU Incorporation Assay 2019 31360115 Inhibition of super enhancer downregulates the expression of KLF5 in basal-like breast cancers Homo sapiens hg38 chr13 73607397 74169928 KLF5 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 HCC1937 CVCL_0290 breast carcinoma cell CL:0000646 Functional perturbation assay, Enhancer activity assay, TF binding assay ChIP-seq CRISPRi, RT-RT-qPCR, Western blot, SRB Cell Viability Assay, Flow Cytometry Cell Cycle Analysis, EdU Incorporation Assay 2019 31767869 LncRNA REG1CP promotes tumorigenesis through an enhancer complex to recruit FANCJ helicase for REG3A transcription Homo sapiens hg38 chr2 79272263 79272447 REG3A Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 LIM1215 CVCL_2049 colorectal carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq, ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, EMSA, shRNA Knockdown 2019 31767869 LncRNA REG1CP promotes tumorigenesis through an enhancer complex to recruit FANCJ helicase for REG3A transcription Homo sapiens hg38 chr2 79272263 79272447 REG3A Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 HT-29 CVCL_0320 colorectal carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq, ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, EMSA, shRNA Knockdown 2019 31767869 LncRNA REG1CP promotes tumorigenesis through an enhancer complex to recruit FANCJ helicase for REG3A transcription Homo sapiens hg38 chr2 79272263 79272447 REG3A Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 SW480 CVCL_0546 colorectal carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq, ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, EMSA, shRNA Knockdown 2019 31767869 LncRNA REG1CP promotes tumorigenesis through an enhancer complex to recruit FANCJ helicase for REG3A transcription Homo sapiens hg38 chr2 79272263 79272447 REG3A Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 COLO 205 CVCL_0218 colorectal carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq, ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, EMSA, shRNA Knockdown 2019 31767869 LncRNA REG1CP promotes tumorigenesis through an enhancer complex to recruit FANCJ helicase for REG3A transcription Homo sapiens hg38 chr2 79272263 79272447 REG3A Enhancer Active Normal Colon UBERON:0001155 FHC CVCL_3806 colon epithelial cell CL:1000348 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq, ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, EMSA, shRNA Knockdown 2023 36803948 eRNA profiling uncovers the enhancer landscape of oesophageal adenocarcinoma and reveals new deregulated pathways Homo sapiens hg38 chr20 43657287 43657942 MYBL2 Enhancer Active Disease esophageal adenocarcinoma MONDO:0004973 DOID:0050861 Esophagus UBERON:0001043 OE19 CVCL_1302 esophageal adenocarcinoma cell CL:0000069 Enhancer activity assay, Functional perturbation assay ATAC-seq, RNA-seq Luciferase Reporter Assay, CRISPR knockout/CRISPRi, RT-RT-qPCR, Western blot 2023 36803948 eRNA profiling uncovers the enhancer landscape of oesophageal adenocarcinoma and reveals new deregulated pathways Homo sapiens hg38 chr20 43657287 43657942 MYBL2 Enhancer Active Disease esophageal adenocarcinoma MONDO:0004973 DOID:0050861 Esophagus UBERON:0001043 CP-A CVCL_6920 esophageal adenocarcinoma cell CL:0000069 Enhancer activity assay, Functional perturbation assay ATAC-seq, RNA-seq Luciferase Reporter Assay, CRISPR knockout/CRISPRi, RT-RT-qPCR, Western blot 2023 36632223 Enhancer RNA promotes resistance to radiotherapy in bone-metastatic prostate cancer by m6A modification Homo sapiens hg38 chr12 122502280 122506427 PSMD9 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Bone UBERON:0001474 PC3 CVCL_0035 prostate carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, TF binding assay RNA-seq, MeRIP-seq, ChIP-seq, Capture Hi-C 3C assay, CLIP, RT-RT-qPCR, Western blot 2023 36632223 Enhancer RNA promotes resistance to radiotherapy in bone-metastatic prostate cancer by m6A modification Homo sapiens hg38 chr12 122502280 122506427 PSMD9 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Bone UBERON:0001474 C4-2B CVCL_4784 prostate carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, TF binding assay RNA-seq, MeRIP-seq, ChIP-seq, Capture Hi-C 3C assay, CLIP, RT-RT-qPCR, Western blot 2023 36632223 Enhancer RNA promotes resistance to radiotherapy in bone-metastatic prostate cancer by m6A modification Homo sapiens hg38 chr12 122502280 122506427 PSMD9 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Bone UBERON:0001474 P-90 prostate carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, TF binding assay RNA-seq, MeRIP-seq, ChIP-seq, Capture Hi-C 3C assay, CLIP, RT-RT-qPCR, Western blot 2026 41651436 Targeting super-enhancer-driven MAB21L2 suppresses neuroblastoma growth and migration Homo sapiens hg38 chr13 150570000 150600000 MAB21L2 Enhancer Active Disease neuroblastoma MONDO:0005070 DOID:769 Adrenal gland UBERON:0002369 SK-N-BE(2) cells CVCL_0528 neuroblastoma cell CL:0000031 Functional perturbation assay ChIP-seq, RNA-seq Luciferase reporter assay, RT-RT-qPCR, Western blot 2026 41355963 Super-enhancer-driven core transcription factor FOXP1 delays endothelial cell senescence via phase separation-mediated SESN3 activation Homo sapiens hg38 chr3 70900000 70903000 FOXP1 Enhancer Active Normal Umbilical vein UBERON:0002066 HUVECs umbilical vein endothelial cell CL:0002615 Enhancer activity assay, Functional perturbation assay CUT&Tag-seq, ATAC-seq, RNA-seq Luciferase reporter assay, CRISPRi, RT-RT-qPCR, Western blot 2026 41355963 Super-enhancer-driven core transcription factor FOXP1 delays endothelial cell senescence via phase separation-mediated SESN3 activation Homo sapiens hg38 chr3 70904000 70907000 FOXP1 Enhancer Active Normal Umbilical vein UBERON:0002066 HUVECs umbilical vein endothelial cell CL:0002615 Enhancer activity assay, Functional perturbation assay CUT&Tag-seq, ATAC-seq, RNA-seq Luciferase reporter assay, CRISPRi, RT-RT-qPCR, Western blot 2026 41355963 Super-enhancer-driven core transcription factor FOXP1 delays endothelial cell senescence via phase separation-mediated SESN3 activation Homo sapiens hg38 chr3 70908000 70911000 FOXP1 Enhancer Active Normal Umbilical vein UBERON:0002066 HUVECs umbilical vein endothelial cell CL:0002615 Enhancer activity assay, Functional perturbation assay CUT&Tag-seq, ATAC-seq, RNA-seq Luciferase reporter assay, CRISPRi, RT-RT-qPCR, Western blot 2025 40208226 Gain-of-function enhancer variant near KCNB1 causes familial ST-depression syndrome Homo sapiens hg38 chr20 49345710 49345732 MEF2A KCNB1 Enhancer Active Normal Heart UBERON:0000948 AC16 cardiomyocytes CVCL_4U18 cardiomyocyte CL:0000746 Enhancer activity assay WGS, RNA-seq, ATAC-seq Luciferase reporter assay, CRISPRa, ChIP-RT-qPCR 2025 40890402 p300/CBP is an essential driver of pathogenic enhancer activity and gene expression in Ewing sarcoma Homo sapiens hg38 chr20 21548504 21587972 NKX2-2 Enhancer Active Disease Ewing sarcoma MONDO:0003368 DOID:3368 Bone UBERON:0001474 A673 cells CVCL_0080 Ewing sarcoma cell CL:0000050 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq CRISPR knockout, ChIP-RT-qPCR, RT-RT-qPCR 2025 40038738 Super-enhancer-hijacking RBBP7 potentiates metastasis and stemness of breast cancer via recruiting NuRD complex subunit LSD1 Homo sapiens hg38 chr11 10200000 10205000 SOX2 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF-7 cells CVCL_0031 breast carcinoma cell CL:0000646 Super-enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq CRISPR knockout, ChIP-RT-qPCR, RT-RT-qPCR 2025 40668918 Modulating immune cell fate and inflammation through CRISPR-mediated DNA methylation editing Homo sapiens hg38 chr2 113127450 113127690 CEBPA IL1B Enhancer Active Normal Blood UBERON:0000178 BLaER cells CVCL_UI64 B cell CL:0000945 Enhancer activity assay, Functional perturbation assay WGBS, ATAC-seq, ChIP-seq CRISPR knockout 2025 40164603 Enhancer RNA transcription pinpoints functional genetic variants linked to asthma Homo sapiens hg38 chr1 213425381 213425881 NR3C1 GCNT1 Enhancer Active Normal Lung UBERON:0002048 BEAS-2B cells CVCL_0168 bronchial epithelial cell CL:0002591 Enhancer activity assay, Functional perturbation assay GRO-seq, ChIP-seq CRISPR knockout 2025 40067892 BTSCs exosomes derived NamiRNA-enhancer network of miR-151a-3p mediates a positive feedback loop and promotes the progression of glioma via FAK phosphorylation Homo sapiens hg38 chr5 58919038 58919746 PDE4D Enhancer Active Disease glioblastoma MONDO:0005142 DOID:3070 Brain UBERON:0000955 U251 glioma cells CVCL_0021 glioblastoma cell CL:0000127 Enhancer activity assay, Functional perturbation assay RNA-seq Luciferase reporter assay, CRISPR knockout, RT-RT-qPCR, Western blot 2025 40067892 BTSCs exosomes derived NamiRNA-enhancer network of miR-151a-3p mediates a positive feedback loop and promotes the progression of glioma via FAK phosphorylation Homo sapiens hg38 chr5 58919038 58919746 PDE4D Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293T cells CVCL_0063 embryonic kidney cell CL:0002139 Enhancer activity assay, Functional perturbation assay RNA-seq Luciferase reporter assay, CRISPR knockout, RT-RT-qPCR, Western blot 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 multiple myeloma MONDO:0005178 DOID:9538 Blood UBERON:0000178 Multiple myeloma cells plasma cell CL:0000945 Enhancer activity assay ATAC-seq, ChIP-seq, CUT&Tag CRISPR knockout, CRISPRi, ChIP-RT-qPCR, FISH 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 multiple myeloma MONDO:0005178 DOID:9538 Blood UBERON:0000178 Multiple myeloma cells plasma cell CL:0000945 Enhancer activity assay ATAC-seq, ChIP-seq, CUT&Tag CRISPR knockout, CRISPRi, ChIP-RT-qPCR, FISH 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 multiple myeloma MONDO:0005178 DOID:9538 Blood UBERON:0000178 Multiple myeloma cells plasma cell CL:0000945 Enhancer activity assay ATAC-seq, ChIP-seq, CUT&Tag CRISPR knockout, CRISPRi, ChIP-RT-qPCR, FISH 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 multiple myeloma MONDO:0005178 DOID:9538 Blood UBERON:0000178 Multiple myeloma cells plasma cell CL:0000945 Enhancer activity assay ATAC-seq, ChIP-seq, CUT&Tag CRISPR knockout, CRISPRi, ChIP-RT-qPCR, FISH 2025 40220379 Bclaf1 mediates super-enhancer-driven activation of POLR2A to enhance chromatin accessibility in nitrosamine-induced esophageal carcinogenesis Homo sapiens hg38 chr17 40250000 40251000 BCLAF1 POLR2A Enhancer Active Disease esophageal squamous cell carcinoma MONDO:0005082 DOID:3748 Esophagus UBERON:0001043 MNNG-M cells CVCL_1360 esophageal squamous cell carcinoma cell CL:0000069 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, CUT&Tag, ChIP-seq Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2025 40220379 Bclaf1 mediates super-enhancer-driven activation of POLR2A to enhance chromatin accessibility in nitrosamine-induced esophageal carcinogenesis Homo sapiens hg38 chr17 40250000 40251000 BCLAF1 POLR2A Enhancer Active Normal Esophagus UBERON:0001043 Het-1A cells CVCL_3703 esophageal epithelial cell CL:0000069 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, CUT&Tag, ChIP-seq Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2025 40220379 Bclaf1 mediates super-enhancer-driven activation of POLR2A to enhance chromatin accessibility in nitrosamine-induced esophageal carcinogenesis Homo sapiens hg38 chr17 40250000 40251000 BCLAF1 POLR2A Enhancer Active Disease esophageal squamous cell carcinoma MONDO:0005082 DOID:3748 Esophagus UBERON:0001043 KYSE-150 cells CVCL_1341 esophageal squamous cell carcinoma cell CL:0000069 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, CUT&Tag, ChIP-seq Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2025 40220379 Bclaf1 mediates super-enhancer-driven activation of POLR2A to enhance chromatin accessibility in nitrosamine-induced esophageal carcinogenesis Homo sapiens hg38 chr17 40252000 40253000 BCLAF1 POLR2A Enhancer Active Disease esophageal squamous cell carcinoma MONDO:0005082 DOID:3748 Esophagus UBERON:0001043 MNNG-M cells CVCL_1360 esophageal squamous cell carcinoma cell CL:0000069 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, CUT&Tag, ChIP-seq Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2025 40220379 Bclaf1 mediates super-enhancer-driven activation of POLR2A to enhance chromatin accessibility in nitrosamine-induced esophageal carcinogenesis Homo sapiens hg38 chr17 40252000 40253000 BCLAF1 POLR2A Enhancer Active Normal Esophagus UBERON:0001043 Het-1A cells CVCL_3703 esophageal epithelial cell CL:0000069 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, CUT&Tag, ChIP-seq Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2025 40220379 Bclaf1 mediates super-enhancer-driven activation of POLR2A to enhance chromatin accessibility in nitrosamine-induced esophageal carcinogenesis Homo sapiens hg38 chr17 40252000 40253000 BCLAF1 POLR2A Enhancer Active Disease esophageal squamous cell carcinoma MONDO:0005082 DOID:3748 Esophagus UBERON:0001043 KYSE-150 cells CVCL_1341 esophageal squamous cell carcinoma cell CL:0000069 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, CUT&Tag, ChIP-seq Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2020 32499651 A distal enhancer at risk locus 11q135 promotes suppression of colitis by Treg cells Homo sapiens hg38 chr11 76586431 76600121 STAT5 LRRC32 Enhancer Active Normal Colon UBERON:0001155 Primary Treg cells regulatory T cell CL:0000815 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, HiChIP, hQTL, eQTL CRISPRa, ChIP-RT-qPCR, RT-RT-qPCR, Flow Cytometry 2025 40604280 Range extender mediates long-distance enhancer activity Homo sapiens hg38 chr16 51623658 51623898 LHX2; LHX9; LEF1 SHH Enhancer Active Normal Embryonic Limb Bud UBERON:0005417 Limb bud mesenchymal cells mesenchymal cell CL:0000134 TF binding assay, Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq Transgenic Reporter Assay, CRISPR Knockout, CRISPR Knock-in, RT-RT-qPCR, Whole-mount in situ hybridization, Skeletal staining, EMSA 2025 40604280 Range extender mediates long-distance enhancer activity Homo sapiens hg38 chr16 51623658 51623898 LHX2; LHX9; LEF1 SHH Enhancer Active Normal Limb Bud UBERON:0005417 Zone of polarizing activity cells mesenchymal cell CL:0000134 TF binding assay, Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq Transgenic Reporter Assay, CRISPR Knockout, CRISPR Knock-in, RT-RT-qPCR, Whole-mount in situ hybridization, Skeletal staining, EMSA 2025 40604280 Range extender mediates long-distance enhancer activity Homo sapiens hg38 chr16 51623899 51624805 SALL1 Enhancer Active Normal Embryonic Limb Bud UBERON:0005417 Limb bud mesenchymal cells mesenchymal cell CL:0000134 Enhancer activity assay, Functional perturbation assay ATAC-seq, scATAC-seq/scRNA-seq multiome, Capture Hi-C Transgenic Reporter Assay, CRISPR Knock-in, Whole-mount in situ hybridization, RT-RT-qPCR 2025 40604280 Range extender mediates long-distance enhancer activity Homo sapiens hg38 chr16 51623899 51624805 SALL1 Enhancer Active Normal Limb Bud UBERON:0005417 Zone of polarizing activity cells mesenchymal cell CL:0000134 Enhancer activity assay, Functional perturbation assay ATAC-seq, scATAC-seq/scRNA-seq multiome, Capture Hi-C Transgenic Reporter Assay, CRISPR Knock-in, Whole-mount in situ hybridization, RT-RT-qPCR 2025 40433695 Super-Enhancer-Driven HCG20 Promotes Pulmonary Hypertension Through U2AF2 Splicing Homo sapiens hg38 chr6 31350000 31355000 USF2 HCG20 Enhancer Active Normal Lung UBERON:0002048 Human Pulmonary Artery Endothelial Cells pulmonary artery endothelial cell CL:1001567 Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq ChIP-RT-qPCR, CRISPR Knockout, RT-RT-qPCR 2024 38592784 Intergenic sequences harboring potential enhancer elements contribute to Axenfeld-Rieger syndrome by regulating PITX2 Homo sapiens hg38 chr4 111397892 111402926 PITX2 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2024 38592784 Intergenic sequences harboring potential enhancer elements contribute to Axenfeld-Rieger syndrome by regulating PITX2 Homo sapiens hg38 chr4 111397892 111402926 PITX2 Enhancer Active Normal Sclera UBERON:0001773 Human embryonic scleral cells scleral fibroblast CL:0000057 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2024 39606421 Single cell variant to enhancer to gene map for coronary artery disease Homo sapiens hg38 chr15 78750919 78751419 CTCF ADAMTS7 Enhancer Active Normal Artery UBERON:0001628 Human Coronary Artery Smooth Muscle Cells (HCASMC) coronary artery smooth muscle cell CL:0000192 TF binding, Chromatin interaction Hi-C, ChIP-seq, ATAC-seq, RNA-seq EMSA 2021 34078608 Epigenomic landscape and 3D genome structure in pediatric high-grade glioma Homo sapiens hg38 chr21 32900000 33260000 OLIG2 OLIG2 Enhancer Active Disease diffuse intrinsic pontine glioma MONDO:0006049 DOID:0080941 Pons UBERON:0000988 Human diffuse intrinsic pontine glioma cell diffuse intrinsic pontine glioma cell CL:0000127 Chromatin interaction assay, Enhancer activity assay, Functional perturbation assay Hi-C, ChIP-seq, ATAC-seq, RNA-seq RT-RT-qPCR, Western blot 2022 34937944 Targeting SWI/SNF ATPases in enhancer-addicted prostate cancer Homo sapiens hg38 chrX 66800000 67800000 AR AR SE Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 Human prostate carcinoma cell prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq, HiChIP qRT-PCR, Western blot, Immunohistochemistry, Cell Viability Assay, In Vivo Xenograft Assay 2020 32284612 Therapeutic base editing of human hematopoietic stem cells Homo sapiens hg38 chr2 60722150 60722350 GATA1 BCL11A Enhancer Active Normal Bone Marrow UBERON:0002371 CD34+ hematopoietic stem/progenitor cells hematopoietic stem cell CL:0001029 Enhancer activity assay, Functional perturbation assay, TF binding assay RNA-seq, ChIP-seq CRISPR Knockout, qRT-PCR, Flow Cytometry 2025 40404660 Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity Homo sapiens hg38 chr1 97306000 97307500 POU4F3 LACZ Enhancer Active Normal Brain UBERON:0000955 iPSC-derived excitatory neurons excitatory neuron CL:0000540 Enhancer activity assay, TF binding assay ATAC-seq, ChIP-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2025 40404660 Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity Homo sapiens hg38 chr5 1230131 1231631 NFYB LACZ Enhancer Active Normal Brain UBERON:0000955 iPSC-derived excitatory neurons excitatory neuron CL:0000540 Enhancer activity assay, TF binding assay ATAC-seq, ChIP-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2025 40404660 Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity Homo sapiens hg38 chr6 156951500 156952500 NR2F1 LACZ Enhancer Active Normal Brain UBERON:0000955 iPSC-derived excitatory neurons excitatory neuron CL:0000540 Enhancer activity assay, TF binding assay ATAC-seq, ChIP-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2025 40404660 Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity Homo sapiens hg38 chr7 5409000 5410500 SP2 LACZ Enhancer Active Normal Brain UBERON:0000955 iPSC-derived excitatory neurons excitatory neuron CL:0000540 Enhancer activity assay, TF binding assay ATAC-seq, ChIP-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2025 40404660 Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity Homo sapiens hg38 chr9 75995000 75996500 CTCF LACZ Enhancer Active Normal Brain UBERON:0000955 iPSC-derived excitatory neurons excitatory neuron CL:0000540 Enhancer activity assay, TF binding assay ATAC-seq, ChIP-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2025 39870618 Genetic coupling of enhancer activity and connectivity in gene expression control Homo sapiens hg38 chr4 76816143 76816143 NAAA Enhancer Active Normal Blood UBERON:0000178 Primary CD14+ monocytes CD14-positive monocyte CL:0001053 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Capture Hi-C, ATAC-seq, RNA-seq, 4C-seq CRISPRi 2025 39870618 Genetic coupling of enhancer activity and connectivity in gene expression control Homo sapiens hg38 chr14 24527672 24527672 CTCF PCK2 Enhancer Active Normal Blood UBERON:0000178 Primary CD14+ monocytes CD14-positive monocyte CL:0001053 Chromatin interaction assay, TF binding assay Capture Hi-C, ATAC-seq, RNA-seq, ChIP-seq (CTCF), 4C-seq qRT-PCR, and ChIP-qPCR 2025 39870618 Genetic coupling of enhancer activity and connectivity in gene expression control Homo sapiens hg38 chr15 39598843 39598843 THBS1 Enhancer Active Normal Blood UBERON:0000178 Primary CD14+ monocytes CD14-positive monocyte CL:0001053 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Capture Hi-C, ATAC-seq, RNA-seq, 4C-seq CRISPRi 2025 39870618 Genetic coupling of enhancer activity and connectivity in gene expression control Homo sapiens hg38 chr15 39607442 39607442 THBS1 Enhancer Active Normal Blood UBERON:0000178 Primary CD14+ monocytes CD14-positive monocyte CL:0001053 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Capture Hi-C, ATAC-seq, RNA-seq, 4C-seq CRISPRi 2023 37945900 Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma Homo sapiens hg38 chr8 127330655 127330840 MYC SE Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 D458 CVCL_1160 medulloblastoma cell CL:0000127 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay Hi-C, ATAC-seq, RNA-seq CRISPRi, qRT-PCR, FISH 2023 37945900 Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma Homo sapiens hg38 chr8 127330840 127330927 MYC SE Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 D458 CVCL_1160 medulloblastoma cell CL:0000127 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay Hi-C, ATAC-seq, RNA-seq CRISPRi, qRT-PCR, FISH 2023 37945900 Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma Homo sapiens hg38 chr8 127330927 127331000 MYC SE Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Brain UBERON:0000955 D458 CVCL_1160 medulloblastoma cell CL:0000127 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay Hi-C, ATAC-seq, RNA-seq CRISPRi, qRT-PCR, FISH 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 EGFR SE Active Disease nasopharyngeal carcinoma MONDO:0005350 DOID:9260 Nasopharynx UBERON:0001729 S18 CVCL_6847 nasopharyngeal carcinoma cell CL:0000069 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq CRISPR Knockout, qRT-PCR, Western blot 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:0005070 DOID:769 Adrenal gland UBERON:0002369 KELLY CVCL_1375 neuroblastoma cell CL:0000031 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq ChIP-RT-qPCR, CRISPR Knockout, qRT-PCR, Western blot 2024 38992040 The transcriptional co-repressor Runx1t1 is essential for MYCN-driven neuroblastoma tumorigenesis Homo sapiens hg38 chr4 13816600 13816900 RUNX1T1 Enhancer Active Disease neuroblastoma MONDO:0005070 DOID:769 Adrenal gland UBERON:0002369 KELLY CVCL_1375 neuroblastoma cell CL:0000031 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq ChIP-RT-qPCR, CRISPR Knockout, qRT-PCR, Western blot 2025 41028522 HSF1-DBC1 axis drives prostate cancer progression by activating a metastatic transcriptional program Homo sapiens hg38 chr22 24114000 24116000 HSF1 MMP11 SE Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 SM1 (mCRPC cell line) prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq CRISPR Knockout, qRT-PCR, Western blot, Transwell Migration Assay, Transwell Invasion Assay 2022 35039581 Targeting of non-coding RNAs encoded by novel MYC enhancers inhibits the proliferation of human hepatic carcinoma cells in vitro Homo sapiens hg38 chr8 128556457 128556814 MYC Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 Huh7 CVCL_0336 hepatocellular carcinoma cell CL:0000182 Functional perturbation assay ChIP-seq, GRO-seq CRISPR Knockout, qRT-PCR 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:2394 Ovary UBERON:0000992 OVCAR5 CVCL_0484 ovarian carcinoma cell CL:0000069 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq ChIP-RT-qPCR, CRISPR-dCas9, qRT-PCR, Western blot 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 adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 A-549 CVCL_0023 lung adenocarcinoma cell CL:0001069 Enhancer activity assay, TF binding assay ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR 2025 39870618 Genetic coupling of enhancer activity and connectivity in gene expression control Homo sapiens hg38 chr15 89000000 89002500 ABHD2 Enhancer Active Normal Blood UBERON:0000178 Primary monocytes monocyte CL:0000576 Enhancer activity assay, Chromatin interaction assay ATAC-seq, Capture Hi-C, RNA-seq CRISPRi, qRT-PCR 2024 39107271 DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression Homo sapiens hg38 chr10 52443566 52444237 AP1 DKK1 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 PANC-1 CVCL_0480 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay ChIP-seq, ATAC-seq Luciferase Reporter Assay 2024 39107271 DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression Homo sapiens hg38 chr10 52443566 52444237 AP1 DKK1 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 HPAC CVCL_1492 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay ChIP-seq, ATAC-seq Luciferase Reporter Assay 2024 39107271 DKK1-SE recruits AP1 to activate the target gene DKK1 thereby promoting pancreatic cancer progression Homo sapiens hg38 chr10 52443566 52444237 AP1 DKK1 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 AsPC-1 CVCL_0152 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay ChIP-seq, ATAC-seq Luciferase Reporter Assay 2024 38454021 MYC activity at enhancers drives prognostic transcriptional programs through an epigenetic switch Homo sapiens hg38 chr1 13820000 13840000 MYC PRDM2 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 BT549 (TNBC) CVCL_1082 breast carcinoma cell CL:0000646 TF binding assay, Gene expression correlation ChIP-seq, ATAC-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2024 39012147 Super-enhancer-driven FOSL1-TCOF1 axis promotes triple-negative breast cancer progression Homo sapiens hg38 chr5 171390000 171400000 FOSL1 TCOF1 SE Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MDA-MB-231 CVCL_0062 breast carcinoma cell CL:0000646 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, qRT-PCR, Western blot 2021 35122059 TNF-??-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer Homo sapiens hg38 chr1 58765000 58766500 CJUN CJUN Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 PANC-1 CVCL_0480 pancreatic ductal adenocarcinoma cell CL:0000066 TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq ChIP-RT-qPCR, siRNA Knockdown, JQ1 Inhibition Assay, RT-RT-qPCR, Western blot 2021 35122059 TNF-??-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer Homo sapiens hg38 chr1 58765000 58766500 CJUN CJUN Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 AsPC-1 CVCL_0152 pancreatic ductal adenocarcinoma cell CL:0000066 TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq ChIP-RT-qPCR, siRNA Knockdown, JQ1 Inhibition Assay, RT-RT-qPCR, Western blot 2021 35122059 TNF-??-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer Homo sapiens hg38 chr1 58765000 58766500 CJUN CJUN Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 primary PDAC cells pancreatic ductal adenocarcinoma cell CL:0000066 TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq ChIP-RT-qPCR, siRNA Knockdown, JQ1 Inhibition Assay, RT-RT-qPCR, Western blot 2021 35122059 TNF-??-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer Homo sapiens hg38 chr1 58770000 58771500 CJUN CJUN Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 PANC-1 CVCL_0480 pancreatic ductal adenocarcinoma cell CL:0000066 TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq ChIP-RT-qPCR, siRNA Knockdown, JQ1 Inhibition Assay, RT-RT-qPCR, Western blot 2021 35122059 TNF-??-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer Homo sapiens hg38 chr1 58770000 58771500 CJUN CJUN Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 AsPC-1 CVCL_0152 pancreatic ductal adenocarcinoma cell CL:0000066 TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq ChIP-RT-qPCR, siRNA Knockdown, JQ1 Inhibition Assay, RT-RT-qPCR, Western blot 2021 35122059 TNF-??-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer Homo sapiens hg38 chr1 58770000 58771500 CJUN CJUN Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 primary PDAC cells pancreatic ductal adenocarcinoma cell CL:0000066 TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq ChIP-RT-qPCR, siRNA Knockdown, JQ1 Inhibition Assay, RT-RT-qPCR, Western blot 2021 35122059 TNF-??-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer Homo sapiens hg38 chr17 31254200 31255700 CJUN CCL2 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 PANC-1 CVCL_0480 pancreatic ductal adenocarcinoma cell CL:0000066 TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq ChIP-RT-qPCR, siRNA Knockdown, RT-RT-qPCR, Western blot, ELISA 2021 35122059 TNF-??-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer Homo sapiens hg38 chr17 31254200 31255700 CJUN CCL2 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 AsPC-1 CVCL_0152 pancreatic ductal adenocarcinoma cell CL:0000066 TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq ChIP-RT-qPCR, siRNA Knockdown, RT-RT-qPCR, Western blot, ELISA 2021 35122059 TNF-??-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer Homo sapiens hg38 chr17 31254200 31255700 CJUN CCL2 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 primary PDAC cells pancreatic ductal adenocarcinoma cell CL:0000066 TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq ChIP-RT-qPCR, siRNA Knockdown, RT-RT-qPCR, Western blot, ELISA 2021 35122059 TNF-??-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer Homo sapiens hg38 chr17 31255800 31256300 CJUN CCL2 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 PANC-1 CVCL_0480 pancreatic ductal adenocarcinoma cell CL:0000066 TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq ChIP-RT-qPCR, siRNA Knockdown, RT-RT-qPCR, Western blot, ELISA 2021 35122059 TNF-??-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer Homo sapiens hg38 chr17 31255800 31256300 CJUN CCL2 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 AsPC-1 CVCL_0152 pancreatic ductal adenocarcinoma cell CL:0000066 TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq ChIP-RT-qPCR, siRNA Knockdown, RT-RT-qPCR, Western blot, ELISA 2021 35122059 TNF-??-producing macrophages determine subtype identity and prognosis via AP1 enhancer reprogramming in pancreatic cancer Homo sapiens hg38 chr17 31255800 31256300 CJUN CCL2 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 primary PDAC cells pancreatic ductal adenocarcinoma cell CL:0000066 TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq ChIP-RT-qPCR, siRNA Knockdown, RT-RT-qPCR, Western blot, ELISA 2018 29364907 HPV integration hijacks and multimerizes a cellular enhancer to generate a viral-cellular super-enhancer that drives high viral oncogene expression Homo sapiens hg38 chr2 28389994 28391994 FOSL2 Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 Cervical-derived cell line 20861 cervical carcinoma cell CL:0000069 Enhancer functional characterization, Chromatin interaction assay ChIP-seq, RNA-seq 3C, ChIP-RT-qPCR, FISH, Immunofluorescence, RT-RT-qPCR 2018 29162563 FOXF1 Defines the Core-Regulatory Circuitry in Gastrointestinal Stromal Tumor Homo sapiens hg38 chr16 86507790 86509790 FOXF1 Enhancer Active Disease gastrointestinal stromal tumor MONDO:0005047 DOID:9253 Gastrointestinal tract UBERON:0005408 Gastrointestinal stromal tumor cells gastrointestinal stromal tumor cell CL:0000066 Super-enhancer regulatory network analysis, Chromatin interaction assay ChIP-seq, ATAC-seq 3C, ChIP-RT-qPCR, RT-RT-qPCR 2017 28774779 Extensive and functional overlap of the STAT6 and RXR cistromes in the active enhancer repertoire of human CD14+ monocyte derived differentiating macrophages Homo sapiens hg38 chr12 57092763 57094763 STAT6 STAT6 Enhancer Active Normal Blood UBERON:0000178 Monocyte-derived macrophages macrophage CL:0000235 Enhancer cistrome analysis, Chromatin interaction assay ChIP-seq, RNA-seq 3C, RT-RT-qPCR 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 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR 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 BIRC2 Enhancer Active Disease nasopharyngeal carcinoma MONDO:0005350 DOID:9260 Nasopharynx UBERON:0008338 5-8F CVCL_6846 nasopharyngeal carcinoma cell CL:0000069 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 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 BIRC2 Enhancer Active Disease nasopharyngeal carcinoma MONDO:0005350 DOID:9260 Nasopharynx UBERON:0008338 HNE1 CVCL_6845 nasopharyngeal carcinoma cell CL:0000069 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2025 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:0005020 DOID:5409 Lung UBERON:0002048 H446 cells CVCL_0049 small cell lung carcinoma cell CL:0000066 Super-enhancer activity assay ChIP-seq, ATAC-seq Luciferase reporter assay, RT-RT-qPCR 2025 40216980 Dynamic interaction of MYC enhancer RNA with YEATS2 protein regulates MYC gene transcription in pancreatic cancer Homo sapiens hg38 chr8 127247000 127248000 MYC Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 MIAPaCa-2 cells CVCL_0428 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay RNA-seq, ChIP-seq, ATAC-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot, shRNA knockdown 2025 40216980 Dynamic interaction of MYC enhancer RNA with YEATS2 protein regulates MYC gene transcription in pancreatic cancer Homo sapiens hg38 chr8 127247000 127248000 MYC Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 AsPC-1 cells CVCL_0152 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay RNA-seq, ChIP-seq, ATAC-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot, shRNA knockdown 2025 41293823 Functional Genomics Link REST to Endothelial Plasticity and Atherosclerosis Homo sapiens hg38 chr1 100690100 100690600 REST SELE Enhancer Silenced Normal Aorta UBERON:0000947 HAECs CVCL_UA48 aortic endothelial cell CL:0002546 Enhancer activity assay ChIP-seq, CUT&Tag, RNA-seq Luciferase reporter assay 2019 30620726 Single-nucleotide human disease mutation inactivates a blood-regenerative GATA2 enhancer Homo sapiens hg38 chr3 128191800 128192300 GATA2 Enhancer Silenced Normal Bone Marrow UBERON:0002371 Hematopoietic stem/progenitor cells hematopoietic stem cell CL:0001029 Enhancer activity assay, Functional perturbation assay RNA-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR 2022 35849129 Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer-promoter interactions Homo sapiens hg38 chr11 5225000 5226000 HBG1 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 Functional perturbation assay CUT&RUN CRISPR Knockout, CRISPRi, RT-RT-qPCR, 3C-RT-qPCR, Western blot 2022 35849129 Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer-promoter interactions Homo sapiens hg38 chr11 5225000 5226000 HBG1 Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Functional perturbation assay CUT&RUN CRISPR Knockout, CRISPRi, RT-RT-qPCR, 3C-RT-qPCR, Western blot 2022 35849129 Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer-promoter interactions Homo sapiens hg38 chr11 5225000 5226000 HBG1 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional perturbation assay CUT&RUN CRISPR Knockout, CRISPRi, RT-RT-qPCR, 3C-RT-qPCR, Western blot 2022 35849129 Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer-promoter interactions Homo sapiens hg38 chr11 5225000 5226000 HBG1 Enhancer Active Disease osteosarcoma MONDO:0005087 DOID:3347 Bone UBERON:0001474 SaOS-2 CVCL_0548 osteosarcoma cell CL:0000062 Functional perturbation assay CUT&RUN CRISPR Knockout, CRISPRi, RT-RT-qPCR, 3C-RT-qPCR, Western blot 2025 40140585 Genome-wide CRISPR screen in human T cells reveals regulators of FOXP3 Homo sapiens hg38 chrX 49238000 49239000 RBPJ FOXP3 Enhancer Silenced Normal Blood UBERON:0000178 Primary CD4+ Treg cells CD4-positive regulatory T cell CL:0000815 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, EMSA, CRISPRi 2024 38110836 Engrailed-1 promotes pancreatic cancer metastasis Homo sapiens hg38 chr2 11000000 11002000 EN1 EN1 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 CFPAC1 CVCL_0019 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR 2024 38994563 SMCHD1 activates genes required for expansion of human myoblasts Homo sapiens hg38 chr12 51000000 51001000 MYF5 Enhancer Active Normal Skeletal muscle UBERON:0001134 Myoblast cells myoblast CL:0000056 Enhancer activity assay RNA-seq, ChIP-seq Luciferase Reporter Assay, RT-RT-qPCR 2024 39122682 Super-enhancer acquisition drives PPP1R15B expression in multiple myeloma Homo sapiens hg38 chr1 204379236 204380236 CEBPB PPP1R15B Enhancer Active Disease multiple myeloma MONDO:0005178 DOID:9538 Bone Marrow UBERON:0002371 NCI-H929 cells CVCL_1600 plasma cell CL:0000945 Super enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq, HiChIP Luciferase Reporter Assay, ChIP-RT-qPCR 2024 38513139 RUNX1 C-terminal mutations impair blood cell differentiation by perturbing specific enhancer-promoter networks Homo sapiens hg38 chr8 128740000 128750000 RUNX1; RUNX1R320*; FOXK2 MYC Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, GRID-seq, RNA-seq CUT&RUN-RT-qPCR, shRNA Knockdown, RT-RT-qPCR, Western blot 2021 34040254 Enhancer release and retargeting activates disease-susceptibility genes Homo sapiens hg38 chr9 37100000 37102000 PAX5 Enhancer Active Normal Embryonic Kidney UBERON:0002113 293T CVCL_0063 embryonic kidney cell CL:0002139 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay Hi-C, ChIA-PET, GRO-seq, RNA-seq CRISPRi, RT-RT-qPCR, 4C-seq 2021 34040254 Enhancer release and retargeting activates disease-susceptibility genes Homo sapiens hg38 chr8 127750000 127752000 MYC Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF-7 CVCL_0031 breast carcinoma cell CL:0000646 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay Hi-C, ChIA-PET, GRO-seq, RNA-seq CRISPRi, RT-RT-qPCR 2021 34078608 Epigenomic landscape and 3D genome structure in pediatric high-grade glioma Homo sapiens hg38 chr15 56000000 58000000 TCF12 TCF12 Enhancer Active Disease diffuse intrinsic pontine glioma MONDO:0006049 DOID:0080941 Pons UBERON:0000988 Human diffuse intrinsic pontine glioma cell diffuse intrinsic pontine glioma cell CL:0000127 Chromatin interaction assay, Enhancer activity assay, Copy number variation analysis Hi-C, ChIP-seq, RNA-seq RT-RT-qPCR 2021 34078608 Epigenomic landscape and 3D genome structure in pediatric high-grade glioma Homo sapiens hg38 chr18 59350000 59950000 FOSL2 CCBE1 Enhancer Active Disease glioblastoma MONDO:0005142 DOID:3070 Pons UBERON:0000988 Human glioblastoma cell glioblastoma cell CL:0000127 Chromatin interaction assay, Enhancer activity assay Hi-C, ChIP-seq, RNA-seq RT-RT-qPCR 2021 33453283 Androglobin gene expression patterns and FOXJ1-dependent regulation indicate its functional association with ciliogenesis Homo sapiens hg38 chr6 146700000 146701000 ADGB Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 Human breast adenocarcinoma cell breast adenocarcinoma cell CL:0000646 Enhancer activity assay ChIP-seq Luciferase Reporter Assay 2021 33453283 Androglobin gene expression patterns and FOXJ1-dependent regulation indicate its functional association with ciliogenesis Homo sapiens hg38 chr6 146775000 146776000 ADGB Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 Human breast adenocarcinoma cell breast adenocarcinoma cell CL:0000646 Enhancer activity assay ChIP-seq Luciferase Reporter Assay 2023 37346447 STAT3-Mediated Promoter-Enhancer Interaction Up-Regulates Inhibitor of DNA Binding 1 (ID1) to Promote Colon Cancer Progression Homo sapiens hg38 chr20 31599000 31602000 ID1 Enhancer Silenced Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Putative enhancer screening ChIP-seq, GRO-seq Dual-luciferase reporter assay 2023 37346447 STAT3-Mediated Promoter-Enhancer Interaction Up-Regulates Inhibitor of DNA Binding 1 (ID1) to Promote Colon Cancer Progression Homo sapiens hg38 chr20 31599000 31602000 ID1 Enhancer Silenced Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 LoVo CVCL_0399 colorectal carcinoma cell CL:0000066 Putative enhancer screening ChIP-seq, GRO-seq Dual-luciferase reporter assay 2023 38040699 SMARCB1 loss activates patient-specific distal oncogenic enhancers in malignant rhabdoid tumors Homo sapiens hg38 chr8 126800000 126900000 MYC SE Active Disease malignant rhabdoid tumor MONDO:0018669 DOID:0050776 Kidney UBERON:0002113 MRT patient-derived organoids (P103) malignant rhabdoid tumor cell CL:0000066 Chromatin interaction assay, Enhancer activity assay, TF binding assay, Functional perturbation assay Hi-C, 3C-seq, ATAC-seq, ChIP-seq, RNA-seq 3C-RT-qPCR, qRT-PCR, Western blot 2023 38040699 SMARCB1 loss activates patient-specific distal oncogenic enhancers in malignant rhabdoid tumors Homo sapiens hg38 chr8 128840000 128890000 MYC SE Active Disease malignant rhabdoid tumor MONDO:0018669 DOID:0050776 Kidney UBERON:0002113 MRT patient-derived organoids (P103) malignant rhabdoid tumor cell CL:0000066 Chromatin interaction assay, Enhancer activity assay, TF binding assay, Functional perturbation assay Hi-C, 3C-seq, ATAC-seq, ChIP-seq, RNA-seq 3C-RT-qPCR, qRT-PCR, Western blot 2023 38040699 SMARCB1 loss activates patient-specific distal oncogenic enhancers in malignant rhabdoid tumors Homo sapiens hg38 chr8 129440000 129740000 MYC SE Active Disease malignant rhabdoid tumor MONDO:0018669 DOID:0050776 Kidney UBERON:0002113 MRT patient-derived organoids (P60) malignant rhabdoid tumor cell CL:0000066 Chromatin interaction assay, Enhancer activity assay, TF binding assay, Functional perturbation assay 3C-seq, ATAC-seq, ChIP-seq, RNA-seq 3C-RT-qPCR, qRT-PCR, Western blot 2025 40765356 Epigenetic remodeling and 3D chromatin reorganization governed by NKX2-1 drive neuroendocrine prostate cancer Homo sapiens hg38 chr12 102818723 103538731 ASCL1 ASCL1 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LuCaP93 PDX patient-derived xenograft prostate carcinoma cell CL:0000066 Chromatin interaction assay, Functional perturbation assay Hi-C, ChIP-seq, RNA-seq siRNA Knockdown, qRT-PCR, Western blot 2024 38454021 MYC activity at enhancers drives prognostic transcriptional programs through an epigenetic switch Homo sapiens hg38 chr20 54119731 54198946 MYC; ESR1 CYP24A1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF7 (ER+) CVCL_0031 breast carcinoma cell CL:0000646 TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Fulvestrant treatment, RT-RT-qPCR 2023 37563118 Enhancer remodeling activates NOTCH3 signaling to confer chemoresistance in advanced nasopharyngeal carcinoma Homo sapiens hg38 chr1 39000000 39645000 HEYL Enhancer Active Disease nasopharyngeal carcinoma MONDO:0005350 DOID:9260 Nasopharynx UBERON:0001714 CNE-2 CVCL_6889 nasopharyngeal carcinoma cell CL:0000069 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2025 40405227 HBV sequence integrated to enhancer acting as oncogenic driver epigenetically promotes hepatocellular carcinoma development Homo sapiens hg38 chr1 207851706 207940358 CD34 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 Huh7 CVCL_0336 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2025 40405227 HBV sequence integrated to enhancer acting as oncogenic driver epigenetically promotes hepatocellular carcinoma development Homo sapiens hg38 chr17 50132536 50229638 COL1A1 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 Huh7 CVCL_0336 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2025 40405227 HBV sequence integrated to enhancer acting as oncogenic driver epigenetically promotes hepatocellular carcinoma development Homo sapiens hg38 chr4 121743874 121852009 CCNA2 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 Huh7 CVCL_0336 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2025 40405227 HBV sequence integrated to enhancer acting as oncogenic driver epigenetically promotes hepatocellular carcinoma development Homo sapiens hg38 chr5 1230131 1337133 TERT Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 Huh7 CVCL_0336 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2025 40640362 Analysis of biased allelic enhancer activity of schizophrenia-linked common variants Homo sapiens hg38 chr8 10368745 10368945 MSRA Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay, Chromatin interaction assay Hi-C Luciferase Reporter Assay 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; CTCF QKI Enhancer Active Normal Brain UBERON:0000955 iPSC-derived excitatory neurons excitatory neuron CL:0000540 Enhancer activity assay, TF binding assay ChIP-seq, ATAC-seq, RNA-seq Transgenic Reporter Assay, qRT-PCR 2020 33176148 ARID1A Mutations Promote P300-Dependent Endometrial Invasion through Super-Enhancer Hyperacetylation Homo sapiens hg38 chr7 100772345 100778921 SERPINE1 Enhancer Active Disease endometriosis MONDO:0005302 DOID:289 Endometrium UBERON:0001295 12Z human endometriosis epithelial cells CVCL_UG04 endometriotic epithelial cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq, CUT&RUN siRNA Knockdown, RT-RT-qPCR, Western blot 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 Huh7 cells CVCL_0336 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay RNA-seq, ATAC-seq Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR 2025 40301309 Drug-induced cis-regulatory elements in human hepatocytes affect molecular phenotypes associated with adverse reactions Homo sapiens hg38 chr2 233764355 233764676 PXR UGT1A1 Enhancer Active Normal Liver UBERON:0002107 Primary hepatocytes hepatocyte CL:0000182 Enhancer activity assay CAGE, ChIP-seq Luciferase reporter assay 2025 40140585 Genome-wide CRISPR screen in human T cells reveals regulators of FOXP3 Homo sapiens hg38 chrX 49245000 49246500 RBPJ FOXP3 Enhancer Silenced Normal Blood UBERON:0000178 Primary CD4+ Treg cells CD4-positive regulatory T cell CL:0000815 Enhancer activity assay, TF binding assay CUT&RUN, ChIP-seq Luciferase Reporter Assay, EMSA 2024 39606421 Single cell variant to enhancer to gene map for coronary artery disease Homo sapiens hg38 chr13 110388102 110388602 EGR1; EGR2 COL4A1 Enhancer Active Normal Artery UBERON:0001628 Human Coronary Artery Smooth Muscle Cells (HCASMC) coronary artery smooth muscle cell CL:0000192 TF binding, Genetic association ATAC-seq, RNA-seq, ChIP-seq RT-RT-qPCR, EMSA 2024 39606421 Single cell variant to enhancer to gene map for coronary artery disease Homo sapiens hg38 chr3 171555500 171556000 AMOTL2 Enhancer Active Normal Artery UBERON:0001621 HCASMC coronary artery smooth muscle cell CL:0000192 Chromatin interaction assay, Functional perturbation assay HiChIP, ATAC-seq, RNA-seq CRISPRi, RT-RT-qPCR 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 NFY SPRY2 Enhancer Active Normal Brain UBERON:0000955 iPSC-derived excitatory neurons excitatory neuron CL:0000540 Enhancer activity assay, TF binding assay ChIP-seq, ATAC-seq, RNA-seq Transgenic Reporter Assay, RT-RT-qPCR 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 Brain UBERON:0000955 iPSC-derived excitatory neurons excitatory neuron CL:0000540 Enhancer activity assay, TF binding assay ChIP-seq, ATAC-seq, RNA-seq Transgenic Reporter Assay, RT-RT-qPCR 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 Brain UBERON:0000955 iPSC-derived excitatory neurons excitatory neuron CL:0000540 Enhancer activity assay, TF binding assay ChIP-seq, ATAC-seq, RNA-seq Transgenic Reporter Assay, RT-RT-qPCR 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; CDX1 GPR63 Enhancer Active Normal Brain UBERON:0000955 iPSC-derived excitatory neurons excitatory neuron CL:0000540 Enhancer activity assay, TF binding assay ChIP-seq, ATAC-seq, RNA-seq Transgenic Reporter Assay, RT-RT-qPCR 2022 36157490 Ultra-conserved non-coding sequences within the FOXF1 enhancer are critical for human lung development Homo sapiens hg38 chr16 86219312 86219780 FOXF1 Enhancer Active Normal Lung UBERON:0002048 IMR-90 CVCL_0034 fetal lung fibroblast CL:0000057 Enhancer activity assay, TF binding assay ChIP-seq Luciferase reporter assay 2025 39905017 Multi-locus CRISPRi targeting with a single truncated guide RNA Homo sapiens hg38 chr1 28883749 28884318 EPB41 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Bone Marrow UBERON:0002371 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional perturbation assay CRISPRi, qRT-PCR 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 carcinoma MONDO:0005075 DOID:3948 Thyroid UBERON:0002046 TPC1 CVCL_6298 thyroid carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIRP-seq, RNA-seq, ChIP-seq RT-RT-qPCR, RIP assay, Western blot 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 carcinoma MONDO:0005075 DOID:3948 Thyroid UBERON:0002046 MDA-T41 CVCL_UC55 thyroid carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIRP-seq, RNA-seq, ChIP-seq RT-RT-qPCR, RIP assay, Western blot 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 carcinoma MONDO:0005075 DOID:3948 Thyroid UBERON:0002046 TPC1 CVCL_6298 thyroid carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIRP-seq, RNA-seq, ChIP-seq RT-RT-qPCR, RIP assay, Western blot 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 carcinoma MONDO:0005075 DOID:3948 Thyroid UBERON:0002046 MDA-T41 CVCL_UC55 thyroid carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIRP-seq, RNA-seq, ChIP-seq RT-RT-qPCR, RIP assay, Western blot 2024 38448444 Dynamic enhancer landscapes in human craniofacial development Homo sapiens hg38 chr8 48579000 48587000 SNAI2 Enhancer Active Normal Embryonic craniofacial tissue UBERON:0000922 Multiple craniofacial cell types mesenchymal cell CL:0000134 Enhancer activity assay ChIP-seq, ATAC-seq, scRNA-seq Transgenic Reporter Assay 2024 39316719 Focal deletions of a promoter tether activate the IRX3 oncogene in T-cell acute lymphoblastic leukemia Homo sapiens hg38 chr16 54926631 54929466 H3K27AC Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 T-ALL cells T lymphoblast CL:0002419 Chromatin conformation capture, Histone modification ChIP-sequencing UMI-4C, H3K27ac HiChIP, H3K27ac ChIP-seq qRT-PCR, and ChIP-qPCR 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Homo sapiens hg38 chr16 86741301 86741644 ANKRD11 Enhancer Active Normal Blood vessel UBERON:0001981 Vascular smooth muscle cells vascular smooth muscle cell CL:0000192 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Homo sapiens hg38 chr2 46315253 46315668 EPAS1 Enhancer Active Normal Blood vessel UBERON:0001981 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Homo sapiens hg38 chr2 46315303 46315474 EPAS1 Enhancer Active Normal Blood vessel UBERON:0001981 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Homo sapiens hg38 chr2 46315425 46315596 EPAS1 Enhancer Active Normal Blood vessel UBERON:0001981 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Homo sapiens hg38 chr2 46315547 46315719 EPAS1 Enhancer Active Normal Blood vessel UBERON:0001981 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2026 41843552 Functional interrogation of candidate cis-regulatory elements at the LDLR locus Homo sapiens hg38 chr19 11090422 11091028 LDLR Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HuH7 cells CVCL_0336 hepatocellular carcinoma cell CL:0000182 Functional perturbation assay CRISPR screen CRISPR knockout, CRISPRi, RT-RT-qPCR 2025 40140585 Genome-wide CRISPR screen in human T cells reveals regulators of FOXP3 Homo sapiens hg38 chrX 49247000 49247500 RBPJ FOXP3 Enhancer Silenced Normal Blood UBERON:0000178 CD4+ T cells CD4-positive T cell CL:0000624 Enhancer activity assay, Functional perturbation assay CUT&RUN, RNA-seq Luciferase reporter assay, EMSA, RT-RT-qPCR 2025 40346084 Large-scale discovery of potent compact erythroid enhancers for gene therapy vectors Homo sapiens hg38 chr8 128041672 128043891 PVT1 Enhancer Active Normal Bone Marrow UBERON:0002371 CD34+ cells hematopoietic stem cell CL:0001029 Functional perturbation assay RNA-seq CRISPR knockout, RT-RT-qPCR 2022 35849129 Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer-promoter interactions Homo sapiens hg38 chr11 17710000 17711000 MYOD1 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 Functional perturbation assay CRISPR Knockout, CRISPRi, RT-RT-qPCR 2022 35849129 Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer-promoter interactions Homo sapiens hg38 chr11 17710000 17711000 MYOD1 Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Functional perturbation assay CRISPR Knockout, CRISPRi, RT-RT-qPCR 2022 35849129 Systematic comparison of CRISPR-based transcriptional activators uncovers gene-regulatory features of enhancer-promoter interactions Homo sapiens hg38 chr11 17710000 17711000 MYOD1 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional perturbation assay CRISPR Knockout, CRISPRi, RT-RT-qPCR 2019 30686579 The cis-Regulatory Atlas of the Mouse Immune System Homo sapiens hg38 chr12 121567800 121568100 Enhancer Active Normal Brain UBERON:0000955 Pvalb GABAergic neurons GABAergic neuron CL:0000099 Enhancer activity assay ATAC-seq, RNA-seq Transgenic Reporter Assay, Luciferase Reporter Assay 2022 35849129 Comparison of dCas9-based transcriptional activators at human enhancer-promoter pairs Homo sapiens hg38 chr6 31130000 31131000 POU5F1 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 Functional perturbation assay CRISPR Knockout, CRISPRi, RT-RT-qPCR 2022 35849129 Comparison of dCas9-based transcriptional activators at human enhancer-promoter pairs Homo sapiens hg38 chr6 31130000 31131000 POU5F1 Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Functional perturbation assay CRISPR Knockout, CRISPRi, RT-RT-qPCR 2022 35849129 Comparison of dCas9-based transcriptional activators at human enhancer-promoter pairs Homo sapiens hg38 chr6 31130000 31131000 POU5F1 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Functional perturbation assay CRISPR Knockout, CRISPRi, RT-RT-qPCR 2025 40433695 Super-Enhancer-Driven HCG20 Promotes Pulmonary Hypertension Through U2AF2 Splicing Homo sapiens hg38 chr6 31356000 31361000 USF2 HCG20 Enhancer Active Normal Lung UBERON:0002048 Human Pulmonary Artery Endothelial Cells pulmonary artery endothelial cell CL:1001567 TF binding assay, Enhancer activity assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2023 37430065 The Mediator complex regulates enhancer-promoter interactions Homo sapiens hg38 chr1 7995001 8260000 ERRFI1 Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 Human colorectal carcinoma cell colorectal carcinoma cell CL:0000066 Chromatin interaction assay, Functional perturbation assay Capture-C, Micro-Capture-C, ChIP-seq, CUT&Tag, ATAC-seq, TT-seq Western blot 2023 37430065 The Mediator complex regulates enhancer-promoter interactions Homo sapiens hg38 chr12 65260000 66115000 HMGA2 Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 Human colorectal carcinoma cell colorectal carcinoma cell CL:0000066 Chromatin interaction assay, Functional perturbation assay Capture-C, Micro-Capture-C, Tiled-MCC, ChIP-seq, CUT&Tag, ATAC-seq, TT-seq Western blot 2023 37430065 The Mediator complex regulates enhancer-promoter interactions Homo sapiens hg38 chr17 40880001 41560000 KRT19 Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 Human colorectal carcinoma cell colorectal carcinoma cell CL:0000066 Chromatin interaction assay, Functional perturbation assay Capture-C, Micro-Capture-C, ChIP-seq, CUT&Tag, ATAC-seq, TT-seq Western blot 2023 37430065 The Mediator complex regulates enhancer-promoter interactions Homo sapiens hg38 chr2 181380000 182280000 ITPRID2 Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 Human colorectal carcinoma cell colorectal carcinoma cell CL:0000066 Chromatin interaction assay, Functional perturbation assay Capture-C, Micro-Capture-C, Tiled-MCC, ChIP-seq, CUT&Tag, ATAC-seq, TT-seq Western blot 2023 36639729 Therapeutic adenine base editing of human hematopoietic stem cells Homo sapiens hg38 chr2 60722750 60722850 BCL11A Enhancer Active Normal Bone Marrow UBERON:0002371 CD34+ hematopoietic stem/progenitor cells hematopoietic stem cell CL:0001029 Functional perturbation assay, Enhancer activity assay RNA-seq CRISPR knockout, Adenine base editing, RT-RT-qPCR, Western blot 2023 37430065 The Mediator complex regulates enhancer-promoter interactions Homo sapiens hg38 chr8 126650000 129950000 MYC Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 Human colorectal carcinoma cell colorectal carcinoma cell CL:0000066 Chromatin interaction assay, Functional perturbation assay Capture-C, Micro-Capture-C, Tiled-MCC, ChIP-seq, CUT&Tag, ATAC-seq, TT-seq Western blot 2023 37430065 The Mediator complex regulates enhancer-promoter interactions Homo sapiens hg38 chr9 21096000 22491000 MTAP Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 Human colorectal carcinoma cell colorectal carcinoma cell CL:0000066 Chromatin interaction assay, Functional perturbation assay Capture-C, Micro-Capture-C, Tiled-MCC, ChIP-seq, CUT&Tag, ATAC-seq, TT-seq Western blot 2025 40404660 Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity Homo sapiens hg38 chr1 97306120 97306390 EGFP Enhancer Active Normal Brain UBERON:0000955 iPSC-derived excitatory neurons excitatory neuron CL:0000540 Enhancer activity assay, TF binding assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay, RT-RT-qPCR 2025 40404660 Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity Homo sapiens hg38 chr5 1230260 1230530 EGFP Enhancer Active Normal Brain UBERON:0000955 iPSC-derived excitatory neurons excitatory neuron CL:0000540 Enhancer activity assay, TF binding assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay, RT-RT-qPCR 2025 40404660 Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity Homo sapiens hg38 chr6 156951620 156951890 EGFP Enhancer Active Normal Brain UBERON:0000955 iPSC-derived excitatory neurons excitatory neuron CL:0000540 Enhancer activity assay, TF binding assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay, RT-RT-qPCR 2025 40404660 Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity Homo sapiens hg38 chr7 5409150 5409420 EGFP Enhancer Active Normal Brain UBERON:0000955 iPSC-derived excitatory neurons excitatory neuron CL:0000540 Enhancer activity assay, TF binding assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay, RT-RT-qPCR 2025 40404660 Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity Homo sapiens hg38 chr9 75995180 75995450 EGFP Enhancer Active Normal Brain UBERON:0000955 iPSC-derived excitatory neurons excitatory neuron CL:0000540 Enhancer activity assay, TF binding assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay, RT-RT-qPCR 2025 39870618 Genetic coupling of enhancer activity and connectivity in gene expression control Homo sapiens hg38 chr4 76817412 76817412 NAAA Enhancer Active Normal Blood UBERON:0000178 Primary CD14+ monocytes CD14-positive monocyte CL:0001053 Enhancer activity assay, Chromatin interaction assay Capture Hi-C, ATAC-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2025 39870618 Genetic coupling of enhancer activity and connectivity in gene expression control Homo sapiens hg38 chr7 1210755 1210755 NAAA (DISTAL) Enhancer Active Normal Blood UBERON:0000178 Primary CD14+ monocytes CD14-positive monocyte CL:0001053 Enhancer activity assay, Chromatin interaction assay Capture Hi-C, ATAC-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2025 39870618 Genetic coupling of enhancer activity and connectivity in gene expression control Homo sapiens hg38 chr7 1210898 1210898 C7ORF50 Enhancer Active Normal Blood UBERON:0000178 Primary CD14+ monocytes CD14-positive monocyte CL:0001053 Enhancer activity assay, Chromatin interaction assay Capture Hi-C, ATAC-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2025 39870618 Genetic coupling of enhancer activity and connectivity in gene expression control Homo sapiens hg38 chr7 1211978 1211978 C7ORF50 Enhancer Active Normal Blood UBERON:0000178 Primary CD14+ monocytes CD14-positive monocyte CL:0001053 Enhancer activity assay, Chromatin interaction assay Capture Hi-C, ATAC-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2025 39870618 Genetic coupling of enhancer activity and connectivity in gene expression control Homo sapiens hg38 chr7 1212211 1212211 C7ORF50 Enhancer Active Normal Blood UBERON:0000178 Primary CD14+ monocytes CD14-positive monocyte CL:0001053 Enhancer activity assay, Chromatin interaction assay Capture Hi-C, ATAC-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2025 39870618 Genetic coupling of enhancer activity and connectivity in gene expression control Homo sapiens hg38 chr7 26135404 26135404 NFE2L3 Enhancer Active Normal Blood UBERON:0000178 Primary CD14+ monocytes CD14-positive monocyte CL:0001053 Enhancer activity assay, Chromatin interaction assay Capture Hi-C, ATAC-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2025 39870618 Genetic coupling of enhancer activity and connectivity in gene expression control Homo sapiens hg38 chr10 129882640 129882640 PTPRE Enhancer Active Normal Blood UBERON:0000178 Primary CD14+ monocytes CD14-positive monocyte CL:0001053 Enhancer activity assay, Chromatin interaction assay Capture Hi-C, ATAC-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2025 39870618 Genetic coupling of enhancer activity and connectivity in gene expression control Homo sapiens hg38 chr10 30092300 30092300 SVIL Enhancer Active Normal Blood UBERON:0000178 Primary CD14+ monocytes CD14-positive monocyte CL:0001053 Enhancer activity assay, Chromatin interaction assay Capture Hi-C, ATAC-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2025 39870618 Genetic coupling of enhancer activity and connectivity in gene expression control Homo sapiens hg38 chr14 90560777 90560777 KCNK13 Enhancer Active Normal Blood UBERON:0000178 Primary CD14+ monocytes CD14-positive monocyte CL:0001053 Enhancer activity assay, Chromatin interaction assay Capture Hi-C, ATAC-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2025 39870618 Genetic coupling of enhancer activity and connectivity in gene expression control Homo sapiens hg38 chr15 39602380 39602380 THBS1 Enhancer Active Normal Blood UBERON:0000178 Primary CD14+ monocytes CD14-positive monocyte CL:0001053 Enhancer activity assay, Chromatin interaction assay Capture Hi-C, ATAC-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2025 39870618 Genetic coupling of enhancer activity and connectivity in gene expression control Homo sapiens hg38 chr15 39606026 39606026 THBS1 Enhancer Active Normal Blood UBERON:0000178 Primary CD14+ monocytes CD14-positive monocyte CL:0001053 Enhancer activity assay, Chromatin interaction assay Capture Hi-C, ATAC-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2025 39870618 Genetic coupling of enhancer activity and connectivity in gene expression control Homo sapiens hg38 chr15 39606089 39606089 THBS1 Enhancer Active Normal Blood UBERON:0000178 Primary CD14+ monocytes CD14-positive monocyte CL:0001053 Enhancer activity assay, Chromatin interaction assay Capture Hi-C, ATAC-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2025 39870618 Genetic coupling of enhancer activity and connectivity in gene expression control Homo sapiens hg38 chr15 39607630 39607630 THBS1 Enhancer Active Normal Blood UBERON:0000178 Primary CD14+ monocytes CD14-positive monocyte CL:0001053 Enhancer activity assay, Chromatin interaction assay Capture Hi-C, ATAC-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2025 39870618 Genetic coupling of enhancer activity and connectivity in gene expression control Homo sapiens hg38 chr15 39607665 39607665 THBS1 Enhancer Active Normal Blood UBERON:0000178 Primary CD14+ monocytes CD14-positive monocyte CL:0001053 Enhancer activity assay, Chromatin interaction assay Capture Hi-C, ATAC-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2025 39870618 Genetic coupling of enhancer activity and connectivity in gene expression control Homo sapiens hg38 chr19 54551115 54551115 TFPT Enhancer Active Normal Blood UBERON:0000178 Primary CD14+ monocytes CD14-positive monocyte CL:0001053 Enhancer activity assay, Chromatin interaction assay Capture Hi-C, ATAC-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2022 34049825 Epigenome editing of the CFTR-locus for treatment of Cystic Fibrosis Homo sapiens hg38 chr7 117504671 117505671 CFTR Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293T CVCL_0063 embryonic kidney cell CL:0002139 Functional perturbation assay CRISPR Knockout, CRISPRi, RT-RT-qPCR, Western blot, Ussing Chamber Assay 2022 34049825 Epigenome editing of the CFTR-locus for treatment of Cystic Fibrosis Homo sapiens hg38 chr7 117504671 117505671 CFTR Enhancer Active Normal Lung UBERON:0002048 UNCCF3T (??F508/??F508 HBE) CVCL_0063 bronchial epithelial cell CL:0002591 Functional perturbation assay CRISPR Knockout, CRISPRi, RT-RT-qPCR, Western blot, Ussing Chamber Assay 2022 34049825 Epigenome editing of the CFTR-locus for treatment of Cystic Fibrosis Homo sapiens hg38 chr7 117523000 117524000 CFTR Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 HT29 CVCL_0320 colorectal carcinoma cell CL:0000066 Functional perturbation assay CRISPR Knockout, CRISPRi, RT-RT-qPCR, Western blot 2015 26663721 The genomic response of macrophages to glucocorticoids Homo sapiens hg38 chr5 172650000 172651200 NR3C1 DUSP1 Enhancer Active Normal Blood UBERON:0000178 Monocyte-derived macrophage (hMDM) macrophage CL:0000235 TF binding assay, Enhancer activity assay ChIP-seq, RNA-seq RT-RT-qPCR 2024 38404767 Germline PDCD1 and CD274 variants modulate clinical outcomes and immune-related adverse events in NSCLC patients treated with immune checkpoint inhibitors Homo sapiens hg38 chr9 5451500 5451650 CEBPA CD274 Enhancer Active Disease non-small cell lung carcinoma MONDO:0005233 DOID:3908 Lung UBERON:0002048 NSCLC cell lines non-small cell lung carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA 2025 40765356 Epigenetic remodeling and 3D chromatin reorganization governed by NKX2-1 drive neuroendocrine prostate cancer Homo sapiens hg38 chr7 27089386 27207428 FOXA2 HOXA1 SE Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LuNE prostate carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq Western blot, qRT-PCR, CCK-8 Assay 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 PTX3 Enhancer Silenced Disease cutaneous squamous cell carcinoma MONDO:0005058 DOID:1749 Skin UBERON:0000014 Met4 cSCC cells CVCL_UE24 cutaneous squamous cell carcinoma cell CL:0000066 Chromatin interaction assay, Functional perturbation assay DamID-seq, RNA-seq CRISPR Knockout, qRT-PCR 2024 38448444 Dynamic enhancer landscapes in human craniofacial development Homo sapiens hg38 chr8 48581000 48583000 SNAI2 Enhancer Active Normal Embryonic craniofacial tissue UBERON:0000922 Human embryonic craniofacial cells mesenchymal cell CL:0000134 Enhancer activity assay ChIP-seq, ATAC-seq, RNA-seq Transgenic Reporter Assay 2024 38448444 Dynamic enhancer landscapes in human craniofacial development Homo sapiens hg38 chr8 98367000 98369000 POP1 Enhancer Active Normal Embryonic craniofacial tissue UBERON:0000922 Human embryonic craniofacial cells mesenchymal cell CL:0000134 Enhancer activity assay ChIP-seq, ATAC-seq, RNA-seq Transgenic Reporter Assay 2024 38448444 Dynamic enhancer landscapes in human craniofacial development Homo sapiens hg38 chr8 98367000 98370806 POP1 Enhancer Active Normal Embryonic craniofacial tissue UBERON:0000922 Maxillary and nasal process cells mesenchymal cell CL:0000134 Enhancer activity assay ChIP-seq, ATAC-seq Transgenic Reporter Assay 2022 36157490 Ultra-conserved non-coding sequences within the FOXF1 enhancer are critical for human lung development Homo sapiens hg38 chr16 86194740 86195815 FOXF1 Enhancer Active Normal Lung UBERON:0002048 IMR90 (fetal lung fibroblasts) CVCL_0034 fetal lung fibroblast CL:0000057 Functional perturbation assay, TF binding assay ChIP-seq siRNA Knockdown, qRT-PCR, Methylation sensitive digestion assay 2021 33863876 Deletion of CTCF sites in the SHH locus alters enhancer-promoter interactions and leads to acheiropodia Homo sapiens hg38 chr7 156816030 156828070 CTCF SHH Enhancer Active Normal Blood UBERON:0000178 Lymphoblastoid lymphoblastoid cell CL:0000945 Chromatin interaction assay, TF binding assay 4C-seq, ChIP-seq 2021 33863876 Deletion of CTCF sites in the SHH locus alters enhancer-promoter interactions and leads to acheiropodia Homo sapiens hg38 chr7 156785000 156786000 CTCF SHH Enhancer Active Normal Blood UBERON:0000178 Patient lymphoblastoid lymphoblastoid cell CL:0000945 Chromatin interaction assay, TF binding assay 4C-seq, ChIP-seq DNA FISH, ChIP-RT-qPCR 2025 40604280 Range extender mediates long-distance enhancer activity Homo sapiens hg38 chr16 51623658 51623900 SHH Enhancer Active Normal Embryonic Limb Bud UBERON:0005417 Limb bud mesenchymal cells mesenchymal cell CL:0000134 Enhancer activity assay, Functional perturbation assay Transgenic Reporter Assay, CRISPR Knock-in, PCR Genotyping, Skeletal staining, RT-RT-qPCR 2017 28487391 Functional Characterization of the GUCY1A3 Coronary Artery Disease Risk Locus Homo sapiens hg38 chr4 155713878 155714284 ZEB1 GUCY1A3 Enhancer Active Normal Blood vessel UBERON:0001981 Endothelial cells endothelial cell CL:0000115 Reporter assay, TF binding, Functional validation ChIP-seq qRT-PCR, and ChIP-qPCR 2017 28971975 TBX4 is involved in the super-enhancer-driven transcriptional programs underlying features specific to lung fibroblasts Homo sapiens hg38 chr17 61449600 61451600 TBX4 Enhancer Active Normal Lung UBERON:0002048 Lung fibroblasts lung fibroblast CL:0000057 Super-enhancer functional study, Chromatin interaction assay RNA-seq 3C, RT-RT-qPCR 2018 29563176 The first enhancer in an enhancer chain safeguards subsequent enhancer-promoter contacts from a distance Homo sapiens hg38 chr16 67559907 67561907 CTCF Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K562 cells CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer chain 3D regulation study, Chromatin interaction assay 3C, RT-RT-qPCR 2019 31053723 Differential methylation of enhancer at IGF2 is associated with abnormal dopamine synthesis in major psychosis Homo sapiens hg38 chr11 2126750 2128050 TH Enhancer Active Normal Brain UBERON:0000955 Primary cortical neurons (NeuN+) neuron CL:0000540 Chromatin interaction assay Hi-C, WGBS, RNA-seq, Illumina MethylationEPIC microarray Targeted bisulfite sequencing, RT-RT-qPCR, Western blot, HPLC 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 IRS1 Enhancer Active Normal Adipose tissue UBERON:0001013 Human Preadipocyte preadipocyte CL:0000136 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay STARR-seq, Hi-C, RNA-seq qRT-PCR, and ChIP-qPCR 2026 41827844 MGMT Promoter and Enhancer Methylation in Melanoma Brain Metastases and Glioblastoma: Shared and Distinct Features Homo sapiens hg38 chr10 128906630 128909942 MGMT Enhancer Active Disease glioblastoma MONDO:0005142 DOID:3070 Brain UBERON:0000955 Primary tumor tissue glioblastoma cell CL:0000127 Enhancer activity assay, Functional perturbation assay Transgenic reporter assay, CRISPR knockout 2026 41843552 Functional interrogation of candidate cis-regulatory elements at the LDLR locus Homo sapiens hg38 chr19 11090550 11090678 LDLR Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HuH7 cells CVCL_0336 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay MPRA Luciferase reporter assay 2025 40132669 Transducin-like enhancer of split 3 protects against lipopolysaccharide-induced inflammation Homo sapiens hg38 chr1 234567000 234577000 TLE3 PPP2R5A Enhancer Silenced Normal Liver UBERON:0002107 Macrophages macrophage CL:0000235 Enhancer activity assay CUT&Tag, RNA-seq Luciferase reporter assay, ChIP-RT-qPCR 2025 40301309 Drug-induced cis-regulatory elements in human hepatocytes affect molecular phenotypes associated with adverse reactions Homo sapiens hg38 chr2 233768020 233768954 UGT1A1 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepaRG cells CVCL_5J53 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay CAGE CRISPRi 2025 40301309 Drug-induced cis-regulatory elements in human hepatocytes affect molecular phenotypes associated with adverse reactions Homo sapiens hg38 chr11 76772927 76773266 TSKU Enhancer Active Normal Liver UBERON:0002107 Hepatocytes hepatocyte CL:0000182 Super-enhancer activity assay CAGE CRISPR knockout 2024 38555298 A conserved NR5A1-responsive enhancer regulates SRY in testis-determination Homo sapiens hg38 chrY 2792658 2792907 SRY Enhancer Silenced Normal Testis UBERON:0000473 hiPSC-derived Sertoli-like cells Sertoli cell CL:0000216 Enhancer activity assay, TF binding assay, Functional perturbation assay Whole Genome Sequencing, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR, Western blot, Sanger Sequencing 2024 38555298 A conserved NR5A1-responsive enhancer regulates SRY in testis-determination Homo sapiens hg38 chrY 2792658 2792907 SRY Enhancer Silenced Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay, TF binding assay, Functional perturbation assay Whole Genome Sequencing, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR, Western blot, Sanger Sequencing 2025 40140585 Genome-wide CRISPR screen in human T cells reveals regulators of FOXP3 Homo sapiens hg38 chrX 49255000 49256300 RBPJ FOXP3 Enhancer Silenced Normal Blood UBERON:0000178 Primary CD4+ Treg cells CD4-positive regulatory T cell CL:0000815 TF binding assay, Enhancer activity assay CUT&RUN, ChIP-seq EMSA, RT-RT-qPCR 2024 39606421 Single cell variant to enhancer to gene map for coronary artery disease Homo sapiens hg38 chr1 59169569 59170069 BACH1; BACH2 HSD17B2 Enhancer Active Normal Artery UBERON:0001628 Human Coronary Artery Smooth Muscle Cells (HCASMC) coronary artery smooth muscle cell CL:0000192 TF binding, Genetic association ATAC-seq, RNA-seq RT-RT-qPCR, EMSA 2020 32284612 Therapeutic base editing of human hematopoietic stem cells Homo sapiens hg38 chr2 6072150 6072450 BCL11A Enhancer Active Normal Bone Marrow UBERON:0002371 CD34+ hematopoietic stem/progenitor cells hematopoietic stem cell CL:0001029 Functional perturbation assay, Enhancer activity assay CRISPR Knockout, qRT-PCR 2022 36157490 Ultra-conserved non-coding sequences within the FOXF1 enhancer are critical for human lung development Homo sapiens hg38 chr16 86194740 86195815 FOXF1 Enhancer Active Normal Lung UBERON:0002048 IMR-90 CVCL_0034 fetal lung fibroblast CL:0000057 Functional perturbation assay, TF binding assay ChIP-seq siRNA knockdown, RT-RT-qPCR, Methylation-sensitive restriction digestion 2023 37591883 High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription Homo sapiens hg38 chr19 40464709 40464990 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K-562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer identification, Transcriptional regulation assay HiS-NET-seq, ChIP-Rx, GRO-cap Dual-luciferase reporter assay 2023 37591883 High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription Homo sapiens hg38 chr1 244970941 244971645 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K-562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer identification, Transcriptional regulation assay HiS-NET-seq, ChIP-Rx, GRO-cap Dual-luciferase reporter assay 2023 37591883 High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription Homo sapiens hg38 chr21 46325282 46325509 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K-562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer identification, Transcriptional regulation assay HiS-NET-seq, ChIP-Rx, GRO-cap Dual-luciferase reporter assay 2023 37591883 High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription Homo sapiens hg38 chr19 48872999 48873182 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K-562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer identification, Transcriptional regulation assay HiS-NET-seq, ChIP-Rx, GRO-cap Dual-luciferase reporter assay 2023 37591883 High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription Homo sapiens hg38 chr19 46786236 46786920 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K-562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer identification, Transcriptional regulation assay HiS-NET-seq, ChIP-Rx, GRO-cap Dual-luciferase reporter assay 2023 37591883 High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription Homo sapiens hg38 chr1 42958018 42958389 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K-562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer identification, Transcriptional regulation assay HiS-NET-seq, ChIP-Rx, GRO-cap Dual-luciferase reporter assay 2023 37591883 High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription Homo sapiens hg38 chr17 51121344 51122474 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K-562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer identification, Transcriptional regulation assay HiS-NET-seq, ChIP-Rx, GRO-cap Dual-luciferase reporter assay 2023 37591883 High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription Homo sapiens hg38 chr19 43754969 43756655 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K-562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer identification, Transcriptional regulation assay HiS-NET-seq, ChIP-Rx, GRO-cap Dual-luciferase reporter assay 2023 37591883 High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription Homo sapiens hg38 chr17 74875718 74876890 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Blood UBERON:0000178 K-562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer identification, Transcriptional regulation assay HiS-NET-seq, ChIP-Rx, GRO-cap Dual-luciferase reporter assay 2023 37591883 High-sensitive nascent transcript sequencing reveals BRD4-specific control of widespread enhancer and target gene transcription Homo sapiens hg38 chr6 28895115 28896348 Enhancer Active Disease Burkitt lymphoma MONDO:0002483 DOID:8582 Lymph node UBERON:0000029 Namalwa (B-lymphocyte) CVCL_0128 Burkitt lymphoma cell CL:0000945 Enhancer identification, Transcriptional regulation assay HiS-NET-seq, ChIP-Rx, GRO-cap Dual-luciferase reporter assay 2025 39796169 Defining Mechanistic Links Between the Non-Coding Variant rs17673553 in CLEC16A and Lupus Susceptibility Homo sapiens hg38 chr16 11075050 11075232 CLEC16A Enhancer Active Normal Heart UBERON:0000948 iPSC-Cardiac Fibroblast iPSC-derived cardiac fibroblast CL:0000057 Functional perturbation assay CRISPR Knockout, RT-RT-qPCR, Western blot 2025 37225984 BRD4 in Cx3cr1-positive macrophages drives proinflammatory transcription in heart failure pathogenesis Homo sapiens hg38 chr17 43574477 43663426 MEOX1 Enhancer Active Normal Heart UBERON:0000948 iPSC-CM CVCL_2514 induced pluripotent stem cell-derived cardiomyocyte CL:0000746 Enhancer activity assay RNA-seq Luciferase Reporter Assay, RT-RT-qPCR 2024 38378865 Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease Homo sapiens hg38 chr9 137494462 137494862 GATA4,SRF,SMAD3,THRA,TBX20 COL5A1 Enhancer Active Normal Endometrium UBERON:0001295 T-HESC (immortalized human endometrial stromal cells) CVCL_UP48 endometrial stromal cell CL:0000066 CRISPR interference (CRISPRi) lentiSTARR-seq, lentiMPRA, scATAC-seq RT-RT-qPCR, FACS, EMSA 2023 37664846 The NR2F2-HAND2 signaling axis regulates progesterone actions in the uterus at early pregnancy Homo sapiens hg38 chr4 173516002 173519662 HAND2 Enhancer Active Disease meningioma MONDO:0005149 DOID:3565 Meninges UBERON:0002360 Patient-derived meningioma primary cells meningioma cell CL:0000127 Enhancer activity assay, Functional perturbation assay CRISPR Activation (CRISPRa), qRT-PCR 2023 37805627 Super-enhancer hijacking drives ectopic expression of hedgehog pathway ligands in meningiomas Homo sapiens hg38 chr2 218000000 218700000 IHH SE Active Normal Breast UBERON:0000310 Breast Adipose Fibroblasts (BAFs) fibroblast CL:0000057 Enhancer activity assay, Chromatin interaction assay HiChIP, H3K27ac ChIP-seq, RNA-seq, WGS, WES Immunofluorescence, Sanger Sequencing 2023 36902090 WNT3a Signaling Inhibits Aromatase Expression in Breast Adipose Fibroblasts-A Possible Mechanism Supporting the Loss of Estrogen Responsiveness of Triple-Negative Breast Cancers Homo sapiens hg38 chr15 51242508 51243030 TCF7L2 CYP19A1 Enhancer Silenced Normal Heart UBERON:0000948 Atrial/ventricular cardiomyocytes cardiomyocyte CL:0000746 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA 2024 39223609 Enhlink infers distal and context-specific enhancer-promoter linkages Homo sapiens hg38 chr7 150955147 150956502 KCNH2 Enhancer Active Normal Blood UBERON:0000178 Primary monocytes monocyte CL:0000576 Enhancer activity assay, Functional perturbation assay CRISPR Knockout 2025 39870618 Genetic coupling of enhancer activity and connectivity in gene expression control Homo sapiens hg38 chr14 24058261 24058761 CTCF PCK2 Enhancer Active Disease glioblastoma MONDO:0005142 DOID:3070 Brain UBERON:0000955 U373MG CVCL_2219 glioblastoma cell CL:0000127 Chromatin interaction assay, TF binding assay ATAC-seq, Capture Hi-C ChIP-RT-qPCR, 4C-seq 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:0005142 DOID:3070 Brain UBERON:0000955 T98G CVCL_0556 glioblastoma cell CL:0000127 Enhancer activity assay, TF binding assay, Functional perturbation assay Microarray, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, siRNA Knockdown, shRNA Knockdown, RT-RT-qPCR, Western blot, Immunohistochemistry 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:0005142 DOID:3070 Brain UBERON:0000955 primary glioblastoma cells (PT#3) glioblastoma cell CL:0000127 Enhancer activity assay, TF binding assay, Functional perturbation assay Microarray, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, siRNA Knockdown, shRNA Knockdown, RT-RT-qPCR, Western blot, Immunohistochemistry 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:0005142 DOID:3070 Brain UBERON:0000955 glioma stem-like cells (GSCs) glioma stem cell CL:0000127 Enhancer activity assay, TF binding assay, Functional perturbation assay Microarray, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, siRNA Knockdown, shRNA Knockdown, RT-RT-qPCR, Western blot, Immunohistochemistry 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 Normal Blood UBERON:0000178 Human monocyte-derived macrophages macrophage CL:0000235 Enhancer activity assay, TF binding assay, Functional perturbation assay Microarray, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, siRNA Knockdown, shRNA Knockdown, RT-RT-qPCR, Western blot, Immunohistochemistry 2021 33976173 A Stat1 bound enhancer promotes Nampt expression and function within tumor associated macrophages Homo sapiens hg38 chr7 109460000 109460600 STAT1 NAMPT Enhancer Active Normal Blood UBERON:0000178 HUDEP-2 cells CVCL_A0NF erythroid progenitor cell CL:0000038 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq 2017 29227829 A long noncoding RNA from the HBS1L-MYB intergenic region on chr6q23 regulates human fetal hemoglobin expression Homo sapiens hg38 chr6 135178878 135180878 MYB Enhancer Active Disease osteosarcoma MONDO:0005087 DOID:3347 Bone UBERON:0001474 Osteosarcoma cells osteosarcoma cell CL:0000062 Enhancer functional validation, Chromatin interaction assay 3C, RT-RT-qPCR, Western blot 2020 31937612 Targeting Super-Enhancer-Associated Oncogenes in Osteosarcoma with THZ2, a Covalent CDK7 Inhibitor Homo sapiens hg38 chr5 69232027 69234027 CDK7 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Bone marrow UBERON:0002371 Leukemia cell lines chronic myeloid leukemia cell CL:0001054 Super-enhancer targeting therapy study, Chromatin interaction assay 3C, RT-RT-qPCR, Western blot 2019 31890812 Expression analysis data of BCL11A and ??-globin genes in KU812 and KG-1 cell lines after CRISPR/Cas9-mediated BCL11A enhancer deletion Homo sapiens hg38 chr2 60447611 60449611 BCL11A Enhancer Active Disease lung carcinoma MONDO:0005061 DOID:1324 Lung UBERON:0002048 Lung carcinoma cells lung carcinoma cell CL:0000066 Enhancer CRISPR perturbation study, Chromatin interaction assay 3C, RT-RT-qPCR 2019 31186707 Long non-coding RNA-neighboring enhancer of FOXA2 inhibits the migration and invasion of small cell lung carcinoma cells by downregulating transforming growth factor-??1 Homo sapiens hg38 chr20 22578327 22580327 FOXA2 Enhancer Active Normal Blood UBERON:0000178 B lymphocytes B cell CL:0000945 LncRNA tumor suppressor study, Chromatin interaction assay 3C, RT-RT-qPCR 2019 31127282 Acute depletion of CTCF directly affects MYC regulation through loss of enhancer-promoter looping Homo sapiens hg38 chr16 67559749 67561749 CTCF Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 Breast carcinoma cells breast carcinoma cell CL:0000646 CTCF 3D genome regulation study, Chromatin interaction assay 3C, RT-RT-qPCR 2019 31826955 FOXA1 upregulation promotes enhancer and transcriptional reprogramming in endocrine-resistant breast cancer Homo sapiens hg38 chr14 37586693 37588693 FOXA1 Enhancer Active Normal Inner cell mass UBERON:0000087 Embryonic stem cells embryonic stem cell CL:0002322 Endocrine resistance enhancer reprogramming study, Chromatin interaction assay 3C, RT-RT-qPCR, Western blot 2019 31827084 A primate-specific retroviral enhancer wires the XACT lncRNA into the core pluripotency network in humans Homo sapiens hg38 chrX 113613674 113615674 XACT Enhancer Active Normal Bronchus UBERON:0002037 Primary airway cells bronchial epithelial cell CL:0002591 Endogenous retroviral enhancer study, Chromatin interaction assay 3C, FISH, RT-RT-qPCR, Western blot 2025 40164603 Enhancer RNA transcription pinpoints functional genetic variants linked to asthma Homo sapiens hg38 chr5 143200112 143200889 NR3C1 Enhancer Silenced Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepaRG cells CVCL_5J53 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay PRO-seq Luciferase reporter assay 2025 40301309 Drug-induced cis-regulatory elements in human hepatocytes affect molecular phenotypes associated with adverse reactions Homo sapiens hg38 chr2 233759112 233759498 UGT1A1 Enhancer Active Normal Liver UBERON:0002107 Hepatocytes hepatocyte CL:0000182 Enhancer activity assay CAGE Luciferase reporter assay 2025 40301309 Drug-induced cis-regulatory elements in human hepatocytes affect molecular phenotypes associated with adverse reactions Homo sapiens hg38 chr20 54103941 54104461 CYP24A1 Enhancer Active Normal Liver UBERON:0002107 Hepatocytes hepatocyte CL:0000182 Super-enhancer activity assay CAGE Luciferase reporter assay 2025 40301309 Drug-induced cis-regulatory elements in human hepatocytes affect molecular phenotypes associated with adverse reactions Homo sapiens hg38 chr20 54107388 54107945 CYP24A1 Enhancer Active Disease glioblastoma MONDO:0005142 DOID:3070 Brain UBERON:0000955 DBTRG-05MG cells CVCL_1166 glioblastoma cell CL:0000127 Super-enhancer activity assay CAGE Luciferase reporter assay 2025 39889913 Enhancer RNA from STAT3 locus affects temozolomide chemoresistance of glioblastoma cells Homo sapiens hg38 chr17 42409879 42412035 STAT3 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 PANC-1 CVCL_0480 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay Luciferase reporter assay, RT-RT-qPCR 2025 40781158 ALDH1A3 promotes aggressive basal-like pancreatic cancer through an AP-1/RUNX2 enhancer network Homo sapiens hg38 chr17 20128500 20157500 MAP2K3 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 PANC-1 CVCL_0480 pancreatic ductal adenocarcinoma cell CL:0000066 TF binding assay, Enhancer activity assay CUT&Tag, RNA-seq RT-RT-qPCR, Western blot 2025 40781158 ALDH1A3 promotes aggressive basal-like pancreatic cancer through an AP-1/RUNX2 enhancer network Homo sapiens hg38 chr4 103422500 103651500 NFKB1 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 PANC-1 CVCL_0480 pancreatic ductal adenocarcinoma cell CL:0000066 TF binding assay, Enhancer activity assay CUT&Tag, RNA-seq RT-RT-qPCR, Western blot 2025 40781158 ALDH1A3 promotes aggressive basal-like pancreatic cancer through an AP-1/RUNX2 enhancer network Homo sapiens hg38 chr4 75314500 75378500 EREG Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 PANC-1 CVCL_0480 pancreatic ductal adenocarcinoma cell CL:0000066 TF binding assay, Enhancer activity assay CUT&Tag, RNA-seq RT-RT-qPCR, Western blot 2025 40781158 ALDH1A3 promotes aggressive basal-like pancreatic cancer through an AP-1/RUNX2 enhancer network Homo sapiens hg38 chr7 55019000 55092000 EGFR Enhancer Active Normal Hypothalamus UBERON:0001898 Primary rat hypothalamic cells rat hypothalamic cell CL:0000540 TF binding assay, Enhancer activity assay CUT&Tag, RNA-seq RT-RT-qPCR, Western blot 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 BDNF Enhancer Active Normal Brainstem UBERON:0002298 Cranial motor neurons motor neuron CL:0000100 Enhancer activity assay GWAS Luciferase Reporter Assay, qRT-PCR 2024 39333082 A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders Homo sapiens hg38 chr11 72308500 72309000 PHOX2A Enhancer Active Normal Brainstem UBERON:0002298 Cranial motor neurons motor neuron CL:0000100 Enhancer activity assay, Chromatin interaction assay scATAC-seq, scRNA-seq, scCUT&Tag Transgenic Reporter Assay 2024 39333082 A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders Homo sapiens hg38 chr22 27493955 27497536 MN1 Enhancer Active Disease pancreatic ductal adenocarcinoma MONDO:0005147 DOID:3490 Pancreas UBERON:0001264 BxPC-3 CVCL_0186 pancreatic ductal adenocarcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay scATAC-seq, scRNA-seq, scCUT&Tag Transgenic Reporter Assay 2025 40611281 LNP-enclosed NamiRNA inhibits pancreatic cancer proliferation and migration via dual pathways Homo sapiens hg38 chr12 6955000 6975000 PTPN6 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepG2 CVCL_0027 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, TF binding assay ChIP-seq ChIP-RT-qPCR, qRT-PCR 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 GDF15 Enhancer Active Normal Skin UBERON:0000014 Human hypertrophic scar fibroblasts (HSFs) fibroblast CL:0000057 Enhancer activity assay Luciferase Reporter Assay 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 HuH7 cells CVCL_0336 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR 2026 41843552 Functional interrogation of candidate cis-regulatory elements at the LDLR locus Homo sapiens hg38 chr19 11090150 11090715 LDLR Enhancer Active Disease tongue squamous cell carcinoma MONDO:0005084 DOID:8648 Tongue UBERON:0001723 SCC25 CVCL_1682 tongue squamous cell carcinoma cell CL:0000069 Enhancer activity assay Transgenic reporter assay 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:0005084 DOID:8648 Tongue UBERON:0001723 CAL27 CVCL_1107 tongue squamous cell carcinoma cell CL:0000069 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 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 Normal Bone Marrow UBERON:0002371 CD34+ hematopoietic stem/progenitor cells hematopoietic stem cell CL:0001029 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2023 36639729 Therapeutic adenine base editing of human hematopoietic stem cells Homo sapiens hg38 chr11 5225440 5225500 HBG1 Enhancer Silenced Normal Bone Marrow UBERON:0002371 CD34+ hematopoietic stem/progenitor cells hematopoietic stem cell CL:0001029 Functional perturbation assay, Enhancer activity assay RNA-seq Adenine base editing, RT-RT-qPCR, RP-HPLC 2023 36639729 Therapeutic adenine base editing of human hematopoietic stem cells Homo sapiens hg38 chr11 5227000 5227060 HBG2 Enhancer Silenced Disease glioblastoma MONDO:0005142 DOID:3070 Brain UBERON:0000955 Primary tumor tissue glioblastoma cell CL:0000127 Functional perturbation assay, Enhancer activity assay RNA-seq Adenine base editing, RT-RT-qPCR, RP-HPLC 2026 41827844 MGMT Promoter and Enhancer Methylation in Melanoma Brain Metastases and Glioblastoma: Shared and Distinct Features Homo sapiens hg38 chr10 128568604 128569741 MGMT Enhancer Active Disease glioblastoma MONDO:0005142 DOID:3070 Brain UBERON:0000955 Primary tumor tissue glioblastoma cell CL:0000127 Enhancer activity assay Transgenic reporter assay 2026 41827844 MGMT Promoter and Enhancer Methylation in Melanoma Brain Metastases and Glioblastoma: Shared and Distinct Features Homo sapiens hg38 chr10 129033193 129034911 MGMT Enhancer Active Disease glioblastoma MONDO:0005142 DOID:3070 Brain UBERON:0000955 Primary tumor tissue glioblastoma cell CL:0000127 Enhancer activity assay Transgenic reporter assay 2026 41827844 MGMT Promoter and Enhancer Methylation in Melanoma Brain Metastases and Glioblastoma: Shared and Distinct Features Homo sapiens hg38 chr10 129605804 129607046 MGMT Enhancer Active Normal Liver UBERON:0002107 Hepatocyte hepatocyte CL:0000182 Enhancer activity assay Transgenic reporter assay 2025 40301309 Drug-induced cis-regulatory elements in human hepatocytes affect molecular phenotypes associated with adverse reactions Homo sapiens hg38 chr11 76773651 76774249 TSKU Enhancer Active Normal Notochord UBERON:0002329 Embryonic notochord notochordal cell CL:0000000 CL:0000182 Super-enhancer activity assay CAGE 2023 36729834 Diverse logics and grammar encode notochord enhancers Homo sapiens hg38 chr18 7076043 7076166 LAMA1 Enhancer Active Normal Heart UBERON:0000948 Ventricular cardiomyocytes cardiomyocyte CL:0000746 Enhancer activity assay Transgenic Reporter Assay 2024 39223609 Enhlink infers distal and context-specific enhancer-promoter linkages Homo sapiens hg38 chr12 110931149 110931877 MYL2 Enhancer Active Normal Heart UBERON:0000948 Ventricular cardiomyocytes cardiomyocyte CL:0000746 Enhancer activity assay qRT-PCR, and ChIP-qPCR 2024 39223609 Enhlink infers distal and context-specific enhancer-promoter linkages Homo sapiens hg38 chr12 110928658 110929096 MYL2 Enhancer Active Normal Heart UBERON:0000948 Ventricular cardiomyocytes cardiomyocyte CL:0000746 Enhancer activity assay qRT-PCR, and ChIP-qPCR 2024 39223609 Enhlink infers distal and context-specific enhancer-promoter linkages Homo sapiens hg38 chr12 110907461 110909456 MYL2 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF-7 CVCL_0031 breast carcinoma cell CL:0000646 Enhancer activity assay qRT-PCR, and ChIP-qPCR 2024 37906431 Metabolomic Rewiring Promotes Endocrine Therapy Resistance in Breast Cancer Homo sapiens hg38 chr21 42879000 42881000 ESR1 TFF1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 T47D CVCL_0553 breast carcinoma cell CL:0000646 Functional perturbation assay, Enhancer activity assay, Chromatin interaction assay Hi-C, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi, Luciferase Reporter Assay, RT-RT-qPCR, Western blot 2024 37906431 Metabolomic Rewiring Promotes Endocrine Therapy Resistance in Breast Cancer Homo sapiens hg38 chr21 42879000 42881000 ESR1 TFF3 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF-7 CVCL_0031 breast carcinoma cell CL:0000646 Functional perturbation assay, Enhancer activity assay, Chromatin interaction assay Hi-C, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi, Luciferase Reporter Assay, RT-RT-qPCR, Western blot 2024 37906431 Metabolomic Rewiring Promotes Endocrine Therapy Resistance in Breast Cancer Homo sapiens hg38 chr6 39090000 39092000 ESR1 KCNK5 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 T47D CVCL_0553 breast carcinoma cell CL:0000646 Functional perturbation assay, Enhancer activity assay, Chromatin interaction assay Hi-C, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi, Luciferase Reporter Assay, RT-RT-qPCR, Western blot 2024 37906431 Metabolomic Rewiring Promotes Endocrine Therapy Resistance in Breast Cancer Homo sapiens hg38 chr6 39090000 39092000 ESR1 KCNK5 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF-7 CVCL_0031 breast carcinoma cell CL:0000646 Functional perturbation assay, Enhancer activity assay, Chromatin interaction assay Hi-C, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi, Luciferase Reporter Assay, RT-RT-qPCR, Western blot 2024 37906431 Metabolomic Rewiring Promotes Endocrine Therapy Resistance in Breast Cancer Homo sapiens hg38 chr11 61600000 61602000 ESR1 P2RY2 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 T47D CVCL_0553 breast carcinoma cell CL:0000646 Functional perturbation assay, Enhancer activity assay, Chromatin interaction assay Hi-C, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi, Luciferase Reporter Assay, RT-RT-qPCR, Western blot 2024 37906431 Metabolomic Rewiring Promotes Endocrine Therapy Resistance in Breast Cancer Homo sapiens hg38 chr11 61600000 61602000 ESR1 P2RY2 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF-7 CVCL_0031 breast carcinoma cell CL:0000646 Functional perturbation assay, Enhancer activity assay, Chromatin interaction assay Hi-C, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi, Luciferase Reporter Assay, RT-RT-qPCR, Western blot 2024 37906431 Metabolomic Rewiring Promotes Endocrine Therapy Resistance in Breast Cancer Homo sapiens hg38 chr11 101800000 101802000 ESR1 PGR Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 T47D CVCL_0553 breast carcinoma cell CL:0000646 Functional perturbation assay, Enhancer activity assay, Chromatin interaction assay Hi-C, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi, Luciferase Reporter Assay, RT-RT-qPCR, Western blot 2024 37906431 Metabolomic Rewiring Promotes Endocrine Therapy Resistance in Breast Cancer Homo sapiens hg38 chr11 101800000 101802000 ESR1 PGR Enhancer Active Normal Lung UBERON:0002048 BEAS-2B human bronchial epithelial cells CVCL_0168 bronchial epithelial cell CL:0002591 Functional perturbation assay, Enhancer activity assay, Chromatin interaction assay Hi-C, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi, Luciferase Reporter Assay, RT-RT-qPCR, Western blot 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 Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 Kasumi-1 CVCL_0589 acute myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay snATAC-seq, Hi-C, ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout/CRISPRi, RT-RT-qPCR, Western blot, 3C-RT-qPCR 2022 36301402 The Tumor Invasion Paradox in Cancer Stem Cell-Driven Solid Tumors Homo sapiens hg38 chr15 40931917 40933388 NSMCE3 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat CVCL_0065 T lymphoblast CL:0002419 Enhancer activity assay, Functional perturbation assay Hi-C, ATAC-seq, CUT&Tag, RNA-seq Luciferase Reporter Assay, CRISPRi, RT-RT-qPCR 2025 41129262 The hematopoietic stem cell MYB enhancer is essential and recurrently amplified during T-cell leukemogenesis Homo sapiens hg38 chr6 135323327 135323580 ETS1 MYB Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepG2 CVCL_0027 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPRi, RT-RT-qPCR 2024 38493444 Integrative regulation of hLMR1 by dietary and genetic factors in nonalcoholic fatty liver disease and hyperlipidemia Homo sapiens hg38 chr16 81157582 81157701 SREBP1C HLMR1 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat cells CVCL_0065 T lymphoblast CL:0002419 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Base Editing, RT-RT-qPCR 2025 41016515 Super-enhancer-driven ELOVL5 promotes T-ALL progression through the MYC-SERBP1 pathway Homo sapiens hg38 chr6 53260000 53270000 ELOVL5 Enhancer Active Normal Heart UBERON:0000948 hPSC-CMs cardiomyocyte CL:0000746 Super-enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq Luciferase reporter assay, CRISPRi, RT-RT-qPCR 2024 39196225 A transcriptional enhancer regulates cardiac maturation Homo sapiens hg38 chr1 154149500 154150000 MEF2A ACTN2 Enhancer Active Disease Burkitt lymphoma MONDO:0002483 DOID:8582 Blood UBERON:0000178 Raji CVCL_0511 Burkitt lymphoma cell CL:0000945 Enhancer activity assay, TF binding assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, RT-RT-qPCR 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 acute monocytic leukemia MONDO:0005025 DOID:0080147 Blood UBERON:0000178 THP-1 CVCL_0006 acute monocytic leukemia cell CL:0000576 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay Hi-C Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, EMSA, RT-RT-qPCR 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 Normal Bronchus UBERON:0002037 HBEC3-KT bronchial epithelial cell CL:0002591 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay Hi-C Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, EMSA, RT-RT-qPCR 2024 38862995 Mechanism of ERBB2 gene overexpression by the formation of super-enhancer with genomic structural abnormalities in lung adenocarcinoma without clinically actionable genetic alterations Homo sapiens hg38 chr17 39611085 39689899 ERBB2 Enhancer Active Normal Bronchus UBERON:0002037 HSAEC1-KT bronchial epithelial cell CL:0002591 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, WGS, Hi-C, RNA-seq CRISPR Knockout, RT-RT-qPCR, FACS, Western blot 2024 38862995 Mechanism of ERBB2 gene overexpression by the formation of super-enhancer with genomic structural abnormalities in lung adenocarcinoma without clinically actionable genetic alterations Homo sapiens hg38 chr17 39611085 39689899 ERBB2 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepG2 CVCL_0027 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, WGS, Hi-C, RNA-seq CRISPR Knockout, RT-RT-qPCR, FACS, Western blot 2025 40393811 Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits Homo sapiens hg38 chr1 178551259 178551689 RALGPS2 Enhancer Active Normal Bone marrow UBERON:0002371 Adipose-Derived Mesenchymal Stem Cells-01 mesenchymal stem cell CL:0000134 Enhancer activity assay, Functional perturbation assay ATAC-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, RT-RT-qPCR 2022 36224171 Lineage-selective super enhancers mediate core regulatory circuitry during adipogenic and osteogenic differentiation of human mesenchymal stem cells Homo sapiens hg38 chr21 36282225 36337655 RUNX1 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 Kasumi-1 CVCL_0589 acute myeloid leukemia cell CL:0001054 Functional perturbation assay, Chromatin interaction assay ChIP-seq, Hi-C CRISPR knockout, RT-RT-qPCR 2022 36301402 The Tumor Invasion Paradox in Cancer Stem Cell-Driven Solid Tumors Homo sapiens hg38 chr2 212609118 212811039 IKZF2 Enhancer Silenced Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 SiHa CVCL_0032 cervical squamous cell carcinoma cell CL:0000069 Chromatin interaction assay, Functional perturbation assay Hi-C, 4C-seq, CUT&Tag, RNA-seq CRISPRi, DNA FISH, RT-RT-qPCR 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 thyroid carcinoma MONDO:0005075 DOID:3948 Thyroid UBERON:0002046 TPC1 CVCL_6298 thyroid carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay ChIP-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, ChIP-RT-qPCR 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 carcinoma MONDO:0005075 DOID:3948 Thyroid UBERON:0002046 MDA-T41 CVCL_UC55 thyroid carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIRP-seq, RNA-seq, ChIP-seq CRISPRi, RT-RT-qPCR, RIP assay, Western blot 2024 39271656 Exploring the transcriptional cooperation between RUNX2 and its associated elncRNA RAIN Homo sapiens hg38 chr7 13905623 13926156 RUNX2 ETV1 Enhancer Active Disease multiple myeloma MONDO:0005178 DOID:9538 Blood UBERON:0000178 Multiple myeloma cells plasma cell CL:0000945 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIRP-seq, RNA-seq, ChIP-seq CRISPRi, RT-RT-qPCR, RIP assay, Western blot 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 Bone Marrow UBERON:0002371 CD34+ HSPCs hematopoietic stem and progenitor cell CL:0008001 Enhancer activity assay ATAC-seq, ChIP-seq, CUT&Tag CRISPR knockout, CRISPRi, ChIP-RT-qPCR, FISH 2020 32284612 Therapeutic base editing of human hematopoietic stem cells Homo sapiens hg38 chr2 60499980 60500080 GATA1 BCL11A Enhancer Active Normal Heart UBERON:0000948 hPSC-CMs cardiomyocyte CL:0000746 Functional perturbation assay ChIP-seq, RNA-seq CRISPR Knockout, RT-RT-qPCR 2024 39196224 Cardiac ACTN2 enhancer regulates cardiometabolism and maturation Homo sapiens hg38 chr1 236783700 236783957 MEF2A ACTN2 Enhancer Active Normal Blood UBERON:0000178 Primary monocytes monocyte CL:0000576 Enhancer activity assay RNA-seq, ChIP-seq, ATAC-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2025 39870618 Genetic coupling of enhancer activity and connectivity in gene expression control Homo sapiens hg38 chr15 39315234 39315720 THBS1 Enhancer Active Disease glioblastoma MONDO:0005142 DOID:3070 Brain UBERON:0000955 U251TR glioblastoma cells CVCL_V635 glioblastoma cell CL:0000127 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ATAC-seq, Capture Hi-C, RNA-seq CRISPRi, 4C-seq, qRT-PCR 2025 40971821 Co-activation of 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:0011998 DOID:8552 Blood UBERON:0000178 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Super-enhancer activity assay, Functional perturbation assay CUT&Tag, RNA-seq Luciferase reporter assay, CRISPRi, ChIP-RT-qPCR 2024 38513139 RUNX1 C-terminal mutations impair blood cell differentiation by perturbing specific enhancer-promoter networks Homo sapiens hg38 chr8 128747000 128748000 RUNX1; RUNX1R320*; FOXK2 MYC Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, GRID-seq, RNA-seq CUT&RUN-RT-qPCR, shRNA Knockdown, RT-RT-qPCR, Western blot 2023 37373188 STAT3-Mediated Promoter-Enhancer Interaction Up-Regulates Inhibitor of DNA Binding 1 (ID1) to Promote Colon Cancer Progression Homo sapiens hg38 chr20 31606000 31608500 ID1 Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 LoVo CVCL_0399 colorectal carcinoma cell CL:0000066 Putative enhancer screening ChIP-seq, GRO-seq Dual-luciferase reporter assay 2023 37373188 STAT3-Mediated Promoter-Enhancer Interaction Up-Regulates Inhibitor of DNA Binding 1 (ID1) to Promote Colon Cancer Progression Homo sapiens hg38 chr20 31606000 31608500 ID1 Enhancer Silenced Normal Heart UBERON:0000948 Cardiac Myeloid macrophage CL:0000235 Putative enhancer screening ChIP-seq, GRO-seq Dual-luciferase reporter assay 2025 39443808 Chromatin remodelling drives immune cell-fibroblast communication in heart failure Homo sapiens hg38 chr2 113580000 113585000 IL1B Enhancer Active Disease osteosarcoma MONDO:0005087 DOID:3347 Bone UBERON:0001474 U2OS osteosarcoma CVCL_0042 osteosarcoma cell CL:0000062 Enhancer activity assay scATAC-seq FISH 2023 37620393 The ABL-MYC axis controls WIPI1-enhanced autophagy in lifespan extension Homo sapiens hg38 chr17 66452427 66453982 MYC; MAX WIPI1 Enhancer Silenced Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay, TF binding assay RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, qRT-PCR, Western blot 2024 38592784 Intergenic sequences harboring potential enhancer elements contribute to Axenfeld-Rieger syndrome by regulating PITX2 Homo sapiens hg38 chr4 111399594 111399691 PITX2 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepG2 CVCL_0027 hepatocellular carcinoma cell CL:0000182 TF binding assay, Functional perturbation assay RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2022 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 GDF15 Enhancer Active Disease neuroblastoma MONDO:0005070 DOID:769 Adrenal gland UBERON:0002369 SK-N-BE(2) CVCL_0528 neuroblastoma cell CL:0000031 Enhancer activity assay Luciferase Reporter Assay 2024 38636893 CDK5RAP3 is a novel super-enhancer-driven gene activated by master TFs and regulates ER-Phagy in neuroblastoma Homo sapiens hg38 chr17 48005000 48010000 MEIS2; HAND2 CDK5RAP3 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LuCaP PDX patient-derived xenograft prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay ChIP-seq, CUT&Tag, RNA-seq Luciferase Reporter Assay, CUT&RUN-RT-qPCR, RT-RT-qPCR, Western blot 2025 39677680 Epigenetic remodeling and 3D chromatin reorganization governed by NKX2-1 drive neuroendocrine prostate cancer Homo sapiens hg38 chr20 20025052 20648767 FOXA2 INSM1 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Chromatin interaction assay Hi-C, ChIP-seq, RNA-seq qRT-PCR 2025 39677680 Epigenetic remodeling and 3D chromatin reorganization governed by NKX2-1 drive neuroendocrine prostate cancer Homo sapiens hg38 chr17 48704466 48768465 AR HOXB13 SE Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq Western blot, qRT-PCR 2025 39677680 Epigenetic remodeling and 3D chromatin reorganization governed by NKX2-1 drive neuroendocrine prostate cancer Homo sapiens hg38 chr3 128453265 128528579 AR GATA2 SE Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq Western blot, qRT-PCR 2025 39677680 Epigenetic remodeling and 3D chromatin reorganization governed by NKX2-1 drive neuroendocrine prostate cancer Homo sapiens hg38 chr17 48529049 48630008 AR MYC SE Active Normal Brain UBERON:0000955 Human neural progenitor cells (hNPCs) neural progenitor cell CL:0002672 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq Western blot, qRT-PCR 2022 35915089 A Ctnnb1 enhancer regulates neocortical neurogenesis by controlling the abundance of intermediate progenitors Homo sapiens hg38 chr3 41119924 41122071 CTNNB1 Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ATAC-seq, ChIP-seq, RNA-seq ChIP-RT-qPCR, qRT-PCR, Western blot 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,GATA6,SOX17,MIXL1 EOMES Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 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,GATA6,SOX17,MIXL1 SOX17 Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 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 EOMES,GATA6,SOX17,MIXL1 GATA6 Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 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,GATA6,SOX17,MIXL1 SOX17 Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 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,GATA6,SOX17,MIXL1 SOX17 Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 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 EOMES,GATA6,SOX17,MIXL1 EOMES Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 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 EOMES,GATA6,SOX17,MIXL1 MIXL1 Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 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,GATA6,SOX17,MIXL1 MIXL1 Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 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,SOX17,MIXL1 GATA6 Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 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,GATA6,SOX17,MIXL1 SOX17 Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 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,SOX17,MIXL1 GATA6 Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 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,GATA6,SOX17,MIXL1 SOX17 Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 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,GATA6,SOX17,MIXL1 EOMES Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 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,GATA6,SOX17,MIXL1 EOMES Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 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 EOMES,GATA6,SOX17,MIXL1 SOX17 Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 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 EOMES,GATA6,SOX17,MIXL1 MIXL1 Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 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 SMAD2,SMAD4,JUN SMAD2 Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 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 EOMES,GATA6,SOX17,MIXL1 SOX17 Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 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 EOMES,GATA6,SOX17,MIXL1 MIXL1 Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 2023 37488417 Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions Homo sapiens hg38 chr18 47918050 47918585 SMAD2,SMAD4,JUN SMAD2 Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 2023 37488417 Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions Homo sapiens hg38 chr18 22101727 22102198 EOMES,GATA6,SOX17,MIXL1 GATA6 Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 2023 37488417 Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions Homo sapiens hg38 chr18 47901736 47902193 SMAD2,SMAD4,JUN SMAD2 Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 2023 37488417 Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions Homo sapiens hg38 chr18 22020271 22020802 EOMES,GATA6,SOX17,MIXL1 GATA6 Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 2023 37488417 Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions Homo sapiens hg38 chr1 226197015 226197408 EOMES,GATA6,SOX17,MIXL1 MIXL1 Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 2023 37488417 Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions Homo sapiens hg38 chr8 54228206 54228505 EOMES,GATA6,SOX17,MIXL1 SOX17 Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 2023 37488417 Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions Homo sapiens hg38 chr12 7970611 7971032 OCT4,SOX2,NANOG NANOG Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 2023 37488417 Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions Homo sapiens hg38 chr18 22032376 22032818 EOMES,GATA6,SOX17,MIXL1 GATA6 Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 2023 37488417 Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions Homo sapiens hg38 chr12 7439885 7440355 OCT4,SOX2,NANOG NANOG Enhancer Active Disease prostate adenocarcinoma MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP prostate cancer cell line CVCL_0395 prostate adenocarcinoma cell CL:0000066 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 2020 32680982 A rare variant of African ancestry activates 8q24 lncRNA hub by modulating cancer associated enhancer Homo sapiens hg38 chr8 127661390 127661641 MYC Enhancer Active Normal Skin UBERON:0000014 Human neonatal foreskin fibroblasts fibroblast CL:0000057 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Luciferase Reporter Assay, 4C, CRISPRi, RT-qPCR 2025 40997217 Mechanosensitive genomic enhancers potentiate the cellular response to matrix stiffness Homo sapiens hg38 chr17 44542500 44543500 FZD2 Enhancer Active Normal Skin UBERON:0000014 Human neonatal foreskin fibroblasts fibroblast CL:0000057 CRISPR interference-based functional screen ATAC-seq, RNA-seq, HiCAR, CRISPRi screening, single-cell RNA-seq Luciferase reporter assay, RT-qPCR, flow cytometry 2025 40997217 Mechanosensitive genomic enhancers potentiate the cellular response to matrix stiffness Homo sapiens hg38 chr22 36656500 36657500 MYH9 Enhancer Active Normal Skin UBERON:0000014 Human neonatal foreskin fibroblasts fibroblast CL:0000057 CRISPR interference-based functional screen ATAC-seq, RNA-seq, HiCAR, CRISPRi screening, single-cell RNA-seq Luciferase reporter assay, RT-qPCR, flow cytometry, immunostaining 2025 40997217 Mechanosensitive genomic enhancers potentiate the cellular response to matrix stiffness Homo sapiens hg38 chr15 40809500 40810500 BMF Enhancer Active Normal Inner cell mass UBERON:0000087 H9 human embryonic stem cells CVCL_9774 embryonic stem cell CL:0002322 CRISPR interference-based functional screen ATAC-seq, RNA-seq, HiCAR, CRISPRi screening, single-cell RNA-seq Luciferase reporter assay, RT-qPCR, flow cytometry, caspase assay 2019 31152430 Core pluripotency factors promote glycolysis of human embryonic stem cells by activating GLUT1 enhancer Homo sapiens hg38 chr1 43094500 43095500 SLC2A1 Enhancer Active Normal Inner cell mass UBERON:0000087 HUES8 human embryonic stem cell line CVCL_2063 embryonic stem cell CL:0002322 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay 3C, CRISPR Knockout, ChIP-qPCR, RT-qPCR 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 EOMES,GATA6,SOX17,MIXL1 SOX17 Enhancer Active Disease medulloblastoma MONDO:0005146 DOID:0050902 Cerebellum UBERON:0002037 D283 cells CVCL_1155 medulloblastoma cell CL:0000127 CRISPR interference-based functional screen CRISPRi screen, RNA-seq, ATAC-seq, ChIP-seq, Hi-C RT-qPCR, flow cytometry, FACS 2025 41338221 Targeting TET3 suppresses group 3 medulloblastoma stemness and progression via impairing hypomethylation of Otx2 super-enhancer Homo sapiens hg38 chr14 56793806 56795906 OTX2 Enhancer Active Normal Blood UBERON:0000178 Lymphoblastoid lymphoblastoid cell CL:0000945 Super-enhancer activity assay, Functional perturbation assay WGBS, CUT&Tag Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR 2021 33863876 Deletion of CTCF sites in the SHH locus alters enhancer-promoter interactions and leads to acheiropodia Homo sapiens hg38 chr7 156790916 156792095 SHH Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa cells CVCL_0030 cervical adenocarcinoma cell CL:0000069 Enhancer activity assay, Chromatin interaction assay 4C-seq, ChIP-seq 2018 31513772 The Nuclear Matrix Protein SAFA Surveils Viral RNA and Facilitates Immunity by Activating Antiviral Enhancers and Super-enhancers Homo sapiens hg38 chr9 21074270 21076270 IFNB1 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LuNE prostate carcinoma cell CL:0000066 Antiviral immune enhancer activation study, Chromatin interaction assay 3C, Immunofluorescence, RT-RT-qPCR, Western blot 2024 39677680 Epigenetic remodeling and 3D chromatin reorganization governed by NKX2-1 drive neuroendocrine prostate cancer Homo sapiens hg38 chr8 127675276 128081453 FOXA2 MYC SE Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LuNE prostate carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq Western blot, qRT-PCR 2024 39677680 Epigenetic remodeling and 3D chromatin reorganization governed by NKX2-1 drive neuroendocrine prostate cancer Homo sapiens hg38 chr9 14296620 14326255 FOXA2 NFIB SE Active Disease Kaposi sarcoma MONDO:0005082 DOID:8632 Skin UBERON:0000014 Human Kaposi sarcoma cell line CVCL_8250 Kaposi sarcoma cell CL:0002581 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq Western blot, qRT-PCR 2018 29909987 A Somatically Acquired Enhancer of the Androgen Receptor Is a Noncoding Driver in Advanced Prostate Cancer Homo sapiens hg38 chrX 67541571 67543571 AR EIF4A3 Enhancer Active Disease Kaposi sarcoma MONDO:0005082 DOID:8632 Skin UBERON:0000014 Human Kaposi sarcoma cell line CVCL_8250 Kaposi sarcoma cell CL:0002581 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq 3C, CRISPR-Cas9, ChIP-RT-qPCR, RT-PCR, RT-RT-qPCR 1993 29958106 CBF?|??-SMMHC Inhibition Triggers Apoptosis by Disrupting MYC Chromatin Dynamics in Acute Myeloid Leukemia Homo sapiens hg38 chr21 34785412 34787412 RUNX1 RUNX1 Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 LS180 colon carcinoma cell line CVCL_0397 colorectal carcinoma cell CL:0000066 Enhancer activity assay, Chromatin interaction assay ChIP-seq, RNA-seq, ATAC-seq 3C, RT-PCR, RT-RT-qPCR 2010 20236932 A Downstream Intergenic Cluster of Regulatory Enhancers Contributes to the Induction of CYP24A1 Expression by 1,25-Dihydroxyvitamin D3 Homo sapiens hg38 chr20 52173000 52174500 VDR CYP24A1 Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 LS180 colon carcinoma cell line CVCL_0397 colorectal carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, ChIP-chip, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, 3C 2010 20236932 A Downstream Intergenic Cluster of Regulatory Enhancers Contributes to the Induction of CYP24A1 Expression by 1,25-Dihydroxyvitamin D3 Homo sapiens hg38 chr20 52157000 52158500 VDR CYP24A1 Enhancer Active Disease Kaposi sarcoma MONDO:0005082 DOID:8632 Skin UBERON:0000014 Kaposi sarcoma cell line CVCL_8250 Kaposi sarcoma cell CL:0002581 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, ChIP-chip, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, 3C 2025 41388312 Nuclear PD-L1 drives IFN-?|??-promoted lung metastasis of triple-negative breast cancer via POLR2A-mediated transcriptional activation of LY6E Homo sapiens hg38 chr8 143015000 143025000 LY6E Enhancer Active Disease lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 A549 cell line CVCL_0023 lung adenocarcinoma cell CL:0001069 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2011 30097539 Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding Homo sapiens hg38 chr3 133743162 133745162 NR3C1 NR3C1 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat cell line CVCL_0065 T lymphoblast CL:0002419 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq, DNase-seq 3C, RT-PCR, RT-RT-qPCR 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 UBERON:0002367 VCaP CVCL_2235 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay 4C-seq, ChIP-seq Luciferase reporter assay, ChIP-RT-qPCR, 3C, RT-RT-qPCR, shRNA knockdown, Western blot 2009 19433513 Long-range activation of FKBP51 transcription by the androgen receptor via distal intronic enhancers Homo sapiens hg38 chr6 35687716 35687816 AR FKBP5 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP cell lines CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2009 19433513 Long-range activation of FKBP51 transcription by the androgen receptor via distal intronic enhancers Homo sapiens hg38 chr6 35687716 35687816 AR FKBP5 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 VCaP CVCL_2235 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2009 19433513 Long-range activation of FKBP51 transcription by the androgen receptor via distal intronic enhancers Homo sapiens hg38 chr6 35717716 35717816 AR FKBP5 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP cell lines CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2009 19433513 Long-range activation of FKBP51 transcription by the androgen receptor via distal intronic enhancers Homo sapiens hg38 chr6 35717716 35717816 AR FKBP5 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 VCaP CVCL_2235 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2009 19433513 Long-range activation of FKBP51 transcription by the androgen receptor via distal intronic enhancers Homo sapiens hg38 chr6 35747716 35747816 AR FKBP5 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP cell lines CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2009 19433513 Long-range activation of FKBP51 transcription by the androgen receptor via distal intronic enhancers Homo sapiens hg38 chr6 35747716 35747816 AR FKBP5 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 VCaP CVCL_2235 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2009 19433513 Long-range activation of FKBP51 transcription by the androgen receptor via distal intronic enhancers Homo sapiens hg38 chr6 35757716 35757816 AR FKBP5 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP cell lines CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2009 19433513 Long-range activation of FKBP51 transcription by the androgen receptor via distal intronic enhancers Homo sapiens hg38 chr6 35757716 35757816 AR FKBP5 Enhancer Active Disease small cell lung carcinoma MONDO:0005020 DOID:5409 Lung UBERON:0002048 SCLC cell line CVCL_1599 small cell lung carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2015 29945888 POU2F3 is a master regulator of a tuft cell-like variant of small cell lung cancer Homo sapiens hg38 chr11 120233455 120235455 POU2F3; ASCL1; NEUROD1; INSM1 POU2F3 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat human CD4+ T leukemia cell line CVCL_0065 T lymphoblast CL:0002419 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq 3C, FISH, Immunofluorescence, RT-PCR, Western blot, RT-RT-qPCR 2016 26957309 Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters Homo sapiens hg38 chr13 39700000 39750000 CD4+ T CELL-SPECIFIC FUNCTIONAL GENES Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon UBERON:0001155 HCT116 cell line CVCL_0291 colorectal carcinoma cell CL:0000066 Enhancer activity assay ChIP-seq Luciferase reporter assay 2012 22337891 Wnt/?|??-Catenin Signaling Regulates Yes-associated Protein Gene Expression in Colorectal Carcinoma Cells Homo sapiens hg38 chr11 101421506 101422130 TCF7L2 YAP1 Enhancer Active Normal Umbilical vein UBERON:0002066 HUVEC cell line CVCL_2959 umbilical vein endothelial cell CL:0002615 Enhancer activity assay ChIP-seq Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR 2012 22645302 Dynamic change of chromatin conformation in response to hypoxia enhances the expression of GLUT3 (SLC2A3) by cooperative interaction of hypoxia-inducible factor 1 and KDM3A Homo sapiens hg38 chr12 4808272 4809572 HIF1A SLC2A3 Enhancer Active Normal Umbilical vein UBERON:0002066 HUVEC cell line CVCL_2959 umbilical vein endothelial cell CL:0002615 Chromatin interaction assay, Enhancer activity assay ChIP-seq, 3C-seq Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR 2012 22645302 Dynamic change of chromatin conformation in response to hypoxia enhances the expression of GLUT3 (SLC2A3) by cooperative interaction of hypoxia-inducible factor 1 and KDM3A Homo sapiens hg38 chr12 4818572 4820072 HIF1A SLC2A3 Enhancer Active Disease neuroepithelioma MONDO:0005357 DOID:2157 Brain UBERON:0000955 SK-N-MC cell line CVCL_0530 neuroepithelioma cell CL:0000031 Chromatin interaction assay, Enhancer activity assay ChIP-seq, 3C-seq Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR 1992 30042132 Epigenome editing of microsatellite repeats defines tumor-specific enhancer functions and dependencies Homo sapiens hg38 chr3 181708868 181710868 SOX2 SOX2 Enhancer Active Normal Kidney UBERON:0002113 COS-7 cell line CVCL_0224 fibroblast-like cell CL:0000057 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq 3C, ChIP-RT-qPCR, RT-PCR, Western blot, RT-RT-qPCR 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:0005087 DOID:3347 Bone UBERON:0001474 LM8-C3H cell line CVCL_UP52 osteosarcoma cell CL:0000062 Enhancer activity assay, TF binding assay ChIP-seq 3C, RT-PCR, RT-RT-qPCR 2018 29927026 Novel lymphoid enhancer-binding factor 1-cytoglobin axis promotes extravasation of osteosarcoma cells into the lungs Homo sapiens hg38 chr4 108044908 108046908 CYGB Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF-7 cells CVCL_0031 breast carcinoma cell CL:0000646 Enhancer activity assay, Functional perturbation assay 3C, CRISPR-Cas9, RT-PCR, Western blot, RT-RT-qPCR 2013 23273978 eRNAs Are Required for p53-Dependent Enhancer Activity and Gene Transcription Homo sapiens hg38 chr1 117752000 117754000 TP53 PAPPA Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF-7 cells CVCL_0031 breast carcinoma cell CL:0000646 Enhancer activity assay 4C-seq Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR 2013 23273978 eRNAs Are Required for p53-Dependent Enhancer Activity and Gene Transcription Homo sapiens hg38 chr1 179369000 179374000 TP53 IER5 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay 4C-seq Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR 2009 19680443 Functional Enhancers at the Gene-Poor 8q24 Cancer-Linked Locus Homo sapiens hg38 chr8 128600697 128601159 AR; FOXA1 MYC Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Enhancer activity assay, TF binding assay ChIP-chip Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA 2007 17277777 Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome Homo sapiens hg38 chr5 131784596 131785596 SLC22A5 Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Reporter gene assay ChIP-chip Luciferase reporter assay 2007 17277777 Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome Homo sapiens hg38 chr5 131790596 131791596 STAT1 Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Reporter gene assay ChIP-chip Luciferase reporter assay 2007 17277777 Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome Homo sapiens hg38 chr7 115940408 115941408 STAT1 Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Reporter gene assay ChIP-chip Luciferase reporter assay 2007 17277777 Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome Homo sapiens hg38 chr9 129175952 129176952 STAT1 Enhancer Active Normal Blood UBERON:0000178 Reporter gene assay ChIP-chip Luciferase reporter assay 2007 17053039 Transcriptional Control of Receptor Activator of Nuclear Factor-B 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 hg38 chr13 42080367 42080909 CREB1 TNFRSF11 Enhancer Active Normal Bone UBERON:0001474 U-2 OS cell CVCL_0042 osteosarcoma cell CL:0000062 Enhancer activity assay, TF binding assay Luciferase reporter assay, ChIP-RT-qPCR, qRT-PCR, EMSA 1999 28637769 Potential contribution of tandem circadian enhancers to nonlinear oscillations in clock gene expression Homo sapiens hg38 chr11 45846943 45846959 CRY2 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF-7 cells CVCL_0031 breast carcinoma cell CL:0000646 Enhancer activity assay Luciferase reporter assay 2013 23273978 eRNAs Are Required for p53-Dependent Enhancer Activity and Gene Transcription Homo sapiens hg38 chr1 117752500 117753100 PAPPA Enhancer Active Normal Lung UBERON:0002048 HFL1 cells CVCL_2949 lung fibroblast CL:0000057 Enhancer activity assay Luciferase reporter assay, RT-RT-qPCR 2012 22260630 Regulation of Human Microsomal Prostaglandin E Synthase-1 by IL-1?|?? Requires a Distal Enhancer Element with a Unique Role for C/EBP?|?? Homo sapiens hg38 chr9 133601400 133601900 CEBPB PTGES Enhancer Active Normal Skin UBERON:0000014 BJ fibroblasts CVCL_3653 fibroblast CL:0000057 Enhancer activity assay Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR 2014 24797517 The Histone Lysine Demethylase JMJD3/KDM6B Is Recruited to p53 Bound Promoters and Enhancer Elements in a p53 Dependent Manner Homo sapiens hg38 chr6 36633472 36634972 TP53 CDKN1A Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Functional perturbation assay ChIP-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2007 17277777 Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome Homo sapiens hg38 chr5 131784000 131784700 SLC22A5 Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Enhancer activity assay ChIP-chip Luciferase Reporter Assay, RT-RT-qPCR 2007 17277777 Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome Homo sapiens hg38 chr5 131790800 131791300 Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Enhancer activity assay ChIP-chip Luciferase Reporter Assay, RT-RT-qPCR 2007 17277777 Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome Homo sapiens hg38 chr7 115940600 115941200 Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Enhancer activity assay ChIP-chip Luciferase Reporter Assay, RT-RT-qPCR 2007 17277777 Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome Homo sapiens hg38 chr9 129176100 129176800 Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Enhancer activity assay ChIP-chip Luciferase Reporter Assay, RT-RT-qPCR 2007 17277777 Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome Homo sapiens hg38 chr21 34091200 34091900 Enhancer Active Normal Bone marrow UBERON:0002371 FDCP-mix CVCL_WT35 hematopoietic progenitor cell CL:0000837 Enhancer activity assay ChIP-chip Luciferase Reporter Assay, RT-RT-qPCR 2007 17637499 mNotch1 signaling and erythropoietin cooperate in erythroid differentiation of multipotent progenitor cells and upregulate beta-globin Homo sapiens hg38 chr11 5246250 5246637 HBB Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Bone marrow UBERON:0002371 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay Luciferase Reporter Assay 2007 17637499 mNotch1 signaling and erythropoietin cooperate in erythroid differentiation of multipotent progenitor cells and upregulate beta-globin Homo sapiens hg38 chr11 5246250 5246637 HBB Enhancer Active Disease esophageal squamous cell carcinoma MONDO:0005082 DOID:3748 Esophagus UBERON:0001043 KYSE-30 CVCL_1351 esophageal squamous cell carcinoma cell CL:0000069 Enhancer activity assay Luciferase Reporter Assay 2014 24788237 The Identification of a ESCC Susceptibility SNP rs920778 That Regulates the Expression of lncRNA HOTAIR via a Novel Intronic Enhancer Homo sapiens hg38 chr12 52644741 52645375 HOTAIR Enhancer Active Normal Bone Marrow UBERON:0002371 Primary Erythroblasts erythroblast CL:0000765 Enhancer activity assay Luciferase Reporter Assay 2007 17715390 Tissue-specific histone modification and transcription factor binding in alpha globin gene expression Homo sapiens hg38 chr16 110000 115000 HBA1 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Bone Marrow UBERON:0002371 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-chip, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2007 17715390 Tissue-specific histone modification and transcription factor binding in alpha globin gene expression Homo sapiens hg38 chr16 110000 115000 HBA1 Enhancer Active Normal Bone Marrow UBERON:0002371 Primary Erythroblasts erythroblast CL:0000765 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-chip, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2007 17715390 Tissue-specific histone modification and transcription factor binding in alpha globin gene expression Homo sapiens hg38 chr16 118000 123000 HBA1 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Bone Marrow UBERON:0002371 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-chip, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2007 17715390 Tissue-specific histone modification and transcription factor binding in alpha globin gene expression Homo sapiens hg38 chr16 118000 123000 HBA1 Enhancer Active Normal Bone Marrow UBERON:0002371 Primary Erythroblasts erythroblast CL:0000765 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-chip, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2007 17715390 Tissue-specific histone modification and transcription factor binding in alpha globin gene expression Homo sapiens hg38 chr16 125000 130000 HBA1 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Bone Marrow UBERON:0002371 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-chip, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2007 17715390 Tissue-specific histone modification and transcription factor binding in alpha globin gene expression Homo sapiens hg38 chr16 125000 130000 HBA1 Enhancer Active Normal Bone Marrow UBERON:0002371 Primary Erythroblasts erythroblast CL:0000765 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-chip, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2007 17715390 Tissue-specific histone modification and transcription factor binding in alpha globin gene expression Homo sapiens hg38 chr16 148000 153000 HBA1 Enhancer Active Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Bone Marrow UBERON:0002371 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-chip, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2007 17715390 Tissue-specific histone modification and transcription factor binding in alpha globin gene expression Homo sapiens hg38 chr16 148000 153000 HBA1 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 PEER CVCL_1913 T lymphoblast CL:0002419 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-chip, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 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 PU1 and HMGA1 Homo sapiens hg38 chr14 98670000 98720000 BCL11B Enhancer Active Normal Connective tissue UBERON:0002384 Pluripotent stem cell pluripotent stem cell CL:0002248 Enhancer activity assay ATAC-seq DNA inhibitory treatment, RT-RT-qPCR 1978 31631012 Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction Homo sapiens hg38 chr2 209421458 209423458 MAP2 Enhancer Active Normal Embryonic cardiac tissue UBERON:0000948 10T1/2 cells CVCL_0190 mesenchymal stem cell CL:0000134 Enhancer activity assay, Chromatin interaction assay 3C, RT-PCR, RT-RT-qPCR 2012 22303449 ISL1 Directly Regulates FGF10 Transcription during Human Cardiac Outflow Formation Homo sapiens hg38 chr5 44421506 44422602 FGF10 Enhancer Active Disease holoprosencephaly MONDO:0019054 DOID:1128 Forebrain UBERON:0001890 COS-1 CVCL_0223 fibroblast CL:0000057 Enhancer activity assay Luciferase reporter assay, Transgenic reporter assay, RT-RT-qPCR 2008 18836447 Regulation of a remote Shh forebrain enhancer by the Six3 homeoprotein Homo sapiens hg38 chr7 155754267 155755366 SIX3 SHH Enhancer Active Normal Forebrain UBERON:0001890 Primary embryonic cells embryonic cell CL:0000000 Enhancer activity assay, TF binding assay, Functional perturbation assay Transgenic Reporter Assay, ChIP-RT-qPCR, EMSA, RT-RT-qPCR 2008 18836447 Regulation of a remote Shh forebrain enhancer by the Six3 homeoprotein Homo sapiens hg38 chr7 155754267 155755366 SIX3 SHH Enhancer Active Normal Inner cell mass UBERON:0000087 Embryonic stem cell embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Functional perturbation assay Transgenic Reporter Assay, ChIP-RT-qPCR, EMSA, RT-RT-qPCR 2014 30527662 Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods Homo sapiens hg38 chr17 30249928 30278499 SIK1 Enhancer Active Normal Embryonic cardiac tissue UBERON:0000948 10T1/2 cells CVCL_0190 mesenchymal stem cell CL:0000134 Enhancer activity assay, Chromatin interaction assay Western blot 2012 22303449 ISL1 Directly Regulates FGF10 Transcription during Human Cardiac Outflow Formation Homo sapiens hg38 chr5 44421506 44422602 FGF10 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 PEER CVCL_1913 T lymphoblast CL:0002419 Enhancer activity assay Luciferase reporter assay, Transgenic reporter assay, RT-RT-qPCR 2007 17308084 Activation of TLX3 and NKX2-5 in t(5;14)(q35;q322) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU1 and HMGA1 Homo sapiens hg38 chr14 97720000 97780000 PU.1 NKX2-5 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 DND-41 CVCL_2022 T lymphoblast CL:0002419 Enhancer activity assay, Functional perturbation assay DNase-seq DNA inhibitory treatment, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, FISH 2007 17308084 Activation of TLX3 and NKX2-5 in t(5;14)(q35;q322) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU1 and HMGA1 Homo sapiens hg38 chr14 97720000 97780000 PU.1 NKX2-5 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 CCRF-CEM CVCL_0207 T lymphoblast CL:0002419 Enhancer activity assay, Functional perturbation assay DNase-seq DNA inhibitory treatment, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, FISH 2007 17308084 Activation of TLX3 and NKX2-5 in t(5;14)(q35;q322) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU1 and HMGA1 Homo sapiens hg38 chr14 97720000 97780000 PU.1 NKX2-5 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 HPB-ALL CVCL_1921 T lymphoblast CL:0002419 Enhancer activity assay, Functional perturbation assay DNase-seq DNA inhibitory treatment, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, FISH 2007 17308084 Activation of TLX3 and NKX2-5 in t(5;14)(q35;q322) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU1 and HMGA1 Homo sapiens hg38 chr14 97720000 97780000 PU.1 NKX2-5 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 PEER CVCL_1913 T lymphoblast CL:0002419 Enhancer activity assay, Functional perturbation assay DNase-seq DNA inhibitory treatment, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, FISH 2007 17308084 Activation of TLX3 and NKX2-5 in t(5;14)(q35;q322) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU1 and HMGA1 Homo sapiens hg38 chr14 97720000 97780000 PU.1 TLX3 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 DND-41 CVCL_2022 T lymphoblast CL:0002419 Enhancer activity assay, Functional perturbation assay DNase-seq DNA inhibitory treatment, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, FISH 2007 17308084 Activation of TLX3 and NKX2-5 in t(5;14)(q35;q322) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU1 and HMGA1 Homo sapiens hg38 chr14 97720000 97780000 PU.1 TLX3 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 CCRF-CEM CVCL_0207 T lymphoblast CL:0002419 Enhancer activity assay, Functional perturbation assay DNase-seq DNA inhibitory treatment, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, FISH 2007 17308084 Activation of TLX3 and NKX2-5 in t(5;14)(q35;q322) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU1 and HMGA1 Homo sapiens hg38 chr14 97720000 97780000 PU.1 TLX3 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 HPB-ALL CVCL_1921 T lymphoblast CL:0002419 Enhancer activity assay, Functional perturbation assay DNase-seq DNA inhibitory treatment, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, FISH 2007 17308084 Activation of TLX3 and NKX2-5 in t(5;14)(q35;q322) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU1 and HMGA1 Homo sapiens hg38 chr14 97720000 97780000 PU.1 TLX3 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 PEER CVCL_1913 T lymphoblast CL:0002419 Enhancer activity assay, Functional perturbation assay DNase-seq DNA inhibitory treatment, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, FISH 2007 17308084 Activation of TLX3 and NKX2-5 in t(5;14)(q35;q322) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU1 and HMGA1 Homo sapiens hg38 chr14 98500000 98710000 BCL11B Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 DND-41 CVCL_2022 T lymphoblast CL:0002419 Enhancer activity assay, Functional perturbation assay DNase-seq DNA inhibitory treatment, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, FISH 2007 17308084 Activation of TLX3 and NKX2-5 in t(5;14)(q35;q322) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU1 and HMGA1 Homo sapiens hg38 chr14 98500000 98710000 BCL11B Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 CCRF-CEM CVCL_0207 T lymphoblast CL:0002419 Enhancer activity assay, Functional perturbation assay DNase-seq DNA inhibitory treatment, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, FISH 2007 17308084 Activation of TLX3 and NKX2-5 in t(5;14)(q35;q322) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU1 and HMGA1 Homo sapiens hg38 chr14 98500000 98710000 BCL11B Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 HPB-ALL CVCL_1921 T lymphoblast CL:0002419 Enhancer activity assay, Functional perturbation assay DNase-seq DNA inhibitory treatment, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, FISH 2007 17308084 Activation of TLX3 and NKX2-5 in t(5;14)(q35;q322) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU1 and HMGA1 Homo sapiens hg38 chr14 98500000 98710000 BCL11B Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 22Rv1 cells CVCL_1045 prostate carcinoma cell CL:0000066 Enhancer activity assay, Functional perturbation assay DNase-seq DNA inhibitory treatment, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, FISH 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 SRRM4 Enhancer Active Normal Connective tissue UBERON:0002384 Pluripotent stem cell pluripotent stem cell CL:0002248 Chromatin interaction assay, Enhancer activity assay, Functional perturbation assay 4C-seq, RNA-seq Luciferase reporter assay, CRISPR knockout, RT-RT-qPCR 2006 31513343 Generation of Nanog reporter mice that distinguish pluripotent stem cells from unipotent primordial germ cells Homo sapiens hg38 chr17 42310596 42312596 STAT3 Enhancer Active Normal Bone marrow UBERON:0002371 G1E cell CVCL_Y439 erythroid progenitor cell CL:0000038 Enhancer activity assay 3C, Immunofluorescence, RT-PCR, RT-RT-qPCR 2008 26443845 Dynamic enhancer-gene body contacts during transcription elongation Homo sapiens hg38 chr16 49740654 49742654 CD47 Enhancer Active Disease testicular cancer MONDO:0005106 DOID:2998 Testis UBERON:0000473 Sustentacular cell Sertoli cell CL:0000216 Enhancer activity assay, Chromatin interaction assay 3C, RT-RT-qPCR 2013 28087634 Genome-wide identification of regulatory elements in Sertoli cells Homo sapiens hg38 chr2 105072843 105076843 WT1 Enhancer Active Normal Bone marrow UBERON:0002371 Mononuclear phagocyte monocyte CL:0000576 Enhancer activity assay ChIP-seq qRT-PCR, and ChIP-qPCR 2014 29514092 Transcription Factor IRF8 Governs Enhancer Landscape Dynamics in Mononuclear Phagocyte Progenitors Homo sapiens hg38 chr19 61151074 61161722 IRF8 CSF2RA Enhancer Active Normal Prostate UBERON:0002367 Enhancer activity assay, TF binding assay ChIP-seq qRT-PCR, and ChIP-qPCR 2008 29514101 Accelerated Evolution in Distinctive Species Reveals Candidate Elements for Clinically Relevant Traits, Including Mutation and Cancer Resistance Homo sapiens hg38 chrX 67541320 67543320 AR Enhancer Active Disease schizophrenia MONDO:0005076 DOID:5419 Brain UBERON:0000955 Neural cell neuron CL:0000540 Enhancer evolution assay DNase-seq 3C, RT-PCR, RT-qPCR 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 SOX2-OT Enhancer Active Disease type 1 diabetes mellitus MONDO:0005147 DOID:9744 Pancreas UBERON:0001264 CD8+ T cell CD8-positive T cell CL:0000625 Enhancer activity assay ATAC-seq 3C, RT-PCR, RT-RT-qPCR 2018 30078552 Conventional and Neo-antigenic Peptides Presented by beta Cells Are Targeted by Circulating Na?ve CD8+ T Cells in Type 1 Diabetic and Healthy Donors Homo sapiens hg38 chr14 92920852 92922852 PTPRN Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa cell CVCL_0030 cervical adenocarcinoma cell CL:0000069 Enhancer activity assay RNA-seq 3C, Immunofluorescence, RT-PCR, RT-RT-qPCR 2019 31679819 R-Loops Promote Antisense Transcription across the Mammalian Genome Homo sapiens hg38 chr12 48826675 48828675 DDX23 Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa cell CVCL_0030 cervical adenocarcinoma cell CL:0000069 Enhancer activity assay 3C, RT-PCR, Western blot, RT-RT-qPCR 2019 31679819 R-Loops Promote Antisense Transcription across the Mammalian Genome Homo sapiens hg38 chr12 48826675 48828675 DDX23 Enhancer Active Normal Blood vessel UBERON:0001981 Endothelial stalk cell endothelial cell CL:0000115 Enhancer activity assay 3C, RT-PCR, Western blot, RT-RT-qPCR 2017 28121289 Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq Homo sapiens hg38 chr6 88202011 88204330 GATA2 Enhancer Active Normal Liver UBERON:0002107 Hepatocyte hepatocyte CL:0000182 Enhancer activity assay, TF binding assay ChIP-seq Luciferase reporter assay, Western blot 2018 30057115 Diet-Induced Circadian Enhancer Remodeling Synchronizes Opposing Hepatic Lipid Metabolic Processes Homo sapiens hg38 chr3 133743395 133745395 Enhancer Active Disease esophageal carcinoma MONDO:0004986 DOID:5041 Esophagus UBERON:0001043 Oesophageal squamous cell esophageal squamous cell CL:0000069 Enhancer activity assay ChIP-seq 3C, RT-PCR, Western blot, RT-RT-qPCR 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 Lung UBERON:0002048 BEAS-2B cells CVCL_0168 bronchial epithelial cell CL:0002591 Enhancer activity assay ChIP-seq 3C, RT-PCR, RT-RT-qPCR 2025 40164603 Enhancer RNA transcription pinpoints functional genetic variants linked to asthma Homo sapiens hg38 chr5 142404236 142405236 NR3C1 Enhancer Active Normal Blood UBERON:0000178 Jurkat E6.1 CVCL_0065 T lymphoblast CL:0002419 Enhancer activity assay, TF binding assay, Chromatin interaction assay GRO-seq, PRO-seq, Micro-C, ATAC-seq Luciferase reporter assay, RT-RT-qPCR 2025 40160815 A pooled CRISPR screen identifies the T??2 enhancer element as a driver of TRA expression in a subset of mature human T lymphocytes Homo sapiens hg38 chr14 22553100 22553200 TRAC Enhancer Active Normal Blood UBERON:0000178 primary human CD3+ T cells T cell CL:0000084 Functional perturbation assay CRISPR screen CRISPR Knockout, CRISPRi, RT-RT-qPCR, Flow Cytometry, Sanger Sequencing 2025 40160815 A pooled CRISPR screen identifies the T??2 enhancer element as a driver of TRA expression in a subset of mature human T lymphocytes Homo sapiens hg38 chr14 22553100 22553200 TRAC Enhancer Active Normal Blood UBERON:0000178 Monocyte-derived macrophage (hMDM) macrophage CL:0000235 Functional perturbation assay CRISPR screen CRISPR Knockout, CRISPRi, RT-RT-qPCR, Flow Cytometry, Sanger Sequencing 2015 26663721 Enhancer Turnover Is Associated with a Divergent Transcriptional Response to Glucocorticoid in Mouse and Human Macrophages Homo sapiens hg38 chr1 109800000 109801100 NR3C1 ADORA3 Enhancer Active Normal Heart UBERON:0000948 hPSC-CMs cardiomyocyte CL:0000746 TF binding assay, Enhancer activity assay ChIP-seq, RNA-seq RT-RT-qPCR 2024 39196225 A transcriptional enhancer regulates cardiac maturation Homo sapiens hg38 chr1 236783100 236784400 ACTN2 Enhancer Active Normal Bone Marrow UBERON:0002371 CD34+ HSPCs hematopoietic stem and progenitor cell CL:0008001 Functional perturbation assay RNA-seq, scRNA-seq CRISPR Knockout, RT-RT-qPCR, Western blot, Calcium Transient Measurement, Seahorse Assay 2020 32170070 MMP9 mediates acute hyperglycemia-induced human cardiac stem cell death by upregulating apoptosis and pyroptosis in vitro Homo sapiens hg38 chr2 60722225 60722425 BCL11A Enhancer Active Disease non-small cell lung carcinoma MONDO:0005233 DOID:3908 Lung UBERON:0002048 NSCLC cell lines non-small cell lung carcinoma cell CL:0000066 Functional perturbation assay, Enhancer activity assay Amplicon deep sequencing, RNA-seq CRISPR Base Editing, RT-RT-qPCR, HPLC, Flow Cytometry, Sickling Assay 2024 39614285 PD-1/PD-L1 immune checkpoint blockade in breast cancer: research insights and sensitization strategies Homo sapiens hg38 chr2 241851500 241851650 STAT3 PDCD1 Enhancer Active Normal Embryonic Limb Bud UBERON:0005417 Limb bud mesenchymal cells mesenchymal cell CL:0000134 Enhancer activity assay, TF binding assay RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA 2025 40604280 Range extender mediates long-distance enhancer activity Mus musculus mm10 chr5 29314497 29315844 Lhx2; Lhx9; Lef1; Ets1; Etv; Hox Shh Enhancer Active Normal Limb Bud UBERON:0005417 Zone of polarizing activity cells mesenchymal cell CL:0000134 TF binding assay, Enhancer activity assay, Functional perturbation assay ATAC-seq, ChIP-seq, Hi-C, scATAC-seq/scRNA-seq multiome, RNA-seq Transgenic Reporter Assay, CRISPR Knockout, CRISPR Knock-in, RT-RT-qPCR, Whole-mount in situ hybridization, Skeletal staining, EMSA, Luciferase Reporter Assay 2025 40604280 Range extender mediates long-distance enhancer activity Mus musculus mm10 chr5 29314497 29315844 Lhx2; Lhx9; Lef1; Ets1; Etv; Hox Shh Enhancer Active Normal Bone Marrow UBERON:0002371 32D Cells CVCL_0C92 myeloid progenitor cell CL:0000837 TF binding assay, Enhancer activity assay, Functional perturbation assay ATAC-seq, ChIP-seq, Hi-C, scATAC-seq/scRNA-seq multiome, RNA-seq Transgenic Reporter Assay, CRISPR Knockout, CRISPR Knock-in, RT-RT-qPCR, Whole-mount in situ hybridization, Skeletal staining, EMSA, Luciferase Reporter Assay 2019 30952671 Identification of a novel enhancer of CEBPE essential for granulocytic differentiation Mus musculus mm10 chr14 54705845 54707084 Cebpa Cebpe Enhancer Active Normal Bone Marrow UBERON:0002371 Primary Mouse Bone Marrow Cells mouse bone marrow cell CL:0000000 TF binding assay, Chromatin interaction assay, Functional perturbation assay, Enhancer activity assay 4C-seq, RNA-seq, ChIP-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR 2019 30952671 Identification of a novel enhancer of CEBPE essential for granulocytic differentiation Mus musculus mm10 chr14 54705845 54707084 Cebpa Cebpe Enhancer Active Normal Brain UBERON:0000955 Neural progenitor cells (NPCs) neural progenitor cell CL:0002672 TF binding assay, Chromatin interaction assay, Functional perturbation assay, Enhancer activity assay 4C-seq, RNA-seq, ChIP-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR 2022 35915089 A Ctnb1 enhancer regulates neocortical neurogenesis by controlling the abundance of intermediate progenitors Mus musculus mm10 chr9 120869524 120870219 Ctnnb1 Enhancer Active Normal Brown adipose tissue UBERON:0001348 Brown adipocytes (SVF) brown adipocyte CL:0000136 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq Transgenic Reporter Assay, CRISPR Knockout, CRISPRi, CRISPRa, 3C, ChIP-RT-qPCR, Luciferase Reporter Assay 2025 39789228 Identification of a distal enhancer of Ucp1 essential for thermogenesis and mitochondrial function in brown fat Mus musculus mm10 chr8 83274000 83275000 Ebf2 Ucp1 Enhancer Active Normal Brown adipose tissue UBERON:0001348 Brown adipocytes (SVF) brown adipocyte CL:0000136 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay 4C-seq, ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, CRISPRi, 3C-RT-qPCR, qRT-PCR, Western blot 2025 39789228 Identification of a distal enhancer of Ucp1 essential for thermogenesis and mitochondrial function in brown fat Mus musculus mm10 chr8 83277000 83278000 Ebf2 Ucp1 Enhancer Active Normal Brain UBERON:0000955 Neural progenitor cells (NPCs) neural progenitor cell CL:0002672 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay 4C-seq, ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, CRISPRi, 3C-RT-qPCR, qRT-PCR, Western blot 2022 35915089 A Ctnnb1 enhancer regulates neocortical neurogenesis by controlling the abundance of intermediate progenitors Mus musculus mm10 chr9 120869062 120871341 Ctnnb1 Enhancer Active Normal Embryo UBERON:0000922 Mouse Embryonic Stem Cells (ESCs) mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, ATAC-seq Transgenic Reporter Assay, Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, CRISPRi, CRISPRa, qRT-PCR, Western blot 2022 35977485 Transcriptomics, regulatory syntax, and enhancer identification in mesoderm-induced ESCs at single-cell resolution Mus musculus mm10 chr4 139771035 139771985 Pax7 Enhancer Active Normal Bone marrow UBERON:0002371 Mouse hematopoietic stem cells (HSCs) mouse hematopoietic stem cell CL:0001029 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ATAC-seq, RNA-seq, ChIP-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, qRT-PCR, Western blot 2025 41129262 The hematopoietic stem cell MYB enhancer is essential for and recurrently amplified during T cell leukemogenesis Mus musculus mm10 chr10 20942490 21160984 Ets1 Myb Enhancer Active Normal Bone Marrow UBERON:0002371 Primary CD19+ pro-B cells pro-B cell CL:0000945 Enhancer activity assay, TF binding assay, Functional perturbation assay, Chromatin interaction assay ChIP-seq, ATAC-seq, Hi-C, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, ChIP-RT-qPCR, qRT-PCR, Western blot 2023 36869028 An Igh distal enhancer modulates antigen receptor diversity by determining locus conformation Mus musculus mm10 chr12 114182511 114183025 Ctcf Igh Enhancer Active Normal Spleen UBERON:0002106 Abl-transformed pro-B cells pro-B cell CL:0000945 Functional perturbation assay, Enhancer activity assay, Chromatin interaction assay, TF binding assay Hi-C, ChIP-seq, RNA-seq, ATAC-seq, VDJ-seq, 3C-seq CRISPR Knockout, RT-RT-qPCR, ChIP-RT-qPCR, 3C assay, 4C assay, FISH, Western blot 2023 36869028 An Igh distal enhancer modulates antigen receptor diversity by determining locus conformation Mus musculus mm10 chr12 114182511 114183025 Ctcf Igh Enhancer Active Normal Spleen UBERON:0002106 Rag1-/- pro-B cells pro-B cell CL:0000945 Functional perturbation assay, Enhancer activity assay, Chromatin interaction assay, TF binding assay Hi-C, ChIP-seq, RNA-seq, ATAC-seq, VDJ-seq, 3C-seq CRISPR Knockout, RT-RT-qPCR, ChIP-RT-qPCR, 3C assay, 4C assay, FISH, Western blot 2023 36869028 An Igh distal enhancer modulates antigen receptor diversity by determining locus conformation Mus musculus mm10 chr12 114182511 114183025 Ctcf Igh Enhancer Active Normal Spleen UBERON:0002106 Rag2-/- pro-B cells pro-B cell CL:0000945 Functional perturbation assay, Enhancer activity assay, Chromatin interaction assay, TF binding assay Hi-C, ChIP-seq, RNA-seq, ATAC-seq, VDJ-seq, 3C-seq CRISPR Knockout, RT-RT-qPCR, ChIP-RT-qPCR, 3C assay, 4C assay, FISH, Western blot 2023 36869028 An Igh distal enhancer modulates antigen receptor diversity by determining locus conformation Mus musculus mm10 chr12 114182511 114183025 Ctcf Igh Enhancer Active Normal Embryo UBERON:0000922 Mouse ESCs mouse embryonic stem cell CL:0002322 Functional perturbation assay, Enhancer activity assay, Chromatin interaction assay, TF binding assay Hi-C, ChIP-seq, RNA-seq, ATAC-seq, VDJ-seq, 3C-seq CRISPR Knockout, RT-RT-qPCR, ChIP-RT-qPCR, 3C assay, 4C assay, FISH, Western blot 2021 34599190 Enhancer-associated H3K4 methylation safeguards in vitro germline competence Mus musculus mm10 chr12 96450000 96452000 Esrrb Enhancer Active Normal Embryo UBERON:0000922 Epiblast-like cells epiblast-like cell CL:0002322 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, Capture Hi-C CRISPR Knockout, RT-RT-qPCR, Flow Cytometry 2021 34599190 Enhancer-associated H3K4 methylation safeguards in vitro germline competence Mus musculus mm10 chr12 96450000 96452000 Esrrb Enhancer Active Normal Embryo UBERON:0000922 Primordial germ cell-like cells primordial germ cell-like cell CL:0000670 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, Capture Hi-C CRISPR Knockout, RT-RT-qPCR, Flow Cytometry 2021 34599190 Enhancer-associated H3K4 methylation safeguards in vitro germline competence Mus musculus mm10 chr12 96450000 96452000 Esrrb Enhancer Active Normal Embryo UBERON:0000922 Mouse ESCs mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, Capture Hi-C CRISPR Knockout, RT-RT-qPCR, Flow Cytometry 2021 34599190 Enhancer-associated H3K4 methylation safeguards in vitro germline competence Mus musculus mm10 chr13 24180000 24182000 Klf5 Enhancer Active Normal Embryo UBERON:0000922 Epiblast-like cells epiblast-like cell CL:0002322 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, Capture Hi-C CRISPR Knockout, RT-RT-qPCR, Flow Cytometry 2021 34599190 Enhancer-associated H3K4 methylation safeguards in vitro germline competence Mus musculus mm10 chr13 24180000 24182000 Klf5 Enhancer Active Normal Embryo UBERON:0000922 Primordial germ cell-like cells primordial germ cell-like cell CL:0000670 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, Capture Hi-C CRISPR Knockout, RT-RT-qPCR, Flow Cytometry 2021 34599190 Enhancer-associated H3K4 methylation safeguards in vitro germline competence Mus musculus mm10 chr13 24180000 24182000 Klf5 Enhancer Active Normal Embryo UBERON:0000922 Mouse ESCs mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, Capture Hi-C CRISPR Knockout, RT-RT-qPCR, Flow Cytometry 2021 34599190 Enhancer-associated H3K4 methylation safeguards in vitro germline competence Mus musculus mm10 chr4 102450000 102452000 Prdm14 Enhancer Active Normal Embryo UBERON:0000922 Epiblast-like cells epiblast-like cell CL:0002322 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, Capture Hi-C CRISPR Knockout, RT-RT-qPCR, Flow Cytometry 2021 34599190 Enhancer-associated H3K4 methylation safeguards in vitro germline competence Mus musculus mm10 chr4 102450000 102452000 Prdm14 Enhancer Active Normal Embryo UBERON:0000922 Primordial germ cell-like cells primordial germ cell-like cell CL:0000670 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, Capture Hi-C CRISPR Knockout, RT-RT-qPCR, Flow Cytometry 2021 34599190 Enhancer-associated H3K4 methylation safeguards in vitro germline competence Mus musculus mm10 chr4 102450000 102452000 Prdm14 Enhancer Active Normal Embryo UBERON:0000922 Mouse ESCs mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, Capture Hi-C CRISPR Knockout, RT-RT-qPCR, Flow Cytometry 2021 34599190 Enhancer-associated H3K4 methylation safeguards in vitro germline competence Mus musculus mm10 chr4 102455000 102457000 Prdm14 Enhancer Active Normal Embryo UBERON:0000922 Epiblast-like cells epiblast-like cell CL:0002322 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, Capture Hi-C CRISPR Knockout, RT-RT-qPCR, Flow Cytometry 2021 34599190 Enhancer-associated H3K4 methylation safeguards in vitro germline competence Mus musculus mm10 chr4 102455000 102457000 Prdm14 Enhancer Active Normal Embryo UBERON:0000922 Primordial germ cell-like cells primordial germ cell-like cell CL:0000670 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, Capture Hi-C CRISPR Knockout, RT-RT-qPCR, Flow Cytometry 2021 34599190 Enhancer-associated H3K4 methylation safeguards in vitro germline competence Mus musculus mm10 chr4 102455000 102457000 Prdm14 Enhancer Active Normal Embryo UBERON:0000922 Mouse ESCs mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, Capture Hi-C CRISPR Knockout, RT-RT-qPCR, Flow Cytometry 2021 34599190 Enhancer-associated H3K4 methylation safeguards in vitro germline competence Mus musculus mm10 chr4 102460000 102462000 Prdm14 Enhancer Active Normal Embryo UBERON:0000922 Epiblast-like cells epiblast-like cell CL:0002322 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, Capture Hi-C CRISPR Knockout, RT-RT-qPCR, Flow Cytometry 2021 34599190 Enhancer-associated H3K4 methylation safeguards in vitro germline competence Mus musculus mm10 chr4 102460000 102462000 Prdm14 Enhancer Active Normal Embryo UBERON:0000922 Primordial germ cell-like cells primordial germ cell-like cell CL:0000670 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, Capture Hi-C CRISPR Knockout, RT-RT-qPCR, Flow Cytometry 2021 34599190 Enhancer-associated H3K4 methylation safeguards in vitro germline competence Mus musculus mm10 chr4 102460000 102462000 Prdm14 Enhancer Active Disease neuroblastoma MONDO:0005070 DOID:769 Brain UBERON:0000955 Neuro2a CVCL_0470 neuroblastoma cell CL:0000031 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, Capture Hi-C CRISPR Knockout, RT-RT-qPCR, Flow Cytometry 2018 30545847 CRISPR-mediated activation of a promoter or enhancer rescues obesity caused by haploinsufficiency Mus musculus mm10 chr10 80245000 80246500 Sim1 Sim1 Enhancer Active Normal Embryo UBERON:0000922 Mouse Embryonic Stem Cells (mESCs; E14TG2a; J1) CVCL_2167 mouse embryonic stem cell CL:0002322 Functional perturbation assay, Enhancer activity assay ChIP-seq, ATAC-seq CRISPR Activation, Luciferase Reporter Assay 2019 31422875 Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from naive pluripotency Mus musculus mm10 chr1 63185000 63188000 Pou5F1 Zdbf2 Enhancer Active Normal Embryo UBERON:0000922 Mouse Embryonic Stem Cells (mESCs; E14TG2a; J1) CVCL_2167 mouse embryonic stem cell CL:0002322 Enhancer activity assay, Chromatin interaction assay, TF binding assay 4C-seq, ATAC-seq, ChIP-seq, RNA-seq, WGBS CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Bisulfite Pyrosequencing 2019 31422875 Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from naive pluripotency Mus musculus mm10 chr1 63185000 63188000 Pou5F1 Zdbf2 Enhancer Active Normal Blood UBERON:0000178 Dendritic cells dendritic cell CL:0000451 Enhancer activity assay, Chromatin interaction assay, TF binding assay 4C-seq, ATAC-seq, ChIP-seq, RNA-seq, WGBS CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Bisulfite Pyrosequencing 2022 36990511 Cis interactions in the Irf8 locus regulate stage-dependent enhancer activation Mus musculus mm10 chr8 121495097 121496097 Irf8 Enhancer Active Normal Blood UBERON:0000178 Myeloid progenitors myeloid progenitor cell CL:0000837 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay RNA-seq, ATAC-seq, ChIP-seq, 4C-seq CRISPR knockout, Transgenic reporter assay, RT-RT-qPCR 2022 36990511 Cis interactions in the Irf8 locus regulate stage-dependent enhancer activation Mus musculus mm10 chr8 121495097 121496097 Irf8 Enhancer Active Normal Blood UBERON:0000178 Dendritic cells dendritic cell CL:0000451 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay RNA-seq, ATAC-seq, ChIP-seq, 4C-seq CRISPR knockout, Transgenic reporter assay, RT-RT-qPCR 2022 36990511 Cis interactions in the Irf8 locus regulate stage-dependent enhancer activation Mus musculus mm10 chr8 121504097 121505097 Irf8 Enhancer Active Normal Blood UBERON:0000178 Myeloid progenitors myeloid progenitor cell CL:0000837 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay RNA-seq, ATAC-seq, ChIP-seq, 4C-seq CRISPR knockout, Transgenic reporter assay, RT-RT-qPCR 2022 36990511 Cis interactions in the Irf8 locus regulate stage-dependent enhancer activation Mus musculus mm10 chr8 121504097 121505097 Irf8 Enhancer Active Normal Blood UBERON:0000178 Dendritic cells dendritic cell CL:0000451 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay RNA-seq, ATAC-seq, ChIP-seq, 4C-seq CRISPR knockout, Transgenic reporter assay, RT-RT-qPCR 2022 36990511 Cis interactions in the Irf8 locus regulate stage-dependent enhancer activation Mus musculus mm10 chr8 121519097 121520097 Irf8 Enhancer Active Normal Blood UBERON:0000178 Myeloid progenitors myeloid progenitor cell CL:0000837 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay RNA-seq, ATAC-seq, ChIP-seq, 4C-seq CRISPR knockout, Transgenic reporter assay, RT-RT-qPCR 2022 36990511 Cis interactions in the Irf8 locus regulate stage-dependent enhancer activation Mus musculus mm10 chr8 121519097 121520097 Irf8 Enhancer Active Normal Artery UBERON:0001637 Primary mouse VSMCs vascular smooth muscle cell CL:0000192 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay RNA-seq, ATAC-seq, ChIP-seq, 4C-seq CRISPR knockout, Transgenic reporter assay, RT-RT-qPCR 2025 40321134 Enhancer-Associated LncRNA-ITGA2 Promotes Vascular Remodeling Through ITGA2 Mus musculus mm10 chr10 87654200 87655200 Srf Itga2 Enhancer Active Normal Artery UBERON:0001637 A7r5 cells CVCL_0137 vascular smooth muscle cell CL:0000192 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase reporter assay, ChIP-RT-qPCR, CRISPRi, RT-RT-qPCR, Western blot, EMSA 2025 40321134 Enhancer-Associated LncRNA-ITGA2 Promotes Vascular Remodeling Through ITGA2 Mus musculus mm10 chr10 87654200 87655200 Srf Itga2 Enhancer Active Normal Artery UBERON:0001637 Primary mouse VSMCs vascular smooth muscle cell CL:0000192 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase reporter assay, ChIP-RT-qPCR, CRISPRi, RT-RT-qPCR, Western blot, EMSA 2025 40321134 Enhancer-Associated LncRNA-ITGA2 Promotes Vascular Remodeling Through ITGA2 Mus musculus mm10 chr10 87657800 87658800 Srf Itga2 Enhancer Active Normal Artery UBERON:0001637 A7r5 cells CVCL_0137 vascular smooth muscle cell CL:0000192 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase reporter assay, ChIP-RT-qPCR, CRISPRi, RT-RT-qPCR, Western blot, EMSA 2025 40321134 Enhancer-Associated LncRNA-ITGA2 Promotes Vascular Remodeling Through ITGA2 Mus musculus mm10 chr10 87657800 87658800 Srf Itga2 Enhancer Active Normal Craniofacial Tissue UBERON:0010368 Primary cranial neural crest cells cranial neural crest cell CL:0000333 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase reporter assay, ChIP-RT-qPCR, CRISPRi, RT-RT-qPCR, Western blot, EMSA 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 Pharyngeal Arch UBERON:0002539 Cranial neural crest cells cranial neural crest cell CL:0000333 Chromatin interaction assay, Functional perturbation assay, Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq, Hi-C, ATAC-seq CRISPR knockout, RT-RT-qPCR, Western blot 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 Enhancer Active Normal Adipose Tissue UBERON:0001013 Mouse preadipocyte cell CVCL_0123 preadipocyte CL:0000136 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, PCHi-C, ChIP-seq, RNA-seq, ATAC-seq CRISPR knockout, RT-RT-qPCR, Whole-mount in situ hybridization, Skeletal staining 2019 31000713 ZFP30 promotes adipogenesis through the KAP1-mediated activation of a retrotransposon-derived Pparg2 enhancer Mus musculus mm10 chr6 115412685 115412777 Zfp30 Pparg2 Enhancer Active Normal Pharyngeal Arch UBERON:0002539 Second pharyngeal arch CNCCs cranial neural crest cell CL:0000333 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, qRT-PCR, Western blot, MITOMI in vitro binding assay 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 H3K27Ac Enhancer Active Normal Pharyngeal Arch UBERON:0002539 Cranial neural crest cells cranial neural crest cell CL:0000333 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, PCHi-C, ChIP-seq, RNA-seq, ATAC-seq CRISPR Knockout, RT-RT-qPCR, Whole-mount in situ hybridization, Skeletal staining 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 H3K27Ac Enhancer Active Normal Craniofacial Tissue UBERON:0010368 Primary cranial neural crest cells cranial neural crest cell CL:0000333 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, ATAC-seq, PCHi-C CRISPR Knockout, RT-RT-qPCR, Whole-mount in situ hybridization, Skeletal staining 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 Enhancer Active Normal Pharyngeal Arch UBERON:0002539 Cranial neural crest cells cranial neural crest cell CL:0000333 Chromatin interaction assay, Functional perturbation assay, Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq, Hi-C, ATAC-seq CRISPR Knockout, RT-RT-qPCR, Western blot 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 H3K27Ac SE Active Normal Craniofacial Tissue UBERON:0010368 Primary cranial neural crest cells cranial neural crest cell CL:0000333 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, ATAC-seq, PCHi-C CRISPR Knockout, RT-RT-qPCR, Whole-mount in situ hybridization, Skeletal staining 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 SE Active Normal Pharyngeal Arch UBERON:0002539 Second pharyngeal arch CNCCs cranial neural crest cell CL:0000333 Chromatin interaction assay, Functional perturbation assay, Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq, Hi-C, ATAC-seq CRISPR Knockout, RT-RT-qPCR, Western blot 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 H3K27Ac SE Active Normal Pharyngeal Arch UBERON:0002539 Cranial neural crest cells cranial neural crest cell CL:0000333 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, PCHi-C, ChIP-seq, RNA-seq, ATAC-seq CRISPR Knockout, RT-RT-qPCR, Whole-mount in situ hybridization, Skeletal staining 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 H3K27Ac SE Active Normal Pituitary gland UBERON:0000007 L??T2 CVCL_B077 gonadotrope cell CL:0000510 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, ATAC-seq, PCHi-C CRISPR Knockout, RT-RT-qPCR, Whole-mount in situ hybridization, Skeletal staining 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 Pituitary gland UBERON:0000007 ??T3-1 CVCL_B078 gonadotrope cell CL:0000510 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay, TF binding assay ATAC-seq, ChIP-seq, UMI-4C-seq, RNA-seq CRISPRi, CRISPRa, ChIP-RT-qPCR, RT-RT-qPCR, 3C, Fluorescence binding assay, Circular dichroism 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 Pituitary gland UBERON:0000007 primary pituitary gonadotrope cells gonadotrope cell CL:0000510 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay, TF binding assay ATAC-seq, ChIP-seq, UMI-4C-seq, RNA-seq CRISPRi, CRISPRa, ChIP-RT-qPCR, RT-RT-qPCR, 3C, Fluorescence binding assay, Circular dichroism 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 Embryo UBERON:0000922 Embryonic Stem Cells (mESCs) mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay, TF binding assay ATAC-seq, ChIP-seq, UMI-4C-seq, RNA-seq CRISPRi, CRISPRa, ChIP-RT-qPCR, RT-RT-qPCR, 3C, Fluorescence binding assay, Circular dichroism 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 Med13L Enhancer Active Normal Extraembryonic Ectoderm UBERON:0004366 Trophoblast Stem Cell trophoblast stem cell CL:0002322 Functional perturbation assay, Chromatin interaction assay ChIP-seq, RNA-seq, Hi-C CRISPR Knockout, RT-RT-qPCR 2019 31301373 Esrrb function is required for proper primordial germ cell development in presomite stage mouse embryos Mus musculus mm10 chr14 53397365 53398765 Esrrb Bmp4 Enhancer Active Normal Spleen UBERON:0002106 Bone Marrow-Derived Macrophages macrophage CL:0000235 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR 2018 30327417 Macrophage-specific MHC II expression is regulated by a remote Ciita enhancer controlled by NFAT5 Mus musculus mm10 chr16 10433585 10433748 Nfat5 Ciita Enhancer Active Normal Spleen UBERON:0002106 Bone Marrow-Derived Macrophages macrophage CL:0000235 Functional perturbation assay ChIP-seq, RNA-seq, 3C-seq CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR 2018 30327417 Macrophage-specific MHC II expression is regulated by a remote Ciita enhancer controlled by NFAT5 Mus musculus mm10 chr16 10480585 10480785 Nfat5 Ciita Enhancer Active Normal Embryo UBERON:0000922 Mouse Embryonic Stem Cells (mESCs; 129xCast F1; v6.5) mouse embryonic stem cell CL:0002322 Functional perturbation assay ChIP-seq, RNA-seq, 3C-seq CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR 2019 31422875 Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs Mus musculus mm10 chr7 3198900 3202780 Pou5F1; Nanog Mir290-295 Enhancer Active Normal Embryo UBERON:0000922 Mouse Embryonic Stem Cells (mESCs; 129xCast F1; v6.5) mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, WGBS, Hi-C Transgenic Reporter Assay (RGM), CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, DNA FISH, Immunofluorescence, Confocal Imaging 2019 31422875 Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs Mus musculus mm10 chr7 3198900 3202780 Pou5F1; Nanog Mir290-295 Enhancer Active Normal Embryo UBERON:0000922 Epiblast-like Cells (EpiLCs) epiblast-like cell CL:0002322 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, WGBS, Hi-C Transgenic Reporter Assay (RGM), CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, DNA FISH, Immunofluorescence, Confocal Imaging 2019 31422875 Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from naive pluripotency Mus musculus mm10 chr1 63240000 63243000 Pou5F1 Zdbf2 Enhancer Active Normal Embryo UBERON:0000922 Differentiated mESCs mouse embryonic stem cell CL:0002322 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay 4C-seq, ATAC-seq, ChIP-seq, RNA-seq, WGBS CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Bisulfite Pyrosequencing 2019 31422875 Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from naive pluripotency Mus musculus mm10 chr1 63240000 63243000 Pou5F1 Zdbf2 Enhancer Active Normal Bone Marrow UBERON:0002371 Hematopoietic Stem Cells hematopoietic stem cell CL:0001029 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay 4C-seq, ATAC-seq, ChIP-seq, RNA-seq, WGBS CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Bisulfite Pyrosequencing 2021 32594099 Gata2 -77 enhancer regulates adult hematopoietic stem cell survival Mus musculus mm10 chr6 88093745 88094001 Gata2 Gata2 Enhancer Active Normal Bone Marrow UBERON:0002371 Primary Mouse Bone Marrow Cells mouse bone marrow cell CL:0000000 Functional perturbation assay, TF binding assay, Chromatin interaction assay RNA-seq, ChIP-seq CRISPR Knockout, RT-RT-qPCR, 3C Assay 2021 32594099 Gata2 -77 enhancer regulates adult hematopoietic stem cell survival Mus musculus mm10 chr6 88093745 88094001 Gata2 Gata2 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Functional perturbation assay, TF binding assay, Chromatin interaction assay RNA-seq, ChIP-seq CRISPR Knockout, RT-RT-qPCR, 3C Assay 2025 41402457 JMJD2 regulates enhancer?Cpromoter interactions via biomolecular condensate formation Mus musculus mm10 chr7 104405000 104415000 Jmjd2C Zscan4C Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Chromatin interaction assay, Functional perturbation assay, TF binding assay 4C-seq, ChIP-seq, RNA-seq CRISPR knockout, ChIP-RT-qPCR, RT-RT-qPCR 2025 40296153 Rewiring of SINE-MIR enhancer topology and Esrrb modulation in expanded and naive pluripotency Mus musculus mm10 chr6 113000000 113001000 Esrrb Klf5 Enhancer Active Normal Blood UBERON:0000178 RAW264.7 CVCL_0493 macrophage CL:0000235 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay Hi-C, HiChIP, RNA-seq, ChIP-seq CRISPR knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2019 31324781 Deletion of a Csf1r enhancer selectively impacts CSF1R expression and development of tissue macrophage populations Mus musculus mm10 chr18 60781333 60781702 Spi1 Csf1R Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, ATAC-seq, RNA-seq, Microarray CRISPR Knockout, Transgenic Reporter Assay, RT-RT-qPCR, Western blot, Flow Cytometry 2019 31324781 Deletion of a Csf1r enhancer selectively impacts CSF1R expression and development of tissue macrophage populations Mus musculus mm10 chr18 60781333 60781702 Spi1 Csf1R Enhancer Active Normal Blood UBERON:0000178 RAW264.7 CVCL_0493 macrophage CL:0000235 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, ATAC-seq, RNA-seq, Microarray CRISPR Knockout, Transgenic Reporter Assay, RT-RT-qPCR, Western blot, Flow Cytometry 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 Brain UBERON:0000955 Mouse primary macrophages macrophage CL:0000235 Functional perturbation assay, Enhancer activity assay, TF binding assay ChIP-seq, ATAC-seq, RNA-seq, Microarray CRISPR Knockout, RT-RT-qPCR, Western blot, Flow Cytometry, Immunohistochemistry, Phagocytosis Assay 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 Skin UBERON:0000014 Langerhans cells Langerhans cell CL:0000453 Functional perturbation assay, Enhancer activity assay, TF binding assay ChIP-seq, ATAC-seq, RNA-seq, Microarray CRISPR Knockout, RT-RT-qPCR, Western blot, Flow Cytometry, Immunohistochemistry, Phagocytosis Assay 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 Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Functional perturbation assay, Enhancer activity assay, TF binding assay ChIP-seq, ATAC-seq, RNA-seq, Microarray CRISPR Knockout, RT-RT-qPCR, Western blot, Flow Cytometry, Immunohistochemistry, Phagocytosis Assay 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 Blood UBERON:0000178 RAW264.7 CVCL_0493 macrophage CL:0000235 Functional perturbation assay, Enhancer activity assay, TF binding assay ChIP-seq, ATAC-seq, RNA-seq, Microarray CRISPR Knockout, RT-RT-qPCR, Western blot, Flow Cytometry, Immunohistochemistry, Phagocytosis Assay 2019 31324781 Deletion of a Csf1r enhancer selectively impacts CSF1R expression and development of tissue macrophage populations Mus musculus mm10 chr18 60917264 60917600 Spi1 Csf1R Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Functional perturbation assay, Enhancer activity assay, TF binding assay ChIP-seq, ATAC-seq, RNA-seq CRISPR Knockout, Transgenic Reporter Assay, RT-RT-qPCR, Western blot, Flow Cytometry, Immunohistochemistry 2019 31324781 Deletion of a Csf1r enhancer selectively impacts CSF1R expression and development of tissue macrophage populations Mus musculus mm10 chr18 60917264 60917600 Spi1 Csf1R Enhancer Active Normal Skin UBERON:0000014 Langerhans cells Langerhans cell CL:0000453 Functional perturbation assay, Enhancer activity assay, TF binding assay ChIP-seq, ATAC-seq, RNA-seq CRISPR Knockout, Transgenic Reporter Assay, RT-RT-qPCR, Western blot, Flow Cytometry, Immunohistochemistry 2019 31324781 Deletion of a Csf1r enhancer selectively impacts CSF1R expression and development of tissue macrophage populations Mus musculus mm10 chr18 60917264 60917600 Spi1 Csf1R Enhancer Active Normal Spleen UBERON:0002106 CD4+ Th1 cells CD4-positive Th1 cell CL:0000897 Functional perturbation assay, Enhancer activity assay, TF binding assay ChIP-seq, ATAC-seq, RNA-seq CRISPR Knockout, Transgenic Reporter Assay, RT-RT-qPCR, Western blot, Flow Cytometry, Immunohistochemistry 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 118373265 118377265 T-Bet Ifng Enhancer Active Normal Spleen UBERON:0002106 CD4+ Th1 cells CD4-positive Th1 cell CL:0000897 Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, Region Capture Micro-C 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR, CRISPR Knockout 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 118393265 118397265 T-Bet Ifng Enhancer Active Normal Spleen UBERON:0002106 CD4+ Th1 cells CD4-positive Th1 cell CL:0000897 Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, Region Capture Micro-C 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR, CRISPR Knockout 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 118405265 118409265 T-Bet Ifng Enhancer Active Normal Spleen UBERON:0002106 CD4+ Th1 cells CD4-positive Th1 cell CL:0000897 Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, Region Capture Micro-C 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR, CRISPR Knockout 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 118421265 118425265 T-Bet Ifng Enhancer Active Normal Spleen UBERON:0002106 CD4+ Th1 cells CD4-positive Th1 cell CL:0000897 Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, Region Capture Micro-C 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR, CRISPR Knockout 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 118445265 118449265 T-Bet Ifng Enhancer Active Normal Spleen UBERON:0002106 CD4+ Th1 cells CD4-positive Th1 cell CL:0000897 Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, Region Capture Micro-C 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR, CRISPR Knockout 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 118456265 118460265 T-Bet Ifng Enhancer Active Normal Embryo UBERON:0000922 Mouse ESCs mouse embryonic stem cell CL:0002322 Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, Region Capture Micro-C 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR, CRISPR Knockout 2015 25486255 CRISPR Reveals a Distal Super-Enhancer Required for Sox2 Expression in Mouse Embryonic Stem Cells Mus musculus mm10 chr3 34619000 34632000 Sox2 SE Active Normal Embryo UBERON:0000922 Mouse ESCs mouse embryonic stem cell CL:0002322 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq, Hi-C, 5C CRISPR Knockout, ChIP-RT-qPCR, qRT-PCR 2024 38511608 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 39441747 39444739 Enhancer Active Normal Heart UBERON:0000948 Embryonic cardiomyocyte embryonic cardiomyocyte CL:0000746 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2020 32251373 Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction Mus musculus mm10 chr12 114462800 114464200 Ighm Enhancer Active Normal Spleen UBERON:0002106 mature B mature B cell CL:0000785 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, GRO-seq, ATAC-seq, 3C-seq 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR, CRISPRa 2020 32251373 Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction Mus musculus mm10 chr12 114465285 114467786 Ighm Enhancer Active Normal Spleen UBERON:0002106 mature B mature B cell CL:0000785 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, GRO-seq, ATAC-seq, 3C-seq 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR, CRISPRa 2020 32251373 Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction Mus musculus mm10 chr12 114479200 114480600 Ighm Enhancer Active Normal Spleen UBERON:0002106 mature B mature B cell CL:0000785 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, GRO-seq, ATAC-seq, 3C-seq 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR, CRISPRa 2020 32251373 Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction Mus musculus mm10 chr12 114481431 114482631 Ighm Enhancer Active Normal Spleen UBERON:0002106 mature B mature B cell CL:0000785 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, GRO-seq, ATAC-seq, 3C-seq 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR, CRISPRa 2020 32251373 Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction Mus musculus mm10 chr12 114461575 114496377 Ighm Enhancer Active Normal Spleen UBERON:0002106 mature B mature B cell CL:0000785 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, GRO-seq, ATAC-seq, Hi-C, 3C-seq 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR, CRISPRa, Flow Cytometry 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 Bone marrow UBERON:0002371 32Dcl3 CVCL_0225 myeloid progenitor cell CL:0000837 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR 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 Bone marrow UBERON:0002371 primary bone marrow bone marrow cell CL:0000000 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR 2015 25801169 Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers Mus musculus mm10 chr17 35600000 35630000 Oct4; Sox2; Nanog Pou5F1 Enhancer Active Normal Embryo UBERON:0000922 mouse ESCs mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout 2015 25801169 Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers Mus musculus mm10 chr4 102500000 102540000 Oct4; Sox2; Nanog Prdm14 Enhancer Active Normal Embryo UBERON:0000922 mouse ESCs mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout 2015 25801169 Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers Mus musculus mm10 chr8 71200000 71240000 Oct4; Sox2; Nanog Mir-290-295 Enhancer Active Normal Embryo UBERON:0000922 mouse ESCs mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout 2015 25801169 Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers Mus musculus mm10 chr10 12800000 12840000 Oct4; Sox2; Nanog Sik1 Enhancer Active Normal Embryo UBERON:0000922 mouse ESCs mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout 2015 25801169 Convergence of developmental and oncogenic signaling pathways at transcriptional super-enhancers Mus musculus mm10 chr8 45600000 45640000 Oct4; Sox2; Nanog Klf2 Enhancer Active Normal Embryo UBERON:0000922 mouse ESCs mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout 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; Nanog; Klf4; Esrrb; Zfx; E2F1; Tfcp2I1 Lefty2 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C CRISPR Knockout, RT-RT-qPCR 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; Nanog; Klf4; Esrrb; Zfx; E2F1; Tfcp2I1 Lefty1 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C CRISPR Knockout, RT-RT-qPCR 2026 41533786 YAP/TAZ-VGLL3 governs adipocyte fate via epigenetic reprogramming of PPAR?? and its target enhancers Mus musculus mm10 chr3 103180000 103230000 Tead Pparg Enhancer Active Normal Adipose tissue UBERON:0001013 C3H10T1/2, primary adipocytes CVCL_0190 mesenchymal cell / adipocyte CL:0000136 Regulatory element functional validation, 3D chromatin architecture analysis, epigenomic profiling ATAC-seq, RNA-seq, ChIP-seq, snRNA-seq, snATAC-seq CRISPRi (dCas9-KRAB-MeCP2), RT-RT-qPCR, ORCA, Western blot, Oil Red O staining 2026 41533786 YAP/TAZ-VGLL3 governs adipocyte fate via epigenetic reprogramming of PPAR?? and its target enhancers Mus musculus mm10 chr3 103470000 103520000 Tead Pparg Enhancer Active Normal Adipose tissue UBERON:0001013 C3H10T1/2, primary adipocytes CVCL_0190 mesenchymal cell / adipocyte CL:0000136 Regulatory element functional validation, 3D chromatin architecture analysis, epigenomic profiling ATAC-seq, RNA-seq, ChIP-seq, snRNA-seq, snATAC-seq CRISPRi (dCas9-KRAB-MeCP2), RT-RT-qPCR, ORCA, Western blot, Oil Red O staining 2025 39626663 Enhancer cooperativity can compensate for loss of activity over large genomic distances Mus musculus mm10 chr17 80721358 80818896 Map4K3 Enhancer Active Normal Embryo UBERON:0000922 Mouse Embryonic Stem Cells (v6.5) mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq Luciferase Reporter Assay, Fluorescent Reporter Assay (mCherry), CRISPR Knockout, RT-RT-qPCR 2024 38729993 Regulation of Myc transcription by an enhancer cluster dedicated to pluripotency and early embryonic expression Mus musculus mm10 chr15 61958143 62188886 Myc Enhancer Active Normal Embryo UBERON:0000922 mESC mouse embryonic stem cell CL:0002322 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay RNA-seq, Hi-C, 4C-seq, ChIP-seq Transgenic Reporter Assay, CRISPR Knockout, Flow Cytometry, Immunofluorescence 2024 38806452 TAD border deletion at the Kit locus causes tissue-specific ectopic activation of a neighboring gene Mus musculus mm10 chr5 75699926 75706926 Kit Enhancer Active Normal Bone Marrow UBERON:0002371 Primary Mast cells mast cell CL:0000097 Functional perturbation assay, Enhancer activity assay ChIP-seq, RNA-seq, Hi-C CRISPR Knockout, qRT-PCR 2024 38806452 TAD border deletion at the Kit locus causes tissue-specific ectopic activation of a neighboring gene Mus musculus mm10 chr5 75825926 75832926 Kit Enhancer Active Normal Skin UBERON:0000014 Primary Melanocytes melanocyte CL:0000148 Functional perturbation assay, Enhancer activity assay ChIP-seq, RNA-seq, Hi-C CRISPR Knockout, qRT-PCR 2024 38806452 TAD border deletion at the Kit locus causes tissue-specific ectopic activation of a neighboring gene Mus musculus mm10 chr5 75699926 75706926 Kdr Enhancer Active Normal Skin UBERON:0000014 Primary Melanocytes (Kit ??30k) melanocyte CL:0000148 Chromatin interaction assay, Functional perturbation assay Hi-C, RNA-seq, ChIP-seq CRISPR Knockout, qRT-PCR, Immunohistochemistry 2024 38806452 TAD border deletion at the Kit locus causes tissue-specific ectopic activation of a neighboring gene Mus musculus mm10 chr5 75825926 75832926 Kdr Enhancer Active Normal Skin UBERON:0000014 Primary Melanocytes (Kit ??30k) melanocyte CL:0000148 Chromatin interaction assay, Functional perturbation assay Hi-C, RNA-seq, ChIP-seq CRISPR Knockout, qRT-PCR, Immunohistochemistry 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 Embryonic gonad UBERON:0005321 Embryonic gonad cells (E11.5) embryonic gonad cell CL:0000000 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, ChIP-seq, CUT&RUN Luciferase Reporter Assay, CRISPR Knockout, qRT-PCR 2021 34260936 Neuronal activity-induced BRG1 phosphorylation regulates enhancer activation Mus musculus mm10 chr12 8570500 8571000 C-Fos Enhancer Active Normal Cerebral cortex UBERON:0000956 Primary mouse cortical neurons mouse cortical neuron CL:0000540 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq ChIP-RT-qPCR, 3C, qRT-PCR, Western blot, CRISPR Knockin 2021 34260936 Neuronal activity-induced BRG1 phosphorylation regulates enhancer activation Mus musculus mm10 chr15 8079500 8080000 Arc Enhancer Active Normal Cerebral cortex UBERON:0000956 Primary mouse cortical neurons mouse cortical neuron CL:0000540 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq ChIP-RT-qPCR, 3C, qRT-PCR, Western blot, CRISPR Knockin 2022 36402859 Hnf1b renal expression directed by a distal enhancer responsive to Pax8 Mus musculus mm10 chr17 63643401 63643706 Pax8 Hnf1B Enhancer Active Normal Kidney UBERON:0002113 MDCK CVCL_0422 kidney epithelial cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, ChIP-seq, DNase-seq Luciferase Reporter Assay, Transgenic Reporter Assay, CRISPR Knockout, EMSA 2022 36402859 Hnf1b renal expression directed by a distal enhancer responsive to Pax8 Mus musculus mm10 chr17 63643401 63643706 Pax8 Hnf1B Enhancer Active Normal Kidney UBERON:0002113 IMCD3 CVCL_5J54 kidney epithelial cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, ChIP-seq, DNase-seq Luciferase Reporter Assay, Transgenic Reporter Assay, CRISPR Knockout, EMSA 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Mus musculus mm10 chrX 7566060 7568152 Foxp3 Enhancer Active Normal Blood UBERON:0000178 CD4+ T cells CD4-positive T cell CL:0000624 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Mus musculus mm10 chrX 7566060 7568152 Foxp3 Enhancer Active Normal Blood UBERON:0000178 Regulatory T cells regulatory T cell CL:0000815 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Mus musculus mm10 chrX 7566060 7568152 Foxp3 Enhancer Active Normal Blood UBERON:0000178 Conventional T cells T cell CL:0000084 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Mus musculus mm10 chrX 7570463 7571424 Foxp3 Enhancer Active Normal Blood UBERON:0000178 CD4+ T cells CD4-positive T cell CL:0000624 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Mus musculus mm10 chrX 7570463 7571424 Foxp3 Enhancer Active Normal Blood UBERON:0000178 Regulatory T cells regulatory T cell CL:0000815 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Mus musculus mm10 chrX 7570463 7571424 Foxp3 Enhancer Active Normal Blood UBERON:0000178 Conventional T cells T cell CL:0000084 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Mus musculus mm10 chrX 7573447 7575334 Foxp3 Enhancer Active Normal Blood UBERON:0000178 CD4+ T cells CD4-positive T cell CL:0000624 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Mus musculus mm10 chrX 7573447 7575334 Foxp3 Enhancer Active Normal Blood UBERON:0000178 Regulatory T cells regulatory T cell CL:0000815 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Mus musculus mm10 chrX 7573447 7575334 Foxp3 Enhancer Active Normal Blood UBERON:0000178 Conventional T cells T cell CL:0000084 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Mus musculus mm10 chrX 7579185 7580141 Foxp3 Enhancer Active Normal Blood UBERON:0000178 CD4+ T cells CD4-positive T cell CL:0000624 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Mus musculus mm10 chrX 7579185 7580141 Foxp3 Enhancer Active Normal Blood UBERON:0000178 Regulatory T cells regulatory T cell CL:0000815 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Mus musculus mm10 chrX 7579185 7580141 Foxp3 Enhancer Active Normal Blood UBERON:0000178 Conventional T cells T cell CL:0000084 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Mus musculus mm10 chrX 7583853 7584485 Foxp3 Enhancer Active Normal Blood UBERON:0000178 CD4+ T cells CD4-positive T cell CL:0000624 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Mus musculus mm10 chrX 7583853 7584485 Foxp3 Enhancer Active Normal Blood UBERON:0000178 Regulatory T cells regulatory T cell CL:0000815 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 2026 41237776 FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry Mus musculus mm10 chrX 7583853 7584485 Foxp3 Enhancer Active Normal Blood UBERON:0000178 Conventional T cells T cell CL:0000084 Functional perturbation assay, Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi 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 Embryo UBERON:0000922 ESCs embryonic stem cell CL:0002322 Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq CRISPR Knockout, RT-RT-qPCR, Western blot 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 Embryo UBERON:0000922 ESCs embryonic stem cell CL:0002322 Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq CRISPR Knockout, RT-RT-qPCR, Western blot 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 Embryo UBERON:0000922 ESCs embryonic stem cell CL:0002322 Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq CRISPR Knockout, RT-RT-qPCR, Western blot 2020 32694829 Super-enhancer-driven metabolic reprogramming promotes cystogenesis in autosomal dominant polycystic kidney disease Mus musculus mm10 chr8 123455000 123472000 Ampd3 Enhancer Active Disease polycystic kidney disease MONDO:0005290 DOID:0111199 Kidney UBERON:0002113 Pkd1-null tubule epithelial cells (PN) kidney epithelial cell CL:0000066 Functional perturbation assay, Enhancer activity assay ChIP-seq, RNA-seq, ATAC-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot, CRISPR Knockout, Flow Cytometry, Immunohistochemistry, HPLC 2020 32694829 Super-enhancer-driven metabolic reprogramming promotes cystogenesis in autosomal dominant polycystic kidney disease Mus musculus mm10 chr8 123455000 123472000 Ampd3 Enhancer Active Normal Kidney UBERON:0002113 Pkd1-heterozygous control tubule epithelial cells (PH) kidney epithelial cell CL:0000066 Functional perturbation assay, Enhancer activity assay ChIP-seq, RNA-seq, ATAC-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot, CRISPR Knockout, Flow Cytometry, Immunohistochemistry, HPLC 2020 32694829 Super-enhancer-driven metabolic reprogramming promotes cystogenesis in autosomal dominant polycystic kidney disease Mus musculus mm10 chr8 123455000 123472000 Ampd3 Enhancer Active Normal Kidney UBERON:0002113 mouse primary renal tubular epithelial cells renal tubular epithelial cell CL:0002306 Functional perturbation assay, Enhancer activity assay ChIP-seq, RNA-seq, ATAC-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot, CRISPR Knockout, Flow Cytometry, Immunohistochemistry, HPLC 2020 32817515 The Atoh7 remote enhancer provides transcriptional robustness during retinal ganglion cell development Mus musculus mm10 chr10 72890000 72895600 Atoh7 Enhancer Active Normal Retina UBERON:0000966 Retinal Progenitor Cells retinal progenitor cell CL:0002672 Functional perturbation assay, Enhancer activity assay ATAC-seq, RNA-seq, ChIP-seq CRISPR Knockout, RT-RT-qPCR, Transgenic Reporter Assay, Electron Microscopy 2020 32817515 The Atoh7 remote enhancer provides transcriptional robustness during retinal ganglion cell development Mus musculus mm10 chr10 72890000 72895600 Atoh7 Enhancer Active Normal Retina UBERON:0000966 Retinal Ganglion Cells retinal ganglion cell CL:0000740 Functional perturbation assay, Enhancer activity assay ATAC-seq, RNA-seq, ChIP-seq CRISPR Knockout, RT-RT-qPCR, Transgenic Reporter Assay, Electron Microscopy 2025 37772400 An Anterior Second Heart Field Enhancer Regulates the Gene Regulatory Network of the Cardiac Outflow Tract Mus musculus mm10 chr5 150830909 150831422 Gata6 Nkx2-5 Enhancer Active Normal Heart UBERON:0000948 Primary embryonic cardiomyocytes cardiomyocyte CL:0000746 Enhancer activity assay, TF binding assay, Functional perturbation assay, Chromatin interaction assay ChIP-seq, ATAC-seq, RNA-seq Transgenic reporter assay, CRISPR knockout, CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR 2025 37772400 An Anterior Second Heart Field Enhancer Regulates the Gene Regulatory Network of the Cardiac Outflow Tract Mus musculus mm10 chr5 150830909 150831422 Gata6 Nkx2-5 Enhancer Active Normal Heart UBERON:0000948 hiPSC-CMs cardiomyocyte CL:0000746 Enhancer activity assay, TF binding assay, Functional perturbation assay, Chromatin interaction assay ChIP-seq, ATAC-seq, RNA-seq Transgenic reporter assay, CRISPR knockout, CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR 2024 38413562 The neutrophil-osteogenic cell axis promotes bone destruction in periodontitis Mus musculus mm10 chr14 78376100 78379511 Stat3 Tnfsf11 Enhancer Active Normal Bone UBERON:0001474 Primary osteoblasts osteoblast CL:0000062 Functional perturbation assay, Enhancer activity assay, TF binding assay ChIP-seq, scRNA-seq, RNA-seq, ATAC-seq CRISPR Knockout, RT-RT-qPCR, Western blot, ChIP-RT-qPCR, ELISA, Micro-CT 2024 38413562 The neutrophil-osteogenic cell axis promotes bone destruction in periodontitis Mus musculus mm10 chr14 78376100 78379511 Stat3 Tnfsf11 Enhancer Active Normal Bone UBERON:0001474 Periodontal ligament cells fibroblast CL:0000057 Functional perturbation assay, Enhancer activity assay, TF binding assay ChIP-seq, scRNA-seq, RNA-seq, ATAC-seq CRISPR Knockout, RT-RT-qPCR, Western blot, ChIP-RT-qPCR, ELISA, Micro-CT 2024 38413562 The neutrophil-osteogenic cell axis promotes bone destruction in periodontitis Mus musculus mm10 chr14 78376100 78379511 Stat3 Tnfsf11 Enhancer Active Normal Bone UBERON:0001474 Osteogenic cells osteoblast CL:0000062 Functional perturbation assay, Enhancer activity assay, TF binding assay ChIP-seq, scRNA-seq, RNA-seq, ATAC-seq CRISPR Knockout, RT-RT-qPCR, Western blot, ChIP-RT-qPCR, ELISA, Micro-CT 2024 38413562 The neutrophil-osteogenic cell axis promotes bone destruction in periodontitis Mus musculus mm10 chr14 78376100 78379511 Stat3 Tnfsf11 Enhancer Active Normal Bone UBERON:0001474 Primary calvarial osteoblasts osteoblast CL:0000062 Functional perturbation assay, Enhancer activity assay, TF binding assay ChIP-seq, scRNA-seq, RNA-seq, ATAC-seq CRISPR Knockout, RT-RT-qPCR, Western blot, ChIP-RT-qPCR, ELISA, Micro-CT 2016 26751055 NANOG alone induces germ cells in primed epiblast in vitro by activation of enhancers Mus musculus mm10 chr6 113009800 113010300 Nanog Prdm1 Enhancer Silenced Normal Embryo UBERON:0000922 Mouse embryonic stem cells (E14TG2a) CVCL_2167 mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, Microarray Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR, CRISPR-Cas9 knockout, Western blot, Immunofluorescence, Flow cytometry 2016 26751055 NANOG alone induces germ cells in primed epiblast in vitro by activation of enhancers Mus musculus mm10 chr4 135009700 135010200 Nanog Prdm14 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Functional perturbation assay, Epigenetic modification assay ChIP-seq, Microarray Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR, CRISPR-Cas9 knockout, Western blot, Immunofluorescence, Flow cytometry, Blastocyst injection assay 2016 26751055 NANOG alone induces germ cells in primed epiblast in vitro by activation of enhancers Mus musculus mm10 chr4 135009700 135010200 Nanog Prdm14 Enhancer Active Normal Embryo UBERON:0000922 EpiLCs epiblast-like cell CL:0002322 Enhancer activity assay, TF binding assay, Functional perturbation assay, Epigenetic modification assay ChIP-seq, Microarray Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR, CRISPR-Cas9 knockout, Western blot, Immunofluorescence, Flow cytometry, Blastocyst injection assay 2016 26751055 NANOG alone induces germ cells in primed epiblast in vitro by activation of enhancers Mus musculus mm10 chr4 135009700 135010200 Nanog Prdm14 Enhancer Active Normal Embryo UBERON:0000922 PGCLCs primordial germ cell-like cell CL:0000670 Enhancer activity assay, TF binding assay, Functional perturbation assay, Epigenetic modification assay ChIP-seq, Microarray Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR, CRISPR-Cas9 knockout, Western blot, Immunofluorescence, Flow cytometry, Blastocyst injection assay 2024 38511608 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 9648563 9650544 Enhancer Active Normal Embryo UBERON:0000922 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2021 34335313 Chromatin accessibility landscape of cardiac pacemaker cells defines an Isl1 enhancer required for sinoatrial node development and function Mus musculus mm10 chr15 103026344 103028143 Hcn4 Enhancer Active Normal Heart UBERON:0000948 Sinoatrial Node Pacemaker sinoatrial node pacemaker cell CL:0000746 Enhancer activity assay, Functional perturbation assay ATAC-seq, RNA-seq, ChIP-seq Transgenic Reporter Assay, CRISPR Knockout, X-gal Staining 2024 38824572 A conserved ACTN2 enhancer regulates cardiomyocyte maturation through mTOR signaling Mus musculus mm10 chr1 179953600 179954900 Mef2A Actn2 Enhancer Active Normal Heart UBERON:0000948 Mouse primary cardiomyocytes mouse cardiomyocyte CL:0000746 Enhancer activity assay, TF binding assay RNA-seq, ChIP-seq, ATAC-seq CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 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 Skeletal muscle UBERON:0001134 Skeletal muscle myocytes skeletal muscle myocyte CL:0000187 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Capture-C, ChIP-seq, ATAC-seq, RNA-seq CRISPR Knockout, qRT-PCR, Southern Blot 2021 33976173 A Stat1 bound enhancer promotes Nampt expression and function within tumor associated macrophages Mus musculus mm10 chr12 32821032 32827114 Stat1 Nampt Enhancer Active Normal Skin UBERON:0000014 Bone Marrow-Derived Macrophages (BMMs) macrophage CL:0000235 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq, scRNA-seq, ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, qRT-PCR, Western blot 2023 36697821 A Prox1 enhancer represses haematopoiesis in the lymphatic vasculature Mus musculus mm10 chr1 190181703 190182534 Gata2 Prox1 Enhancer Active Normal Lymphatic vasculature UBERON:0001473 Lymphatic endothelial cells (LECs) lymphatic endothelial cell CL:0002546 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, 3C-seq Transgenic Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, qRT-PCR, Immunostaining 2020 33049031 LncRNA Platr22 promotes super-enhancer activity and stem cell pluripotency Mus musculus mm10 chr1 136650000 136700000 Zfp281 Zfp281 SE Active Normal Embryo UBERON:0000922 Mouse Embryonic Stem Cells (mESCs) mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, ChIA-PET, GRID-seq, GRO-seq, DNase-seq ChIP-RT-qPCR, CRISPR Knockout, CRISPRa, qRT-PCR, RNA FISH, 3C, RIP, RNA pull-down, Co-IP 2021 33976173 A Stat1 bound enhancer promotes Nampt expression and function within tumor associated macrophages Mus musculus mm10 chr12 32821032 32827113 Stat1 Nampt Enhancer Active Normal Bone marrow UBERON:0002371 Bone marrow-derived macrophages (BMMs) macrophage CL:0000235 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, scRNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, qRT-PCR, Western blot 2021 33976173 A Stat1 bound enhancer promotes Nampt expression and function within tumor associated macrophages Mus musculus mm10 chr12 32821787 32821864 Stat1 Nampt Enhancer Active Normal Blood UBERON:0000178 RAW 264.7 CVCL_0493 macrophage CL:0000235 Enhancer activity assay, TF binding assay ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, qRT-PCR 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 Pancreas UBERON:0001264 Pancreatic Multipotent Progenitor Cells (MPCs) pancreatic multipotent progenitor cell CL:0002583 Functional perturbation assay, Enhancer activity assay ChIP-seq, scRNA-seq, scATAC-seq CRISPR Knockout, qRT-PCR, Immunofluorescence 2021 33974869 Distinct Foxp3 enhancer elements coordinate development, maintenance and function of regulatory T cells Mus musculus mm10 chrX 7570674 7571274 Stat5A Foxp3 Enhancer Active Normal Thymus UBERON:0002370 CD4+Foxp3+ Regulatory T Cells (Treg) regulatory T cell CL:0000815 Functional perturbation assay, TF binding assay, Enhancer activity assay ChIP-seq, ATAC-seq, RNA-seq, Bisulfite-seq CRISPR Knockout, ChIP-RT-qPCR, qRT-PCR, Western blot, Flow Cytometry 2024 39085358 SMC3 contributes to heart development by regulating superenhancer associated genes Mus musculus mm10 chr16 95745432 95912361 Ets2 Enhancer Silenced Normal Heart UBERON:0000948 Outflow tract cardiac muscle cells cardiomyocyte CL:0000746 Functional perturbation assay, Enhancer activity assay ChIP-seq, RNA-seq, snRNA-seq CRISPR Knockout, RT-RT-qPCR, Western blot, H&E Staining 2025 40604280 Range extender mediates long-distance enhancer activity Mus musculus mm10 chr16 95847911 95849564 Ets2 Enhancer Active Normal Embryonic Limb Bud UBERON:0005417 Limb bud mesenchymal cells mesenchymal cell CL:0000134 Enhancer activity assay, Functional perturbation assay ATAC-seq, scATAC-seq/scRNA-seq multiome, Capture Hi-C Transgenic Reporter Assay, CRISPR Knock-in, Whole-mount in situ hybridization, Skeletal staining 2025 40604280 Range extender mediates long-distance enhancer activity Mus musculus mm10 chr16 95847911 95849564 Ets2 Enhancer Active Normal Limb Bud UBERON:0005417 Zone of polarizing activity cells mesenchymal cell CL:0000134 Enhancer activity assay, Functional perturbation assay ATAC-seq, scATAC-seq/scRNA-seq multiome, Capture Hi-C Transgenic Reporter Assay, CRISPR Knock-in, Whole-mount in situ hybridization, Skeletal staining 2025 40604280 Range extender mediates long-distance enhancer activity Mus musculus mm10 chr2 60785660 60787563 Rbms1 Enhancer Active Normal Embryonic Limb Bud UBERON:0005417 Limb bud mesenchymal cells mesenchymal cell CL:0000134 Enhancer activity assay, Functional perturbation assay scATAC-seq/scRNA-seq multiome, Capture Hi-C Transgenic Reporter Assay, CRISPR Knock-in, Whole-mount in situ hybridization, Skeletal staining 2025 40604280 Range extender mediates long-distance enhancer activity Mus musculus mm10 chr4 154707415 154711162 Prdm16 Enhancer Active Normal Embryonic Limb Bud UBERON:0005417 Limb bud mesenchymal cells mesenchymal cell CL:0000134 Enhancer activity assay, Functional perturbation assay scATAC-seq/scRNA-seq multiome, Capture Hi-C Transgenic Reporter Assay, CRISPR Knock-in, Whole-mount in situ hybridization, Skeletal staining 2019 31120998 HoxA9 binds and represses the Cebpa +8 kb enhancer Mus musculus mm10 chr7 35860000 35860514 Hoxa9 Cebpa Enhancer Silenced Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 Mouse myeloid progenitor cell mouse myeloid progenitor cell CL:0000837 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, EMSA, RT-RT-qPCR, Western blot 2019 31120998 HoxA9 binds and represses the Cebpa +8 kb enhancer Mus musculus mm10 chr7 35860000 35860514 Hoxa9 Cebpa Enhancer Silenced Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 MUTZ-3 CVCL_1435 acute myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, EMSA, RT-RT-qPCR, Western blot 2019 31120998 HoxA9 binds and represses the Cebpa +8 kb enhancer Mus musculus mm10 chr7 35860000 35860514 Hoxa9 Cebpa Enhancer Silenced Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 Primary murine myeloid progenitor cells mouse myeloid progenitor cell CL:0000837 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, EMSA, RT-RT-qPCR, Western blot 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 Ranbp17 Enhancer Active Normal Embryo UBERON:0000922 Embryonic Stem Cells (mESCs) mouse embryonic stem cell CL:0002322 Functional perturbation assay ChIP-seq, RNA-seq CRISPR Knockout, RT-RT-qPCR 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 Macf1 Enhancer Active Normal Embryo UBERON:0000922 Embryonic Stem Cells (mESCs) mouse embryonic stem cell CL:0002322 Functional perturbation assay ChIP-seq, RNA-seq CRISPR Knockout, RT-RT-qPCR 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 Thymus UBERON:0002370 NKT thymocyte and ILCP T cell CL:0000084 Functional perturbation assay ATAC-seq, ChIP-seq CRISPR Knockout 2017 29038421 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 Thymus UBERON:0002370 NKT thymocyte and ILCP T cell CL:0000084 Functional perturbation assay ATAC-seq, ChIP-seq CRISPR Knockout 2019 31591447 Distinct enhancer signatures in the mouse gastrula delineate progressive cell fate continuum during embryo development Mus musculus mm10 chr16 21480000 21482000 2510009E07Rik Enhancer Active Normal Embryo UBERON:0000922 mouse gastrula mouse embryo CL:0000000 Enhancer activity assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq Transgenic Reporter Assay, CRISPR Knockout, CRISPRi 2019 31591447 Distinct enhancer signatures in the mouse gastrula delineate progressive cell fate continuum during embryo development Mus musculus mm10 chr16 21480000 21482000 2510009E07Rik Enhancer Active Normal Embryo UBERON:0000922 mouse embryo E11.5 mouse embryo CL:0000000 Enhancer activity assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq Transgenic Reporter Assay, CRISPR Knockout, CRISPRi 2018 30130256 Super-enhancers maintain renin-expressing cell identity Mus musculus mm10 chr1 133345000 133350000 Creb1 Ren1C Enhancer Active Normal Kidney UBERON:0002113 Juxtaglomerular cell juxtaglomerular cell CL:0000647 Functional perturbation assay ChIP-seq, RNA-seq CRISPR Knockout, RT-RT-qPCR 2018 30328555 STAT5-Driven Enhancers Tightly Control Temporal Expression of Mammary-Specific Genes Mus musculus mm10 chr10 127850000 127852000 Stat5A Socs2 Enhancer Active Normal Mammary Gland UBERON:0001911 Mammary epithelial cells mammary epithelial cell CL:0000066 Functional perturbation assay ChIP-seq, RNA-seq CRISPR Knockout, RT-RT-qPCR, Western blot 2022 35210422 A fast Myosin super enhancer dictates muscle fiber phenotype through competitive interactions with Myosin genes Mus musculus mm10 chr11 97938123 97980122 Myh2 Enhancer Active Normal Skeletal muscle UBERON:0001134 Myofibers skeletal muscle myofiber CL:0000187 Chromatin interaction assay, Functional perturbation assay, Enhancer activity assay ATAC-seq, 4C-seq, RNA-seq CRISPR knockout, Transgenic reporter assay, RT-RT-qPCR 2022 35210422 A fast Myosin super enhancer dictates muscle fiber phenotype through competitive interactions with Myosin genes Mus musculus mm10 chr11 97938123 97980122 Myh1 Enhancer Active Normal Skeletal muscle UBERON:0001134 Myofibers skeletal muscle myofiber CL:0000187 Chromatin interaction assay, Functional perturbation assay, Enhancer activity assay ATAC-seq, 4C-seq, RNA-seq CRISPR knockout, Transgenic reporter assay, RT-RT-qPCR 2022 35210422 A fast Myosin super enhancer dictates muscle fiber phenotype through competitive interactions with Myosin genes Mus musculus mm10 chr11 97938123 97980122 Myh4 Enhancer Active Normal Skeletal muscle UBERON:0001134 Myofibers skeletal muscle myofiber CL:0000187 Chromatin interaction assay, Functional perturbation assay, Enhancer activity assay ATAC-seq, 4C-seq, RNA-seq CRISPR knockout, Transgenic reporter assay, RT-RT-qPCR 2022 35210422 A fast Myosin super enhancer dictates muscle fiber phenotype through competitive interactions with Myosin genes Mus musculus mm10 chr11 97938123 97980122 Myh8 Enhancer Active Normal Skeletal muscle UBERON:0001134 Myofibers skeletal muscle myofiber CL:0000187 Chromatin interaction assay, Functional perturbation assay, Enhancer activity assay ATAC-seq, 4C-seq, RNA-seq CRISPR knockout, Transgenic reporter assay, RT-RT-qPCR 2022 35210422 A fast Myosin super enhancer dictates muscle fiber phenotype through competitive interactions with Myosin genes Mus musculus mm10 chr11 97938123 97980122 Myh13 Enhancer Active Normal Skeletal muscle UBERON:0001134 Myofibers skeletal muscle myofiber CL:0000187 Chromatin interaction assay, Functional perturbation assay, Enhancer activity assay ATAC-seq, 4C-seq, RNA-seq CRISPR knockout, Transgenic reporter assay, RT-RT-qPCR 2021 34245781 Diet-dependent natriuretic peptide receptor C expression in adipose tissue is mediated by PPAR?? via long-range distal enhancers Mus musculus mm10 chr16 17266000 17266100 Nprc Enhancer Active Normal Adipose tissue UBERON:0001013 3T3-L1 adipocytes CVCL_0123 adipocyte CL:0000136 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq Luciferase Reporter Assay, 3C, ChIP-RT-qPCR, RT-RT-qPCR 2021 34245781 Diet-dependent natriuretic peptide receptor C expression in adipose tissue is mediated by PPAR?? via long-range distal enhancers Mus musculus mm10 chr16 17253000 17253100 Nprc Enhancer Active Normal Adipose tissue UBERON:0001013 3T3-L1 adipocytes CVCL_0123 adipocyte CL:0000136 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq Luciferase Reporter Assay, 3C, ChIP-RT-qPCR, RT-RT-qPCR 2020 32817427 Enhancer dependence of cell-type?Cspecific gene expression increases with developmental age Mus musculus mm10 chr12 111517811 111518523 Gata1 Tnfaip2 Enhancer Active Normal Bone Marrow UBERON:0002371 Erythroblasts erythroblast CL:0000765 Functional perturbation assay, Chromatin interaction assay, TF binding assay HiChIP, ChIP-seq, RNA-seq, ATAC-seq CRISPR Knockout, RT-RT-qPCR 2020 32817427 Enhancer dependence of cell-type?Cspecific gene expression increases with developmental age Mus musculus mm10 chr12 111517811 111518523 Gata1 Tnfaip2 Enhancer Active Normal Fetal Liver UBERON:0002107 MEL Cells CVCL_2109 erythroid progenitor cell CL:0000038 Functional perturbation assay, Chromatin interaction assay, TF binding assay HiChIP, ChIP-seq, RNA-seq, ATAC-seq CRISPR Knockout, RT-RT-qPCR 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 Bhlhe41 Enhancer Active Normal Blood UBERON:0000178 RAW 264.7 macrophage cells CVCL_0493 macrophage CL:0000235 Enhancer activity assay DNase-seq, RNA-seq, ChIP-seq Luciferase reporter assay 2025 40378239 C/EBP?? 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 Bone marrow UBERON:0002371 Myeloid cells myeloid cell CL:0000837 Functional perturbation assay ChIP-seq, RNA-seq CRISPR knockout, ChIP-RT-qPCR 2025 40604280 Range extender mediates long-distance enhancer activity Mus musculus mm10 chr8 89454508 89455383 Sall1 Enhancer Active Normal Embryonic Limb Bud UBERON:0005417 Limb bud mesenchymal cells mesenchymal cell CL:0000134 Enhancer activity assay, Functional perturbation assay ATAC-seq, scATAC-seq/scRNA-seq multiome, Capture Hi-C Transgenic Reporter Assay, CRISPR Knock-in, Whole-mount in situ hybridization, RT-RT-qPCR 2025 40604280 Range extender mediates long-distance enhancer activity Mus musculus mm10 chr8 89454508 89455383 Sall1 Enhancer Active Normal Limb Bud UBERON:0005417 Zone of polarizing activity cells mesenchymal cell CL:0000134 Enhancer activity assay, Functional perturbation assay ATAC-seq, scATAC-seq/scRNA-seq multiome, Capture Hi-C Transgenic Reporter Assay, CRISPR Knock-in, Whole-mount in situ hybridization, RT-RT-qPCR 2024 39394696 Identification and characterization of an enhancer element regulating expression of Cdkn1c (p57 gene) Mus musculus mm10 chr7 142855000 142857000 Cdkn1C Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells (mESCs) mouse embryonic stem cell CL:0002322 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay 4C, RNA-seq, ChIP-seq CRISPR knockout, CRISPRi, RT-RT-qPCR, Western blot 2025 40163145 Disease-Associated Mutations of the STAT5B SH2 Domain Regulate Cytokine-Driven Enhancer Function and Mammary Development Mus musculus mm10 chr11 98480000 98510000 Stat5A Wap Enhancer Active Normal Mammary Gland UBERON:0001911 Mammary alveolar epithelial cells mammary alveolar epithelial cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq RT-RT-qPCR, Western blot, CRISPR knockout 2025 40163145 Disease-Associated Mutations of the STAT5B SH2 Domain Regulate Cytokine-Driven Enhancer Function and Mammary Development Mus musculus mm10 chr19 12600000 12650000 Stat5A Olah Enhancer Active Normal Mammary Gland UBERON:0001911 Mammary alveolar epithelial cells mammary alveolar epithelial cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq RT-RT-qPCR, CRISPR knockout 2025 40163145 Disease-Associated Mutations of the STAT5B SH2 Domain Regulate Cytokine-Driven Enhancer Function and Mammary Development Mus musculus mm10 chr5 86800000 87200000 Stat5A Csn1S1 Enhancer Active Normal Mammary Gland UBERON:0001911 Mammary alveolar epithelial cells mammary alveolar epithelial cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq RT-RT-qPCR, Western blot, CRISPR knockout 2025 40163145 Disease-Associated Mutations of the STAT5B SH2 Domain Regulate Cytokine-Driven Enhancer Function and Mammary Development Mus musculus mm10 chr5 86800000 87200000 Stat5A Csn2 Enhancer Active Normal Mammary Gland UBERON:0001911 Mammary alveolar epithelial cells mammary alveolar epithelial cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq RT-RT-qPCR, Western blot, CRISPR knockout 2017 29042628 A DNA Contact Map for the Mouse Runx1 Gene Identifies Novel Haematopoietic Enhancers Mus musculus mm10 chr16 93024000 93024500 Runx1 Runx1 Enhancer Active Normal Bone Marrow UBERON:0002371 Mouse hematopoietic progenitor cell hematopoietic progenitor cell CL:0000837 Functional perturbation assay ChIP-seq, Hi-C Transgenic Reporter Assay, Luciferase Reporter Assay, RT-RT-qPCR 2017 29042628 A DNA Contact Map for the Mouse Runx1 Gene Identifies Novel Haematopoietic Enhancers Mus musculus mm10 chr16 93142000 93142471 Runx1 Enhancer Active Normal Bone Marrow UBERON:0002371 Mouse hematopoietic progenitor cell hematopoietic progenitor cell CL:0000837 Enhancer activity assay, Chromatin interaction assay 4C-seq, ChIP-seq, DNase-seq Transgenic Reporter Assay, Luciferase Reporter Assay 2017 29042628 A DNA Contact Map for the Mouse Runx1 Gene Identifies Novel Haematopoietic Enhancers Mus musculus mm10 chr16 93224000 93224529 Runx1 Enhancer Active Normal Bone Marrow UBERON:0002371 Mouse hematopoietic progenitor cell hematopoietic progenitor cell CL:0000837 Enhancer activity assay, Chromatin interaction assay 4C-seq, ChIP-seq, DNase-seq Transgenic Reporter Assay, Luciferase Reporter Assay 2017 29042628 A DNA Contact Map for the Mouse Runx1 Gene Identifies Novel Haematopoietic Enhancers Mus musculus mm10 chr16 93310000 93310579 Runx1 Enhancer Active Normal Bone Marrow UBERON:0002371 Mouse hematopoietic progenitor cell hematopoietic progenitor cell CL:0000837 Enhancer activity assay, Chromatin interaction assay 4C-seq, ChIP-seq, DNase-seq Transgenic Reporter Assay, Luciferase Reporter Assay 2024 38233525 Affinity-optimizing enhancer variants disrupt development Mus musculus mm10 chr5 28395077 28395877 Ets1 Shh Enhancer Active Normal Embryonic Limb Bud UBERON:0005417 Embryonic limb bud mesenchymal cells mesenchymal cell CL:0000134 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq Transgenic Reporter Assay, EMSA, in situ hybridization, CRISPR Knockout 2023 37932452 GATA transcription factors drive initial Xist upregulation after fertilization through direct activation of long-range enhancers Mus musculus mm10 chrX 103345000 103346000 Xist Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Functional perturbation assay CUT&Tag, RNA-seq, ATAC-seq Luciferase assay, CRISPRi, qRT-PCR, RNA-FISH 2023 37932452 GATA transcription factors drive initial Xist upregulation after fertilization through direct activation of long-range enhancers Mus musculus mm10 chrX 103365000 103366000 Xist Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Functional perturbation assay CUT&Tag, RNA-seq, ATAC-seq Luciferase assay, CRISPRi, qRT-PCR, RNA-FISH 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 Pancreas UBERON:0001264 Pancreatic islet cells pancreatic islet cell CL:0000168 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, RNA-seq CRISPR Knockout, Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2015 26673693 Dynamic recruitment of Ets1 to both nucleosome-occupied and -depleted enhancer regions mediates a transcriptional program switch during early T-cell differentiation Mus musculus mm10 chr14 53210000 53210600 Ets1 Tcra Enhancer Active Normal Thymus UBERON:0002370 Double-negative thymocytes double-negative thymocyte CL:0000894 Functional perturbation assay ChIP-seq, RNA-seq CRISPR Knockout, RT-RT-qPCR, Western blot 2018 29335546 Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming Mus musculus mm10 chr6 122663482 122708482 Oct4; Klf4; Cebpa Nanog Enhancer Active Normal Bone marrow UBERON:0002371 primary bone marrow-derived pre-B pre-B cell CL:0000945 Time-resolved multi-omic profiling of cell reprogramming in situ Hi-C, RNA-seq, ChIP-seq, ATAC-seq, 4C-seq qRT-PCR 2023 37832549 Genome-wide CRISPR activation screening in senescent cells reveals SOX5 as a driver and therapeutic target of rejuvenation Mus musculus mm10 chr9 112500000 112502800 Sox5 Hmgb2 Enhancer Active Normal Cartilage UBERON:0002418 Mouse Mesenchymal Progenitor mesenchymal progenitor cell CL:0000134 Enhancer activity assay ChIP-seq, ATAC-seq CRISPRa, RT-RT-qPCR 2023 37922339 Distinct use of super-enhancer elements controls cell type-specific CD25 transcription and function Mus musculus mm10 chr2 11621753 11635500 Stat5,Rbpj Il2Ra Enhancer Active Normal Thymus UBERON:0002370 DN thymocytes double-negative thymocyte CL:0000894 Regulatory element functional validation, 3D chromatin interaction mapping ChIP-seq, HiChIP, RNA-seq CRISPR-Cas9 deletion, flow cytometry, reporter assay 2023 37922339 Distinct use of super-enhancer elements controls cell type-specific CD25 transcription and function Mus musculus mm10 chr2 11656369 11660078 Stat5 Il2Ra Enhancer Active Normal Spleen UBERON:0002106 CD8+ T CD8-positive T cell CL:0000625 Regulatory element functional validation, 3D chromatin interaction mapping ChIP-seq, HiChIP, RNA-seq CRISPR-Cas9 deletion, flow cytometry, reporter assay 2018 30404009 Genetic Models Reveal cis and trans Immune-Regulatory Activities for lincRNA-Cox2 Mus musculus mm10 chr1 152006173 152012078 Ptgs2 Enhancer Active Normal Lung UBERON:0002048 BMDM macrophage CL:0000235 Enhancer activity assay, Functional perturbation assay RNA-seq, ChIP-seq Transgenic Reporter Assay, CRISPR Knockout, CRISPRi, RT-RT-qPCR, Western blot 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 Uterus UBERON:0000995 Uterine stromal cells endometrial stromal cell CL:0002255 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, CRISPR Activation (CRISPRa), qRT-PCR, Western blot 2024 38729993 Regulation of Myc transcription by an enhancer cluster dedicated to pluripotency and early embryonic expression Mus musculus mm10 chr15 61990505 62014068 Myc Enhancer Active Normal Embryo UBERON:0000922 mESC (naive pluripotency) mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq, ChIP-seq CRISPR Knockout, Flow Cytometry, Immunofluorescence, qRT-PCR 2024 38729993 Regulation of Myc transcription by an enhancer cluster dedicated to pluripotency and early embryonic expression Mus musculus mm10 chr15 62078497 62099928 Myc Enhancer Active Normal Embryo UBERON:0000922 EpiLC (formative pluripotency) epiblast-like cell CL:0002322 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq, ChIP-seq CRISPR Knockout, Flow Cytometry, Immunofluorescence, qRT-PCR 2025 40089598 In vivo deletion of a GWAS identified Myb distal enhancer acts on Myb expression, globin switching, and clinical erythroid parameters in ??-thalassemia Mus musculus mm10 chr10 21241829 21242175 Gata1 Myb Enhancer Active Normal Fetal liver UBERON:0002107 Erythroid progenitor erythroid progenitor cell CL:0000038 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, ATAC-seq, Capture-C, RNA-seq CRISPR Knockout, qRT-PCR, Flow cytometry 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 Gonad UBERON:0000991 Embryonic gonadal cells embryonic gonad cell CL:0000000 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq, ATAC-seq Luciferase Reporter Assay, CRISPR Knockout, EMSA, qRT-PCR 2022 36402763 PPAR?? lipodystrophy mutants reveal intermolecular interactions required for enhancer activation Mus musculus mm10 chr8 19275272 19275342 Pparg; Rxra Lpl Enhancer Active Normal Embryo UBERON:0000922 MEF CVCL_0003 mouse embryonic fibroblast CL:0000057 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq, ATAC-seq Luciferase Reporter Assay, Western blot, EMSA, qRT-PCR 2022 36402763 PPAR?? lipodystrophy mutants reveal intermolecular interactions required for enhancer activation Mus musculus mm10 chr6 14570800 14570870 Pparg; Rxra Cidec Enhancer Active Normal Embryo UBERON:0000922 MEF CVCL_0003 mouse embryonic fibroblast CL:0000057 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq, ATAC-seq Luciferase Reporter Assay, Western blot, EMSA, qRT-PCR 2023 36707514 Epigenetic regulation of Neuregulin 1 promotes breast cancer progression associated to hyperglycemia Mus musculus mm10 chr8 32199690 32200290 Nrg1 Enhancer Active Disease breast cancer MONDO:0006120 DOID:1612 Mammary gland UBERON:0001911 Met1 CVCL_UP55 breast carcinoma cell CL:0000646 Enhancer activity assay, TF binding assay, Functional perturbation assay FAIRE-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, qRT-PCR, Western blot 2020 32321991 The interdependence of mammary-specific super-enhancers and their native promoters facilitates gene activation during pregnancy Mus musculus mm10 chr11 10077283 10077800 Stat5; Nfib; Nr3C1 Wap Enhancer Active Normal Mammary Gland UBERON:0001911 Primary Mouse Mammary Epithelial mouse mammary epithelial cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi, RT-RT-qPCR 2020 32321991 The interdependence of mammary-specific super-enhancers and their native promoters facilitates gene activation during pregnancy Mus musculus mm10 chr11 10070908 10071400 Stat5; Nfib; Nr3C1 Wap Enhancer Active Normal Mammary Gland UBERON:0001911 Primary Mouse Mammary Epithelial mouse mammary epithelial cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi, RT-RT-qPCR 2020 32321991 The interdependence of mammary-specific super-enhancers and their native promoters facilitates gene activation during pregnancy Mus musculus mm10 chr11 10070908 10082508 Stat5; Nfib; Nr3C1 Wap Enhancer Active Normal Mammary Gland UBERON:0001911 Primary Mouse Mammary Epithelial mouse mammary epithelial cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi, RT-RT-qPCR 2017 28213503 Temporal regulation of LPS-induced transcription by IL-10 reveals distinct enhancer deactivation kinetics Mus musculus mm10 chr11 96750000 96755000 Nfkb1; Ikbz Il12B Enhancer Active Normal Bone marrow UBERON:0002371 Bone Marrow Derived Macrophages (BMDM) macrophage CL:0000235 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq Luciferase Reporter Assay, EMSA, RT-RT-qPCR 2016 27376239 Hierarchy within the mammary STAT5-driven Wap super-enhancer Mus musculus mm10 chr11 103459000 103463000 Stat5A Wap Enhancer Active Normal Mammary gland UBERON:0001911 Mammary epithelial cell mammary epithelial cell CL:0000066 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR 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; Hif1A; Stat3; Stat5A; Stat6; Arnt; Clock; Arntl; Npas2 Fgf23 Enhancer Active Normal Kidney UBERON:0002113 Conventional dendritic cells conventional dendritic cell CL:0000451 Functional genomics assay, Epigenomic profiling assay, Genome editing assay, In vivo functional assay ChIP-seq, Microarray CRISPR-Cas9 enhancer deletion, RT-RT-qPCR, FGF23 ELISA, Serum biochemical analysis, In vivo LPS stimulation assay, In vivo CKD model assay 2020 33229569 Chromatin topology and the timing of enhancer action at the mouse HoxD locus Mus musculus mm10 chr2 74925621 74939634 Hoxd9 Enhancer Active Normal Limb UBERON:0002101 Chromatin interaction assay, Functional perturbation assay 3C-seq, RNA-seq CRISPR knockout, CRISPRi, RT-RT-qPCR 2020 33229569 Chromatin topology and the timing of enhancer action at the mouse HoxD locus Mus musculus mm10 chr2 75081283 75094718 Hoxd4 Enhancer Active Normal Limb UBERON:0002101 Chromatin interaction assay, Functional perturbation assay 3C-seq, RNA-seq CRISPR knockout, CRISPRi, RT-RT-qPCR 2020 33229569 Chromatin topology and the timing of enhancer action at the mouse HoxD locus Mus musculus mm10 chr2 75128401 75162753 Hoxd11 Enhancer Active Normal Limb UBERON:0002101 Chromatin interaction assay, Functional perturbation assay 3C-seq, RNA-seq CRISPR knockout, CRISPRi, RT-RT-qPCR 2020 33229569 Chromatin topology and the timing of enhancer action at the mouse HoxD locus Mus musculus mm10 chr2 75194928 75211234 Hoxd11 Enhancer Active Normal Limb UBERON:0002101 Chromatin interaction assay, Functional perturbation assay 3C-seq, RNA-seq CRISPR knockout, CRISPRi, RT-RT-qPCR 2020 33229569 Chromatin topology and the timing of enhancer action at the mouse HoxD locus Mus musculus mm10 chr2 75420048 75444960 Hoxd11 Enhancer Active Normal Limb UBERON:0002101 Chromatin interaction assay, Functional perturbation assay 3C-seq, RNA-seq CRISPR knockout, CRISPRi, RT-RT-qPCR 2020 31685980 Zfp422 promotes skeletal muscle differentiation by regulating EphA7 to induce appropriate myoblast apoptosis Mus musculus mm10 chr4 28176897 28177065 Epha7 Enhancer Active Normal Skeletal Muscle UBERON:0001134 Primary myoblasts myoblast CL:0000056 Enhancer activity assay, Functional perturbation assay RNA-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR, Western blot 2020 31685980 Zfp422 promotes skeletal muscle differentiation by regulating EphA7 to induce appropriate myoblast apoptosis Mus musculus mm10 chr4 28176897 28177065 Epha7 Enhancer Active Normal Skeletal Muscle UBERON:0001134 Satellite cells satellite cell CL:0000593 Enhancer activity assay, Functional perturbation assay RNA-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR, Western blot 2021 33313982 The anxiety and ethanol intake controlling GAL51 enhancer is epigenetically modulated by, and controls preference for, high-fat diet Mus musculus mm10 chr19 3441054 3441445 Gal Enhancer Silenced Disease neuroblastoma MONDO:0005070 DOID:769 Brain UBERON:0000955 SH-SY5Y CVCL_0019 neuroblastoma cell CL:0000031 Enhancer activity assay, Epigenetic modulation assay, Functional perturbation assay Luciferase Reporter Assay, Bisulfite Pyrosequencing, RT-RT-qPCR, CRISPR Knockout 2021 33313982 The anxiety and ethanol intake controlling GAL51 enhancer is epigenetically modulated by, and controls preference for, high-fat diet Mus musculus mm10 chr19 3441054 3441445 Gal Enhancer Silenced Normal Hypothalamus UBERON:0001898 Primary hypothalamic neurons neuron CL:0000540 Enhancer activity assay, Epigenetic modulation assay, Functional perturbation assay Luciferase Reporter Assay, Bisulfite Pyrosequencing, RT-RT-qPCR, CRISPR Knockout 2021 33313982 The anxiety and ethanol intake controlling GAL51 enhancer is epigenetically modulated by, and controls preference for, high-fat diet Mus musculus mm10 chr19 3441054 3441445 Gal Enhancer Silenced Normal Amygdala UBERON:0001876 Primary amygdala neurons neuron CL:0000540 Enhancer activity assay, Epigenetic modulation assay, Functional perturbation assay Luciferase Reporter Assay, Bisulfite Pyrosequencing, RT-RT-qPCR, CRISPR Knockout 2025 41081394 Generation and characterization of a knockout mouse of an enhancer of EBF3 Mus musculus mm10 chr7 136083275 136084434 Ebf3 Enhancer Active Normal Forebrain UBERON:0000955 Mouse Embryonic Brain Cells mouse embryonic brain cell CL:0000540 Functional Perturbation Assay, Chromatin Interaction Assay Hi-C, RNA-seq, PacBio HiFi Whole-Genome Sequencing CRISPR Knockout, RT-RT-qPCR, PCR Genotyping 2019 31000713 ZFP30 promotes adipogenesis through the KAP1-mediated activation of a retrotransposon-derived Pparg2 enhancer Mus musculus mm10 chr6 113041000 113041700 Pparg2 Enhancer Active Normal Cerebral Cortex UBERON:0000956 Mouse embryo fibroblast cell mouse embryonic fibroblast CL:0000057 Enhancer activity assay,Functional perturbation assay Luciferase Reporter Assay,CRISPR Knockout,qRT-PCR 2017 29042628 A DNA Contact Map for the Mouse Runx1 Gene Identifies Novel Haematopoietic Enhancers Mus musculus mm10 chr16 92332000 92333000 Runx1 Runx1 Enhancer Active Normal Bone Marrow UBERON:0002371 Mouse hematopoietic progenitor cell hematopoietic progenitor cell CL:0000837 Enhancer activity assay, Chromatin interaction assay 4C-seq, ChIP-seq, RNA-seq Transgenic Reporter Assay, RT-RT-qPCR 2017 29042628 A DNA Contact Map for the Mouse Runx1 Gene Identifies Novel Haematopoietic Enhancers Mus musculus mm10 chr16 92414000 92415000 Runx1 Runx1 Enhancer Active Normal Bone Marrow UBERON:0002371 Mouse hematopoietic progenitor cell hematopoietic progenitor cell CL:0000837 Enhancer activity assay, Chromatin interaction assay 4C-seq, ChIP-seq, RNA-seq Transgenic Reporter Assay, RT-RT-qPCR 2024 38528203 Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development Mus musculus mm10 chr13 53802995 53810985 Meis2; Dlx5 Drd1 Enhancer Active Normal Forebrain UBERON:0000955 Mouse neuroblastoma cell mouse neuroblastoma cell CL:0000031 Enhancer activity assay, TF binding assay ChIP-seq Luciferase Reporter Assay 2020 32251373 Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction Mus musculus mm10 chr6 122498000 122499500 Aicda Enhancer Active Normal Spleen UBERON:0002106 mature B mature B cell CL:0000785 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, GRO-seq, ATAC-seq, 3C-seq 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR 2020 32251373 Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction Mus musculus mm10 chr6 122502000 122503500 Aicda Enhancer Active Normal Spleen UBERON:0002106 mature B mature B cell CL:0000785 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, GRO-seq, ATAC-seq, 3C-seq 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR 2020 32251373 Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction Mus musculus mm10 chr6 122506000 122507500 Aicda Enhancer Active Normal Spleen UBERON:0002106 mature B mature B cell CL:0000785 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, GRO-seq, ATAC-seq, 3C-seq 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR 2020 32251373 Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction Mus musculus mm10 chr6 122510000 122511500 Aicda Enhancer Active Normal Spleen UBERON:0002106 mature B mature B cell CL:0000785 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, GRO-seq, ATAC-seq, 3C-seq 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR 2020 32251373 Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction Mus musculus mm10 chr15 61825000 62125000 Myc Enhancer Active Normal Spleen UBERON:0002106 mature B mature B cell CL:0000785 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, GRO-seq, ATAC-seq, 3C-seq 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45582000 45582499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 double-negative thymocyte double-negative thymocyte CL:0000894 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45582000 45582499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 double-positive thymocyte double-positive thymocyte CL:0000895 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45582000 45582499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 naive CD4-positive T cell naive CD4-positive T cell CL:0000896 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45582000 45582499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 Th1 CD4-positive Th1 cell CL:0000897 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45586000 45586499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 double-negative thymocyte double-negative thymocyte CL:0000894 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45586000 45586499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 double-positive thymocyte double-positive thymocyte CL:0000895 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45586000 45586499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 naive CD4-positive T cell naive CD4-positive T cell CL:0000896 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45586000 45586499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 Th1 CD4-positive Th1 cell CL:0000897 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45590000 45590499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 double-negative thymocyte double-negative thymocyte CL:0000894 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45590000 45590499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 double-positive thymocyte double-positive thymocyte CL:0000895 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45590000 45590499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 naive CD4-positive T cell naive CD4-positive T cell CL:0000896 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45590000 45590499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 Th1 CD4-positive Th1 cell CL:0000897 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45594000 45594499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 double-negative thymocyte double-negative thymocyte CL:0000894 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45594000 45594499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 double-positive thymocyte double-positive thymocyte CL:0000895 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45594000 45594499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 naive CD4-positive T cell naive CD4-positive T cell CL:0000896 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45594000 45594499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 Th1 CD4-positive Th1 cell CL:0000897 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45598000 45598499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 double-negative thymocyte double-negative thymocyte CL:0000894 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45598000 45598499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 double-positive thymocyte double-positive thymocyte CL:0000895 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45598000 45598499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 naive CD4-positive T cell naive CD4-positive T cell CL:0000896 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45598000 45598499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 Th1 CD4-positive Th1 cell CL:0000897 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45602000 45602499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 double-negative thymocyte double-negative thymocyte CL:0000894 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45602000 45602499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 double-positive thymocyte double-positive thymocyte CL:0000895 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45602000 45602499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 naive CD4-positive T cell naive CD4-positive T cell CL:0000896 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45602000 45602499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 Th1 CD4-positive Th1 cell CL:0000897 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45606000 45606499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 double-negative thymocyte double-negative thymocyte CL:0000894 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45606000 45606499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 double-positive thymocyte double-positive thymocyte CL:0000895 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45606000 45606499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 naive CD4-positive T cell naive CD4-positive T cell CL:0000896 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45606000 45606499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 Th1 CD4-positive Th1 cell CL:0000897 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45610000 45610499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 double-negative thymocyte double-negative thymocyte CL:0000894 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45610000 45610499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 double-positive thymocyte double-positive thymocyte CL:0000895 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45610000 45610499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 naive CD4-positive T cell naive CD4-positive T cell CL:0000896 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45610000 45610499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 Th1 CD4-positive Th1 cell CL:0000897 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45614000 45614499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 double-negative thymocyte double-negative thymocyte CL:0000894 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45614000 45614499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 double-positive thymocyte double-positive thymocyte CL:0000895 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45614000 45614499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 naive CD4-positive T cell naive CD4-positive T cell CL:0000896 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45614000 45614499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 Th1 CD4-positive Th1 cell CL:0000897 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45618000 45618499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 double-negative thymocyte double-negative thymocyte CL:0000894 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45618000 45618499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 double-positive thymocyte double-positive thymocyte CL:0000895 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45618000 45618499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 naive CD4-positive T cell naive CD4-positive T cell CL:0000896 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45618000 45618499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 Th1 CD4-positive Th1 cell CL:0000897 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45622000 45622499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 double-negative thymocyte double-negative thymocyte CL:0000894 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45622000 45622499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 double-positive thymocyte double-positive thymocyte CL:0000895 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45622000 45622499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 naive CD4-positive T cell naive CD4-positive T cell CL:0000896 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2020 32814051 Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation Mus musculus mm10 chr11 45622000 45622499 Lef1 Enhancer Active Normal Thymus UBERON:0002370 Th1 CD4-positive Th1 cell CL:0000897 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, 3C-seq qRT-PCR, and ChIP-qPCR 2015 26494787 Lhx1 functions together with Otx2, Foxa2, and Ldb1 to govern anterior mesendoderm, node, and midline development Mus musculus mm10 chr10 61645000 61646000 Lhx1 Nodal Enhancer Active Normal Embryo UBERON:0000922 Mouse Embryonic Stem mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2015 26494787 Lhx1 functions together with Otx2, Foxa2, and Ldb1 to govern anterior mesendoderm, node, and midline development Mus musculus mm10 chr14 54950000 54951000 Lhx1 Otx2 Enhancer Active Normal Embryo UBERON:0000922 Mouse Embryonic Stem mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2015 26494787 Lhx1 functions together with Otx2, Foxa2, and Ldb1 to govern anterior mesendoderm, node, and midline development Mus musculus mm10 chr2 146950000 146951000 Lhx1 Foxa2 Enhancer Active Normal Embryo UBERON:0000922 Mouse Embryonic Stem mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2015 25810254 RNA transcribed from a distal enhancer is required for activating the chromatin at the promoter of the gonadotropin ??-subunit gene Mus musculus mm10 chr6 84520000 84524600 Cga Enhancer Active Normal Pituitary gland UBERON:0000007 alphaT3-1 CVCL_0141 gonadotrope cell CL:0000510 Enhancer activity assay, Chromatin interaction assay RNA-seq Luciferase Reporter Assay, 3C assay 2025 37225984 BRD4 in Cx3cr1-positive macrophages drives proinflammatory transcription in heart failure pathogenesis Mus musculus mm10 chr2 129318595 129323595 Il1B Enhancer Active Normal Heart UBERON:0000948 Macrophage macrophage CL:0000235 Enhancer activity assay scATAC-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR 2022 36427307 XLID syndrome gene Med12 promotes Ig isotype switching through chromatin modification and enhancer RNA regulation Mus musculus mm10 chr12 117170000 117198000 Igh Enhancer Active Normal Spleen UBERON:0002106 CH12F3-2A CVCL_7161 B cell CL:0000945 Regulatory element functional validation, super-enhancer activation analysis CRISPR-dCas9 enhancer activation, siRNA knockdown, ASO-mediated eRNA knockdown, 3C assay, ChIP-RT-qPCR, RT-RT-qPCR, flow cytometry 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 Intervertebral disc UBERON:0001066 Annulus fibrosus annulus fibrosus cell CL:0000060 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, EMSA, RT-RT-qPCR, Co-immunoprecipitation, Transgenic Reporter Assay 2016 27881681 A Novel Regulatory Mechanism of Type II Collagen Expression via a SOX9-Dependent Enhancer in Intron 6 Mus musculus mm10 chr15 71595 72481 Sox9 Col2A1 Enhancer Active Normal Cartilage UBERON:0002418 Primary chondrocytes chondrocyte CL:0000138 Enhancer activity assay, TF binding assay ChIP-seq EMSA, CRISPR knockout 2025 39626663 Enhancer cooperativity can compensate for loss of activity over large genomic distances Mus musculus mm10 chr6 100282437 100393986 Rybp Enhancer Active Normal Embryo UBERON:0000922 Mouse Embryonic Stem Cells (v6.5) mouse embryonic stem cell CL:0002322 Enhancer activity assay ChIP-seq, ATAC-seq Luciferase Reporter Assay, Fluorescent Reporter Assay (mCherry), RT-RT-qPCR 2025 39626663 Enhancer cooperativity can compensate for loss of activity over large genomic distances Mus musculus mm10 chr3 34546571 34552571 Sox2 Enhancer Active Normal Embryo UBERON:0000922 Mouse Embryonic Stem Cells (v6.5) mouse embryonic stem cell CL:0002322 Enhancer activity assay ChIP-seq, ATAC-seq Luciferase Reporter Assay, Fluorescent Reporter Assay (mCherry), RT-RT-qPCR 2024 39256730 Early inhibition of BRD4 facilitates iPSC reprogramming via accelerating rDNA dynamic expression Mus musculus mm10 chr15 1 1000 Ubf 47S Rrna Enhancer Active Normal Embryo UBERON:0000922 MEF CVCL_0003 mouse embryonic fibroblast CL:0000057 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, CRISPR Knockout, qRT-PCR, Western blot 2020 32647123 The chromatin remodeling enzyme Chd4 regulates genome architecture in the mouse brain Mus musculus mm10 chr4 49550000 49600000 Aldob Enhancer Active Normal Cerebellum UBERON:0002037 Mouse Cerebellar Granule Neurons cerebellar granule neuron CL:0001031 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, DNaseI-seq Conditional Knockout, qRT-PCR, Western blot 2020 32647123 The chromatin remodeling enzyme Chd4 regulates genome architecture in the mouse brain Mus musculus mm10 chr13 28260000 29080000 Sox4 SE Active Normal Cerebellum UBERON:0002037 Mouse Cerebellar Granule Neurons cerebellar granule neuron CL:0001031 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, DNaseI-seq Conditional Knockout, qRT-PCR, Western blot 2020 32647123 The chromatin remodeling enzyme Chd4 regulates genome architecture in the mouse brain Mus musculus mm10 chr4 95048663 95059853 Jun Enhancer Active Normal Cerebellum UBERON:0002037 Mouse Cerebellar Granule Neurons cerebellar granule neuron CL:0001031 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, DNaseI-seq Conditional Knockout, qRT-PCR, Western blot 2020 32647123 The chromatin remodeling enzyme Chd4 regulates genome architecture in the mouse brain Mus musculus mm10 chr10 117390000 117760000 SE Active Normal Cerebellum UBERON:0002037 Mouse Cerebellar Granule Neurons cerebellar granule neuron CL:0001031 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, DNaseI-seq Conditional Knockout, qRT-PCR, Western blot 2021 33707608 Dmrt2 promotes transition of endochondral bone formation by linking Sox9 and Runx2 Mus musculus mm10 chr19 25728596 25729301 Dmrt2 Enhancer Active Normal Cartilage UBERON:0002418 Primary chondrocytes chondrocyte CL:0000138 Enhancer activity assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, qRT-PCR 2020 32647123 The chromatin remodeling enzyme Chd4 regulates genome architecture in the mouse brain Mus musculus mm10 chr4 95630001 95639906 Chd4; Smc1 Jun Enhancer Active Normal Cerebellum UBERON:0002037 Cerebellar granule neurons cerebellar granule neuron CL:0001031 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ChIP-seq, DNaseI-seq, RNA-seq RT-RT-qPCR, Western blot 2022 35831318 A SOX17-PDGFB signaling axis regulates aortic root development Mus musculus mm10 chr15 79849001 79850000 Sox17 Pdgfb Enhancer Active Normal Aorta UBERON:0000947 Cardiac endothelial cells (MCECs) cardiac endothelial cell CL:0000115 TF binding assay, Enhancer activity assay ChIP-seq, RNA-seq ChIP-RT-qPCR, Luciferase Reporter Assay 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 Limb bud UBERON:0005417 Embryonic limb mesenchyme limb mesenchyme cell CL:0000134 Enhancer activity assay, TF binding assay, Chromatin interaction assay ATAC-seq, ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA 2024 38528203 Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development Mus musculus mm10 chr4 156021490 156022916 Tnfrsf18 Enhancer Active Normal Immune System UBERON:0002405 Primary mouse regulatory T cells mouse regulatory T cell CL:0000815 Functional perturbation assay RNA-seq, ATAC-seq CRISPRi, Stain-and-sort screen, Flow Cytometry 2019 31096644 A Critical E-box in Barhl1 3' Enhancer Is Essential for Auditory Hair Cell Differentiation Mus musculus mm10 chr2 44123800 44124118 Barhl1 Enhancer Active Normal Inner Ear UBERON:0001846 mESC differentiated hair cell hair cell CL:0000202 Enhancer activity assay, Functional perturbation assay Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR 2018 30295986 Identification of Novel Gata3 Distal Enhancers Active in Mouse Embryonic Lens Mus musculus mm10 chr2 9895741 9898314 Gata3 Gata3 Enhancer Active Normal Lens UBERON:0000965 Lens epithelial cells lens epithelial cell CL:0002224 Enhancer activity assay ChIP-seq Luciferase Reporter Assay, Transgenic Reporter Assay, RT-RT-qPCR 2018 30295986 Identification of Novel Gata3 Distal Enhancers Active in Mouse Embryonic Lens Mus musculus mm10 chr2 9897700 9898314 Gata3 Gata3 Enhancer Active Normal Lens UBERON:0000965 Lens epithelial cells lens epithelial cell CL:0002224 Enhancer activity assay ChIP-seq Luciferase Reporter Assay, Transgenic Reporter Assay, RT-RT-qPCR 2018 30295986 Identification of Novel Gata3 Distal Enhancers Active in Mouse Embryonic Lens Mus musculus mm10 chr2 9895741 9896397 Gata3 Gata3 Enhancer Active Normal Lens UBERON:0000965 Lens epithelial cells lens epithelial cell CL:0002224 Enhancer activity assay ChIP-seq Luciferase Reporter Assay, Transgenic Reporter Assay, RT-RT-qPCR 2018 30295986 Identification of Novel Gata3 Distal Enhancers Active in Mouse Embryonic Lens Mus musculus mm10 chr2 9881939 9882773 Gata3 Gata3 Enhancer Active Normal Lens UBERON:0000965 Lens epithelial cells lens epithelial cell CL:0002224 Enhancer activity assay ChIP-seq Luciferase Reporter Assay, Transgenic Reporter Assay, RT-RT-qPCR 2018 29358217 Homeostatic response of mouse renin gene transcription in a hypertensive environment is mediated by a novel 5' enhancer Mus musculus mm10 chr1 13344600 13346900 Ren1 Enhancer Active Normal Kidney UBERON:0002113 JG cells juxtaglomerular cell CL:0000647 Functional perturbation assay CRISPR Knockout, Luciferase Reporter Assay, RT-RT-qPCR 2020 32376415 Immunity-related GTPase induces lipophagy to prevent excess hepatic lipid accumulation Mus musculus mm10 chr18 60211000 60212000 Foxo1 Ifgga2 Enhancer Active Normal Liver UBERON:0002107 Primary hepatocytes hepatocyte CL:0000182 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq EMSA, RT-RT-qPCR, Western blot 2020 32376415 Immunity-related GTPase induces lipophagy to prevent excess hepatic lipid accumulation Mus musculus mm10 chr18 60211000 60212000 Foxo1 Ifgga2 Enhancer Active Normal Liver UBERON:0002107 McArdle hepatocytes hepatocyte CL:0000182 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq EMSA, RT-RT-qPCR, Western blot 2020 32376415 Immunity-related GTPase induces lipophagy to prevent excess hepatic lipid accumulation Mus musculus mm10 chr18 60211000 60212000 Foxo1 Ifgga2 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293T cells CVCL_0063 embryonic kidney cell CL:0002139 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq EMSA, RT-RT-qPCR, Western blot 2020 32376415 Immunity-related GTPase induces lipophagy to prevent excess hepatic lipid accumulation Mus musculus mm10 chr18 60211000 60212000 Foxo1 Ifgga4 Enhancer Active Normal Liver UBERON:0002107 Primary hepatocytes hepatocyte CL:0000182 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq EMSA, RT-RT-qPCR, Western blot 2020 32376415 Immunity-related GTPase induces lipophagy to prevent excess hepatic lipid accumulation Mus musculus mm10 chr18 60211000 60212000 Foxo1 Ifgga4 Enhancer Active Normal Liver UBERON:0002107 McArdle hepatocytes hepatocyte CL:0000182 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq EMSA, RT-RT-qPCR, Western blot 2020 32376415 Immunity-related GTPase induces lipophagy to prevent excess hepatic lipid accumulation Mus musculus mm10 chr18 60211000 60212000 Foxo1 Ifgga4 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293T cells CVCL_0063 embryonic kidney cell CL:0002139 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq EMSA, RT-RT-qPCR, Western blot 2019 31406377 An Nfil3-Zeb2-Id2 pathway imposes Irf8 enhancer switching during cDC1 development Mus musculus mm10 chr8 124380000 124380454 E2A; Tcf4 Irf8 Enhancer Active Normal Bone Marrow UBERON:0002371 Common Dendritic Cell Progenitor (CDP) dendritic cell progenitor CL:0000451 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq, scRNA-seq Retroviral Reporter Assay, Site-directed Mutagenesis, RT-RT-qPCR, Flow Cytometry 2019 31406377 An Nfil3-Zeb2-Id2 pathway imposes Irf8 enhancer switching during cDC1 development Mus musculus mm10 chr8 124380000 124380454 E2A; Tcf4 Irf8 Enhancer Active Normal Bone Marrow UBERON:0002371 Pre-cDC1 conventional dendritic cell CL:0000451 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq, scRNA-seq Retroviral Reporter Assay, Site-directed Mutagenesis, RT-RT-qPCR, Flow Cytometry 2019 31406377 An Nfil3-Zeb2-Id2 pathway imposes Irf8 enhancer switching during cDC1 development Mus musculus mm10 chr8 124380000 124380454 E2A; Tcf4 Irf8 Enhancer Active Normal Bone Marrow UBERON:0002371 Plasmacytoid Dendritic Cells (pDC) plasmacytoid dendritic cell CL:0000945 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq, scRNA-seq Retroviral Reporter Assay, Site-directed Mutagenesis, RT-RT-qPCR, Flow Cytometry 2020 31915147 Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types Mus musculus mm10 chr14 48579937 48581029 Otx2 Enhancer Active Normal Retina UBERON:0000966 Primary Mouse Embryonic Retinal Explant Cells mouse embryonic retinal cell CL:0000540 Enhancer activity assay RNA-seq, ATAC-seq, ChIP-seq Transgenic Reporter Assay, RT-RT-qPCR 2020 31915147 Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types Mus musculus mm10 chr14 48584564 48585012 Otx2 Enhancer Active Normal Retina UBERON:0000966 Primary Mouse Embryonic Retinal Explant Cells mouse embryonic retinal cell CL:0000540 Enhancer activity assay RNA-seq, ATAC-seq, ChIP-seq Transgenic Reporter Assay, RT-RT-qPCR 2020 31915147 Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types Mus musculus mm10 chr14 48593170 48594188 Otx2 Enhancer Active Normal Retina UBERON:0000966 Primary Mouse Embryonic Retinal Explant Cells mouse embryonic retinal cell CL:0000540 Enhancer activity assay RNA-seq, ATAC-seq, ChIP-seq qRT-PCR, and ChIP-qPCR 2020 31915147 Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types Mus musculus mm10 chr14 48606973 48608016 Otx2 Enhancer Active Normal Retina UBERON:0000966 Primary Mouse Embryonic Retinal Explant Cells mouse embryonic retinal cell CL:0000540 Enhancer activity assay RNA-seq, ATAC-seq, ChIP-seq Transgenic Reporter Assay, RT-RT-qPCR 2020 31915147 Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types Mus musculus mm10 chr14 48608144 48609697 Otx2 Enhancer Active Normal Retina UBERON:0000966 Primary Mouse Embryonic Retinal Explant Cells mouse embryonic retinal cell CL:0000540 Enhancer activity assay RNA-seq, ATAC-seq, ChIP-seq Transgenic Reporter Assay, RT-RT-qPCR 2020 31915147 Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types Mus musculus mm10 chr14 48616314 48617497 Otx2 Enhancer Active Normal Retina UBERON:0000966 Primary Mouse Embryonic Retinal Explant Cells mouse embryonic retinal cell CL:0000540 Enhancer activity assay RNA-seq, ATAC-seq, ChIP-seq Transgenic Reporter Assay, RT-RT-qPCR 2020 31915147 Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types Mus musculus mm10 chr14 48624486 48626389 Otx2 Enhancer Active Normal Retina UBERON:0000966 Primary Mouse Embryonic Retinal Explant Cells mouse embryonic retinal cell CL:0000540 Enhancer activity assay RNA-seq, ATAC-seq, ChIP-seq Transgenic Reporter Assay, RT-RT-qPCR 2020 31915147 Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types Mus musculus mm10 chr14 48662841 48663211 Otx2 Enhancer Active Normal Retina UBERON:0000966 Primary Mouse Embryonic Retinal Explant Cells mouse embryonic retinal cell CL:0000540 Enhancer activity assay RNA-seq, ATAC-seq, ChIP-seq Transgenic Reporter Assay, RT-RT-qPCR 2025 41253710 The Ets2 super-enhancer modulates endothelial-mesenchymal transition during cardiac aging Mus musculus mm10 chr16 95721049 95979933 Ets2 Enhancer Active Normal Heart UBERON:0000948 Cardiac endothelial cells endothelial cell CL:0000115 Functional perturbation assay RNA-seq, ATAC-seq CRISPR knockout, RT-RT-qPCR, Western blot 2025 41253710 The Ets2 super-enhancer modulates endothelial-mesenchymal transition during cardiac aging Mus musculus mm10 chr16 95721049 95979933 Ets2 Enhancer Active Normal Heart UBERON:0000948 Aortic endothelial cells aortic endothelial cell CL:0002546 Functional perturbation assay RNA-seq, ATAC-seq CRISPR knockout, RT-RT-qPCR, Western blot 2025 40382324 Auricular malformations are driven by copy number variations in a hierarchical enhancer cluster and a dominant enhancer recapitulates human pathogenesis Mus musculus mm10 chr5 12345678 12346478 Hmx1 Enhancer Active Normal Embryonic Craniofacial Tissue UBERON:0010368 Mouse cranial neural crest cells mouse cranial neural crest cell CL:0000333 Enhancer activity assay, Functional perturbation assay ATAC-seq, RNA-seq Transgenic Reporter Assay, CRISPR Knockout, RT-RT-qPCR 2025 40604280 Range extender mediates long-distance enhancer activity Mus musculus mm10 chr5 29314881 29315667 Shh Enhancer Active Normal Limb Bud UBERON:0005417 Zone of polarizing activity cells mesenchymal cell CL:0000134 Enhancer activity assay ATAC-seq, Hi-C Luciferase Reporter Assay 2017 29042628 A DNA Contact Map for the Mouse Runx1 Gene Identifies Novel Haematopoietic Enhancers Mus musculus mm10 chr16 92829000 92829471 Runx1 Enhancer Active Normal Bone Marrow UBERON:0002371 Mouse hematopoietic progenitor cell hematopoietic progenitor cell CL:0000837 Enhancer activity assay, Chromatin interaction assay 4C-seq, ChIP-seq, DNase-seq Transgenic Reporter Assay 2017 29042628 A DNA Contact Map for the Mouse Runx1 Gene Identifies Novel Haematopoietic Enhancers Mus musculus mm10 chr16 92832000 92832471 Runx1 Enhancer Active Normal Bone Marrow UBERON:0002371 Mouse hematopoietic progenitor cell hematopoietic progenitor cell CL:0000837 Enhancer activity assay, Chromatin interaction assay 4C-seq, ChIP-seq, DNase-seq Transgenic Reporter Assay 2017 29042628 A DNA Contact Map for the Mouse Runx1 Gene Identifies Novel Haematopoietic Enhancers Mus musculus mm10 chr16 92846000 92846471 Runx1 Enhancer Active Normal Bone Marrow UBERON:0002371 Mouse hematopoietic progenitor cell hematopoietic progenitor cell CL:0000837 Enhancer activity assay, Chromatin interaction assay 4C-seq, ChIP-seq, DNase-seq Transgenic Reporter Assay 2017 29042628 A DNA Contact Map for the Mouse Runx1 Gene Identifies Novel Haematopoietic Enhancers Mus musculus mm10 chr16 92879000 92879471 Runx1 Enhancer Active Normal Bone Marrow UBERON:0002371 Mouse hematopoietic progenitor cell hematopoietic progenitor cell CL:0000837 Enhancer activity assay, Chromatin interaction assay 4C-seq, ChIP-seq, DNase-seq Transgenic Reporter Assay 2017 29042628 A DNA Contact Map for the Mouse Runx1 Gene Identifies Novel Haematopoietic Enhancers Mus musculus mm10 chr16 92897000 92897471 Runx1 Enhancer Active Normal Bone Marrow UBERON:0002371 Mouse hematopoietic progenitor cell hematopoietic progenitor cell CL:0000837 Enhancer activity assay, Chromatin interaction assay 4C-seq, ChIP-seq, DNase-seq Transgenic Reporter Assay 2017 29042628 A DNA Contact Map for the Mouse Runx1 Gene Identifies Novel Haematopoietic Enhancers Mus musculus mm10 chr16 93110000 93110500 Spi1 Runx1 Enhancer Active Normal Bone Marrow UBERON:0002371 Mouse hematopoietic progenitor cell hematopoietic progenitor cell CL:0000837 Enhancer activity assay ChIP-seq, DNase-seq Transgenic Reporter Assay, Luciferase Reporter Assay, RT-RT-qPCR 2017 29042628 A DNA Contact Map for the Mouse Runx1 Gene Identifies Novel Haematopoietic Enhancers Mus musculus mm10 chr16 93152000 93152471 Runx1 Enhancer Active Normal Bone Marrow UBERON:0002371 Mouse hematopoietic progenitor cell hematopoietic progenitor cell CL:0000837 Enhancer activity assay, Chromatin interaction assay 4C-seq, ChIP-seq, DNase-seq Transgenic Reporter Assay 2024 38528203 Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development Mus musculus mm10 chr14 23090994 23098987 Meis2; Dlx5; Lhx6 Zfp503 Enhancer Active Normal Forebrain UBERON:0000955 Mouse neuroblastoma cell mouse neuroblastoma cell CL:0000031 Enhancer activity assay, TF binding assay ChIP-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2024 38528203 Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development Mus musculus mm10 chr19 14773960 14781991 Meis2; Dlx5; Lhx6 Tle4 Enhancer Active Normal Forebrain UBERON:0000955 Mouse neuroblastoma cell mouse neuroblastoma cell CL:0000031 Enhancer activity assay, TF binding assay ChIP-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2024 38528203 Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development Mus musculus mm10 chr2 115721983 115729990 Meis2; Dlx5; Lhx6 Meis2 Enhancer Active Normal Forebrain UBERON:0000955 Mouse neuroblastoma cell mouse neuroblastoma cell CL:0000031 Enhancer activity assay, TF binding assay ChIP-seq Luciferase Reporter Assay 2024 38528203 Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development Mus musculus mm10 chr6 15366783 15417517 Meis2; Dlx5; Pbx1 Foxp2 Enhancer Active Normal Forebrain UBERON:0000955 Mouse neuroblastoma cell mouse neuroblastoma cell CL:0000031 Enhancer activity assay, TF binding assay ChIP-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2024 38528203 Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development Mus musculus mm10 chr6 15408978 15417000 Meis2; Dlx5; Lhx6 Foxp2 Enhancer Active Normal Forebrain UBERON:0000955 Mouse neuroblastoma cell mouse neuroblastoma cell CL:0000031 Enhancer activity assay, TF binding assay ChIP-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2021 34335313 Transcriptional and Epigenetic Landscape of Cardiac Pacemaker Cells: Insights Into Cellular Specialization in the Sinoatrial Node Mus musculus mm10 chr1 172411511 172413110 Rgs6 Enhancer Active Normal Heart UBERON:0000948 Sinoatrial Node Pacemaker sinoatrial node pacemaker cell CL:0000746 Enhancer activity assay ATAC-seq, RNA-seq, ChIP-seq Transgenic Reporter Assay, X-gal Staining 2021 34335313 Chromatin accessibility landscape of cardiac pacemaker cells defines an Isl1 enhancer required for sinoatrial node development and function Mus musculus mm10 chr12 4704343 4706142 Ptgfr Enhancer Active Normal Heart UBERON:0000948 Sinoatrial Node Pacemaker sinoatrial node pacemaker cell CL:0000746 Enhancer activity assay ATAC-seq, RNA-seq, ChIP-seq Transgenic Reporter Assay, X-gal Staining 2016 26751055 NANOG alone induces germ cells in primed epiblast in vitro by activation of enhancers Mus musculus mm10 chr6 113010000 113010100 Nanog Prdm1 Enhancer Active Normal Embryo UBERON:0000922 EpiLCs epiblast-like cell CL:0002322 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2016 26751055 NANOG alone induces germ cells in primed epiblast in vitro by activation of enhancers Mus musculus mm10 chr6 113010000 113010100 Nanog Prdm1 Enhancer Active Normal Embryo UBERON:0000922 PGCLCs primordial germ cell-like cell CL:0000670 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2016 26751055 NANOG alone induces germ cells in primed epiblast in vitro by activation of enhancers Mus musculus mm10 chr4 135010000 135010100 Nanog Prdm14 Enhancer Active Normal Embryo UBERON:0000922 EpiLCs epiblast-like cell CL:0002322 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2016 26751055 NANOG alone induces germ cells in primed epiblast in vitro by activation of enhancers Mus musculus mm10 chr4 135010000 135010100 Nanog Prdm14 Enhancer Active Normal Embryo UBERON:0000922 PGCLCs primordial germ cell-like cell CL:0000670 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2015 26593423 Chromosomal Loop Domains Direct the Recombination of Antigen Receptor Genes Mus musculus mm10 chr1 88392925 88392988 Enhancer Active Normal Bone marrow UBERON:0002371 Primary pro-B pro-B cell CL:0000945 Enhancer activity assay, Chromatin interaction assay ChIP-seq, Hi-C qRT-PCR, and ChIP-qPCR 2015 26593423 Chromosomal Loop Domains Direct the Recombination of Antigen Receptor Genes Mus musculus mm10 chr1 120286768 120286837 Enhancer Enhancer Active Normal Bone marrow UBERON:0002371 Primary pro-B pro-B cell CL:0000945 Enhancer activity assay, Chromatin interaction assay ChIP-seq, Hi-C qRT-PCR, and ChIP-qPCR 2015 26593423 Chromosomal Loop Domains Direct the Recombination of Antigen Receptor Genes Mus musculus mm10 chr1 167519257 167519314 Enhancer Enhancer Active Normal Bone marrow UBERON:0002371 Primary pro-B pro-B cell CL:0000945 Enhancer activity assay, Chromatin interaction assay ChIP-seq, Hi-C qRT-PCR, and ChIP-qPCR 2015 26593423 Chromosomal Loop Domains Direct the Recombination of Antigen Receptor Genes Mus musculus mm10 chr1 167572056 167572182 Enhancer Enhancer Active Normal Bone marrow UBERON:0002371 Primary pro-B pro-B cell CL:0000945 Enhancer activity assay, Chromatin interaction assay ChIP-seq, Hi-C qRT-PCR, and ChIP-qPCR 2015 26593423 Chromosomal Loop Domains Direct the Recombination of Antigen Receptor Genes Mus musculus mm10 chr1 173848852 173848903 Enhancer Active Normal Bone marrow UBERON:0002371 Primary pro-B pro-B cell CL:0000945 Enhancer activity assay, Chromatin interaction assay ChIP-seq, Hi-C qRT-PCR, and ChIP-qPCR 2015 26593423 Chromosomal Loop Domains Direct the Recombination of Antigen Receptor Genes Mus musculus mm10 chr16 95636899 95636961 Enhancer Active Normal Bone marrow UBERON:0002371 Primary pro-B pro-B cell CL:0000945 Enhancer activity assay, Chromatin interaction assay ChIP-seq, Hi-C qRT-PCR, and ChIP-qPCR 2015 26593423 Chromosomal Loop Domains Direct the Recombination of Antigen Receptor Genes Mus musculus mm10 chr16 95640070 95640137 Enhancer Active Normal Bone marrow UBERON:0002371 Primary pro-B pro-B cell CL:0000945 Enhancer activity assay, Chromatin interaction assay ChIP-seq, Hi-C qRT-PCR, and ChIP-qPCR 2015 26593423 Chromosomal Loop Domains Direct the Recombination of Antigen Receptor Genes Mus musculus mm10 chr18 86761026 86761110 Enhancer Enhancer Active Normal Bone marrow UBERON:0002371 Primary pro-B pro-B cell CL:0000945 Enhancer activity assay, Chromatin interaction assay ChIP-seq, Hi-C qRT-PCR, and ChIP-qPCR 2015 26593423 Chromosomal Loop Domains Direct the Recombination of Antigen Receptor Genes Mus musculus mm10 chr18 86772479 86772600 Enhancer Enhancer Active Normal Bone marrow UBERON:0002371 Primary pro-B pro-B cell CL:0000945 Enhancer activity assay, Chromatin interaction assay ChIP-seq, Hi-C qRT-PCR, and ChIP-qPCR 2015 26593423 Chromosomal Loop Domains Direct the Recombination of Antigen Receptor Genes Mus musculus mm10 chr18 86773163 86773345 Enhancer Enhancer Active Normal Bone marrow UBERON:0002371 Primary pro-B pro-B cell CL:0000945 Enhancer activity assay, Chromatin interaction assay ChIP-seq, Hi-C qRT-PCR, and ChIP-qPCR 2015 26593423 Chromosomal Loop Domains Direct the Recombination of Antigen Receptor Genes Mus musculus mm10 chr2 121974537 121974595 Enhancer Enhancer Active Normal Bone marrow UBERON:0002371 Primary pro-B pro-B cell CL:0000945 Enhancer activity assay, Chromatin interaction assay ChIP-seq, Hi-C qRT-PCR, and ChIP-qPCR 2015 26593423 Chromosomal Loop Domains Direct the Recombination of Antigen Receptor Genes Mus musculus mm10 chr6 48626570 48626638 Enhancer Active Normal Bone marrow UBERON:0002371 Primary pro-B pro-B cell CL:0000945 Enhancer activity assay, Chromatin interaction assay ChIP-seq, Hi-C qRT-PCR, and ChIP-qPCR 2019 31685615 SHH signaling mediated by a prechordal and brain enhancer controls forebrain organization Mus musculus mm10 chr5 28369548 28371047 Shh Enhancer Active Normal Forebrain UBERON:0000955 Mouse Embryonic Neural Progenitor mouse neural progenitor cell CL:0002672 Enhancer activity assay, Functional perturbation assay ChIP-seq Transgenic Reporter Assay, CRISPR Knockout, Whole-mount in situ Hybridization, Micro-CT 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 Heart UBERON:0000948 Cardiac progenitor cells cardiac progenitor cell CL:0002248 Enhancer activity assay ChIP-seq Luciferase reporter assay, Transgenic reporter assay, ChIP-RT-qPCR 2015 25940622 The SOX9 upstream region prone to chromosomal aberrations causing campomelic dysplasia contains multiple cartilage enhancers Mus musculus mm10 chr11 111805000 111805100 Sox5 Sox9 Enhancer Active Normal Cartilage UBERON:0002418 Primary chondrocytes chondrocyte CL:0000138 Enhancer activity assay, TF binding assay ChIP-seq Transgenic Reporter Assay, Luciferase Reporter Assay, EMSA 2015 25940622 The SOX9 upstream region prone to chromosomal aberrations causing campomelic dysplasia contains multiple cartilage enhancers Mus musculus mm10 chr11 111916000 111916100 Sox9 Enhancer Active Normal Cartilage UBERON:0002418 Primary chondrocytes chondrocyte CL:0000138 Enhancer activity assay ChIP-seq Transgenic Reporter Assay, Luciferase Reporter Assay 2015 25940622 The SOX9 upstream region prone to chromosomal aberrations causing campomelic dysplasia contains multiple cartilage enhancers Mus musculus mm10 chr11 111930000 111930100 Sox9 Sox9 Enhancer Active Normal Cartilage UBERON:0002418 Primary chondrocytes chondrocyte CL:0000138 Enhancer activity assay, TF binding assay ChIP-seq Transgenic Reporter Assay, Luciferase Reporter Assay, EMSA 2011 21797989 Differentiation and fiber type-specific activity of a muscle creatine kinase intronic enhancer Mus musculus mm10 chr7 19145920 19146014 Myod Ckm Enhancer Active Normal Skeletal Muscle UBERON:0001134 C2C12 CVCL_0188 myoblast CL:0000187 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq Luciferase Reporter Assay, Transgenic Reporter Assay, ChIP-RT-qPCR 2011 21797989 Differentiation and fiber type-specific activity of a muscle creatine kinase intronic enhancer Mus musculus mm10 chr7 19145920 19146014 Myod Ckm Enhancer Active Normal Skeletal Muscle UBERON:0001134 Primary Myocytes myocyte CL:0000187 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq Luciferase Reporter Assay, Transgenic Reporter Assay, ChIP-RT-qPCR 2011 21368066 The Gonadotropin-Releasing Hormone Cell-Specific Element Is Required for Normal Puberty and Estrous Cyclicity Mus musculus mm10 chr14 64201000 64201728 Gnrh1 Enhancer Active Normal Hypothalamus UBERON:0001898 GnRH neurons GnRH neuron CL:0000111 Enhancer activity assay, Functional perturbation assay Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR, Immunohistochemistry 2011 21368066 The Gonadotropin-Releasing Hormone Cell-Specific Element Is Required for Normal Puberty and Estrous Cyclicity Mus musculus mm10 chr14 64201000 64201728 Gnrh1 Enhancer Active Normal Hypothalamus UBERON:0001898 Ovarian surface epithelial cells ovarian surface epithelial cell CL:0000066 Enhancer activity assay, Functional perturbation assay Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR, Immunohistochemistry 2011 21368066 The Gonadotropin-Releasing Hormone Cell-Specific Element Is Required for Normal Puberty and Estrous Cyclicity Mus musculus mm10 chr14 64201000 64201728 Gnrh1 Enhancer Active Normal Hypothalamus UBERON:0001898 Granulosa cells granulosa cell CL:0000501 Enhancer activity assay, Functional perturbation assay Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR, Immunohistochemistry 2024 pending A distal enhancer of GATA3 regulates Th2 differentiation and allergic inflammation Mus musculus mm10 chr2 8936092 8980864 Gata3 Enhancer Active Disease asthma MONDO:0004607 DOID:2841 Lung UBERON:0002048 primary CD4+ T cell (Th2) CD4-positive Th2 cell CL:0000899 Functional perturbation assay, Chromatin interaction assay 4C-seq CRISPR Knockout 2022 36402859 Hnf1b renal expression directed by a distal enhancer responsive to Pax8 Mus musculus mm10 chr11 55120386 55120691 Pax8 Hnf1B Enhancer Active Normal Kidney UBERON:0002113 MDCK CVCL_0422 kidney epithelial cell CL:0000066 Enhancer activity assay, TF binding assay ATAC-seq, ChIP-seq Luciferase Reporter Assay, EMSA, qRT-PCR 2022 36402763 PPAR?? lipodystrophy mutants reveal intermolecular interactions required for enhancer activation Mus musculus mm10 chr3 14761800 14762300 Pparg; Rxra Fabp4 Enhancer Active Normal Adipose tissue UBERON:0001013 MEF CVCL_0003 mouse embryonic fibroblast CL:0000057 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq, ATAC-seq Western blot, qRT-PCR 2022 36402763 PPAR?? lipodystrophy mutants reveal intermolecular interactions required for enhancer activation Mus musculus mm10 chr3 14759100 14759600 Pparg; Rxra Fabp4 Enhancer Active Normal Adipose tissue UBERON:0001013 MEF CVCL_0003 mouse embryonic fibroblast CL:0000057 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq, ATAC-seq Western blot, qRT-PCR 2020 32318068 NCOR1 Orchestrates Transcriptional Landscapes and Effector Functions of CD4+ T Cells Mus musculus mm10 chr10 118409500 118410500 Ncor1 Ifng Enhancer Silenced Normal Spleen UBERON:0002106 Primary Naive CD4+ T naive CD4-positive T cell CL:0000896 TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq RT-RT-qPCR 2020 32318068 NCOR1 Orchestrates Transcriptional Landscapes and Effector Functions of CD4+ T Cells Mus musculus mm10 chr10 118409500 118410500 Ncor1 Ifng Enhancer Silenced Normal Lymph Node UBERON:0002429 In vitro Differentiated Th1 CD4-positive Th1 cell CL:0000897 TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq RT-RT-qPCR 2021 34145235 Coordination of two enhancers drives expression of olfactory trace amine-associated receptors Mus musculus mm10 chr10 23929882 23931253 Taar1 Enhancer Active Normal Olfactory epithelium UBERON:0001997 Olfactory sensory neuron (OSN) olfactory sensory neuron CL:0000206 Functional perturbation assay, Enhancer activity assay ATAC-seq, RNA-seq CRISPR Knockout, CRISPRi, Transgenic Reporter Assay, RT-RT-qPCR 2021 34145235 Coordination of two enhancers drives expression of olfactory trace amine-associated receptors Mus musculus mm10 chr10 23987372 23988804 Taar1 Enhancer Active Normal Olfactory epithelium UBERON:0001997 Olfactory sensory neuron (OSN) olfactory sensory neuron CL:0000206 Functional perturbation assay, Enhancer activity assay ATAC-seq, RNA-seq CRISPR Knockout, CRISPRi, Transgenic Reporter Assay, RT-RT-qPCR 2024 39085358 SMC3 contributes to heart development by regulating superenhancer associated genes Mus musculus mm10 chr3 98010000 98160000 Notch2 Enhancer Silenced Disease atrial fibrillation MONDO:0004978 DOID:0060224 Heart UBERON:0000948 Atrial cardiomyocyte cell line atrial cardiomyocyte CL:0000746 Functional perturbation assay, Enhancer activity assay ChIP-seq, RNA-seq, snRNA-seq RT-RT-qPCR, Western blot, ChIP-RT-qPCR 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr1 135324502 135324868 Fmod Enhancer Active Normal Blood vessel UBERON:0001981 Vascular smooth muscle cells vascular smooth muscle cell CL:0000192 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr1 193272679 193273133 Traf5 Enhancer Active Normal Cerebral Cortex UBERON:0000956 Oligodendrocyte precursor cells oligodendrocyte precursor cell CL:0000128 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr1 36539161 36539602 Unc50 Enhancer Active Normal Blood vessel UBERON:0001981 Vascular smooth muscle cells vascular smooth muscle cell CL:0000192 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr10 116270311 116271768 Ptprb Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr10 24493568 24493998 Slc18B1 Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr10 24824503 24825197 Enpp1 Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr11 106382395 106382923 Icam2 Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr12 85455100 85455928 Dpf3 Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr13 60897338 60897768 Ctla2A Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr13 60936496 60937061 Ctla2A Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr13 97579897 97580928 Gm41030 Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr13 97580240 97580407 Gm41030 Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr14 50995230 50995698 Pnp Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr14 50995280 50995470 Pnp Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr14 50995418 50995609 Pnp Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr14 50995561 50995752 Pnp Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr15 72034077 72034453 Gm19782 Enhancer Active Normal Blood vessel UBERON:0001981 Vascular smooth muscle cells vascular smooth muscle cell CL:0000192 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr15 75001522 75001829 Ly6A Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr15 75001571 75001879 Ly6A Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr15 85574338 85575028 Gtse1 Enhancer Active Normal Cerebral Cortex UBERON:0000956 Oligodendrocyte precursor cells oligodendrocyte precursor cell CL:0000128 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr16 18703897 18705643 Cldn5 Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr16 32512896 32513882 Heg1 Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr16 38432836 38433208 Fstl1 Enhancer Active Normal Blood vessel UBERON:0001981 Vascular smooth muscle cells vascular smooth muscle cell CL:0000192 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr17 31905602 31906289 Notch4 Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr19 34733020 34733442 Slc16A12 Enhancer Active Normal Blood vessel UBERON:0001981 Vascular smooth muscle cells vascular smooth muscle cell CL:0000192 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr19 38027995 38028468 Sorbs1 Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr2 152155608 152156274 Id1 Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr2 157506804 157507303 Myl9 Enhancer Active Normal Blood vessel UBERON:0001981 Vascular smooth muscle cells vascular smooth muscle cell CL:0000192 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr2 181487538 181488198 Sox18 Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr2 26575785 26576489 Egfl7 Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr2 57116616 57117116 Gpd2 Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr4 118489677 118490197 Tie1 Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr4 119043893 119045511 Tie1 Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr4 119044310 119044536 Tie1 Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr4 47237059 47237485 Erp44 Enhancer Active Normal Blood vessel UBERON:0001981 Vascular smooth muscle cells vascular smooth muscle cell CL:0000192 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr4 55670153 55670693 Klf4 Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr5 104397936 104398396 Tgfbr3 Enhancer Active Normal Blood vessel UBERON:0001981 Vascular smooth muscle cells vascular smooth muscle cell CL:0000192 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr5 142905691 142906292 Arpc1B Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr6 142544854 142545576 Gm31108 Enhancer Active Normal Blood vessel UBERON:0001981 Vascular smooth muscle cells vascular smooth muscle cell CL:0000192 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr6 58623144 58623738 Abcg2 Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr7 18884015 18884799 Pglyrp1 Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr7 46746201 46746883 Rcn3 Enhancer Active Normal Blood vessel UBERON:0001981 Vascular smooth muscle cells vascular smooth muscle cell CL:0000192 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr7 99694197 99694747 Aqp11 Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr9 37400589 37400968 Esam Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr9 37401768 37402146 Robo4 Enhancer Active Normal Blood vessel UBERON:0001986 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2025 40403729 A suite of enhancer AAVs and transgenic mouse lines for genetic access to cortical cell types Mus musculus mm10 chr9 57597959 57598486 Cyp11A1 Enhancer Active Normal Cerebral Cortex UBERON:0000956 Oligodendrocyte precursor cells oligodendrocyte precursor cell CL:0000128 Enhancer activity assay ATAC-seq, RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay 2019 31120998 HoxA9 binds and represses the Cebpa +8 kb enhancer Mus musculus mm10 chr7 35940000 35940455 Hoxa9 Cebpa Enhancer Silenced Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 Primary murine myeloid progenitor cells myeloid progenitor cell CL:0000837 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq Transgenic Reporter Assay, Flow Cytometry, RT-RT-qPCR 2019 31120998 HoxA9 binds and represses the Cebpa +8 kb enhancer Mus musculus mm10 chr7 35940000 35940455 Hoxa9 Cebpa Enhancer Silenced Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 Common myeloid progenitor cells common myeloid progenitor cell CL:0000837 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq Transgenic Reporter Assay, Flow Cytometry, RT-RT-qPCR 2019 31120998 HoxA9 binds and represses the Cebpa +8 kb enhancer Mus musculus mm10 chr7 35940000 35940455 Hoxa9 Cebpa Enhancer Silenced Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 Granulocyte-monocyte progenitor cells granulocyte-monocyte progenitor cell CL:0000837 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq Transgenic Reporter Assay, Flow Cytometry, RT-RT-qPCR 2019 31120998 HoxA9 binds and represses the Cebpa +8 kb enhancer Mus musculus mm10 chr7 35940000 35940455 Hoxa9 Cebpa Enhancer Silenced Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 LSK cells hematopoietic stem cell CL:0001029 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq Transgenic Reporter Assay, Flow Cytometry, RT-RT-qPCR 2011 21487009 Mouse Rankl expression is regulated in T cells by c-Fos and NFAT Mus musculus mm10 chr14 78469483 78470483 C-Fos Tnfsf11 Enhancer Active Disease Blood UBERON:0000178 Enhancer activity assay, TF binding assay, Chromatin interaction assay Luciferase Reporter Assay, ChIP-RT-qPCR, 3C 2018 29514092 Transcription Factor IRF8 Governs Enhancer Landscape Dynamics in Mononuclear Phagocyte Progenitors Mus musculus mm10 chr11 98040000 98080000 Irf8; Spi1; Cebpa Csf3R Enhancer Active Normal Bone Marrow UBERON:0002371 Neutrophils neutrophil CL:0000775 Immunological functional assay, Functional genomics assay, Epigenomic profiling assay, Transcriptional regulation assay ChIP-seq [targets: H3K4me1, H3K27ac], RNA-seq, Gene Expression Microarray Flow Cytometry, FACS, qRT-PCR, ChIP-RT-qPCR, Western blot 2018 29514092 Transcription Factor IRF8 Governs Enhancer Landscape Dynamics in Mononuclear Phagocyte Progenitors Mus musculus mm10 chr12 10710000 10750000 Irf8; Spi1; Batf3; Zbtb46 Batf3 Enhancer Active Normal Bone Marrow UBERON:0002371 Monocyte-dendritic cell progenitor cells monocyte-dendritic cell progenitor CL:0000837 Immunological functional assay, Functional genomics assay, Epigenomic profiling assay, Transcriptional regulation assay, In vitro functional assay, In vivo functional assay ChIP-seq [targets: H3K4me1, H3K27ac, Irf8], RNA-seq, Gene Expression Microarray Flow Cytometry, FACS, qRT-PCR, ChIP-RT-qPCR, Western blot, Histological Analysis 2018 29514092 Transcription Factor IRF8 Governs Enhancer Landscape Dynamics in Mononuclear Phagocyte Progenitors Mus musculus mm10 chr13 48580000 48620000 Irf8; Spi1; Runx1; Rbpj Unc93B1 Enhancer Active Normal Bone Marrow UBERON:0002371 Monocyte-dendritic cell progenitor cells monocyte-dendritic cell progenitor CL:0000837 Immunological functional assay, Functional genomics assay, Epigenomic profiling assay, Transcriptional regulation assay ChIP-seq [targets: H3K4me1, H3K27ac, Irf8], RNA-seq, Gene Expression Microarray Flow Cytometry, FACS, qRT-PCR, ChIP-RT-qPCR, Western blot 2018 29514092 Transcription Factor IRF8 Governs Enhancer Landscape Dynamics in Mononuclear Phagocyte Progenitors Mus musculus mm10 chr16 16980000 17020000 Irf8; Spi1; Bcl6 Bcl6 Enhancer Active Normal Bone Marrow UBERON:0002371 B lymphocytes B cell CL:0000945 Immunological functional assay, Functional genomics assay, Epigenomic profiling assay, Transcriptional regulation assay ChIP-seq [targets: H3K4me1, H3K27ac, Irf8], RNA-seq, Gene Expression Microarray Flow Cytometry, FACS, qRT-PCR, ChIP-RT-qPCR, Western blot, Histological Analysis 2018 29514092 Transcription Factor IRF8 Governs Enhancer Landscape Dynamics in Mononuclear Phagocyte Progenitors Mus musculus mm10 chr19 61222000 61250000 Irf8; Spi1; Cebpa; Runx1 Csf2Ra Enhancer Active Normal Bone Marrow UBERON:0002371 Granulocyte-monocyte progenitor cells granulocyte-monocyte progenitor cell CL:0000837 Immunological functional assay, Functional genomics assay, Epigenomic profiling assay, Transcriptional regulation assay, In vitro functional assay, In vivo functional assay, Developmental biology assay ChIP-seq [targets: H3K4me1, H3K4me3, H3K27ac, Irf8, Spi1], RNA-seq, Gene Expression Microarray Flow Cytometry, FACS, qRT-PCR, ChIP-RT-qPCR, Single-Cell Colony Formation Assay, Western blot, Immunofluorescence Microscopy 2018 29514092 Transcription Factor IRF8 Governs Enhancer Landscape Dynamics in Mononuclear Phagocyte Progenitors Mus musculus mm10 chr2 103295000 103314000 Irf8; Spi1; Batf3; Relb Ehf Enhancer Active Normal Bone Marrow UBERON:0002371 Monocyte-dendritic cell progenitor cells monocyte-dendritic cell progenitor CL:0000837 Immunological functional assay, Functional genomics assay, Epigenomic profiling assay, Transcriptional regulation assay, In vitro functional assay, In vivo functional assay ChIP-seq [targets: H3K4me1, H3K27ac, Irf8], RNA-seq, Gene Expression Microarray Flow Cytometry, FACS, qRT-PCR, ChIP-RT-qPCR, Single-Cell Colony Formation Assay, Western blot, Histological Analysis 2018 29514092 Transcription Factor IRF8 Governs Enhancer Landscape Dynamics in Mononuclear Phagocyte Progenitors Mus musculus mm10 chr2 143822000 143865000 Irf8; Spi1; Cebpb Bfsp1 Enhancer Active Normal Bone Marrow UBERON:0002371 Ly6C+ classical monocytes classical monocyte CL:0000576 Immunological functional assay, Functional genomics assay, Epigenomic profiling assay, Transcriptional regulation assay, In vitro functional assay, In vivo functional assay ChIP-seq [targets: H3K4me1, H3K27ac, Irf8], RNA-seq, Gene Expression Microarray Flow Cytometry, FACS, qRT-PCR, ChIP-RT-qPCR, Single-Cell Colony Formation Assay, Western blot 2018 29514092 Transcription Factor IRF8 Governs Enhancer Landscape Dynamics in Mononuclear Phagocyte Progenitors Mus musculus mm10 chr7 114280000 114320000 Irf8; Spi1; Cebpa Ceacam1 Enhancer Active Normal Bone Marrow UBERON:0002371 Neutrophils neutrophil CL:0000775 Immunological functional assay, Functional genomics assay, Epigenomic profiling assay, Transcriptional regulation assay ChIP-seq [targets: H3K4me1, H3K27ac], RNA-seq, Gene Expression Microarray Flow Cytometry, FACS, qRT-PCR, ChIP-RT-qPCR, Western blot 2018 29514092 Transcription Factor IRF8 Governs Enhancer Landscape Dynamics in Mononuclear Phagocyte Progenitors Mus musculus mm10 chr8 44910000 44930000 Irf8; Spi1; Maf Bach2 Enhancer Active Normal Bone Marrow UBERON:0002371 Ly6C+ classical monocytes classical monocyte CL:0000576 Immunological functional assay, Functional genomics assay, Epigenomic profiling assay, Transcriptional regulation assay, In vitro functional assay, In vivo functional assay ChIP-seq [targets: H3K4me1, H3K27ac, Irf8], RNA-seq, Gene Expression Microarray Flow Cytometry, FACS, qRT-PCR, ChIP-RT-qPCR, Western blot, Immunofluorescence Microscopy, In Vivo Hematopoietic Reconstitution Assay 2018 30404006 Genetic Models Reveal cis and trans Immune-Regulatory Activities for lincRNA-Cox2 Mus musculus mm10 chr1 152006173 152012078 Ptgs2 Enhancer Active Disease Lung UBERON:0002048 Bone Marrow-Derived Macrophages (BMDMs) macrophage CL:0000235 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2019 31406377 An Nfil3-Zeb2-Id2 pathway imposes Irf8 enhancer switching during cDC1 development Mus musculus mm10 chr8 124371000 124371500 Batf3; Irf8 Irf8 Enhancer Active Normal Spleen UBERON:0002106 Mature cDC1 conventional dendritic cell CL:0000451 Enhancer activity assay, TF binding assay ATAC-seq, ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2019 31406377 An Nfil3-Zeb2-Id2 pathway imposes Irf8 enhancer switching during cDC1 development Mus musculus mm10 chr8 124371000 124371500 Batf3; Irf8 Irf8 Enhancer Active Normal Bone Marrow UBERON:0002371 Pre-cDC1 conventional dendritic cell CL:0000451 Enhancer activity assay, TF binding assay ATAC-seq, ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2020 33382813 Decreased sensitivity to the anorectic effects of leptin in mice that lack a Pomc-specific neural enhancer Mus musculus mm10 chr12 103026200 103027200 Pomc Enhancer Active Normal Hypothalamus UBERON:0001898 Mouse primary neurons mouse neuron CL:0000540 Functional perturbation assay RNA-seq CRISPR Knockout, CRISPRi, RT-RT-qPCR 2018 29514092 Transcription Factor IRF8 Governs Enhancer Landscape Dynamics in Mononuclear Phagocyte Progenitors Mus musculus mm10 chr17 34210000 34250000 Irf8; Spi1; Rfx; Creb1 H2-Aa Enhancer Active Normal Bone marrow UBERON:0002371 Monocyte-dendritic cell progenitor cells monocyte-dendritic cell progenitor CL:0000837 Immunological functional assay, Functional genomics assay, Epigenomic profiling assay, Transcriptional regulation assay ChIP-seq, RNA-seq, Microarray Flow cytometry, FACS, RT-RT-qPCR, ChIP-RT-qPCR, MLR assay, Western blot 2018 29514092 Transcription Factor IRF8 Governs Enhancer Landscape Dynamics in Mononuclear Phagocyte Progenitors Mus musculus mm10 chr8 124580000 124620000 Irf8; Spi1; Batf3; Nfil3; Bcl6 Irf8 Enhancer Active Normal Bone marrow UBERON:0002371 Ly6C+ classical monocytes classical monocyte CL:0000576 Immunological functional assay, Functional genomics assay, Epigenomic profiling assay, Transcriptional regulation assay, In vitro functional assay, In vivo functional assay ChIP-seq, RNA-seq, Microarray Flow cytometry, FACS, RT-RT-qPCR, ChIP-RT-qPCR, Single-cell colony formation assay, Western blot, Immunofluorescence microscopy, In vivo hematopoietic reconstitution assay 2018 29514092 Transcription Factor IRF8 Governs Enhancer Landscape Dynamics in Mononuclear Phagocyte Progenitors Mus musculus mm10 chr9 124480000 124520000 Irf8; Spi1; Jun; Fos; Nfkb1 Il18 Enhancer Active Normal Bone marrow UBERON:0002371 Ly6C+ classical monocytes classical monocyte CL:0000576 Immunological functional assay, Functional genomics assay, Epigenomic profiling assay, Transcriptional regulation assay ChIP-seq, RNA-seq, Microarray Flow cytometry, FACS, RT-RT-qPCR, ChIP-RT-qPCR, ELISA, Western blot 2024 38724692 Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters Mus musculus mm10 chr1 12189000 12190000 Lamc1 Enhancer Active Normal Embryoid Body UBERON:0010001 Pluripotent cells pluripotent cell CL:0002248 Enhancer activity assay scRNA-seq, scATAC-seq, MPRA Single-cell Quantitative Expression Reporter Assay (scQers), Luciferase Reporter Assay 2024 38724692 Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters Mus musculus mm10 chr1 12189000 12190000 Lamc1 Enhancer Active Normal Embryoid Body UBERON:0010001 Parietal endoderm cells parietal endoderm cell CL:0002322 Enhancer activity assay scRNA-seq, scATAC-seq, MPRA Single-cell Quantitative Expression Reporter Assay (scQers), Luciferase Reporter Assay 2024 38724692 Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters Mus musculus mm10 chr12 21830000 21831000 Lamb1 Enhancer Active Normal Embryoid Body UBERON:0010001 Parietal endoderm cells parietal endoderm cell CL:0002322 Enhancer activity assay scRNA-seq, scATAC-seq, MPRA Single-cell Quantitative Expression Reporter Assay (scQers), Luciferase Reporter Assay 2019 30686579 The cis-Regulatory Atlas of the Mouse Immune System Mus musculus mm10 chr15 65218400 65218700 Enhancer Active Normal Cerebral Cortex UBERON:0000956 L5_IT glutamatergic neurons glutamatergic neuron CL:0000540 Enhancer activity assay ATAC-seq, RNA-seq Transgenic Reporter Assay, Luciferase Reporter Assay 2019 30686579 The cis-Regulatory Atlas of the Mouse Immune System Mus musculus mm10 chr2 78542600 78542900 Enhancer Active Normal Cerebral Cortex UBERON:0000956 L5_ET glutamatergic neurons glutamatergic neuron CL:0000540 Enhancer activity assay ATAC-seq, RNA-seq Transgenic Reporter Assay, Luciferase Reporter Assay 2019 30686579 The cis-Regulatory Atlas of the Mouse Immune System Mus musculus mm10 chr4 98754300 98754600 Enhancer Active Normal Cerebral Cortex UBERON:0000956 Astrocytes astrocyte CL:0000127 Enhancer activity assay ATAC-seq, RNA-seq Transgenic Reporter Assay, Luciferase Reporter Assay 2025 40433695 Super-Enhancer-Driven HCG20 Promotes Pulmonary Hypertension Through U2AF2 Splicing Mus musculus mm10 chr17 34520000 34525000 Hcg20 Enhancer Active Normal Lung UBERON:0002048 Mouse Pulmonary Artery Endothelial Cells pulmonary artery endothelial cell CL:1001567 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq RT-RT-qPCR, Western blot 2025 40163145 Disease-Associated Mutations of the STAT5B SH2 Domain Regulate Cytokine-Driven Enhancer Function and Mammary Development Mus musculus mm10 chr10 127950000 127955000 Stat5A Socs2 Enhancer Active Normal Mammary Gland UBERON:0001911 Mammary alveolar epithelial cells mammary alveolar epithelial cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq RT-RT-qPCR 2025 40163145 Disease-Associated Mutations of the STAT5B SH2 Domain Regulate Cytokine-Driven Enhancer Function and Mammary Development Mus musculus mm10 chr11 100950000 100955000 Stat5A Stat5A Enhancer Active Normal Mammary Gland UBERON:0001911 Mammary alveolar epithelial cells mammary alveolar epithelial cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq RT-RT-qPCR 2025 40163145 Disease-Associated Mutations of the STAT5B SH2 Domain Regulate Cytokine-Driven Enhancer Function and Mammary Development Mus musculus mm10 chr11 100950000 100955000 Stat5B Stat5B Enhancer Active Normal Mammary Gland UBERON:0001911 Mammary alveolar epithelial cells mammary alveolar epithelial cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq RT-RT-qPCR 2025 40163145 Disease-Associated Mutations of the STAT5B SH2 Domain Regulate Cytokine-Driven Enhancer Function and Mammary Development Mus musculus mm10 chr15 98450000 98455000 Stat5A Lalba Enhancer Active Normal Mammary Gland UBERON:0001911 Mammary alveolar epithelial cells mammary alveolar epithelial cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq RT-RT-qPCR 2025 40163145 Disease-Associated Mutations of the STAT5B SH2 Domain Regulate Cytokine-Driven Enhancer Function and Mammary Development Mus musculus mm10 chr17 30950000 30955000 Stat5A Xdh Enhancer Active Normal Mammary Gland UBERON:0001911 Mammary alveolar epithelial cells mammary alveolar epithelial cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq RT-RT-qPCR 2025 40163145 Disease-Associated Mutations of the STAT5B SH2 Domain Regulate Cytokine-Driven Enhancer Function and Mammary Development Mus musculus mm10 chr2 151850000 151855000 Stat5A Elf5 Enhancer Active Normal Mammary Gland UBERON:0001911 Mammary alveolar epithelial cells mammary alveolar epithelial cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq RT-RT-qPCR 2025 40163145 Disease-Associated Mutations of the STAT5B SH2 Domain Regulate Cytokine-Driven Enhancer Function and Mammary Development Mus musculus mm10 chr4 100450000 100455000 Stat5A Fabp3 Enhancer Active Normal Mammary Gland UBERON:0001911 Mammary alveolar epithelial cells mammary alveolar epithelial cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq RT-RT-qPCR 2025 40163145 Disease-Associated Mutations of the STAT5B SH2 Domain Regulate Cytokine-Driven Enhancer Function and Mammary Development Mus musculus mm10 chr4 142900000 142905000 Stat5A Slc9A4 Enhancer Active Normal Mammary Gland UBERON:0001911 Mammary alveolar epithelial cells mammary alveolar epithelial cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq RT-RT-qPCR 2025 40163145 Disease-Associated Mutations of the STAT5B SH2 Domain Regulate Cytokine-Driven Enhancer Function and Mammary Development Mus musculus mm10 chr5 87140000 87145000 Stat5A Csn1S2B Enhancer Active Normal Mammary Gland UBERON:0001911 Mammary alveolar epithelial cells mammary alveolar epithelial cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq RT-RT-qPCR 2025 40163145 Disease-Associated Mutations of the STAT5B SH2 Domain Regulate Cytokine-Driven Enhancer Function and Mammary Development Mus musculus mm10 chr8 19550000 19555000 Stat5B Defb1 Enhancer Active Normal Mammary Gland UBERON:0001911 Mammary alveolar epithelial cells mammary alveolar epithelial cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq RT-RT-qPCR 2019 30686579 The cis-Regulatory Atlas of the Mouse Immune System Mus musculus mm10 chr11 94321500 94321800 Gm20063 Enhancer Active Normal Cerebral Cortex UBERON:0000956 L2-3_IT glutamatergic neurons glutamatergic neuron CL:0000540 Enhancer activity assay ATAC-seq, RNA-seq Transgenic Reporter Assay, Luciferase Reporter Assay 2019 30686579 The cis-Regulatory Atlas of the Mouse Immune System Mus musculus mm10 chr12 102567800 102568100 Nos1 Enhancer Active Normal Cerebral Cortex UBERON:0000956 Sst_Chodl GABAergic neurons GABAergic neuron CL:0000099 Enhancer activity assay ATAC-seq, RNA-seq Transgenic Reporter Assay, Luciferase Reporter Assay 2019 30686579 The cis-Regulatory Atlas of the Mouse Immune System Mus musculus mm10 chr16 89765300 89765600 Nectin3 Enhancer Active Normal Cerebral Cortex UBERON:0000956 GABAergic neurons GABAergic neuron CL:0000099 Enhancer activity assay ATAC-seq, RNA-seq Transgenic Reporter Assay, Luciferase Reporter Assay 2019 30686579 The cis-Regulatory Atlas of the Mouse Immune System Mus musculus mm10 chr3 145217900 145218200 Cplx3 Enhancer Active Normal Cerebral Cortex UBERON:0000956 L6b glutamatergic neurons glutamatergic neuron CL:0000540 Enhancer activity assay ATAC-seq, RNA-seq Transgenic Reporter Assay, Luciferase Reporter Assay 2019 30686579 The cis-Regulatory Atlas of the Mouse Immune System Mus musculus mm10 chr5 32156800 32157100 Ws1 Enhancer Active Normal Cerebral Cortex UBERON:0000956 Astrocytes astrocyte CL:0000127 Enhancer activity assay ATAC-seq, RNA-seq Transgenic Reporter Assay, Luciferase Reporter Assay 2019 30686579 The cis-Regulatory Atlas of the Mouse Immune System Mus musculus mm10 chr7 128945200 128945500 Rga Enhancer Active Normal Cerebral Cortex UBERON:0000956 L2-3_IT glutamatergic neurons glutamatergic neuron CL:0000540 Enhancer activity assay ATAC-seq, RNA-seq Transgenic Reporter Assay, Luciferase Reporter Assay 2019 31217582 Noncoding deletions reveal a gene that is critical for intestinal function Mus musculus mm10 chr17 25313666 25315178 Lacz Enhancer Active Normal Stomach UBERON:0000945 Enteroendocrine cells enteroendocrine cell CL:0000164 Enhancer activity assay, Functional perturbation assay RNA-seq Transgenic Reporter Assay, CRISPR Knockout, RT-RT-qPCR, Western blot 2018 29514092 Transcription Factor IRF8 Governs Enhancer Landscape Dynamics in Mononuclear Phagocyte Progenitors Mus musculus mm10 chr4 55630000 55650000 Irf8 Klf4 Enhancer Active Normal Bone Marrow UBERON:0002371 Monocyte-dendritic cell progenitor cells monocyte-dendritic cell progenitor CL:0000837 Immunological functional assay, Functional genomics assay, Epigenomic profiling assay, Transcriptional regulation assay, In vitro functional assay, In vivo functional assay ChIP-seq, RNA-seq, Gene expression microarray Flow cytometry, FACS, RT-RT-qPCR, ChIP-RT-qPCR, Western blot 2018 29358044 CRISPR-Based Chromatin Remodeling of the Endogenous Oct4 or Sox2 Locus Enables Reprogramming to Pluripotency Mus musculus mm10 chr17 34540000 34542000 Sox2 Sox2 Enhancer Active Normal Embryo UBERON:0000922 Tail tip fibroblasts fibroblast CL:0000057 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2016 26748758 Foxd3 Promotes Exit from Naive Pluripotency through Enhancer Decommissioning and Inhibits Germline Specification Mus musculus mm10 chr5 141952000 141952800 Foxd3; Pou5F1; Sox2; Nanog Tbx3 Enhancer Silenced Normal Embryo UBERON:0000922 Mouse embryonic stem cells (LF2 strain) mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Functional perturbation assay, Enhancer decommissioning assay ChIP-seq, Strand-specific RNA-seq GFP reporter assay, ChIP-RT-qPCR, RT-RT-qPCR, Co-immunoprecipitation, Western blot, EpiLC differentiation assay, Alkaline phosphatase staining 2016 26748758 Foxd3 Promotes Exit from Naive Pluripotency through Enhancer Decommissioning and Inhibits Germline Specification Mus musculus mm10 chr7 122684500 122685300 Foxd3; Pou5F1; Sox2; Nanog Nanos3 Enhancer Silenced Normal Embryo UBERON:0000922 Mouse embryonic stem cells (LF2 strain) mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Functional perturbation assay, Germline specification assay ChIP-seq, Strand-specific RNA-seq GFP reporter assay, ChIP-RT-qPCR, RT-RT-qPCR, Co-immunoprecipitation, Western blot, EpiLC differentiation assay, PGCLC induction assay, Flow cytometry 2016 26748758 Foxd3 Promotes Exit from Naive Pluripotency through Enhancer Decommissioning and Inhibits Germline Specification Mus musculus mm10 chr13 74521600 74522400 Foxd3; Pou5F1; Sox2; Nanog Tfap2C Enhancer Silenced Normal Embryo UBERON:0000922 Mouse embryonic stem cells (LF2 strain) mouse embryonic stem cell CL:0002322 TF binding assay, Functional perturbation assay, Enhancer decommissioning assay, Germline specification assay ChIP-seq, Strand-specific RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Co-immunoprecipitation, Western blot, EpiLC differentiation assay, PGCLC induction assay, Flow cytometry 2016 26748758 Foxd3 Promotes Exit from Naive Pluripotency through Enhancer Decommissioning and Inhibits Germline Specification Mus musculus mm10 chr4 103876200 103877000 Foxd3; Pou5F1; Sox2; Nanog Prdm14 Enhancer Silenced Normal Embryo UBERON:0000922 Mouse embryonic stem cells (LF2 strain) mouse embryonic stem cell CL:0002322 Functional perturbation assay, Enhancer decommissioning assay, Germline specification assay ChIP-seq, Strand-specific RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Co-immunoprecipitation, Western blot, EpiLC differentiation assay, PGCLC induction assay, Flow cytometry 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 Midbrain UBERON:0001891 mDA progenitors/neurons (E12.5) dopaminergic neuron CL:0000700 Enhancer activity assay, TF binding assay (ChIP-supported) ChIP-seq, RNA-seq Transgenic Reporter Assay, ChIP-RT-qPCR 2015 25775043 Functional annotation of native enhancers with a Cas9-histone demethylase fusion Mus musculus mm10 chr17 35602100 35602600 Pou5F1 Enhancer Active Normal Embryo UBERON:0000922 mouse ESCs mouse embryonic stem cell CL:0002322 Functional perturbation assay ATAC-seq CRISPRi 2011 20942803 The pancreatic islet ??-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 Pancreas UBERON:0001264 ??TC-3 CVCL_B077 pancreatic beta cell CL:0000169 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA 2011 20942803 The pancreatic islet ??-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 Pancreas UBERON:0001264 ??TC-6 CVCL_B078 pancreatic beta cell CL:0000169 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA 2011 20942803 The pancreatic islet ??-cell-enriched transcription factor Pdx-1 regulates Slc30a8 gene transcription through an intronic enhancer Mus musculus mm10 chr15 52153900 52154520 Pdx1 Slc30A8 Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA 2017 28357464 CRISPR/Cas9-mediated deletion of lncRNA Gm26878 in the distant Foxf1 enhancer region Mus musculus mm10 chr8 120880096 120882495 Foxf1 Enhancer Active Normal Lung UBERON:0002048 Embryonic lung tissue embryonic lung cell CL:0000000 Functional perturbation assay RNA-seq CRISPR Knockout, RT-RT-qPCR, Sanger Sequencing 2024 39196225 A transcriptional enhancer regulates cardiac maturation Mus musculus mm10 chr1 154150000 154150500 Mef2C Actn2 Enhancer Active Normal Heart UBERON:0000948 Mouse embryonic/Adult cardiomyocytes cardiomyocyte CL:0000746 TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2024 39196225 A transcriptional enhancer regulates cardiac maturation Mus musculus mm10 chr1 154150500 154151000 Tead1 Actn2 Enhancer Active Normal Heart UBERON:0000948 Mouse embryonic/Adult cardiomyocytes cardiomyocyte CL:0000746 TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2024 39196225 A transcriptional enhancer regulates cardiac maturation Mus musculus mm10 chr1 154151000 154151500 Gata4 Actn2 Enhancer Active Normal Heart UBERON:0000948 Mouse embryonic/Adult cardiomyocytes cardiomyocyte CL:0000746 TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2025 40604280 Range extender mediates long-distance enhancer activity Mus musculus mm10 chr4 154706480 154712089 Shh Enhancer Active Normal Embryonic Limb Bud UBERON:0005417 Limb bud mesenchymal cells mesenchymal cell CL:0000134 Enhancer activity assay, Functional perturbation assay Transgenic Reporter Assay, CRISPR Knock-in, Whole-mount in situ hybridization, Skeletal staining 2020 31658410 A distal enhancer that directs Otx2 expression in the retinal pigment epithelium and neuroretina Mus musculus mm10 chr14 48799494 48801489 Pax6 Otx2 Enhancer Active Disease Retina UBERON:0000966 Enhancer activity assay, TF binding assay ChIP-seq Transgenic Reporter Assay, qRT-PCR, Immunohistochemistry 2024 38528203 Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development Mus musculus mm10 chr12 118718991 118721980 Meis2; Dlx5; Lhx6 Mbip Enhancer Active Normal Forebrain UBERON:0001890 Mouse embryonic GE progenitor ganglionic eminence progenitor CL:0002672 Enhancer activity assay, TF binding assay ChIP-seq Transgenic Reporter Assay 2024 38528203 Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development Mus musculus mm10 chr2 63090990 63093985 Meis2; Dlx5; Lhx6 Arhgap15 Enhancer Active Normal Forebrain UBERON:0001890 Mouse embryonic GE progenitor ganglionic eminence progenitor CL:0002672 Enhancer activity assay, TF binding assay ChIP-seq Transgenic Reporter Assay 2024 38528203 Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development Mus musculus mm10 chr2 72425536 72428482 Meis2; Dlx5; Lhx6 Sp4 Enhancer Active Normal Forebrain UBERON:0001890 Mouse embryonic GE progenitor ganglionic eminence progenitor CL:0002672 Enhancer activity assay, TF binding assay ChIP-seq Transgenic Reporter Assay 2024 38528203 Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development Mus musculus mm10 chr9 118718991 118721980 Meis2; Dlx5; Lhx6 Tle1 Enhancer Active Normal Forebrain UBERON:0001890 Mouse embryonic GE progenitor ganglionic eminence progenitor CL:0002672 Enhancer activity assay, TF binding assay ChIP-seq Transgenic Reporter Assay 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 44280890 44281890 Nfil3 Il12B Enhancer Active Disease Blood UBERON:0000178 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA 2011 21673114 Combinatorial Regulation of Photoreceptor Differentiation Factor, Neural Retina Leucine Zipper Gene Nrl, Revealed by in Vivo Promoter Analysis Mus musculus mm10 chr14 95982949 95983230 Nrl Enhancer Active Disease Retina UBERON:0000966 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, In Vivo Reporter Assay, EMSA 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 Bone UBERON:0001474 mOS-482 CVCL_WT34 osteosarcoma cell CL:0000062 Enhancer activity assay Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2018 30404901 Promoter-enhancer looping and shadow enhancers of the mouse ??A-crystallin locus Mus musculus mm10 chr17 34048994 34049208 Cryaa Enhancer Active Normal Lens UBERON:0000965 Lens epithelial cells lens epithelial cell CL:0002224 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay 3C, RNA-seq qRT-PCR, and ChIP-qPCR 2018 30404901 Promoter-enhancer looping and shadow enhancers of the mouse ??A-crystallin locus Mus musculus mm10 chr17 34048994 34049208 Cryaa Enhancer Active Normal Lens UBERON:0000965 Lens fiber cells lens fiber cell CL:0002225 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay 3C, RNA-seq qRT-PCR, and ChIP-qPCR 2018 30404901 Promoter-enhancer looping and shadow enhancers of the mouse ??A-crystallin locus Mus musculus mm10 chr17 34049209 34050661 Cryaa Enhancer Active Normal Lens UBERON:0000965 Lens epithelial cells lens epithelial cell CL:0002224 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay 3C, RNA-seq qRT-PCR, and ChIP-qPCR 2018 30404901 Promoter-enhancer looping and shadow enhancers of the mouse ??A-crystallin locus Mus musculus mm10 chr17 34049209 34050661 Cryaa Enhancer Active Normal Lens UBERON:0000965 Lens fiber cells lens fiber cell CL:0002225 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay 3C, RNA-seq qRT-PCR, and ChIP-qPCR 2018 30404901 Promoter-enhancer looping and shadow enhancers of the mouse ??A-crystallin locus Mus musculus mm10 chr17 34060350 34061356 Cryaa Enhancer Active Normal Lens UBERON:0000965 Lens epithelial cells lens epithelial cell CL:0002224 Enhancer activity assay, Chromatin interaction assay 3C, RNA-seq qRT-PCR, and ChIP-qPCR 2018 30404901 Promoter-enhancer looping and shadow enhancers of the mouse ??A-crystallin locus Mus musculus mm10 chr17 34060350 34061356 Cryaa Enhancer Active Normal Lens UBERON:0000965 Lens fiber cells lens fiber cell CL:0002225 Enhancer activity assay, Chromatin interaction assay 3C, RNA-seq qRT-PCR, and ChIP-qPCR 2025 39863595 The ??-globin super-enhancer acts in an orientation-dependent manner Mus musculus mm10 chr11 32160121 32161120 Hba-A1 Enhancer Active Normal Blood UBERON:0000178 mESC-derived erythroid cells erythroid progenitor cell CL:0000038 Functional perturbation assay CRISPR knockout, RT-RT-qPCR 2025 39863595 The ??-globin super-enhancer acts in an orientation-dependent manner Mus musculus mm10 chr11 32166121 32167120 Hba-A1 Enhancer Active Normal Blood UBERON:0000178 mESC-derived erythroid cells erythroid progenitor cell CL:0000038 Functional perturbation assay CRISPR knockout, RT-RT-qPCR 2023 37932452 GATA transcription factors drive initial Xist upregulation after fertilization through direct activation of long-range enhancers Mus musculus mm10 chrX 103455000 103456000 Xist Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Functional perturbation assay CRISPRi, RT-RT-qPCR 2023 37932452 GATA transcription factors drive initial Xist upregulation after fertilization through direct activation of long-range enhancers Mus musculus mm10 chrX 103455000 103456000 Xist Enhancer Active Normal Embryo UBERON:0000922 Mouse embryo cells mouse embryo cell CL:0000000 Functional perturbation assay CRISPRi, RT-RT-qPCR 2017 29042628 A DNA Contact Map for the Mouse Runx1 Gene Identifies Novel Haematopoietic Enhancers Mus musculus mm10 chr16 92629000 92629500 Erg Runx1 Enhancer Active Normal Bone Marrow UBERON:0002371 Mouse hematopoietic progenitor cell hematopoietic progenitor cell CL:0000837 Enhancer activity assay ChIP-seq, DNase-seq Transgenic Reporter Assay, RT-RT-qPCR 2017 29042628 A DNA Contact Map for the Mouse Runx1 Gene Identifies Novel Haematopoietic Enhancers Mus musculus mm10 chr16 92632000 92632500 Erg Runx1 Enhancer Active Normal Bone Marrow UBERON:0002371 Mouse hematopoietic progenitor cell hematopoietic progenitor cell CL:0000837 Enhancer activity assay ChIP-seq, DNase-seq Transgenic Reporter Assay, RT-RT-qPCR 2017 29042628 A DNA Contact Map for the Mouse Runx1 Gene Identifies Novel Haematopoietic Enhancers Mus musculus mm10 chr16 92679000 92679500 Spi1 Runx1 Enhancer Active Normal Bone Marrow UBERON:0002371 Mouse hematopoietic progenitor cell hematopoietic progenitor cell CL:0000837 Enhancer activity assay ChIP-seq, DNase-seq Transgenic Reporter Assay, RT-RT-qPCR 2017 29042628 A DNA Contact Map for the Mouse Runx1 Gene Identifies Novel Haematopoietic Enhancers Mus musculus mm10 chr16 92697000 92697500 Tal1 Runx1 Enhancer Active Normal Bone Marrow UBERON:0002371 Mouse hematopoietic progenitor cell hematopoietic progenitor cell CL:0000837 Enhancer activity assay ChIP-seq, DNase-seq Transgenic Reporter Assay, RT-RT-qPCR 2017 29042628 A DNA Contact Map for the Mouse Runx1 Gene Identifies Novel Haematopoietic Enhancers Mus musculus mm10 chr16 92629000 92629500 Erg Runx1 Enhancer Active Disease Bone Marrow UBERON:0002371 Mouse hematopoietic progenitor cell hematopoietic progenitor cell CL:0000837 Enhancer activity assay ChIP-seq, DNase-seq Transgenic Reporter Assay, RT-RT-qPCR 2017 29042628 A DNA Contact Map for the Mouse Runx1 Gene Identifies Novel Haematopoietic Enhancers Mus musculus mm10 chr16 92632000 92632500 Erg Runx1 Enhancer Active Disease Bone Marrow UBERON:0002371 Mouse hematopoietic progenitor cell hematopoietic progenitor cell CL:0000837 Enhancer activity assay ChIP-seq, DNase-seq Transgenic Reporter Assay, RT-RT-qPCR 2017 29042628 A DNA Contact Map for the Mouse Runx1 Gene Identifies Novel Haematopoietic Enhancers Mus musculus mm10 chr16 92679000 92679500 Spi1 Runx1 Enhancer Active Disease Bone Marrow UBERON:0002371 Mouse hematopoietic progenitor cell hematopoietic progenitor cell CL:0000837 Enhancer activity assay ChIP-seq, DNase-seq Transgenic Reporter Assay, RT-RT-qPCR 2017 29042628 A DNA Contact Map for the Mouse Runx1 Gene Identifies Novel Haematopoietic Enhancers Mus musculus mm10 chr16 92697000 92697500 Tal1 Runx1 Enhancer Active Disease Bone Marrow UBERON:0002371 Mouse hematopoietic progenitor cell hematopoietic progenitor cell CL:0000837 Enhancer activity assay ChIP-seq, DNase-seq Transgenic Reporter Assay, RT-RT-qPCR 2024 38528203 Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development Mus musculus mm10 chr1 92390990 92393985 Meis2; Dlx5; Lhx6 Prox1 Enhancer Active Normal Forebrain UBERON:0001890 Mouse embryonic GE progenitor ganglionic eminence progenitor CL:0002672 Enhancer activity assay, TF binding assay ChIP-seq Transgenic Reporter Assay 2024 38528203 Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development Mus musculus mm10 chr12 39300010 39302995 Meis2; Dlx5; Lhx6 Prkd1 Enhancer Active Normal Forebrain UBERON:0001890 Mouse embryonic GE progenitor ganglionic eminence progenitor CL:0002672 Enhancer activity assay, TF binding assay ChIP-seq Transgenic Reporter Assay 2024 38528203 Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development Mus musculus mm10 chr12 51000995 51003991 Meis2; Dlx5; Lhx6 Prox1 Enhancer Active Normal Forebrain UBERON:0001890 Mouse embryonic GE progenitor ganglionic eminence progenitor CL:0002672 Enhancer activity assay, TF binding assay ChIP-seq Transgenic Reporter Assay 2024 38528203 Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development Mus musculus mm10 chr12 56457933 56460958 Meis2; Dlx5; Lhx6 Sp9 Enhancer Active Normal Forebrain UBERON:0001890 Mouse embryonic GE progenitor ganglionic eminence progenitor CL:0002672 Enhancer activity assay, TF binding assay ChIP-seq Transgenic Reporter Assay 2024 38528203 Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development Mus musculus mm10 chr16 15601990 15604980 Meis2; Dlx5; Lhx6 Evt1 Enhancer Active Normal Forebrain UBERON:0001890 Mouse embryonic GE progenitor ganglionic eminence progenitor CL:0002672 Enhancer activity assay, TF binding assay ChIP-seq Transgenic Reporter Assay 2024 38528203 Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development Mus musculus mm10 chr18 8042971 8045972 Meis2; Dlx5; Lhx6 Fzd8 Enhancer Active Normal Forebrain UBERON:0001890 Mouse embryonic GE progenitor ganglionic eminence progenitor CL:0002672 Enhancer activity assay, TF binding assay ChIP-seq Transgenic Reporter Assay 2024 38528203 Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development Mus musculus mm10 chr2 72425536 72428482 Meis2; Dlx5; Lhx6 Tle1 Enhancer Active Normal Forebrain UBERON:0001890 Mouse embryonic GE progenitor ganglionic eminence progenitor CL:0002672 Enhancer activity assay, TF binding assay ChIP-seq Transgenic Reporter Assay 2024 38528203 Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development Mus musculus mm10 chr4 71482992 71486006 Meis2; Dlx5; Lhx6 Prkd1 Enhancer Active Normal Forebrain UBERON:0001890 Mouse embryonic GE progenitor ganglionic eminence progenitor CL:0002672 Enhancer activity assay, TF binding assay ChIP-seq Transgenic Reporter Assay 2024 38528203 Spatial enhancer activation influences inhibitory neuron identity during mouse embryonic development Mus musculus mm10 chr8 94090990 94093985 Meis2; Dlx5; Lhx6 Pou3F2 Enhancer Active Normal Forebrain UBERON:0001890 Mouse embryonic GE progenitor ganglionic eminence progenitor CL:0002672 Enhancer activity assay, TF binding assay ChIP-seq Transgenic Reporter Assay 2022 36201590 A noncoding single-nucleotide polymorphism at 8q24 drives IDH1-mutant glioma formation Mus musculus mm10 chr15 62345678 62345743 Myc Enhancer Active Normal Brain UBERON:0000955 Neural stem neural stem cell CL:0002672 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay RNA-seq, GAM, 4C-seq Transgenic Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, Immunofluorescence 2016 26957309 Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters Mus musculus mm10 chr2 86750000 86800000 Neural Development Genes Enhancer Active Normal Forebrain UBERON:0000955 Mouse embryonic day 11.5 forebrain tissue embryonic forebrain cell CL:0000000 Enhancer activity assay ChIP-seq Transgenic Reporter Assay 2016 26748758 Foxd3 Promotes Exit from Naive Pluripotency through Enhancer Decommissioning and Inhibits Germline Specification Mus musculus mm10 chr8 92145800 92146600 Foxd3 Foxd3 Enhancer Active Normal Embryo UBERON:0000922 mESC mouse embryonic stem cell CL:0002322 TF binding assay ChIP-seq ChIP-RT-qPCR 2015 25940622 The SOX9 upstream region prone to chromosomal aberrations causing campomelic dysplasia contains multiple cartilage enhancers Mus musculus mm10 chr11 111750000 111750100 Sox9 Enhancer Active Normal Cartilage UBERON:0002418 Primary chondrocytes chondrocyte CL:0000138 Enhancer activity ChIP-seq Reporter assay 2015 25651906 Wnt3a signal pathways activate MyoD expression by targeting cis-elements inside and outside its distal enhancer Mus musculus mm10 chr7 46069079 46073575 Myod1 Enhancer Active Normal Skeletal muscle UBERON:0001134 C2C12 myoblasts CVCL_0188 myoblast CL:0000187 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2015 25651906 Wnt3a signal pathways activate MyoD expression by targeting cis-elements inside and outside its distal enhancer Mus musculus mm10 chr7 46084867 46086466 Pax3 Myod1 Enhancer Active Normal Skeletal muscle UBERON:0001134 C2C12 myoblasts CVCL_0188 myoblast CL:0000187 Enhancer activity assay, TF binding assay, Functional perturbation assay Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2015 25651906 Wnt3a signal pathways activate MyoD expression by targeting cis-elements inside and outside its distal enhancer Mus musculus mm10 chr7 46001197 46005694 Myod1 Enhancer Active Normal Skeletal muscle UBERON:0001134 C2C12 CVCL_0188 myoblast CL:0000187 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2015 25651906 Wnt3a signal pathways activate MyoD expression by targeting cis-elements inside and outside its distal enhancer Mus musculus mm10 chr7 46016985 46018584 Pax3 Myod1 Enhancer Active Normal Skeletal muscle UBERON:0001134 C2C12 CVCL_0188 myoblast CL:0000187 Enhancer activity assay, TF binding assay, Functional perturbation assay Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2015 25644599 Wnt signaling regulates MyoD expression through ??-catenin/TCF and NFAT pathways in myogenic cells Mus musculus mm10 chr7 44970000 44970300 Myod1 Enhancer Active Normal Skeletal muscle UBERON:0001134 C2C12 CVCL_0188 myoblast CL:0000187 Enhancer activity assay Luciferase Reporter Assay 2021 34890222 Conditionally pathogenic genetic variants of a hematopoietic disease-suppressing enhancer Mus musculus mm10 chr6 88180000 88180500 Gata2 Enhancer Active Normal Bone marrow UBERON:0002371 Hematopoietic stem cells, HSPCs hematopoietic stem cell CL:0001029 Regulatory element functional validation, in vivo mouse model validation CRISPR-Cas9 point mutation, RT-RT-qPCR, flow cytometry, competitive bone marrow transplantation 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 Intervertebral disc UBERON:0001066 Annulus fibrosus annulus fibrosus cell CL:0000060 Enhancer activity assay, TF binding assay RNA-seq Luciferase Reporter Assay, EMSA, RT-RT-qPCR 2014 24157522 A novel regulatory element for Shh expression in the lung and gut of mouse embryos Mus musculus mm10 chr5 28820000 28821700 Shh Enhancer Active Normal Lung UBERON:0002048 Embryonic endodermal epithelial cells endodermal epithelial cell CL:0000066 Enhancer activity assay, Chromatin interaction assay Transgenic reporter assay, Luciferase reporter assay, 3C assay 2014 25209250 A regulatory network controls nephrocan expression and midgut patterning Mus musculus mm10 chr11 96201500 96202300 Sox17 Nepn Enhancer Active Normal Endoderm UBERON:0000925 P19 cells CVCL_2151 embryonal carcinoma cell CL:0000031 Enhancer activity assay, TF binding assay Luciferase reporter assay, EMSA, RT-RT-qPCR 2014 25209250 A regulatory network controls nephrocan expression and midgut patterning Mus musculus mm10 chr11 96200000 96202300 Rara Nepn Enhancer Active Normal Endoderm UBERON:0000925 P19 cells CVCL_2151 embryonal carcinoma cell CL:0000031 Enhancer activity assay, TF binding assay, Transgenic reporter assay Luciferase reporter assay, EMSA, Transgenic reporter assay, RT-RT-qPCR 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 Spinal cord UBERON:0002240 Primary oligodendrocytes oligodendrocyte CL:0000128 Enhancer activity assay, TF binding assay Luciferase reporter assay, Transgenic reporter assay, ChIP-RT-qPCR, EMSA, RT-RT-qPCR 2015 25804738 Genome-wide characterisation of Foxa1 binding sites reveals several mechanisms for regulating neuronal differentiation in midbrain dopamine cells Mus musculus mm10 chr11 72560000 72561500 Foxa1 Smarca1 Enhancer Active Normal Midbrain UBERON:0001891 mDA progenitors/neurons (E12.5) dopaminergic neuron CL:0000700 TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Loss-of-function assay 2015 25775043 Functional annotation of native enhancers with a Cas9-assisted histone demethylase fusion Mus musculus mm10 chr5 142010000 142010300 Lsd1 Tbx3 Enhancer Active Normal Embryo UBERON:0000922 mESC mouse embryonic stem cell CL:0002322 TF binding assay ChIP-seq ChIP-RT-qPCR 2011 20864515 Prep1 Controls Insulin Glucoregulatory Function in Liver by Transcriptional Targeting of SHP1 Tyrosine Phosphatase Mus musculus mm10 chr6 124695557 124695892 Prep1 Ptpn6 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepG2 CVCL_0027 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR 2011 20864515 Prep1 Controls Insulin Glucoregulatory Function in Liver by Transcriptional Targeting of SHP1 Tyrosine Phosphatase Mus musculus mm10 chr6 124695557 124695892 Prep1 Ptpn6 Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR 2011 20864515 Prep1 Controls Insulin Glucoregulatory Function in Liver by Transcriptional Targeting of SHP1 Tyrosine Phosphatase Mus musculus mm10 chr6 124695557 124695892 Prep1 Ptpn6 Enhancer Active Normal Liver UBERON:0002107 NMuLi hepatocyte CL:0000182 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR 2011 20942803 The pancreatic islet ??-cell-enriched transcription factor Pdx-1 regulates Slc30a8 gene transcription through an intronic enhancer Mus musculus mm10 chr15 52159003 52159479 Slc30A8 Enhancer Active Normal Pancreas UBERON:0001264 ??TC-3 CVCL_B077 pancreatic beta cell CL:0000169 Enhancer activity assay Luciferase Reporter Assay 2011 20942803 The pancreatic islet ??-cell-enriched transcription factor Pdx-1 regulates Slc30a8 gene transcription through an intronic enhancer Mus musculus mm10 chr15 52159003 52159479 Slc30A8 Enhancer Active Normal Pancreas UBERON:0001264 ??TC-6 CVCL_B078 pancreatic beta cell CL:0000169 Enhancer activity assay Luciferase Reporter Assay 2011 20942803 The pancreatic islet ??-cell-enriched transcription factor Pdx-1 regulates Slc30a8 gene transcription through an intronic enhancer Mus musculus mm10 chr15 52159003 52159479 Slc30A8 Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Enhancer activity assay Luciferase Reporter Assay 2011 21464046 Nkx2-5 represses Gata1 gene expression and modulates its hematopoietic enhancer Mus musculus mm10 chrX 7826505 7830405 Gata1 Enhancer Silenced Disease chronic myeloid leukemia MONDO:0011998 DOID:8552 Bone marrow UBERON:0002371 K562 CVCL_0004 chronic myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, Transgenic Reporter Assay 2011 21464046 Nkx2-5 represses Gata1 gene expression and modulates its hematopoietic enhancer Mus musculus mm10 chrX 7826505 7830405 Gata1 Enhancer Silenced Normal Bone marrow UBERON:0002371 ES embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, Transgenic Reporter Assay 2011 21326212 Tbx6-dependent Sox2 regulation determines neural vs mesodermal fate in axial stem cells Mus musculus mm10 chr3 14768 15068 Tbx6 Sox2 Enhancer Active Normal Embryo UBERON:0000922 Axial stem cells axial stem cell CL:0000037 Enhancer activity assay, Functional perturbation assay Transgenic Reporter Assay, CRISPR Knockout, EMSA, RT-RT-qPCR 2011 21652669 Suppression of the Pancreatic Duodenal Homeodomain Transcription Factor-1 (Pdx-1) Promoter by Sterol Regulatory Element-binding Protein-1c (SREBP-1c) Mus musculus mm10 chr12 53052517 53052542 Pdx1 Enhancer Active Normal Pancreatic islet UBERON:0001264 INS-1 CVCL_0352 pancreatic beta cell CL:0000169 Enhancer activity assay Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA 2011 21652669 Suppression of the Pancreatic Duodenal Homeodomain Transcription Factor-1 (Pdx-1) Promoter by Sterol Regulatory Element-binding Protein-1c (SREBP-1c) Mus musculus mm10 chr12 53052517 53052542 Pdx1 Enhancer Active Normal Pancreatic islet UBERON:0001264 HIT CVCL_0294 pancreatic beta cell CL:0000169 Enhancer activity assay Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA 2010 20036227 Estrogen regulates the expression of N-methyl-D-aspartate (NMDA) receptor subunit epsilon 4 (Grin2d), that is essential for the normal sexual behavior in female mice Mus musculus mm10 chr7 6720559 6721159 Grin2D Enhancer Active Normal Hypothalamus UBERON:0001898 Primary Hypothalamic Cells hypothalamic cell CL:0000540 Enhancer activity assay, Functional perturbation assay RT-RT-qPCR, CRISPR Knockout 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 Pancreas UBERON:0001264 Islet pancreatic islet cell CL:0000168 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA 2009 19584292 Activating Transcription Factor 2 and c-Jun-Mediated Induction of FoxP3 for Experimental Therapy of Mammary Tumor in the Mouse Mus musculus mm10 chrX 4905800 4906065 Atf2 Foxp3 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Mammary Gland UBERON:0001911 4T1 CVCL_0125 breast carcinoma cell CL:0000646 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA, RT-RT-qPCR 2009 19584292 Activating Transcription Factor 2 and c-Jun-Mediated Induction of FoxP3 for Experimental Therapy of Mammary Tumor in the Mouse Mus musculus mm10 chrX 4905800 4906065 Atf2 Foxp3 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Mammary Gland UBERON:0001911 TSA CVCL_Z585 breast carcinoma cell CL:0000646 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA, RT-RT-qPCR 2009 19584292 Activating Transcription Factor 2 and c-Jun-Mediated Induction of FoxP3 for Experimental Therapy of Mammary Tumor in the Mouse Mus musculus mm10 chrX 4905800 4906065 Atf2 Foxp3 Enhancer Active Normal Mammary Gland UBERON:0001911 Primary Mammary Epithelial Cells mammary epithelial cell CL:0000066 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA, RT-RT-qPCR 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 Silenced Normal Embryo UBERON:0000922 NIH3T3 CVCL_0594 fibroblast CL:0000057 Enhancer activity assay, TF binding assay, Functional perturbation assay Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA, RT-RT-qPCR 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 Silenced Normal Embryo UBERON:0000922 MEF CVCL_0003 mouse embryonic fibroblast CL:0000057 Enhancer activity assay, TF binding assay, Functional perturbation assay Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA, RT-RT-qPCR 2005 15798193 Identification of Neuronal Enhancers of the Proopiomelanocortin Gene by Transgenic Mouse Analysis and Phylogenetic Footprinting Mus musculus mm10 chr12 103437276 103437876 Pomc Enhancer Active Normal Hypothalamus UBERON:0001898 POMC Arcuate Neuron POMC neuron CL:0000540 Enhancer activity assay Transgenic Reporter Assay, CRISPR Knockout 2000 11120820 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 37389739 37389753 Ahr Il2 Enhancer Active Normal Thymus UBERON:0002370 Thymocytes thymocyte CL:0000893 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, EMSA, RT-RT-qPCR, ELISA 2000 11120820 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 37389739 37389753 Ahr Il2 Enhancer Active Normal Thymus UBERON:0002370 Splenic T cells T cell CL:0000084 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, EMSA, RT-RT-qPCR, ELISA 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 Igh Enhancer Active Disease plasmacytoma MONDO:0005105 DOID:2090 Lymphoid tissue UBERON:0001745 X63-Ag8 CVCL_3415 plasmacytoma cell CL:0000945 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, EMSA 2019 31085606 Hepatic BMP9 improves glucose and lipid metabolism via SREBP-1c suppression Mus musculus mm10 chr10 89234500 89236669 Luc Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepG2 CVCL_0027 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay Luciferase Reporter Assay 2024 38504114 Multicenter integrated analysis of noncoding CRISPRi screens Mus musculus mm10 chr4 156021490 156022916 Tnfrsf18 Enhancer Active Normal Spleen UBERON:0002106 Primary mouse regulatory T cells regulatory T cell CL:0000815 Functional perturbation assay, Enhancer activity assay CRISPRi screening, ATAC-seq Flow cytometry 2023 36747241 CEBP??/miR-101b-3p promotes meningoencephalitis in mice infected with Angiostrongylus cantonensis by promoting microglial pyroptosis Mus musculus mm10 chr19 29129170 29131699 Mmu-Mir-101B-3P Enhancer Active Disease Brain UBERON:0000955 BV2 microglia CVCL_0182 microglial cell CL:0000129 Enhancer activity assay, TF binding assay RNA-seq Luciferase Reporter Assay, qRT-PCR, Western blot 2023 36969227 A cis-element at the Rorc locus regulates the development of type 3 innate lymphoid cells Mus musculus mm10 chr3 93993657 93995818 Rorc Enhancer Active Normal Small intestine UBERON:0002108 ILC3s innate lymphoid cell CL:0000945 Functional perturbation assay RNA-seq CRISPR Knockout, qRT-PCR 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 Normal Adipose tissue UBERON:0001013 3T3-L1 preadipocytes CVCL_0123 preadipocyte CL:0000136 Enhancer activity assay, TF binding assay RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, qRT-PCR 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 Normal Adipose tissue UBERON:0001013 3T3-L1 preadipocytes CVCL_0123 preadipocyte CL:0000136 Enhancer activity assay, TF binding assay RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, qRT-PCR 2024 38448444 Dynamic enhancer landscapes in human craniofacial development Mus musculus mm10 chr15 34751000 34754612 Pop1 Enhancer Silenced Normal Embryonic craniofacial tissue UBERON:0000922 Embryonic craniofacial cells mesenchymal cell CL:0000134 Enhancer activity assay ChIP-seq Transgenic Reporter Assay 2017 29273679 The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes Mus musculus mm10 chr2 73970064 73983434 Hoxd9 Enhancer Active Normal Limb bud UBERON:0005417 Primary limb cells limb mesenchyme cell CL:0000134 Enhancer activity assay Hi-C, 4C-seq LacZ Reporter Assay, RT-RT-qPCR 2018 29284139 Coordinated D-cyclin/Foxd1 activation drives mitogenic activity of the Sonic Hedgehog signaling pathway Mus musculus mm10 chr13 98353215 98355279 Foxd1 Enhancer Active Normal Face UBERON:0001456 iMEFs mouse embryonic fibroblast CL:0000057 Functional perturbation assay CRISPR Knockout, RT-RT-qPCR 2024 38923989 A distal enhancer of GATA3 regulates Th2 differentiation and allergic inflammation Mus musculus mm10 chr2 8936092 8980864 Gata3 Enhancer Active Normal Thymus UBERON:0002370 CD4+ T cell CD4-positive T cell CL:0000624 Functional perturbation assay CRISPR Knockout 2014 25223790 Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers Mus musculus mm10 chr17 35500000 35501700 46299 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic fibroblasts CVCL_0003 mouse embryonic fibroblast CL:0000057 Enhancer activity assay, Functional perturbation assay Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Flow Cytometry 2014 25223790 Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers Mus musculus mm10 chr6 12265000 12266000 Nanog Enhancer Active Normal Embryo UBERON:0000922 Epiblast stem cells epiblast stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Flow Cytometry 2015 25644605 PRDM16 enhances nuclear receptor-dependent transcription of the brown fat-specific Ucp1 gene through interactions with Mediator subunit MED1 Mus musculus mm10 chr8 105552148 105552347 Prdm16 Ucp1 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic fibroblasts CVCL_0003 mouse embryonic fibroblast CL:0000057 Enhancer activity assay, TF binding assay, Chromatin interaction assay Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, Co-IP, In vitro transcription assay 2015 25644605 PRDM16 enhances nuclear receptor-dependent transcription of the brown fat-specific Ucp1 gene through interactions with Mediator subunit MED1 Mus musculus mm10 chr8 123453500 123453720 Ucp1 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic fibroblasts CVCL_0003 mouse embryonic fibroblast CL:0000057 Enhancer activity assay Luciferase Reporter Assay 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 Gpr63 Enhancer Active Normal Brain UBERON:0000955 Neurons neuron CL:0000540 Enhancer activity assay RNA-seq, ATAC-seq Transgenic Reporter Assay 2018 30537984 Enhancers in the Peril lincRNA locus regulate distant but not local genes Mus musculus mm10 chr3 34765000 34767361 Mccc1 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay MPRA, RNA-seq, Hi-C qRT-PCR, and ChIP-qPCR 2015 25490687 Identification of Hypothalamic Arcuate Nucleus-Specific Enhancer Region of Kiss1 Gene in Mice Mus musculus mm10 chr10 74487110 74497835 Esr1 Kiss1 Enhancer Active Normal Hypothalamus UBERON:0001898 Arcuate nucleus neurons arcuate nucleus neuron CL:0000540 Enhancer activity assay, Chromatin interaction assay, TF binding assay Transgenic Reporter Assay, 3C, ChIP-RT-qPCR, Immunofluorescence 2015 26364592 A highly conserved NF-??B-responsive enhancer is critical for thymic expression of Aire in mice Mus musculus mm10 chr10 177510950 177511040 Aire Enhancer Active Normal Thymus UBERON:0002370 mTEC medullary thymic epithelial cell CL:0002366 Enhancer activity assay Luciferase Reporter Assay 2015 26110280 An insulator element located at the cyclin B1 interacting protein 1 gene locus is highly conserved among mammalian species Mus musculus mm10 chr11 96840000 96840185 Ccnb1Ip1 Enhancer Active Normal Embryo UBERON:0000922 E9.5 embryo mouse embryo CL:0000000 Enhancer activity assay Luciferase Reporter Assay 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr13 84638399 84640848 Mir9-2 Enhancer Active Normal Forebrain UBERON:0001890 transgenic mouse embryo mouse embryo CL:0000000 CRISPR deletion, Transgenic reporter assay Capture Hi-C RT-RT-qPCR, lacZ whole-mount staining 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr13 84751727 84752626 Mir9-2 Enhancer Active Normal Forebrain UBERON:0001890 transgenic mouse embryo mouse embryo CL:0000000 CRISPR deletion, Transgenic reporter assay Capture Hi-C RT-RT-qPCR, lacZ whole-mount staining 2013 24009265 The control of hematopoietic stem cell maintenance, self-renewal, and differentiation by Mysm1-mediated epigenetic regulation Mus musculus mm10 chr11 98250000 98285000 Gata2 Gfi1 Enhancer Active Normal Bone marrow UBERON:0002371 Hematopoietic stem cells hematopoietic stem cell CL:0001029 Enhancer activity assay, TF binding assay ChIP-RT-qPCR, Luciferase reporter assay 2011 21652712 Suppression of the Pancreatic Duodenal Homeodomain Transcription Factor-1 (Pdx-1) Promoter by Sterol Regulatory Element-binding Protein-1c Mus musculus mm10 chr5 148601086 148601161 Pdx1 Enhancer Silenced Normal Pancreas UBERON:0001264 INS-1 CVCL_0352 pancreatic beta cell CL:0000169 Enhancer activity assay, TF binding assay, Functional perturbation assay Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, RNAi 2011 21652712 Suppression of the Pancreatic Duodenal Homeodomain Transcription Factor-1 (Pdx-1) Promoter by Sterol Regulatory Element-binding Protein-1c Mus musculus mm10 chr5 148601086 148601161 Pdx1 Enhancer Silenced Normal Pancreas UBERON:0001264 ?? cell lines Enhancer activity assay, TF binding assay, Functional perturbation assay Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, RNAi 2011 21454523 Cohesin Mediates Chromatin Interactions That Regulate Mammalian ??-globin Expression Mus musculus mm10 chr7 103826000 103826500 Rad21 Hbb-B1 Enhancer Active Normal Fetal liver UBERON:0002107 MEL erythroleukemia cells CVCL_2109 erythroid progenitor cell CL:0000038 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay 3C, ChIP-loop, ChIP-RT-qPCR, siRNA Knockdown, RT-RT-qPCR 2009 19584292 Activating Transcription Factor 2 and c-Jun-Mediated Induction of FoxP3 for Experimental Therapy of Mammary Tumor in the Mouse Mus musculus mm10 chrX 4899200 4899465 Atf2 Foxp3 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Mammary Gland UBERON:0001911 4T1 CVCL_0125 breast carcinoma cell CL:0000646 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR 2009 19584292 Activating Transcription Factor 2 and c-Jun-Mediated Induction of FoxP3 for Experimental Therapy of Mammary Tumor in the Mouse Mus musculus mm10 chrX 4899200 4899465 Atf2 Foxp3 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Mammary Gland UBERON:0001911 TSA CVCL_Z585 breast carcinoma cell CL:0000646 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR 2008 18552207 Stem cell-specific epigenetic priming and B cell-specific transcriptional activation at the mouse Cd19 locus Mus musculus mm10 chr7 1911568 1911832 E2A Cd19 Enhancer Active Normal Bone Marrow UBERON:0002371 Pro-B cells pro-B cell CL:0000945 Enhancer activity assay, TF binding assay DNase-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2008 18552207 Stem cell-specific epigenetic priming and B cell-specific transcriptional activation at the mouse Cd19 locus Mus musculus mm10 chr7 1911568 1911832 E2A Cd19 Enhancer Active Normal Bone Marrow UBERON:0002371 B cells B cell CL:0000945 Enhancer activity assay, TF binding assay DNase-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2008 18552207 Stem cell-specific epigenetic priming and B cell-specific transcriptional activation at the mouse Cd19 locus Mus musculus mm10 chr7 1911568 1911832 E2A Cd19 Enhancer Active Normal Bone Marrow UBERON:0002371 Multipotent Progenitors multipotent progenitor cell CL:0000837 Enhancer activity assay, TF binding assay DNase-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2006 16709834 CD86 Stimulation on a B Cell Activates the Phosphatidylinositol 3-Kinase/Akt and Phospholipase Cgamma2/Protein Kinase C Signaling Pathways Mus musculus mm10 chr12 114450000 114450225 Nfkb1 Ighg1 Enhancer Active Normal Spleen UBERON:0002106 CH12.LX CVCL_5199 B cell CL:0000945 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, ELISA 2006 16709834 CD86 Stimulation on a B Cell Activates the Phosphatidylinositol 3-Kinase/Akt and Phospholipase Cgamma2/Protein Kinase C Signaling Pathways Mus musculus mm10 chr12 114450000 114450225 Nfkb1 Ighg1 Enhancer Active Disease B-cell lymphoma MONDO:0005029 DOID:164 Spleen UBERON:0002106 A20 CVCL_1940 B cell lymphoma cell CL:0000945 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, ELISA 2006 16709834 CD86 Stimulation on a B Cell Activates the Phosphatidylinositol 3-Kinase/Akt and Phospholipase Cgamma2/Protein Kinase C Signaling Pathways Mus musculus mm10 chr12 114450000 114450225 Nfkb1 Ighg1 Enhancer Active Normal Spleen UBERON:0002106 Primary B Cells B cell CL:0000945 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, ELISA 2019 31290539 A 50bp enhancer of the mouse Acrv1 gene activates round spermatid-specific transcription in vivo Mus musculus mm10 chr9 110254800 110254851 Luc Enhancer Active Normal Testis UBERON:0000473 Round spermatids spermatid CL:0000018 Enhancer activity assay Transgenic Reporter Assay, Luciferase Reporter Assay 2019 30739802 The cis-Regulatory Atlas of the Mouse Immune System Mus musculus mm10 chr6 71233400 71233600 Cd8A Enhancer Active Normal Thymus UBERON:0002370 CD8+ T CD8-positive T cell CL:0000625 Enhancer activity assay ATAC-seq, RNA-seq Transgenic Reporter Assay 2019 31290539 A 50bp enhancer of the mouse Acrv1 gene activates round spermatid-specific transcription in vivo Mus musculus mm10 chr9 59048862 59048913 Acrv1 Enhancer Active Normal Testis UBERON:0000473 Round spermatids spermatid CL:0000018 Enhancer activity assay, TF binding assay Transgenic Reporter Assay, Luciferase Reporter Assay 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 Flk1 (Kdr) Enhancer Active Normal Embryo UBERON:0000922 Mouse Embryonic Stem Cells (mESCs) mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay miRNA sequencing, RNA-seq Luciferase Reporter Assay, ChIP-PCR, qRT-PCR, Western blot 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 Nes Enhancer Active Normal Central nervous system UBERON:0001017 Embryonic neuroprogenitor cells neural progenitor cell CL:0002672 Functional perturbation assay, Enhancer activity assay CRISPR Knockout, qRT-PCR, In situ hybridization, Immunohistochemistry 2024 38448444 Dynamic enhancer landscapes in human craniofacial development Mus musculus mm10 chr9 55546300 55546600 Isl2 Enhancer Active Normal Embryonic craniofacial tissue UBERON:0000922 Sensory neurons sensory neuron CL:0000101 Enhancer activity assay snATAC-seq, scRNA-seq Transgenic Reporter Assay 2024 38448444 Dynamic enhancer landscapes in human craniofacial development Mus musculus mm10 chr9 55546300 55546600 Scaper Enhancer Active Normal Embryonic craniofacial tissue UBERON:0000922 epithelial cells epithelial cell CL:0000066 Enhancer activity assay snATAC-seq, scRNA-seq Transgenic Reporter Assay 2024 38448444 Dynamic enhancer landscapes in human craniofacial development Mus musculus mm10 chr7 66376000 66378000 Lrrk1 Enhancer Active Normal Embryonic craniofacial tissue UBERON:0000922 Epithelial cells epithelial cell CL:0000066 Enhancer activity assay snATAC-seq, scRNA-seq Transgenic Reporter Assay 2023 36749647 Prdm6 drives ductus arteriosus closure by promoting ductus arteriosus smooth muscle cell identity and contractility Mus musculus mm10 chr15 100452350 100452650 Prdm6 Acta2 Enhancer Active Normal Heart UBERON:0000948 Mouse outflow tract smooth muscle smooth muscle cell CL:0000192 TF binding assay ChIP-seq qRT-PCR, and ChIP-qPCR 2018 29284139 Coordinated D-cyclin/Foxd1 activation drives mitogenic activity of the Sonic Hedgehog signaling pathway Mus musculus mm10 chr7 150644800 150646500 Foxd1 Enhancer Silenced Normal Face UBERON:0001456 iMEFs mouse embryonic fibroblast CL:0000057 Enhancer activity assay Luciferase Reporter Assay, RT-RT-qPCR 2018 30537984 Enhancers in the Peril lincRNA locus regulate distant but not local genes Mus musculus mm10 chr11 3650000 3652019 Morc2A Enhancer Active Normal Skeletal Muscle UBERON:0001134 Mouse myoblast cell CVCL_0188 myoblast CL:0000056 Enhancer activity assay MPRA qRT-PCR, and ChIP-qPCR 2018 30537984 Enhancers in the Peril lincRNA locus regulate distant but not local genes Mus musculus mm10 chr13 10543000 10544508 Enc1 Enhancer Active Normal Skeletal Muscle UBERON:0001134 Mouse myoblast cell CVCL_0188 myoblast CL:0000056 Enhancer activity assay MPRA qRT-PCR, and ChIP-qPCR 2018 30537984 Enhancers in the Peril lincRNA locus regulate distant but not local genes Mus musculus mm10 chr17 29065000 29066050 Cdkn1A Enhancer Active Normal Skeletal Muscle UBERON:0001134 Mouse myoblast cell CVCL_0188 myoblast CL:0000056 Enhancer activity assay MPRA qRT-PCR, and ChIP-qPCR 2018 30537984 Enhancers in the Peril lincRNA locus regulate distant but not local genes Mus musculus mm10 chr17 29072000 29073308 Cdkn1A Enhancer Active Normal Skeletal Muscle UBERON:0001134 Mouse myoblast cell CVCL_0188 myoblast CL:0000056 Enhancer activity assay MPRA qRT-PCR, and ChIP-qPCR 2025 37225984 BRD4 in Cx3cr1-positive macrophages drives proinflammatory transcription in heart failure pathogenesis Mus musculus mm10 chr3 54351833 54571175 Creb5; Runx2; Arid5A Meox1 Enhancer Active Disease Heart UBERON:0000948 Cardiac Fibroblast cardiac fibroblast CL:0002547 Chromatin interaction assay scATAC-seq ChIP-RT-qPCR, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr13 84570044 84572517 Mir9-2 Enhancer Active Normal Neural tube UBERON:0000934 transgenic mouse embryo mouse embryo CL:0000000 CRISPR deletion, Transgenic reporter assay Capture Hi-C RT-RT-qPCR, lacZ whole-mount staining 2016 26645089 Characterizing a distal muscle enhancer in the mouse Igf2 locus Mus musculus mm10 chr7 142580000 142580293 Igf2 Enhancer Active Normal Skeletal muscle UBERON:0001134 C3H10T1/2 CVCL_0190 mesenchymal stem cell CL:0000134 Enhancer activity assay, Functional perturbation assay Transgenic reporter assay, RT-RT-qPCR, Western blot 2016 26645089 Characterizing a distal muscle enhancer in the mouse Igf2 locus Mus musculus mm10 chr7 142580000 142580293 Igf2 Enhancer Active Normal Skeletal muscle UBERON:0001134 Myoblasts myoblast CL:0000056 Enhancer activity assay, Functional perturbation assay Transgenic reporter assay, RT-RT-qPCR, Western blot 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 Msi1 Enhancer Active Normal Nervous system UBERON:0001016 NS/PCs neural stem cell CL:0002672 Enhancer activity assay Luciferase Reporter Assay 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 Msi1 Enhancer Active Normal Nervous system UBERON:0001016 ESCs embryonic stem cell CL:0002322 Enhancer activity assay Luciferase Reporter Assay 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 Sox2 Msi1 Enhancer Active Normal Nervous system UBERON:0001016 NS/PCs neural stem cell CL:0002672 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR 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 Sox2 Msi1 Enhancer Active Normal Nervous system UBERON:0001016 ESCs embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR 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 Blood UBERON:0000178 RAW264 CVCL_0493 macrophage CL:0000235 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR 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 Blood UBERON:0000178 38B9 CVCL_UE53 pre-B cell CL:0000945 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR 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 Disease B-cell lymphoma MONDO:0005029 DOID:164 Blood UBERON:0000178 A20 CVCL_1940 B cell lymphoma cell CL:0000945 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR 2023 37542287 FACT regulates pluripotency through proximal and distal regulation of gene expression in murine embryonic stem cells Mus musculus mm10 chr6 122612768 122617768 Nanog SE Active Normal Embryo UBERON:0000922 murine embryonic stem cells (mESCs) mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Chromatin interaction assay Luciferase Reporter Assay, ChIP-RT-qPCR, qRT-PCR 2023 37542287 FACT regulates pluripotency through proximal and distal regulation of gene expression in murine embryonic stem cells Mus musculus mm10 chr6 122652768 122657768 Nanog SE Active Normal Embryo UBERON:0000922 murine embryonic stem cells (mESCs) mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Chromatin interaction assay Luciferase Reporter Assay, ChIP-RT-qPCR, qRT-PCR 2023 37542287 FACT regulates pluripotency through proximal and distal regulation of gene expression in murine embryonic stem cells Mus musculus mm10 chr6 122717768 122722768 Nanog SE Active Normal Embryo UBERON:0000922 murine embryonic stem cells (mESCs) mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Chromatin interaction assay Luciferase Reporter Assay, ChIP-RT-qPCR, qRT-PCR 2023 37542287 FACT regulates pluripotency through proximal and distal regulation of gene expression in murine embryonic stem cells Mus musculus mm10 chr3 34756748 34761748 Sox2 SE Active Normal Embryo UBERON:0000922 murine embryonic stem cells (mESCs) mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Chromatin interaction assay Luciferase Reporter Assay, ChIP-RT-qPCR, qRT-PCR 2024 39333082 A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders Mus musculus mm10 chr13 116000000 116001000 Isl1 Enhancer Active Normal Brainstem UBERON:0002298 Cranial motor neurons motor neuron CL:0000100 Enhancer activity assay, Chromatin interaction assay scATAC-seq, scRNA-seq, scCUT&Tag Transgenic Reporter Assay 2024 39333082 A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders Mus musculus mm10 chr13 116002000 116003000 Isl1 Enhancer Active Normal Brainstem UBERON:0002298 Cranial motor neurons motor neuron CL:0000100 Enhancer activity assay, Chromatin interaction assay scATAC-seq, scRNA-seq, scCUT&Tag Transgenic Reporter Assay 2024 39333082 A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders Mus musculus mm10 chr13 116004000 116005000 Isl1 Enhancer Active Normal Brainstem UBERON:0002298 Cranial motor neurons motor neuron CL:0000100 Enhancer activity assay, Chromatin interaction assay scATAC-seq, scRNA-seq, scCUT&Tag Transgenic Reporter Assay 2024 39333082 A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders Mus musculus mm10 chr13 116006000 116007000 Isl1 Enhancer Active Normal Brainstem UBERON:0002298 Cranial motor neurons motor neuron CL:0000100 Enhancer activity assay, Chromatin interaction assay scATAC-seq, scRNA-seq, scCUT&Tag Transgenic Reporter Assay 2018 30404901 Promoter-enhancer looping and shadow enhancers of the mouse ??A-crystallin locus Mus musculus mm10 chr17 31321000 31322000 Cryaa Enhancer Active Normal Lens UBERON:0000965 Embryonic lens vesicle lens vesicle cell CL:0002224 Enhancer activity assay, Chromatin interaction assay qRT-PCR, and ChIP-qPCR 2018 30404901 Promoter-enhancer looping and shadow enhancers of the mouse ??A-crystallin locus Mus musculus mm10 chr17 31322000 31323000 Cryaa Enhancer Active Normal Lens UBERON:0000965 Embryonic lens vesicle lens vesicle cell CL:0002224 Enhancer activity assay, Chromatin interaction assay qRT-PCR, and ChIP-qPCR 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 Forebrain UBERON:0001890 Embryonic neural progenitor neural progenitor cell CL:0002672 Enhancer activity assay, TF binding assay Transgenic Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2019 31278164 The Prrx1 limb enhancer marks an adult subpopulation of injury-responsive dermal fibroblasts Mus musculus mm10 chr1 17147835 17150235 Prrx1 Enhancer Active Normal Embryonic Limb Bud UBERON:0005417 Limb mesenchymal progenitors mesenchymal progenitor cell CL:0000134 Enhancer activity assay RNA-seq, FACS Transgenic Reporter Assay, Lineage tracing, Immunohistochemistry, Whole-mount imaging 2019 31278164 The Prrx1 limb enhancer marks an adult subpopulation of injury-responsive dermal fibroblasts Mus musculus mm10 chr1 17147835 17150235 Prrx1 Enhancer Active Normal Dermis UBERON:0002067 Dermal fibroblasts dermal fibroblast CL:0000057 Enhancer activity assay RNA-seq, FACS Transgenic Reporter Assay, Lineage tracing, Immunohistochemistry, Whole-mount imaging 2020 32817515 The Atoh7 remote enhancer provides transcriptional robustness during retinal ganglion cell development Mus musculus mm10 chr10 72890000 72890392 Atoh7 Enhancer Active Normal Retina UBERON:0000966 Retinal Progenitor Cells retinal progenitor cell CL:0002672 Enhancer activity assay Transgenic Reporter Assay 2020 32817515 The Atoh7 remote enhancer provides transcriptional robustness during retinal ganglion cell development Mus musculus mm10 chr10 72890000 72890392 Atoh7 Enhancer Active Normal Retina UBERON:0000966 Retinal Ganglion Cells retinal ganglion cell CL:0000740 Enhancer activity assay Transgenic Reporter Assay 2020 32817515 The Atoh7 remote enhancer provides transcriptional robustness during retinal ganglion cell development Mus musculus mm10 chr10 72894616 72895600 Atoh7 Enhancer Active Normal Retina UBERON:0000966 Retinal Progenitor Cells retinal progenitor cell CL:0002672 Enhancer activity assay Transgenic Reporter Assay 2020 32817515 The Atoh7 remote enhancer provides transcriptional robustness during retinal ganglion cell development Mus musculus mm10 chr10 72894616 72895600 Atoh7 Enhancer Active Normal Retina UBERON:0000966 Retinal Ganglion Cells retinal ganglion cell CL:0000740 Enhancer activity assay Transgenic Reporter Assay 2020 33229569 Chromatin topology and the timing of enhancer function at the HoxD locus Mus musculus mm10 chr2 74558139 74559639 Hoxd9 Enhancer Active Normal Limb UBERON:0002101 Not available Enhancer activity assay Transgenic Reporter Assay 2020 33229569 Chromatin topology and the timing of enhancer function at the HoxD locus Mus musculus mm10 chr2 74558139 74559639 Hoxd11 Enhancer Active Normal Limb UBERON:0002101 Not available Enhancer activity assay Transgenic Reporter Assay 2020 33229569 Chromatin topology and the timing of enhancer function at the HoxD locus Mus musculus mm10 chr2 74560139 74561639 Hoxd9 Enhancer Active Normal Limb UBERON:0002101 Not available Enhancer activity assay Transgenic Reporter Assay 2020 33229569 Chromatin topology and the timing of enhancer function at the HoxD locus Mus musculus mm10 chr2 74560139 74561639 Hoxd11 Enhancer Active Normal Limb UBERON:0002101 Not available Enhancer activity assay Transgenic Reporter Assay 2020 33229569 Chromatin topology and the timing of enhancer function at the HoxD locus Mus musculus mm10 chr2 74728139 74729639 Hoxd9 Enhancer Active Normal Limb UBERON:0002101 Not available Enhancer activity assay Transgenic Reporter Assay 2020 33229569 Chromatin topology and the timing of enhancer function at the HoxD locus Mus musculus mm10 chr2 74728139 74729639 Hoxd11 Enhancer Active Normal Limb UBERON:0002101 Not available Enhancer activity assay Transgenic Reporter Assay 2020 33229569 Chromatin topology and the timing of enhancer function at the HoxD locus Mus musculus mm10 chr2 74808139 74809639 Hoxd9 Enhancer Active Normal Limb UBERON:0002101 Not available Enhancer activity assay Transgenic Reporter Assay 2020 33229569 Chromatin topology and the timing of enhancer function at the HoxD locus Mus musculus mm10 chr2 74808139 74809639 Hoxd11 Enhancer Active Normal Limb UBERON:0002101 Not available Enhancer activity assay Transgenic Reporter Assay 2020 33229569 Chromatin topology and the timing of enhancer function at the HoxD locus Mus musculus mm10 chr2 74888139 74889639 Hoxd9 Enhancer Active Normal Limb UBERON:0002101 Not available Enhancer activity assay Transgenic Reporter Assay 2020 33229569 Chromatin topology and the timing of enhancer function at the HoxD locus Mus musculus mm10 chr2 74888139 74889639 Hoxd11 Enhancer Active Normal Limb UBERON:0002101 Not available Enhancer activity assay Transgenic Reporter Assay 2003 12732147 A Global Control Region Defines a Chromosomal Regulatory Landscape Containing the HoxD Cluster Mus musculus mm10 chr2 74460000 74500000 Hoxd13 Enhancer Active Normal Limb UBERON:0002101 Enhancer activity assay, Functional perturbation assay Transgenic Reporter Assay, Southern Blot, Whole-mount In Situ Hybridization 2003 12732147 A Global Control Region Defines a Chromosomal Regulatory Landscape Containing the HoxD Cluster Mus musculus mm10 chr2 74460000 74500000 Hoxd12 Enhancer Active Normal Limb UBERON:0002101 Enhancer activity assay, Functional perturbation assay Transgenic Reporter Assay, Southern Blot, Whole-mount In Situ Hybridization 2003 12732147 A Global Control Region Defines a Chromosomal Regulatory Landscape Containing the HoxD Cluster Mus musculus mm10 chr2 74460000 74500000 Hoxd11 Enhancer Active Normal Limb UBERON:0002101 Enhancer activity assay, Functional perturbation assay Transgenic Reporter Assay, Southern Blot, Whole-mount In Situ Hybridization 2003 12732147 A Global Control Region Defines a Chromosomal Regulatory Landscape Containing the HoxD Cluster Mus musculus mm10 chr2 74460000 74500000 Hoxd10 Enhancer Active Normal Limb UBERON:0002101 Enhancer activity assay, Functional perturbation assay Transgenic Reporter Assay, Southern Blot, Whole-mount In Situ Hybridization 2003 12732147 A Global Control Region Defines a Chromosomal Regulatory Landscape Containing the HoxD Cluster Mus musculus mm10 chr2 74460000 74500000 Evx2 Enhancer Active Normal Limb UBERON:0002101 Enhancer activity assay, Functional perturbation assay Transgenic Reporter Assay, Southern Blot, Whole-mount In Situ Hybridization 2003 12732147 A Global Control Region Defines a Chromosomal Regulatory Landscape Containing the HoxD Cluster Mus musculus mm10 chr2 74460000 74500000 Lnp Enhancer Active Normal Limb UBERON:0002101 Enhancer activity assay, Functional perturbation assay Transgenic Reporter Assay, Southern Blot, Whole-mount In Situ Hybridization 2015 26490266 Identification of the 187 bp EphA7 Genomic DNA as the Dorsal Midline-Specific Enhancer of the Diencephalon and Mesencephalon Mus musculus mm10 chr4 84506800 84506986 Epha7 Enhancer Active Normal Brain UBERON:0000955 Embryonic tissue embryonic tissue CL:0000000 Enhancer activity assay qRT-PCR, and ChIP-qPCR 2018 29301908 Deletion of a Long-Range Dlx5 Enhancer Disrupts Inner Ear Development in Mice Mus musculus mm10 chr6 6163229 6163674 Dlx5 Enhancer Active Normal Embryo UBERON:0000922 Embryonic whole mount mouse embryo CL:0000000 Enhancer activity assay qRT-PCR, and ChIP-qPCR 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 Aicda Enhancer Active Normal Lymph node UBERON:0000029 Germinal center B cells germinal center B cell CL:0000945 Enhancer activity assay, Functional perturbation assay Transgenic reporter assay, RT-RT-qPCR, FACS 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 Aicda Enhancer Active Normal Lymph node UBERON:0000029 Germinal center B cells germinal center B cell CL:0000945 Enhancer activity assay, Functional perturbation assay Transgenic reporter assay, RT-RT-qPCR, FACS 2015 25652130 Enhancer cooperativity as a novel mechanism underlying the transcriptional regulation of E-cadherin during mesenchymal to epithelial transition Mus musculus mm10 chr8 125454150 125454370 Hnf4A Cdh1 Enhancer Active Normal Mammary gland UBERON:0001911 NMuMG cells CVCL_0077 mammary epithelial cell CL:0000066 TF binding assay ChIP-RT-qPCR 1996 8977525 Specific versus cooperative regulatory mechanisms of the cytokine genes that are clustered on the same chromosome Mus musculus mm10 chr11 53495000 53501000 Cat Enhancer Active Normal Blood UBERON:0000178 Murine T Lymphocytes T cell CL:0000084 Enhancer activity assay CAT Reporter Assay, DNase I Hypersensitivity Assay 2023 36729834 Diverse logics and grammar encode notochord enhancers Mus musculus mm10 chr17 67749535 67749594 Lama1 Enhancer Active Normal Notochord UBERON:0002329 Embryonic notochord notochordal cell CL:0000000 Enhancer activity assay Transgenic Reporter Assay 2023 36729834 Diverse logics and grammar encode notochord enhancers Mus musculus mm10 chr17 8396191 8396849 Enhancer Active Normal Notochord UBERON:0002329 Embryonic notochord notochordal cell CL:0000000 Enhancer activity assay Transgenic Reporter Assay 2023 36729834 Diverse logics and grammar encode notochord enhancers Mus musculus mm10 chr17 8444218 8444317 Enhancer Active Normal Notochord UBERON:0002329 Embryonic notochord notochordal cell CL:0000000 Enhancer activity assay Transgenic Reporter Assay 2019 30990414 Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from naive pluripotency Mus musculus mm10 chr1 63189000 63192000 Pou5F1 Zdbf2 Enhancer Active Normal Embryo UBERON:0000922 Mouse Embryonic Stem Cells (mESCs) mouse embryonic stem cell CL:0002322 Enhancer activity assay, Chromatin interaction assay, TF binding assay 4C-seq, ATAC-seq, ChIP-seq, RNA-seq, WGBS CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Bisulfite Pyrosequencing 2019 30990414 Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from naive pluripotency Mus musculus mm10 chr1 63189000 63192000 Pou5F1 Zdbf2 Enhancer Active Normal Embryo UBERON:0000922 E14TG2a CVCL_2167 mouse embryonic stem cell CL:0002322 Enhancer activity assay, Chromatin interaction assay, TF binding assay 4C-seq, ATAC-seq, ChIP-seq, RNA-seq, WGBS CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Bisulfite Pyrosequencing 2019 30990414 Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from naive pluripotency Mus musculus mm10 chr1 63189000 63192000 Pou5F1 Zdbf2 Enhancer Active Normal Embryo UBERON:0000922 J1) CVCL_2167 mouse embryonic stem cell CL:0002322 Enhancer activity assay, Chromatin interaction assay, TF binding assay 4C-seq, ATAC-seq, ChIP-seq, RNA-seq, WGBS CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Bisulfite Pyrosequencing 2019 30990414 Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from naive pluripotency Mus musculus mm10 chr1 63193000 63196000 Pou5F1 Zdbf2 Enhancer Active Normal Embryo UBERON:0000922 Mouse Embryonic Stem Cells (mESCs) mouse embryonic stem cell CL:0002322 Enhancer activity assay, Chromatin interaction assay, TF binding assay 4C-seq, ATAC-seq, ChIP-seq, RNA-seq, WGBS CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Bisulfite Pyrosequencing 2019 30990414 Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from naive pluripotency Mus musculus mm10 chr1 63193000 63196000 Pou5F1 Zdbf2 Enhancer Active Normal Embryo UBERON:0000922 E14TG2a CVCL_2167 mouse embryonic stem cell CL:0002322 Enhancer activity assay, Chromatin interaction assay, TF binding assay 4C-seq, ATAC-seq, ChIP-seq, RNA-seq, WGBS CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Bisulfite Pyrosequencing 2019 30990414 Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from naive pluripotency Mus musculus mm10 chr1 63193000 63196000 Pou5F1 Zdbf2 Enhancer Active Normal Embryo UBERON:0000922 J1) CVCL_2167 mouse embryonic stem cell CL:0002322 Enhancer activity assay, Chromatin interaction assay, TF binding assay 4C-seq, ATAC-seq, ChIP-seq, RNA-seq, WGBS CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Bisulfite Pyrosequencing 2016 27376235 Genetic dissection of the alpha-globin super-enhancer in vivo Mus musculus mm10 chr11 32115000 32145000 Gata1 Hba1 Enhancer Active Normal Bone marrow UBERON:0002371 Erythroid progenitor erythroid progenitor cell CL:0000038 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay ChIP-seq, RNA-seq, 3C CRISPR Knockout, Transgenic Reporter Assay 2018 30328555 STAT5-Driven Enhancers Tightly Control Temporal Expression of Mammary-Specific Genes Mus musculus mm10 chr11 100810000 100812000 Stat5A Stat5A Enhancer Active Normal Mammary Gland UBERON:0001911 Mammary epithelial cells mammary epithelial cell CL:0000066 Functional perturbation assay ChIP-seq, RNA-seq, 3C-seq CRISPR Knockout, RT-RT-qPCR, Western blot 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 40942777 40944397 Enhancer Active Normal Heart UBERON:0000948 embryonic cardiomyocyte CL:0000746 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 41143611 41146744 Enhancer Active Normal Eye UBERON:0000970 embryonic ocular cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 41603697 41606058 Enhancer Active Normal Forebrain UBERON:0001890 embryonic forebrain cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 42365513 42367630 Enhancer Active Normal Forebrain UBERON:0001890 embryonic forebrain cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 42538429 42540496 Enhancer Active Normal Forebrain UBERON:0001890 embryonic forebrain cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 75770058 75773197 Enhancer Active Normal Limb UBERON:0002101 embryonic limb cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 86488603 86493027 Enhancer Active Normal Heart UBERON:0000948 embryonic cardiomyocyte CL:0000746 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 92718827 92721406 Enhancer Active Normal Heart UBERON:0000948 embryonic cardiomyocyte CL:0000746 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 155038871 155039989 Enhancer Active Normal Heart UBERON:0000948 embryonic cardiomyocyte CL:0000746 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 163361752 163364252 Enhancer Active Normal Limb UBERON:0002101 embryonic limb cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 169343173 169345241 Enhancer Active Normal Limb UBERON:0002101 embryonic limb cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 190655086 190655625 Enhancer Active Normal Forebrain UBERON:0001890 embryonic forebrain cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 190727026 190730523 Enhancer Active Normal Forebrain UBERON:0001890 embryonic forebrain cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr10 3393773 3395290 Enhancer Active Normal Heart UBERON:0000948 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr10 21082099 21084259 Enhancer Active Normal Eye UBERON:0000970 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr10 31052886 31054461 Enhancer Active Normal Heart UBERON:0000948 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr10 31228851 31230590 Enhancer Active Normal Heart UBERON:0000948 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr10 45894288 45894827 Enhancer Active Normal Limb UBERON:0002101 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr10 49983887 49986266 Enhancer Active Normal Limb UBERON:0002101 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr10 53324321 53325988 Enhancer Active Normal Heart UBERON:0000948 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr10 87324145 87327333 Enhancer Active Normal Midbrain UBERON:0001891 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr10 92555796 92557968 Enhancer Active Normal Forebrain UBERON:0001890 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr10 96707809 96707988 Enhancer Active Normal Heart UBERON:0000948 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 11955959 11958746 Enhancer Active Normal Heart UBERON:0000948 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 18915780 18919026 Enhancer Active Normal Forebrain UBERON:0001890 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 22077830 22079309 Enhancer Active Normal Midbrain UBERON:0001891 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 24096035 24096394 Enhancer Active Normal Forebrain UBERON:0001890 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 24330054 24333979 Enhancer Active Normal Hindbrain UBERON:0002028 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 24369946 24372657 Enhancer Active Normal Forebrain UBERON:0001890 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 25287174 25289345 Enhancer Active Normal Face UBERON:0001456 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 25531402 25532001 Enhancer Active Normal Midbrain UBERON:0001891 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 26006299 26007590 Enhancer Active Normal Limb UBERON:0002101 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 26120058 26122427 Enhancer Active Normal Dorsal root ganglion UBERON:0001685 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 44799152 44801733 Enhancer Active Normal Neural tube UBERON:0000934 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 45549323 45551898 Enhancer Active Normal Limb UBERON:0002101 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 54879406 54883911 Enhancer Active Normal Heart UBERON:0000948 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 59638982 59640132 Enhancer Active Normal Heart UBERON:0000948 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 64898966 64900764 Enhancer Active Normal Face UBERON:0001456 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 65209858 65211177 Enhancer Active Normal Heart UBERON:0000948 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 65648676 65651675 Enhancer Active Normal Heart UBERON:0000948 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 75048409 75050731 Enhancer Active Normal Limb UBERON:0002101 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 77422172 77424768 Enhancer Active Normal Heart UBERON:0000948 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 84495459 84496979 Enhancer Active Normal Hindbrain UBERON:0002028 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 84765200 84766279 Enhancer Active Normal Limb UBERON:0002101 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 85856960 85860695 Enhancer Active Normal Midbrain UBERON:0001891 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 85875857 85878048 Enhancer Active Normal Limb UBERON:0002101 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 85962963 85963802 Enhancer Active Normal Limb UBERON:0002101 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 98338371 98340241 Enhancer Active Normal Midbrain UBERON:0001891 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 106133614 106136287 Enhancer Active Normal Heart UBERON:0000948 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 111563103 111564513 Enhancer Active Normal Limb UBERON:0002101 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 111568057 111570396 Enhancer Active Normal Pharyngeal arch UBERON:0003066 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 111827949 111829442 Enhancer Active Normal Limb UBERON:0002101 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 114335424 114336143 Enhancer Active Normal Forebrain UBERON:0001890 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 5266607 5270082 Enhancer Active Normal Ear UBERON:0001690 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 12178866 12180524 Enhancer Active Normal Heart UBERON:0000948 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 12866488 12867793 Enhancer Active Normal Midbrain UBERON:0001891 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 34219098 34222003 Enhancer Active Normal Limb UBERON:0002101 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 38435899 38436969 Enhancer Active Normal Hindbrain UBERON:0002028 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 49944259 49946938 Enhancer Active Normal Forebrain UBERON:0001890 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 49973819 49974898 Enhancer Active Normal Hindbrain UBERON:0002028 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 50120052 50121911 Enhancer Active Normal Forebrain UBERON:0001890 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 52227850 52229485 Enhancer Active Normal Heart UBERON:0000948 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 53873637 53876199 Enhancer Active Normal Heart UBERON:0000948 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 55643171 55644130 Enhancer Active Normal Forebrain UBERON:0001890 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 56114427 56116838 Enhancer Active Normal Hindbrain UBERON:0002028 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 56458924 56460465 Enhancer Active Normal Forebrain UBERON:0001890 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 57290916 57292614 Enhancer Active Normal Midbrain UBERON:0001891 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 69757650 69759599 Enhancer Active Normal Heart UBERON:0000948 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 79795735 79797174 Enhancer Active Normal Blood vessel UBERON:0001981 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 85453982 85456023 Enhancer Active Normal Heart UBERON:0000948 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 86800395 86804134 Enhancer Active Normal Neural tube UBERON:0000934 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 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 Sox2 Klf5 SE Active Normal Embryonic tissue UBERON:0000922 Mouse Embryonic Stem Cells (E14) CVCL_2167 mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, 4C-seq, scRNA-seq, ATAC-seq CRISPR Knockout, CRISPRa, qRT-PCR, Western blot, 3C-PCR 2017 27881681 A Novel Regulatory Mechanism of Type II Collagen Expression via a SOX9-dependent Enhancer in Intron 6 Mus musculus mm10 chr11 96800000 96801500 Sox9 Col2A1 Enhancer Active Normal Cartilage UBERON:0002418 RCS chondrocytes CVCL_5256 chondrocyte CL:0000138 Enhancer activity assay, TF binding assay ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA, CRISPR Knockout 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 Embryo UBERON:0000922 ESCs embryonic stem cell CL:0002322 Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq CRISPR Knockout, RT-RT-qPCR, Western blot 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 19698786 19700794 Enhancer Active Normal Hindbrain UBERON:0002028 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 39945410 39950481 Enhancer Active Normal Dorsal root ganglion UBERON:0001685 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 41165774 41167470 Enhancer Active Normal Midbrain UBERON:0001891 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 41274809 41277330 Enhancer Active Normal Hindbrain UBERON:0002028 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 41274477 41276046 Enhancer Active Normal Midbrain UBERON:0001891 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 41389098 41390679 Enhancer Active Normal Neural tube UBERON:0000934 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 41558620 41559699 Enhancer Active Normal Dorsal root ganglion UBERON:0001685 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 41936018 41937045 Enhancer Active Normal Pharyngeal arch UBERON:0003066 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 41980560 41982826 Enhancer Active Normal Hindbrain UBERON:0002028 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 42242028 42244560 Enhancer Active Normal Midbrain UBERON:0001891 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 42740097 42742436 Enhancer Active Normal Hindbrain UBERON:0002028 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 42888276 42890025 Enhancer Active Normal Neural tube UBERON:0000934 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 56287621 56287740 Enhancer Active Normal Pharyngeal arch UBERON:0003066 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 59333610 59335295 Enhancer Active Normal Somite UBERON:0002329 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 59340469 59342458 Enhancer Active Normal Midbrain UBERON:0001891 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 61202186 61204482 Enhancer Active Normal Face UBERON:0001456 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 67795652 67796989 Enhancer Active Normal Neural tube UBERON:0000934 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 68045495 68048139 Enhancer Active Normal Hindbrain UBERON:0002028 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 75784481 75787064 Enhancer Active Normal Limb UBERON:0002101 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 75832340 75835632 Enhancer Active Normal Limb UBERON:0002101 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 78058902 78059702 Enhancer Active Normal Skin UBERON:0000014 embryonic melanocyte CL:0000148 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 89713239 89715218 Enhancer Active Normal Limb UBERON:0002101 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 89750247 89752564 Enhancer Active Normal Hindbrain UBERON:0002028 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 89847226 89849959 Enhancer Active Normal Forebrain UBERON:0001890 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 90752845 90755953 Enhancer Active Normal Somite UBERON:0002329 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 91962915 91965571 Enhancer Active Normal Pharyngeal arch UBERON:0003066 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 92786133 92787932 Enhancer Active Normal Hindbrain UBERON:0002028 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 92789742 92792954 Enhancer Active Normal Limb UBERON:0002101 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 97538458 97543032 Enhancer Active Normal Neural tube UBERON:0000934 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 118776992 118777951 Enhancer Active Normal Hindbrain UBERON:0002028 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 120023430 120025609 Enhancer Active Normal Embryo UBERON:0000922 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 132332673 132334764 Enhancer Active Normal Hindbrain UBERON:0002028 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 133079543 133081905 Enhancer Active Normal Neural tube UBERON:0000934 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 133491760 133493483 Enhancer Active Normal Blood vessel UBERON:0001981 embryonic vascular cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 138498963 138501215 Enhancer Active Normal Hindbrain UBERON:0002028 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 158265584 158268273 Enhancer Active Normal Hindbrain UBERON:0002028 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 162074122 162077977 Enhancer Active Normal Somite UBERON:0002329 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 162829985 162833284 Enhancer Active Normal Neural tube UBERON:0000934 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 163897046 163900155 Enhancer Active Normal Limb UBERON:0002101 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 166047034 166051082 Enhancer Active Normal Neural tube UBERON:0000934 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 168341325 168343770 Enhancer Active Normal Hindbrain UBERON:0002028 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 168356497 168358717 Enhancer Active Normal Hindbrain UBERON:0002028 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 169384774 169387004 Enhancer Active Normal Hindbrain UBERON:0002028 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 177151814 177152053 Enhancer Active Normal Neural tube UBERON:0000934 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 179385555 179387659 Enhancer Active Normal Midbrain UBERON:0001891 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 187907873 187909312 Enhancer Active Normal Cranial nerve UBERON:0001785 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 189186446 189189286 Enhancer Active Normal Neural tube UBERON:0000934 embryonic cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 191238682 191241679 Enhancer Active Normal Neural tube UBERON:0000934 embryonic neural tube cell CL:0000000 Enhancer capture Hi-C assay, In vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR-Cas9 knockout, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 192798078 192799697 Enhancer Active Normal Somite UBERON:0002329 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr1 193140090 193141613 Enhancer Active Normal Limb UBERON:0002101 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr10 14462982 14465275 Enhancer Active Normal Limb UBERON:0002101 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr10 17228620 17231920 Enhancer Active Normal Hindbrain UBERON:0002028 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr10 36483060 36486674 Enhancer Active Normal Midbrain UBERON:0001891 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr10 38551938 38556574 Enhancer Active Normal Neural tube UBERON:0000934 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr10 45228796 45231475 Enhancer Active Normal Limb UBERON:0002101 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr10 51257317 51258816 Enhancer Active Normal Midbrain UBERON:0001891 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr10 52741597 52745163 Enhancer Active Normal Neural tube UBERON:0000934 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr10 87292824 87294448 Enhancer Active Normal Midbrain UBERON:0001891 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr10 87445090 87449904 Enhancer Active Normal Hindbrain UBERON:0002028 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr10 87472791 87473750 Enhancer Active Normal Neural tube UBERON:0000934 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr10 91880854 91881573 Enhancer Active Normal Midbrain UBERON:0001891 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr10 120551807 120554146 Enhancer Active Normal Neural tube UBERON:0000934 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr10 120646283 120649237 Enhancer Active Normal Hindbrain UBERON:0002028 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr10 125809640 125811484 Enhancer Active Normal Somite UBERON:0002329 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 17448900 17451834 Enhancer Active Normal Hindbrain UBERON:0002028 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 18357518 18358569 Enhancer Active Normal Hindbrain UBERON:0002028 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 24426421 24428736 Enhancer Active Normal Midbrain UBERON:0001891 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 25356124 25357143 Enhancer Active Normal Neural tube UBERON:0000934 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 26771684 26773636 Enhancer Active Normal Hindbrain UBERON:0002028 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 32245096 32247223 Enhancer Active Normal Heart UBERON:0000948 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 33299155 33301650 Enhancer Active Normal Hindbrain UBERON:0002028 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 33399382 33401384 Enhancer Active Normal Neural tube UBERON:0000934 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 44634961 44636269 Enhancer Active Normal Neural tube UBERON:0000934 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 44656049 44658617 Enhancer Active Normal Neural tube UBERON:0000934 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 45136282 45138321 Enhancer Active Normal Limb UBERON:0002101 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 46201700 46203391 Enhancer Active Normal Pharyngeal arch UBERON:0003066 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 62983610 62986909 Enhancer Active Normal Neural tube UBERON:0000934 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 77905947 77908190 Enhancer Active Normal Hindbrain UBERON:0002028 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 81611872 81614511 Enhancer Active Normal Neural tube UBERON:0000934 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 86167051 86168070 Enhancer Active Normal Embryo UBERON:0000922 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 88274108 88276472 Enhancer Active Normal Neural tube UBERON:0000934 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 94159442 94162241 Enhancer Active Normal Hindbrain UBERON:0002028 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 94880838 94883684 Enhancer Active Normal Neural tube UBERON:0000934 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 96883943 96888120 Enhancer Active Normal Hindbrain UBERON:0002028 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 98496932 98499144 Enhancer Active Normal Neural tube UBERON:0000934 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 103840502 103842458 Enhancer Active Normal Neural tube UBERON:0000934 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 107761860 107764266 Enhancer Active Normal Embryo UBERON:0000922 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 109269018 109271202 Enhancer Active Normal Neural tube UBERON:0000934 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 112411851 112414154 Enhancer Active Normal Limb UBERON:0002101 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 113012998 113015716 Enhancer Active Normal Limb UBERON:0002101 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 113307250 113310296 Enhancer Active Normal Neural tube UBERON:0000934 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 113783986 113787857 Enhancer Active Normal Neural tube UBERON:0000934 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr11 120314730 120315389 Enhancer Active Normal Dorsal root ganglion UBERON:0001685 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 8385536 8387745 Enhancer Active Normal Heart UBERON:0000948 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 9338781 9340056 Enhancer Active Normal Somite UBERON:0002329 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 12707452 12712121 Enhancer Active Normal Midbrain UBERON:0001891 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 25890817 25892310 Enhancer Active Normal Forebrain UBERON:0001890 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 27564419 27567345 Enhancer Active Normal Neural tube UBERON:0000934 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 28817230 28818444 Enhancer Active Normal Hindbrain UBERON:0002028 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 31309806 31310405 Enhancer Active Normal Dorsal root ganglion UBERON:0001685 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 34198954 34201589 Enhancer Active Normal Hindbrain UBERON:0002028 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 34215806 34216763 Enhancer Active Normal Limb UBERON:0002101 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 39300476 39302395 Enhancer Active Normal Forebrain UBERON:0001890 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 39341105 39343483 Enhancer Active Normal Hindbrain UBERON:0002028 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 44402329 44404831 Enhancer Active Normal Midbrain UBERON:0001891 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 46020387 46022607 Enhancer Active Normal Neural tube UBERON:0000934 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 49991668 49994699 Enhancer Active Normal Hindbrain UBERON:0002028 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 56482102 56482581 Enhancer Active Normal Hindbrain UBERON:0002028 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 79846147 79848987 Enhancer Active Normal Limb UBERON:0002101 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr12 83072708 83074410 Enhancer Active Normal Midbrain UBERON:0001891 Enhancer capture Hi-C, in vivo functional validation Capture Hi-C, ChIP-seq, RNA-seq, Bisulfite-seq CRISPR/Cas9 knockout, RT-qPCR 2017 28982762 A dynamic interplay of enhancer elements regulates Klf4 expression in naive pluripotency Mus musculus mm10 chr4 55559000 55560500 Pou5F1 Klf4 Enhancer Active Normal Embryo UBERON:0000922 Mouse JM8.N4 ESCs CVCL_2155 mouse embryonic stem cell CL:0002322 Functional perturbation assay ChIP-exo, ATAC-seq, RNA-seq CRISPR Knockout, Luciferase Reporter Assay, RT-RT-qPCR, ChIP-RT-qPCR 2018 30328555 STAT5-Driven Enhancers Tightly Control Temporal Expression of Mammary-Specific Genes Mus musculus mm10 chr11 98346350 98346550 Stat5A Wap Enhancer Active Normal Mammary Gland UBERON:0001911 Mammary epithelial cells mammary epithelial cell CL:0000066 Functional perturbation assay ChIP-seq, RNA-seq CRISPR Knockout, RT-RT-qPCR, Western blot 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 Bone Marrow UBERON:0002371 Erythroblasts erythroblast CL:0000765 Functional perturbation assay, Chromatin interaction assay, TF binding assay HiChIP, ChIP-seq, RNA-seq, ATAC-seq CRISPR Knockout, RT-RT-qPCR 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 Fetal Liver UBERON:0002107 MEL Cells CVCL_2109 erythroid progenitor cell CL:0000038 Functional perturbation assay, Chromatin interaction assay, TF binding assay HiChIP, ChIP-seq, RNA-seq, ATAC-seq CRISPR Knockout, RT-RT-qPCR 2025 40570123 Reactivation of mammalian regeneration by turning on an evolutionarily disabled genetic switch Mus musculus mm10 chr10 87230000 87234000 Aldh1A2 Enhancer Active Normal Ear pinna UBERON:0001847 Wound-induced Fibroblast fibroblast CL:0000057 Functional perturbation assay RNA-seq Transgenic Reporter Assay, RT-RT-qPCR 2015 25644605 PRDM16 enhances nuclear receptor-dependent transcription of the brown fat-specific Ucp1 gene through interactions with Mediator subunit MED1 Mus musculus mm10 chr8 84109163 84109362 Prdm16 Ucp1 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic fibroblasts CVCL_0003 mouse embryonic fibroblast CL:0000057 TF binding assay, Functional perturbation assay ChIP-RT-qPCR, RT-RT-qPCR 2018 29301908 Deletion of a Long-Range Dlx5 Enhancer Disrupts Inner Ear Development in Mice Mus musculus mm10 chr6 6058554 6059028 Dlx5 Enhancer Active Normal Embryo UBERON:0000922 Embryonic whole mount embryonic cell CL:0000000 Enhancer activity assay qRT-PCR, and ChIP-qPCR 2011 21673114 Combinatorial Regulation of Photoreceptor Differentiation Factor, Neural Retina Leucine Zipper Gene Nrl Mus musculus mm10 chr11 75210000 75210304 Nrl Enhancer Active Normal Retina UBERON:0000966 Primary Retinal Cells retinal cell CL:0000540 Enhancer activity assay Transgenic Reporter Assay 2007 17715390 Tissue-specific histone modification and transcription factor binding in alpha globin gene expression Mus musculus mm10 chr11 3210000 3215000 Hba1 Enhancer Active Normal Bone Marrow UBERON:0002371 Primary Murine Erythroblasts mouse erythroblast CL:0000765 Enhancer activity assay, TF binding assay ChIP-chip ChIP-RT-qPCR, RT-RT-qPCR 2022 35885978 Transcriptional Interference Regulates the Evolutionary Development of Speech Mus musculus mm10 chr4 10329803 10537032 Gdf6 Enhancer Active Normal Limb bud UBERON:0005417 Limb bud limb bud cell CL:0000000 Enhancer activity assay Transgenic Reporter Assay 2022 35885978 Transcriptional Interference Regulates the Evolutionary Development of Speech Mus musculus mm10 chr4 10329803 10537032 Gdf6 Enhancer Active Normal Limb bud UBERON:0005417 Embryonic tissue embryonic cell CL:0000000 Enhancer activity assay Transgenic Reporter Assay 2009 19041414 Smad3 activates the Sox9-dependent transcription on chromatin Mus musculus mm10 chr15 98129939 98130247 Sox9 Col2A1 Enhancer Active Normal Cartilage UBERON:0002418 Enhancer activity assay, TF binding assay ChIP-RT-qPCR, EMSA 2020 32321991 The interdependence of mammary-specific super-enhancers and their native promoters facilitates gene activation during pregnancy Mus musculus mm10 chr11 10081501 10082508 Stat5; Nfib; Nr3C1 Wap Enhancer Active Normal Mammary Gland UBERON:0001911 Primary Mouse Mammary Epithelial mouse mammary epithelial cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq CRISPR Knockout, CRISPRi, RT-RT-qPCR 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 97550000 97553161 Sry; Sf1; Sox9 Sox9 Enhancer Active Normal Gonad UBERON:0000991 Fetal gonadal somatic cells gonadal somatic cell CL:0000000 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq Transgenic Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout 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 97551000 97552292 Sry; Sf1; Sox9 Sox9 Enhancer Active Normal Gonad UBERON:0000991 Fetal gonadal somatic cells gonadal somatic cell CL:0000000 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq Transgenic Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout 2024 38341433 Matrin3 mediates differentiation through stabilizing chromatin loop-domain interactions and YY1 mediated enhancer-promoter interactions Mus musculus mm10 chr7 67890000 67910000 Mphosph8 Enhancer Active Normal Skeletal muscle UBERON:0001134 C2C12 myoblasts CVCL_0188 myoblast CL:0000187 Chromatin interaction assay, Functional perturbation assay Hi-C, ATAC-seq CRISPR Knockout, RT-RT-qPCR 2020 32251373 Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction Mus musculus mm10 chr12 114664163 114667348 Ighm Enhancer Active Normal Spleen UBERON:0002106 mature B mature B cell CL:0000785 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, GRO-seq, ATAC-seq, 3C-seq 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR 2025 39443808 Chromatin remodelling drives immune cell-fibroblast communication in heart failure Mus musculus mm10 chr2 129323600 129328600 Il1B Enhancer Active Disease atherosclerosis MONDO:0005147 DOID:1936 Heart UBERON:0000948 Macrophage macrophage CL:0000235 Enhancer activity assay scATAC-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR 2025 39443808 Chromatin remodelling drives immune cell-fibroblast communication in heart failure Mus musculus mm10 chr11 101828402 101833529 Creb5; Runx2 Postn Enhancer Active Disease cardiac fibrosis MONDO:0004976 DOID:3770 Heart UBERON:0000948 Cardiac Fibroblast cardiac fibroblast CL:0002547 Chromatin interaction assay scATAC-seq ChIP-RT-qPCR, RT-RT-qPCR 2024 38509385 Increased enhancer-promoter interactions during developmental enhancer activation in mammals Mus musculus mm10 chr9 90690384 90694866 Zic1 Enhancer Active Normal Midbrain UBERON:0001891 transgenic mouse embryo mouse embryo CL:0000000 CRISPR deletion, Transgenic reporter assay Capture Hi-C RT-RT-qPCR, lacZ whole-mount staining 2019 30686579 The cis-Regulatory Atlas of the Mouse Immune System Mus musculus mm10 chr11 44112300 44112500 Pu.1 Spi1 Enhancer Active Normal Bone marrow UBERON:0002371 B B cell CL:0000945 Enhancer activity assay ATAC-seq, RNA-seq ChIP-RT-qPCR 2011 21673114 Combinatorial Regulation of Photoreceptor Differentiation Factor, Neural Retina Leucine Zipper Gene Nrl, Revealed by in Vivo Promoter Analysis Mus musculus mm10 chr14 54721862 54722816 Nrl Enhancer Active Normal Retina UBERON:0000966 Rod photoreceptor rod photoreceptor CL:0000740 Enhancer activity assay Transgenic Reporter Assay, Luciferase Reporter Assay 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 37283342 37283854 C-Maf Il21 Enhancer Active Disease T-cell lymphoma MONDO:0005114 DOID:0050747 Lymph node UBERON:0000029 EL4 CVCL_0255 T lymphoma cell CL:0000084 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA 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 37283342 37283854 C-Maf Il21 Enhancer Active Normal Embryonic Kidney UBERON:0002113 293T CVCL_0063 embryonic kidney cell CL:0002139 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA 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 37283342 37283854 C-Maf Il21 Enhancer Active Normal Blood UBERON:0000178 CD4+ T cell CD4-positive T cell CL:0000624 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA 2001 11263787 Activation of a Fibroblast-Specific Enhancer of the Proalpha2(I) Collagen Gene in Tight-Skin Mice Mus musculus mm10 chr6 122479265 122485265 Col1A2 Enhancer Active Disease scleroderma MONDO:0005100 DOID:418 Skin UBERON:0000014 Dermal Fibroblast dermal fibroblast CL:0000057 Enhancer activity assay Transgenic Reporter Assay, Luciferase Reporter Assay 2001 11263787 Activation of a Fibroblast-Specific Enhancer of the Proalpha2(I) Collagen Gene in Tight-Skin Mice Mus musculus mm10 chr6 122481665 122483665 Col1A2 Enhancer Active Disease scleroderma MONDO:0005100 DOID:418 Skin UBERON:0000014 Dermal Fibroblast dermal fibroblast CL:0000057 Enhancer activity assay Transgenic Reporter Assay, Luciferase Reporter Assay 2015 25775043 Functional annotation of native enhancers with a Cas9-assisted histone demethylase fusion Mus musculus mm10 chr17 35605300 35605800 Pou5F1 Enhancer Active Normal Embryo UBERON:0000922 mESC mouse embryonic stem cell CL:0002322 Enhancer activity assay Luciferase Reporter Assay 2015 25486239 Identification of hypothalamic arcuate nucleus-specific enhancer region of Kiss1 gene in mice Mus musculus mm10 chr10 128065200 128076800 Esr1 Kiss1 Enhancer Active Normal Hypothalamus UBERON:0001898 Arcuate nucleus primary arcuate nucleus cell CL:0000540 Enhancer activity assay, Chromatin interaction assay, TF binding assay Transgenic Reporter Assay, 3C assay, ChIP-RT-qPCR 2015 25486239 Identification of hypothalamic arcuate nucleus-specific enhancer region of Kiss1 gene in mice Mus musculus mm10 chr10 74487110 74497835 Esr1 Kiss1 Enhancer Active Normal Hypothalamus UBERON:0001898 Arcuate nucleus neurons arcuate nucleus neuron CL:0000540 Enhancer activity assay, Chromatin interaction assay, TF binding assay Transgenic Reporter Assay, Chromosome Conformation Capture (3C), ChIP-RT-qPCR, Immunofluorescence 2005 15798195 Identification of Neuronal Enhancers of the Proopiomelanocortin Gene by Transgenic Mouse Analysis and Phylogenetic Footprinting Mus musculus mm10 chr12 103439326 103439476 Pomc Enhancer Active Normal Hypothalamus UBERON:0001898 POMC Arcuate Neuron POMC neuron CL:0000540 Enhancer activity assay Transgenic Reporter Assay, CRISPR Knockout 2000 11120820 Peroxisome proliferator activator receptor-gamma agonists and 15-deoxy-Delta(12,14)(12,14)-PGJ(2) induce apoptosis in normal and malignant B-lineage cells Mus musculus mm10 chr3 37390149 37390163 Ahr Il2 Enhancer Active Normal Thymus UBERON:0002370 Thymocytes thymocyte CL:0000893 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, EMSA, RT-RT-qPCR, ELISA 2000 11120820 Peroxisome proliferator activator receptor-gamma agonists and 15-deoxy-Delta(12,14)(12,14)-PGJ(2) induce apoptosis in normal and malignant B-lineage cells Mus musculus mm10 chr3 37390149 37390163 Ahr Il2 Enhancer Active Normal Thymus UBERON:0002370 Splenic T cells T cell CL:0000084 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, EMSA, RT-RT-qPCR, ELISA 2000 11120820 Peroxisome proliferator activator receptor-gamma agonists and 15-deoxy-Delta(12,14)(12,14)-PGJ(2) induce apoptosis in normal and malignant B-lineage cells Mus musculus mm10 chr3 37390185 37390199 Ahr Il2 Enhancer Active Normal Thymus UBERON:0002370 Thymocytes thymocyte CL:0000893 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, EMSA, RT-RT-qPCR, ELISA 2000 11120820 Peroxisome proliferator activator receptor-gamma agonists and 15-deoxy-Delta(12,14)(12,14)-PGJ(2) induce apoptosis in normal and malignant B-lineage cells Mus musculus mm10 chr3 37390185 37390199 Ahr Il2 Enhancer Active Normal Thymus UBERON:0002370 Splenic T cells T cell CL:0000084 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, EMSA, RT-RT-qPCR, ELISA 2017 28405742 CRISPR/Cas9-mediated deletion of lncRNA Gm26878 in the distant Foxf1 enhancer region Mus musculus mm10 chr8 120880096 120882492 Foxf1 Enhancer Active Normal Lung UBERON:0002048 Embryonic lung tissue embryonic lung cell CL:0000000 Functional perturbation assay CRISPR Knockout, RT-RT-qPCR, Sanger Sequencing 2018 30146478 Combinatorial CRISPR/Cas9 Approach to Elucidate a Far-Upstream Enhancer Complex for Tissue-Specific Sox9 Expression Mus musculus mm10 chr11 111838889 111839334 Sox9 Enhancer Active Normal Cartilage UBERON:0002418 Primary Chondrocytes chondrocyte CL:0000138 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay 3C-seq qRT-PCR, and ChIP-qPCR 2018 30146478 Combinatorial CRISPR/Cas9 Approach to Elucidate a Far-Upstream Enhancer Complex for Tissue-Specific Sox9 Expression Mus musculus mm10 chr11 111838889 111839334 Sox9 Enhancer Active Normal Cartilage UBERON:0002418 ATDC5 CVCL_3894 chondrogenic cell CL:0000138 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay 3C-seq qRT-PCR, and ChIP-qPCR 2018 30146478 Combinatorial CRISPR/Cas9 Approach to Elucidate a Far-Upstream Enhancer Complex for Tissue-Specific Sox9 Expression Mus musculus mm10 chr11 111838889 111839334 Sox9 Enhancer Active Normal Cartilage UBERON:0002418 C3H10T1/2 CVCL_0190 mesenchymal stem cell CL:0000134 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay 3C-seq qRT-PCR, and ChIP-qPCR 2025 39626663 Enhancer cooperativity can compensate for loss of activity over large genomic distances Mus musculus mm10 chr6 122698567 122721126 Nanog Nanog Enhancer Active Normal Embryo UBERON:0000922 Mouse Embryonic Stem Cells (v6.5) mouse embryonic stem cell CL:0002322 Enhancer activity assay ChIP-seq, ATAC-seq Luciferase Reporter Assay, Fluorescent Reporter Assay (mCherry), Flow-FISH, RT-RT-qPCR 2022 35831318 A SOX17-PDGFB signaling axis regulates aortic root development Mus musculus mm10 chr15 79850614 79850824 Sox17 Pdgfb Enhancer Active Normal Heart UBERON:0000948 Mouse Cardiac Endothelial Cells (MCECs) cardiac endothelial cell CL:0000115 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, qRT-PCR, Western blot 2011 21673114 Combinatorial Regulation of Photoreceptor Differentiation Factor, Neural Retina Leucine Zipper Gene Nrl, Revealed by in Vivo Promoter Analysis Mus musculus mm10 chr14 54721862 54722143 Nrl Enhancer Active Normal Retina UBERON:0000966 Rod photoreceptor rod photoreceptor CL:0000740 Enhancer activity assay Transgenic Reporter Assay, Luciferase Reporter Assay, EMSA 2011 21673114 Combinatorial Regulation of Photoreceptor Differentiation Factor, Neural Retina Leucine Zipper Gene Nrl, Revealed by in Vivo Promoter Analysis Mus musculus mm10 chr14 54722765 54722816 Nrl Enhancer Active Normal Retina UBERON:0000966 Rod photoreceptor rod photoreceptor CL:0000740 Enhancer activity assay Transgenic Reporter Assay, Luciferase Reporter Assay, EMSA 2021 33976173 A Stat1 bound enhancer promotes Nampt expression and function within tumor associated macrophages Mus musculus mm10 chr9 102705800 102706400 Stat1 Nampt Enhancer Active Disease tumor microenvironment MONDO:0005070 DOID:162 Bone marrow UBERON:0002371 Bone marrow-derived macrophages (BMMs) macrophage CL:0000235 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq, scRNA-seq, ChIP-seq qRT-PCR, and ChIP-qPCR 2021 33976173 A Stat1 bound enhancer promotes Nampt expression and function within tumor associated macrophages Mus musculus mm10 chr9 102705800 102706400 Stat1 Nampt Enhancer Active Disease tumor microenvironment MONDO:0005070 DOID:162 Bone marrow UBERON:0002371 RAW 264.7 cell line CVCL_0493 macrophage CL:0000235 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq, scRNA-seq, ChIP-seq qRT-PCR, and ChIP-qPCR 2021 33976173 A Stat1 bound enhancer promotes Nampt expression and function within tumor associated macrophages Mus musculus mm10 chr9 102705800 102706400 Stat1 Nampt Enhancer Active Disease tumor microenvironment MONDO:0005070 DOID:162 Bone marrow UBERON:0002371 tumor-associated macrophages (TAMs) macrophage CL:0000235 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq, scRNA-seq, ChIP-seq qRT-PCR, and ChIP-qPCR 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 chr12 53054974 53055029 Usf1 Pdx1 Enhancer Active Normal Pancreatic islet UBERON:0001264 INS-1 CVCL_0352 pancreatic beta cell CL:0000169 TF binding assay Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR 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 chr12 53054974 53055029 Usf1 Pdx1 Enhancer Active Normal Pancreatic islet UBERON:0001264 HIT CVCL_0294 pancreatic beta cell CL:0000169 TF binding assay Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR 2015 25652130 Enhancer cooperativity as a novel mechanism underlying the transcriptional regulation of E-cadherin during mesenchymal to epithelial transition Mus musculus mm10 chr8 125450780 125451000 Cdh1 Enhancer Active Normal Mammary gland UBERON:0001911 NMuMG CVCL_0077 mammary epithelial cell CL:0000066 Enhancer activity assay Luciferase Reporter Assay 2023 37821107 Allelic chromatin structure precedes imprinted expression of Kcnk9 during neurogenesis Mus musculus mm10 chr15 72250000 72250650 Ctcf Kcnk9 Enhancer Silenced Normal Brain UBERON:0000955 Embryonic Stem Cells (ESCs) embryonic stem cell CL:0002322 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ChIP-seq, RNA-seq CRISPR Knockout, ChIP-qPCR, RT-qPCR, Western blot, Region Capture Hi-C 2023 37821107 Allelic chromatin structure precedes imprinted expression of Kcnk9 during neurogenesis Mus musculus mm10 chr15 72290000 72290650 Ctcf Kcnk9 Enhancer Silenced Normal Brain UBERON:0000955 Embryonic Stem Cells (ESCs) embryonic stem cell CL:0002322 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ChIP-seq, RNA-seq CRISPR Knockout, ChIP-qPCR, RT-qPCR, Western blot, Region Capture Hi-C 2017 29272704 AP-1 transcription factors and the SWI/SNF complex mediate signal-dependent enhancer selection Mus musculus mm10 chr17 45790442 45800636 Fos Vegfa Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic fibroblasts (MEFs) CVCL_0003 mouse embryonic fibroblast CL:0000057 Enhancer activity assay, Signal-dependent regulation study ChIP-seq, ATAC-seq, RNA-seq Co-IP, Western blot, CRISPR knock-in 2013 23321477 Hypoxic adaptation engages the CBP/CREST-induced coactivator complex of Creb-HIF-1?|?? in transactivating murine neuroblastic glucose transporter Mus musculus mm10 chr11 119715961 119716245 Hif1A Slc2A3 Enhancer Active Normal Brain UBERON:0000955 Neuro-2a (N2A) cells CVCL_0470 neuroblastoma cell CL:0000031 Enhancer activity assay Luciferase reporter assay, ChIP-qPCR, EMSA 2019 31422875 Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs Mus musculus mm10 chr3 34752523 34766449 Pou5F1; Nanog Sox2 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells (129¡ÁCast F1; v6.5) CVCL_2167 mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, WGBS, ATAC-seq Transgenic Reporter Assay, CRISPR Knockout, ChIP-qPCR, RT-qPCR, DNA FISH, Immunofluorescence, Confocal Imaging 2019 31422875 Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs Mus musculus mm10 chr3 34752523 34766449 Pou5F1; Nanog Sox2 Enhancer Active Normal Embryo UBERON:0000922 v6.5) mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, WGBS, ATAC-seq Transgenic Reporter Assay, CRISPR Knockout, ChIP-qPCR, RT-qPCR, DNA FISH, Immunofluorescence, Confocal Imaging 2021 33930308 Distinct Foxp3 enhancer elements coordinate development, maintenance, and function of regulatory T cells Mus musculus mm10 chrX 76054800 76055800 Stat5 Foxp3 Enhancer Active Normal Thymus UBERON:0002370 Primary CD4+ T cells CD4-positive regulatory T cell CL:0000815 Functional perturbation assay, Chromatin interaction assay, TF binding assay HiChIP, ChIP-seq, ATAC-seq CRISPR Knockout, CRISPRi, ChIP-qPCR 2021 33930308 Distinct Foxp3 enhancer elements coordinate development, maintenance, and function of regulatory T cells Mus musculus mm10 chrX 76054800 76055800 Stat5 Foxp3 Enhancer Active Normal Thymus UBERON:0002370 thymocytes thymocyte CL:0000893 Functional perturbation assay, Chromatin interaction assay, TF binding assay HiChIP, ChIP-seq, ATAC-seq CRISPR Knockout, CRISPRi, ChIP-qPCR 2021 33930308 Distinct Foxp3 enhancer elements coordinate development, maintenance, and function of regulatory T cells Mus musculus mm10 chrX 76071800 76072800 C-Rel Foxp3 Enhancer Active Normal Thymus UBERON:0002370 Primary CD4+ T cells CD4-positive regulatory T cell CL:0000815 Functional perturbation assay, Chromatin interaction assay, TF binding assay HiChIP, ChIP-seq, ATAC-seq CRISPR Knockout, CRISPRi, ChIP-qPCR 2021 33930308 Distinct Foxp3 enhancer elements coordinate development, maintenance, and function of regulatory T cells Mus musculus mm10 chrX 76071800 76072800 C-Rel Foxp3 Enhancer Active Normal Thymus UBERON:0002370 thymocytes thymocyte CL:0000893 Functional perturbation assay, Chromatin interaction assay, TF binding assay HiChIP, ChIP-seq, ATAC-seq CRISPR Knockout, CRISPRi, ChIP-qPCR 2018 29930091 Coactivator condensation at super-enhancers links phase separation and gene control Mus musculus mm10 chr6 122620000 122660000 Nanog Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells CVCL_2167 mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay ChIP-seq, ATAC-seq Luciferase Reporter Assay, RT-qPCR 2023 36717694 Enhancer-promoter interactions can bypass CTCF-mediated boundaries and contribute to phenotypic robustness Mus musculus mm10 chr3 34824938 34837938 Oct4,Sox2,Nanog Sox2 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells CVCL_2167 mouse embryonic stem cell CL:0002322 CRISPR deletion functional assay Capture Hi-C, ChIP-seq, CUT&RUN RT-qPCR, Immunofluorescence staining 2025 40966339 Functional maps of a genomic locus reveal confinement of an enhancer by its target gene Mus musculus mm10 chr3 34824938 34837938 Oct4,Sox2,Nanog Sox2 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells CVCL_2167 mouse embryonic stem cell CL:0002322 CRISPR deletion functional assay ATAC-seq, ChIP-seq, Micro-C, transposon integration mapping RT-qPCR, flow cytometry 2018 29141987 BRACHYURY directs histone acetylation to target loci during mesoderm development Mus musculus mm10 chr17 86425000 86432000 Tbxt Tbxt Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 CRISPR knockout enhancer assay ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2018 29141987 BRACHYURY directs histone acetylation to target loci during mesoderm development Mus musculus mm10 chr2 27480000 27480400 Tbxt Lmo2 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 CRISPR enhancer knockout assay ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 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 113005000 113005100 Igh Enhancer Active Normal Lymph node UBERON:0000029 Primary resting B lymphocytes resting B cell CL:0000945 Functional perturbation assay, Chromatin topology assay ATAC-seq CRISPR Knockout, CRISPRi, RT-qPCR, FISH 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 113010000 113010100 Igh Enhancer Active Normal Lymph node UBERON:0000029 Primary resting B lymphocytes resting B cell CL:0000945 Functional perturbation assay, Chromatin topology assay ATAC-seq CRISPR Knockout, CRISPRi, RT-qPCR, FISH 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 113015000 113015100 Igh Enhancer Active Normal Lymph node UBERON:0000029 Primary resting B lymphocytes resting B cell CL:0000945 Functional perturbation assay, Chromatin topology assay ATAC-seq CRISPR Knockout, CRISPRi, RT-qPCR, FISH 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 113019000 113019100 Igh Enhancer Active Normal Lymph node UBERON:0000029 Primary resting B lymphocytes resting B cell CL:0000945 Functional perturbation assay, Chromatin topology assay ATAC-seq CRISPR Knockout, CRISPRi, RT-qPCR, FISH 2021 33334884 Genome editing demonstrates that the -5 kb Nanog enhancer regulates Nanog expression by modulating RNAPII initiation and/or recruitment Mus musculus mm10 chr6 122655000 122657500 Nanog Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Functional perturbation assay CRISPR Knockout, RT-qPCR 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 Pax5 Enhancer Active Normal Bone marrow UBERON:0002371 Primary B cell progenitors pro-B cell CL:0000945 Enhancer activity assay, TF binding assay Transgenic Reporter Assay, Luciferase Reporter Assay 2018 30349647 3'Igh enhancers hs3b/hs4 are dispensable for Myc deregulation in mouse plasmacytomas with T(12;15) translocations Mus musculus mm10 chr12 113005000 113005100 Myc Enhancer Active Disease plasmacytoma MONDO:0005086 DOID:1324 Lymph node UBERON:0000029 Primary plasmacytoma cells plasma cell CL:0000786 Functional perturbation assay, Tumorigenesis assay RNA-seq qRT-PCR, and ChIP-qPCR 2018 30349647 3'Igh enhancers hs3b/hs4 are dispensable for Myc deregulation in mouse plasmacytomas with T(12;15) translocations Mus musculus mm10 chr12 113005000 113005100 Myc Enhancer Active Disease plasmacytoma MONDO:0005086 DOID:1324 Lymph node UBERON:0000029 plasma cells plasma cell CL:0000786 Functional perturbation assay, Tumorigenesis assay RNA-seq qRT-PCR, and ChIP-qPCR 2018 30349647 3'Igh enhancers hs3b/hs4 are dispensable for Myc deregulation in mouse plasmacytomas with T(12;15) translocations Mus musculus mm10 chr12 113010000 113010100 Myc Enhancer Active Disease plasmacytoma MONDO:0005086 DOID:1324 Lymph node UBERON:0000029 Primary plasmacytoma cells plasma cell CL:0000786 Functional perturbation assay, Tumorigenesis assay RNA-seq qRT-PCR, and ChIP-qPCR 2018 30349647 3'Igh enhancers hs3b/hs4 are dispensable for Myc deregulation in mouse plasmacytomas with T(12;15) translocations Mus musculus mm10 chr12 113010000 113010100 Myc Enhancer Active Disease plasmacytoma MONDO:0005086 DOID:1324 Lymph node UBERON:0000029 plasma cells plasma cell CL:0000786 Functional perturbation assay, Tumorigenesis assay RNA-seq qRT-PCR, and ChIP-qPCR 2018 30349647 3'Igh enhancers hs3b/hs4 are dispensable for Myc deregulation in mouse plasmacytomas with T(12;15) translocations Mus musculus mm10 chr12 113015000 113015100 Myc Enhancer Active Disease plasmacytoma MONDO:0005086 DOID:1324 Lymph node UBERON:0000029 Primary plasmacytoma cells plasma cell CL:0000786 Functional perturbation assay, Tumorigenesis assay RNA-seq qRT-PCR, and ChIP-qPCR 2018 30349647 3'Igh enhancers hs3b/hs4 are dispensable for Myc deregulation in mouse plasmacytomas with T(12;15) translocations Mus musculus mm10 chr12 113015000 113015100 Myc Enhancer Active Disease plasmacytoma MONDO:0005086 DOID:1324 Lymph node UBERON:0000029 plasma cells plasma cell CL:0000786 Functional perturbation assay, Tumorigenesis assay RNA-seq qRT-PCR, and ChIP-qPCR 2018 30349647 3'Igh enhancers hs3b/hs4 are dispensable for Myc deregulation in mouse plasmacytomas with T(12;15) translocations Mus musculus mm10 chr12 113019000 113019100 Myc Enhancer Active Disease plasmacytoma MONDO:0005086 DOID:1324 Lymph node UBERON:0000029 Primary plasmacytoma cells plasma cell CL:0000786 Functional perturbation assay, Tumorigenesis assay RNA-seq qRT-PCR, and ChIP-qPCR 2018 30349647 3'Igh enhancers hs3b/hs4 are dispensable for Myc deregulation in mouse plasmacytomas with T(12;15) translocations Mus musculus mm10 chr12 113019000 113019100 Myc Enhancer Active Disease plasmacytoma MONDO:0005086 DOID:1324 Lymph node UBERON:0000029 plasma cells plasma cell CL:0000786 Functional perturbation assay, Tumorigenesis assay RNA-seq qRT-PCR, and ChIP-qPCR 2023 37858706 YY1 Binding to Regulatory Elements That Lack Enhancer Activity Promotes Locus Folding and Gene Activation Mus musculus mm10 chr16 19007329 19008187 E2A Igkv1-110 Enhancer Active Normal Lymph node UBERON:0000029 103/BCL-2 pre-B cells pre-B cell CL:0000945 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-qPCR 2025 40456823 Divergent combinations of enhancers encode spatial gene expression Mus musculus mm10 chr6 64732005 64901125 Atoh1 Enhancer Active Normal Spinal cord UBERON:0002240 Neurons neuron CL:0000540 Enhancer activity assay, Functional perturbation assay ATAC-seq, RNA-seq Transgenic Reporter Assay, CRISPR Knockout, qRT-PCR, FISH 2019 31387996 TonEBP/NFAT5 promotes obesity and insulin resistance by epigenetic suppression of white adipose tissue beiging Mus musculus mm10 chr8 115656318 115662318 Adrb3 Enhancer Silenced Normal Adipose tissue UBERON:0001013 3T3-L1 Adipocytes CVCL_0123 adipocyte CL:0000136 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, qRT-PCR, Western blot, EMSA, Bisulfite Sequencing, Co-Immunoprecipitation 2017 28575180 MyoD- and FoxO3-mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation Mus musculus mm10 chr1 136170803 136192554 Myod1; Foxo3 Myog Enhancer Active Normal Skeletal muscle UBERON:0001134 C2C12 myoblast cell line CVCL_0188 myoblast CL:0000187 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, RNA-seq, 3C-seq Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, 3C-RT-qPCR, RT-RT-qPCR, Co-IP, DNA pulldown, Western blot 2017 28749941 Krox20 hindbrain regulation incorporates multiple modes of cooperation between cis-acting elements Mus musculus mm10 chr10 72782000 72783500 Egr2 Egr2 Enhancer Active Normal Brain UBERON:0000955 Primary mouse embryonic hindbrain cells embryonic hindbrain neuron CL:0000540 Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq CRISPR Knockout, Luciferase Reporter Assay, 3C, RT-RT-qPCR 2017 28749941 Krox20 hindbrain regulation incorporates multiple modes of cooperation between cis-acting elements Mus musculus mm10 chr10 72855000 72856500 Hoxa1 Egr2 Enhancer Active Normal Brain UBERON:0000955 Primary mouse embryonic hindbrain cells embryonic hindbrain neuron CL:0000540 Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq CRISPR Knockout, Luciferase Reporter Assay, 3C, RT-RT-qPCR 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 Skeletal muscle UBERON:0001134 Mouse myoblast/myotube cell CVCL_0188 myoblast/myotube CL:0000187 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq, 3C-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, RT-RT-qPCR, 3C-PCR 2017 28575289 MyoD- and FoxO3-mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation Mus musculus mm10 chr1 136170803 136192554 Myod1 Myog SE Active Normal Skeletal muscle UBERON:0001134 Mouse myoblast/myotube cell CVCL_0188 myoblast/myotube CL:0000187 Enhancer activity assay ChIP-seq, RNA-seq, 3C-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, RT-RT-qPCR, Western blot, Immunofluorescence Staining 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 Skeletal muscle UBERON:0001134 Mouse myoblast/myotube cell CVCL_0188 myoblast/myotube CL:0000187 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, 3C-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, RT-RT-qPCR, 3C-PCR 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 Skeletal muscle UBERON:0001134 Mouse myoblast/myotube cell CVCL_0188 myoblast/myotube CL:0000187 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, 3C-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, RT-RT-qPCR, 3C-PCR, DNA Pulldown Assay, Immunoprecipitation 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 Skeletal muscle UBERON:0001134 Mouse myoblast/myotube cell CVCL_0188 myoblast/myotube CL:0000187 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, 3C-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, RT-RT-qPCR, 3C-PCR 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 Skeletal muscle UBERON:0001134 Mouse myoblast/myotube cell CVCL_0188 myoblast/myotube CL:0000187 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, 3C-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, RT-RT-qPCR, 3C-PCR 2015 26595656 Stimulus-specific combinatorial functionality of neuronal c-fos enhancers Mus musculus mm10 chr12 85460146 85464510 Creb1 Fos Enhancer Active Normal Cerebral Cortex UBERON:0000956 Primary mouse cortical neurons cortical neuron CL:0000540 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPRi, 3C, RT-RT-qPCR, ChIP-RT-qPCR 2015 26595656 Stimulus-specific combinatorial functionality of neuronal c-fos enhancers Mus musculus mm10 chr12 85486555 85490135 Creb1 Fos Enhancer Active Normal Cerebral Cortex UBERON:0000956 Primary mouse cortical neurons cortical neuron CL:0000540 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPRi, 3C, RT-RT-qPCR, ChIP-RT-qPCR 2015 26595656 Stimulus-specific combinatorial functionality of neuronal c-fos enhancers Mus musculus mm10 chr12 85505903 85509655 Creb1 Fos Enhancer Active Normal Cerebral Cortex UBERON:0000956 Primary mouse cortical neurons cortical neuron CL:0000540 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPRi, 3C, RT-RT-qPCR, ChIP-RT-qPCR 2021 33473108 SOX-5 activates a novel ROR?|??t enhancer to facilitate experimental autoimmune encephalomyelitis by promoting Th17 cell differentiation Mus musculus mm10 chr3 94170946 94172113 Sox5 Rorc Enhancer Active Disease experimental autoimmune encephalomyelitis MONDO:0005257 DOID:3310 Spleen UBERON:0002106 CD4+ Th17 cells CD4-positive Th17 cell CL:0000899 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, 3C-RT-qPCR, ChIP-loop assay, CRISPR Knockout, RT-RT-qPCR, ELISA, Flow Cytometry 2021 33473108 SOX-5 activates a novel ROR?|??t enhancer to facilitate experimental autoimmune encephalomyelitis by promoting Th17 cell differentiation Mus musculus mm10 chr3 94170946 94172113 Sox5 Rorc Enhancer Active Disease experimental autoimmune encephalomyelitis MONDO:0005257 DOID:3310 Spleen UBERON:0002106 Naive CD4+ T cells naive CD4-positive T cell CL:0000896 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR knockout, ChIP-RT-qPCR, 3C-RT-qPCR, ChIP-loop assay, RT-RT-qPCR, Western blot, Co-IP, Flow cytometry, ELISA 2015 26538132 Stimulus-specific combinatorial functionality of neuronal c-fos enhancers Mus musculus mm10 chr12 85425800 85426300 Creb1 Fos Enhancer Active Normal Brain UBERON:0000955 Cortical neurons cortical neuron CL:0000540 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, RNA-seq Luciferase Reporter Assay, 3C, ChIP-RT-qPCR, CRISPRi 2020 32701507 ERG orchestrates chromatin interactions to drive prostate cell fate reprogramming Mus musculus mm10 chr16 25400000 25900000 Trp63 SE Silenced Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 Mouse Prostate Epithelial Organoids mouse prostate epithelial organoid cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, ATAC-seq CRISPR Knockout, qRT-PCR, Western blot, Immunofluorescence 2019 31636200 Long-range Pitx2c enhancer-promoter interactions prevent predisposition to atrial fibrillation Mus musculus mm10 chr3 128750000 128770000 Ctcf Pitx2C Enhancer Active Disease atrial fibrillation MONDO:0004978 DOID:0060224 Heart UBERON:0000948 Left Atrial Cardiomyocytes atrial cardiomyocyte CL:0000746 Functional perturbation assay, Chromatin interaction assay, Enhancer activity assay 4C-seq, ChIP-seq, ATAC-seq, RNA-seq CRISPR Knockout, RT-RT-qPCR, Programmed Intracardiac Pacing 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 Heart UBERON:0000948 Mouse cardiomyocyte cell cardiomyocyte CL:0000746 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq, ATAC-seq CRISPR knockout, RT-RT-qPCR, Luciferase Reporter Assay, Western blot 2019 31666509 An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo Mus musculus mm10 chr9 119377827 119389749 Tbx3 Scn5A Enhancer Active Normal Heart UBERON:0000948 Cardiomyocytes cardiomyocyte CL:0000746 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, ATAC-seq, 4C-seq Transgenic Reporter Assay, CRISPR Knockout, RT-RT-qPCR, Western blot, in vivo electrophysiology 2015 26595767 Stimulus-specific combinatorial functionality of neuronal c-fos enhancers Mus musculus mm10 chr12 85454000 85457752 Creb1 Fos Enhancer Active Normal Brain UBERON:0000955 Primary mouse cortical neurons cortical neuron CL:0000540 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPRi, 3C, RT-RT-qPCR 2024 38855864 Chromatin profiling identifies chondrocyte-specific Sox9 enhancers important for skeletal development Mus musculus mm10 chr11 112334364 112335294 Pitx1 Sox9 Enhancer Active Normal Cartilage UBERON:0002418 Primary Mouse Chondrocytes chondrocyte CL:0000138 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, Alcian Blue Staining, DNA Pull-Down Assay 2024 38855864 Chromatin profiling identifies chondrocyte-specific Sox9 enhancers important for skeletal development Mus musculus mm10 chr11 112334364 112335294 Pitx1 Sox9 Enhancer Active Normal Limb bud UBERON:0005417 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, Alcian Blue Staining, DNA Pull-Down Assay 2024 38855864 Chromatin profiling identifies chondrocyte-specific Sox9 enhancers important for skeletal development Mus musculus mm10 chr11 112334364 112335294 Pitx1 Sox9 Enhancer Active Normal Cartilage UBERON:0002418 ATDC5 CVCL_3894 chondrogenic cell CL:0000138 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, Alcian Blue Staining, DNA Pull-Down Assay 2024 38855864 Chromatin profiling identifies chondrocyte-specific Sox9 enhancers important for skeletal development Mus musculus mm10 chr11 112334364 112335294 Pitx1 Sox9 Enhancer Active Normal Cartilage UBERON:0002418 C3H10T1/2 CVCL_0190 mesenchymal stem cell CL:0000134 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, Alcian Blue Staining, DNA Pull-Down Assay 2024 38855864 Chromatin profiling identifies chondrocyte-specific Sox9 enhancers important for skeletal development Mus musculus mm10 chr11 112482190 112483273 Pitx1 Sox9 Enhancer Active Normal Cartilage UBERON:0002418 Primary Mouse Chondrocytes chondrocyte CL:0000138 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, Alcian Blue Staining, DNA Pull-Down Assay 2024 38855864 Chromatin profiling identifies chondrocyte-specific Sox9 enhancers important for skeletal development Mus musculus mm10 chr11 112482190 112483273 Pitx1 Sox9 Enhancer Active Normal Limb bud UBERON:0005417 HEK293 CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, Alcian Blue Staining, DNA Pull-Down Assay 2024 38855864 Chromatin profiling identifies chondrocyte-specific Sox9 enhancers important for skeletal development Mus musculus mm10 chr11 112482190 112483273 Pitx1 Sox9 Enhancer Active Normal Cartilage UBERON:0002418 ATDC5 CVCL_3894 chondrogenic cell CL:0000138 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, Alcian Blue Staining, DNA Pull-Down Assay 2024 38855864 Chromatin profiling identifies chondrocyte-specific Sox9 enhancers important for skeletal development Mus musculus mm10 chr11 112482190 112483273 Pitx1 Sox9 Enhancer Active Normal Cartilage UBERON:0002418 C3H10T1/2 CVCL_0190 mesenchymal stem cell CL:0000134 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, Alcian Blue Staining, DNA Pull-Down Assay 2021 34183853 Orphan CpG islands amplify poised enhancer regulatory activity and determine target gene responsiveness Mus musculus mm10 chr8 12428828 12432474 Enhancer Silenced Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay ChIP-seq, RNA-seq, 4C-seq CRISPR Knockout, CRISPR Knock-in, RT-RT-qPCR, ChIP-RT-qPCR, Bisulfite Sequencing, Immunofluorescence 2017 28520978 LDB1-mediated enhancer looping can be established independent of mediator and cohesin Mus musculus mm10 chr7 103816000 103817000 Gata1 Hbb-B1 Enhancer Active Normal Fetal liver UBERON:0002107 MEL (mouse erythroleukemia) cell line CVCL_2109 erythroid progenitor cell CL:0000038 Chromatin interaction assay, Functional perturbation assay ChIP-seq, Hi-C, RNA-seq 3C, ChIP-RT-qPCR, CRISPR Knockout, RT-RT-qPCR, Western blot 2017 28575180 MyoD- and FoxO3-mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation Mus musculus mm10 chr1 136178700 136179145 Myod1 Myog Enhancer Silenced Normal Skeletal muscle UBERON:0001134 C2C12 myoblast cell line CVCL_0188 myoblast CL:0000187 Functional perturbation assay ChIP-seq CRISPR Knockout, Luciferase Reporter Assay, RT-RT-qPCR 2020 32293525 Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection Mus musculus mm10 chr18 37169500 37170500 Ctcf Pcdha Enhancer Active Normal Cerebral cortex UBERON:0000956 Cortical neurons cortical neuron CL:0000540 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, 5C, QHR-4C, Single-cell RNA-seq CRISPR Knockout, CRISPR Inversion, dCas9 Blocking 2020 32293525 Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection Mus musculus mm10 chr18 37169500 37170500 Ctcf Pcdha Enhancer Active Normal Endometrium UBERON:0001295 HEC-1-B cells CVCL_0294 endometrial carcinoma cell CL:0000069 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, 5C, QHR-4C, Single-cell RNA-seq CRISPR Knockout, CRISPR Inversion, dCas9 Blocking 2020 32293525 Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection Mus musculus mm10 chr18 37172000 37173000 Pcdha Enhancer Active Normal Cerebral cortex UBERON:0000956 Cortical neurons cortical neuron CL:0000540 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, 5C, QHR-4C CRISPR Knockout, CRISPR Inversion 2020 32293525 Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection Mus musculus mm10 chr18 37172000 37173000 Pcdhb Enhancer Active Normal Endometrium UBERON:0001295 HEC-1-B cells CVCL_0294 endometrial carcinoma cell CL:0000069 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, 5C, QHR-4C CRISPR Knockout, CRISPR Inversion 2020 32293525 Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection Mus musculus mm10 chr18 37000000 37100000 Ctcf Pcdhb Enhancer Active Normal Cerebral cortex UBERON:0000956 Cortical neurons CVCL_0470 cortical neuron CL:0000540 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, 5C, QHR-4C CRISPR Knockout, dCas9 Blocking 2020 32293525 Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection Mus musculus mm10 chr18 37000000 37100000 Ctcf Pcdhg Enhancer Active Normal Brain UBERON:0000955 Neuro-2A cells CVCL_0470 neuroblastoma cell CL:0000031 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, 5C, QHR-4C CRISPR Knockout, dCas9 Blocking 2015 25486255 CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells Mus musculus mm10 chr3 3464735 3477735 Pou5F1; Sox2; Nanog Sox2 SE Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Functional perturbation assay, Chromatin interaction assay ChIP-seq, RNA-seq, Hi-C CRISPR Knockout, qRT-PCR, Western blot 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 Heart UBERON:0000948 Mouse cardiomyocyte cell cardiomyocyte CL:0000746 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR, Western blot 2015 26595656 Stimulus-specific combinatorial functionality of neuronal c-fos enhancers Mus musculus mm10 chr12 85471268 85473533 Mef2 Fos Enhancer Active Normal Cerebral Cortex UBERON:0000956 Primary mouse cortical neurons cortical neuron CL:0000540 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPRi, RT-RT-qPCR, ChIP-RT-qPCR 2025 39863595 The ?|??-globin super-enhancer acts in an orientation-dependent manner Mus musculus mm10 chr11 32144500 32150000 Gata1 Hba-A1 Enhancer Active Normal Fetal Liver UBERON:0002107 Erythroid cells erythroid cell CL:0000038 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ATAC-seq, ChIP-seq, 3C-seq CRISPR Knockout, RT-RT-qPCR 2025 39863595 The ?|??-globin super-enhancer acts in an orientation-dependent manner Mus musculus mm10 chr11 32145000 32145500 Gata1 Hba-A1 Enhancer Active Normal Fetal Liver UBERON:0002107 Erythroid cells erythroid cell CL:0000038 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ATAC-seq, ChIP-seq, 3C-seq CRISPR Knockout, RT-RT-qPCR 2025 39863595 The ?|??-globin super-enhancer acts in an orientation-dependent manner Mus musculus mm10 chr11 32146000 32146500 Gata1 Hba-A1 Enhancer Active Normal Fetal Liver UBERON:0002107 Erythroid cells erythroid cell CL:0000038 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ATAC-seq, ChIP-seq, 3C-seq CRISPR Knockout, RT-RT-qPCR 2025 39863595 The ?|??-globin super-enhancer acts in an orientation-dependent manner Mus musculus mm10 chr11 32147000 32147500 Gata1 Hba-A1 Enhancer Active Normal Fetal Liver UBERON:0002107 Erythroid cells erythroid cell CL:0000038 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ATAC-seq, ChIP-seq, 3C-seq CRISPR Knockout, RT-RT-qPCR 2025 39863595 The ?|??-globin super-enhancer acts in an orientation-dependent manner Mus musculus mm10 chr11 32148000 32148500 Gata1 Hba-A1 Enhancer Active Normal Fetal Liver UBERON:0002107 Erythroid cells erythroid cell CL:0000038 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ATAC-seq, ChIP-seq, 3C-seq CRISPR Knockout, RT-RT-qPCR 2025 39863595 The ?|??-globin super-enhancer acts in an orientation-dependent manner Mus musculus mm10 chr11 32149000 32149500 Gata1 Hba-A1 Enhancer Active Normal Fetal Liver UBERON:0002107 Erythroid cells erythroid cell CL:0000038 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ATAC-seq, ChIP-seq, 3C-seq CRISPR Knockout, RT-RT-qPCR 2013 24285714 Role of SWI/SNF in acute leukemia maintenance and enhancer-mediated Myc regulation Mus musculus mm10 chr15 97300000 97400000 Myc Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 RN2 AML cell line CVCL_WT32 acute myeloid leukemia cell CL:0001054 Enhancer activity assay, Chromatin interaction assay ChIP-seq, RNA-seq Luciferase reporter assay, ChIP-RT-qPCR, 3C-RT-qPCR 2020 32991700 NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure brown and beige adipocyte differentiation Mus musculus mm10 chr3 3103577 3104077 Nfia Pparg Enhancer Active Normal Skeletal muscle UBERON:0001134 C2C12 myoblast CVCL_0188 myoblast CL:0000187 Enhancer activity assay, TF binding assay, Functional perturbation assay FAIRE-seq, ChIP-seq, RNA-seq ChIP-RT-qPCR, FAIRE-RT-qPCR, CRISPRi, Luciferase Reporter Assay, RT-RT-qPCR, Oil-Red-O Staining 2020 32991700 NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure brown and beige adipocyte differentiation Mus musculus mm10 chr3 3103577 3104077 Nfia Pparg Enhancer Active Normal Adipose tissue UBERON:0001013 3T3-F442A preadipocyte CVCL_5246 preadipocyte CL:0000136 Enhancer activity assay, TF binding assay, Functional perturbation assay FAIRE-seq, ChIP-seq, RNA-seq ChIP-RT-qPCR, FAIRE-RT-qPCR, CRISPRi, Luciferase Reporter Assay, RT-RT-qPCR, Oil-Red-O Staining 2017 28575180 MyoD- and FoxO3-mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation Mus musculus mm10 chr1 136185800 136186245 Myod1; Foxo3 Myog Enhancer Active Normal Skeletal muscle UBERON:0001134 C2C12 myoblast cell line CVCL_0188 myoblast CL:0000187 Chromatin interaction assay, TF binding assay ChIP-seq, 3C-seq 3C-RT-qPCR, ChIP-RT-qPCR, Luciferase Reporter Assay, DNA pulldown, Co-IP 2018 29342133 A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies Mus musculus mm10 chr15 63442671 63443111 Spi1 Myc Enhancer Silenced Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 LSK Cells hematopoietic stem cell CL:0001029 Functional perturbation assay ChIP-seq, ATAC-seq CRISPR Knockout, RT-RT-qPCR 2018 29342133 A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies Mus musculus mm10 chr15 63479681 63480222 Runx1 Myc Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 LT-HSCs long-term hematopoietic stem cell CL:0001029 Functional perturbation assay ChIP-seq, RNA-seq CRISPR Knockout, RT-RT-qPCR 2025 39626660 Long-range regulation of transcription scales with genomic distance in a gene-specific manner Mus musculus mm10 chr5 98680000 98682000 Fgf5 Enhancer Active Normal Embryo UBERON:0000922 EpiLCs epiblast-like cell CL:0002322 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPRa, RT-RT-qPCR 2025 39626660 Long-range regulation of transcription scales with genomic distance in a gene-specific manner Mus musculus mm10 chr5 98660000 98662000 Fgf5 Enhancer Active Normal Embryo UBERON:0000922 EpiLCs epiblast-like cell CL:0002322 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq, ATAC-seq CRISPRa, RT-RT-qPCR 2020 32499651 A distal enhancer at risk locus 11q135 promotes suppression of colitis by Treg cells Mus musculus mm10 chr7 105711382 105713753 Stat5 Lrrc32 Enhancer Active Disease colitis MONDO:0005075 DOID:0060180 Colon UBERON:0001155 Primary Treg cells regulatory T cell CL:0000815 Functional perturbation assay, Enhancer activity assay, TF binding assay RNA-seq, ChIP-seq, ATAC-seq CRISPR Knockout, ChIP-RT-qPCR, qRT-PCR, Flow Cytometry 2021 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 Heart UBERON:0000948 Not available cardiomyocyte CL:0000746 Enhancer activity assay, Functional perturbation assay ATAC-seq, RNA-seq, ChIP-seq Transgenic Reporter Assay, CRISPR knockout, X-gal Staining 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 Bone Marrow UBERON:0002371 Bone marrow-derived macrophages macrophage CL:0000235 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, RNA-seq, GRO-seq, 3C-seq ChIP-RT-qPCR, RT-RT-qPCR, Luciferase Reporter Assay, 3C-RT-RT-qPCR 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 Bone Marrow UBERON:0002371 Bone marrow-derived macrophages macrophage CL:0000235 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, GRO-seq, 3C-seq ChIP-RT-qPCR, RT-RT-qPCR, Luciferase Reporter Assay, 3C-RT-RT-qPCR, ELISA, CAM Assay 2020 32251373 Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction Mus musculus mm10 chr12 114462800 114464200 Ighm,Ighg1 Enhancer Active Normal Spleen UBERON:0002106 Primary mature B cells (activated with LPS + IL-4) activated B cell CL:0000945 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, GRO-seq, ATAC-seq, 3C-seq 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR, CRISPRa 2020 32251373 Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction Mus musculus mm10 chr12 114465285 114467786 Ighm,Ighg1 Enhancer Active Normal Spleen UBERON:0002106 Primary mature B cells (activated with LPS + IL-4) activated B cell CL:0000945 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, GRO-seq, ATAC-seq, 3C-seq 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR, CRISPRa 2020 32251373 Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction Mus musculus mm10 chr12 114479200 114480600 Ighm,Ighg1 Enhancer Active Normal Spleen UBERON:0002106 Primary mature B cells (activated with LPS + IL-4) activated B cell CL:0000945 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, GRO-seq, ATAC-seq, 3C-seq 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR, CRISPRa 2020 32251373 Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction Mus musculus mm10 chr12 114481431 114482631 Ighm,Ighg1 Enhancer Active Normal Spleen UBERON:0002106 Primary mature B cells (activated with LPS + IL-4) activated B cell CL:0000945 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, GRO-seq, ATAC-seq, 3C-seq 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR, CRISPRa 2020 32251373 Spt5-mediated enhancer transcription directly couples enhancer activation with physical promoter interaction Mus musculus mm10 chr12 114461575 114496377 Ighm,Ighg3,Igha Enhancer Active Normal Spleen UBERON:0002106 Primary mature B cells (activated with LPS + IL-4) activated B cell CL:0000945 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, GRO-seq, ATAC-seq, Hi-C, 3C-seq 3C-RT-qPCR, ChIP-RT-qPCR, RT-RT-qPCR, CRISPRa, Flow cytometry 2015 26595767 Stimulus-specific combinatorial functionality of neuronal c-fos enhancers Mus musculus mm10 chr12 85488233 85490498 Mef2A Fos Enhancer Active Normal Brain UBERON:0000955 Primary mouse cortical neurons cortical neuron CL:0000540 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPRi, RT-RT-qPCR 2020 32701507 ERG orchestrates chromatin interactions to drive prostate cell fate reprogramming Mus musculus mm10 chr15 102000000 102800000 Krt8 SE Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 Mouse Prostate Epithelial Organoids mouse prostate epithelial organoid cell CL:0000066 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, ATAC-seq shRNA Knockdown, qRT-PCR, Western blot, Immunofluorescence 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; Creb5; Ets1; Tgif1; Smad3 Nfatc1 Enhancer Active Disease proliferative vitreoretinopathy MONDO:0006007 DOID:0080067 Retina UBERON:0000966 Primary retinal pigment epithelium (RPE) cells retinal pigment epithelial cell CL:0002586 Enhancer activity assay, TF binding assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot, CRISPRi (shRNA), Immunofluorescence 2018 29903884 Sex reversal following deletion of a single far upstream enhancer of Sox9 Mus musculus mm10 chr11 10954273 10955559 Sox9 Enhancer Active Disease sex reversal MONDO:0008637 DOID:14450 Testis UBERON:0000473 Sertoli cells 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 2012 22264824 Intragenic enhancers act as alternative promoters Mus musculus mm10 chr11 32154500 32155500 Gata1 Hba-A1 Enhancer Active Normal Fetal Liver UBERON:0002107 Primary erythroid cells erythroid cell CL:0000038 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay ChIP-seq, RNA-seq, DNase-seq CRISPR Knockout, RT-PCR, qRT-PCR, Northern Blot, RNA-FISH, Western blot 2012 22264824 Intragenic enhancers act as alternative promoters Mus musculus mm10 chr11 32156045 32157045 Gata1 Hba-A1 Enhancer Active Normal Fetal Liver UBERON:0002107 Primary erythroid cells erythroid cell CL:0000038 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay ChIP-seq, RNA-seq, DNase-seq CRISPR Knockout, RT-PCR, qRT-PCR, Northern Blot, RNA-FISH, Western blot 2012 22264824 Intragenic enhancers act as alternative promoters Mus musculus mm10 chr11 32158500 32159500 Gata1 Hba-A1 Enhancer Active Normal Fetal Liver UBERON:0002107 Primary erythroid cells erythroid cell CL:0000038 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay ChIP-seq, RNA-seq, DNase-seq CRISPR Knockout, RT-PCR, qRT-PCR, Northern Blot, RNA-FISH, Western blot 2012 22264824 Intragenic enhancers act as alternative promoters Mus musculus mm10 chr11 32160500 32161500 Gata1 Hba-A1 Enhancer Active Normal Fetal Liver UBERON:0002107 Primary erythroid cells erythroid cell CL:0000038 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay ChIP-seq, RNA-seq, DNase-seq CRISPR Knockout, RT-PCR, qRT-PCR, Northern Blot, RNA-FISH, Western blot 2012 22264824 Intragenic enhancers act as alternative promoters Mus musculus mm10 chr11 32163000 32164000 Gata1 Hba-A1 Enhancer Active Normal Fetal Liver UBERON:0002107 Primary erythroid cells erythroid cell CL:0000038 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay ChIP-seq, RNA-seq, DNase-seq CRISPR Knockout, RT-PCR, qRT-PCR, Northern Blot, RNA-FISH, Western blot 2016 26446995 An autoregulatory enhancer controls mammary-specific STAT5 functions Mus musculus mm10 chr11 9746900 9747200 Stat5A Stat5A Enhancer Active Normal Mammary gland UBERON:0001911 Primary MECs mammary epithelial cell CL:0000066 Functional perturbation assay ChIP-seq, RNA-seq CRISPR Knockout, RT-RT-qPCR 2016 27166834 Long-range enhancers modulate Foxf1 transcription in blood vessels of pulmonary vascular network Mus musculus mm10 chr8 123400044 123400756 Gata Foxf1 Enhancer Active Disease pulmonary vascular disease MONDO:0005022 DOID:1307 Lung UBERON:0002048 Embryonic lung cells embryonic lung cell CL:0000000 Chromatin interaction assay ChIP-seq 3C-seq, Luciferase Reporter Assay 2016 27166834 Long-range enhancers modulate Foxf1 transcription in blood vessels of pulmonary vascular network Mus musculus mm10 chr8 123406634 123407310 Gli1 Foxf1 Enhancer Active Disease pulmonary vascular disease MONDO:0005022 DOID:1307 Lung UBERON:0002048 Embryonic lung cells embryonic lung cell CL:0000000 Chromatin interaction assay ChIP-seq 3C-seq, Luciferase Reporter Assay, RT-RT-qPCR 2018 29342133 A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies Mus musculus mm10 chr15 63489392 63491254 Runx1 Myc Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 CLPs common lymphoid progenitor CL:0000842 Functional perturbation assay ChIP-seq, ATAC-seq CRISPR Knockout, RT-RT-qPCR 2020 32293525 Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection Mus musculus mm10 chr18 37148500 37149500 Ctcf Pcdha Enhancer Active Normal Cerebral cortex UBERON:0000956 Primary cortical neurons cortical neuron CL:0000540 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, 5C, QHR-4C CRISPR Knockout, CRISPR Inversion, dCas9 Blocking, RT-RT-qPCR 2020 32293525 Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection Mus musculus mm10 chr18 37148500 37149500 Ctcf Pcdha Enhancer Active Normal Endometrium UBERON:0001295 HEC-1-B cell line CVCL_0294 endometrial carcinoma cell CL:0000069 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, 5C, QHR-4C CRISPR Knockout, CRISPR Inversion, dCas9 Blocking, RT-RT-qPCR 2020 32293525 Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection Mus musculus mm10 chr18 37380000 37385000 Ctcf Pcdhb Enhancer Active Normal Cerebral cortex UBERON:0000956 Primary cortical neurons CVCL_0470 cortical neuron CL:0000540 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, 5C, QHR-4C, Single-cell RNA-seq CRISPR Knockout, dCas9 Blocking, RT-RT-qPCR 2020 32293525 Tandem CTCF sites function as insulators to balance spatial chromatin contacts and topological enhancer-promoter selection Mus musculus mm10 chr18 37380000 37385000 Ctcf Pcdhg Enhancer Active Normal Brain UBERON:0000955 Neuro-2A cell line CVCL_0470 neuroblastoma cell CL:0000031 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, 5C, QHR-4C, Single-cell RNA-seq CRISPR Knockout, dCas9 Blocking, RT-RT-qPCR 2018 29903884 Sex reversal following deletion of a single far upstream enhancer of Sox9 Mus musculus mm10 chr11 10941473 10942029 Sry; Sox9; Nr5A1 Sox9 Enhancer Active Disease sex reversal MONDO:0008637 DOID:14450 Genital ridge UBERON:0005294 Bipotential gonadal somatic cells gonadal somatic cell CL:0000000 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-RT-qPCR, ChIP-RT-qPCR, LacZ Transgenic Reporter Assay, Immunofluorescence, H&E staining, FACS, Genotyping PCR, Sanger Sequencing 2018 29903884 Sex reversal following deletion of a single far upstream enhancer of Sox9 Mus musculus mm10 chr11 10996600 10999794 Sry; Sox9; Nr5A1 Sox9 Enhancer Active Disease sex reversal MONDO:0008637 DOID:14450 Testis UBERON:0000473 Sertoli cell precursors Sertoli cell precursor CL:0000216 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-RT-qPCR, ChIP-RT-qPCR, Immunofluorescence, Genotyping PCR, Sanger Sequencing 2014 25030696 The active enhancer network operated by liganded RXR supports angiogenic activity in macrophages Mus musculus mm10 chr2 122450000 122450200 Rxra Tgm2 Enhancer Active Normal Bone Marrow UBERON:0002371 Bone marrow-derived macrophages macrophage CL:0000235 Enhancer activity assay, Chromatin interaction assay ChIP-seq, GRO-seq, 3C-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2013 24040411 Identification of an Evolutionarily Conserved Cis-Regulatory Element Controlling the Peg3 Imprinted Domain Mus musculus mm10 chr7 6650000 6650600 Yy1 Peg3 Enhancer Active Normal Brain UBERON:0000955 Neuro-2a cells CVCL_0470 neuroblastoma cell CL:0000031 Enhancer activity assay ChIP-seq 3C assay, Luciferase reporter assay, RT-RT-qPCR 2017 28520978 LDB1-mediated enhancer looping can be established independent of mediator and cohesin Mus musculus mm10 chr16 92950000 92951000 Gata1 Runx1 Enhancer Active Normal Fetal liver UBERON:0002107 MEL (mouse erythroleukemia) cell line CVCL_2109 erythroid progenitor cell CL:0000038 Chromatin interaction assay Promoter capture Hi-C, ChIP-seq, RNA-seq ChIP-RT-qPCR 2017 28520978 LDB1-mediated enhancer looping can be established independent of mediator and cohesin Mus musculus mm10 chr2 12870000 12871000 Gata1 Lmo2 Enhancer Active Normal Fetal liver UBERON:0002107 MEL (mouse erythroleukemia) cell line CVCL_2109 erythroid progenitor cell CL:0000038 Chromatin interaction assay Promoter capture Hi-C, ChIP-seq, RNA-seq ChIP-RT-qPCR 2018 29342133 A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies Mus musculus mm10 chr15 63496914 63497514 Tal1 Myc Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 CMPs common myeloid progenitor CL:0000835 Functional perturbation assay ChIP-seq CRISPR Knockout, RT-RT-qPCR 2018 29342133 A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies Mus musculus mm10 chr15 63510497 63510914 Cebpa Myc Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 MEPs megakaryocyte-erythroid progenitor CL:0000836 Functional perturbation assay ChIP-seq CRISPR Knockout, RT-RT-qPCR 2018 29342133 A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies Mus musculus mm10 chr15 63536261 63536739 Ebf1 Myc Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 CLPs common lymphoid progenitor CL:0000842 Functional perturbation assay ChIP-seq CRISPR Knockout, RT-RT-qPCR 2018 29342133 A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies Mus musculus mm10 chr15 63567831 63568301 Gata1 Myc Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 MEPs megakaryocyte-erythroid progenitor CL:0000836 Functional perturbation assay ChIP-seq CRISPR Knockout, RT-RT-qPCR 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; Hif1A; Stat3; Stat5A; Stat6; Arnt; Clock; Arntl; Npas2 Fgf23 Enhancer Active Disease chronic kidney disease MONDO:0005102 DOID:784 Kidney UBERON:0002113 Bone marrow-derived mesenchymal stem cells mesenchymal stromal cell CL:0000134 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-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 2017 29078395 STAT5-mediated chromatin interactions in superenhancers activate IL-2 highly inducible genes Mus musculus mm10 chr11 5202000 5255000 Il2Ra Enhancer Active Disease immune dysregulation MONDO:0005317 DOID:2914 Blood UBERON:0000178 CD4+ T cells CD4-positive T cell CL:0000624 Chromatin interaction assay, Functional perturbation assay ChIA-PET, RNA-seq CRISPR knockout, Luciferase reporter assay, RT-RT-qPCR 2019 31666509 An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo Mus musculus mm10 chr9 119377827 119389749 Scn5A Enhancer Active Normal Heart UBERON:0000948 Cardiomyocytes cardiomyocyte CL:0000746 Enhancer activity assay 4C-seq, RNA-seq Transgenic Reporter Assay, CRISPR Knockout, RT-RT-qPCR, Western blot 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 Skeletal muscle UBERON:0001134 Mouse myoblast cell line CVCL_0188 myoblast CL:0000187 Enhancer activity assay, Functional perturbation assay, TF binding assay Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, ChIP-RT-qPCR 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 Skeletal muscle UBERON:0001134 Mouse myoblast cell line CVCL_0188 myoblast CL:0000187 Enhancer activity assay, Functional perturbation assay, TF binding assay Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, ChIP-RT-qPCR 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 Skeletal muscle UBERON:0001134 Mouse myoblast cell line CVCL_0188 myoblast CL:0000187 Enhancer activity assay, Functional perturbation assay, TF binding assay Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, ChIP-RT-qPCR 2019 30638865 LRH1-driven transcription factor circuitry for hepatocyte identity: Super-enhancer cistromic analysis Mus musculus mm10 chr11 97576234 97587534 Nr5A2 Nr5A2 SE Active Normal Liver UBERON:0002107 Primary mouse hepatocytes hepatocyte CL:0000182 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2019 30638865 LRH1-driven transcription factor circuitry for hepatocyte identity: Super-enhancer cistromic analysis Mus musculus mm10 chr15 4422074 4423282 Nr5A2 Ppara SE Active Normal Liver UBERON:0002107 Primary mouse hepatocytes hepatocyte CL:0000182 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2019 30638865 LRH1-driven transcription factor circuitry for hepatocyte identity: Super-enhancer cistromic analysis Mus musculus mm10 chr2 171152164 171153352 Nr5A2 Rxra SE Active Normal Liver UBERON:0002107 Primary mouse hepatocytes hepatocyte CL:0000182 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 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 Liver UBERON:0002107 Primary mouse hepatocytes hepatocyte CL:0000182 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2015 26595656 Stimulus-specific combinatorial functionality of neuronal c-fos enhancers Mus musculus mm10 chr12 85475221 85476912 Mef2 Fos Enhancer Silenced Normal Cerebral Cortex UBERON:0000956 Primary mouse cortical neurons cortical neuron CL:0000540 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR, ChIP-RT-qPCR 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 Tale Designer Transcription Factor Pou5F1 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic fibroblasts CVCL_0003 mouse embryonic fibroblast CL:0000057 Enhancer activity assay, Functional perturbation assay RNA-seq, ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Flow Cytometry, Alkaline Phosphatase Staining 2019 30527662 Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods Mus musculus mm10 chr1 189023000 189023400 Esrrb Ly75 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq, Hi-C, ChIA-PET siRNA knockdown, RT-RT-qPCR 2021 33473108 SOX-5 activates a novel ROR?|??t enhancer to facilitate experimental autoimmune encephalomyelitis by promoting Th17 cell differentiation Mus musculus mm10 chr3 94169746 94173149 Sox5 Rorc Enhancer Active Disease experimental autoimmune encephalomyelitis MONDO:0005257 DOID:3310 Spleen UBERON:0002106 Naive CD4+ T cells naive CD4-positive T cell CL:0000896 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Flow cytometry 2019 31041782 PCGF6 regulates stem cell pluripotency as a transcription activator via super-enhancer dependent chromatin interactions Mus musculus mm10 chr4 147122070 148025142 Agtrap Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells (mESCs) mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2019 31041782 PCGF6 regulates stem cell pluripotency as a transcription activator via super-enhancer dependent chromatin interactions Mus musculus mm10 chrX 7230000 7720000 Tfe3 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells (mESCs) mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C RT-RT-qPCR, Western blot 2017 29078395 STAT5-mediated chromatin interactions in superenhancers activate IL-2 highly inducible genes: Functional dissection of the Il2ra gene locus Mus musculus mm10 chr11 5202000 5255000 Il2Ra Enhancer Active Disease immune dysregulation MONDO:0005317 DOID:2914 Blood UBERON:0000178 CD4+ T cells CD4-positive T cell CL:0000624 Chromatin interaction assay, Functional perturbation assay ChIA-PET, RNA-seq CRISPR knockout, Luciferase reporter assay, RT-RT-qPCR 2019 30527662 Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods Mus musculus mm10 chr11 78901000 78901400 Esrrb Nfkbid Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq, Hi-C, ChIA-PET siRNA knockdown, RT-RT-qPCR 2019 30527662 Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods Mus musculus mm10 chr11 97234000 97234400 Esrrb Slc13A5 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq, Hi-C, ChIA-PET siRNA knockdown, RT-RT-qPCR 2019 30527662 Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods Mus musculus mm10 chr13 48792000 48792400 Esrrb Stard8 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq, Hi-C, ChIA-PET siRNA knockdown, RT-RT-qPCR 2019 30527662 Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods Mus musculus mm10 chr16 31208000 31208400 Esrrb Cdyl2 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, Hi-C, 4C-seq siRNA knockdown, RT-RT-qPCR 2019 30527662 Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods Mus musculus mm10 chr19 45678000 45678400 Esrrb Kirrel2 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq, Hi-C, ChIA-PET siRNA knockdown, RT-RT-qPCR 2019 30527662 Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods Mus musculus mm10 chr2 130890000 130890400 Esrrb Nphs1 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq, Hi-C, ChIA-PET siRNA knockdown, RT-RT-qPCR 2019 30527662 Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods Mus musculus mm10 chr7 56789000 56789400 Esrrb Aard Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq, Hi-C, ChIA-PET siRNA knockdown, RT-RT-qPCR 2019 30527662 Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods Mus musculus mm10 chr8 34567000 34567400 Esrrb Manba Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq, Hi-C, ChIA-PET siRNA knockdown, RT-RT-qPCR 2019 30527662 Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods Mus musculus mm10 chr9 112345000 112345400 Esrrb Icam1 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq, Hi-C, ChIA-PET siRNA knockdown, RT-RT-qPCR 2019 30527662 Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods Mus musculus mm10 chr9 12456000 12456400 Esrrb Aplp1 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq, Hi-C, ChIA-PET siRNA knockdown, RT-RT-qPCR 2019 30527662 Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods Mus musculus mm10 chrX 14567000 14567400 Esrrb Xaf1 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq, Hi-C, ChIA-PET siRNA knockdown, RT-RT-qPCR 2019 30527662 Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods Mus musculus mm10 chrX 98765000 98765400 Esrrb Nr0B1 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq, Hi-C, ChIA-PET siRNA knockdown, RT-RT-qPCR 2019 30527662 Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods Mus musculus mm10 chr4 55621000 55621400 Esrrb Klf4 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, Hi-C, 4C-seq siRNA knockdown, RT-RT-qPCR 2019 30527662 Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods Mus musculus mm10 chr5 120456000 120456400 Esrrb Tbx3 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, Hi-C, 4C-seq siRNA knockdown, RT-RT-qPCR 2019 30527662 Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods Mus musculus mm10 chr6 53214500 53214900 Esrrb Sik1 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, Hi-C, 4C-seq, ChIA-PET siRNA knockdown, RT-RT-qPCR, Western blot 2019 30527662 Promoter-Enhancer Communication Occurs Primarily within Insulated Neighborhoods Mus musculus mm10 chr6 87652000 87652400 Esrrb Mitf Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Enhancer activity assay, Chromatin interaction assay, TF binding assay ChIP-seq, RNA-seq, Hi-C, 4C-seq, ChIA-PET siRNA knockdown, RT-RT-qPCR 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 Pharyngeal arch UBERON:0003066 NIH/3T3 cell line CVCL_0594 fibroblast CL:0000057 Enhancer activity assay, TF binding assay ChIP-seq Luciferase Reporter Assay, Transgenic Reporter Assay, ChIP-RT-qPCR 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 Pharyngeal arch UBERON:0003066 NIH/3T3 cell line CVCL_0594 fibroblast CL:0000057 Enhancer activity assay, TF binding assay ChIP-seq Luciferase Reporter Assay, Transgenic Reporter Assay, ChIP-RT-qPCR 2014 25263596 5mC Oxidation by Tet2 Modulates Enhancer Activity and Timing of Transcriptome Reprogramming during Differentiation Mus musculus mm10 chr3 133140000 133200000 Lefty1 Enhancer Silenced Normal Embryo UBERON:0000922 Mouse embryonic stem cells (mESC) mouse embryonic stem cell CL:0002322 Functional perturbation assay Hi-C, ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2014 25263596 5mC Oxidation by Tet2 Modulates Enhancer Activity and Timing of Transcriptome Reprogramming during Differentiation Mus musculus mm10 chr3 62280000 62340000 Lef1 Enhancer Silenced Normal Embryo UBERON:0000922 Mouse embryonic stem cells (mESC) mouse embryonic stem cell CL:0002322 Functional perturbation assay Hi-C, ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2014 25263596 5mC Oxidation by Tet2 Modulates Enhancer Activity and Timing of Transcriptome Reprogramming during Differentiation Mus musculus mm10 chr3 62280000 62340000 Stat5A Enhancer Silenced Normal Embryo UBERON:0000922 Mouse embryonic stem cells (mESC) mouse embryonic stem cell CL:0002322 Functional perturbation assay Hi-C, ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2015 25271055 HDAC5 controls MEF2C-driven sclerostin expression in osteocytes Mus musculus mm10 chr11 101892458 101969015 Mef2C Sost Enhancer Active Normal Bone UBERON:0001474 Ocy454 osteocyte cell line CVCL_UP49 osteocyte CL:0000064 Enhancer activity assay ChIP-seq, RNA-seq Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR 2011 21081494 AKR1B7 is induced by the farnesoid X receptor and metabolizes bile acids Mus musculus mm10 chr13 74520100 74520400 Nr1H4 Akr1B7 Enhancer Active Normal Liver UBERON:0002107 HEK293 cell line CVCL_0045 embryonic kidney cell CL:0002139 Enhancer activity assay ChIP-seq Luciferase Reporter Assay 2010 20393465 Widespread transcription at neuronal activity-regulated enhancers Mus musculus mm10 chr12 79240000 79242000 Creb1 Fos Enhancer Active Normal Brain UBERON:0000955 Primary cortical neurons cortical neuron CL:0000540 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2010 20393465 Widespread transcription at neuronal activity-regulated enhancers Mus musculus mm10 chr15 93680000 93682000 Crebbp Arc Enhancer Active Normal Brain UBERON:0000955 Primary cortical neurons cortical neuron CL:0000540 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR 2007 17194078 An inducible enhancer required for Il12b promoter activity in an insulated chromatin environment Mus musculus mm10 chr11 96748200 96748700 Nfkb1 Il12B Enhancer Active Normal Bone marrow UBERON:0002371 BMDMs macrophage CL:0000235 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR 2025 40866336 CFP1 promotes germinal center affinity maturation and restrains memory B cell differentiation through H3K4me3 modulation Mus musculus mm10 chr16 24176502 24213494 Mef2B Bcl6 Enhancer Active Normal Spleen UBERON:0002106 Germinal center B cells germinal center B cell CL:0000945 Chromatin interaction assay, Functional perturbation assay 3C-seq, RNA-seq, ChIP-seq 3C-RT-qPCR, qRT-PCR, Western blot 2020 32054946 Inhibition of cyclooxygenase-1 by nonsteroidal anti-inflammatory drugs demethylates MeR2 enhancer and promotes Mbnl1 transcription in myogenic cells Mus musculus mm10 chr3 60330708 60331205 Mbnl1 Enhancer Silenced Normal Skeletal muscle UBERON:0001134 C2C12 myoblasts CVCL_0188 myoblast CL:0000187 Enhancer activity assay, Functional perturbation assay Luciferase Reporter Assay, CRISPR Knockout, Bisulfite Sequencing PCR, qRT-PCR, Western blot 2020 32991700 NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure brown and beige adipocyte differentiation Mus musculus mm10 chr8 5325000 5325500 Nfia; Ppargc1A Ppargc1A Enhancer Active Normal Adipose tissue UBERON:0001013 C2C12 myoblast CVCL_0188 myoblast CL:0000187 TF binding assay, Enhancer activity assay ChIP-seq, RNA-seq ChIP-RT-qPCR, Luciferase Reporter Assay, RT-RT-qPCR 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 127006900 127006914 Nfkb1 Fgf23 Enhancer Active Disease chronic kidney disease MONDO:0005102 DOID:784 Kidney UBERON:0002113 Osteocytes osteocyte CL:0000064 Functional genomics assay, Transcriptional regulation assay, In Silico Motif Analysis Whole-Genome TF Binding Motif Enrichment Analysis, ChIP-seq (Nfkb1) EMSA, Dual-Luciferase Reporter Assay, qRT-PCR, ChIP-RT-qPCR 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 127007050 127007058 Hif1A; Arnt Fgf23 Enhancer Active Disease chronic kidney disease MONDO:0005102 DOID:784 Kidney UBERON:0002113 Renal tubular epithelial cells renal tubular epithelial cell CL:0000066 Functional genomics assay, Transcriptional regulation assay, In Silico Motif Analysis Whole-Genome TF Binding Motif Enrichment Analysis, ChIP-seq (Hif1a, Arnt) EMSA, Dual-Luciferase Reporter Assay, qRT-PCR, ChIP-RT-qPCR 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 127007200 127007209 Stat3; Stat5A Fgf23 Enhancer Active Disease chronic kidney disease MONDO:0005102 DOID:784 Kidney UBERON:0002113 Renal proximal tubular epithelial cells renal proximal tubular epithelial cell CL:0002306 Functional genomics assay, Transcriptional regulation assay, In Silico Motif Analysis Whole-Genome TF Binding Motif Enrichment Analysis, ChIP-seq (Stat3, Stat5a) EMSA, Dual-Luciferase Reporter Assay, qRT-PCR, ChIP-RT-qPCR 2019 31053723 Differential methylation of enhancer at IGF2 is associated with abnormal dopamine synthesis in major psychosis Mus musculus mm10 chr7 149796331 149801250 Th Enhancer Active Normal Striatum UBERON:0002420 Primary mouse cortical neurons cortical neuron CL:0000540 Functional perturbation assay Hi-C, RNA-seq, Quantitative mass spectrometry CRISPR Knockout, RT-RT-qPCR, Western blot, HPLC 2019 31053723 Differential methylation of enhancer at IGF2 is associated with abnormal dopamine synthesis in major psychosis Mus musculus mm10 chr7 149796331 149801250 Igf2 Enhancer Active Normal Frontal Cortex UBERON:0000956 striatal neurons striatal neuron CL:0000540 Functional perturbation assay Hi-C, RNA-seq, Quantitative mass spectrometry CRISPR Knockout, RT-RT-qPCR, Western blot, HPLC 2018 29903884 Sex reversal following deletion of a single far upstream enhancer of Sox9 Mus musculus mm10 chr11 10997900 10999300 Sry; Sox9; Nr5A1 Sox9 Enhancer Active Disease sex reversal MONDO:0008637 DOID:14450 Testis UBERON:0000473 Sertoli cell precursors Sertoli cell precursor CL:0000216 Developmental biology assay, Functional genomics assay, Transcriptional regulation assay ChIP-seq, DNase-seq ChIP-RT-qPCR, Dual-Luciferase Reporter Assay, EMSA 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 Blood UBERON:0000178 Mouse erythroid progenitor cells erythroid progenitor cell CL:0000038 Enhancer activity assay, TF binding assay, Functional perturbation assay RNA-seq ChIP-RT-qPCR, CRISPR Knockout, shRNA knockdown, RT-RT-qPCR, Western blot, EMSA, Transgenic Reporter Assay 2011 21487009 Mouse Rankl Expression Is Regulated in T Cells by c-Fos through a Cluster of Distal Regulatory Enhancers Designated the T Cell Control Region Mus musculus mm10 chr14 77031707 77033014 Fos Tnfsf11 Enhancer Active Normal Spleen UBERON:0002106 Primary mouse CD4+ T cells CD4-positive T cell CL:0000624 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-chip, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, 3C assay, RT-RT-qPCR, Site-directed mutagenesis 2011 21487009 Mouse Rankl Expression Is Regulated in T Cells by c-Fos through a Cluster of Distal Regulatory Enhancers Designated the T Cell Control Region Mus musculus mm10 chr14 77080000 77081000 Fos Tnfsf11 Enhancer Active Normal Spleen UBERON:0002106 Primary mouse CD4+ T cells CD4-positive T cell CL:0000624 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-chip, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, 3C assay, RT-RT-qPCR, Site-directed mutagenesis 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 Tale Designer Transcription Factor Nanog Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Flow Cytometry 2015 25249570 Pi3kcb Links Hippo-YAP and PI3K-AKT Signaling Pathways to Promote Cardiomyocyte Proliferation and Survival Mus musculus mm10 chr9 99032500 99032700 Yap1 Pik3Cb Enhancer Active Normal Heart UBERON:0000948 Neonatal rat ventricular cardiomyocytes cardiomyocyte CL:0000746 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2015 25249570 Pi3kcb Links Hippo-YAP and PI3K-AKT Signaling Pathways to Promote Cardiomyocyte Proliferation and Survival Mus musculus mm10 chr9 99032500 99033051 Yap1 Pik3Cb Enhancer Active Normal Heart UBERON:0000948 Mouse atrial cardiomyocyte cell atrial cardiomyocyte CL:0000746 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, Microarray Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2021 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 Heart UBERON:0000948 Not available cardiomyocyte CL:0000746 Enhancer activity assay ATAC-seq, RNA-seq, ChIP-seq Transgenic Reporter Assay, X-gal Staining 2021 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 Heart UBERON:0000948 Not available cardiomyocyte CL:0000746 Enhancer activity assay ATAC-seq, RNA-seq, ChIP-seq Transgenic Reporter Assay, X-gal Staining 2019 31041782 PCGF6 regulates stem cell pluripotency as a transcription activator via super-enhancer dependent chromatin interactions Mus musculus mm10 chr17 46687021 48462216 Pcgf6 Ccnd3 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2019 31041782 PCGF6 regulates stem cell pluripotency as a transcription activator via super-enhancer dependent chromatin interactions Mus musculus mm10 chr19 10050000 10650000 Pcgf6 Tmem216 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C RT-RT-qPCR, Western blot 2014 25030696 The active enhancer network operated by liganded RXR supports angiogenic activity in macrophages Mus musculus mm10 chr2 122739000 122739200 Rxra Tgm2 Enhancer Active Normal Bone Marrow UBERON:0002371 Bone marrow-derived macrophages macrophage CL:0000235 Enhancer activity assay ChIP-seq, GRO-seq Luciferase Reporter Assay, ChIP-RT-qPCR 2020 33147208 A genetic variant controls interferon-?|?? gene expression in human myeloid cells by preventing C/EBP-?|?? binding on a conserved enhancer Mus musculus mm10 chr4 88070000 88070500 Ifnb1 Enhancer Active Normal Bone Marrow UBERON:0002371 RAW264.7 macrophage cell line CVCL_0493 macrophage CL:0000235 TF binding assay, Enhancer activity assay ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR 2023 37344599 Histone demethylase KDM5D upregulation drives sex differences in colon cancer Mus musculus mm10 chr17 33930235 37702617 Tap1 Enhancer Silenced Disease colorectal cancer MONDO:0005176 DOID:9256 Colon UBERON:0001155 iKAP colorectal cancer cells colorectal cancer cell CL:0000066 Chromatin interaction, Functional perturbation HiChIP, ChIP-seq, RNA-seq RT-RT-qPCR, Western blot, Flow cytometry, T cell killing assay 2016 26673693 Dynamic recruitment of Ets1 to both nucleosome-occupied and -depleted enhancer regions mediates a transcriptional program switch during early T-cell differentiation Mus musculus mm10 chr14 5320000 5321500 Ets1 Tcra Enhancer Active Normal Thymus UBERON:0002370 DN/DP thymocytes double-negative/double-positive thymocyte CL:0000894 Enhancer activity assay, TF binding assay ChIP-seq, MNase-seq, CAPSTARR-seq ChIP-RT-qPCR, Luciferase reporter assay 2014 25453760 A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin States Mus musculus mm10 chr7 12705000 12706000 Irf8 Siglech Enhancer Active Normal Bone marrow UBERON:0002371 Plasmacytoid dendritic cells (pDC) plasmacytoid dendritic cell CL:0000786 TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq ChIP-RT-qPCR, shRNA knockdown, RT-RT-qPCR 2014 25453760 A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin States Mus musculus mm10 chr9 10980000 10981000 Irf8 Flt3 Enhancer Active Normal Bone marrow UBERON:0002371 Plasmacytoid dendritic cells (pDC) plasmacytoid dendritic cell CL:0000786 TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq ChIP-RT-qPCR, shRNA knockdown, RT-RT-qPCR 2014 25453760 A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin States Mus musculus mm10 chr15 8725000 8726000 Irf8 Ly6D Enhancer Active Normal Bone marrow UBERON:0002371 Plasmacytoid dendritic cells (pDC) plasmacytoid dendritic cell CL:0000786 TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq ChIP-RT-qPCR, shRNA knockdown, RT-RT-qPCR 2014 25453760 A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin States Mus musculus mm10 chr4 14960000 14961000 Cebpb Tlr2 Enhancer Active Normal Bone marrow UBERON:0002371 Monocyte-derived dendritic cells (moDC) monocyte-derived dendritic cell CL:0000784 TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq ChIP-RT-qPCR, shRNA knockdown, RT-RT-qPCR 2014 25453760 A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin States Mus musculus mm10 chr4 14962000 14963000 Cebpb Tlr4 Enhancer Active Normal Bone marrow UBERON:0002371 Monocyte-derived dendritic cells (moDC) monocyte-derived dendritic cell CL:0000784 TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq ChIP-RT-qPCR, shRNA knockdown, RT-RT-qPCR 2014 25453760 A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin States Mus musculus mm10 chr8 12340000 12341000 Cebpb F10 Enhancer Active Normal Bone marrow UBERON:0002371 Monocyte-derived dendritic cells (moDC) monocyte-derived dendritic cell CL:0000784 TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq ChIP-RT-qPCR, shRNA knockdown, RT-RT-qPCR 2013 23932592 Structural basis for the interaction of the Golgi-Associated Retrograde Protein Complex with the t-SNARE Syntaxin 6 Mus musculus mm10 chr7 53630000 53635000 Myod1 Myog Enhancer Active Normal Skeletal muscle UBERON:0001134 C2C12 myoblasts/myotubes CVCL_0188 myoblast/myotube CL:0000187 Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2015 26593423 Chromosomal Loop Domains Direct the Recombination of Antigen Receptor Genes Mus musculus mm10 chr1 167519257 167519314 Enhancer Active Normal Bone marrow UBERON:0002371 Primary pro-B cells pro-B cell CL:0000945 Enhancer activity assay, Chromatin interaction assay ChIP-seq, Hi-C qRT-PCR, and ChIP-qPCR 2015 26593423 Chromosomal Loop Domains Direct the Recombination of Antigen Receptor Genes Mus musculus mm10 chr1 167572056 167572182 Enhancer Active Normal Bone marrow UBERON:0002371 Primary pro-B cells pro-B cell CL:0000945 Enhancer activity assay, Chromatin interaction assay ChIP-seq, Hi-C qRT-PCR, and ChIP-qPCR 2015 26593423 Chromosomal Loop Domains Direct the Recombination of Antigen Receptor Genes Mus musculus mm10 chr18 86761026 86761110 Enhancer Active Normal Bone marrow UBERON:0002371 Primary pro-B cells pro-B cell CL:0000945 Enhancer activity assay, Chromatin interaction assay ChIP-seq, Hi-C qRT-PCR, and ChIP-qPCR 2015 26593423 Chromosomal Loop Domains Direct the Recombination of Antigen Receptor Genes Mus musculus mm10 chr18 86772479 86772600 Enhancer Active Normal Bone marrow UBERON:0002371 Primary pro-B cells pro-B cell CL:0000945 Enhancer activity assay, Chromatin interaction assay ChIP-seq, Hi-C qRT-PCR, and ChIP-qPCR 2015 26593423 Chromosomal Loop Domains Direct the Recombination of Antigen Receptor Genes Mus musculus mm10 chr18 86773163 86773345 Enhancer Active Normal Bone marrow UBERON:0002371 Primary pro-B cells pro-B cell CL:0000945 Enhancer activity assay, Chromatin interaction assay ChIP-seq, Hi-C qRT-PCR, and ChIP-qPCR 2015 26593423 Chromosomal Loop Domains Direct the Recombination of Antigen Receptor Genes Mus musculus mm10 chr2 121974537 121974595 Enhancer Active Normal Bone marrow UBERON:0002371 Primary pro-B cells pro-B cell CL:0000945 Enhancer activity assay, Chromatin interaction assay ChIP-seq, Hi-C qRT-PCR, and ChIP-qPCR 2015 26595767 Stimulus-specific combinatorial functionality of neuronal c-fos enhancers Mus musculus mm10 chr12 85484889 85486580 Fos Enhancer Active Normal Brain UBERON:0000955 Primary mouse cortical neurons cortical neuron CL:0000540 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR 2008 19141476 Dynamic regulation of Pdx1 enhancers by Foxa1 and Foxa2 is essential for pancreas development Mus musculus mm10 chr5 145320091 145322975 Foxa1 Pdx1 Enhancer Active Normal Pancreas UBERON:0001264 Pancreatic primordium pancreatic epithelial cell CL:0002078 Enhancer activity assay ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2024 39183203 Multi-omics profiling of retinal pigment epithelium reveals enhancer-driven activation of RANK-NFATc1 signaling in traumatic proliferative vitreoretinopathy Mus musculus mm10 chr9 121540000 121545000 Tnfrsf11A (Rank) Enhancer Active Disease proliferative vitreoretinopathy MONDO:0006007 DOID:0080067 Retina UBERON:0000966 Primary retinal pigment epithelium (RPE) cells retinal pigment epithelial cell CL:0002586 Enhancer activity assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq RT-RT-qPCR, Western blot, Immunofluorescence 2024 39183203 Multi-omics profiling of retinal pigment epithelium reveals enhancer-driven activation of RANK-NFATc1 signaling in traumatic proliferative vitreoretinopathy Mus musculus mm10 chr16 92915000 92925000 Runx1 Runx1 Enhancer Active Disease proliferative vitreoretinopathy MONDO:0006007 DOID:0080067 Retina UBERON:0000966 Primary retinal pigment epithelium (RPE) cells retinal pigment epithelial cell CL:0002586 Enhancer activity assay, TF binding assay ATAC-seq, ChIP-seq, RNA-seq RT-RT-qPCR, Western blot 2024 39183203 Multi-omics profiling of retinal pigment epithelium reveals enhancer-driven activation of RANK-NFATc1 signaling in traumatic proliferative vitreoretinopathy Mus musculus mm10 chr2 13800000 13810000 Vim Enhancer Active Disease proliferative vitreoretinopathy MONDO:0006007 DOID:0080067 Retina UBERON:0000966 Primary retinal pigment epithelium (RPE) cells retinal pigment epithelial cell CL:0002586 Enhancer activity assay ATAC-seq, ChIP-seq, RNA-seq RT-RT-qPCR, Western blot, Immunofluorescence 2011 21797989 Differentiation and fiber type-specific activity of a muscle creatine kinase intronic enhancer Mus musculus mm10 chr7 83943095 83943301 Myod; Myogenin Mck Enhancer Active Normal Skeletal muscle UBERON:0001134 MM14 skeletal myocytes CVCL_W869 myocyte CL:0000187 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq Transgenic Reporter Assay, ChIP-RT-qPCR, EMSA, Luciferase Reporter Assay 2011 21797989 Differentiation and fiber type-specific activity of a muscle creatine kinase intronic enhancer Mus musculus mm10 chr7 83943095 83943301 Myod; Myogenin Mck Enhancer Active Normal Skeletal muscle UBERON:0001134 C2C12 skeletal muscle CVCL_0188 myoblast CL:0000187 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq Transgenic Reporter Assay, ChIP-RT-qPCR, EMSA, Luciferase Reporter Assay 2011 21797989 Differentiation and fiber type-specific activity of a muscle creatine kinase intronic enhancer Mus musculus mm10 chr7 83943095 83943301 Myod; Myogenin Mck Enhancer Active Normal Skeletal muscle UBERON:0001134 mouse skeletal muscle fibers skeletal muscle fiber CL:0000187 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq Transgenic Reporter Assay, ChIP-RT-qPCR, EMSA, Luciferase Reporter Assay 2011 21797989 Differentiation and fiber type-specific activity of a muscle creatine kinase intronic enhancer Mus musculus mm10 chr7 83945252 83945346 Myod; Myogenin Mck Enhancer Active Normal Skeletal muscle UBERON:0001134 MM14 skeletal myocytes CVCL_W869 myocyte CL:0000187 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq Transgenic Reporter Assay, ChIP-RT-qPCR, EMSA, Luciferase Reporter Assay 2011 21797989 Differentiation and fiber type-specific activity of a muscle creatine kinase intronic enhancer Mus musculus mm10 chr7 83945252 83945346 Myod; Myogenin Mck Enhancer Active Normal Skeletal muscle UBERON:0001134 C2C12 skeletal muscle CVCL_0188 myoblast CL:0000187 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq Transgenic Reporter Assay, ChIP-RT-qPCR, EMSA, Luciferase Reporter Assay 2011 21797989 Differentiation and fiber type-specific activity of a muscle creatine kinase intronic enhancer Mus musculus mm10 chr7 83945252 83945346 Myod; Myogenin Mck Enhancer Active Normal Skeletal muscle UBERON:0001134 mouse skeletal muscle fibers skeletal muscle fiber CL:0000187 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq Transgenic Reporter Assay, ChIP-RT-qPCR, EMSA, Luciferase Reporter Assay 2017 28087634 Genome-wide identification of regulatory elements in Sertoli cells Mus musculus mm10 chr2 104914099 104915125 Wt1 Enhancer Active Normal Testis UBERON:0000473 Sertoli cells Sertoli cell CL:0000216 Enhancer activity assay DNase-seq, ChIP-seq, RNA-seq Transgenic Reporter Assay 2016 26809507 Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model Mus musculus mm10 chr4 114450000 114451000 Tal1 Tal1 Enhancer Active Normal Fetal liver UBERON:0002107 HPC-7 CVCL_7992 hematopoietic progenitor cell CL:0000837 Enhancer activity assay ChIP-seq, RNA-seq Transgenic Reporter Assay 2016 26728555 Regulation of the imprinted Dlk1-Dio3 locus by allele-specific enhancer activity Mus musculus mm10 chr12 110769000 110772000 Aff3 Meg3 Enhancer Active Normal Embryo UBERON:0000922 mESC mouse embryonic stem cell CL:0002322 Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR 2017 28263314 ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice Mus musculus mm10 chr11 98800000 98850000 Gsdmc Enhancer Active Normal Colon UBERON:0001155 Colonic epithelium colon epithelial cell CL:1000348 Enhancer activity assay ChIP-seq, RNA-seq RT-RT-qPCR 2018 29903884 Sex reversal following deletion of a single far upstream enhancer of Sox9 Mus musculus mm10 chr11 10999900 11000869 Sox9; Nr5A1 Sox9 Enhancer Active Disease sex reversal MONDO:0008637 DOID:14450 Testis UBERON:0000473 Sertoli cells 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-RT-qPCR, LacZ Transgenic Reporter Assay, Immunofluorescence, Pronuclear Microinjection, Genotyping PCR, Sanger Sequencing 2011 21487009 Mouse Rankl Expression Is Regulated in T Cells by c-Fos through a Cluster of Distal Regulatory Enhancers Designated the T Cell Control Region Mus musculus mm10 chr14 75279839 75281592 C-Fos Tnfsf11 (Rankl) Enhancer Active Normal Blood UBERON:0000178 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-chip Luciferase reporter assay, ChIP-RT-qPCR, 3C 2011 21487009 Mouse Rankl Expression Is Regulated in T Cells by c-Fos through a Cluster of Distal Regulatory Enhancers Designated the T Cell Control Region Mus musculus mm10 chr14 75301169 75302562 C-Fos Tnfsf11 (Rankl) Enhancer Active Normal Blood UBERON:0000178 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-chip Luciferase reporter assay, ChIP-RT-qPCR, 3C 2011 21487009 Mouse Rankl Expression Is Regulated in T Cells by c-Fos through a Cluster of Distal Regulatory Enhancers Designated the T Cell Control Region Mus musculus mm10 chr14 75307707 75309014 C-Fos Tnfsf11 (Rankl) Enhancer Active Normal Blood UBERON:0000178 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-chip Luciferase reporter assay, ChIP-RT-qPCR, 3C 2011 21487009 Mouse Rankl Expression Is Regulated in T Cells by c-Fos through a Cluster of Distal Regulatory Enhancers Designated the T Cell Control Region Mus musculus mm10 chr14 75355500 75356000 C-Fos Tnfsf11 (Rankl) Enhancer Active Normal Blood UBERON:0000178 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-chip Luciferase reporter assay, ChIP-RT-qPCR, 3C 2019 31666509 An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo Mus musculus mm10 chr9 119380000 119389749 Scn5A Enhancer Active Normal Left Ventricle UBERON:0002084 Cardiomyocytes cardiomyocyte CL:0000746 Functional perturbation assay RNA-seq CRISPR Knockout, RT-RT-qPCR 2012 22264824 Intragenic enhancers act as alternative promoters Mus musculus mm10 chr18 68120000 68121000 Gata1 D18Ertd653E Enhancer Active Normal Fetal Liver UBERON:0002107 Primary erythroid cells erythroid cell CL:0000038 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq, DNase-seq RT-PCR, RT-RT-qPCR, Northern blot 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 Blood UBERON:0000178 Mouse erythroblast cell erythroblast CL:0000765 Chromatin interaction assay, Functional perturbation assay ChIP-seq, Micro-C, RNA-seq, TT-seq ChIP-RT-qPCR, Western blot, RT-RT-qPCR 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 Blood UBERON:0000178 Mouse erythroblast cell erythroblast CL:0000765 Chromatin interaction assay, Functional perturbation assay ChIP-seq, Micro-C, RNA-seq, TT-seq ChIP-RT-qPCR, Western blot, RT-RT-qPCR 2024 39210046 YY1-controlled regulatory connectivity and transcription are influenced by the cell cycle Mus musculus mm10 chr5 142650068 142650435 Yy1 Nbr1 Enhancer Active Normal Blood UBERON:0000178 Mouse erythroblast cell erythroblast CL:0000765 TF binding assay, Enhancer activity assay ChIP-seq, RNA-seq, TT-seq ChIP-RT-qPCR, Western blot, RT-RT-qPCR 2024 39210046 YY1-controlled regulatory connectivity and transcription are influenced by the cell cycle Mus musculus mm10 chr6 125380026 125380393 Yy1 Cd4 Enhancer Active Normal Blood UBERON:0000178 Mouse erythroblast cell erythroblast CL:0000765 TF binding assay, Enhancer activity assay ChIP-seq, RNA-seq, TT-seq ChIP-RT-qPCR, Western blot, RT-RT-qPCR 2024 39210046 YY1-controlled regulatory connectivity and transcription are influenced by the cell cycle Mus musculus mm10 chr7 27930056 27930423 Yy1 Yy1 Enhancer Active Normal Blood UBERON:0000178 Mouse erythroblast cell erythroblast CL:0000765 TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq, TT-seq ChIP-RT-qPCR, Western blot, RT-RT-qPCR 2024 39210046 YY1-controlled regulatory connectivity and transcription are influenced by the cell cycle Mus musculus mm10 chr9 120150022 120150389 Yy1 Lro41 Enhancer Active Normal Blood UBERON:0000178 Mouse erythroblast cell erythroblast CL:0000765 Chromatin interaction assay, Functional perturbation assay ChIP-seq, Micro-C, RNA-seq, TT-seq ChIP-RT-qPCR, Western blot, RT-RT-qPCR 2016 26673693 Dynamic recruitment of Ets1 to both nucleosome-occupied and -depleted enhancer regions mediates a transcriptional program switch during early T-cell differentiation Mus musculus mm10 chr6 122500000 122502000 Cd8 Enhancer Active Normal Thymus UBERON:0002370 Double-positive thymocytes double-positive thymocyte CL:0000895 Functional perturbation assay RNA-seq CRISPR knockout 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 Testis UBERON:0000473 Sertoli cells Sertoli cell CL:0000216 Enhancer activity assay, Functional perturbation assay, TF binding assay RNA-seq CRISPR knockout, RT-RT-qPCR, Immunofluorescence, ChIP-RT-qPCR 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 Testis UBERON:0000473 Sertoli cells Sertoli cell CL:0000216 Enhancer activity assay, Functional perturbation assay, TF binding assay RNA-seq CRISPR knockout, RT-RT-qPCR, Immunofluorescence, ChIP-RT-qPCR, Transgenic Reporter Assay 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 Thymus UBERON:0002370 CD4-positive, CD8-positive thymocyte double-positive thymocyte CL:0000895 Genome-wide regulatory element profiling ChIP-seq, Strand-specific RNA-seq, FAIRE-seq qRT-PCR, and ChIP-qPCR 2017 28262751 The SWI/SNF chromatin remodelling complex is required for maintenance of lineage specific enhancers Mus musculus mm10 chr7 134235000 134355000 Spn Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic fibroblast CVCL_0003 mouse embryonic fibroblast CL:0000057 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Western blot, Immunoprecipitation, In vitro HAT assay 2017 28262751 The SWI/SNF chromatin remodelling complex is required for maintenance of lineage specific enhancers Mus musculus mm10 chr4 96790000 97810000 Nfia Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic fibroblast CVCL_0003 mouse embryonic fibroblast CL:0000057 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Western blot, Immunoprecipitation, In vitro HAT assay 2014 25209250 A regulatory network controls nephrocan expression and midgut patterning Mus musculus mm10 chr2 123456678 123456750 Sox17 Nepn Enhancer Active Normal Embryo UBERON:0000922 P19 cells CVCL_2151 embryonal carcinoma cell CL:0000031 Enhancer activity assay, TF binding assay Luciferase reporter assay, EMSA, RT-RT-qPCR 2014 25185713 The Runx-PU1 pathway preserves normal and AML/ETO9a leukemic stem cells Mus musculus mm10 chr2 28950000 28970000 Runx1 Spi1 Enhancer Active Normal Bone marrow UBERON:0002371 LSK hematopoietic stem cells hematopoietic stem cell CL:0001029 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay 3C-RT-qPCR, Luciferase reporter assay, ChIP-RT-qPCR, RT-RT-qPCR 2011 21507944 Mouse Rankl Expression Is Regulated in T Cells by c-Fos through a Cluster of Distal Regulatory Enhancers Mus musculus mm10 chr14 77129438 77130831 Tnfsf11 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat T cells CVCL_0065 T lymphoblast CL:0002419 Enhancer activity assay ChIP-chip, RNA-seq Luciferase Reporter Assay, RT-RT-qPCR 2011 20942803 The pancreatic islet ?|??-cell-enriched transcription factor Pdx-1 regulates Slc30a8 gene transcription through an intronic enhancer Mus musculus mm10 chr16 13020425 13021045 Pdx-1 Slc30A8 Enhancer Active Normal Pancreatic islet UBERON:0000006 ¦ÂTC-3 CVCL_B077 pancreatic beta cell CL:0000169 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2011 20942803 The pancreatic islet ?|??-cell-enriched transcription factor Pdx-1 regulates Slc30a8 gene transcription through an intronic enhancer Mus musculus mm10 chr16 13020425 13021045 Pdx-1 Slc30A8 Enhancer Active Normal Pancreatic islet UBERON:0000006 ¦ÂTC-6 CVCL_B078 pancreatic beta cell CL:0000169 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2011 20942803 The pancreatic islet ?|??-cell-enriched transcription factor Pdx-1 regulates Slc30a8 gene transcription through an intronic enhancer Mus musculus mm10 chr16 13020425 13021045 Pdx-1 Slc30A8 Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2011 21331042 Tbx6-dependent Sox2 regulation determines neural or mesodermal fate in axial stem cells Mus musculus mm10 chr3 34668260 34668560 Lef1 Sox2 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay Transgenic Reporter Assay, CRISPR Knockout, EMSA, in situ Hybridization, Immunohistochemistry 2011 21331042 Tbx6-dependent Sox2 regulation determines neural or mesodermal fate in axial stem cells Mus musculus mm10 chr3 34668260 34668560 Lef1 Sox2 Enhancer Active Normal Embryo UBERON:0000922 primary embryonic tissue embryonic cell CL:0000000 Enhancer activity assay, Functional perturbation assay Transgenic Reporter Assay, CRISPR Knockout, EMSA, in situ Hybridization, Immunohistochemistry 2017 28262751 The SWI/SNF chromatin remodelling complex is required for maintenance of lineage specific enhancers Mus musculus mm10 chr7 134235000 134355000 Smarca4; Smarcc1; Smarcb1 Spn Enhancer Active Normal Embryo UBERON:0000922 Mouse Embryonic Fibroblast (MEF) CVCL_0003 mouse embryonic fibroblast CL:0000057 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Western blot, Immunoprecipitation, In vitro HAT Assay 2016 27941798 ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice Mus musculus mm10 chr15 63606018 63757541 Gsdmc Enhancer Active Normal Colon UBERON:0001155 Colonic epithelial colon epithelial cell CL:1000348 Enhancer activity assay ChIP-seq, RNA-seq RT-RT-qPCR 2020 32290491 Expression of a Constitutively Active Form of Hck in Chondrocytes Activates Wnt and Hedgehog Signaling Pathways, and Induces Chondrocyte Proliferation in Mice Mus musculus mm10 chr2 155134800 155135200 Runx2 Hck Enhancer Active Normal Cartilage UBERON:0002418 Primary Mouse Chondrocytes chondrocyte CL:0000138 TF binding assay, Functional perturbation assay CAGE, ChIP-seq, RNA-seq, Microarray ChIP-RT-qPCR, RT-RT-qPCR 2020 32290491 Expression of a Constitutively Active Form of Hck in Chondrocytes Activates Wnt and Hedgehog Signaling Pathways, and Induces Chondrocyte Proliferation in Mice Mus musculus mm10 chr2 155134800 155135200 Runx2 Hck Enhancer Active Normal Cartilage UBERON:0002418 ATDC5 Chondrogenic CVCL_3894 chondrocyte CL:0000138 TF binding assay, Functional perturbation assay CAGE, ChIP-seq, RNA-seq, Microarray ChIP-RT-qPCR, RT-RT-qPCR 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 126984000 126986000 Ctcf Fgf23 Enhancer Active Disease chronic kidney disease MONDO:0005102 DOID:784 Kidney UBERON:0002113 Osteocytes osteocyte CL:0000064 Functional genomics assay, Epigenomic profiling assay, Transcriptional regulation assay ChIP-seq ChIP-RT-qPCR, qRT-PCR, Genotyping PCR, Sanger Sequencing 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 127030000 127032000 Ctcf Fgf23 Enhancer Active Disease chronic kidney disease MONDO:0005102 DOID:784 Kidney UBERON:0002113 Osteocytes osteocyte CL:0000064 Functional genomics assay, Epigenomic profiling assay, Transcriptional regulation assay ChIP-seq ChIP-RT-qPCR, qRT-PCR, Genotyping PCR, Sanger Sequencing 2017 28121289 Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq Mus musculus mm10 chr4 114743698 114748936 Lacz Enhancer Active Normal Blood vessel UBERON:0001981 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ChIP-seq (Ep300 bioChIP-seq) Transgenic Reporter Assay (LacZ) 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 44203545 44203644 Nfil3 Il12B Enhancer Active Normal Bone Marrow UBERON:0002371 Bone marrow-derived macrophages macrophage CL:0000235 Enhancer activity assay, TF binding assay, Functional perturbation assay Luciferase Reporter Assay, qRT-PCR, Western blot, EMSA, Knockout Mouse Model, Mass Spectrometry 2016 26809507 Integrated genome-scale analysis of the transcriptional regulatory landscape in a blood stem/progenitor cell model Mus musculus mm10 chr4 114484000 114485000 Tal1 Tal1 Enhancer Active Normal Fetal liver UBERON:0002107 HPC-7 CVCL_7992 hematopoietic progenitor cell CL:0000837 Enhancer activity assay ChIP-seq Transgenic Reporter Assay 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 Fetal liver UBERON:0002107 HPC-7 CVCL_7992 hematopoietic progenitor cell CL:0000837 Enhancer activity assay ChIP-seq Transgenic Reporter Assay 2017 28614915 Identification of an Enhancer Critical for the ephrin-A5 Gene Expression in the Posterior Region of the Mesencephalon Mus musculus mm10 chr1 134714823 134715623 Ascl1 Efna5 Enhancer Active Normal Brain UBERON:0000955 Primary mouse mesencephalic cells neuron CL:0000540 Enhancer activity assay Transgenic Reporter Assay, Luciferase Reporter Assay, EMSA 2007 17053039 Transcriptional Control of Receptor Activator of Nuclear Factor-B 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 Blood UBERON:0000178 Enhancer activity assay, TF binding assay Luciferase reporter assay, ChIP-RT-qPCR, qRT-PCR, EMSA 2007 17053039 Transcriptional Control of Receptor Activator of Nuclear Factor-B 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 75357027 Creb1 Tnfsf11 Enhancer Active Normal Blood UBERON:0000178 Enhancer activity assay, TF binding assay Luciferase reporter assay, ChIP-RT-qPCR, qRT-PCR, EMSA 2007 17053039 Transcriptional Control of Receptor Activator of Nuclear Factor-B 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 Blood UBERON:0000178 Enhancer activity assay, TF binding assay Luciferase reporter assay, ChIP-RT-qPCR, qRT-PCR, EMSA 2007 17053039 Transcriptional Control of Receptor Activator of Nuclear Factor-B 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 Blood UBERON:0000178 Enhancer activity assay, TF binding assay Luciferase reporter assay, ChIP-RT-qPCR, qRT-PCR, EMSA 2007 17053039 Transcriptional Control of Receptor Activator of Nuclear Factor-B 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 Blood UBERON:0000178 Enhancer activity assay, TF binding assay Luciferase reporter assay, ChIP-RT-qPCR, qRT-PCR, EMSA 2007 17053039 Transcriptional Control of Receptor Activator of Nuclear Factor-B 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 Blood UBERON:0000178 Enhancer activity assay, TF binding assay Luciferase reporter assay, ChIP-RT-qPCR, qRT-PCR, EMSA 2007 17053039 Transcriptional Control of Receptor Activator of Nuclear Factor-B 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 Blood UBERON:0000178 Enhancer activity assay, TF binding assay Luciferase reporter assay, ChIP-RT-qPCR, qRT-PCR, EMSA 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 Bone UBERON:0001474 Primary mouse osteoblasts osteoblast CL:0000062 Enhancer activity assay, TF binding assay Transgenic Reporter Assay, Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, GST-pulldown 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 Bone UBERON:0001474 Primary mouse osteoblasts osteoblast CL:0000062 Enhancer activity assay, TF binding assay, Functional perturbation assay Transgenic Reporter Assay, Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, GST-pulldown, Site-directed Mutagenesis 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 Bone UBERON:0001474 Primary mouse osteoblasts osteoblast CL:0000062 Enhancer activity assay, TF binding assay Transgenic Reporter Assay, Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, GST-pulldown 2019 31666509 An enhancer cluster controls gene activity and topology of the SCN5A-SCN10A locus in vivo Mus musculus mm10 chr9 119385000 119387000 Scn5A Enhancer Active Normal Heart UBERON:0000948 Cardiomyocytes cardiomyocyte CL:0000746 Functional perturbation assay CRISPR Knockout, RT-RT-qPCR 2017 28121289 Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq Mus musculus mm10 chr11 32145270 32146411 Lacz Enhancer Active Normal Blood vessel UBERON:0001981 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ChIP-seq (Ep300 bioChIP-seq) Transgenic Reporter Assay (LacZ) 2017 28121289 Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq Mus musculus mm10 chr13 28809515 28811310 Lacz Enhancer Active Normal Blood vessel UBERON:0001981 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ChIP-seq (Ep300 bioChIP-seq) Transgenic Reporter Assay (LacZ) 2017 28121289 Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq Mus musculus mm10 chr17 12982583 12985936 Lacz Enhancer Active Normal Blood vessel UBERON:0001981 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ChIP-seq (Ep300 bioChIP-seq) Transgenic Reporter Assay (LacZ) 2017 28121289 Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq Mus musculus mm10 chr3 87786601 87790798 Lacz Enhancer Active Normal Blood vessel UBERON:0001981 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ChIP-seq (Ep300 bioChIP-seq) Transgenic Reporter Assay (LacZ) 2017 28121289 Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq Mus musculus mm10 chr5 93426293 93427320 Lacz Enhancer Active Normal Blood vessel UBERON:0001981 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ChIP-seq (Ep300 bioChIP-seq) Transgenic Reporter Assay (LacZ) 2017 28121289 Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq Mus musculus mm10 chr7 116256647 116260817 Lacz Enhancer Active Normal Heart UBERON:0000948 Cardiomyocytes cardiomyocyte CL:0000746 Enhancer activity assay ChIP-seq (Ep300 bioChIP-seq) Transgenic Reporter Assay (LacZ) 2017 28121289 Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq Mus musculus mm10 chr8 28216799 28218903 Lacz Enhancer Active Normal Blood vessel UBERON:0001981 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ChIP-seq (Ep300 bioChIP-seq) Transgenic Reporter Assay (LacZ) 2017 28121289 Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq Mus musculus mm10 chr8 28216817 28218896 Lacz Enhancer Active Normal Blood vessel UBERON:0001981 Endothelial cells endothelial cell CL:0000115 Enhancer activity assay ChIP-seq (Ep300 bioChIP-seq) Transgenic Reporter Assay (LacZ) 2017 27920250 Renal Anemia Model Mouse Established by Transgenic Rescue with Erythropoietin Gene Lacking Kidney-specific Regulatory Elements Mus musculus mm10 chr5 137487678 137501478 Epo Enhancer Active Normal Kidney UBERON:0002113 Renal EPO-producing cells renal erythropoietin-producing cell CL:0000647 Enhancer activity assay, Functional perturbation assay Transgenic Reporter Assay, CRISPR knockout, CRISPRi, RT-RT-qPCR 2016 26673693 Dynamic recruitment of Ets1 to both nucleosome-occupied and -depleted enhancer regions mediates a transcriptional program switch during early T-cell differentiation Mus musculus mm10 chr14 53200000 53202000 Ets1 Tcra Enhancer Active Normal Thymus UBERON:0002370 Double-negative thymocytes double-negative thymocyte CL:0000894 Enhancer activity assay ChIP-seq ChIP-RT-qPCR 2016 26673693 Dynamic recruitment of Ets1 to both nucleosome-occupied and -depleted enhancer regions mediates a transcriptional program switch during early T-cell differentiation Mus musculus mm10 chr6 72100000 72102000 Ets1 Tcrb Enhancer Active Normal Thymus UBERON:0002370 Double-negative thymocytes double-negative thymocyte CL:0000894 Enhancer activity assay ChIP-seq ChIP-RT-qPCR 2014 25030696 The active enhancer network operated by liganded RXR supports angiogenic activity in macrophages Mus musculus mm10 chr10 95800000 95800200 Rxr Angptl4 Enhancer Active Normal Bone Marrow UBERON:0002371 Bone marrow-derived macrophages macrophage CL:0000235 Enhancer activity assay ChIP-seq, GRO-seq ChIP-RT-qPCR, RT-RT-qPCR 2014 25030696 The active enhancer network operated by liganded RXR supports angiogenic activity in macrophages Mus musculus mm10 chr11 82100000 82100200 Rxr Ccl2 Enhancer Active Normal Bone Marrow UBERON:0002371 Bone marrow-derived macrophages macrophage CL:0000235 TF binding assay ChIP-seq ChIP-RT-qPCR 2014 25030696 The active enhancer network operated by liganded RXR supports angiogenic activity in macrophages Mus musculus mm10 chr4 5320000 5320100 Rxr Abca1 Enhancer Active Normal Bone Marrow UBERON:0002371 Bone marrow-derived macrophages macrophage CL:0000235 Enhancer activity assay ChIP-seq, GRO-seq ChIP-RT-qPCR, RT-RT-qPCR 2016 27920250 Renal Anemia Model Mouse Established by Transgenic Rescue with Erythropoietin Gene Lacking Kidney-specific Regulatory Elements Mus musculus mm10 chr5 137531500 137531600 Hif1A; Hif2A Epo Enhancer Active Normal Liver UBERON:0002107 Hepatocytes hepatocyte CL:0000182 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, Transgenic Reporter Assay, EMSA 2009 19212405 ChIP-seq accurately predicts tissue-specific activity of enhancers Mus musculus mm10 chr1 134976575 134977476 Enhancer Active Normal Forebrain UBERON:0001890 Transgenic mouse embryo embryonic cell CL:0000000 Transgenic reporter assay ChIP-seq In vivo transgenic reporter assay 2009 19212405 ChIP-seq accurately predicts tissue-specific activity of enhancers Mus musculus mm10 chr1 140396600 140397726 Enhancer Active Normal Forebrain UBERON:0001890 Transgenic mouse embryo embryonic cell CL:0000000 Transgenic reporter assay ChIP-seq In vivo transgenic reporter assay 2009 19212405 ChIP-seq accurately predicts tissue-specific activity of enhancers Mus musculus mm10 chr1 165828000 165828801 Enhancer Active Normal Midbrain UBERON:0001891 Transgenic mouse embryo embryonic cell CL:0000000 Transgenic reporter assay ChIP-seq In vivo transgenic reporter assay 2009 19212405 ChIP-seq accurately predicts tissue-specific activity of enhancers Mus musculus mm10 chr1 167864800 167866051 Enhancer Active Normal Forebrain UBERON:0001890 Transgenic mouse embryo embryonic cell CL:0000000 Transgenic reporter assay ChIP-seq In vivo transgenic reporter assay 2009 19212405 ChIP-seq accurately predicts tissue-specific activity of enhancers Mus musculus mm10 chr1 192551300 192552876 Enhancer Active Normal Forebrain UBERON:0001890 Transgenic mouse embryo embryonic cell CL:0000000 Transgenic reporter assay ChIP-seq In vivo transgenic reporter assay 2009 19212405 ChIP-seq accurately predicts tissue-specific activity of enhancers Mus musculus mm10 chr1 41975300 41976076 Enhancer Active Normal Forebrain UBERON:0001890 Transgenic mouse embryo embryonic cell CL:0000000 Transgenic reporter assay ChIP-seq In vivo transgenic reporter assay 2009 19212405 ChIP-seq accurately predicts tissue-specific activity of enhancers Mus musculus mm10 chr2 137073600 137074376 Enhancer Active Normal Midbrain UBERON:0001891 Transgenic mouse embryo embryonic cell CL:0000000 Transgenic reporter assay ChIP-seq In vivo transgenic reporter assay 2009 19212405 ChIP-seq accurately predicts tissue-specific activity of enhancers Mus musculus mm10 chr3 141901125 141902126 Enhancer Active Normal Midbrain UBERON:0001891 Transgenic mouse embryo embryonic cell CL:0000000 Transgenic reporter assay ChIP-seq In vivo transgenic reporter assay 2009 19212405 ChIP-seq accurately predicts tissue-specific activity of enhancers Mus musculus mm10 chr3 30006475 30007726 Enhancer Active Normal Midbrain UBERON:0001891 Transgenic mouse embryo embryonic cell CL:0000000 Transgenic reporter assay ChIP-seq In vivo transgenic reporter assay 2009 19212405 ChIP-seq accurately predicts tissue-specific activity of enhancers Mus musculus mm10 chr3 34986900 34988201 Enhancer Active Normal Forebrain UBERON:0001890 Transgenic mouse embryo embryonic cell CL:0000000 Transgenic reporter assay ChIP-seq In vivo transgenic reporter assay 2009 19212405 ChIP-seq accurately predicts tissue-specific activity of enhancers Mus musculus mm10 chr3 5224600 5225676 Enhancer Active Normal Forebrain UBERON:0001890 Transgenic mouse embryo embryonic cell CL:0000000 Transgenic reporter assay ChIP-seq In vivo transgenic reporter assay 2009 19212405 ChIP-seq accurately predicts tissue-specific activity of enhancers Mus musculus mm10 chr3 55558975 55559751 Enhancer Active Normal Limb UBERON:0002101 Transgenic mouse embryo embryonic cell CL:0000000 Transgenic reporter assay ChIP-seq In vivo transgenic reporter assay 2009 19212405 ChIP-seq accurately predicts tissue-specific activity of enhancers Mus musculus mm10 chr3 84741550 84742501 Enhancer Active Normal Forebrain UBERON:0001890 Transgenic mouse embryo embryonic cell CL:0000000 Transgenic reporter assay ChIP-seq In vivo transgenic reporter assay 2009 19212405 ChIP-seq accurately predicts tissue-specific activity of enhancers Mus musculus mm10 chr4 44864575 44865251 Enhancer Active Normal Limb UBERON:0002101 Transgenic mouse embryo embryonic cell CL:0000000 Transgenic reporter assay ChIP-seq In vivo transgenic reporter assay 2009 19212405 ChIP-seq accurately predicts tissue-specific activity of enhancers Mus musculus mm10 chr4 5888950 5890926 Enhancer Active Normal Forebrain UBERON:0001890 Transgenic mouse embryo embryonic cell CL:0000000 Transgenic reporter assay ChIP-seq In vivo transgenic reporter assay 2009 19212405 ChIP-seq accurately predicts tissue-specific activity of enhancers Mus musculus mm10 chr4 6840325 6841401 Enhancer Active Normal Forebrain UBERON:0001890 Transgenic mouse embryo embryonic cell CL:0000000 Transgenic reporter assay ChIP-seq In vivo transgenic reporter assay 2009 19212405 ChIP-seq accurately predicts tissue-specific activity of enhancers Mus musculus mm10 chr4 71828300 71829751 Enhancer Active Normal Forebrain UBERON:0001890 Transgenic mouse embryo embryonic cell CL:0000000 Transgenic reporter assay ChIP-seq In vivo transgenic reporter assay 2009 19212405 ChIP-seq accurately predicts tissue-specific activity of enhancers Mus musculus mm10 chr4 97774675 97775901 Enhancer Active Normal Forebrain UBERON:0001890 Transgenic mouse embryo embryonic cell CL:0000000 Transgenic reporter assay ChIP-seq In vivo transgenic reporter assay 2009 19212405 ChIP-seq accurately predicts tissue-specific activity of enhancers Mus musculus mm10 chr5 74828975 74829601 Enhancer Active Normal Limb UBERON:0002101 Transgenic mouse embryo embryonic cell CL:0000000 Transgenic reporter assay ChIP-seq In vivo transgenic reporter assay 2009 19212405 ChIP-seq accurately predicts tissue-specific activity of enhancers Mus musculus mm10 chr6 144260800 144262201 Enhancer Active Normal Midbrain UBERON:0001891 Transgenic mouse embryo embryonic cell CL:0000000 Transgenic reporter assay ChIP-seq In vivo transgenic reporter assay 2009 19212405 ChIP-seq accurately predicts tissue-specific activity of enhancers Mus musculus mm10 chr6 28346175 28347126 Enhancer Active Normal Forebrain UBERON:0001890 Transgenic mouse embryo embryonic cell CL:0000000 Transgenic reporter assay ChIP-seq In vivo transgenic reporter assay 2009 19212405 ChIP-seq accurately predicts tissue-specific activity of enhancers Mus musculus mm10 chr6 51026850 51028001 Enhancer Active Normal Forebrain UBERON:0001890 Transgenic mouse embryo embryonic cell CL:0000000 Transgenic reporter assay ChIP-seq In vivo transgenic reporter assay 2009 19212405 ChIP-seq accurately predicts tissue-specific activity of enhancers Mus musculus mm10 chr6 51146275 51148026 Enhancer Active Normal Midbrain UBERON:0001891 Transgenic mouse embryo embryonic cell CL:0000000 Transgenic reporter assay ChIP-seq In vivo transgenic reporter assay 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 Thymus UBERON:0002370 Thymocytes (ETP/DN/DP/CD4 SP) thymocyte CL:0000893 Enhancer activity assay, TF binding assay, Functional perturbation assay Transgenic reporter assay, CRISPR knockout, ChIP-RT-qPCR, RT-RT-qPCR 2016 26673693 Dynamic recruitment of Ets1 to both nucleosome-occupied and -depleted enhancer regions mediates a transcriptional program switch during early T-cell differentiation Mus musculus mm10 chr6 42300000 42301500 Ets1 Tcrb Enhancer Active Normal Thymus UBERON:0002370 DN/DP thymocytes thymocyte CL:0000894 Enhancer activity assay, TF binding assay ChIP-seq, MNase-seq ChIP-RT-qPCR 2014 24920384 Functional analysis of limb transcriptional enhancers in the mouse Mus musculus mm10 chr1 165827290 165830012 Kifap3 Enhancer Active Normal Limb bud UBERON:0005417 Limb mesenchymal cells mesenchymal cell CL:0000134 Enhancer activity assay, Functional perturbation assay Transgenic reporter assay, CRISPR knockout, RT-RT-qPCR, Whole mount in situ hybridization 2014 24905168 Reorganization of Enhancer Patterns in Transition from Naive to Primed Pluripotency Mus musculus mm10 chr5 115320000 115320500 Pou5F1; Otx2 Fgf5 Enhancer Active Normal Embryo UBERON:0000922 Embryonic stem cells (ESC) embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq ChIP-RT-qPCR 2014 24905168 Reorganization of Enhancer Patterns in Transition from Naive to Primed Pluripotency Mus musculus mm10 chr5 115345000 115345600 Pou5F1; Otx2 Fgf5 Enhancer Active Normal Embryo UBERON:0000922 Embryonic stem cells (ESC) embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay ChIP-seq, RNA-seq ChIP-RT-qPCR 2014 24905168 Reorganization of Enhancer Patterns in Transition from Naive to Primed Pluripotency Mus musculus mm10 chr5 142680000 142680600 Pou5F1; Esrrb Tbx3 Enhancer Silenced Normal Embryo UBERON:0000922 Embryonic stem cells (ESC) embryonic stem cell CL:0002322 Enhancer activity assay ChIP-seq, RNA-seq Transgenic reporter assay 2014 24905168 Reorganization of Enhancer Patterns in Transition from Naive to Primed Pluripotency Mus musculus mm10 chr4 101250000 101250600 Pou5F1; Otx2 Pou3F1 Enhancer Active Normal Embryo UBERON:0000922 Epiblast-like cells (EpiLC) epiblast-like cell CL:0002322 Enhancer activity assay ChIP-seq, RNA-seq Transgenic reporter assay 2011 21498522 Mouse Rankl Expression Is Regulated in T Cells by c-Fos through a Cluster of Distal Regulatory Enhancers Designated the T Cell Control Region Mus musculus mm10 chr14 77129438 77130831 Rankl Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat cells CVCL_0065 T lymphoblast CL:0002419 Enhancer activity assay Luciferase Reporter Assay 2011 21797989 Differentiation and fiber type-specific activity of a muscle creatine kinase intronic enhancer Mus musculus mm10 chr19 4473287 4473381 Myod Mck Enhancer Active Normal Skeletal muscle UBERON:0001134 MM14 myocytes CVCL_W869 myocyte CL:0000187 Enhancer activity assay, TF binding assay ChIP-seq CAT Reporter Assay, Transgenic Reporter Assay, ChIP-RT-qPCR, EMSA 2011 21797989 Differentiation and fiber type-specific activity of a muscle creatine kinase intronic enhancer Mus musculus mm10 chr19 4473287 4473381 Myod Mck Enhancer Active Normal Skeletal muscle UBERON:0001134 C2C12 myocytes CVCL_0188 myoblast CL:0000187 Enhancer activity assay, TF binding assay ChIP-seq CAT Reporter Assay, Transgenic Reporter Assay, ChIP-RT-qPCR, EMSA 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 lymphoma MONDO:0005029 DOID:164 Blood UBERON:0000178 M12 B cells B cell lymphoma cell CL:0000945 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, EMSA, RT-RT-qPCR 2020 32290615 Expression of a Constitutively Active Form of Hck in Chondrocytes Activates Wnt and Hedgehog Signaling Pathways, and Induces Chondrocyte Proliferation in Mice Mus musculus mm10 chr2 171850200 171850400 Runx2 Hck Enhancer Active Normal Cartilage UBERON:0002418 Primary Chondrocytes chondrocyte CL:0000138 TF binding assay, Functional perturbation assay RNA-seq, CAGE, ChIP-seq ChIP-RT-qPCR, qRT-PCR, siRNA Knockdown, Adenoviral Overexpression 2023 37365500 Identification and characterization of transcribed enhancers during cerebellar development through enhancer RNA analysis Mus musculus mm10 chr4 82235567 82235814 Atoh1 Nfib Enhancer Active Normal Cerebellum UBERON:0002037 Cerebellar granule cells cerebellar granule cell CL:0001031 TF binding assay, Enhancer activity assay CAGE-seq, ChIP-seq RNAscope FISH, Colorimetric in situ hybridization 2023 37365500 Identification and characterization of transcribed enhancers during cerebellar development through enhancer RNA analysis Mus musculus mm10 chr4 81219772 81219968 Atoh1 Nfib Enhancer Active Normal Cerebellum UBERON:0002037 Cerebellar granule cells cerebellar granule cell CL:0001031 TF binding assay, Enhancer activity assay CAGE-seq, ChIP-seq RNAscope FISH, Colorimetric in situ hybridization 2023 37365500 Identification and characterization of transcribed enhancers during cerebellar development through enhancer RNA analysis Mus musculus mm10 chr4 82185096 82185615 Atoh1 Nfib Enhancer Active Normal Cerebellum UBERON:0002037 Cerebellar granule cells cerebellar granule cell CL:0001031 TF binding assay, Enhancer activity assay CAGE-seq, ChIP-seq Colorimetric in situ hybridization 2023 37365500 Identification and characterization of transcribed enhancers during cerebellar development through enhancer RNA analysis Mus musculus mm10 chr4 81212120 81212422 Atoh1 Nfib Enhancer Active Normal Cerebellum UBERON:0002037 Cerebellar granule cells cerebellar granule cell CL:0001031 TF binding assay CAGE-seq, ChIP-seq qRT-PCR, and ChIP-qPCR 2011 21486496 Identification of a novel intronic enhancer responsible for the transcriptional regulation of musashi1 in neural stem/progenitor cells Mus musculus mm10 chr18 12947300 12947895 Msi1 Enhancer Active Normal Brain UBERON:0000955 Neural stem/progenitor neural stem cell CL:0002672 Enhancer activity assay, Functional perturbation assay RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay, BAC deletion assay, RT-RT-qPCR, Flow cytometry, Immunohistochemistry 2011 21486496 Identification of a novel intronic enhancer responsible for the transcriptional regulation of musashi1 in neural stem/progenitor cells Mus musculus mm10 chr18 12947300 12947895 Msi1 Enhancer Active Normal Brain UBERON:0000955 Mouse embryonic stem embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay RNA-seq Luciferase Reporter Assay, Transgenic Reporter Assay, BAC deletion assay, RT-RT-qPCR, Flow cytometry, Immunohistochemistry 2011 21486496 Identification of a novel intronic enhancer responsible for the transcriptional regulation of musashi1 in neural stem/progenitor cells Mus musculus mm10 chr18 12880000 12880676 Msi1 Enhancer Active Normal Brain UBERON:0000955 Neural stem/progenitor neural stem cell CL:0002672 Enhancer activity assay, Functional perturbation assay RNA-seq Luciferase Reporter Assay, BAC deletion assay, RT-RT-qPCR 2011 21486496 Identification of a novel intronic enhancer responsible for the transcriptional regulation of musashi1 in neural stem/progenitor cells Mus musculus mm10 chr18 12880000 12880676 Msi1 Enhancer Active Normal Brain UBERON:0000955 Mouse embryonic stem embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay RNA-seq Luciferase Reporter Assay, BAC deletion assay, RT-RT-qPCR 2011 20942803 The pancreatic islet ?|??-cell-enriched transcription factor Pdx-1 regulates Slc30a8 gene transcription through an intronic enhancer Mus musculus mm10 chr16 13020625 13020824 Pdx-1 Slc30A8 Enhancer Active Normal Pancreatic islet UBERON:0000006 ¦ÂTC-3 CVCL_B077 pancreatic beta cell CL:0000169 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, EMSA, ChIP-RT-qPCR, Site-directed Mutagenesis 2011 20864515 Prep1 Controls Insulin Glucoregulatory Function in Liver by Transcriptional Targeting of SHP1 Tyrosine Phosphatase Mus musculus mm10 chr6 1778 2113 Prep1; Pbx1 Ptpn6 Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepG2 CVCL_0027 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, TF binding assay, Functional perturbation assay Luciferase Reporter Assay, ChIP-RT-qPCR, Re-ChIP, RT-RT-qPCR, Western blot, Euglycemic Hyperinsulinemic Clamp, Antisense Oligonucleotide Silencing 2011 20864515 Prep1 Controls Insulin Glucoregulatory Function in Liver by Transcriptional Targeting of SHP1 Tyrosine Phosphatase Mus musculus mm10 chr6 1778 2113 Prep1; Pbx1 Ptpn6 Enhancer Active Normal Liver UBERON:0002107 NMuLi hepatocyte CL:0000182 Enhancer activity assay, TF binding assay, Functional perturbation assay Luciferase Reporter Assay, ChIP-RT-qPCR, Re-ChIP, RT-RT-qPCR, Western blot, Euglycemic Hyperinsulinemic Clamp, Antisense Oligonucleotide Silencing 2011 20864515 Prep1 Controls Insulin Glucoregulatory Function in Liver by Transcriptional Targeting of SHP1 Tyrosine Phosphatase Mus musculus mm10 chr6 1778 2113 Prep1; Pbx1 Ptpn6 Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Enhancer activity assay, TF binding assay, Functional perturbation assay Luciferase Reporter Assay, ChIP-RT-qPCR, Re-ChIP, RT-RT-qPCR, Western blot, Euglycemic Hyperinsulinemic Clamp, Antisense Oligonucleotide Silencing 2019 31784100 ETV2/ER71 regulates the generation of FLK1+ cells from mouse embryonic stem cells through miR-126-MAPK signaling Mus musculus mm10 chr5 75546054 75548325 Etv2 Flk1 (Vegfr2) Enhancer Active Normal Embryo UBERON:0000922 Mouse Embryonic Stem Cells (mESCs) mouse embryonic stem cell CL:0002322 Enhancer activity assay, TF binding assay miRNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, Flow Cytometry 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; Smad4; Tcf4 Dlx5 Enhancer Active Normal Skeletal muscle UBERON:0001134 C2C12 cells CVCL_0188 myoblast CL:0000187 Enhancer activity assay, TF binding assay, Chromatin interaction assay Luciferase Reporter Assay, ChIP-RT-qPCR, GST Pull-down, Co-IP, RT-RT-qPCR, Western blot 2016 26787680 Desmin enters the nucleus of cardiac stem cells and modulates Nkx25 expression by participating in transcription factor complexes that interact with the nkx25 gene Mus musculus mm10 chr17 26841565 26842075 Nkx2-5 Enhancer Active Normal Heart UBERON:0000948 Cardiac progenitors cardiac progenitor cell CL:0002248 Enhancer activity assay Luciferase Reporter Assay, RT-RT-qPCR, Western blot 2016 26787680 Desmin enters the nucleus of cardiac stem cells and modulates Nkx25 expression by participating in transcription factor complexes that interact with the nkx25 gene Mus musculus mm10 chr17 26839438 26839943 Nkx2-5 Enhancer Active Normal Heart UBERON:0000948 Cardiac progenitors cardiac progenitor cell CL:0002248 Enhancer activity assay Luciferase Reporter Assay, RT-RT-qPCR 2018 29967281 A Muscle-Specific Enhancer RNA Mediates Cohesin Recruitment and Regulates Transcription in Trans Mus musculus mm10 chr7 53627200 53627771 Myog Enhancer Active Normal Skeletal muscle UBERON:0001134 C2C12 myoblasts CVCL_0188 myoblast CL:0000187 Enhancer activity assay, RNA-mediated regulation assay RNA-seq qRT-PCR, and ChIP-qPCR 2017 27920250 Renal Anemia Model Mouse Established by Transgenic Rescue with Erythropoietin Gene Lacking Kidney-specific Regulatory Elements Mus musculus mm10 chr5 135080000 135100000 Epo Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 Human hepatocellular carcinoma cell hepatocellular carcinoma cell CL:0000182 Enhancer activity assay Luciferase Reporter Assay 2014 24734888 A mouse renin distal enhancer is essential for blood pressure homeostasis in BAC-rescued renin-null mutant mice Mus musculus mm10 chr1 133452484 133452725 Ren-1C Enhancer Active Normal Kidney UBERON:0002113 Mouse juxtaglomerular cells juxtaglomerular cell CL:0000647 Enhancer activity assay, Functional perturbation assay BAC Transgenic Reporter Assay, Luciferase Reporter Assay, Northern blot, RT-RT-qPCR, Radioimmunoassay, In situ hybridization, Conditional knockout rescue 2017 27920250 Renal Anemia Model Mouse Established by Transgenic Rescue with Erythropoietin Gene Lacking Kidney-specific Regulatory Elements Mus musculus mm10 chr5 135091600 135091864 Epo Enhancer Active Normal Kidney UBERON:0002113 Renal EPO-producing cells renal erythropoietin-producing cell CL:0000647 Enhancer activity assay Luciferase Reporter Assay 2016 27920250 Renal Anemia Model Mouse Established by Transgenic Rescue with Erythropoietin Gene Lacking Kidney-specific Regulatory Elements Mus musculus mm10 chr5 137521712 137522012 Epo Enhancer Active Normal Kidney UBERON:0002113 Renal EPO-producing cells renal erythropoietin-producing cell CL:0000647 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, Transgenic Reporter Assay, RT-RT-qPCR 2003 30146317 The Evf2 Ultraconserved Enhancer lncRNA Functionally and Spatially Organizes Megabase Distant Genes in the Developing Forebrain Mus musculus mm10 chr15 76897064 76899064 Lsm8 Enhancer Active Normal Forebrain UBERON:0001890 Embryonic forebrain cell neural progenitor cell CL:0002672 Enhancer activity assay, Chromatin interaction assay 3C, Immunofluorescence, RT-PCR, RT-RT-qPCR 2016 27867070 The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances Mus musculus mm10 chr5 29641240 29642424 Shh Enhancer Active Normal Limb bud UBERON:0005417 Mouse E14 ESCs CVCL_2167 mouse embryonic stem cell CL:0002322 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay 4C-seq LacZ transgenic reporter assay, Cre-loxP genome rearrangement, RT-RT-qPCR, Whole-mount in situ hybridization, Skeletal preparation 2016 27867070 The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances Mus musculus mm10 chr5 29641240 29642424 Shh Enhancer Active Normal Limb bud UBERON:0005417 E11.5 embryonic limb bud cells limb bud cell CL:0000000 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay 4C-seq LacZ transgenic reporter assay, Cre-loxP genome rearrangement, RT-RT-qPCR, Whole-mount in situ hybridization, Skeletal preparation 2023 37537334 Transcription modulates chromatin dynamics and locus configuration sampling Mus musculus mm10 chr2 105300000 105310000 Pax6 Enhancer Active Normal Pancreatic islet UBERON:0000006 ¦ÂTC-3 cells CVCL_B077 pancreatic beta cell CL:0000169 Chromatin interaction assay, Enhancer activity assay Capture-C, ATAC-seq, ChIP-chip 3D DNA FISH, Computational modeling 2023 37537334 Transcription modulates chromatin dynamics and locus configuration sampling Mus musculus mm10 chr2 105480000 105490000 Pax6 Enhancer Active Normal Pancreatic islet UBERON:0000006 ¦ÂTC-3 cells CVCL_B077 pancreatic beta cell CL:0000169 Chromatin interaction assay, Enhancer activity assay Capture-C, ATAC-seq, ChIP-chip 3D DNA FISH, Computational modeling 2016 26957309 Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters Mus musculus mm10 chr8 62860000 62865000 Neural Development Genes Enhancer Active Normal Forebrain UBERON:0001890 Mouse embryonic day 11.5 forebrain tissue neural progenitor cell CL:0002672 Enhancer activity assay ChIP-seq Transgenic reporter assay 2014 24920384 Functional analysis of limb transcriptional enhancers in the mouse Mus musculus mm10 chr4 117063735 117065404 Tmem53 Enhancer Active Normal Limb bud UBERON:0005417 Limb mesenchymal cells mesenchymal cell CL:0000134 Enhancer activity assay, Functional perturbation assay Transgenic reporter assay, CRISPR knockout, RT-RT-qPCR, Whole mount in situ hybridization 2014 24915132 Identification of two regulatory elements controlling Fucosyltransferase 7 transcription in murine CD4+ T cells Mus musculus mm10 chr2 25276566 25277137 Fut7 Enhancer Active Normal Blood UBERON:0000178 Primary CD4+ Th1 cells CD4-positive Th1 cell CL:0000897 Enhancer activity assay ChIP-on-chip Luciferase reporter assay 2014 24915132 Identification of two regulatory elements controlling Fucosyltransferase 7 transcription in murine CD4+ T cells Mus musculus mm10 chr2 25277864 25279387 Fut7 Enhancer Active Normal Blood UBERON:0000178 Primary CD4+ Th1 cells CD4-positive Th1 cell CL:0000897 Enhancer activity assay ChIP-on-chip Luciferase reporter assay 2014 25209250 A regulatory network controls nephrocan expression and midgut patterning Mus musculus mm10 chr2 123454700 123457000 Nepn Enhancer Active Normal Embryo UBERON:0000922 Mouse embryo tissue embryonic cell CL:0000000 Enhancer activity assay Transgenic reporter assay, Luciferase reporter assay 2014 25263592 Enhancer RNA facilitates NELF release from immediate early genes Mus musculus mm10 chr15 8271300 8272300 Arc Enhancer Active Normal Cerebral cortex UBERON:0000956 Primary mouse cortical neurons cortical neuron CL:0000540 Chromatin interaction assay 3C, RT-RT-qPCR 2014 25263592 Enhancer RNA facilitates NELF release from immediate early genes Mus musculus mm10 chr6 135005780 135006780 Gadd45B Enhancer Active Normal Cerebral cortex UBERON:0000956 Primary mouse cortical neurons cortical neuron CL:0000540 Chromatin interaction assay 3C, RT-RT-qPCR 2011 21498522 Mouse Rankl Expression Is Regulated in T Cells by c-Fos through a Cluster of Distal Regulatory Enhancers Designated the T Cell Control Region Mus musculus mm10 chr14 77122986 77124293 C-Fos Rankl Enhancer Active Normal Spleen UBERON:0002106 CD4+ T cells CD4-positive T cell CL:0000624 Enhancer activity assay, TF binding assay ChIP-chip Luciferase Reporter Assay, ChIP-RT-qPCR 2011 21498522 Mouse Rankl Expression Is Regulated in T Cells by c-Fos through a Cluster of Distal Regulatory Enhancers Designated the T Cell Control Region Mus musculus mm10 chr14 77122986 77124293 C-Fos Rankl Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat cells CVCL_0065 T lymphoblast CL:0002419 Enhancer activity assay, TF binding assay ChIP-chip Luciferase Reporter Assay, ChIP-RT-qPCR 2010 19940492 c-Maf activates the promoter and enhancer of the IL-21 gene, and TGF-?|?? inhibits c-Maf-induced IL-21 production in CD4+ T cells Mus musculus mm10 chr3 90502261 90502522 Il21 Enhancer Active Normal Blood UBERON:0000178 CD4+ T cell CD4-positive T cell CL:0000624 Enhancer activity assay Luciferase Reporter Assay 1991 1827138 Cloning of Murine TCF-1, a T Cell-specific Transcription Factor Interacting with Functional Motifs in the CD3-E and T Cell Receptor alpha Enhancers Mus musculus mm10 chr11 105000000 105000100 Tcf7 Cd3E Enhancer Active Disease T-cell lymphoma MONDO:0005114 DOID:0050747 Lymph node UBERON:0000029 EL4 cells CVCL_0255 T lymphoma cell CL:0000084 Enhancer activity assay, TF binding assay EMSA, Luciferase Reporter Assay 1991 1827138 Cloning of Murine TCF-1, a T Cell-specific Transcription Factor Interacting with Functional Motifs in the CD3-E and T Cell Receptor alpha Enhancers Mus musculus mm10 chr14 54000000 54000100 Tcf7 Tcra Enhancer Active Disease T-cell lymphoma MONDO:0005114 DOID:0050747 Lymph node UBERON:0000029 EL4 cells CVCL_0255 T lymphoma cell CL:0000084 Enhancer activity assay, TF binding assay EMSA, Luciferase Reporter Assay 2023 37365500 Identification and characterization of transcribed enhancers during cerebellar development through enhancer RNA analysis Mus musculus mm10 chr2 74292472 74294212 Lacz Enhancer Active Normal Cerebellum UBERON:0002037 Embryonic cerebellar cells neural progenitor cell CL:0002672 Enhancer activity assay CAGE-seq, ChIP-seq Transgenic Reporter Assay 2024 38559809 Functional analysis of a first hindlimb positioning enhancer via Gdf11 expression Mus musculus mm10 chr10 128326106 128327832 Egfp Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic cells (E8.5) embryonic cell CL:0000000 Enhancer activity assay, Functional perturbation assay Transgenic Reporter Assay, CRISPR Knockout, qRT-PCR, Whole-mount in situ hybridization 2011 20942803 The pancreatic islet ?|??-cell-enriched transcription factor Pdx-1 regulates Slc30a8 gene transcription through an intronic enhancer Mus musculus mm10 chr16 13025528 13026004 Slc30A8 Enhancer Active Normal Pancreatic islet UBERON:0000006 ¦ÂTC-3 CVCL_B077 pancreatic beta cell CL:0000169 Enhancer activity assay Luciferase Reporter Assay, Site-directed Mutagenesis 2011 20942803 The pancreatic islet ?|??-cell-enriched transcription factor Pdx-1 regulates Slc30a8 gene transcription through an intronic enhancer Mus musculus mm10 chr16 13025528 13026004 Slc30A8 Enhancer Active Normal Pancreatic islet UBERON:0000006 ¦ÂTC-6 CVCL_B078 pancreatic beta cell CL:0000169 Enhancer activity assay Luciferase Reporter Assay, Site-directed Mutagenesis 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; Smad4; Tcf4 Msx2 Enhancer Active Normal Skeletal muscle UBERON:0001134 C2C12 CVCL_0188 myoblast CL:0000187 Enhancer activity assay, TF binding assay, Chromatin interaction assay Luciferase Reporter Assay, ChIP-RT-qPCR, GST Pull-down, Co-IP, RT-RT-qPCR, Western blot 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; Smad4; Tcf4 Runx2 Enhancer Active Normal Bone UBERON:0001474 MC3T3-E1 CVCL_0D73 osteoblast CL:0000062 Enhancer activity assay, TF binding assay, Chromatin interaction assay Luciferase Reporter Assay, ChIP-RT-qPCR, GST Pull-down, Co-IP, RT-RT-qPCR, Western blot 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; Smad4; Tcf4 Enhancer Active Normal Bone marrow UBERON:0002371 BM-MSC mesenchymal stem cell CL:0000134 Enhancer activity assay, TF binding assay, Chromatin interaction assay Luciferase Reporter Assay, ChIP-RT-qPCR, GST Pull-down, Co-IP, RT-RT-qPCR, Western blot 2011 20878775 Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways Mus musculus mm10 chr13 114453916 114454191 Smad1; Smad4; Tcf4 Msx2 Enhancer Active Normal Skeletal muscle UBERON:0001134 C2C12 CVCL_0188 myoblast CL:0000187 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2011 20878775 Conserved regulatory motifs in osteogenic gene promoters integrate cooperative effects of canonical Wnt and BMP pathways Mus musculus mm10 chr13 114453916 114454191 Smad1; Smad4; Tcf4 Msx2 Enhancer Active Normal Bone UBERON:0001474 MC3T3-E1 CVCL_0D73 osteoblast CL:0000062 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 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; Smad4; Tcf4 Runx2 Enhancer Active Normal Skeletal muscle UBERON:0001134 C2C12 CVCL_0188 myoblast CL:0000187 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 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; Smad4; Tcf4 Runx2 Enhancer Active Normal Bone UBERON:0001474 MC3T3-E1 CVCL_0D73 osteoblast CL:0000062 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 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; Smad4; Tcf4 Runx2 Enhancer Active Normal Bone marrow UBERON:0002371 BM-MSC mesenchymal stem cell CL:0000134 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2010 20042469 c-Maf activates the promoter and enhancer of the IL-21 gene, and TGF-?|?? inhibits c-Maf-induced IL-21 production in CD4+ T cells Mus musculus mm10 chr3 2931 3443 C-Maf; Foxp3 Il21 Enhancer Silenced Normal Lymph node UBERON:0000029 CD4+ T CD4-positive T cell CL:0000624 Enhancer activity assay, TF binding assay, Functional perturbation assay Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, Flow Cytometry, Coimmunoprecipitation 2010 20042469 c-Maf activates the promoter and enhancer of the IL-21 gene, and TGF-?|?? inhibits c-Maf-induced IL-21 production in CD4+ T cells Mus musculus mm10 chr3 2931 3443 C-Maf; Foxp3 Il21 Enhancer Active Disease T-cell lymphoma MONDO:0005114 DOID:0050747 Lymph node UBERON:0000029 EL4 CVCL_0255 T lymphoma cell CL:0000084 Enhancer activity assay, TF binding assay, Functional perturbation assay Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, Flow Cytometry, Coimmunoprecipitation 2010 20042469 c-Maf activates the promoter and enhancer of the IL-21 gene, and TGF-?|?? inhibits c-Maf-induced IL-21 production in CD4+ T cells Mus musculus mm10 chr3 2931 3443 C-Maf; Foxp3 Il21 Enhancer Silenced Normal Embryonic Kidney UBERON:0002113 293T CVCL_0063 embryonic kidney cell CL:0002139 Enhancer activity assay, TF binding assay, Functional perturbation assay Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, Flow Cytometry, Coimmunoprecipitation 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 Limb bud UBERON:0005417 Hypertrophic chondrocytes hypertrophic chondrocyte CL:0000138 Enhancer activity assay, TF binding assay Transgenic Reporter Assay, EMSA, ChIP-RT-qPCR, RT-RT-qPCR 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 Limb bud UBERON:0005417 Hypertrophic chondrocytes hypertrophic chondrocyte CL:0000138 Enhancer activity assay, TF binding assay Transgenic Reporter Assay, EMSA, ChIP-RT-qPCR, RT-RT-qPCR 2011 21859967 Runx2 Contributes to Murine Col10a1 Gene Regulation Through Direct Interaction With Its Cis-Enhancer Mus musculus mm10 chr10 12845732 12845743 Runx2 Col10A1 Enhancer Active Normal Cartilage UBERON:0002418 Hypertrophic MCT chondrocytes hypertrophic chondrocyte CL:0000138 TF binding assay EMSA 2005 15798207 Long-Range Interactions between Three Transcriptional Enhancers, Active VGene Promoters, and a 3Boundary Sequence Spanning 46 Kilobases Mus musculus mm10 chr6 70500000 70500100 E47 Igk Enhancer Active Disease plasmacytoma MONDO:0005086 DOID:1324 Blood UBERON:0000178 MPC-11 cells CVCL_UE61 plasmacytoma cell CL:0000945 Chromatin interaction assay, TF binding assay 3C-seq ChIP-RT-qPCR 2005 15798207 Long-Range Interactions between Three Transcriptional Enhancers, Active VGene Promoters, and a 3Boundary Sequence Spanning 46 Kilobases Mus musculus mm10 chr6 70500000 70500100 E47 Igk Enhancer Active Normal Blood UBERON:0000178 Primary B cells B cell CL:0000945 Chromatin interaction assay, TF binding assay 3C-seq ChIP-RT-qPCR 2005 15798207 Long-Range Interactions between Three Transcriptional Enhancers, Active VGene Promoters, and a 3Boundary Sequence Spanning 46 Kilobases Mus musculus mm10 chr6 70522000 70522100 E47 Igk Enhancer Active Disease plasmacytoma MONDO:0005086 DOID:1324 Blood UBERON:0000178 MPC-11 cells CVCL_UE61 plasmacytoma cell CL:0000945 Chromatin interaction assay, TF binding assay 3C-seq ChIP-RT-qPCR 2005 15798207 Long-Range Interactions between Three Transcriptional Enhancers, Active VGene Promoters, and a 3Boundary Sequence Spanning 46 Kilobases Mus musculus mm10 chr6 70522000 70522100 E47 Igk Enhancer Active Normal Blood UBERON:0000178 Primary B cells B cell CL:0000945 Chromatin interaction assay, TF binding assay 3C-seq ChIP-RT-qPCR 2005 15798207 Long-Range Interactions between Three Transcriptional Enhancers, Active VGene Promoters, and a 3Boundary Sequence Spanning 46 Kilobases Mus musculus mm10 chr6 70546000 70546100 E47 Igk Enhancer Active Disease plasmacytoma MONDO:0005086 DOID:1324 Blood UBERON:0000178 MPC-11 cells CVCL_UE61 plasmacytoma cell CL:0000945 Chromatin interaction assay, TF binding assay 3C-seq ChIP-RT-qPCR 2005 15798207 Long-Range Interactions between Three Transcriptional Enhancers, Active VGene Promoters, and a 3Boundary Sequence Spanning 46 Kilobases Mus musculus mm10 chr6 70546000 70546100 E47 Igk Enhancer Active Normal Blood UBERON:0000178 Primary B cells B cell CL:0000945 Chromatin interaction assay, TF binding assay 3C-seq ChIP-RT-qPCR 2019 31636200 Long-range Pitx2c enhancer-promoter interactions prevent predisposition to atrial fibrillation Mus musculus mm10 chr9 119540800 119544032 Scn5A Enhancer Active Normal Heart UBERON:0000948 Cardiomyocyte cardiomyocyte CL:0000746 Enhancer activity assay Transgenic Reporter Assay 2019 31636200 Long-range Pitx2c enhancer-promoter interactions prevent predisposition to atrial fibrillation Mus musculus mm10 chr9 119378051 119379479 Scn5A Enhancer Active Normal Heart UBERON:0000948 Cardiomyocyte cardiomyocyte CL:0000746 Enhancer activity assay Transgenic Reporter Assay 2017 28087634 Genome-wide identification of regulatory elements in Sertoli cells Mus musculus mm10 chr11 112638000 112639300 Sox9 Enhancer Active Normal Testis UBERON:0000473 Sertoli cells Sertoli cell CL:0000216 Enhancer activity assay DNase-seq Transgenic Reporter Assay 2017 27920250 Renal Anemia Model Mouse Established by Transgenic Rescue with Erythropoietin Gene Lacking Kidney-specific Regulatory Elements Mus musculus mm10 chr5 135082600 135096400 Epo Enhancer Active Normal Kidney UBERON:0002113 Renal EPO-producing cells renal erythropoietin-producing cell CL:0000647 Functional perturbation assay Transgenic Reporter Assay 2016 27920250 Renal Anemia Model Mouse Established by Transgenic Rescue with Erythropoietin Gene Lacking Kidney-specific Regulatory Elements Mus musculus mm10 chr5 137512712 137526512 Epo Enhancer Active Normal Kidney UBERON:0002113 Renal EPO-producing cells renal erythropoietin-producing cell CL:0000647 Enhancer activity assay Transgenic Reporter Assay, RT-RT-qPCR 2016 27920250 Renal Anemia Model Mouse Established by Transgenic Rescue with Erythropoietin Gene Lacking Kidney-specific Regulatory Elements Mus musculus mm10 chr5 137512712 137518112 Epo Enhancer Active Normal Kidney UBERON:0002113 Renal EPO-producing cells renal erythropoietin-producing cell CL:0000647 Enhancer activity assay Transgenic Reporter Assay 2016 27920250 Renal Anemia Model Mouse Established by Transgenic Rescue with Erythropoietin Gene Lacking Kidney-specific Regulatory Elements Mus musculus mm10 chr5 137518112 137521712 Epo Enhancer Active Normal Kidney UBERON:0002113 Renal EPO-producing cells renal erythropoietin-producing cell CL:0000647 Enhancer activity assay Transgenic Reporter Assay 2016 27920250 Renal Anemia Model Mouse Established by Transgenic Rescue with Erythropoietin Gene Lacking Kidney-specific Regulatory Elements Mus musculus mm10 chr5 137526512 137530112 Epo Enhancer Active Normal Kidney UBERON:0002113 Renal EPO-producing cells renal erythropoietin-producing cell CL:0000647 Enhancer activity assay Transgenic Reporter Assay, RT-RT-qPCR 2015 25548254 A novel Cd8-cis-regulatory element preferentially directs expression in CD44hiCD62L+ CD8+ T cells and in CD8aa+ dendritic cells Mus musculus mm10 chr6 71252310 71308680 Runx3 Hcd2 Enhancer Active Normal Blood UBERON:0000178 Effector memory CD8+ T cells effector memory CD8+ T cell CL:0000625 Enhancer activity assay, TF binding assay Transgenic Reporter Assay, ChIP-RT-qPCR 2015 25548254 A novel Cd8-cis-regulatory element preferentially directs expression in CD44hiCD62L+ CD8+ T cells and in CD8aa+ dendritic cells Mus musculus mm10 chr6 71272801 71273297 Bcl11B Cd8A Enhancer Active Normal Blood UBERON:0000178 Effector memory CD8+ T cells effector memory CD8+ T cell CL:0000625 Enhancer activity assay, TF binding assay Transgenic Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2015 25548254 A novel Cd8-cis-regulatory element preferentially directs expression in CD44hiCD62L+ CD8+ T cells Mus musculus mm10 chr6 71275200 71275697 Runx3 Cd8A Enhancer Active Normal Blood UBERON:0000178 CD8+ T cells CD8-positive T cell CL:0000625 Enhancer activity assay, TF binding assay Transgenic Reporter Assay, ChIP-RT-qPCR 2016 26808502 Lineage-affiliated transcription factors bind the Gata3 Tce1 enhancer to mediate lineage-specific programs Mus musculus mm10 chr2 9515156 9516356 Gata3 Enhancer Active Normal Thymus UBERON:0002370 Thymocytes thymocyte CL:0000893 Enhancer activity assay Transgenic reporter assay 2011 21859967 Runx2 Contributes to Murine Col10a1 Gene Regulation Through Direct Interaction With Its Cis-Enhancer Mus musculus mm10 chr10 12845723 12845872 Col10A1 Enhancer Active Normal Cartilage UBERON:0002418 Hypertrophic MCT chondrocytes hypertrophic chondrocyte CL:0000138 Enhancer activity assay Transgenic Reporter Assay 2007 17715390 Tissue-specific histone modification and transcription factor binding in alpha globin gene expression Mus musculus mm10 chr11 3217000 3222000 Hba1 Enhancer Active Normal Bone Marrow UBERON:0002371 Primary Murine Erythroblasts erythroblast CL:0000765 Enhancer activity assay, TF binding assay ChIP-chip ChIP-RT-qPCR, RT-RT-qPCR 2007 17715390 Tissue-specific histone modification and transcription factor binding in alpha globin gene expression Mus musculus mm10 chr11 3222000 3227000 Hba1 Enhancer Active Normal Bone Marrow UBERON:0002371 Primary Mur qRT-PCR, and ChIP-qPCR 1991 1827138 Cloning of Murine TCF-1, a T Cell-specific Transcription Factor Interacting with Functional Motifs in the CD3-E and T Cell Receptor alpha Enhancers Mus musculus mm10 chr11 105000000 105000100 Tcf7 Cd3E Enhancer Active Normal Blood UBERON:0000178 EL4 cells CVCL_0255 T lymphoma cell CL:0000084 Enhancer activity assay, TF binding assay EMSA, Luciferase Reporter Assay 1991 1827138 Cloning of Murine TCF-1, a T Cell-specific Transcription Factor Interacting with Functional Motifs in the CD3-E and T Cell Receptor alpha Enhancers Mus musculus mm10 chr14 54000000 54000100 Tcf7 Tcra Enhancer Active Normal Blood UBERON:0000178 EL4 cells CVCL_0255 T lymphoma cell CL:0000084 Enhancer activity assay, TF binding assay EMSA, Luciferase Reporter Assay 2007 17715390 Tissue-specific histone modification and transcription factor binding in alpha globin gene expression Mus musculus mm10 chr11 3222000 3227000 Hba1 Enhancer Active Normal Bone Marrow UBERON:0002371 Primary Murine Erythroblasts erythroblast CL:0000765 Enhancer activity assay, TF binding assay ChIP-chip ChIP-RT-qPCR, RT-RT-qPCR 2007 17715390 Tissue-specific histone modification and transcription factor binding in alpha globin gene expression Mus musculus mm10 chr11 3231000 3236000 Hba1 Enhancer Active Normal Bone Marrow UBERON:0002371 Primary Murine Erythroblasts erythroblast CL:0000765 Enhancer activity assay, TF binding assay ChIP-chip ChIP-RT-qPCR, RT-RT-qPCR 2007 17715390 Tissue-specific histone modification and transcription factor binding in alpha globin gene expression Mus musculus mm10 chr11 3235000 3240000 Hba1 Enhancer Active Normal Bone Marrow UBERON:0002371 Primary Murine Erythroblasts erythroblast CL:0000765 Enhancer activity assay, TF binding assay ChIP-chip ChIP-RT-qPCR, RT-RT-qPCR 1992 1429727 Immunoglobulin K Gene Enhancers Synergistically Activate Gene Expression but Independently Determine Chromatin Structure Mus musculus mm10 chr6 70989543 70989643 Igkc Enhancer Active Disease plasmacytoma MONDO:0005086 DOID:1324 Blood UBERON:0000178 S194 plasmacytoma cells CVCL_V125 plasmacytoma cell CL:0000945 Functional perturbation assay RT-RT-qPCR 1992 1429727 Immunoglobulin K Gene Enhancers Synergistically Activate Gene Expression but Independently Determine Chromatin Structure Mus musculus mm10 chr6 70999043 70999143 Igkc Enhancer Active Disease plasmacytoma MONDO:0005086 DOID:1324 Blood UBERON:0000178 S194 plasmacytoma cells CVCL_V125 plasmacytoma cell CL:0000945 Functional perturbation assay RT-RT-qPCR 2011 21331042 Tbx6-dependent Sox2 regulation determines neural or mesodermal fate in axial stem cells Mus musculus mm10 chr3 34668443 34668497 Sox2 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic tissue embryonic cell CL:0000000 Enhancer activity assay Transgenic Reporter Assay, Site-directed Mutagenesis, in situ Hybridization 2019 31773374 The wmN1 Enhancer Region of the Mouse Myelin Proteolipid Protein Gene (mPlp1) is Indispensable for Expression of an mPlp1-lacZ Transgene in Both the CNS and PNS Mus musculus mm10 chrX 100581771 100582950 Plp1 Enhancer Active Normal Brain UBERON:0000955 Oligodendrocytes oligodendrocyte CL:0000128 Enhancer activity assay, Functional perturbation assay Transgenic Reporter Assay, Cre-loxP Mediated Knockout, ?|??-Galactosidase Enzyme Assay, X-gal Staining, Immunohistochemistry 2019 31773374 The wmN1 Enhancer Region of the Mouse Myelin Proteolipid Protein Gene (mPlp1) is Indispensable for Expression of an mPlp1-lacZ Transgene in Both the CNS and PNS Mus musculus mm10 chrX 100581771 100582950 Plp1 Enhancer Active Normal Brain UBERON:0000955 Oligodendrocyte Precursor oligodendrocyte precursor cell CL:0002453 Enhancer activity assay, Functional perturbation assay Transgenic Reporter Assay, Cre-loxP Mediated Knockout, ?|??-Galactosidase Enzyme Assay, X-gal Staining, Immunohistochemistry 2019 31773374 The wmN1 Enhancer Region of the Mouse Myelin Proteolipid Protein Gene (mPlp1) is Indispensable for Expression of an mPlp1-lacZ Transgene in Both the CNS and PNS Mus musculus mm10 chrX 100581771 100582950 Plp1 Enhancer Active Normal Brain UBERON:0000955 Olfactory Ensheathing olfactory ensheathing cell CL:0002023 Enhancer activity assay, Functional perturbation assay Transgenic Reporter Assay, Cre-loxP Mediated Knockout, ?|??-Galactosidase Enzyme Assay, X-gal Staining, Immunohistochemistry 2019 31773374 The wmN1 Enhancer Region of the Mouse Myelin Proteolipid Protein Gene (mPlp1) is Indispensable for Expression of an mPlp1-lacZ Transgene in Both the CNS and PNS Mus musculus mm10 chrX 100581771 100582950 Plp1 Enhancer Active Normal Brain UBERON:0000955 Schwann Schwann cell CL:0002573 Enhancer activity assay, Functional perturbation assay Transgenic Reporter Assay, Cre-loxP Mediated Knockout, ?|??-Galactosidase Enzyme Assay, X-gal Staining, Immunohistochemistry 2019 31773374 The wmN1 Enhancer Region of the Mouse Myelin Proteolipid Protein Gene (mPlp1) is Indispensable for Expression of an mPlp1-lacZ Transgene in Both the CNS and PNS Mus musculus mm10 chrX 100581771 100582950 Plp1 Enhancer Active Normal Brain UBERON:0000955 Neurons neuron CL:0000540 Enhancer activity assay, Functional perturbation assay Transgenic Reporter Assay, Cre-loxP Mediated Knockout, ?|??-Galactosidase Enzyme Assay, X-gal Staining, Immunohistochemistry 2015 26595656 Stimulus-specific combinatorial functionality of neuronal c-fos enhancers Mus musculus mm10 chr12 85427000 85427500 Creb Fos Enhancer Active Normal Cerebral cortex UBERON:0000956 Cortical neurons cortical neuron CL:0000540 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, RNA-seq Luciferase Reporter Assay, 3C, ChIP-RT-qPCR, CRISPRi 2015 26595656 Stimulus-specific combinatorial functionality of neuronal c-fos enhancers Mus musculus mm10 chr12 85428000 85428500 Mef2A Fos Enhancer Active Normal Cerebral cortex UBERON:0000956 Cortical neurons cortical neuron CL:0000540 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, RNA-seq Luciferase Reporter Assay, 3C, ChIP-RT-qPCR, CRISPRi 2015 26595656 Stimulus-specific combinatorial functionality of neuronal c-fos enhancers Mus musculus mm10 chr12 85429000 85429500 Srf Fos Enhancer Active Normal Cerebral cortex UBERON:0000956 Cortical neurons cortical neuron CL:0000540 Enhancer activity assay, TF binding assay, Chromatin interaction assay ChIP-seq, RNA-seq Luciferase Reporter Assay, 3C, ChIP-RT-qPCR, CRISPRi 2015 26595656 Stimulus-specific combinatorial functionality of neuronal c-fos enhancers Mus musculus mm10 chr12 85471518 85475098 Creb Fos Enhancer Active Normal Brain UBERON:0000955 Primary mouse cortical neurons cortical neuron CL:0000540 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPRi, 3C, RT-RT-qPCR 2015 26595656 Stimulus-specific combinatorial functionality of neuronal c-fos enhancers Mus musculus mm10 chr12 85499955 85504319 Creb Fos Enhancer Active Normal Brain UBERON:0000955 Primary mouse cortical neurons cortical neuron CL:0000540 Enhancer activity assay ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPRi, 3C, RT-RT-qPCR 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 Skeletal muscle UBERON:0001134 C2C12 CVCL_0188 myoblast CL:0000187 Enhancer activity assay ChIP-seq Luciferase Reporter Assay, CRISPR Knockout 2020 32991581 NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure brown and beige adipocyte differentiation Mus musculus mm10 chr3 3109577 3110077 Nfia Pparg Enhancer Active Normal Adipose tissue UBERON:0001013 C2C12 myoblast CVCL_0188 myoblast CL:0000187 Enhancer activity assay, TF binding assay FAIRE-seq, ChIP-seq, RNA-seq ChIP-RT-qPCR, FAIRE-RT-qPCR, CRISPRi, Luciferase Reporter Assay 2017 29224777 YY1 Is a Structural Regulator of Enhancer-Promoter Loops Mus musculus mm10 chr6 115598005 115604631 Yy1 Raf1 Enhancer Active Normal Embryo UBERON:0000922 mESC mouse embryonic stem cell CL:0002322 Chromatin interaction assay, Functional perturbation assay ChIP-seq, Hi-C CRISPR Knockout, 4C-seq, RT-RT-qPCR 2017 29224777 YY1 Is a Structural Regulator of Enhancer-Promoter Loops Mus musculus mm10 chr6 115598005 115604631 Yy1 Raf1 Enhancer Active Normal Embryo UBERON:0000922 Embryonic stem cell embryonic stem cell CL:0002322 Chromatin interaction assay, Functional perturbation assay ChIP-seq, Hi-C CRISPR Knockout, 4C-seq, RT-RT-qPCR 2025 39626660 Long-range regulation of transcription scales with genomic distance in a gene-specific manner Mus musculus mm10 chr5 98716000 98718000 Fgf5 Enhancer Active Normal Embryo UBERON:0000922 mESCs mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay ChIP-seq, RNA-seq, ORCA, ATAC-seq CRISPRa, RT-RT-qPCR, ChIP-RT-qPCR 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 Nervous system UBERON:0001016 Neural progenitor neural progenitor cell CL:0002672 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq CRISPR Knockout, Transgenic Reporter Assay 2017 27986456 Isoform-specific expression and feedback regulation of E protein TCF4 control dendritic cell lineage specification Mus musculus mm10 chr19 45700000 45702000 Tcf4 Tcf4 Enhancer Active Normal Bone marrow UBERON:0002371 Plasmacytoid dendritic cell (pDC) plasmacytoid dendritic cell CL:0000786 Functional perturbation assay ATAC-seq, ChIP-seq CRISPR Knockout, RT-RT-qPCR 2017 28575289 MyoD- and FoxO3-mediated hotspot interaction orchestrates super-enhancer activity during myogenic differentiation Mus musculus mm10 chr1 136188400 136188845 Myod Myog Enhancer Active Normal Skeletal muscle UBERON:0001134 C2C12 CVCL_0188 myoblast CL:0000187 Functional perturbation assay ChIP-seq CRISPR Knockout, RT-RT-qPCR 2016 27867070 The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances Mus musculus mm10 chr14 97485490 97486674 Shh Enhancer Silenced Normal Limb bud UBERON:0005417 Mouse E14 ESCs CVCL_2167 mouse embryonic stem cell CL:0002322 Enhancer activity assay, Functional perturbation assay, Genome rearrangement assay LacZ transgenic reporter assay, Cre-loxP genome rearrangement, RT-RT-qPCR, Whole-mount in situ hybridization, Skeletal preparation 2016 27867070 The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances Mus musculus mm10 chr14 97485490 97486674 Shh Enhancer Silenced Normal Limb bud UBERON:0005417 E11.5 embryonic limb bud cells limb bud cell CL:0000000 Enhancer activity assay, Functional perturbation assay, Genome rearrangement assay LacZ transgenic reporter assay, Cre-loxP genome rearrangement, RT-RT-qPCR, Whole-mount in situ hybridization, Skeletal preparation 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 Cartilage UBERON:0002418 Hypertrophic MCT chondrocytes hypertrophic chondrocyte CL:0000138 TF binding assay EMSA 2011 21673114 Combinatorial regulation of photoreceptor differentiation factor, neural retina leucine zipper gene NRL, revealed by in vivo promoter analysis Mus musculus mm10 chr11 75210600 75210904 Nrl Enhancer Active Normal Retina UBERON:0000966 Primary Retinal Cells retinal cell CL:0000540 TF binding assay EMSA 2011 20878775 Conserved Regulatory Motifs in Osteogenic Gene Promoters Integrate Cooperative Effects of Canonical Wnt and BMP Pathways Mus musculus mm10 chr14 52100000 52101066 Dlx5 Enhancer Active Normal Skeletal muscle UBERON:0001134 C2C12 CVCL_0188 myoblast CL:0000187 Enhancer activity assay Luciferase Reporter Assay 2011 20878775 Conserved Regulatory Motifs in Osteogenic Gene Promoters Integrate Cooperative Effects of Canonical Wnt and BMP Pathways Mus musculus mm10 chr13 11003340 11003615 Msx2 Enhancer Active Normal Skeletal muscle UBERON:0001134 C2C12 CVCL_0188 myoblast CL:0000187 Enhancer activity assay Luciferase Reporter Assay 2011 20878775 Conserved Regulatory Motifs in Osteogenic Gene Promoters Integrate Cooperative Effects of Canonical Wnt and BMP Pathways Mus musculus mm10 chr17 45201170 45201388 Runx2 Enhancer Active Normal Skeletal muscle UBERON:0001134 C2C12 CVCL_0188 myoblast CL:0000187 Enhancer activity assay Luciferase Reporter Assay 2011 21464046 Nkx2-5 Represses Gata1 Gene Expression and Modulates the Cellular Fate of Cardiac Progenitors during Embryogenesis Mus musculus mm10 chrX 10068000 10071900 Gata1 Enhancer Silenced Normal Heart UBERON:0000948 ES cells embryonic stem cell CL:0002322 Enhancer activity assay RNA-seq Luciferase Reporter Assay 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 90505451 90505963 Il21 Enhancer Active Normal Blood UBERON:0000178 CD4+ T cell CD4-positive T cell CL:0000624 Enhancer activity assay Luciferase Reporter Assay 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 147228000 147228250 Pdx1 Enhancer Silenced Normal Pancreatic islet UBERON:0001264 INS-1 CVCL_0352 pancreatic beta cell CL:0000169 Enhancer activity assay Luciferase Reporter Assay 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 147228000 147228250 Pdx1 Enhancer Silenced Normal Pancreatic islet UBERON:0001264 HIT CVCL_0294 pancreatic beta cell CL:0000169 Enhancer activity assay Luciferase Reporter Assay 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 147228000 147228250 Pdx1 Enhancer Silenced Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 HepG2 CVCL_0027 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay Luciferase Reporter Assay 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 60725000 60725403 Csf1R Enhancer Active Normal Bone marrow UBERON:0002371 38B9 CVCL_UE53 pre-B cell CL:0000945 Enhancer activity assay Luciferase Reporter Assay 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 60725000 60725403 Csf1R Enhancer Active Disease B-cell lymphoma MONDO:0005029 DOID:164 Bone marrow UBERON:0002371 A20 CVCL_1940 B cell lymphoma cell CL:0000945 Enhancer activity assay Luciferase Reporter Assay 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 60725000 60725403 Csf1R Enhancer Active Normal Bone marrow UBERON:0002371 Pro-B Cells pro-B cell CL:0000945 Enhancer activity assay Luciferase Reporter Assay 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 lymphoma MONDO:0005029 DOID:164 Blood UBERON:0000178 M12 B cells B cell lymphoma cell CL:0000945 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, EMSA, RT-RT-qPCR 2025 40866336 CFP1 promotes germinal center affinity maturation and restrains memory B cell differentiation through H3K4me3 modulation Mus musculus mm10 chr16 24132522 24174993 Mef2B Bcl6 Enhancer Active Normal Spleen UBERON:0002106 Germinal center B cells germinal center B cell CL:0000945 Chromatin interaction assay, Functional perturbation assay 3C-seq, RNA-seq, ChIP-seq 3C-RT-qPCR, qRT-PCR, Western blot 2020 32991581 NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure brown and beige adipocyte differentiation Mus musculus mm10 chr8 83360000 83360500 Nfia; Ppar?|?? Ucp1 Enhancer Active Normal Adipose tissue UBERON:0001013 C2C12 myoblast CVCL_0188 myoblast CL:0000187 TF binding assay, Enhancer activity assay ChIP-seq, RNA-seq ChIP-RT-qPCR, Luciferase Reporter Assay, RT-RT-qPCR 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 44203400 44203700 Nfil3 Il12B Enhancer Silenced Normal Bone marrow UBERON:0002371 BMDM macrophage CL:0000235 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA, RT-RT-qPCR 2009 19041414 Smad3 activates the Sox9-dependent transcription on chromatin Mus musculus mm10 chr15 98750000 98750480 Sox9 Col2A1 Enhancer Active Disease chondrosarcoma MONDO:0005172 DOID:3369 Cartilage UBERON:0002418 SW1353 chondrosarcoma cells CVCL_0543 chondrosarcoma cell CL:0000138 Enhancer activity assay, TF binding assay Luciferase Reporter Assay, EMSA, In vitro transcription assay 2008 19141476 Dynamic regulation of Pdx1 enhancers by Foxa1 and Foxa2 is essential for pancreas development Mus musculus mm10 chr5 145326114 145328962 Foxa1 Pdx1 Enhancer Active Normal Pancreas UBERON:0001264 Fetal pancreatic pancreatic epithelial cell CL:0002078 TF binding assay ChIP-seq ChIP-RT-qPCR 2011 21487009 Mouse Rankl Expression Is Regulated in T Cells by c-Fos through a Cluster of Distal Regulatory Enhancers Designated the T Cell Control Region Mus musculus mm10 chr14 77150408 77152161 Rankl Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat cells CVCL_0065 T lymphoblast CL:0002419 Enhancer activity assay Luciferase Reporter Assay 2011 21566115 A Distal Enhancer in Il12b Is the Target of Transcriptional Repression by the STAT3 Pathway and Requires the Basic Leucine Zipper Protein NFIL3 Mus musculus mm10 chr11 44203545 44203644 Nfil3 Il12B Enhancer Silenced Normal Bone marrow UBERON:0002371 BMDM macrophage CL:0000235 Enhancer activity assay, TF binding assay, Functional perturbation assay Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA, RT-RT-qPCR 2011 21566115 A Distal Enhancer in Il12b Is the Target of Transcriptional Repression by the STAT3 Pathway and Requires the Basic Leucine Zipper Protein NFIL3 Mus musculus mm10 chr11 44203545 44203644 Nfil3 Il12B Enhancer Silenced Normal Bone marrow UBERON:0002371 PDM macrophage CL:0000235 Enhancer activity assay, TF binding assay, Functional perturbation assay Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA, RT-RT-qPCR 2011 21566115 A Distal Enhancer in Il12b Is the Target of Transcriptional Repression by the STAT3 Pathway and Requires the Basic Leucine Zipper Protein NFIL3 Mus musculus mm10 chr11 44203545 44203644 Nfil3 Il12B Enhancer Silenced Normal Bone marrow UBERON:0002371 RAW264.7 CVCL_0493 macrophage CL:0000235 Enhancer activity assay, TF binding assay, Functional perturbation assay Luciferase Reporter Assay, ChIP-RT-qPCR, EMSA, RT-RT-qPCR 2011 21797989 Differentiation and fiber type-specific activity of a muscle creatine kinase intronic enhancer Mus musculus mm10 chr19 4472130 4472336 Myod Mck Enhancer Active Normal Skeletal muscle UBERON:0001134 MM14 myocytes CVCL_W869 myocyte CL:0000187 Enhancer activity assay, TF binding assay ChIP-seq CAT Reporter Assay, Transgenic Reporter Assay, ChIP-RT-qPCR, EMSA 2011 21797989 Differentiation and fiber type-specific activity of a muscle creatine kinase intronic enhancer Mus musculus mm10 chr19 4472130 4472336 Myod Mck Enhancer Active Normal Skeletal muscle UBERON:0001134 C2C12 myocytes CVCL_0188 myoblast CL:0000187 Enhancer activity assay, TF binding assay ChIP-seq CAT Reporter Assay, Transgenic Reporter Assay, ChIP-RT-qPCR, EMSA 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 Embryo UBERON:0000922 Mouse E14 embryonic stem cells CVCL_2167 mouse 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 2016 26771354 BMP Sustains Embryonic Stem Cell Self-Renewal through Distinct Functions of Different Kr?¡§?1ppel-like Factors Mus musculus mm10 chr13 74952000 74953000 Smad1 Id1 Enhancer Active Normal Embryo UBERON:0000922 E14 mouse embryonic stem cells CVCL_2167 mouse embryonic stem cell CL:0002322 Functional perturbation assay, TF binding assay ChIP-seq, RNA-seq CRISPR Knockout, RT-qPCR, Luciferase Reporter Assay 2024 39695228 Nucleosome fibre topology guides transcription factor binding to enhancers Mus musculus mm10 chr6 122656000 122657000 Oct4,Sox2,Klf4 Nanog Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic fibroblasts CVCL_0003 mouse embryonic fibroblast CL:0000057 Enhancer reporter assay snATAC-seq, snRNA-seq, Micro-C, MNase-seq, ChIP-seq EMSA, immunoprecipitation, flow cytometry, immunostaining 2024 39695228 Nucleosome fibre topology guides transcription factor binding to enhancers Mus musculus mm10 chr6 122656000 122657000 Oct4,Sox2,Klf4 Nanog Enhancer Active Normal Embryo UBERON:0000922 embryonic stem cells embryonic stem cell CL:0002322 Enhancer reporter assay snATAC-seq, snRNA-seq, Micro-C, MNase-seq, ChIP-seq EMSA, immunoprecipitation, flow cytometry, immunostaining 2018 29254942 Transcription factor activity rhythms and tissue-specific chromatin interactions explain circadian gene expression across organs Mus musculus mm10 chr6 72190000 72200000 Dbp Enhancer Silenced Normal Liver UBERON:0002107 Primary hepatocytes hepatocyte CL:0000182 Chromatin interaction assay, Circadian regulation assay 4C-seq, RNA-seq qRT-PCR, and ChIP-qPCR 2018 29256171 Multiple enhancer regions govern the transcription of CCN2 during embryonic development Mus musculus mm10 chr10 24200250 24202250 Ets1 Ccn2 Enhancer Active Normal Blood vessel UBERON:0001981 Endothelial cells endothelial cell CL:0000115 Transgenic reporter assay, Developmental regulation assay ChIP-seq qRT-PCR, and ChIP-qPCR 2018 29256171 Multiple enhancer regions govern the transcription of CCN2 during embryonic development Mus musculus mm10 chr10 24165250 24167250 Sox9 Ccn2 Enhancer Active Normal Cartilage UBERON:0002418 Chondrocytes chondrocyte CL:0000138 Transgenic reporter assay, Developmental regulation assay ChIP-seq qRT-PCR, and ChIP-qPCR 2018 29256171 Multiple enhancer regions govern the transcription of CCN2 during embryonic development Mus musculus mm10 chr10 24102250 24104250 Runx2 Ccn2 Enhancer Active Normal Connective tissue UBERON:0002384 Fibroblasts fibroblast CL:0000057 Transgenic reporter assay, Developmental regulation assay ChIP-seq qRT-PCR, and ChIP-qPCR 2018 29256171 Multiple enhancer regions govern the transcription of CCN2 during embryonic development Mus musculus mm10 chr10 24071250 24073250 Runx2 Ccn2 Enhancer Active Normal Bone UBERON:0001474 Osteoblasts osteoblast CL:0000062 Transgenic reporter assay, Developmental regulation assay ChIP-seq qRT-PCR, and ChIP-qPCR 2022 36097291 Cohesin is required for long-range enhancer action at the Shh locus Mus musculus mm10 chr5 28718122 28719021 Shh Enhancer Active Normal Limb bud UBERON:0005417 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Functional perturbation assay, Chromatin interaction assay Hi-C RT-qPCR, RNA FISH 2022 36097291 Cohesin is required for long-range enhancer action at the Shh locus Mus musculus mm10 chr5 29155811 29156811 Shh Enhancer Active Normal Limb bud UBERON:0005417 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Functional perturbation assay, Chromatin interaction assay Hi-C RT-qPCR, RNA FISH 2022 36097291 Cohesin is required for long-range enhancer action at the Shh locus Mus musculus mm10 chr5 29465811 29466811 Shh Enhancer Active Normal Limb bud UBERON:0005417 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Functional perturbation assay, Chromatin interaction assay Hi-C RT-qPCR, RNA FISH 2015 25487574 MyoR modulates cardiac conduction by repressing Gata4 Mus musculus mm10 chr16 20740332 20744432 Gata4 Cx30.2 (Gjd3) Enhancer Active Normal Kidney UBERON:0002113 COS7 CVCL_0224 fibroblast-like cell CL:0000057 Enhancer activity assay, TF binding assay, Functional perturbation assay Microarray Luciferase Reporter Assay, Transgenic Reporter Assay, ChIP-RT-qPCR, qRT-PCR, Western blot 2020 32991581 NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure brown and beige adipocyte differentiation Mus musculus mm10 chr3 3122577 3123077 Nfia Pparg Enhancer Active Normal Adipose tissue UBERON:0001013 C2C12 myoblast CVCL_0188 myoblast CL:0000187 Enhancer activity assay, TF binding assay FAIRE-seq, ChIP-seq, RNA-seq ChIP-RT-qPCR, FAIRE-RT-qPCR 2020 32991581 NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure brown and beige adipocyte differentiation Mus musculus mm10 chr3 3125577 3126077 Nfia Pparg Enhancer Active Normal Adipose tissue UBERON:0001013 C2C12 myoblast CVCL_0188 myoblast CL:0000187 Enhancer activity assay, TF binding assay FAIRE-seq, ChIP-seq, RNA-seq ChIP-RT-qPCR, FAIRE-RT-qPCR 2020 32991581 NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure brown and beige adipocyte differentiation Mus musculus mm10 chr3 3139577 3140077 Nfia Pparg Enhancer Active Normal Adipose tissue UBERON:0001013 C2C12 myoblast CVCL_0188 myoblast CL:0000187 Enhancer activity assay, TF binding assay FAIRE-seq, ChIP-seq, RNA-seq ChIP-RT-qPCR, FAIRE-RT-qPCR 2020 32991581 NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure brown and beige adipocyte differentiation Mus musculus mm10 chr3 3159577 3160077 Nfia Pparg Enhancer Active Normal Adipose tissue UBERON:0001013 C2C12 myoblast CVCL_0188 myoblast CL:0000187 Enhancer activity assay, TF binding assay FAIRE-seq, ChIP-seq, RNA-seq ChIP-RT-qPCR, FAIRE-RT-qPCR 2020 32991581 NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure brown and beige adipocyte differentiation Mus musculus mm10 chr3 3180577 3181077 Pparg Enhancer Active Normal Adipose tissue UBERON:0001013 C2C12 myoblast CVCL_0188 myoblast CL:0000187 Enhancer activity assay, Functional perturbation assay RNA-seq CRISPRi, RT-RT-qPCR 2020 32991581 NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure brown and beige adipocyte differentiation Mus musculus mm10 chr7 46550546 46551046 Nfia; Klf5 Myod1 Enhancer Silenced Normal Skeletal muscle UBERON:0001134 C2C12 myoblast CVCL_0188 myoblast CL:0000187 TF binding assay, Enhancer activity assay FAIRE-seq, ChIP-seq, RNA-seq ChIP-RT-qPCR, FAIRE-RT-qPCR, RT-RT-qPCR 2020 32991581 NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure brown and beige adipocyte differentiation Mus musculus mm10 chr7 46556546 46557046 Nfia Myod1 Enhancer Silenced Normal Skeletal muscle UBERON:0001134 C2C12 myoblast CVCL_0188 myoblast CL:0000187 TF binding assay, Enhancer activity assay FAIRE-seq, ChIP-seq, RNA-seq ChIP-RT-qPCR, FAIRE-RT-qPCR, RT-RT-qPCR 2020 32991581 NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure brown and beige adipocyte differentiation Mus musculus mm10 chr7 46565546 46566046 Nfia; Klf5 Myod1 Enhancer Silenced Normal Skeletal muscle UBERON:0001134 C2C12 myoblast CVCL_0188 myoblast CL:0000187 TF binding assay, Enhancer activity assay, Functional perturbation assay FAIRE-seq, ChIP-seq, RNA-seq ChIP-RT-qPCR, FAIRE-RT-qPCR, RT-RT-qPCR, Western blot 2020 32991581 NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure brown and beige adipocyte differentiation Mus musculus mm10 chr7 46568546 46569046 Nfia Myod1 Enhancer Silenced Normal Skeletal muscle UBERON:0001134 C2C12 myoblast CVCL_0188 myoblast CL:0000187 TF binding assay, Enhancer activity assay FAIRE-seq, ChIP-seq, RNA-seq ChIP-RT-qPCR, FAIRE-RT-qPCR, RT-RT-qPCR 2020 32991581 NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure brown and beige adipocyte differentiation Mus musculus mm10 chr7 46587546 46588046 Nfia Myod1 Enhancer Silenced Normal Skeletal muscle UBERON:0001134 C2C12 myoblast CVCL_0188 myoblast CL:0000187 Enhancer activity assay, Functional perturbation assay FAIRE-seq, ChIP-seq, RNA-seq RT-RT-qPCR, ChIP-RT-qPCR 2020 32991581 NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure brown and beige adipocyte differentiation Mus musculus mm10 chr7 46594146 46594646 Nfia Myod1 Enhancer Silenced Normal Skeletal muscle UBERON:0001134 C2C12 myoblast CVCL_0188 myoblast CL:0000187 TF binding assay, Enhancer activity assay FAIRE-seq, ChIP-seq, RNA-seq ChIP-RT-qPCR, FAIRE-RT-qPCR, RT-RT-qPCR 2020 32991581 NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure brown and beige adipocyte differentiation Mus musculus mm10 chr7 46595846 46596346 Nfia Myod1 Enhancer Silenced Normal Skeletal muscle UBERON:0001134 C2C12 myoblast CVCL_0188 myoblast CL:0000187 TF binding assay, Enhancer activity assay FAIRE-seq, ChIP-seq, RNA-seq ChIP-RT-qPCR, FAIRE-RT-qPCR, RT-RT-qPCR 2020 32991581 NFIA differentially controls adipogenic and myogenic gene program through distinct pathways to ensure brown and beige adipocyte differentiation Mus musculus mm10 chr7 35120000 35120500 Nfia Cebpa Enhancer Active Normal Adipose tissue UBERON:0001013 C2C12 myoblast CVCL_0188 myoblast CL:0000187 TF binding assay, Enhancer activity assay FAIRE-seq, ChIP-seq, RNA-seq ChIP-RT-qPCR, FAIRE-RT-qPCR 2011 21368045 The Gonadotropin-Releasing Hormone Cell-Specific Element Is Required for Normal Puberty and Estrous Cyclicity Mus musculus mm10 chr14 62018722 62019450 Gnrh1 Enhancer Active Normal Hypothalamus UBERON:0001898 GnRH neuron GnRH neuron CL:0000111 Functional perturbation assay CRISPR Knockout, Transgenic Reporter Assay, Luciferase Reporter Assay, RT-RT-qPCR 2018 29979962 A Muscle-Specific Enhancer RNA Mediates Cohesin Recruitment and Regulates Transcription in Trans Mus musculus mm10 chr7 53626726 53628851 Myod1 Myod1 Enhancer Active Normal Skeletal muscle UBERON:0001134 C2C12 myoblasts CVCL_0188 myoblast CL:0000187 Enhancer activity assay, Functional perturbation assay ChIP-seq, RNA-seq qRT-PCR, and ChIP-qPCR 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 Embryo UBERON:0000922 Embryonic stem cells (ESCs) embryonic stem cell CL:0002322 Enhancer activity assay, Chromatin interaction assay, TF binding assay, Functional perturbation assay 4C-seq, ChIP-seq, RNA-seq FISH, ChIP-RT-qPCR, shRNA knockdown, Overexpression assay, Immunoprecipitation, RT-RT-qPCR, Western blot 2015 26593423 Chromosomal Loop Domains Direct the Recombination of Antigen Receptor Genes Mus musculus mm10 chr1 120286768 120286837 Enhancer Active Normal Bone marrow UBERON:0002371 Primary pro-B cells pro-B cell CL:0000945 Enhancer activity assay, Chromatin interaction assay ChIP-seq, Hi-C qRT-PCR, and ChIP-qPCR 2018 29514092 Transcription Factor IRF8 Governs Enhancer Landscape Dynamics in Mononuclear Phagocyte Progenitors Mus musculus mm10 chr11 96880000 96920000 Irf8; Spi1; Klf2 Nr4A1 Enhancer Active Normal Bone marrow UBERON:0002371 Non-classical monocytes non-classical monocyte CL:0000576 Immunological functional assay, Functional genomics assay, Epigenomic profiling assay, Transcriptional regulation assay ChIP-seq [targets: H3K4me1, H3K27ac, Irf8], RNA-seq, Gene Expression Microarray Flow Cytometry, FACS, qRT-PCR, ChIP-RT-qPCR, Western blot, Immunofluorescence Microscopy 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 13192908 13194140 Mitf Hdc Enhancer Active Disease mastocytosis MONDO:0005300 DOID:2488 Bone marrow UBERON:0002371 BMMC mast cell CL:0000097 Luciferase-based enhancer assay ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 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 13192908 13194140 Mitf Hdc Enhancer Active Disease mastocytosis MONDO:0005300 DOID:2488 Bone marrow UBERON:0002371 Mast cells mast cell CL:0000097 Luciferase-based enhancer assay ChIP-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2019 30672333 The putative Neuronatin imprint control region is an enhancer that also regulates the Blcap gene Mus musculus mm10 chr2 150860120 150860367 Nnat Enhancer Active Normal Brain UBERON:0000955 Primary Mouse Tissues mouse brain cell CL:0000540 Enhancer activity assay, Functional perturbation assay CRISPR knockout, Transgenic reporter assay, ChIP-RT-qPCR, RT-RT-qPCR 2019 30672333 The putative Neuronatin imprint control region is an enhancer that also regulates the Blcap gene Mus musculus mm10 chr2 150860120 150860367 Nnat Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa Cells CVCL_0030 cervical adenocarcinoma cell CL:0000069 Enhancer activity assay, Functional perturbation assay CRISPR knockout, Transgenic reporter assay, ChIP-RT-qPCR, RT-RT-qPCR 2019 30672333 The putative Neuronatin imprint control region is an enhancer that also regulates the Blcap gene Mus musculus mm10 chr2 150860120 150860367 Blcap Enhancer Active Normal Brain UBERON:0000955 Primary Mouse Tissues mouse brain cell CL:0000540 Enhancer activity assay, Functional perturbation assay CRISPR knockout, Transgenic reporter assay, ChIP-RT-qPCR, RT-RT-qPCR 2019 30672333 The putative Neuronatin imprint control region is an enhancer that also regulates the Blcap gene Mus musculus mm10 chr2 150860120 150860367 Blcap Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervix UBERON:0000002 HeLa Cells CVCL_0030 cervical adenocarcinoma cell CL:0000069 Enhancer activity assay, Functional perturbation assay CRISPR knockout, Transgenic reporter assay, ChIP-RT-qPCR, RT-RT-qPCR 2019 31028121 Runx1 and ROR??t Cooperate to Upregulate IL-22 Expression in Th Cells through Its Distal Enhancer Mus musculus mm10 chr12 31875800 31876373 Runx1 Il22 Enhancer Active Normal Spleen UBERON:0002106 CD4+ T cells CD4-positive T cell CL:0000624 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay Luciferase Reporter Assay, 3C-seq, ChIP-RT-qPCR, RT-RT-qPCR 2019 30711920 H2AFY promoter deletion causes PITX1 endoactivation and Liebenberg syndrome Mus musculus mm10 chr13 69400000 69410000 Pitx1 Enhancer Active Normal Limb bud UBERON:0005417 Mouse embryonic fibroblasts (MEFs) CVCL_0003 mouse embryonic fibroblast CL:0000057 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay RNA-seq CRISPR Knockout (Pitx1-lieb), RT-RT-qPCR, Whole-mount in situ hybridisation 2019 30711920 H2AFY promoter deletion causes PITX1 endoactivation and Liebenberg syndrome Mus musculus mm10 chr13 69400000 69410000 Pitx1 Enhancer Active Normal Limb bud UBERON:0005417 E11.5 mouse forelimb/hindlimb buds embryonic limb bud cell CL:0000000 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay RNA-seq CRISPR Knockout (Pitx1-lieb), RT-RT-qPCR, Whole-mount in situ hybridisation 2020 33313982 The anxiety and ethanol intake controlling GAL51 enhancer is epigenetically modulated by, and controls preference for, high-fat diet Mus musculus mm10 chr19 3441054 3441445 Gal Enhancer Active Normal Hypothalamus UBERON:0001898 Galaninergic Neuron galaninergic neuron CL:0000540 Enhancer activity assay, Functional perturbation assay Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR, Pyrosequencing 2019 30545847 CRISPR-mediated activation of a promoter or enhancer rescues obesity caused by haploinsufficiency Mus musculus mm10 chr10 87141000 87142000 Sim1 Enhancer Active Normal Hypothalamus UBERON:0001898 Primary neurons neuron CL:0000540 Functional perturbation assay RNA-seq CRISPR Knockout/CRISPRi, RT-RT-qPCR 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 Igl Enhancer Active Normal Bone marrow UBERON:0002371 pro-B cell pro-B cell CL:0000945 Enhancer activity assay, Functional perturbation assay Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR 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 Igl Enhancer Active Normal Bone marrow UBERON:0002371 B cell B cell CL:0000945 Enhancer activity assay, Functional perturbation assay Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR 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 Igl Enhancer Active Normal Bone marrow UBERON:0002371 pro-B cell pro-B cell CL:0000945 Enhancer activity assay, Functional perturbation assay Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR 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 Igl Enhancer Active Normal Bone marrow UBERON:0002371 B cell B cell CL:0000945 Enhancer activity assay, Functional perturbation assay Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR 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 Pomc Enhancer Active Normal Hypothalamus UBERON:0001898 Mouse primary neurons neuron CL:0000540 Functional perturbation assay RNA-seq CRISPR Knockout, CRISPRi, RT-RT-qPCR 2018 29514092 Transcription Factor IRF8 Governs Enhancer Landscape Dynamics in Mononuclear Phagocyte Progenitors Mus musculus mm10 chr16 5510000 5550000 Irf8; Spi1; Relb; Nfkb1 Cd80 Enhancer Active Normal Bone marrow UBERON:0002371 B lymphocytes B cell CL:0000945 Immunological functional assay, Functional genomics assay, Epigenomic profiling assay, Transcriptional regulation assay ChIP-seq, RNA-seq, Microarray Flow cytometry, FACS, RT-RT-qPCR, ChIP-RT-qPCR, MLR assay, Western blot 2024 38724692 Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters Mus musculus mm10 chr3 34757100 34758037 Sox2 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Enhancer activity assay scRNA-seq, scATAC-seq, MPRA Single-cell Quantitative Expression Reporter Assay (scQers), Luciferase Reporter Assay 2024 38724692 Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters Mus musculus mm10 chr3 34757100 34758037 Sox2 Enhancer Active Normal Embryoid body UBERON:0010001 Pluripotent cells from 21-day mouse embryoid bodies pluripotent stem cell CL:0002248 Enhancer activity assay scRNA-seq, scATAC-seq, MPRA Single-cell Quantitative Expression Reporter Assay (scQers), Luciferase Reporter Assay 2024 38724692 Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters Mus musculus mm10 chr3 34761100 34762000 Sox2 Enhancer Active Normal Embryo UBERON:0000922 Mouse embryonic stem cells mouse embryonic stem cell CL:0002322 Enhancer activity assay scRNA-seq, scATAC-seq, MPRA Single-cell Quantitative Expression Reporter Assay (scQers), Luciferase Reporter Assay 2024 38724692 Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters Mus musculus mm10 chr3 34761100 34762000 Sox2 Enhancer Active Normal Embryoid body UBERON:0010001 Pluripotent cells from 21-day mouse embryoid bodies pluripotent stem cell CL:0002248 Enhancer activity assay scRNA-seq, scATAC-seq, MPRA Single-cell Quantitative Expression Reporter Assay (scQers), Luciferase Reporter Assay 2024 38724692 Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters Mus musculus mm10 chr4 8201000 8202000 Bend5 Enhancer Active Normal Embryoid body UBERON:0010001 Parietal endoderm cells parietal endoderm cell CL:0002322 Enhancer activity assay scRNA-seq, scATAC-seq, MPRA Single-cell Quantitative Expression Reporter Assay (scQers), Luciferase Reporter Assay 2015 26626481 NSD3-short is an adaptor protein that couples BRD4 to the CHD8 chromatin remodeler Mus musculus mm10 chr15 61978434 61986531 Myc Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone marrow UBERON:0002371 RN2 CVCL_WT32 acute myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR 2015 26663721 Enhancer Turnover Is Associated with a Divergent Transcriptional Response to Glucocorticoid in Mouse and Human Macrophages Mus musculus mm10 chr13 101200000 101201200 Nr3C1 Dusp1 Enhancer Active Normal Blood UBERON:0000178 Bone marrow-derived macrophage (mBMDM) macrophage CL:0000235 TF binding assay, Enhancer activity assay ChIP-seq, RNA-seq RT-RT-qPCR 2015 26663721 Enhancer Turnover Is Associated with a Divergent Transcriptional Response to Glucocorticoid in Mouse and Human Macrophages Mus musculus mm10 chr8 72500000 72501100 Nr3C1 F13A1 Enhancer Active Normal Blood UBERON:0000178 Bone marrow-derived macrophage (mBMDM) macrophage CL:0000235 TF binding assay, Enhancer activity assay ChIP-seq, RNA-seq RT-RT-qPCR 2024 39196225 A transcriptional enhancer regulates cardiac maturation Mus musculus mm10 chr1 154149500 154150000 Mef2A Actn2 Enhancer Active Normal Heart UBERON:0000948 Mouse embryonic/Adult cardiomyocytes cardiomyocyte CL:0000746 TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2026 41526337 Temporal constraints on enhancer usage shape the regulation of limb gene transcription Mus musculus mm39 chr3 66550000 66650000 Hoxa13 Shox2 Enhancer Active Normal Limb bud UBERON:0005417 Limb mesenchymal cells mesenchymal cell CL:0000134 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay ChIP-seq, ATAC-seq, Capture Hi-C, RNA-seq Transgenic Reporter Assay, CRISPR Knockout, qRT-PCR, EMSA 2026 41526337 Temporal constraints on enhancer usage shape the regulation of limb gene transcription Mus musculus mm39 chr3 66850000 66950000 Hoxa13 Shox2 Enhancer Active Normal Limb bud UBERON:0005417 Limb mesenchymal cells mesenchymal cell CL:0000134 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay ChIP-seq, ATAC-seq, Capture Hi-C, RNA-seq Transgenic Reporter Assay, CRISPR Knockout, qRT-PCR 2024 38413562 The neutrophil-osteogenic cell axis promotes bone destruction in periodontitis Mus musculus mm39 chr14 78613540 78616951 Stat3 Tnfsf11 Enhancer Active Normal Bone UBERON:0001474 Primary osteoblasts osteoblast CL:0000062 Functional perturbation assay, Enhancer activity assay, TF binding assay ChIP-seq, scRNA-seq, RNA-seq, ATAC-seq CRISPR Knockout, RT-RT-qPCR, Western blot, ChIP-RT-qPCR, ELISA, Micro-CT 2024 38413562 The neutrophil-osteogenic cell axis promotes bone destruction in periodontitis Mus musculus mm39 chr14 78613540 78616951 Stat3 Tnfsf11 Enhancer Active Normal Bone UBERON:0001474 Periodontal ligament cells fibroblast CL:0000057 Functional perturbation assay, Enhancer activity assay, TF binding assay ChIP-seq, scRNA-seq, RNA-seq, ATAC-seq CRISPR Knockout, RT-RT-qPCR, Western blot, ChIP-RT-qPCR, ELISA, Micro-CT 2024 38413562 The neutrophil-osteogenic cell axis promotes bone destruction in periodontitis Mus musculus mm39 chr14 78613540 78616951 Stat3 Tnfsf11 Enhancer Active Normal Bone UBERON:0001474 Osteogenic cells osteoblast CL:0000062 Functional perturbation assay, Enhancer activity assay, TF binding assay ChIP-seq, scRNA-seq, RNA-seq, ATAC-seq CRISPR Knockout, RT-RT-qPCR, Western blot, ChIP-RT-qPCR, ELISA, Micro-CT 2024 38413562 The neutrophil-osteogenic cell axis promotes bone destruction in periodontitis Mus musculus mm39 chr14 78613540 78616951 Stat3 Tnfsf11 Enhancer Active Normal Bone UBERON:0001474 Primary calvarial osteoblasts osteoblast CL:0000062 Functional perturbation assay, Enhancer activity assay, TF binding assay ChIP-seq, scRNA-seq, RNA-seq, ATAC-seq CRISPR Knockout, RT-RT-qPCR, Western blot, ChIP-RT-qPCR, ELISA, Micro-CT 2026 41526337 Temporal constraints on enhancer usage shape the regulation of limb gene transcription Mus musculus mm39 chr3 66750000 66850000 Meis1 Shox2 Enhancer Active Normal Limb bud UBERON:0005417 Limb mesenchymal cells mesenchymal cell CL:0000134 Enhancer activity assay, Chromatin interaction assay ChIP-seq, ATAC-seq, Capture Hi-C, RNA-seq Transgenic Reporter Assay, qRT-PCR 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 Snca Enhancer Active Normal Brain UBERON:0000955 Primary midbrain dopaminergic neurons dopaminergic neuron CL:0000700 Functional perturbation assay CRISPR knockout, CRISPRi, RT-RT-qPCR, Western blot, FISH 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 Bdnf Enhancer Active Normal Amygdala UBERON:0001876 Mouse amygdala tissue mouse amygdala cell CL:0000540 Functional perturbation assay, Enhancer activity assay RNA-seq CRISPR Knockout, qRT-PCR, Transgenic Reporter Assay 2008 18202151 An Enhancer Twenty Kilobases Upstream of the Human Receptor Activator of Nuclear Factor Kappa B Ligand Gene Mediates Dominant Activation by 1,25 Dihydroxyvitamin D3 Mus musculus mm39 chr14 75391059 75392159 Tnfsf11 Enhancer Active Normal Bone marrow UBERON:0002371 ST2 CVCL_2205 mesenchymal stem cell CL:0000134 Enhancer activity assay Luciferase Reporter Assay 2008 18202151 An Enhancer Twenty Kilobases Upstream of the Human Receptor Activator of Nuclear Factor Kappa B Ligand Gene Mediates Dominant Activation by 1,25 Dihydroxyvitamin D3 Mus musculus mm39 chr14 75331459 75332459 Tnfsf11 Enhancer Active Normal Bone marrow UBERON:0002371 ST2 CVCL_2205 mesenchymal stem cell CL:0000134 Enhancer activity assay Luciferase Reporter Assay 2024 39362902 Developmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in Drosophila Drosophila melanogaster dm6 chr2L 1000000 1000300 NA Enhancer Active Normal None NA NA Embryo UBERON:0000922 S2 cell CVCL_TZ72 late embryonic Drosophila melanogaster cell CL:0007006 Enhancer activity assay STARR-seq Luciferase Reporter Assay 2024 39362902 Developmental and housekeeping transcriptional programs display distinct modes of enhancer-enhancer cooperativity in Drosophila Drosophila melanogaster dm6 chr2L 1001000 1001300 RpS12 Enhancer Active Normal None NA NA Embryo UBERON:0000922 S2 cell CVCL_TZ72 late embryonic Drosophila melanogaster cell CL:0007006 Enhancer activity assay STARR-seq Luciferase Reporter Assay 2020 32342858 Disparate expression specificities coded by a shared Hox-C enhancer Drosophila melanogaster dm6 chr3R 7795000 7796400 exd pb Enhancer Active Normal None NA NA Embryo UBERON:0000922 embryonic cell NA embryonic cell NA Enhancer activity assay; TF binding assay; Functional perturbation assay ChIP-seq; RNA-seq Transgenic Reporter Assay; CRISPR Knockout; RT-qPCR; In situ hybridization 2020 32342858 Disparate expression specificities coded by a shared Hox-C enhancer Drosophila melanogaster dm6 chr3R 7795000 7796400 exd zen2 Enhancer Active Normal None NA NA Embryo UBERON:0000922 embryonic cell NA embryonic cell NA Enhancer activity assay; TF binding assay; Functional perturbation assay ChIP-seq; RNA-seq Transgenic Reporter Assay; CRISPR Knockout; RT-qPCR; In situ hybridization 2020 33057197 Dense and pleiotropic regulatory information in a developmental enhancer Drosophila melanogaster dm6 chr2R 10788877 10789168 hth svb,lacZ Enhancer Active Normal None NA NA Embryo UBERON:0000922 embryonic epithelial cell NA embryonic epithelial cell NA Enhancer activity assay; TF binding assay; Functional perturbation assay RNA-seq Transgenic Reporter Assay; ChIP-qPCR; CRISPR Knockout; RT-qPCR; Western blot; EMSA 2023 38086419 Cell type directed design of synthetic enhancers Drosophila melanogaster dm6 chr3L 8670850 8671350 NA Enhancer Active Normal None NA NA Brain UBERON:0000955 Kenyon cell NA Kenyon cell CL:0000523 Enhancer activity assay ATAC-seq Transgenic Reporter Assay 2020 32541043 Regulation of spatiotemporal limits of developmental gene expression via enhancer grammar Drosophila melanogaster dm6 chr2R 5208000 5208523 T48 Enhancer Active Normal None NA NA Embryo UBERON:0000922 nc14 embryo NA embryonic cell NA Enhancer activity assay; Functional perturbation assay RNA-seq Transgenic Reporter Assay; RT-qPCR 2018 30038397 Dynamic interplay between enhancer-promoter topology and gene activity Drosophila melanogaster dm6 chr2R 9974054 9974699 eve Enhancer Active Normal None NA NA Embryo UBERON:0000922 blastoderm cell NA embryonic cell NA Enhancer activity assay; Chromatin interaction assay; Functional perturbation assay qRT-PCR; ChIP-qPCR 2018 30038397 Dynamic interplay between enhancer-promoter topology and gene activity Drosophila melanogaster dm6 chr2R 9975013 9975699 eve Enhancer Active Normal None NA NA Embryo UBERON:0000922 blastoderm cell NA embryonic cell NA Enhancer activity assay; Chromatin interaction assay; Functional perturbation assay qRT-PCR; ChIP-qPCR 2018 30038397 Dynamic interplay between enhancer-promoter topology and gene activity Drosophila melanogaster dm6 chr2R 9984101 9984849 eve Enhancer Active Normal None NA NA Embryo UBERON:0000922 blastoderm cell NA embryonic cell NA Enhancer activity assay; Chromatin interaction assay; Functional perturbation assay qRT-PCR; ChIP-qPCR 2018 30038397 Dynamic interplay between enhancer-promoter topology and gene activity Drosophila melanogaster dm6 chr2R 9985221 9985886 eve Enhancer Active Normal None NA NA Embryo UBERON:0000922 blastoderm cell NA embryonic cell NA Enhancer activity assay; Chromatin interaction assay; Functional perturbation assay qRT-PCR; ChIP-qPCR 2019 31223115 Dissecting the sharp response of a canonical developmental enhancer reveals multiple sources of cooperativity Drosophila melanogaster dm6 chr3 4669900 4670243 hb Enhancer Active Normal None NA NA Embryo UBERON:0000922 blastoderm embryo NA embryonic cell NA Enhancer activity assay Transgenic Reporter Assay 2019 32541043 Regulation of spatiotemporal limits of developmental gene expression via enhancer grammar Drosophila melanogaster dm6 chr3R 26880000 26880523 CG5507 Enhancer Active Normal None NA NA Embryo UBERON:0000922 embryo NA embryonic cell NA Enhancer activity assay; Functional perturbation assay Transgenic Reporter Assay; RT-qPCR 2020 31340149 Distinct Roles of Broadly Expressed Repressors Support Dynamic Enhancer Action and Change in Time Drosophila melanogaster dm6 chrX 18719542 18720191 Su(H) sog Enhancer Active Normal None NA NA Embryo UBERON:0000922 blastoderm embryo NA embryonic cell NA Enhancer activity assay; TF binding assay Transgenic Reporter Assay; ChIP-qPCR 2020 31340149 Distinct Roles of Broadly Expressed Repressors Support Dynamic Enhancer Action and Change in Time Drosophila melanogaster dm6 chrX 18741042 18741691 Su(H) sog Enhancer Active Normal None NA NA Embryo UBERON:0000922 blastoderm embryo NA embryonic cell NA Enhancer activity assay; TF binding assay Transgenic Reporter Assay; ChIP-qPCR 2023 38086419 Cell type directed design of synthetic enhancers Drosophila melanogaster dm6 chrX 15547650 15548150 NA Enhancer Active Normal None NA NA Brain UBERON:0000955 Kenyon cell NA Kenyon cell CL:0000523 Enhancer activity assay ATAC-seq Transgenic Reporter Assay 2023 38086419 Cell type directed design of synthetic enhancers Drosophila melanogaster dm6 chrX 4010500 4011000 NA Enhancer Active Normal None NA NA Brain UBERON:0000955 Kenyon cell NA Kenyon cell CL:0000523 Enhancer activity assay ATAC-seq Transgenic Reporter Assay 2023 38086419 Cell type directed design of synthetic enhancers Drosophila melanogaster dm6 chrX 9786300 9786800 NA Enhancer Active Normal None NA NA Brain UBERON:0000955 Kenyon cell NA Kenyon cell CL:0000523 Enhancer activity assay ATAC-seq Transgenic Reporter Assay 2021 33465092 A regulatory sub-circuit downstream of Wnt signaling controls developmental transitions in neural crest formation Gallus gallus galGal6 chr2 5221179 5221678 LEF1 AXUD1 Enhancer Active Normal None NA NA Cranial neural crest UBERON:0003099 neural crest cell NA neural crest cell CL:0000333 Enhancer activity assay; TF binding assay; Functional perturbation assay ATAC-seq; CUT&RUN; ChIP-seq Transgenic Reporter Assay; ChIP-qPCR; CRISPR Knockout; RT-PCR; FISH 2021 33465092 A regulatory sub-circuit downstream of Wnt signaling controls developmental transitions in neural crest formation Gallus gallus galGal6 chr2 5218800 5221678 LEF1 AXUD1 Enhancer Active Normal None NA NA Cranial neural crest UBERON:0003099 neural crest cell NA neural crest cell CL:0000333 Enhancer activity assay; TF binding assay; Chromatin interaction assay ATAC-seq; CUT&RUN; ChIP-seq; 3C-seq Transgenic Reporter Assay; ChIP-qPCR; RT-qPCR 2021 33465092 A regulatory sub-circuit downstream of Wnt signaling controls developmental transitions in neural crest formation Gallus gallus galGal6 chr2 5218800 5219499 AXUD1 Enhancer Active Normal None NA NA Cranial neural crest UBERON:0003099 neural crest cell NA neural crest cell CL:0000333 Enhancer activity assay; Functional perturbation assay ATAC-seq Transgenic Reporter Assay; CRISPR Knockout; RT-PCR; FISH 2023 37567873 Spinal cord repair is modulated by the neurogenic factor Hb-egf under direction of a regeneration-associated enhancer Danio rerio GRCz11 chr14 6760805 6761115 hbegfa Enhancer Active Normal None 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 2020 33239788 A map of cis-regulatory elements and 3D genome structures in zebrafish Danio rerio GRCz11 chr9 31332828 31334322 egfp Enhancer Active Normal None NA NA Brain UBERON:0000955 neuron NA neuron CL:0000540 Enhancer activity assay ChIP-seq; ATAC-seq Transgenic Reporter Assay 2020 33239788 A map of cis-regulatory elements and 3D genome structures in zebrafish Danio rerio GRCz11 chr8 44088636 44090085 egfp Enhancer Active Normal None NA NA Brain UBERON:0000955 neuron NA neuron CL:0000540 Enhancer activity assay ChIP-seq; ATAC-seq Transgenic Reporter Assay 2020 33239788 A map of cis-regulatory elements and 3D genome structures in zebrafish Danio rerio GRCz11 chr5 49025012 49026815 egfp Enhancer Active Normal None NA NA Heart UBERON:0000948 cardiomyocyte NA cardiomyocyte CL:0000746 Enhancer activity assay ChIP-seq; ATAC-seq Transgenic Reporter Assay 2020 33239788 A map of cis-regulatory elements and 3D genome structures in zebrafish Danio rerio GRCz11 chr7 7439474 7441474 egfp Enhancer Active Normal None NA NA Heart UBERON:0000948 cardiomyocyte NA cardiomyocyte CL:0000746 Enhancer activity assay ChIP-seq; ATAC-seq Transgenic Reporter Assay 2020 33239788 A map of cis-regulatory elements and 3D genome structures in zebrafish Danio rerio GRCz11 chr23 5735883 5736938 egfp Enhancer Active Normal None NA NA Heart UBERON:0000948 cardiomyocyte NA cardiomyocyte CL:0000746 Enhancer activity assay ChIP-seq; ATAC-seq Transgenic Reporter Assay 2020 33239788 A map of cis-regulatory elements and 3D genome structures in zebrafish Danio rerio GRCz11 chr7 18138313 18139545 egfp Enhancer Active Normal None NA NA Heart UBERON:0000948 cardiomyocyte NA cardiomyocyte CL:0000746 Enhancer activity assay ChIP-seq; ATAC-seq Transgenic Reporter Assay 2020 33239788 A map of cis-regulatory elements and 3D genome structures in zebrafish Danio rerio GRCz11 chr1 47366207 47368074 egfp Enhancer Active Normal None NA NA Heart UBERON:0000948 cardiomyocyte NA cardiomyocyte CL:0000746 Enhancer activity assay ChIP-seq; ATAC-seq Transgenic Reporter Assay 2020 33239788 A map of cis-regulatory elements and 3D genome structures in zebrafish Danio rerio GRCz11 chr8 2567791 2569300 egfp Enhancer Active Normal None NA NA Heart UBERON:0000948 cardiomyocyte NA cardiomyocyte CL:0000746 Enhancer activity assay ChIP-seq; ATAC-seq Transgenic Reporter Assay 2020 33239788 A map of cis-regulatory elements and 3D genome structures in zebrafish Danio rerio GRCz11 chr25 17938108 17939563 egfp Enhancer Active Normal None NA NA Kidney UBERON:0002113 embryonic kidney cell NA embryonic kidney cell NA Enhancer activity assay ChIP-seq; ATAC-seq Transgenic Reporter Assay 2020 33239788 A map of cis-regulatory elements and 3D genome structures in zebrafish Danio rerio GRCz11 chr5 61665365 61667095 egfp Enhancer Active Normal None NA NA Kidney UBERON:0002113 embryonic kidney cell NA embryonic kidney cell NA Enhancer activity assay ChIP-seq; ATAC-seq Transgenic Reporter Assay 2020 33239788 A map of cis-regulatory elements and 3D genome structures in zebrafish Danio rerio GRCz11 chr25 17939264 17940252 egfp Enhancer Active Normal None NA NA Kidney UBERON:0002113 embryonic kidney cell NA embryonic kidney cell NA Enhancer activity assay ChIP-seq; ATAC-seq Transgenic Reporter Assay 2020 33239788 A map of cis-regulatory elements and 3D genome structures in zebrafish Danio rerio GRCz11 chr6 43661350 43663650 egfp Enhancer Active Normal None NA NA Brain UBERON:0000955 neuron NA neuron CL:0000540 Enhancer activity assay ChIP-seq; ATAC-seq Transgenic Reporter Assay 2020 33239788 A map of cis-regulatory elements and 3D genome structures in zebrafish Danio rerio GRCz11 chr1 19433791 19434807 egfp Enhancer Active Normal None NA NA Skeletal muscle UBERON:0001134 embryonic myocyte NA embryonic myocyte CL:0000187 Enhancer activity assay ChIP-seq; ATAC-seq Transgenic Reporter Assay 2020 33239788 A map of cis-regulatory elements and 3D genome structures in zebrafish Danio rerio GRCz11 chr1 7624913 7626890 egfp Enhancer Active Normal None NA NA Skeletal muscle UBERON:0001134 embryonic myocyte NA embryonic myocyte CL:0000187 Enhancer activity assay ChIP-seq; ATAC-seq Transgenic Reporter Assay 2020 33239788 A map of cis-regulatory elements and 3D genome structures in zebrafish Danio rerio GRCz11 chr6 99012350 99015100 egfp Enhancer Active Normal None NA NA Skeletal muscle UBERON:0001134 embryonic myocyte NA embryonic myocyte CL:0000187 Enhancer activity assay ChIP-seq; ATAC-seq Transgenic Reporter Assay 2022 36284357 CRISPR-Cas9-mediated functional dissection of the foxc1 genomic region in zebrafish identifies critical conserved cis-regulatory elements Danio rerio GRCz11 chr2 716946 717020 foxf2a Enhancer Active Normal None NA NA Embryo UBERON:0000922 embryonic cell NA embryonic cell NA Functional perturbation assay CRISPR Knockout; qRT-PCR 2022 36284357 CRISPR-Cas9-mediated functional dissection of the foxc1 genomic region in zebrafish identifies critical conserved cis-regulatory elements Danio rerio GRCz11 chr20 26689284 26689441 foxf2b Enhancer Active Normal None NA NA Embryo UBERON:0000922 embryonic cell NA embryonic cell NA Functional perturbation assay CRISPR Knockout; qRT-PCR 2022 36284357 CRISPR-Cas9-mediated functional dissection of the foxc1 genomic region in zebrafish identifies critical conserved cis-regulatory elements Danio rerio GRCz11 chr2 684320 684414 foxc1a Enhancer Active Normal None NA NA Embryo UBERON:0000922 embryonic cell NA embryonic cell NA Functional perturbation assay CRISPR Knockout; qRT-PCR; Whole-mount in situ hybridization 2022 36284357 CRISPR-Cas9-mediated functional dissection of the foxc1 genomic region in zebrafish identifies critical conserved cis-regulatory elements Danio rerio GRCz11 chr2 577491 577557 foxc1a Enhancer Active Normal None NA NA Embryo UBERON:0000922 embryonic cell NA embryonic cell NA Functional perturbation assay CRISPR Knockout; qRT-PCR; Whole-mount in situ hybridization 2022 36284357 CRISPR-Cas9-mediated functional dissection of the foxc1 genomic region in zebrafish identifies critical conserved cis-regulatory elements Danio rerio GRCz11 chr2 535659 535798 foxc1a Enhancer Active Normal None NA NA Embryo UBERON:0000922 embryonic cell NA embryonic cell NA Functional perturbation assay CRISPR Knockout; qRT-PCR; Whole-mount in situ hybridization 2023 37563180 Spinal cord repair is modulated by the neurogenic factor Hb-egf under direction of a regeneration-associated enhancer Danio rerio GRCz11 chr14 6760805 6761115 hbegfa Enhancer Active Normal None NA NA Spinal cord UBERON:0002240 ependymo-radial glial cell NA radial glial cell CL:0000681 Enhancer activity assay ATAC-seq qRT-PCR; ChIP-qPCR 2021 33359848 Comparative sequence analysis and functional validation identified a retina-specific enhancer around zic5 and zic2a Danio rerio GRCz11 chr7 20447000 20447290 zic5 Enhancer Active Normal None NA NA Retina UBERON:0000966 embryonic cell NA retinal progenitor cell NA Enhancer activity assay Transgenic Reporter Assay 2023 38019918 An injury-responsive mmp14b enhancer is required for heart regeneration Danio rerio GRCz11 chr2 38181326 38182075 NA Enhancer Active Normal None NA NA Heart UBERON:0000948 cardiac endothelial cell NA cardiac endothelial cell CL:0000115 Regulatory element functional validation; chromatin accessibility analysis ATAC-seq; RNA-seq RT-qPCR; EMSA; Transgenic Reporter Assay 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:0002600 NA NA gamma Kenyon cell CL:0000669 in vivo reporter assay NA Enhancer-GFP reporter; site-directed mutagenesis 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:0002600 NA NA gamma Kenyon cell CL:0000669 in vivo reporter assay NA Enhancer-GFP reporter; site-directed mutagenesis 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:0002600 NA NA gamma Kenyon cell CL:0000669 in vivo reporter assay NA Enhancer-GFP reporter; site-directed mutagenesis 2022 34987221 Decoding gene regulation in the fly brain Drosophila melanogaster dm6 chrX 534837 535834 Mamo Appl Enhancer Silenced Normal NA NA NA brain UBERON:0002600 NA NA gamma Kenyon cell CL:0000669 in vivo reporter assay NA Enhancer-GFP reporter; site-directed mutagenesis 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:0002600 NA NA gamma Kenyon cell CL:0000669 in vivo reporter assay NA Enhancer-GFP reporter 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:0002600 NA NA gamma Kenyon cell CL:0000669 in vivo reporter assay NA Enhancer-GFP reporter 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:0002600 NA NA gamma Kenyon cell CL:0000669 in vivo reporter assay NA Enhancer-GFP reporter; site-directed mutagenesis 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:0002600 NA NA gamma Kenyon cell CL:0000669 in vivo reporter assay NA Enhancer-GFP reporter; site-directed mutagenesis 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:0002600 NA NA gamma Kenyon cell CL:0000669 in vivo reporter assay NA Enhancer-GFP reporter; site-directed mutagenesis 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:0002600 NA NA gamma Kenyon cell CL:0000669 in vivo reporter assay NA Enhancer-GFP reporter; site-directed mutagenesis 2022 34987221 Decoding gene regulation in the fly brain Drosophila melanogaster dm6 chrX 18554916 18555296 Mamo Bx Enhancer Silenced Normal NA NA NA brain UBERON:0002600 NA NA gamma Kenyon cell CL:0000669 in vivo reporter assay NA Enhancer-GFP reporter; site-directed mutagenesis 2022 34987221 Decoding gene regulation in the fly brain Drosophila melanogaster dm6 chrX 18554916 18555296 Lola-PF Bx Enhancer Silenced Normal NA NA NA brain UBERON:0002600 NA NA gamma Kenyon cell CL:0000669 in vivo reporter assay NA Enhancer-GFP reporter; site-directed mutagenesis 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:0002600 NA NA gamma Kenyon cell CL:0000669 in vivo reporter assay NA Enhancer-GFP reporter; site-directed mutagenesis 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:0002600 NA NA gamma Kenyon cell CL:0000669 in vivo reporter assay NA Enhancer-GFP reporter; site-directed mutagenesis 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:0002600 NA NA gamma Kenyon cell CL:0000669 in vivo reporter assay NA Enhancer-GFP reporter; site-directed mutagenesis 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:0002600 NA NA gamma Kenyon cell CL:0000669 in vivo reporter assay NA Enhancer-GFP reporter; site-directed mutagenesis 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:0002600 NA NA gamma Kenyon cell CL:0000669 in vivo reporter assay NA Enhancer-GFP reporter; site-directed mutagenesis 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:0002600 NA NA gamma Kenyon cell CL:0000669 in vivo reporter assay NA Enhancer-GFP reporter; site-directed mutagenesis 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:0002600 NA NA gamma Kenyon cell CL:0000669 in vivo reporter assay NA Enhancer-GFP reporter; site-directed mutagenesis 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:0002600 NA NA gamma Kenyon cell CL:0000669 in vivo reporter assay NA Enhancer-GFP reporter; site-directed mutagenesis 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:0002600 NA NA gamma Kenyon cell CL:0000669 in vivo reporter assay NA Enhancer-GFP reporter; site-directed mutagenesis 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:0002600 NA NA gamma Kenyon cell CL:0000669 in vivo reporter assay NA Enhancer-GFP reporter; site-directed mutagenesis 2022 34987221 Decoding gene regulation in the fly brain Drosophila melanogaster dm6 chr2L 20040500 20041072 Mamo sNPF Enhancer Silenced Normal NA NA NA brain UBERON:0002600 NA NA gamma Kenyon cell CL:0000669 in vivo reporter assay NA Enhancer-GFP reporter; site-directed mutagenesis 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:0002600 NA NA gamma Kenyon cell CL:0000669 in vivo reporter assay NA Enhancer-GFP reporter; site-directed mutagenesis 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:0002600 NA NA gamma Kenyon cell CL:0000669 in vivo reporter assay NA Enhancer-GFP reporter; site-directed mutagenesis 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:0002600 NA NA gamma Kenyon cell CL:0000669 in vivo reporter assay NA Enhancer-GFP reporter; site-directed mutagenesis 2025 40369080 A human-specific enhancer fine-tunes radial glia potency and corticogenesis Homo sapiens hg38 chr10 35949193 35950411 NR FZD8 Enhancer Active Normal NA NA NA cerebral cortex UBERON:0000956 NA NA radial glial cell CL:0000680 in vivo reporter assay; genome editing RNA-seq; scRNA-seq; ChIP-qPCR; CRISPRi Immunohistochemistry; luciferase reporter assay; RT-qPCR 2020 32095812 Looping of upstream cis-regulatory elements is required for CFTR expression in human airway epithelial cells Homo sapiens hg19 chr7 117043000 117044500 CEBPB CFTR Enhancer Active Normal Airway epithelium UBERON:0003684 16HBE14o- human bronchial epithelial CVCL_0112 bronchial epithelial cell CL:0002591 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, ATAC-seq, 4C-seq, RNA-seq CRISPR Knockout, Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2020 32095812 Looping of upstream cis-regulatory elements is required for CFTR expression in human airway epithelial cells Homo sapiens hg19 chr7 117043000 117044500 CEBPB CFTR Enhancer Active Disease lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 Calu3 CVCL_0609 lung adenocarcinoma cell CL:0001069 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, ATAC-seq, 4C-seq, RNA-seq CRISPR Knockout, Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR 2020 32095812 Looping of upstream cis-regulatory elements is required for CFTR expression in human airway epithelial cells Homo sapiens hg19 chr7 117052000 117053500 CFTR Enhancer Active Normal Airway epithelium UBERON:0003684 16HBE14o- human bronchial epithelial CVCL_0112 bronchial epithelial cell CL:0002591 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, ATAC-seq, 4C-seq, RNA-seq CRISPR Knockout, Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Sulforaphane Treatment 2020 32095812 Looping of upstream cis-regulatory elements is required for CFTR expression in human airway epithelial cells Homo sapiens hg19 chr7 117052000 117053500 CFTR Enhancer Active Disease lung adenocarcinoma MONDO:0005032 DOID:3905 Lung UBERON:0002048 Calu3 CVCL_0609 lung adenocarcinoma cell CL:0001069 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, ATAC-seq, 4C-seq, RNA-seq CRISPR Knockout, Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Sulforaphane Treatment 2023 37904237 Landscape of enhancer disruption and functional screen in melanoma cells Homo sapiens hg19 chr10 89986509 89987396 PTEN Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 Melanoma cell line melanoma cell CL:0002573 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay HiChIP, ATAC-seq, ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, 3C-seq, 4C-seq, RT-RT-qPCR, Western blot 2023 37904237 Landscape of enhancer disruption and functional screen in melanoma cells Homo sapiens hg19 chr15 99982353 99983277 MEF2A Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 Melanoma cell line melanoma cell CL:0002573 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay HiChIP, ATAC-seq, ChIP-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, 3C-seq, 4C-seq, RT-RT-qPCR, Western blot 2021 33712565 EphA2 super-enhancer promotes tumor progression by recruiting FOSL2 and TCF7L2 to activate the target gene EphA2 Homo sapiens hg19 chr1 16479332 16539780 EPHA2 Enhancer Active Disease cervical cancer MONDO:0001156 DOID:2871 Cervical Epithelium UBERON:0000002 HeLa CVCL_0030 cervical adenocarcinoma cell CL:0000069 Functional perturbation assay, Enhancer activity assay ChIP-seq, RNA-seq, ATAC-seq CRISPR Knockout, Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2021 33712565 EphA2 super-enhancer promotes tumor progression by recruiting FOSL2 and TCF7L2 to activate the target gene EphA2 Homo sapiens hg19 chr1 16479332 16539780 EPHA2 Enhancer Active Disease colorectal carcinoma MONDO:0005132 DOID:9256 Colon Epithelium UBERON:0001155 HCT116 CVCL_0291 colorectal carcinoma cell CL:0000066 Functional perturbation assay, Enhancer activity assay ChIP-seq, RNA-seq, ATAC-seq CRISPR Knockout, Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2021 33712565 EphA2 super-enhancer promotes tumor progression by recruiting FOSL2 and TCF7L2 to activate the target gene EphA2 Homo sapiens hg19 chr1 16479332 16539780 EPHA2 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast Epithelium UBERON:0000310 MCF7 CVCL_0031 breast carcinoma cell CL:0000066 Functional perturbation assay, Enhancer activity assay ChIP-seq, RNA-seq, ATAC-seq CRISPR Knockout, Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr8 130550000 130551100 EVI1 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 Primary AML blasts myeloid leukemia cell CL:0001054 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, 3C-seq, 4C-seq CRISPR Knockout, RT-RT-qPCR, Western blot, Flow Cytometry 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr8 130550000 130551100 EVI1 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Peripheral Blood UBERON:0000178 K562 CVCL_0004 K562 erythroleukemia cell CL:0001054 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, 3C-seq, 4C-seq CRISPR Knockout, RT-RT-qPCR, Western blot, Flow Cytometry 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr8 130550000 130551100 EVI1 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 CD34+ HSPCs CD34-positive hematopoietic stem cell CL:0001029 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, 3C-seq, 4C-seq CRISPR Knockout, RT-RT-qPCR, Western blot, Flow Cytometry 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr8 130580000 130581100 EVI1 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Peripheral Blood UBERON:0000178 K562 CVCL_0004 K562 erythroleukemia cell CL:0001054 TF binding assay, Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, 4C-seq, RNA-seq, ATAC-seq CRISPR Knockout, RT-RT-qPCR, Western blot, FISH, Flow Cytometry 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr8 130580000 130581100 EVI1 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 Primary AML blasts myeloid leukemia cell CL:0001054 TF binding assay, Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, 4C-seq, RNA-seq, ATAC-seq CRISPR Knockout, RT-RT-qPCR, Western blot, FISH, Flow Cytometry 2021 34584081 The leukemic oncogene EVI1 hijacks a MYC super-enhancer by CTCF-facilitated loops Homo sapiens hg19 chr8 130580000 130581100 EVI1 Enhancer Active Disease acute myeloid leukemia MONDO:0018874 DOID:9119 Bone Marrow UBERON:0002371 CD34+ HSPCs CD34-positive hematopoietic stem cell CL:0001029 TF binding assay, Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, 4C-seq, RNA-seq, ATAC-seq CRISPR Knockout, RT-RT-qPCR, Western blot, FISH, Flow Cytometry 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 Normal Peripheral Blood UBERON:0000178 SC monocyte-derived cells monocyte-derived cell CL:0000576 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay RNA-seq, ChIP-seq, ATAC-seq, 3C-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, CRISPRa, ChIP-RT-qPCR, 3C assay, 4C assay, EMSA, RT-RT-qPCR, Western blot 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 Normal Peripheral Blood UBERON:0000178 Primary CD14+ monocytes CD14-positive monocyte CL:0001053 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay RNA-seq, ChIP-seq, ATAC-seq, 3C-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, CRISPRa, ChIP-RT-qPCR, 3C assay, 4C assay, EMSA, RT-RT-qPCR, Western blot 2020 32238901 Accelerated evolution of an Lhx2 enhancer shapes mammalian social hierarchies Homo sapiens hg19 chr9 126770367 126771183 CTCF LHX2 Enhancer Active Disease Brain UBERON:0000955 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C, ATAC-seq Luciferase Reporter Assay, Transgenic Reporter Assay, CRISPR Knockout, CRISPRi, qRT-PCR 2019 30659195 Aberrant enhancer hypomethylation contributes to hepatic carcinogenesis through global transcriptional reprogramming Homo sapiens hg19 chr20 48900221 48901229 CEBPB Enhancer Active Normal Liver UBERON:0002107 Human normal liver cell hepatocyte CL:0000182 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay MBDCap-seq, WGBS, ChIP-seq, RNA-seq, Hi-C Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, Bisulfite pyrosequencing 2019 31251802 Enhancer-mediated enrichment of interacting JMJD3a???DDX21 to ENPP2 locus prevents R-loop formation and promotes transcription Homo sapiens hg19 chr8 120733232 120735226 RELA ENPP2 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293 CVCL_0063 embryonic kidney cell CL:0002139 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, RT-RT-qPCR, Western blot 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 SPRED2 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293T CVCL_0063 embryonic kidney cell CL:0002139 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ATAC-seq, ChIP-seq CRISPR knockout, Luciferase Reporter Assay, RT-RT-qPCR, Western blot 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 ACTR2 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293T CVCL_0063 embryonic kidney cell CL:0002139 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ATAC-seq, ChIP-seq CRISPR knockout, Luciferase Reporter Assay, RT-RT-qPCR, Western blot 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 Normal Embryonic Kidney UBERON:0002113 HEK293T CVCL_0063 embryonic kidney cell CL:0002139 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ATAC-seq, ChIP-seq CRISPR knockout, Luciferase Reporter Assay, RT-RT-qPCR, Western blot 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 SPRED2 Enhancer Active Normal Embryonic Kidney UBERON:0002113 HEK293T CVCL_0063 embryonic kidney cell CL:0002139 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ATAC-seq, ChIP-seq CRISPR knockout, Luciferase Reporter Assay, RT-RT-qPCR, Western blot 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:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat cells CVCL_0065 T lymphoblast CL:0002419 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ATAC-seq, ChIP-seq, RNA-seq Luciferase reporter assay, CRISPR knockout, ChIP-RT-qPCR, RT-RT-qPCR, 3C-seq 2016 26776159 A p53-bound enhancer region controls a long intergenic noncoding RNA required for p53 stress response Homo sapiens hg19 chr9 89630000 89631000 TP53 LINC00475 Enhancer Active Disease T-cell acute lymphoblastic leukemia MONDO:0004947 DOID:0050890 Blood UBERON:0000178 MOLT-4 cells CVCL_0013 T lymphoblast CL:0002419 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, 3C-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, CRISPR Knockout, Western blot 2016 26776159 A p53-bound enhancer region controls a long intergenic noncoding RNA required for p53 stress response Homo sapiens hg19 chr9 89630000 89631000 TP53 LINC00475 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 MCF7 CVCL_0031 breast carcinoma cell CL:0000646 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, 3C-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, CRISPR Knockout, Western blot 2016 26776159 A p53-bound enhancer region controls a long intergenic noncoding RNA required for p53 stress response Homo sapiens hg19 chr9 89630000 89631000 TP53 LINC00475 Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 MALME-3M CVCL_1438 melanoma cell CL:0002573 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, 3C-seq Luciferase Reporter Assay, ChIP-RT-qPCR, RT-RT-qPCR, CRISPR Knockout, Western blot 2016 27803105 BET inhibitors suppress ALDH activity by targeting ALDH1A1 super-enhancer Homo sapiens hg19 chr9 133401000 133404500 BRD4 ALDH1A1 Enhancer Active Disease breast carcinoma MONDO:0006120 DOID:1612 Breast UBERON:0000310 ZR-75-1 CVCL_0588 breast carcinoma cell CL:0000646 Enhancer activity assay, Functional perturbation assay, Chromatin interaction assay ChIP-seq, RNA-seq, 3C Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR 2017 29149598 Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene Homo sapiens hg19 chr12 47732000 47733500 FOSL2 AMIGO2 Enhancer Active Disease ovarian carcinoma MONDO:0005140 DOID:2394 Ovary UBERON:0000992 OVCAR3 CVCL_0465 ovarian carcinoma cell CL:0000069 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR 2017 29149598 Harnessing BET Inhibitor Sensitivity Reveals AMIGO2 as a Melanoma Survival Gene Homo sapiens hg19 chr12 47732000 47733500 FOSL2 AMIGO2 Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 SKmel147 CVCL_3876 melanoma cell CL:0002573 Enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR 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 PAX5 ETV6 Enhancer Active Disease skin melanoma MONDO:0005105 DOID:1909 Skin UBERON:0000014 501MEL CVCL_4633 melanoma cell CL:0002573 Enhancer activity assay, Functional perturbation assay Hi-C, RNA-seq, ChIP-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR 2024 38356460 ETV6::ACSL6 translocation-driven super-enhancer activation leads to eosinophilia in acute lymphoblastic leukemia through IL-3 overexpression Homo sapiens hg19 chr12 11680000 11718964 FOXJ1 ETV6 Enhancer Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0080545 Bone Marrow UBERON:0002371 Primary ALL cells B lymphoblast CL:0000945 Enhancer activity assay, Functional perturbation assay Hi-C, RNA-seq, ChIP-seq Luciferase Reporter Assay, CRISPR Knockout, RT-RT-qPCR 2016 26813977 A New Class of Temporarily Phenotypic Enhancers Identified by CRISPR/Cas9 Mediated Genetic Screening Homo sapiens hg19 chr6 30904342 30904788 POU5F1 Enhancer Active Disease B-cell acute lymphoblastic leukemia MONDO:0004945 DOID:0080545 Bone Marrow UBERON:0002371 Primary ALL cells B lymphoblast CL:0000945 Functional perturbation assay, Enhancer activity assay ChIP-seq, RNA-seq, 4C-seq CRISPR Knockout, CRISPRi, Luciferase Reporter Assay, RT-RT-qPCR 2019 31251802 Enhancer-mediated enrichment of interacting JMJD3a???DDX21 to ENPP2 locus prevents R-loop formation and promotes transcription Homo sapiens hg19 chr8 120733232 120735226 RELA ENPP2 Enhancer Active Disease histiocytic lymphoma MONDO:0004854 DOID:5408 Hematopoietic UBERON:0002405 U-937 CVCL_0007 histiocytic lymphoma cell CL:0000576 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, RNA-seq, Hi-C Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, RT-RT-qPCR, Western blot 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:0004947 DOID:0050890 Blood UBERON:0000178 Jurkat CVCL_0065 T lymphoblast CL:0002419 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, ATAC-seq, Hi-C, 4C-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 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:0004947 DOID:0050890 Blood UBERON:0000178 RPMI-8402 CVCL_1667 T lymphoblast CL:0002419 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, ATAC-seq, Hi-C, 4C-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 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:0004947 DOID:0050890 Blood UBERON:0000178 Primary T-ALL cells T lymphoblast CL:0002419 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay ChIP-seq, ATAC-seq, Hi-C, 4C-seq Luciferase Reporter Assay, CRISPR Knockout, CRISPRi, ChIP-RT-qPCR, RT-RT-qPCR, Western blot 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:0005280 Synovial tissue UBERON:0002407 MH7A CVCL_0427 synovial fibroblast CL:0000057 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ATAC-seq, ChIP-seq CRISPR knockout, Luciferase Reporter Assay, RT-RT-qPCR, Western blot 2019 30659195 Aberrant enhancer hypomethylation contributes to hepatic carcinogenesis through global transcriptional reprogramming Homo sapiens hg19 chr20 48900221 48901229 CEBPB Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 Human hepatocellular carcinoma cell hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay MBDCap-seq, WGBS, ChIP-seq, RNA-seq, Hi-C Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, Bisulfite pyrosequencing 2019 30659195 Aberrant enhancer hypomethylation contributes to hepatic carcinogenesis through global transcriptional reprogramming Homo sapiens hg19 chr20 48900221 48901229 CEBPB Enhancer Active Disease hepatocellular carcinoma MONDO:0007256 DOID:684 Liver UBERON:0002107 Huh7 CVCL_0336 hepatocellular carcinoma cell CL:0000182 Enhancer activity assay, TF binding assay, Chromatin interaction assay, Functional perturbation assay MBDCap-seq, WGBS, ChIP-seq, RNA-seq, Hi-C Luciferase Reporter Assay, CRISPR Knockout, ChIP-RT-qPCR, RT-RT-qPCR, Western blot, Bisulfite pyrosequencing 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 SPRED2 Enhancer Active Disease rheumatoid arthritis MONDO:0005280 Synovial tissue UBERON:0002407 MH7A CVCL_0427 synovial fibroblast CL:0000057 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ATAC-seq, ChIP-seq CRISPR knockout, Luciferase Reporter Assay, RT-RT-qPCR, Western blot 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 ACTR2 Enhancer Active Disease rheumatoid arthritis MONDO:0005280 Synovial tissue UBERON:0002407 MH7A CVCL_0427 synovial fibroblast CL:0000057 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ATAC-seq, ChIP-seq CRISPR knockout, Luciferase Reporter Assay, RT-RT-qPCR, Western blot 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 SPRED2 Enhancer Active Disease rheumatoid arthritis MONDO:0005280 Synovial tissue UBERON:0002407 MH7A CVCL_0427 synovial fibroblast CL:0000057 Enhancer activity assay, Chromatin interaction assay, Functional perturbation assay Hi-C, ATAC-seq, ChIP-seq CRISPR knockout, Luciferase Reporter Assay, RT-RT-qPCR, Western blot 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:0005176 DOID:9256 Colon UBERON:0001155 HT29 CVCL_0320 colorectal carcinoma cell CL:0000066 Super enhancer activity assay, Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq CRISPRi, Luciferase Reporter Assay 2021 33975627 Functional mapping of androgen receptor enhancer activity Homo sapiens hg19 chr19 51354200 51354400 AR KLK3 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, STARRseq, RNA-seq Luciferase Reporter Assay, CRISPRi, qRT-PCR 2021 33975627 Functional mapping of androgen receptor enhancer activity Homo sapiens hg19 chr6 15109500 15110350 AR FKBP5 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, STARRseq, ChIA-PET, RNA-seq Luciferase Reporter Assay, CRISPRi, qRT-PCR 2021 33975627 Functional mapping of androgen receptor enhancer activity Homo sapiens hg19 chr7 45025000 45025850 AR STEAP4 Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, STARRseq, ChIA-PET, RNA-seq Luciferase Reporter Assay, CRISPRi, qRT-PCR 2021 33975627 Functional mapping of androgen receptor enhancer activity Homo sapiens hg19 chr2 74155000 74155850 AR DBI Enhancer Active Disease prostate cancer MONDO:0008315 DOID:10283 Prostate UBERON:0002367 LNCaP CVCL_0395 prostate carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, STARRseq, ChIA-PET, RNA-seq Luciferase Reporter Assay, CRISPRi, qRT-PCR 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:0006120 DOID:1612 Breast UBERON:0000310 MCF7 CVCL_0031 breast carcinoma cell CL:0000066 Enhancer activity assay, TF binding assay, Functional perturbation assay ChIP-seq, RNA-seq Luciferase Reporter Assay, ChIP-RT-qPCR, CRISPR Knockout, CRISPRi, qRT-PCR, Western blot 2019 31761532 Functional Enhancers Shape Extrachromosomal Oncogene Amplifications Homo sapiens hg19 chr7 54932020 54934020 SOX2 EGFR Enhancer Active Disease glioblastoma MONDO:0005142 DOID:3070 Brain UBERON:0000955 G361 glioblastoma CVCL_1220 glioblastoma cell CL:0000127 Functional perturbation assay ChIP-seq, ATAC-seq, RNA-seq, 4C-seq, CRISPRi screen CRISPRi, RT-RT-qPCR, Alamar Blue Assay