Pubmed	Chromosome	Start_position	End_position	Enhancer_related_genes	Description	Species	Tissue_class	Experiment_class	Title	SNP_related	SNP_id	Disease	Cell_class	Enhancer_id	Enhancer_experiment	Enhancer_tar_ex_De	Enhancer_type	target_gene_strong_experiment	target_gene_weak_experiment	target_gene_other_name	Enhancer_function	Enhancer_function_experiment	En_function_ex_de	TF_other_name	Experiment	SNP_position	SNP_experiment	Target_gene	TF_name	target_gene_experiment_description	TF_experiment_de
29364907	chr2	28389994	28391994	FOSL2	FOSL2 levels were only minimally reduced, indicating that 20861 cell proliferation is completely dependent on expression of the E6 and E7 oncogenes.	human	Cervix	High+Lowthroughput	HPV integration hijacks and multimerizes a cellular enhancer to generate a viral-cellular super-enhancer that drives high viral oncogene expression	否		HPV positive tumors	cervical-derived cell line 20861	E_01_0001	Southern blot,ChIP-seq,Immunofluorescence,ChIP-qPCR,RNA-seq,FISH	FOSL2 levels were only minimally reduced, indicating that 20861 cell proliferation is completely dependent on expression of the E6 and E7 oncogenes.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		FOSL2 levels were only minimally reduced, indicating that 20861 cell proliferation is completely dependent on expression of the E6 and E7 oncogenes.	Immunohistochemical staining	FOSL2 levels were only minimally reduced, indicating that 20861 cell proliferation is completely dependent on expression of the E6 and E7 oncogenes.		Southern blot,ChIP-seq,Immunofluorescence,ChIP-qPCR,RNA-seq,FISH				FOSL2		FOSL2 levels were only minimally reduced, indicating that 20861 cell proliferation is completely dependent on expression of the E6 and E7 oncogenes.
29363938	chr2	207527779	207529779	CREB1	The addition of AuNP-p(T)DNA to HeLa lysate containing GFP, GCN5, CREB1, and XBP-1S mRNA increased protein synthesis by 1.80, 1.99, 1.95 and 2.20-fold respectively.	human	Cervix	High+Lowthroughput	Universal mRNA Translation Enhancement with Gold Nanoparticles Conjugated to Oligonucleotides with a Poly(T) Sequence	否		cervical cancer	HeLa cell	E_01_0002	Western blot,RT-PCR,PCR	The addition of AuNP-p(T)DNA to HeLa lysate containing GFP, GCN5, CREB1, and XBP-1S mRNA increased protein synthesis by 1.80, 1.99, 1.95 and 2.20-fold respectively.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The addition of AuNP-p(T)DNA to HeLa lysate containing GFP, GCN5, CREB1, and XBP-1S mRNA increased protein synthesis by 1.80, 1.99, 1.95 and 2.20-fold respectively.	Immunohistochemical staining	The addition of AuNP-p(T)DNA to HeLa lysate containing GFP, GCN5, CREB1, and XBP-1S mRNA increased protein synthesis by 1.80, 1.99, 1.95 and 2.20-fold respectively.		Western blot,RT-PCR,PCR				CREB1		The addition of AuNP-p(T)DNA to HeLa lysate containing GFP, GCN5, CREB1, and XBP-1S mRNA increased protein synthesis by 1.80, 1.99, 1.95 and 2.20-fold respectively.
29357419	chr7	148804764	148806764	EZH2	Polycomb group proteins,EZH2, and menin binds at PAX2 gene and has been demonstrated to decrease transcription of PAX2	human	Kidney	High+Lowthroughput	Modulation of apolipoprotein L1-microRNA-193a axis prevents podocyte dedifferentiation in high-glucose milieu	否		kidney disease	epithelial cell	E_01_0003	Western blot,Immunofluorescence,Transfection	Polycomb group proteins,EZH2, and menin binds at PAX2 gene and has been demonstrated to decrease transcription of PAX2	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Polycomb group proteins,EZH2, and menin binds at PAX2 gene and has been demonstrated to decrease transcription of PAX2	Immunohistochemical staining	Polycomb group proteins,EZH2, and menin binds at PAX2 gene and has been demonstrated to decrease transcription of PAX2		Western blot,Immunofluorescence,Transfection				EZH2		Polycomb group proteins,EZH2, and menin binds at PAX2 gene and has been demonstrated to decrease transcription of PAX2
29344674	chr7	148805135	148807135	EZH2	In addition, H19 was found to regulate the expression of oncogene enhancer of zeste homolog 2 (EZH2) by competing with miR‑138; the inhibition of miR-138 attenuated the inhibitory effects of H19 knockdown on OSCC cells.	human	Oral cavity	High+Lowthroughput	Long non-coding RNA H1 promotes cell proliferation and invasion by acting as a ceRNA of miR?138 and releasing EZH2 in oral squamous cell carcinoma	否		oral squamous cell carcinoma	oral squamous cell carcinoma cell	E_01_0004	RT-qPCR,transfection,Western blot	In addition, H19 was found to regulate the expression of oncogene enhancer of zeste homolog 2 (EZH2) by competing with miR‑138; the inhibition of miR-138 attenuated the inhibitory effects of H19 knockdown on OSCC cells.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In addition, H19 was found to regulate the expression of oncogene enhancer of zeste homolog 2 (EZH2) by competing with miR‑138; the inhibition of miR-138 attenuated the inhibitory effects of H19 knockdown on OSCC cells.	Immunohistochemical staining	In addition, H19 was found to regulate the expression of oncogene enhancer of zeste homolog 2 (EZH2) by competing with miR‑138; the inhibition of miR-138 attenuated the inhibitory effects of H19 knockdown on OSCC cells.		RT-qPCR,transfection,Western blot				EZH2		In addition, H19 was found to regulate the expression of oncogene enhancer of zeste homolog 2 (EZH2) by competing with miR‑138; the inhibition of miR-138 attenuated the inhibitory effects of H19 knockdown on OSCC cells.
29344090	chr12	102954386	102956386	ASCL1	As a consequence of the rearrangement ASCL1 was brought into proximity of the IGHJ-Cμ enhancer and was highly overexpressed in the aberrant B-cells of the patient, as shown by qPCR and immunohistochemistry.	human	Bone marrow and lymphatic	High+Lowthroughput	Overexpression of the proneural transcription factor ASCL1 in chronic lymphocytic leukemia with a t(12;14)(q23.2;q32.3)	否		chronic lymphocytic leukemia	chronic lymphocytic leukemia cell	E_01_0005	qPCR,FISH	As a consequence of the rearrangement ASCL1 was brought into proximity of the IGHJ-Cμ enhancer and was highly overexpressed in the aberrant B-cells of the patient, as shown by qPCR and immunohistochemistry.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		As a consequence of the rearrangement ASCL1 was brought into proximity of the IGHJ-Cμ enhancer and was highly overexpressed in the aberrant B-cells of the patient, as shown by qPCR and immunohistochemistry.	Immunohistochemical staining	As a consequence of the rearrangement ASCL1 was brought into proximity of the IGHJ-Cμ enhancer and was highly overexpressed in the aberrant B-cells of the patient, as shown by qPCR and immunohistochemistry.		qPCR,FISH				ASCL1		As a consequence of the rearrangement ASCL1 was brought into proximity of the IGHJ-Cμ enhancer and was highly overexpressed in the aberrant B-cells of the patient, as shown by qPCR and immunohistochemistry.
29344006	chr6	113930322	113932322	HDAC2	HDAC2 can attenuate lipopolysaccharide-induced inflammation by regulating c-Jun and PAI-1 expression in macrophages.	human	Connective	High+Lowthroughput	Histone deacetylase 2 (HDAC2) attenuates lipopolysaccharide (LPS)-induced inflammation by regulating PAI-1 expression	否		Sepsis	macrophage	E_01_0006	ChIP,qRT-PCR,Western blot	HDAC2 can attenuate lipopolysaccharide-induced inflammation by regulating c-Jun and PAI-1 expression in macrophages.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		HDAC2 can attenuate lipopolysaccharide-induced inflammation by regulating c-Jun and PAI-1 expression in macrophages.	Immunohistochemical staining	HDAC2 can attenuate lipopolysaccharide-induced inflammation by regulating c-Jun and PAI-1 expression in macrophages.		ChIP,qRT-PCR,Western blot			HDAC2	TNF	HDAC2 can attenuate lipopolysaccharide-induced inflammation by regulating c-Jun and PAI-1 expression in macrophages.	Results revealed that PAI-1, TNF, and MIP-2 expression were inhibited by theophylline, an HDAC2 enhancer, in a RAW macrophage cell line, following LPS-induced inflammation.
29342503	chr5	173229371	173231371	NKX2-5	NKX2-5 is a homeobox transcription factor required for the formation of the heart and vessels during development, with significant postnatal downregulation and reactivation in disease states characterised by vascular remodelling.	human	Vascular	High+Lowthroughput	Molecular Basis for Dysregulated Activation of NKX2-5 in the Vascular Remodeling of Systemic Sclerosis	是	rs3095870	scleroderma associated pulmonary hypertensio	smooth muscle cell of the pulmonary artery	E_01_0007	Western blot,qPCR	NKX2-5 is a homeobox transcription factor required for the formation of the heart and vessels during development, with significant postnatal downregulation and reactivation in disease states characterised by vascular remodelling.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		NKX2-5 is a homeobox transcription factor required for the formation of the heart and vessels during development, with significant postnatal downregulation and reactivation in disease states characterised by vascular remodelling.	Immunohistochemical staining	NKX2-5 is a homeobox transcription factor required for the formation of the heart and vessels during development, with significant postnatal downregulation and reactivation in disease states characterised by vascular remodelling.		Western blot,qPCR				NKX2-5,TEAD1		NKX2-5 is a homeobox transcription factor required for the formation of the heart and vessels during development, with significant postnatal downregulation and reactivation in disease states characterised by vascular remodelling.;TEAD1 is a member of TEA/ATTS domain family transcription regulators with distinct and important roles in VSMC differentiation and in cardiovascular disease
29339538	chr7	55016139	55018139	EGFR	Whole genome ChIP-seq and RNA-seq results revealed that CaSki cells contained super-enhancers in the proto-oncogenes EGFR and c-MET.	human	Cervix	High+Lowthroughput	E6 Protein Expressed by High-Risk HPV Activates Super-Enhancers of the EGFR and c-MET Oncogenes by Destabilizing the Histone Demethylase KDM5C	否		human papillomaviruses	CaSki cell(human cervical cancer cell line)	E_01_0008	ChIP-seq,RNA-seq	Whole genome ChIP-seq and RNA-seq results revealed that CaSki cells contained super-enhancers in the proto-oncogenes EGFR and c-MET.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Whole genome ChIP-seq and RNA-seq results revealed that CaSki cells contained super-enhancers in the proto-oncogenes EGFR and c-MET.	Immunohistochemical staining	Whole genome ChIP-seq and RNA-seq results revealed that CaSki cells contained super-enhancers in the proto-oncogenes EGFR and c-MET.		ChIP-seq,RNA-seq				EGFR,KDM5C		Whole genome ChIP-seq and RNA-seq results revealed that CaSki cells contained super-enhancers in the proto-oncogenes EGFR and c-MET.;Restoration of KDM5C significantly suppressed the tumorigenicity of CaSki cells, an HPV16-positive cervical cancer cell line.
29339121	chr8	144288666	144290666	HSF1	HSF1 was found to promote proliferation, migration and invasion of gastric cancer cells.	human	Gastric cancer	High+Lowthroughput	HSF1, in association with MORC2, downregulates ArgBP2 via the PRC2 family in gastric cancer cells	否		gastric cancer	gastric cancer cell	E_01_0009	ChIP,Real-time PCR,Western blot	HSF1 was found to promote proliferation, migration and invasion of gastric cancer cells.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		HSF1 was found to promote proliferation, migration and invasion of gastric cancer cells.	Immunohistochemical staining	HSF1 was found to promote proliferation, migration and invasion of gastric cancer cells.		ChIP,Real-time PCR,Western blot			MORC2	HSF1,EZH2	In view of this, we speculated that HSF1 may regulate ArgBP2 as well as associate with MORC2	HSF1 was found to promote proliferation, migration and invasion of gastric cancer cells.;EZH2, as the core and contributing catalytic subunit of PRC2, which is composed of EED
29337370	chr16	28929378	28931378	CD19	GM12878 LCL and P3HR-1 Burkitt lymphoma cells stably expressing activating dCas9-VP64 were transduced with either control sgRNA or sgRNAs targeting the indicated genes(CD19 or CD86).	human	Lymphoid tissue bone marrow	High+Lowthroughput	Modulating Gene Expression in Epstein-Barr Virus (EBV)-Positive B Cell Lines with CRISPRa and CRISPRi	否		Epstein-Barr virus	B cell	E_01_0010	ChIP-seq,ChIA-PET,RT-PCR	GM12878 LCL and P3HR-1 Burkitt lymphoma cells stably expressing activating dCas9-VP64 were transduced with either control sgRNA or sgRNAs targeting the indicated genes(CD19 or CD86).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		GM12878 LCL and P3HR-1 Burkitt lymphoma cells stably expressing activating dCas9-VP64 were transduced with either control sgRNA or sgRNAs targeting the indicated genes(CD19 or CD86).	Immunohistochemical staining	GM12878 LCL and P3HR-1 Burkitt lymphoma cells stably expressing activating dCas9-VP64 were transduced with either control sgRNA or sgRNAs targeting the indicated genes(CD19 or CD86).		ChIP-seq,ChIA-PET,RT-PCR			CD19	CD86	GM12878 LCL and P3HR-1 Burkitt lymphoma cells stably expressing activating dCas9-VP64 were transduced with either control sgRNA or sgRNAs targeting the indicated genes(CD19 or CD86).	GM12878 LCL and P3HR-1 Burkitt lymphoma cells stably expressing activating dCas9-VP64 were transduced with either control sgRNA or sgRNAs targeting the indicated genes(CD19 or CD86).
29334376	chr1	94526560	94528560	F3	We further show that genetic deletion of a single Met-VEL at the F3 locus blocks metastatic cell outgrowth in the lung.	human	Osteosarcoma	High+Lowthroughput	Positively selected enhancer elements endow osteosarcoma cells with metastatic competence	否		Osteosarcoma	osteosarcoma cell	E_01_0011	RNA-seq,ChIP–seq	We further show that genetic deletion of a single Met-VEL at the F3 locus blocks metastatic cell outgrowth in the lung.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We further show that genetic deletion of a single Met-VEL at the F3 locus blocks metastatic cell outgrowth in the lung.	Immunohistochemical staining	We further show that genetic deletion of a single Met-VEL at the F3 locus blocks metastatic cell outgrowth in the lung.		RNA-seq,ChIP–seq			F3		We further show that genetic deletion of a single Met-VEL at the F3 locus blocks metastatic cell outgrowth in the lung.	
29331016	chr10	112947442	112949442	TCF7L2	The SNP rs7903146 at the transcription factor 7-like 2 (TCF7L2) locus is established as the strongest known genetic marker for type 2 diabetes via genome-wide association studies.	human	Liver	High+Lowthroughput	A candidate functional SNP rs7074440 in TCF7L2 alters gene expression through C-FOS in hepatocytes	是	rs7903146	type 2 diabetes	hepatocyte	E_01_0012	qRT-PCR,ChIP,Transfection	The SNP rs7903146 at the transcription factor 7-like 2 (TCF7L2) locus is established as the strongest known genetic marker for type 2 diabetes via genome-wide association studies.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The SNP rs7903146 at the transcription factor 7-like 2 (TCF7L2) locus is established as the strongest known genetic marker for type 2 diabetes via genome-wide association studies.	Immunohistochemical staining	The SNP rs7903146 at the transcription factor 7-like 2 (TCF7L2) locus is established as the strongest known genetic marker for type 2 diabetes via genome-wide association studies.		qRT-PCR,ChIP,Transfection				TCF7L2		The SNP rs7903146 at the transcription factor 7-like 2 (TCF7L2) locus is established as the strongest known genetic marker for type 2 diabetes via genome-wide association studies.
29327713	chr7	148804434	148806434	EZH2	EZH2 is an important enzymatic subunit of the epigenetic regulator polycomb repressive complex 2 (PRC2), which controls gene silencing through post-translational modification, and is overexpressed in various carcinomas and hematopoietic neoplasms.	human	Lymphoid	High+Lowthroughput	Expression of enhancer of zeste homolog 2 (EZH2) protein in histiocytic and dendritic cell neoplasms with evidence for p-ERK1/2-related, but not MYC- or p-STAT3-related cell signaling	否		histiocytic and dendritic cell neoplasms	histiocytic and dendritic cell neoplasm cell	E_01_0013	Immunohistochemical staining	EZH2 is an important enzymatic subunit of the epigenetic regulator polycomb repressive complex 2 (PRC2), which controls gene silencing through post-translational modification, and is overexpressed in various carcinomas and hematopoietic neoplasms.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		EZH2 is an important enzymatic subunit of the epigenetic regulator polycomb repressive complex 2 (PRC2), which controls gene silencing through post-translational modification, and is overexpressed in various carcinomas and hematopoietic neoplasms.	Immunohistochemical staining	EZH2 is an important enzymatic subunit of the epigenetic regulator polycomb repressive complex 2 (PRC2), which controls gene silencing through post-translational modification, and is overexpressed in various carcinomas and hematopoietic neoplasms.		Immunohistochemical staining				EZH2		EZH2 is an important enzymatic subunit of the epigenetic regulator polycomb repressive complex 2 (PRC2), which controls gene silencing through post-translational modification, and is overexpressed in various carcinomas and hematopoietic neoplasms.
29325110	chr5	56096484	56098484	ANKRD55	As an example, we found that rs71624119, shared with three other autoimmune diseases and located in a primed enhancer (H3K4me1) with potential binding for STAT transcription factors, significantly associates with ANKRD55 expression.	human	Lymphoid	High+Lowthroughput	Impact of genetic risk loci for multiple sclerosis on expression of proximal genes in patients	是	rs71624119	multiple sclerosis	peripheral blood mononuclear cell	E_01_0014	RNA-Seq	As an example, we found that rs71624119, shared with three other autoimmune diseases and located in a primed enhancer (H3K4me1) with potential binding for STAT transcription factors, significantly associates with ANKRD55 expression.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		As an example, we found that rs71624119, shared with three other autoimmune diseases and located in a primed enhancer (H3K4me1) with potential binding for STAT transcription factors, significantly associates with ANKRD55 expression.	Immunohistochemical staining	As an example, we found that rs71624119, shared with three other autoimmune diseases and located in a primed enhancer (H3K4me1) with potential binding for STAT transcription factors, significantly associates with ANKRD55 expression.		RNA-Seq			ANKRD55		As an example, we found that rs71624119, shared with three other autoimmune diseases and located in a primed enhancer (H3K4me1) with potential binding for STAT transcription factors, significantly associates with ANKRD55 expression.	
29323272	chr19	10958350	10960350	SMARCA4	Mutation of SMARCA4 (BRG1), the ATPase of BAF (mSWI/SNF) and PBAF complexes, contributes to a range of malignancies and neurologic disorders.	human	Tumor	High+Lowthroughput	Dominant-negative SMARCA4 mutants alter the accessibility landscape of tissue-unrestricted enhancers	否		Tumor	embryonic stem cell	E_01_0015	Western blot,ATAC-seq,ChIP-seq,RNA-seq	Mutation of SMARCA4 (BRG1), the ATPase of BAF (mSWI/SNF) and PBAF complexes, contributes to a range of malignancies and neurologic disorders.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Mutation of SMARCA4 (BRG1), the ATPase of BAF (mSWI/SNF) and PBAF complexes, contributes to a range of malignancies and neurologic disorders.	Immunohistochemical staining	Mutation of SMARCA4 (BRG1), the ATPase of BAF (mSWI/SNF) and PBAF complexes, contributes to a range of malignancies and neurologic disorders.		Western blot,ATAC-seq,ChIP-seq,RNA-seq				SMARCA4		Mutation of SMARCA4 (BRG1), the ATPase of BAF (mSWI/SNF) and PBAF complexes, contributes to a range of malignancies and neurologic disorders.
29316219	chr9	81580914	81582914	TLE1	These studies identify 150 direct FOXG1 targets, several of which are also TLE1 targets, involved in cell proliferation, differentiation, survival,chemotaxis and angiogenesis.	human	Brain	High+Lowthroughput	Characterization of a FOXG1:TLE1 transcriptional network in glioblastoma-initiating cells	否		Glioblastoma	glioblastoma-initiating cells	E_01_0016	ChIP-Seq,RNA-Seq,RT-qPCR	These studies identify 150 direct FOXG1 targets, several of which are also TLE1 targets, involved in cell proliferation, differentiation, survival,chemotaxis and angiogenesis.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		These studies identify 150 direct FOXG1 targets, several of which are also TLE1 targets, involved in cell proliferation, differentiation, survival,chemotaxis and angiogenesis.	Immunohistochemical staining	These studies identify 150 direct FOXG1 targets, several of which are also TLE1 targets, involved in cell proliferation, differentiation, survival,chemotaxis and angiogenesis.		ChIP-Seq,RNA-Seq,RT-qPCR				TLE1		These studies identify 150 direct FOXG1 targets, several of which are also TLE1 targets, involved in cell proliferation, differentiation, survival,chemotaxis and angiogenesis.
29311615	chr12	54030827	54032827	HOXC5	Deregulation of HOXC5 and mir-615-3p expression may contribute to the activation of hTERT in human cancers.	human	Somatic	High+Lowthroughput	HoxC5 and miR-615-3p target newly evolved genomic regions to repress hTERT and inhibit tumorigenesis	否		Tumor	somatic cell	E_01_0017	Luciferase reporter assay,Western blot,ChIP-Seq,qRT-PCR,3C-qPCR	Deregulation of HOXC5 and mir-615-3p expression may contribute to the activation of hTERT in human cancers.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Deregulation of HOXC5 and mir-615-3p expression may contribute to the activation of hTERT in human cancers.	Immunohistochemical staining	Deregulation of HOXC5 and mir-615-3p expression may contribute to the activation of hTERT in human cancers.		Luciferase reporter assay,Western blot,ChIP-Seq,qRT-PCR,3C-qPCR				HOXC5		Deregulation of HOXC5 and mir-615-3p expression may contribute to the activation of hTERT in human cancers.
29309299	chr19	19143072	19145072	MEF2B	Myocyte enhancer binding factor 2B (MEF2B) is a transcriptional activator of the BCL6 proto-oncogene in normal germinal center (GC) B-cells.	human	Lymphoid	High+Lowthroughput	Comparison of Myocyte Enhancer Factor 2B Versus Other Germinal Center-associated Antigens in the Differential Diagnosis of B-Cell Non-Hodgkin Lymphomas	否		Lymphomas	B cell	E_01_0018	Immunohistochemical Staining	Myocyte enhancer binding factor 2B (MEF2B) is a transcriptional activator of the BCL6 proto-oncogene in normal germinal center (GC) B-cells.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Myocyte enhancer binding factor 2B (MEF2B) is a transcriptional activator of the BCL6 proto-oncogene in normal germinal center (GC) B-cells.	Immunohistochemical staining	Myocyte enhancer binding factor 2B (MEF2B) is a transcriptional activator of the BCL6 proto-oncogene in normal germinal center (GC) B-cells.		Immunohistochemical Staining			MEF2B		Myocyte enhancer binding factor 2B (MEF2B) is a transcriptional activator of the BCL6 proto-oncogene in normal germinal center (GC) B-cells.	
29307778	chr17	43750876	43752876	SOST	The SOST gene encodes sclerostin, a C-terminal cysteine knot-like domain containing key negative regulator of osteoblastic bone formation that inhibits LRP5/6-mediated canonical Wnt signaling.	human	Bone	High+Lowthroughput	Computational and functional characterization of four SNPs in the SOST locus associated with osteoporosis	是	rs1230399,rs7220711,rs1107748,rs75901553	osteoporosis	Germinal center B-cells	E_01_0019	Luciferase reporter assay,ChIP,qPCR	The SOST gene encodes sclerostin, a C-terminal cysteine knot-like domain containing key negative regulator of osteoblastic bone formation that inhibits LRP5/6-mediated canonical Wnt signaling.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The SOST gene encodes sclerostin, a C-terminal cysteine knot-like domain containing key negative regulator of osteoblastic bone formation that inhibits LRP5/6-mediated canonical Wnt signaling.	Immunohistochemical staining	The SOST gene encodes sclerostin, a C-terminal cysteine knot-like domain containing key negative regulator of osteoblastic bone formation that inhibits LRP5/6-mediated canonical Wnt signaling.		Luciferase reporter assay,ChIP,qPCR			SOST	CTCF	The SOST gene encodes sclerostin, a C-terminal cysteine knot-like domain containing key negative regulator of osteoblastic bone formation that inhibits LRP5/6-mediated canonical Wnt signaling.	The SOST gene encodes sclerostin, a C-terminal cysteine knot-like domain containing key negative regulator of osteoblastic bone formation that inhibits LRP5/6-mediated canonical Wnt signaling.
29304378	chr6	151654024	151656024	ESR1	Only variants in ESR1 and close proximity to RANKL showed a clear effect dependency on age.	human	Bone	High+Lowthroughput	Life-Course Genome-wide Association Study Meta-analysis of Total Body BMD and Assessment of Age-Specific Effects	是	rs2982562	osteoporosis	osteocyte	E_01_0020	Knockout	Only variants in ESR1 and close proximity to RANKL showed a clear effect dependency on age.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Only variants in ESR1 and close proximity to RANKL showed a clear effect dependency on age.	Immunohistochemical staining	Only variants in ESR1 and close proximity to RANKL showed a clear effect dependency on age.		Knockout				ESR1		Only variants in ESR1 and close proximity to RANKL showed a clear effect dependency on age.
29303507	chr11	68036369	68038369	TCIRG1	These findings suggest that TCIRG1 functions as a metastatic enhancer by modulating growth, death and EMT in HCC cells.	human	HCC	High+Lowthroughput	T-cell immune regulator 1 enhances metastasis in hepatocellular carcinoma	否		hepatocellular carcinoma	HCC cell lines	E_01_0021	Western blot,transfection	These findings suggest that TCIRG1 functions as a metastatic enhancer by modulating growth, death and EMT in HCC cells.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		These findings suggest that TCIRG1 functions as a metastatic enhancer by modulating growth, death and EMT in HCC cells.	Immunohistochemical staining	These findings suggest that TCIRG1 functions as a metastatic enhancer by modulating growth, death and EMT in HCC cells.		Western blot,transfection			TCIRG1		These findings suggest that TCIRG1 functions as a metastatic enhancer by modulating growth, death and EMT in HCC cells.	
29300379	chr15	67061032	67063032	SMAD3	These variants regulate SMAD3 transcription in an allele-specific manner through enhancer elements in introns of SMAD3.	human	Thyroid	High+Lowthroughput	The role of SMAD3 in the genetic predisposition to papillary thyroid carcinoma	是	rs17293632,rs4562997	papillary thyroid carcinoma	thyroid cancer cell lines	E_01_0022	ChIP,siRNA Knockdown,Luciferase reporter assay,Transfection,qPCR	These variants regulate SMAD3 transcription in an allele-specific manner through enhancer elements in introns of SMAD3.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		These variants regulate SMAD3 transcription in an allele-specific manner through enhancer elements in introns of SMAD3.	Immunohistochemical staining	These variants regulate SMAD3 transcription in an allele-specific manner through enhancer elements in introns of SMAD3.		ChIP,siRNA Knockdown,Luciferase reporter assay,Transfection,qPCR			SPRY4	SMAD3	The sprouty RTK signaling antagonist 4 (SPRY4)gene was found to be the second-most dysregulated candidate gene	These variants regulate SMAD3 transcription in an allele-specific manner through enhancer elements in introns of SMAD3.
29300302	chrX	129537551	129539551	OCRL	The OCRL1 protein contains several domains, including an N-terminal pleckstrin homology (PH) domain, a central 5-phosphatase catalytic domain, an ASH (ASPM, SPD-2, Hydin) domain,and a C-terminal noncatalytic Rho-GTPase activating protein (GAP) domain	human	Kidney	High+Lowthroughput	Splicing Analysis of Exonic OCRL Mutations Causing Lowe Syndrome or Dent-2 Disease	否		Lowe syndrome and Dent-2 disease	COS7 cells	E_01_0023	Transfection,RT-PCR	The OCRL1 protein contains several domains, including an N-terminal pleckstrin homology (PH) domain, a central 5-phosphatase catalytic domain, an ASH (ASPM, SPD-2, Hydin) domain,and a C-terminal noncatalytic Rho-GTPase activating protein (GAP) domain	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The OCRL1 protein contains several domains, including an N-terminal pleckstrin homology (PH) domain, a central 5-phosphatase catalytic domain, an ASH (ASPM, SPD-2, Hydin) domain,and a C-terminal noncatalytic Rho-GTPase activating protein (GAP) domain	Immunohistochemical staining	The OCRL1 protein contains several domains, including an N-terminal pleckstrin homology (PH) domain, a central 5-phosphatase catalytic domain, an ASH (ASPM, SPD-2, Hydin) domain,and a C-terminal noncatalytic Rho-GTPase activating protein (GAP) domain		Transfection,RT-PCR			OCRL		The OCRL1 protein contains several domains, including an N-terminal pleckstrin homology (PH) domain, a central 5-phosphatase catalytic domain, an ASH (ASPM, SPD-2, Hydin) domain,and a C-terminal noncatalytic Rho-GTPase activating protein (GAP) domain	
29294297	chr7	148804388	148806388	EZH2	We conclude that EZH2 plays a negative role during the odontogenic differentiation of hDPCs.	human	Dental pulp	High+Lowthroughput	EZH2 Impairs Human Dental Pulp Cell Mineralization via the Wnt/β-Catenin Pathway	否		Oral Diseases	dental pulp cell	E_01_0024	ChIP	We conclude that EZH2 plays a negative role during the odontogenic differentiation of hDPCs.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We conclude that EZH2 plays a negative role during the odontogenic differentiation of hDPCs.	Immunohistochemical staining	We conclude that EZH2 plays a negative role during the odontogenic differentiation of hDPCs.		ChIP				EZH2		We conclude that EZH2 plays a negative role during the odontogenic differentiation of hDPCs.
29294065	chr19	33297489	33299489	CEBPA	Therefore, CEBPA is likely to bind to the “c” region of the PCP4 promoter.	human	Adrenal	High+Lowthroughput	Purkinje Cell Protein 4 Expression Is Associated With DNA Methylation Status in Aldosterone-Producing Adenoma	否		adrenocortical adenoma	cortical cell of adrenal gland	E_01_0025	qPCR,ChIP	Therefore, CEBPA is likely to bind to the “c” region of the PCP4 promoter.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Therefore, CEBPA is likely to bind to the “c” region of the PCP4 promoter.	Immunohistochemical staining	Therefore, CEBPA is likely to bind to the “c” region of the PCP4 promoter.		qPCR,ChIP				CEBPA		Therefore, CEBPA is likely to bind to the “c” region of the PCP4 promoter.
29286144	chr7	148804229	148806229	EZH2	Overall, the present study demonstrated that the lncrna PVt1 may contribute to the tumorigenesis and metastasis of melanoma through binding to eZH2 and regulating the expression of mir-200c.	human	Melanoma	High+Lowthroughput	Effect of long non-coding RNA PVT1 on cell proliferation and migration in melanoma	否		Melanoma	melanoma cells	E_01_0026	Western blot,ChIP	Overall, the present study demonstrated that the lncrna PVt1 may contribute to the tumorigenesis and metastasis of melanoma through binding to eZH2 and regulating the expression of mir-200c.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Overall, the present study demonstrated that the lncrna PVt1 may contribute to the tumorigenesis and metastasis of melanoma through binding to eZH2 and regulating the expression of mir-200c.	Immunohistochemical staining	Overall, the present study demonstrated that the lncrna PVt1 may contribute to the tumorigenesis and metastasis of melanoma through binding to eZH2 and regulating the expression of mir-200c.		Western blot,ChIP				EZH2		Overall, the present study demonstrated that the lncrna PVt1 may contribute to the tumorigenesis and metastasis of melanoma through binding to eZH2 and regulating the expression of mir-200c.
29286132	chr7	148804179	148806179	EZH2	Its ability to facilitate invasion makes EZH2 a promising target for the management of advanced RCC	human	Kidney	High+Lowthroughput	EZH2 enhances the invasive capability of renal cell carcinoma cells via activation of STAT3	否		renal cell carcinoma	nephrocyte	E_01_0027	Western blot	Its ability to facilitate invasion makes EZH2 a promising target for the management of advanced RCC	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Its ability to facilitate invasion makes EZH2 a promising target for the management of advanced RCC	Immunohistochemical staining	Its ability to facilitate invasion makes EZH2 a promising target for the management of advanced RCC		Western blot				EZH2		Its ability to facilitate invasion makes EZH2 a promising target for the management of advanced RCC
29259014	chr7	55016411	55018411	EGFR	We therefore performed a genome-wide CRISPR/Cas9 enhancer/suppressor screen in EGFR-dependent lung cancer PC9 cells treated with erlotinib þ THZ1 (CDK7/12 inhibitor) combination therapy, a combination previously shown to suppress drug-tolerant cells in this setting.	human	Lung	High+Lowthroughput	"ER Stress Signaling Promotes the Survival of Cancer ""Persister Cells"" Tolerant to EGFR Tyrosine Kinase Inhibitors"	否		Tumor	PC9 cells	E_01_0028	qRT-PCR,RNA-seq	We therefore performed a genome-wide CRISPR/Cas9 enhancer/suppressor screen in EGFR-dependent lung cancer PC9 cells treated with erlotinib þ THZ1 (CDK7/12 inhibitor) combination therapy, a combination previously shown to suppress drug-tolerant cells in this setting.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We therefore performed a genome-wide CRISPR/Cas9 enhancer/suppressor screen in EGFR-dependent lung cancer PC9 cells treated with erlotinib þ THZ1 (CDK7/12 inhibitor) combination therapy, a combination previously shown to suppress drug-tolerant cells in this setting.	Immunohistochemical staining	We therefore performed a genome-wide CRISPR/Cas9 enhancer/suppressor screen in EGFR-dependent lung cancer PC9 cells treated with erlotinib þ THZ1 (CDK7/12 inhibitor) combination therapy, a combination previously shown to suppress drug-tolerant cells in this setting.		qRT-PCR,RNA-seq				EGFR		We therefore performed a genome-wide CRISPR/Cas9 enhancer/suppressor screen in EGFR-dependent lung cancer PC9 cells treated with erlotinib þ THZ1 (CDK7/12 inhibitor) combination therapy, a combination previously shown to suppress drug-tolerant cells in this setting.
29256825	chr4	108045000	108047000	LEF1	β-catenin nuclear translocation, T cell factor (TCF) and lymphoid enhancerbinding factor (LEF) up-regulation have been shown to be involved in canonical Wnt pathways [20], and in our studies, Western blot results showed that the amount of β- catenin protein in nuclei was increased in treated cells	human	Liver	High+Lowthroughput	Salvianolic Acid B Enhances Hepatic Differentiation of Human Embryonic Stem Cells Through Upregulation of WNT Pathway and Inhibition of Notch Pathway	否		Liver disease	Hepatocytes	E_01_0029	qRT-PCR,Immunofluorescence staining,PCR,Western blot	β-catenin nuclear translocation, T cell factor (TCF) and lymphoid enhancerbinding factor (LEF) up-regulation have been shown to be involved in canonical Wnt pathways [20], and in our studies, Western blot results showed that the amount of β- catenin protein in nuclei was increased in treated cells	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		β-catenin nuclear translocation, T cell factor (TCF) and lymphoid enhancerbinding factor (LEF) up-regulation have been shown to be involved in canonical Wnt pathways [20], and in our studies, Western blot results showed that the amount of β- catenin protein in nuclei was increased in treated cells	Immunohistochemical staining	β-catenin nuclear translocation, T cell factor (TCF) and lymphoid enhancerbinding factor (LEF) up-regulation have been shown to be involved in canonical Wnt pathways [20], and in our studies, Western blot results showed that the amount of β- catenin protein in nuclei was increased in treated cells		qRT-PCR,Immunofluorescence staining,PCR,Western blot				LEF1		β-catenin nuclear translocation, T cell factor (TCF) and lymphoid enhancerbinding factor (LEF) up-regulation have been shown to be involved in canonical Wnt pathways [20], and in our studies, Western blot results showed that the amount of β- catenin protein in nuclei was increased in treated cells
29249800	chr18	27930050	27932050	CDH2	DBC1 functions as a coactivator for AR-V7 and is required for the expression of AR-V7 target genes including CDH2, a mesenchymal marker linked to CRPC progression.	human	CRPC	High+Lowthroughput	DBC1 promotes castration-resistant prostate cancer by positively regulating DNA binding and stability of AR-V7	否		castration-resistant prostate cancer	castration-resistant prostate cancer cell	E_01_0030	qRT-PCR,ChIP,3C	DBC1 functions as a coactivator for AR-V7 and is required for the expression of AR-V7 target genes including CDH2, a mesenchymal marker linked to CRPC progression.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		DBC1 functions as a coactivator for AR-V7 and is required for the expression of AR-V7 target genes including CDH2, a mesenchymal marker linked to CRPC progression.	Immunohistochemical staining	DBC1 functions as a coactivator for AR-V7 and is required for the expression of AR-V7 target genes including CDH2, a mesenchymal marker linked to CRPC progression.		qRT-PCR,ChIP,3C				CDH2		DBC1 functions as a coactivator for AR-V7 and is required for the expression of AR-V7 target genes including CDH2, a mesenchymal marker linked to CRPC progression.
29248547	chr7	148804663	148806663	EZH2	Here we report that enhancer of zeste homolog 2 (EZH2), the catalytic subunit of polycomb repressive complex 2 (PRC2) which mediates histone H3 lysine 27 trimethylation(H3K27me3), is over-expressed in CD30+ anaplastic cells in PCALCL and large-cell transformed CTCL.	human	PCALCL	High+Lowthroughput	Dual Role of EZH2 in Cutaneous Anaplastic Large Cell Lymphoma: Promoting Tumor Cell Survival and Regulating Tumor Microenvironment	否		cutaneous CD30+ lymphoproliferative disease	Primary cutaneous anaplastic T cell lymphoma cell	E_01_0031	ChIP,qRT-PCR,Western blot	Here we report that enhancer of zeste homolog 2 (EZH2), the catalytic subunit of polycomb repressive complex 2 (PRC2) which mediates histone H3 lysine 27 trimethylation(H3K27me3), is over-expressed in CD30+ anaplastic cells in PCALCL and large-cell transformed CTCL.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Here we report that enhancer of zeste homolog 2 (EZH2), the catalytic subunit of polycomb repressive complex 2 (PRC2) which mediates histone H3 lysine 27 trimethylation(H3K27me3), is over-expressed in CD30+ anaplastic cells in PCALCL and large-cell transformed CTCL.	Immunohistochemical staining	Here we report that enhancer of zeste homolog 2 (EZH2), the catalytic subunit of polycomb repressive complex 2 (PRC2) which mediates histone H3 lysine 27 trimethylation(H3K27me3), is over-expressed in CD30+ anaplastic cells in PCALCL and large-cell transformed CTCL.		ChIP,qRT-PCR,Western blot				EZH2		Here we report that enhancer of zeste homolog 2 (EZH2), the catalytic subunit of polycomb repressive complex 2 (PRC2) which mediates histone H3 lysine 27 trimethylation(H3K27me3), is over-expressed in CD30+ anaplastic cells in PCALCL and large-cell transformed CTCL.
29233846	chr6	47504530	47506530	Ezh2	Ezh2 is the catalytic subunit containing a SET domain, which harbors the active site for histone H3 trimethylation on lysine 27 (H3K27me3), although Suz12 and Eed association is needed for optimal enzymatic activity8.	mouse	Ovarian	High+Lowthroughput	VE-Cadherin-Mediated Epigenetic Regulation of Endothelial Gene Expression	否		Ovarian carcinoma	endothelial cell	E_01_0032	Immunofluorescence,Western blot,RNA-seq ,qRT–PCR,ChIP	Ezh2 is the catalytic subunit containing a SET domain, which harbors the active site for histone H3 trimethylation on lysine 27 (H3K27me3), although Suz12 and Eed association is needed for optimal enzymatic activity8.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Ezh2 is the catalytic subunit containing a SET domain, which harbors the active site for histone H3 trimethylation on lysine 27 (H3K27me3), although Suz12 and Eed association is needed for optimal enzymatic activity8.	Immunohistochemical staining	Ezh2 is the catalytic subunit containing a SET domain, which harbors the active site for histone H3 trimethylation on lysine 27 (H3K27me3), although Suz12 and Eed association is needed for optimal enzymatic activity8.		Immunofluorescence,Western blot,RNA-seq ,qRT–PCR,ChIP			Ezh2		Ezh2 is the catalytic subunit containing a SET domain, which harbors the active site for histone H3 trimethylation on lysine 27 (H3K27me3), although Suz12 and Eed association is needed for optimal enzymatic activity8.	
29231261	chr7	148804801	148806801	EZH2	LncRNA AWPPH can promote cell proliferation, autophagy and migration, as well as inhibit cell apoptosis in BC by inhibiting SMAD4 via EZH2.	human	Bladder	High+Lowthroughput	LncRNA AWPPH inhibits SMAD4 via EZH2 to regulate bladder cancer progression	否		bladder cancer	human bladder epithelial cell line	E_01_0033	Transfection,qRT-PCR,Western blot,ChIP	LncRNA AWPPH can promote cell proliferation, autophagy and migration, as well as inhibit cell apoptosis in BC by inhibiting SMAD4 via EZH2.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		LncRNA AWPPH can promote cell proliferation, autophagy and migration, as well as inhibit cell apoptosis in BC by inhibiting SMAD4 via EZH2.	Immunohistochemical staining	LncRNA AWPPH can promote cell proliferation, autophagy and migration, as well as inhibit cell apoptosis in BC by inhibiting SMAD4 via EZH2.		Transfection,qRT-PCR,Western blot,ChIP				EZH2		LncRNA AWPPH can promote cell proliferation, autophagy and migration, as well as inhibit cell apoptosis in BC by inhibiting SMAD4 via EZH2.
29227829	chr6	135178878	135180878	MYB	HMI-LNCRNA might be a potential therapeutic target for HbF induction treatment in sickle cell disease and β-thalassemia.	human	Hematopoietic	High+Lowthroughput	A long noncoding RNA from the HBS1L-MYB intergenic region on chr6q23 regulates human fetal hemoglobin expression	是	rs66650371	sickle cell disease and β-thalassemia	HUDEP-2 cell	E_01_0034	RT–PCR,qPCR,Western blot	HMI-LNCRNA might be a potential therapeutic target for HbF induction treatment in sickle cell disease and β-thalassemia.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		HMI-LNCRNA might be a potential therapeutic target for HbF induction treatment in sickle cell disease and β-thalassemia.	Immunohistochemical staining	HMI-LNCRNA might be a potential therapeutic target for HbF induction treatment in sickle cell disease and β-thalassemia.		RT–PCR,qPCR,Western blot			MYB,HBS1L		HMI-LNCRNA might be a potential therapeutic target for HbF induction treatment in sickle cell disease and β-thalassemia.;HMI-LNCRNA might be a potential therapeutic target for HbF induction treatment in sickle cell disease and β-thalassemia.	
29207119	chr7	148804312	148806312	EZH2	Enhancer of zeste homologue 2 (EZH2), a catalytic subunit of polycomb repressive complex 2, is overexpressed in a number of different tumors including breast cancer, and serves important roles in cell cycle regulation, proliferation, apoptosis, tumorigenesis and drug resistance.	human	Breast	High+Lowthroughput	EZH2 inhibition sensitizes tamoxifen?resistant breast cancer cells through cell cycle regulation	否		breast cancer	breast cancer cell	E_01_0035	Transfection,RT-qPCR,Western blot	Enhancer of zeste homologue 2 (EZH2), a catalytic subunit of polycomb repressive complex 2, is overexpressed in a number of different tumors including breast cancer, and serves important roles in cell cycle regulation, proliferation, apoptosis, tumorigenesis and drug resistance.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Enhancer of zeste homologue 2 (EZH2), a catalytic subunit of polycomb repressive complex 2, is overexpressed in a number of different tumors including breast cancer, and serves important roles in cell cycle regulation, proliferation, apoptosis, tumorigenesis and drug resistance.	Immunohistochemical staining	Enhancer of zeste homologue 2 (EZH2), a catalytic subunit of polycomb repressive complex 2, is overexpressed in a number of different tumors including breast cancer, and serves important roles in cell cycle regulation, proliferation, apoptosis, tumorigenesis and drug resistance.		Transfection,RT-qPCR,Western blot				EZH2		Enhancer of zeste homologue 2 (EZH2), a catalytic subunit of polycomb repressive complex 2, is overexpressed in a number of different tumors including breast cancer, and serves important roles in cell cycle regulation, proliferation, apoptosis, tumorigenesis and drug resistance.
29180489	chr12	114350941	114352941	TBX5	TBX5 deficiency-mediated downregulation of NFAT3 is crucial for the high cytokine-producing activity of T cells.	human	Lymphoid	High+Lowthroughput	Downregulation of NFAT3 Due to Lack of T-Box Transcription Factor TBX5 Is Crucial for Cytokine Expression in T Cells	否			T cell	E_01_0036	Transfection	TBX5 deficiency-mediated downregulation of NFAT3 is crucial for the high cytokine-producing activity of T cells.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		TBX5 deficiency-mediated downregulation of NFAT3 is crucial for the high cytokine-producing activity of T cells.	Immunohistochemical staining	TBX5 deficiency-mediated downregulation of NFAT3 is crucial for the high cytokine-producing activity of T cells.		Transfection				TBX5		TBX5 deficiency-mediated downregulation of NFAT3 is crucial for the high cytokine-producing activity of T cells.
29177481	chr7	148804952	148806952	EZH2	The fact that EZH2 catalyzes the methylation of H3K27me3, a repressive mark known to be induced at DNA damage sites,prompted us to test whether the level of H3K27me3 at damage sites is affected by CDYL1.	human		High+Lowthroughput	CDYL1 fosters double-strand break-induced transcription silencing and promotes homology-directed repair	否				E_01_0037	Transfection,Immunofluorescence,Western blot,ChIP	The fact that EZH2 catalyzes the methylation of H3K27me3, a repressive mark known to be induced at DNA damage sites,prompted us to test whether the level of H3K27me3 at damage sites is affected by CDYL1.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The fact that EZH2 catalyzes the methylation of H3K27me3, a repressive mark known to be induced at DNA damage sites,prompted us to test whether the level of H3K27me3 at damage sites is affected by CDYL1.	Immunohistochemical staining	The fact that EZH2 catalyzes the methylation of H3K27me3, a repressive mark known to be induced at DNA damage sites,prompted us to test whether the level of H3K27me3 at damage sites is affected by CDYL1.		Transfection,Immunofluorescence,Western blot,ChIP				EZH2		The fact that EZH2 catalyzes the methylation of H3K27me3, a repressive mark known to be induced at DNA damage sites,prompted us to test whether the level of H3K27me3 at damage sites is affected by CDYL1.
29175454	chr10	68557509	68559509	TET1	To gain an understanding into how iAs might impact TET expression, we found that iAs inhibits the binding of CTCF at the proximal, weak CTCF binding sites of the TET1 and TET2 gene promoters and enhances CTCF binding at the stronger distal binding site.	human	Tumor	High+Lowthroughput	Selective inhibition of CTCF binding by iAs directs TET-mediated reprogramming of 5-hydroxymethylation patterns in iAs-transformed cells	否		iAs-mediated carcinogenesis	transformed cell	E_01_0038	qRT-PCR,ChIP	To gain an understanding into how iAs might impact TET expression, we found that iAs inhibits the binding of CTCF at the proximal, weak CTCF binding sites of the TET1 and TET2 gene promoters and enhances CTCF binding at the stronger distal binding site.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		To gain an understanding into how iAs might impact TET expression, we found that iAs inhibits the binding of CTCF at the proximal, weak CTCF binding sites of the TET1 and TET2 gene promoters and enhances CTCF binding at the stronger distal binding site.	Immunohistochemical staining	To gain an understanding into how iAs might impact TET expression, we found that iAs inhibits the binding of CTCF at the proximal, weak CTCF binding sites of the TET1 and TET2 gene promoters and enhances CTCF binding at the stronger distal binding site.		qRT-PCR,ChIP			TET2	TET1,CTCF	To gain an understanding into how iAs might impact TET expression, we found that iAs inhibits the binding of CTCF at the proximal, weak CTCF binding sites of the TET1 and TET2 gene promoters and enhances CTCF binding at the stronger distal binding site.	To gain an understanding into how iAs might impact TET expression, we found that iAs inhibits the binding of CTCF at the proximal, weak CTCF binding sites of the TET1 and TET2 gene promoters and enhances CTCF binding at the stronger distal binding site.;To gain an understanding into how iAs might impact TET expression, we found that iAs inhibits the binding of CTCF at the proximal, weak CTCF binding sites of the TET1 and TET2 gene promoters and enhances CTCF binding at the stronger distal binding site.
29162563	chr16	86507790	86509790	FOXF1	We uncover that FOXF1 defi nes the core-regulatory circuitry in GIST through both direct transcriptional regulation and pioneer factor function.	human	Gastrointestinal tract	High+Lowthroughput	FOXF1 Defines the Core-Regulatory Circuitry in Gastrointestinal Stromal Tumor	否		gastrointestinal stromal tumor	gastrointestinal stromal tumor cell	E_01_0039	siRNA Transfection,qRT-PCR,ChIP,ChIP-qPCR,ATAC-seq,ChIP-seq	We uncover that FOXF1 defi nes the core-regulatory circuitry in GIST through both direct transcriptional regulation and pioneer factor function.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We uncover that FOXF1 defi nes the core-regulatory circuitry in GIST through both direct transcriptional regulation and pioneer factor function.	Immunohistochemical staining	We uncover that FOXF1 defi nes the core-regulatory circuitry in GIST through both direct transcriptional regulation and pioneer factor function.		siRNA Transfection,qRT-PCR,ChIP,ChIP-qPCR,ATAC-seq,ChIP-seq				FOXF1,ETV1,KIT		We uncover that FOXF1 defi nes the core-regulatory circuitry in GIST through both direct transcriptional regulation and pioneer factor function.;Here, we uncover that in gastrointestinal stromal tumor (GIST), the forkhead family member FOXF1 directly controls the transcription of two master regulators, KIT and ETV1, both required for GIST precursor-interstitial cells of Cajal lineage specifi cation and GIST tumorigenesis;Here, we uncover that in gastrointestinal stromal tumor (GIST), the forkhead family member FOXF1 directly controls the transcription of two master regulators, KIT and ETV1, both required for GIST precursor-interstitial cells of Cajal lineage specifi cation and GIST tumorigenesis
29162511	chr1	11782707	11784707	MTHFR	Little is still known about the contribution of MTHFR, MTR and MTRR polymorphisms in clinical subtypes of autoimmune diseases, except for some controversial studies suggesting a possible contribution of MTHFR polymorphisms to both risk and response to methotrexate treatment of rheumatoid arthritis	human	Thymus	High+Lowthroughput	The thymidylate synthase enhancer region (TSER) polymorphism increases the risk of thymic lymphoid hyperplasia in patients with Myasthenia Gravis	是	rs1801133	thymic lymphoid hyperplasia	B cell	E_01_0040		Little is still known about the contribution of MTHFR, MTR and MTRR polymorphisms in clinical subtypes of autoimmune diseases, except for some controversial studies suggesting a possible contribution of MTHFR polymorphisms to both risk and response to methotrexate treatment of rheumatoid arthritis	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Little is still known about the contribution of MTHFR, MTR and MTRR polymorphisms in clinical subtypes of autoimmune diseases, except for some controversial studies suggesting a possible contribution of MTHFR polymorphisms to both risk and response to methotrexate treatment of rheumatoid arthritis	Immunohistochemical staining	Little is still known about the contribution of MTHFR, MTR and MTRR polymorphisms in clinical subtypes of autoimmune diseases, except for some controversial studies suggesting a possible contribution of MTHFR polymorphisms to both risk and response to methotrexate treatment of rheumatoid arthritis					MTHFR,MTR,TYMS,MTRR		Little is still known about the contribution of MTHFR, MTR and MTRR polymorphisms in clinical subtypes of autoimmune diseases, except for some controversial studies suggesting a possible contribution of MTHFR polymorphisms to both risk and response to methotrexate treatment of rheumatoid arthritis;Little is still known about the contribution of MTHFR, MTR and MTRR polymorphisms in clinical subtypes of autoimmune diseases, except for some controversial studies suggesting a possible contribution of MTHFR polymorphisms to both risk and response to methotrexate treatment of rheumatoid arthritis;Therefore, the lack of association that we observed between the TYMS TSER polymorphism and thymoma risk might be due to different histological, molecular and pathological pathways leading to either thymoma or follicular hyperplasia in MG patients;Little is still known about the contribution of MTHFR, MTR and MTRR polymorphisms in clinical subtypes of autoimmune diseases, except for some controversial studies suggesting a possible contribution of MTHFR polymorphisms to both risk and response to methotrexate treatment of rheumatoid arthritis	
29154949	chr12	56115695	56117695	ESYT1	We demonstrate the robustness and specificity of this cell-based assay, by the identification of siRNAs acting both as ANO1 traffic enhancer and inhibitor, targeting respectively COPB1 and ESYT1 (extended synaptotagmin-1), the latter involved in coupling of the endoplasmic reticulum to the PM at specific microdomains.	human	Lung CF	High+Lowthroughput	A novel microscopy-based assay identifies extended synaptotagmin-1 (ESYT1) as a positive regulator of anoctamin 1 traffic	否		Cystic Fibrosis	bronchial epithelial cell	E_01_0041	siRNA transfection,Immunostaining	We demonstrate the robustness and specificity of this cell-based assay, by the identification of siRNAs acting both as ANO1 traffic enhancer and inhibitor, targeting respectively COPB1 and ESYT1 (extended synaptotagmin-1), the latter involved in coupling of the endoplasmic reticulum to the PM at specific microdomains.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We demonstrate the robustness and specificity of this cell-based assay, by the identification of siRNAs acting both as ANO1 traffic enhancer and inhibitor, targeting respectively COPB1 and ESYT1 (extended synaptotagmin-1), the latter involved in coupling of the endoplasmic reticulum to the PM at specific microdomains.	Immunohistochemical staining	We demonstrate the robustness and specificity of this cell-based assay, by the identification of siRNAs acting both as ANO1 traffic enhancer and inhibitor, targeting respectively COPB1 and ESYT1 (extended synaptotagmin-1), the latter involved in coupling of the endoplasmic reticulum to the PM at specific microdomains.		siRNA transfection,Immunostaining			ESYT1,COPB1	ANO1	We demonstrate the robustness and specificity of this cell-based assay, by the identification of siRNAs acting both as ANO1 traffic enhancer and inhibitor, targeting respectively COPB1 and ESYT1 (extended synaptotagmin-1), the latter involved in coupling of the endoplasmic reticulum to the PM at specific microdomains.;We demonstrate the robustness and specificity of this cell-based assay, by the identification of siRNAs acting both as ANO1 traffic enhancer and inhibitor, targeting respectively COPB1 and ESYT1 (extended synaptotagmin-1), the latter involved in coupling of the endoplasmic reticulum to the PM at specific microdomains.	We demonstrate the robustness and specificity of this cell-based assay, by the identification of siRNAs acting both as ANO1 traffic enhancer and inhibitor, targeting respectively COPB1 and ESYT1 (extended synaptotagmin-1), the latter involved in coupling of the endoplasmic reticulum to the PM at specific microdomains.
29129693	chr17	76133482	76135482	FOXJ1	FOXJ1 as a tumor inducer in bladder cancer and an enhancer in glycolysis.	human	Bladder cancer	High+Lowthroughput	FOXJ1 promotes bladder cancer cell growth and regulates Warburg effect	否		bladder cancer	bladder cancer cell	E_01_0042	Western blot	FOXJ1 as a tumor inducer in bladder cancer and an enhancer in glycolysis.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		FOXJ1 as a tumor inducer in bladder cancer and an enhancer in glycolysis.	Immunohistochemical staining	FOXJ1 as a tumor inducer in bladder cancer and an enhancer in glycolysis.		Western blot				FOXJ1		FOXJ1 as a tumor inducer in bladder cancer and an enhancer in glycolysis.
29127222	chr15	99562705	99564705	MEF2A	These findings suggest individual members of MEF2 family distinctively regulate 40 cytotrophoblast proliferation, invasion, and differentiation.	human	Placental	High+Lowthroughput	MEF2 transcription factors in human placenta and involvement in cytotrophoblast invasion and differentiation	否		placenta-related pregnancy disorders	cytotrophoblast cell lines	E_01_0043	Transfection,Immunofluorescence,Western blot,ChIP,RT-PCR	These findings suggest individual members of MEF2 family distinctively regulate 40 cytotrophoblast proliferation, invasion, and differentiation.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		These findings suggest individual members of MEF2 family distinctively regulate 40 cytotrophoblast proliferation, invasion, and differentiation.	Immunohistochemical staining	These findings suggest individual members of MEF2 family distinctively regulate 40 cytotrophoblast proliferation, invasion, and differentiation.		Transfection,Immunofluorescence,Western blot,ChIP,RT-PCR			MEF2B,MEF2D	MEF2A,MEF2C	These findings suggest individual members of MEF2 family distinctively regulate 40 cytotrophoblast proliferation, invasion, and differentiation.;These findings suggest individual members of MEF2 family distinctively regulate 40 cytotrophoblast proliferation, invasion, and differentiation.	These findings suggest individual members of MEF2 family distinctively regulate 40 cytotrophoblast proliferation, invasion, and differentiation.;These findings suggest individual members of MEF2 family distinctively regulate 40 cytotrophoblast proliferation, invasion, and differentiation.
29106960	chr7	148804589	148806589	EZH2	Thus, SIRT1/EZH2 regulation could be used as a new therapeutic strategy for fibrogenesis.	human	Liver	High+Lowthroughput	Carnosol-mediated Sirtuin 1 activation inhibits Enhancer of Zeste Homolog 2 to attenuate liver fibrosis	否		hepatic fibrosis	Myofibroblast	E_01_0044	Western blot, RT-PCR,Immunofluorescence staining,Transfection	Thus, SIRT1/EZH2 regulation could be used as a new therapeutic strategy for fibrogenesis.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Thus, SIRT1/EZH2 regulation could be used as a new therapeutic strategy for fibrogenesis.	Immunohistochemical staining	Thus, SIRT1/EZH2 regulation could be used as a new therapeutic strategy for fibrogenesis.		Western blot, RT-PCR,Immunofluorescence staining,Transfection				EZH2		Thus, SIRT1/EZH2 regulation could be used as a new therapeutic strategy for fibrogenesis.
29089464	chr7	148804445	148806445	EZH2	Histone methylation is a member of the histone modifications with histone methyltransferase activity, wherein SET and MYND domain containing 3 (SMYD3) and Enhancer of Zeste Homolog 2 (EZH2) are reported to be involved in the development of multiple cancers and play important roles in transcriptional regulation	human	Breast cancer	High+Lowthroughput	Correlations of EZH2 and SMYD3 gene polymorphisms with breast cancer susceptibility and prognosis	否		breast cancer	breast cancer cell	E_01_0045	RT-qPCR,Western blot	Histone methylation is a member of the histone modifications with histone methyltransferase activity, wherein SET and MYND domain containing 3 (SMYD3) and Enhancer of Zeste Homolog 2 (EZH2) are reported to be involved in the development of multiple cancers and play important roles in transcriptional regulation	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Histone methylation is a member of the histone modifications with histone methyltransferase activity, wherein SET and MYND domain containing 3 (SMYD3) and Enhancer of Zeste Homolog 2 (EZH2) are reported to be involved in the development of multiple cancers and play important roles in transcriptional regulation	Immunohistochemical staining	Histone methylation is a member of the histone modifications with histone methyltransferase activity, wherein SET and MYND domain containing 3 (SMYD3) and Enhancer of Zeste Homolog 2 (EZH2) are reported to be involved in the development of multiple cancers and play important roles in transcriptional regulation		RT-qPCR,Western blot				EZH2		Histone methylation is a member of the histone modifications with histone methyltransferase activity, wherein SET and MYND domain containing 3 (SMYD3) and Enhancer of Zeste Homolog 2 (EZH2) are reported to be involved in the development of multiple cancers and play important roles in transcriptional regulation
29070695	chr17	19492823	19494823	SLC47A1	These results suggest that the 5’ CpG island of SLC47A1 acts as an enhancer for SLC47A1, and DNA methylation in the CpG island plays an important role in inter-individual differences in hepatic MATE1 expression.	human	Liver	High+Lowthroughput	Relationship between DNA Methylation in the 5' CpG Island of the SLC47A1 (Multidrug and Toxin Extrusion Protein MATE1) Gene and Interindividual Variability in MATE1 Expression in the Human Liver	否			HepG2 cell	E_01_0046	qRT-PCR	These results suggest that the 5’ CpG island of SLC47A1 acts as an enhancer for SLC47A1, and DNA methylation in the CpG island plays an important role in inter-individual differences in hepatic MATE1 expression.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		These results suggest that the 5’ CpG island of SLC47A1 acts as an enhancer for SLC47A1, and DNA methylation in the CpG island plays an important role in inter-individual differences in hepatic MATE1 expression.	Immunohistochemical staining	These results suggest that the 5’ CpG island of SLC47A1 acts as an enhancer for SLC47A1, and DNA methylation in the CpG island plays an important role in inter-individual differences in hepatic MATE1 expression.		qRT-PCR			SLC47A1		These results suggest that the 5’ CpG island of SLC47A1 acts as an enhancer for SLC47A1, and DNA methylation in the CpG island plays an important role in inter-individual differences in hepatic MATE1 expression.	
29059175	chr16	67559364	67561364	CTCF	Because CTCF is a multifunctional TF that can function as either an activator or a repressor of transcription, we first confirmed the role of CTCF in regulation of MSMP expression using siRNA.	human	Tumor	High+Lowthroughput	Induction of anti-VEGF therapy resistance by upregulated expression of microseminoprotein (MSMP)	否		Tumor	cancer cell	E_01_0047	qRT–PCR,Immunostaining,Western blot	Because CTCF is a multifunctional TF that can function as either an activator or a repressor of transcription, we first confirmed the role of CTCF in regulation of MSMP expression using siRNA.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Because CTCF is a multifunctional TF that can function as either an activator or a repressor of transcription, we first confirmed the role of CTCF in regulation of MSMP expression using siRNA.	Immunohistochemical staining	Because CTCF is a multifunctional TF that can function as either an activator or a repressor of transcription, we first confirmed the role of CTCF in regulation of MSMP expression using siRNA.		qRT–PCR,Immunostaining,Western blot			MSMP	CTCF	These findings imply that MSMP inhibition combined with the use of antiangiogenesis drugs may be a new strategy to overcome resistance to antiangiogenesis therapy	Because CTCF is a multifunctional TF that can function as either an activator or a repressor of transcription, we first confirmed the role of CTCF in regulation of MSMP expression using siRNA.
29053336	chr7	148804334	148806334	EZH2	These findings suggest that a novel and functionally interdependent interplay between EZH2 and G9a regulates histone methylation-mediated epigenetic repression of the antifibrotic CXCL10 gene in IPF. This interdependent interplay may prove to be a target for epigenetic intervention to restore the expression of CXCL10 and other anti-fibrotic genes in IPF.	human	Lung	High+Lowthroughput	Interplay between EZH2 and G9a Regulates CXCL10 Gene Repression in Idiopathic Pulmonary Fibrosis	否		Pulmonary Fibrosis		E_01_0048	ChIP	These findings suggest that a novel and functionally interdependent interplay between EZH2 and G9a regulates histone methylation-mediated epigenetic repression of the antifibrotic CXCL10 gene in IPF. This interdependent interplay may prove to be a target for epigenetic intervention to restore the expression of CXCL10 and other anti-fibrotic genes in IPF.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		These findings suggest that a novel and functionally interdependent interplay between EZH2 and G9a regulates histone methylation-mediated epigenetic repression of the antifibrotic CXCL10 gene in IPF. This interdependent interplay may prove to be a target for epigenetic intervention to restore the expression of CXCL10 and other anti-fibrotic genes in IPF.	Immunohistochemical staining	These findings suggest that a novel and functionally interdependent interplay between EZH2 and G9a regulates histone methylation-mediated epigenetic repression of the antifibrotic CXCL10 gene in IPF. This interdependent interplay may prove to be a target for epigenetic intervention to restore the expression of CXCL10 and other anti-fibrotic genes in IPF.		ChIP				EZH2		These findings suggest that a novel and functionally interdependent interplay between EZH2 and G9a regulates histone methylation-mediated epigenetic repression of the antifibrotic CXCL10 gene in IPF. This interdependent interplay may prove to be a target for epigenetic intervention to restore the expression of CXCL10 and other anti-fibrotic genes in IPF.
29044515	chr12	32787839	32789839	PKP2	Moreover, our data suggest that Plakophilin-2 may act as an antagonist of β-catenin/TCF complexes on Wnt-activated promoters.	human	Colon	High+Lowthroughput	The human PKP2/plakophilin-2 gene is induced by Wnt/β-catenin in normal and colon cancer-associated fibroblasts	否		colon cancer	colon cancer-associated fibroblast	E_01_0049	RNA-Seq,RT-qPCR,Western blot	Moreover, our data suggest that Plakophilin-2 may act as an antagonist of β-catenin/TCF complexes on Wnt-activated promoters.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Moreover, our data suggest that Plakophilin-2 may act as an antagonist of β-catenin/TCF complexes on Wnt-activated promoters.	Immunohistochemical staining	Moreover, our data suggest that Plakophilin-2 may act as an antagonist of β-catenin/TCF complexes on Wnt-activated promoters.		RNA-Seq,RT-qPCR,Western blot			PKP2		Moreover, our data suggest that Plakophilin-2 may act as an antagonist of β-catenin/TCF complexes on Wnt-activated promoters.	
28994199	chr1	47213269	47215269	TAL1	Here, addition of PD0325901 to the culture was associated with increased transcript levels of GATA1, LMO2, TAL1 and FOG which are known to be the key transcription factors for normal erythroid differentiation	human	Haematopoietic	High+Lowthroughput	Inhibition of MEK/ERK signalling pathway promotes erythroid differentiation and reduces HSCs engraftment in ex?vivo expanded haematopoietic stem cells	否			hematopoietic stem cell	E_01_0050	qPCR,Immunohistochemical staining	Here, addition of PD0325901 to the culture was associated with increased transcript levels of GATA1, LMO2, TAL1 and FOG which are known to be the key transcription factors for normal erythroid differentiation	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Here, addition of PD0325901 to the culture was associated with increased transcript levels of GATA1, LMO2, TAL1 and FOG which are known to be the key transcription factors for normal erythroid differentiation	Immunohistochemical staining	Here, addition of PD0325901 to the culture was associated with increased transcript levels of GATA1, LMO2, TAL1 and FOG which are known to be the key transcription factors for normal erythroid differentiation		qPCR,Immunohistochemical staining				TAL1		Here, addition of PD0325901 to the culture was associated with increased transcript levels of GATA1, LMO2, TAL1 and FOG which are known to be the key transcription factors for normal erythroid differentiation
28974397	chr7	148804688	148806688	EZH2	A promising epigenetic target is EZH2 (enhancer of zeste homolog 2), the catalytic subunit of the polycomb repressive complex 2 that methylates the 27th H3K27.	human	Soft	High+Lowthroughput	Comprehensive Genomic Sequencing of Urothelial Tumors Identifies Rare SMARCB1 (INI-1)-Deficient Carcinomas of the Urinary?System	否		urothelial carcinoma	tumor cell	E_01_0051	Immunohistochemical staining	A promising epigenetic target is EZH2 (enhancer of zeste homolog 2), the catalytic subunit of the polycomb repressive complex 2 that methylates the 27th H3K27.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		A promising epigenetic target is EZH2 (enhancer of zeste homolog 2), the catalytic subunit of the polycomb repressive complex 2 that methylates the 27th H3K27.	Immunohistochemical staining	A promising epigenetic target is EZH2 (enhancer of zeste homolog 2), the catalytic subunit of the polycomb repressive complex 2 that methylates the 27th H3K27.		Immunohistochemical staining			SMARCB1	EZH2	Functioning as a tumor suppressor, biallelic loss of SMARCB1/INI1 through mutation or deletion results in tumor formation.	A promising epigenetic target is EZH2 (enhancer of zeste homolog 2), the catalytic subunit of the polycomb repressive complex 2 that methylates the 27th H3K27.
28971975	chr17	61449600	61451600	TBX4	Transcriptome analysis revealed that TBX4 could broadly regulate fibroblast-related pathways and partly contribute to super-enhancer-mediated transcriptional programs.	human		High+Lowthroughput	TBX4 is involved in the super-enhancer-driven transcriptional programs underlying features specific to lung fibroblasts	否		pathogenesis of respiratory diseases	lung fibroblasts cell	E_01_0052	RNA-seq,RT-PCR	Transcriptome analysis revealed that TBX4 could broadly regulate fibroblast-related pathways and partly contribute to super-enhancer-mediated transcriptional programs.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Transcriptome analysis revealed that TBX4 could broadly regulate fibroblast-related pathways and partly contribute to super-enhancer-mediated transcriptional programs.	Immunohistochemical staining	Transcriptome analysis revealed that TBX4 could broadly regulate fibroblast-related pathways and partly contribute to super-enhancer-mediated transcriptional programs.		RNA-seq,RT-PCR				TBX4		Transcriptome analysis revealed that TBX4 could broadly regulate fibroblast-related pathways and partly contribute to super-enhancer-mediated transcriptional programs.
28939663	chr7	148804966	148806966	EZH2	As CCRK drives hepatocarcinogenesis through upregulation of EZH2,which can function as a transcriptional activator of NF-κB targets	human	Liver	High+Lowthroughput	Hepatoma-intrinsic CCRK inhibition diminishes myeloid-derived suppressor cell immunosuppression and enhances immune-checkpoint blockade efficacy	否		hepatocellular carcinoma	Myeloid-derived suppressor cell	E_01_0053	Transfection	As CCRK drives hepatocarcinogenesis through upregulation of EZH2,which can function as a transcriptional activator of NF-κB targets	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		As CCRK drives hepatocarcinogenesis through upregulation of EZH2,which can function as a transcriptional activator of NF-κB targets	Immunohistochemical staining	As CCRK drives hepatocarcinogenesis through upregulation of EZH2,which can function as a transcriptional activator of NF-κB targets		Transfection				EZH2		As CCRK drives hepatocarcinogenesis through upregulation of EZH2,which can function as a transcriptional activator of NF-κB targets
28925507	chr7	148804490	148806490	EZH2	In accord with this, we confirmed that EGCG and GSK343 could both significantly arrest the G0/G1 phase in RKO cell cycle, suggesting EGCG and EZH2 inhibitor share a common mechanism of action in RKO cells.	human	CRC	High+Lowthroughput	(-)-Epigallocatechin-3-gallate and EZH2 inhibitor GSK343 have similar inhibitory effects and mechanisms of action on colorectal cancer cells	否		colorectal cancer	colorectal cancer (CRC) cell line	E_01_0054	Western blot,Immunofluorescence	In accord with this, we confirmed that EGCG and GSK343 could both significantly arrest the G0/G1 phase in RKO cell cycle, suggesting EGCG and EZH2 inhibitor share a common mechanism of action in RKO cells.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In accord with this, we confirmed that EGCG and GSK343 could both significantly arrest the G0/G1 phase in RKO cell cycle, suggesting EGCG and EZH2 inhibitor share a common mechanism of action in RKO cells.	Immunohistochemical staining	In accord with this, we confirmed that EGCG and GSK343 could both significantly arrest the G0/G1 phase in RKO cell cycle, suggesting EGCG and EZH2 inhibitor share a common mechanism of action in RKO cells.		Western blot,Immunofluorescence				EZH2		In accord with this, we confirmed that EGCG and GSK343 could both significantly arrest the G0/G1 phase in RKO cell cycle, suggesting EGCG and EZH2 inhibitor share a common mechanism of action in RKO cells.
28925391	chr7	148804797	148806797	EZH2	Here, we show enhancer of zeste homolog 2(EZH2), an enzyme that catalyzes H3 lysine trimethylation and associates with oncogenic function, contributes to PARPi sensitivity in breast cancer cells.	human	Tumor	High+Lowthroughput	EZH2 contributes to the response to PARP inhibitors through its PARP-mediated poly-ADP ribosylation in breast cancer	否		breast cancer	breast cancer cell	E_01_0055	ChIP,qPCR,RT-qPCR,Western blot	Here, we show enhancer of zeste homolog 2(EZH2), an enzyme that catalyzes H3 lysine trimethylation and associates with oncogenic function, contributes to PARPi sensitivity in breast cancer cells.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Here, we show enhancer of zeste homolog 2(EZH2), an enzyme that catalyzes H3 lysine trimethylation and associates with oncogenic function, contributes to PARPi sensitivity in breast cancer cells.	Immunohistochemical staining	Here, we show enhancer of zeste homolog 2(EZH2), an enzyme that catalyzes H3 lysine trimethylation and associates with oncogenic function, contributes to PARPi sensitivity in breast cancer cells.		ChIP,qPCR,RT-qPCR,Western blot				EZH2		Here, we show enhancer of zeste homolog 2(EZH2), an enzyme that catalyzes H3 lysine trimethylation and associates with oncogenic function, contributes to PARPi sensitivity in breast cancer cells.
28923345	chr10	67881952	67883952	SIRT1	Thus, SIRT1 is a novel transcriptional enhancer of GR-induced transcriptional activity possibly by functioning as a scaffold for the transcriptional complex formed on GR.	human		High+Lowthroughput	SIRT1 is a transcriptional enhancer of the glucocorticoid receptor acting independently to its deacetylase activity	否			HeLa cell	E_01_0056	Transfection,Western blot,RNA-seq,PCR,ChIP	Thus, SIRT1 is a novel transcriptional enhancer of GR-induced transcriptional activity possibly by functioning as a scaffold for the transcriptional complex formed on GR.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Thus, SIRT1 is a novel transcriptional enhancer of GR-induced transcriptional activity possibly by functioning as a scaffold for the transcriptional complex formed on GR.	Immunohistochemical staining	Thus, SIRT1 is a novel transcriptional enhancer of GR-induced transcriptional activity possibly by functioning as a scaffold for the transcriptional complex formed on GR.		Transfection,Western blot,RNA-seq,PCR,ChIP				SIRT1		Thus, SIRT1 is a novel transcriptional enhancer of GR-induced transcriptional activity possibly by functioning as a scaffold for the transcriptional complex formed on GR.
28922471	chr19	35742614	35744614	PSENEN	The co-existence of the two disorders was recently found to result from mutations in PSENEN, encoding protein presenilin enhancer gamma-secretase subunit.	human		High+Lowthroughput	A phenotype combining hidradenitis suppurativa with Dowling-Degos disease caused by a founder mutation in PSENEN	否		Dowling-Degos disease	keratinocyte cell	E_01_0057	qRT-PCR	The co-existence of the two disorders was recently found to result from mutations in PSENEN, encoding protein presenilin enhancer gamma-secretase subunit.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The co-existence of the two disorders was recently found to result from mutations in PSENEN, encoding protein presenilin enhancer gamma-secretase subunit.	Immunohistochemical staining	The co-existence of the two disorders was recently found to result from mutations in PSENEN, encoding protein presenilin enhancer gamma-secretase subunit.		qRT-PCR			PSENEN		The co-existence of the two disorders was recently found to result from mutations in PSENEN, encoding protein presenilin enhancer gamma-secretase subunit.	
28902616	chr5	88714680	88716680	MEF2C	The MADS-box transcription factor myocyte enhancer factor 2C (MEF2C) is required for the cardiac development and postnatal adaptation and in mice-targeted disruption of the MEF2C gene results in dilated cardiomyopathy (DCM).	human	Heart	High+Lowthroughput	MEF2C loss-of-function mutation associated with familial dilated cardiomyopathy	否		dilated cardiomyopathy	HeLa cell	E_01_0058	Transfection,dual-luciferase reporter assay	The MADS-box transcription factor myocyte enhancer factor 2C (MEF2C) is required for the cardiac development and postnatal adaptation and in mice-targeted disruption of the MEF2C gene results in dilated cardiomyopathy (DCM).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The MADS-box transcription factor myocyte enhancer factor 2C (MEF2C) is required for the cardiac development and postnatal adaptation and in mice-targeted disruption of the MEF2C gene results in dilated cardiomyopathy (DCM).	Immunohistochemical staining	The MADS-box transcription factor myocyte enhancer factor 2C (MEF2C) is required for the cardiac development and postnatal adaptation and in mice-targeted disruption of the MEF2C gene results in dilated cardiomyopathy (DCM).		Transfection,dual-luciferase reporter assay				MEF2C		The MADS-box transcription factor myocyte enhancer factor 2C (MEF2C) is required for the cardiac development and postnatal adaptation and in mice-targeted disruption of the MEF2C gene results in dilated cardiomyopathy (DCM).
28862715	chr7	148804307	148806307	EZH2	EZH2 positivity was significantly correlated with WHO tumor grade and worse prognosis in gliomas.	human	Tumor	High+Lowthroughput	Prognostic role of EZH2 in gliomas: a meta-analysis	否		gliomas	tumor cell	E_01_0059	Meta-analysis	EZH2 positivity was significantly correlated with WHO tumor grade and worse prognosis in gliomas.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		EZH2 positivity was significantly correlated with WHO tumor grade and worse prognosis in gliomas.	Immunohistochemical staining	EZH2 positivity was significantly correlated with WHO tumor grade and worse prognosis in gliomas.		Meta-analysis				EZH2		EZH2 positivity was significantly correlated with WHO tumor grade and worse prognosis in gliomas.
28858300	chr7	148804693	148806693	EZH2	Aberrant activity of enhancer of zeste homolog 2 (EZH2) is associated with a wide range of human cancers.	human	Tumor	High+Lowthroughput	Development of a high-throughput fluorescence polarization assay for the discovery of EZH2-EED interaction inhibitors	否		Tumor	cancer cell	E_01_0060	PCR	Aberrant activity of enhancer of zeste homolog 2 (EZH2) is associated with a wide range of human cancers.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Aberrant activity of enhancer of zeste homolog 2 (EZH2) is associated with a wide range of human cancers.	Immunohistochemical staining	Aberrant activity of enhancer of zeste homolog 2 (EZH2) is associated with a wide range of human cancers.		PCR				EZH2		Aberrant activity of enhancer of zeste homolog 2 (EZH2) is associated with a wide range of human cancers.
28811072	chr16	81236	83236	NPRL3	One globin gene cluster, linked to the gene NPRL3, is preserved in all vertebrates, including a gene cluster encoding the highly divergent globins from jawless vertebrates.	human		High+Lowthroughput	Evolution of hemoglobin loci and their regulatory elements	否			erythroid cell	E_01_0061		One globin gene cluster, linked to the gene NPRL3, is preserved in all vertebrates, including a gene cluster encoding the highly divergent globins from jawless vertebrates.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		One globin gene cluster, linked to the gene NPRL3, is preserved in all vertebrates, including a gene cluster encoding the highly divergent globins from jawless vertebrates.	Immunohistochemical staining	One globin gene cluster, linked to the gene NPRL3, is preserved in all vertebrates, including a gene cluster encoding the highly divergent globins from jawless vertebrates.					NPRL3		One globin gene cluster, linked to the gene NPRL3, is preserved in all vertebrates, including a gene cluster encoding the highly divergent globins from jawless vertebrates.	
28810932	chr7	148804688	148806688	EZH2	RIP and ChIP assays suggest that NEAT1 is recruited to the E-cadherin promoter by EZH2 (enhancer of zeste homolog 2), where it represses E-cadherin expression. These findings indicate that NEAT1 exerts oncogenic effects in CCA.	human	CCA	High+Lowthroughput	Long Noncoding RNA NEAT1 Promotes Growth and Metastasis of Cholangiocarcinoma Cells	否		cholangiocarcinoma	Cholangiocarcinoma Cell	E_01_0062	qRT-PCR,ChIP,Western blot	RIP and ChIP assays suggest that NEAT1 is recruited to the E-cadherin promoter by EZH2 (enhancer of zeste homolog 2), where it represses E-cadherin expression. These findings indicate that NEAT1 exerts oncogenic effects in CCA.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		RIP and ChIP assays suggest that NEAT1 is recruited to the E-cadherin promoter by EZH2 (enhancer of zeste homolog 2), where it represses E-cadherin expression. These findings indicate that NEAT1 exerts oncogenic effects in CCA.	Immunohistochemical staining	RIP and ChIP assays suggest that NEAT1 is recruited to the E-cadherin promoter by EZH2 (enhancer of zeste homolog 2), where it represses E-cadherin expression. These findings indicate that NEAT1 exerts oncogenic effects in CCA.		qRT-PCR,ChIP,Western blot				EZH2		RIP and ChIP assays suggest that NEAT1 is recruited to the E-cadherin promoter by EZH2 (enhancer of zeste homolog 2), where it represses E-cadherin expression. These findings indicate that NEAT1 exerts oncogenic effects in CCA.
28796375	chr7	148804611	148806611	EZH2	Consequently, we find that EZH2 promotes LA cell invasion and metastasis by inhibiting SPRY4-IT1 expression. This article is protected by copyright.	human	LA	High+Lowthroughput	Effects of long noncoding RNA SPRY4-IT1-mediated EZH2 on the invasion and migration of lung adenocarcinoma	否		lung adenocarcinoma	lung adenocarcinoma (LA) cell	E_01_0063	Western blot,RT-qPCR	Consequently, we find that EZH2 promotes LA cell invasion and metastasis by inhibiting SPRY4-IT1 expression. This article is protected by copyright.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Consequently, we find that EZH2 promotes LA cell invasion and metastasis by inhibiting SPRY4-IT1 expression. This article is protected by copyright.	Immunohistochemical staining	Consequently, we find that EZH2 promotes LA cell invasion and metastasis by inhibiting SPRY4-IT1 expression. This article is protected by copyright.		Western blot,RT-qPCR				EZH2		Consequently, we find that EZH2 promotes LA cell invasion and metastasis by inhibiting SPRY4-IT1 expression. This article is protected by copyright.
28795320	chr7	148804483	148806483	EZH2	Taken together, our results suggest that EZH2 regulates cell proliferation potentially by targeting RUNX3 through the Wnt/b-catenin signaling pathway in laryngeal carcinoma.	human	Laryngeal carcinoma	High+Lowthroughput	EZH2 promotes cell proliferation by regulating the expression of RUNX3 in laryngeal carcinoma	否		laryngeal carcinoma	laryngeal carcinoma cell	E_01_0064	Western blot,qRT-PCR	Taken together, our results suggest that EZH2 regulates cell proliferation potentially by targeting RUNX3 through the Wnt/b-catenin signaling pathway in laryngeal carcinoma.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Taken together, our results suggest that EZH2 regulates cell proliferation potentially by targeting RUNX3 through the Wnt/b-catenin signaling pathway in laryngeal carcinoma.	Immunohistochemical staining	Taken together, our results suggest that EZH2 regulates cell proliferation potentially by targeting RUNX3 through the Wnt/b-catenin signaling pathway in laryngeal carcinoma.		Western blot,qRT-PCR				EZH2		Taken together, our results suggest that EZH2 regulates cell proliferation potentially by targeting RUNX3 through the Wnt/b-catenin signaling pathway in laryngeal carcinoma.
28774779	chr12	57092763	57094763	STAT6	Our results suggest that there is a novel, so far uncharacterized cistromic crosstalk between RXR and STAT6 that is likely to contribute to the formation of the active enhancer repertoire, transcriptome and differential signal-specific gene regulation of polarized macrophages.	human		High+Lowthroughput	Extensive and functional overlap of the STAT6 and RXR cistromes in the active enhancer repertoire of human CD14+ monocyte derived differentiating macrophages	否			macrophage	E_01_0065	ChIP,ChIP-seq,RNA-Seq,qPCR	Our results suggest that there is a novel, so far uncharacterized cistromic crosstalk between RXR and STAT6 that is likely to contribute to the formation of the active enhancer repertoire, transcriptome and differential signal-specific gene regulation of polarized macrophages.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Our results suggest that there is a novel, so far uncharacterized cistromic crosstalk between RXR and STAT6 that is likely to contribute to the formation of the active enhancer repertoire, transcriptome and differential signal-specific gene regulation of polarized macrophages.	Immunohistochemical staining	Our results suggest that there is a novel, so far uncharacterized cistromic crosstalk between RXR and STAT6 that is likely to contribute to the formation of the active enhancer repertoire, transcriptome and differential signal-specific gene regulation of polarized macrophages.		ChIP,ChIP-seq,RNA-Seq,qPCR				STAT6		Our results suggest that there is a novel, so far uncharacterized cistromic crosstalk between RXR and STAT6 that is likely to contribute to the formation of the active enhancer repertoire, transcriptome and differential signal-specific gene regulation of polarized macrophages.
28763207	chr7	148804454	148806454	EZH2		human		High+Lowthroughput	Inhibition of Human Enhancer of Zeste Homolog 2 with Tambjamine Analogs	否				E_01_0066	Immunofluorescence staining		Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq			Immunohistochemical staining			Immunofluorescence staining			SET,AEBP2	EZH2		
28722764	chr7	148804258	148806258	EZH2	We previously demonstrated that Enhancer Zeste of Homolog 2 (EZH2), the catalytic subunits of PRC2 complex, contributes to inhibit muscle differentiation in eRMS and its down-regulation causes a partial recovery of myogenesis.	human		High+Lowthroughput	12-O-tetradecanoylphorbol-13-acetate and EZH2 inhibition: A novel approach for promoting myogenic differentiation in embryonal rhabdomyosarcoma cells	否		Rhabdomyosarcoma	myocyte	E_01_0067	Western blot,Real-Time PCR	We previously demonstrated that Enhancer Zeste of Homolog 2 (EZH2), the catalytic subunits of PRC2 complex, contributes to inhibit muscle differentiation in eRMS and its down-regulation causes a partial recovery of myogenesis.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We previously demonstrated that Enhancer Zeste of Homolog 2 (EZH2), the catalytic subunits of PRC2 complex, contributes to inhibit muscle differentiation in eRMS and its down-regulation causes a partial recovery of myogenesis.	Immunohistochemical staining	We previously demonstrated that Enhancer Zeste of Homolog 2 (EZH2), the catalytic subunits of PRC2 complex, contributes to inhibit muscle differentiation in eRMS and its down-regulation causes a partial recovery of myogenesis.		Western blot,Real-Time PCR				EZH2		We previously demonstrated that Enhancer Zeste of Homolog 2 (EZH2), the catalytic subunits of PRC2 complex, contributes to inhibit muscle differentiation in eRMS and its down-regulation causes a partial recovery of myogenesis.
28718381	chr7	148804593	148806593	EZH2	Third, the involvement of EZH2 and epigenetic changes as shown in this study lends further support for the notion that endometriosis is an epigenetic disease79 and justifies the use of HDACIs as therapeutics for endometriosis.	human	Ectopic endometrial	High+Lowthroughput	Histological and Immunohistochemical Characterization of the Similarity and Difference Between Ovarian Endometriomas and Deep Infiltrating Endometriosis	否		Ovarian endometrioma (OMA) and deep infiltrating endometriosis (DIE)	endothelial cell	E_01_0068	immunostaining	Third, the involvement of EZH2 and epigenetic changes as shown in this study lends further support for the notion that endometriosis is an epigenetic disease79 and justifies the use of HDACIs as therapeutics for endometriosis.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Third, the involvement of EZH2 and epigenetic changes as shown in this study lends further support for the notion that endometriosis is an epigenetic disease79 and justifies the use of HDACIs as therapeutics for endometriosis.	Immunohistochemical staining	Third, the involvement of EZH2 and epigenetic changes as shown in this study lends further support for the notion that endometriosis is an epigenetic disease79 and justifies the use of HDACIs as therapeutics for endometriosis.		immunostaining				EZH2		Third, the involvement of EZH2 and epigenetic changes as shown in this study lends further support for the notion that endometriosis is an epigenetic disease79 and justifies the use of HDACIs as therapeutics for endometriosis.
28681918	chr7	148804320	148806320	EZH2	Human gene of enhancer of zeste homolog 2 (EZH2) was originally found to encode a histone methyltransferase forming the catalytic component of the polycomb repressive complex-2, thus exerting functional regulations on epigenetic silencing during the process of cell fate decisions	human	Cervical epithelial	High+Lowthroughput	MicroRNA-137 is negatively associated with clinical outcome and regulates tumor development through EZH2 in cervical cancer	否		cervical cancer	CC cell line	E_01_0069	qPCR,Dual-luciferase reporter assay	Human gene of enhancer of zeste homolog 2 (EZH2) was originally found to encode a histone methyltransferase forming the catalytic component of the polycomb repressive complex-2, thus exerting functional regulations on epigenetic silencing during the process of cell fate decisions	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Human gene of enhancer of zeste homolog 2 (EZH2) was originally found to encode a histone methyltransferase forming the catalytic component of the polycomb repressive complex-2, thus exerting functional regulations on epigenetic silencing during the process of cell fate decisions	Immunohistochemical staining	Human gene of enhancer of zeste homolog 2 (EZH2) was originally found to encode a histone methyltransferase forming the catalytic component of the polycomb repressive complex-2, thus exerting functional regulations on epigenetic silencing during the process of cell fate decisions		qPCR,Dual-luciferase reporter assay				EZH2		Human gene of enhancer of zeste homolog 2 (EZH2) was originally found to encode a histone methyltransferase forming the catalytic component of the polycomb repressive complex-2, thus exerting functional regulations on epigenetic silencing during the process of cell fate decisions
28681114	chr7	148804493	148806493	EZH2	Enhancer of zeste homolog 2 (EZH2), a stemness factor, plays roles in regulation of cell differentiation and embryonic development as well as cancer progression.	human	Tumor	High+Lowthroughput	Predicting the Correlation of EZH2 and Cancer Stem Cell Markers in Esophageal Squamous Cell Carcinoma	否		Esophageal Squamous Cell Carcinoma	Cancer Stem Cell	E_01_0070	qRT-PCR	Enhancer of zeste homolog 2 (EZH2), a stemness factor, plays roles in regulation of cell differentiation and embryonic development as well as cancer progression.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Enhancer of zeste homolog 2 (EZH2), a stemness factor, plays roles in regulation of cell differentiation and embryonic development as well as cancer progression.	Immunohistochemical staining	Enhancer of zeste homolog 2 (EZH2), a stemness factor, plays roles in regulation of cell differentiation and embryonic development as well as cancer progression.		qRT-PCR				EZH2		Enhancer of zeste homolog 2 (EZH2), a stemness factor, plays roles in regulation of cell differentiation and embryonic development as well as cancer progression.
28462489	chr5	179729425	179731425	MAML1	In the present study, we analyzed cross talk between NOTCH pathway and HOX genes through assessment of probable correlation betweenMAML1 and MEIS1 as the main transcription factor of NOTCH pathway and enhancer of HOX transcriptional machinery, respectively in esophageal squamous cell carcinoma (ESCC) patients.	human	Tumor	High+Lowthroughput	Role of MAML1 and MEIS1 in Esophageal Squamous Cell Carcinoma Depth of Invasion	否		esophageal squamous cell carcinoma	tumor cell	E_01_0071	qRT-PCR	In the present study, we analyzed cross talk between NOTCH pathway and HOX genes through assessment of probable correlation betweenMAML1 and MEIS1 as the main transcription factor of NOTCH pathway and enhancer of HOX transcriptional machinery, respectively in esophageal squamous cell carcinoma (ESCC) patients.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In the present study, we analyzed cross talk between NOTCH pathway and HOX genes through assessment of probable correlation betweenMAML1 and MEIS1 as the main transcription factor of NOTCH pathway and enhancer of HOX transcriptional machinery, respectively in esophageal squamous cell carcinoma (ESCC) patients.	Immunohistochemical staining	In the present study, we analyzed cross talk between NOTCH pathway and HOX genes through assessment of probable correlation betweenMAML1 and MEIS1 as the main transcription factor of NOTCH pathway and enhancer of HOX transcriptional machinery, respectively in esophageal squamous cell carcinoma (ESCC) patients.		qRT-PCR			MAML1,MEIS1		In the present study, we analyzed cross talk between NOTCH pathway and HOX genes through assessment of probable correlation betweenMAML1 and MEIS1 as the main transcription factor of NOTCH pathway and enhancer of HOX transcriptional machinery, respectively in esophageal squamous cell carcinoma (ESCC) patients.;In the present study, we analyzed cross talk between NOTCH pathway and HOX genes through assessment of probable correlation betweenMAML1 and MEIS1 as the main transcription factor of NOTCH pathway and enhancer of HOX transcriptional machinery, respectively in esophageal squamous cell carcinoma (ESCC) patients.	
28442495	chr13	27958465	27960465	CDX2	CDX2, a transcription factor required to form intestinal epithelium, is a target of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signalling, which can be inhibited by aspirin.	human		High+Lowthroughput	Aspirin prevents NF-κB activation and CDX2 expression stimulated by acid and bile salts in oesophageal squamous cells of patients with Barrett's oesophagus	否		Esophageal Diseases	oesophageal squamous cell	E_01_0072	Western blot	CDX2, a transcription factor required to form intestinal epithelium, is a target of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signalling, which can be inhibited by aspirin.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		CDX2, a transcription factor required to form intestinal epithelium, is a target of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signalling, which can be inhibited by aspirin.	Immunohistochemical staining	CDX2, a transcription factor required to form intestinal epithelium, is a target of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signalling, which can be inhibited by aspirin.		Western blot				CDX2		CDX2, a transcription factor required to form intestinal epithelium, is a target of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) signalling, which can be inhibited by aspirin.
28027119	chr4	108044503	108046503	LEF1	Lymphoid enhancer-factor 1 (LEF1), a recently emerged marker, is part of the Wnt pathway with b-catenin but has not been studied in DTF	human	Soft	High+Lowthroughput	Comparison of β-Catenin and LEF1 Immunohistochemical Stains in Desmoid-type Fibromatosis and its Selected Mimickers, With Unexpected Finding of LEF1 Positivity in Scars	否		desmoid-type fibromatosis		E_01_0073	Immunohistochemical staining	Lymphoid enhancer-factor 1 (LEF1), a recently emerged marker, is part of the Wnt pathway with b-catenin but has not been studied in DTF	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Lymphoid enhancer-factor 1 (LEF1), a recently emerged marker, is part of the Wnt pathway with b-catenin but has not been studied in DTF	Immunohistochemical staining	Lymphoid enhancer-factor 1 (LEF1), a recently emerged marker, is part of the Wnt pathway with b-catenin but has not been studied in DTF		Immunohistochemical staining				LEF1		Lymphoid enhancer-factor 1 (LEF1), a recently emerged marker, is part of the Wnt pathway with b-catenin but has not been studied in DTF
27997051	chr7	44101517	44103517	AEBP1	Adipocyte enhancer binding protein 1 (AEBP1) activates inflammatory responses via the NF-κB pathway in macrophages and regulates adipogenesis in preadipocytes	human	Hippocampal	High+Lowthroughput	Association of adipocyte enhancer-binding protein 1 with Alzheimer's disease pathology in human hippocampi	否		Alzheimer’s disease	smooth muscle cell line	E_01_0074	Western blot	Adipocyte enhancer binding protein 1 (AEBP1) activates inflammatory responses via the NF-κB pathway in macrophages and regulates adipogenesis in preadipocytes	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Adipocyte enhancer binding protein 1 (AEBP1) activates inflammatory responses via the NF-κB pathway in macrophages and regulates adipogenesis in preadipocytes	Immunohistochemical staining	Adipocyte enhancer binding protein 1 (AEBP1) activates inflammatory responses via the NF-κB pathway in macrophages and regulates adipogenesis in preadipocytes		Western blot			AEBP1		Adipocyte enhancer binding protein 1 (AEBP1) activates inflammatory responses via the NF-κB pathway in macrophages and regulates adipogenesis in preadipocytes	
27845419	chr7	87500277	87502277	ABCB1	These results suggest that genetic variation in ABCC1 and ABCB1 may contribute to irinotecan-induced neutropenia by altering expression of transporters involved in irinotecan metabolite disposition.	human	Liver	High+Lowthroughput	ABC transporter polymorphisms are associated with irinotecan pharmacokinetics and neutropenia	是	rs12720066,rs6498588	Neutropenia	Hep G2 cell	E_01_0075	Enhancer Assay	These results suggest that genetic variation in ABCC1 and ABCB1 may contribute to irinotecan-induced neutropenia by altering expression of transporters involved in irinotecan metabolite disposition.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		These results suggest that genetic variation in ABCC1 and ABCB1 may contribute to irinotecan-induced neutropenia by altering expression of transporters involved in irinotecan metabolite disposition.	Immunohistochemical staining	These results suggest that genetic variation in ABCC1 and ABCB1 may contribute to irinotecan-induced neutropenia by altering expression of transporters involved in irinotecan metabolite disposition.		Enhancer Assay				ABCB1		These results suggest that genetic variation in ABCC1 and ABCB1 may contribute to irinotecan-induced neutropenia by altering expression of transporters involved in irinotecan metabolite disposition.
28860350	chr2	43219398	43221398	ZFP36L2	Notably, ZFP36L2 is associated with super-enhancer in healthy oesophageal mucosa; Dna hypermethylation in its super-enhancer reduced active histone markers in squamous cancer cells, suggesting an epigenetic inactivation of a super-enhancerassociated Scc suppressor	human	Non-malignant oesophagus	High+Lowthroughput	Identification of distinct mutational patterns and new driver genes in oesophageal squamous cell carcinomas and adenocarcinomas	否		Oesophageal squamous cell carcinoma (OScc) and adenocarcinoma (Oac)	squamous cell line	E_01_0076	ChIP-seq,WGBS	Notably, ZFP36L2 is associated with super-enhancer in healthy oesophageal mucosa; Dna hypermethylation in its super-enhancer reduced active histone markers in squamous cancer cells, suggesting an epigenetic inactivation of a super-enhancerassociated Scc suppressor	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Notably, ZFP36L2 is associated with super-enhancer in healthy oesophageal mucosa; Dna hypermethylation in its super-enhancer reduced active histone markers in squamous cancer cells, suggesting an epigenetic inactivation of a super-enhancerassociated Scc suppressor	Immunohistochemical staining	Notably, ZFP36L2 is associated with super-enhancer in healthy oesophageal mucosa; Dna hypermethylation in its super-enhancer reduced active histone markers in squamous cancer cells, suggesting an epigenetic inactivation of a super-enhancerassociated Scc suppressor		ChIP-seq,WGBS			ZFP36L2		Notably, ZFP36L2 is associated with super-enhancer in healthy oesophageal mucosa; Dna hypermethylation in its super-enhancer reduced active histone markers in squamous cancer cells, suggesting an epigenetic inactivation of a super-enhancerassociated Scc suppressor	
31975641	chr1	118880199	118882199	TBX15	Our findings from GWAS index, proxy, and imputed SNPs suggest that a few SNPs, including three in a 0.7-kb cluster, act as causal regulatory variants to fine-tune TBX15 expression and, thereby, affect both obesity and osteoporosis risk.	human	bone marrow	High+Lowthroughput	Osteoporosis- and obesity-risk interrelationships: an epigenetic analysis of GWAS-derived SNPs at the developmental gene TBX15	是	rs61730011,rs984222,rs1106529,rs9659323,rs12742627,rs961470,rs17023223	Osteoporosis	cementoblast	E_01_0077	RNA SEQ, GWAS derived SNPs and LD analysis	Our findings from GWAS index, proxy, and imputed SNPs suggest that a few SNPs, including three in a 0.7-kb cluster, act as causal regulatory variants to fine-tune TBX15 expression and, thereby, affect both obesity and osteoporosis risk.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Our findings from GWAS index, proxy, and imputed SNPs suggest that a few SNPs, including three in a 0.7-kb cluster, act as causal regulatory variants to fine-tune TBX15 expression and, thereby, affect both obesity and osteoporosis risk.	Immunohistochemical staining	Our findings from GWAS index, proxy, and imputed SNPs suggest that a few SNPs, including three in a 0.7-kb cluster, act as causal regulatory variants to fine-tune TBX15 expression and, thereby, affect both obesity and osteoporosis risk.		 RNA-seq，GWAS衍生的SNPs和LD分析				TBX15		Our findings from GWAS index, proxy, and imputed SNPs suggest that a few SNPs, including three in a 0.7-kb cluster, act as causal regulatory variants to fine-tune TBX15 expression and, thereby, affect both obesity and osteoporosis risk.
31969149	chr1	8001716	8003716	ERRFI1	 The minor allele rs72635708 (rs72635708-C) might affect the ERRFI1 promoter activity, which results in unstable expression of ERRFI1, enhancing the risk of psoriasis via disruption of lipid metabolism and skin cell proliferation. 	human	lung	High+Lowthroughput	An integrated analysis of public genomic data unveils a possible functional mechanism of psoriasis risk via a long-range ERRFI1 enhancer	是	rs72635708	psoriasis	IMR-90 cell	E_01_0078	ChIP-seq	 The minor allele rs72635708 (rs72635708-C) might affect the ERRFI1 promoter activity, which results in unstable expression of ERRFI1, enhancing the risk of psoriasis via disruption of lipid metabolism and skin cell proliferation. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		 The minor allele rs72635708 (rs72635708-C) might affect the ERRFI1 promoter activity, which results in unstable expression of ERRFI1, enhancing the risk of psoriasis via disruption of lipid metabolism and skin cell proliferation. 	Immunohistochemical staining	 The minor allele rs72635708 (rs72635708-C) might affect the ERRFI1 promoter activity, which results in unstable expression of ERRFI1, enhancing the risk of psoriasis via disruption of lipid metabolism and skin cell proliferation. 		ChIP-seq			ERRFI1		 The minor allele rs72635708 (rs72635708-C) might affect the ERRFI1 promoter activity, which results in unstable expression of ERRFI1, enhancing the risk of psoriasis via disruption of lipid metabolism and skin cell proliferation. 	
31967103	chr7	148804333	148806333	EZH2	We tested UNC1999, a small molecule inhibitor that blocks enhancer of zeste homolog 2, an enzyme that maintains closed polycomb chromatin. 	human	kidney	High+Lowthroughput	Site-directed targeting of transcriptional activation-associated proteins to repressed chromatin restores CRISPR activity	否			HEK293 cell	E_01_0079	Transfection, luciferase assay, flow cytometry, chip qPCR,	We tested UNC1999, a small molecule inhibitor that blocks enhancer of zeste homolog 2, an enzyme that maintains closed polycomb chromatin. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We tested UNC1999, a small molecule inhibitor that blocks enhancer of zeste homolog 2, an enzyme that maintains closed polycomb chromatin. 	Immunohistochemical staining	We tested UNC1999, a small molecule inhibitor that blocks enhancer of zeste homolog 2, an enzyme that maintains closed polycomb chromatin. 		转染，荧光素酶分析，流式细胞术，ChIP-qPCR，				EZH2		We tested UNC1999, a small molecule inhibitor that blocks enhancer of zeste homolog 2, an enzyme that maintains closed polycomb chromatin. 
31963554	chr10	52311442	52313442	DKK1	Taken together, these observations suggest that 1,25D3 promotes the mineralization of osteoblasts through activation of DKK1 followed by an increase of C/EBPβ.	human	Bone, mesenchymal	High+Lowthroughput	DKK1 Induced by 1,25D3 Is Required for the Mineralization of Osteoblasts	否		Osteoporosis	osteogenitorcell,cementoblast，SaOS2 cell	E_01_0080	QPCR, Western blot, immunofluorescence, luciferase assay, chromatin immunoprecipitation assay	Taken together, these observations suggest that 1,25D3 promotes the mineralization of osteoblasts through activation of DKK1 followed by an increase of C/EBPβ.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Taken together, these observations suggest that 1,25D3 promotes the mineralization of osteoblasts through activation of DKK1 followed by an increase of C/EBPβ.	Immunohistochemical staining	Taken together, these observations suggest that 1,25D3 promotes the mineralization of osteoblasts through activation of DKK1 followed by an increase of C/EBPβ.		qPCR，Western Blot，免疫荧光，荧光素酶分析，染色质免疫沉淀分析			DKK1		Taken together, these observations suggest that 1,25D3 promotes the mineralization of osteoblasts through activation of DKK1 followed by an increase of C/EBPβ.	
31961892	chr11	55334650	55336650	Atox1	Nuclear translocation of Atox1 potentiates activin A-induced cell migration and colony formation in colon cancer	mouse	colon	High+Lowthroughput	Nuclear translocation of Atox1 potentiates activin A-induced cell migration and colony formation in colon cancer	否		Colon cancer	SW480 cell	E_01_0081	Immunofluorescence, Western blot, transfection, cell colony assay	Nuclear translocation of Atox1 potentiates activin A-induced cell migration and colony formation in colon cancer	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Nuclear translocation of Atox1 potentiates activin A-induced cell migration and colony formation in colon cancer	Immunohistochemical staining	Nuclear translocation of Atox1 potentiates activin A-induced cell migration and colony formation in colon cancer		免疫荧光，Western blot，转染，细胞集落实验			Atox1		Nuclear translocation of Atox1 potentiates activin A-induced cell migration and colony formation in colon cancer	
31954402	chr7	148804633	148806633	EZH2	Expression of enhancer of zeste homolog 2 (EZH2) was significantly (P < 0.01) down regulated indicating that genes involved in epigenetic regulation are also differentially expressed in SD patients during the early stage of infection.	human	blood	High+Lowthroughput	Differential expression of microRNA, miR-150 and enhancer of zeste homolog 2 (EZH2) in peripheral blood cells as early prognostic markers of severe forms of dengue	否		dengue fever		E_01_0082	qRT-PCR	Expression of enhancer of zeste homolog 2 (EZH2) was significantly (P < 0.01) down regulated indicating that genes involved in epigenetic regulation are also differentially expressed in SD patients during the early stage of infection.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Expression of enhancer of zeste homolog 2 (EZH2) was significantly (P < 0.01) down regulated indicating that genes involved in epigenetic regulation are also differentially expressed in SD patients during the early stage of infection.	Immunohistochemical staining	Expression of enhancer of zeste homolog 2 (EZH2) was significantly (P < 0.01) down regulated indicating that genes involved in epigenetic regulation are also differentially expressed in SD patients during the early stage of infection.		qRT-PCR				EZH2		Expression of enhancer of zeste homolog 2 (EZH2) was significantly (P < 0.01) down regulated indicating that genes involved in epigenetic regulation are also differentially expressed in SD patients during the early stage of infection.
31953940	chr4	108045068	108047068	LEF1	LEF1 is not expressed in most CD5-positive MZLs and LPLs; therefore, it is a reliable marker for distinguishing them from CLL/SLL. LEF1 may be expressed in CD5-positive FLs.	human		High+Lowthroughput	Immunohistochemical Expression of Lymphoid Enhancer Binding Factor 1 in CD5-Positive Marginal Zone, Lymphoplasmacytic, and Follicular Lymphomas.	否		Lymphoplasmacytoma, follicular lymphoma	tumor cell	E_01_0083	Immunohistochemistry, flow cytometry, fluorescence in situ hybridization, QRT PCR	LEF1 is not expressed in most CD5-positive MZLs and LPLs; therefore, it is a reliable marker for distinguishing them from CLL/SLL. LEF1 may be expressed in CD5-positive FLs.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		LEF1 is not expressed in most CD5-positive MZLs and LPLs; therefore, it is a reliable marker for distinguishing them from CLL/SLL. LEF1 may be expressed in CD5-positive FLs.	Immunohistochemical staining	LEF1 is not expressed in most CD5-positive MZLs and LPLs; therefore, it is a reliable marker for distinguishing them from CLL/SLL. LEF1 may be expressed in CD5-positive FLs.		免疫组化，流式细胞术，荧光原位杂交技术，qRT-PCR				LEF1		LEF1 is not expressed in most CD5-positive MZLs and LPLs; therefore, it is a reliable marker for distinguishing them from CLL/SLL. LEF1 may be expressed in CD5-positive FLs.
31953319	chr22	39516679	39518679	ATF4	Activating transcription factor 4 (ATF4) promotes skeletal muscle atrophy by forming a heterodimer with the transcriptional regulator C/EBPβ.	human	skeletal muscle	High+Lowthroughput	Activating transcription factor 4 (ATF4) promotes skeletal muscle atrophy by forming a heterodimer with the transcriptional regulator C/EBPβ	否		Skeletal muscle atrophy	mouse cell of skeletal muscle	E_01_0084	Western blot, transfection, qPCR, agarose gel electrophoresis	Activating transcription factor 4 (ATF4) promotes skeletal muscle atrophy by forming a heterodimer with the transcriptional regulator C/EBPβ.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Activating transcription factor 4 (ATF4) promotes skeletal muscle atrophy by forming a heterodimer with the transcriptional regulator C/EBPβ.	Immunohistochemical staining	Activating transcription factor 4 (ATF4) promotes skeletal muscle atrophy by forming a heterodimer with the transcriptional regulator C/EBPβ.		Western Blot，转染，qPCR，琼脂糖凝胶电泳				ATF4		Activating transcription factor 4 (ATF4) promotes skeletal muscle atrophy by forming a heterodimer with the transcriptional regulator C/EBPβ.
31952907	chr7	148804371	148806371	EZH2	Taken together, EZH2 in CD4 T cells from RA patients was attenuated, which suppressed FOXP3 transcription through downregulating RUNX1 and upregulating SMAD7 in CD4 T cells, and ultimately suppressed Tregs differentiation. IL17 in RA synovial fluid might promote downregulation of EZH2 in CD4 T cells. Defective EZH2 in CD4 T cells might contribute to Treg deficiency in RA.	human	Connective tissue, peripheral blood	High+Lowthroughput	EZH2 deficiency attenuates Treg differentiation in rheumatoid arthritis	否		Rheumatoid arthritis	synovial cell，peripheral blood mononuclear cell，Jurkat T cell	E_01_0085	Western blot，RT-qPCR	Taken together, EZH2 in CD4 T cells from RA patients was attenuated, which suppressed FOXP3 transcription through downregulating RUNX1 and upregulating SMAD7 in CD4 T cells, and ultimately suppressed Tregs differentiation. IL17 in RA synovial fluid might promote downregulation of EZH2 in CD4 T cells. Defective EZH2 in CD4 T cells might contribute to Treg deficiency in RA.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Taken together, EZH2 in CD4 T cells from RA patients was attenuated, which suppressed FOXP3 transcription through downregulating RUNX1 and upregulating SMAD7 in CD4 T cells, and ultimately suppressed Tregs differentiation. IL17 in RA synovial fluid might promote downregulation of EZH2 in CD4 T cells. Defective EZH2 in CD4 T cells might contribute to Treg deficiency in RA.	Immunohistochemical staining	Taken together, EZH2 in CD4 T cells from RA patients was attenuated, which suppressed FOXP3 transcription through downregulating RUNX1 and upregulating SMAD7 in CD4 T cells, and ultimately suppressed Tregs differentiation. IL17 in RA synovial fluid might promote downregulation of EZH2 in CD4 T cells. Defective EZH2 in CD4 T cells might contribute to Treg deficiency in RA.		Western blot，RT-qPCR				EZH2		Taken together, EZH2 in CD4 T cells from RA patients was attenuated, which suppressed FOXP3 transcription through downregulating RUNX1 and upregulating SMAD7 in CD4 T cells, and ultimately suppressed Tregs differentiation. IL17 in RA synovial fluid might promote downregulation of EZH2 in CD4 T cells. Defective EZH2 in CD4 T cells might contribute to Treg deficiency in RA.
31951295	chr15	88633030	88635030	ISG20	Our findings suggest that ISG20 exerts the anti-HBV activity by acting as a putative repressor binding to the HBV EnhII/Cp region.	human	liver	High+Lowthroughput	Antiviral activity of interferon-stimulated gene 20, as a putative repressor binding to hepatitis B virus enhancer II and core promoter	否		hepatitis B	HepG2，HepG2 NTCP，HepAD38 cell	E_01_0086	Immunohistochemistry, luciferase analysis, transfection, Southern blot, Northern blot, Western blot, RT-PCR, chromatin immunoprecipitation analysis, microarray data analysis	Our findings suggest that ISG20 exerts the anti-HBV activity by acting as a putative repressor binding to the HBV EnhII/Cp region.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Our findings suggest that ISG20 exerts the anti-HBV activity by acting as a putative repressor binding to the HBV EnhII/Cp region.	Immunohistochemical staining	Our findings suggest that ISG20 exerts the anti-HBV activity by acting as a putative repressor binding to the HBV EnhII/Cp region.		免疫组化，荧光素酶分析，转染，Southern blot ，Northern blot，Western blot，RT-PCR ，染色质免疫沉淀分析，微阵列数据分析			ISG20		Our findings suggest that ISG20 exerts the anti-HBV activity by acting as a putative repressor binding to the HBV EnhII/Cp region.	
31938642	chr9	81581120	81583120	TLE1	Frequency of Transducer-like Enhancer of Split 1 Immunohistochemical Expression in Synovial Sarcoma: An Institution-based Cross-sectional Study	human		High+Lowthroughput	Frequency of Transducer-like Enhancer of Split 1 Immunohistochemical Expression in Synovial Sarcoma: An Institution-based Cross-sectional Study	否		Soft tissue sarcoma		E_01_0087	Immunohistochemistry	Frequency of Transducer-like Enhancer of Split 1 Immunohistochemical Expression in Synovial Sarcoma: An Institution-based Cross-sectional Study	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Frequency of Transducer-like Enhancer of Split 1 Immunohistochemical Expression in Synovial Sarcoma: An Institution-based Cross-sectional Study	Immunohistochemical staining	Frequency of Transducer-like Enhancer of Split 1 Immunohistochemical Expression in Synovial Sarcoma: An Institution-based Cross-sectional Study		免疫组化				TLE1		Frequency of Transducer-like Enhancer of Split 1 Immunohistochemical Expression in Synovial Sarcoma: An Institution-based Cross-sectional Study
31937612	chr5	69232027	69234027	CDK7	Targeting Super-Enhancer-Associated Oncogenes in Osteosarcoma with THZ2, a Covalent CDK7 Inhibitor	human	bone	High+Lowthroughput	Targeting Super-Enhancer-Associated Oncogenes in Osteosarcoma with THZ2, a Covalent CDK7 Inhibitor	否		Osteosarcoma	SJSA-1 cell，U2-OS cell，HOS cell，G-292 cell，MNNG/HOS cell，143B cell，MG-63 cell，cementoblast	E_01_0088	Chromatin immunoprecipitation, microarray, transfection, cell viability assay, Transwell, Western blot, RT qPCR	Targeting Super-Enhancer-Associated Oncogenes in Osteosarcoma with THZ2, a Covalent CDK7 Inhibitor	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Targeting Super-Enhancer-Associated Oncogenes in Osteosarcoma with THZ2, a Covalent CDK7 Inhibitor	Immunohistochemical staining	Targeting Super-Enhancer-Associated Oncogenes in Osteosarcoma with THZ2, a Covalent CDK7 Inhibitor		染色质免疫沉淀，微阵列，转染，细胞活力检测，Transwell，Western blot，RT-qPCR			CDK7		Targeting Super-Enhancer-Associated Oncogenes in Osteosarcoma with THZ2, a Covalent CDK7 Inhibitor	
31933869	chr11	113406893	113408893	DRD2	This case-control evaluation involving the Chinese Han population suggests that the rs4648317 and rs7131056 polymorphisms and the haplotype GTGATCGCGCAGGC inside the DRD2 gene could be possible markers to forecast vulnerability to MDD.	human	Peripheral blood	High+Lowthroughput	Functional tag SNPs inside the DRD2 gene as a genetic risk factor for major depressive disorder in the Chinese Han population	是	rs4648317,rs7131056	Major depressive disorder	peripheral blood mononuclear cell	E_01_0089	PCR	This case-control evaluation involving the Chinese Han population suggests that the rs4648317 and rs7131056 polymorphisms and the haplotype GTGATCGCGCAGGC inside the DRD2 gene could be possible markers to forecast vulnerability to MDD.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		This case-control evaluation involving the Chinese Han population suggests that the rs4648317 and rs7131056 polymorphisms and the haplotype GTGATCGCGCAGGC inside the DRD2 gene could be possible markers to forecast vulnerability to MDD.	Immunohistochemical staining	This case-control evaluation involving the Chinese Han population suggests that the rs4648317 and rs7131056 polymorphisms and the haplotype GTGATCGCGCAGGC inside the DRD2 gene could be possible markers to forecast vulnerability to MDD.		PCR			DRD2		This case-control evaluation involving the Chinese Han population suggests that the rs4648317 and rs7131056 polymorphisms and the haplotype GTGATCGCGCAGGC inside the DRD2 gene could be possible markers to forecast vulnerability to MDD.	
31933740	chr9	81580946	81582946	TLE1	TLE1 is a specific and sensitive diagnostic immunomarker for SS and can be helpful to distinguish SS from other mesenchymal neoplasms.	human		High+Lowthroughput	Transducer-like enhancer of split 1 (TLE1) as a novel biomarker for diagnosis of synovial sarcoma correlates with translocation t(X;18): a study of 155 cases in China	否		Synovial sarcoma		E_01_0090	Immunohistochemistry, fluorescence in situ hybridization	TLE1 is a specific and sensitive diagnostic immunomarker for SS and can be helpful to distinguish SS from other mesenchymal neoplasms.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		TLE1 is a specific and sensitive diagnostic immunomarker for SS and can be helpful to distinguish SS from other mesenchymal neoplasms.	Immunohistochemical staining	TLE1 is a specific and sensitive diagnostic immunomarker for SS and can be helpful to distinguish SS from other mesenchymal neoplasms.		免疫组化，荧光原位杂交				TLE1		TLE1 is a specific and sensitive diagnostic immunomarker for SS and can be helpful to distinguish SS from other mesenchymal neoplasms.
31929803	chr4	108044497	108046497	LEF1	We conclude that high LEF1 expression was a favorable prognostic marker which can define AML patient risk and outcome independent from assessing the serum galectin.3 level.	human		High+Lowthroughput	Prognostic Impact of Lymphoid Enhancer Factor 1 Expression and Serum Galectin.3 in Egyptian AML Patients	否		Acute myeloid leukemia		E_01_0091	RT qPCR, ELISA	We conclude that high LEF1 expression was a favorable prognostic marker which can define AML patient risk and outcome independent from assessing the serum galectin.3 level.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We conclude that high LEF1 expression was a favorable prognostic marker which can define AML patient risk and outcome independent from assessing the serum galectin.3 level.	Immunohistochemical staining	We conclude that high LEF1 expression was a favorable prognostic marker which can define AML patient risk and outcome independent from assessing the serum galectin.3 level.		RT-qPCR，联酶免疫吸附反应				LEF1		We conclude that high LEF1 expression was a favorable prognostic marker which can define AML patient risk and outcome independent from assessing the serum galectin.3 level.
31928966	chr6	10978082	10980082	ELOVL2	rs953413 Regulates Polyunsaturated Fatty Acid Metabolism by Modulating ELOVL2 Expression	human	liver	High+Lowthroughput	rs953413 Regulates Polyunsaturated Fatty Acid Metabolism by Modulating ELOVL2 Expression	是	rs953413	liver cancer	HepG2 cell	E_01_0092	As qPCR, chip SEQ, gene knockdown, QRT PCR, chromatin immunoprecipitation, luciferase reporter	rs953413 Regulates Polyunsaturated Fatty Acid Metabolism by Modulating ELOVL2 Expression	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		rs953413 Regulates Polyunsaturated Fatty Acid Metabolism by Modulating ELOVL2 Expression	Immunohistochemical staining	rs953413 Regulates Polyunsaturated Fatty Acid Metabolism by Modulating ELOVL2 Expression		AS-qPCR，ChIP-seq，基因敲除，qRT-PCR，染色质免疫沉淀，荧光素酶报告基因			ELOVL2		rs953413 Regulates Polyunsaturated Fatty Acid Metabolism by Modulating ELOVL2 Expression	
31914533	chr19	19142448	19144448	MEF2B	The expression of MEF2B in MCL is related to the pathological subtypes, structural subtypes and the expression of SOX11, but not to the proliferation and prognosis. 	human		High+Lowthroughput	Expression of myocyte enhancer factor 2B in mantle cell lymphoma and its clinical significance	否		Mantle cell lymphoma		E_01_0093	He staining, immunohistochemistry, fluorescence in situ hybridization	The expression of MEF2B in MCL is related to the pathological subtypes, structural subtypes and the expression of SOX11, but not to the proliferation and prognosis. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The expression of MEF2B in MCL is related to the pathological subtypes, structural subtypes and the expression of SOX11, but not to the proliferation and prognosis. 	Immunohistochemical staining	The expression of MEF2B in MCL is related to the pathological subtypes, structural subtypes and the expression of SOX11, but not to the proliferation and prognosis. 		HE染色，免疫组化，荧光原位杂交			MEF2B		The expression of MEF2B in MCL is related to the pathological subtypes, structural subtypes and the expression of SOX11, but not to the proliferation and prognosis. 	
31914083	chr5	51380063	51382063	ISL1	ISL1 promotes cardiomyocyte differentiation and plays important roles in heart development.	human		High+Lowthroughput	Correlations between ISL1 rs1017 polymorphism and congenital heart disease risk: A PRISMA-compliant meta-analysis	是	rs1017	Congenital heart disease	cardiac muscle cell (sensu Arthopoda)	E_01_0094		ISL1 promotes cardiomyocyte differentiation and plays important roles in heart development.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		ISL1 promotes cardiomyocyte differentiation and plays important roles in heart development.	Immunohistochemical staining	ISL1 promotes cardiomyocyte differentiation and plays important roles in heart development.						ISL1		ISL1 promotes cardiomyocyte differentiation and plays important roles in heart development.
31910882	chr11	306685	308685	IFITM1	Increased expression of the IFITM1 gene is required for LPS-stimulated hMSC migration. 	human	bone marrow	High+Lowthroughput	Epigenetic regulation of IFITM1 expression in lipopolysaccharide-stimulated human mesenchymal stromal cells	否			hMSC cell	E_01_0095	QRT PCR, ELISA, Western blot, immunocytochemistry, chromatin immunoprecipitation PCR, chip SEQ, scratch assay, gene knockdown, luciferase reporter assay	Increased expression of the IFITM1 gene is required for LPS-stimulated hMSC migration. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Increased expression of the IFITM1 gene is required for LPS-stimulated hMSC migration. 	Immunohistochemical staining	Increased expression of the IFITM1 gene is required for LPS-stimulated hMSC migration. 		qRT-PCR，酶联免疫吸附试验，Western blot，免疫细胞化学，染色质免疫沉淀PCR，ChIP-seq，划痕实验，基因敲降，荧光素酶报告试验			IFITM1		Increased expression of the IFITM1 gene is required for LPS-stimulated hMSC migration. 	
31902945	chr22	27745785	27747785	MN1	Ectopia associated MN1 fusions and aberrant activation in myeloid neoplasms with t(12;22)(p13;q12)	human	bone marrow	High+Lowthroughput	Ectopia associated MN1 fusions and aberrant activation in myeloid neoplasms with t(12;22)(p13;q12)	否		Myeloid neoplasms	Bone marrow monocytes	E_01_0096	Whole genome sequencing, RT-PCR, fluorescence in situ hybridization, Sanger sequencing	Ectopia associated MN1 fusions and aberrant activation in myeloid neoplasms with t(12;22)(p13;q12)	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Ectopia associated MN1 fusions and aberrant activation in myeloid neoplasms with t(12;22)(p13;q12)	Immunohistochemical staining	Ectopia associated MN1 fusions and aberrant activation in myeloid neoplasms with t(12;22)(p13;q12)		全基因组测序，RT-PCR，荧光原位杂交，sanger测序			MN1		Ectopia associated MN1 fusions and aberrant activation in myeloid neoplasms with t(12;22)(p13;q12)	
31900258	chr5	1250197	1252197	TERT	Epigenetically cotargeting Brd4 and Cdks suppresses human neuroblastoma with TERT overexpression by inhibiting the TERT-associated gene expression networks.	human		High+Lowthroughput		否		Neuroblastoma	neuroblastoma cells，SK-N-AS cell	E_01_0097	Chip – qPCR, RT qPCR, Western blot, cell viability assay	Epigenetically cotargeting Brd4 and Cdks suppresses human neuroblastoma with TERT overexpression by inhibiting the TERT-associated gene expression networks.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Epigenetically cotargeting Brd4 and Cdks suppresses human neuroblastoma with TERT overexpression by inhibiting the TERT-associated gene expression networks.	Immunohistochemical staining	Epigenetically cotargeting Brd4 and Cdks suppresses human neuroblastoma with TERT overexpression by inhibiting the TERT-associated gene expression networks.		ChIP–qPCR，RT-qPCR，Western blot，细胞活力检测				TERT		Epigenetically cotargeting Brd4 and Cdks suppresses human neuroblastoma with TERT overexpression by inhibiting the TERT-associated gene expression networks.
31899875	chr14	100776332	100778332	MEG3	Furthermore, as a target gene of MIR-376B-3P, HMGA2 served as an oncogene in pituitary adenoma and could be negatively regulated by MEG3 via enriching MIR-376B-3P.	human	ovarian follicle	High+Lowthroughput	MEG3/MIR-376B-3P/HMGA2 axis is involved in pituitary tumor invasiveness	否		Pituitary tumors		E_01_0098	Dual luciferase reporter assay, immunofluorescence, IHC, RT qPCR, Western blot, flow cytometry, TUNEL staining, transfection, cell viability assay, Transwell, scratch assay	Furthermore, as a target gene of MIR-376B-3P, HMGA2 served as an oncogene in pituitary adenoma and could be negatively regulated by MEG3 via enriching MIR-376B-3P.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Furthermore, as a target gene of MIR-376B-3P, HMGA2 served as an oncogene in pituitary adenoma and could be negatively regulated by MEG3 via enriching MIR-376B-3P.	Immunohistochemical staining	Furthermore, as a target gene of MIR-376B-3P, HMGA2 served as an oncogene in pituitary adenoma and could be negatively regulated by MEG3 via enriching MIR-376B-3P.		双荧光素酶报告基因，免疫荧光，，免疫组化，RT-qPCR，Western blot，流式细胞术，TUNEL染色，转染，细胞活力检测，Transwell，划痕实验			MEG3		Furthermore, as a target gene of MIR-376B-3P, HMGA2 served as an oncogene in pituitary adenoma and could be negatively regulated by MEG3 via enriching MIR-376B-3P.	
31897846	chr19	2974615	2976615	TLE6	Expanding the genetic and phenotypic spectrum of female infertility caused by TLE6 mutations	human		High+Lowthroughput	Expanding the genetic and phenotypic spectrum of female infertility caused by TLE6 mutations	否		Infertility		E_01_0099	Whole exome sequencing, Sanger sequencing	Expanding the genetic and phenotypic spectrum of female infertility caused by TLE6 mutations	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Expanding the genetic and phenotypic spectrum of female infertility caused by TLE6 mutations	Immunohistochemical staining	Expanding the genetic and phenotypic spectrum of female infertility caused by TLE6 mutations		全外显子组测序，Sanger测序			TLE6		Expanding the genetic and phenotypic spectrum of female infertility caused by TLE6 mutations	
31897220	chr1	6098734	6100734	CHD5	In conclusion, since CHD5 regulated multiple cancer-related targets, its expression may be a useful prognostic biomarker in patients with gastric cancer.	human	Stomach, cervix	High+Lowthroughput	Clinical significance of chromatin remodeling factor CHD5 expression in gastric cancer	否		gastric cancer	AGS cell, KATO III cell, MKN45 cell, NCI-N87 cell, NUGC-3 cell, OCUM‑1 cell,HeLa cell 	E_01_0100	Immunohistochemistry, scratch assay, cell viability assay, Transwell, Western blot, RT ＾ PCR	In conclusion, since CHD5 regulated multiple cancer-related targets, its expression may be a useful prognostic biomarker in patients with gastric cancer.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In conclusion, since CHD5 regulated multiple cancer-related targets, its expression may be a useful prognostic biomarker in patients with gastric cancer.	Immunohistochemical staining	In conclusion, since CHD5 regulated multiple cancer-related targets, its expression may be a useful prognostic biomarker in patients with gastric cancer.		免疫组化，划痕实验，细胞活力检测，Transwell，western blot，RT‑PCR			CHD5		In conclusion, since CHD5 regulated multiple cancer-related targets, its expression may be a useful prognostic biomarker in patients with gastric cancer.	
31897216	chr4	7751333	7753333	AFAP1-AS1	 In conclusion, AFAP1-AS1 accelerates the proliferative and metastatic abilities of A549/DDP cells, whereas inhibits the apoptosis of A549/DDP cells, by interacting with EZH2 to activate the PI3K/AKT pathway; thus, inducing DDP resistance in NSCLC.	human	lung	High+Lowthroughput	AFAP1-AS1 induces cisplatin resistance in non-small cell lung cancer through PI3K/AKT pathway	否		Non small cell lung cancer	A549 cell	E_01_0101	RNA immunoprecipitation, flow cytometry, Western blot, Transwell, RT ‐qpcr	 In conclusion, AFAP1-AS1 accelerates the proliferative and metastatic abilities of A549/DDP cells, whereas inhibits the apoptosis of A549/DDP cells, by interacting with EZH2 to activate the PI3K/AKT pathway; thus, inducing DDP resistance in NSCLC.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		 In conclusion, AFAP1-AS1 accelerates the proliferative and metastatic abilities of A549/DDP cells, whereas inhibits the apoptosis of A549/DDP cells, by interacting with EZH2 to activate the PI3K/AKT pathway; thus, inducing DDP resistance in NSCLC.	Immunohistochemical staining	 In conclusion, AFAP1-AS1 accelerates the proliferative and metastatic abilities of A549/DDP cells, whereas inhibits the apoptosis of A549/DDP cells, by interacting with EZH2 to activate the PI3K/AKT pathway; thus, inducing DDP resistance in NSCLC.		RNA免疫沉淀，流式细胞术，Western blot，Transwell，RT‑qPCR			AFAP1-AS1		 In conclusion, AFAP1-AS1 accelerates the proliferative and metastatic abilities of A549/DDP cells, whereas inhibits the apoptosis of A549/DDP cells, by interacting with EZH2 to activate the PI3K/AKT pathway; thus, inducing DDP resistance in NSCLC.	
31893185	chr9	81580729	81582729	TLE1	TLE1 may be a reliable immunostain for diagnosing SS, but its expression is not limited to SS. Its expression should be interpreted in the light of morphological features and a panel of antibodies.	human		High+Lowthroughput	Is TLE1 Expression Limited to Synovial Sarcoma? Our Experience at Shifa International Hospital, Pakistan	否		Synovial sarcoma		E_01_0102	Immunohistochemistry	TLE1 may be a reliable immunostain for diagnosing SS, but its expression is not limited to SS. Its expression should be interpreted in the light of morphological features and a panel of antibodies.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		TLE1 may be a reliable immunostain for diagnosing SS, but its expression is not limited to SS. Its expression should be interpreted in the light of morphological features and a panel of antibodies.	Immunohistochemical staining	TLE1 may be a reliable immunostain for diagnosing SS, but its expression is not limited to SS. Its expression should be interpreted in the light of morphological features and a panel of antibodies.		免疫组化				TLE1		TLE1 may be a reliable immunostain for diagnosing SS, but its expression is not limited to SS. Its expression should be interpreted in the light of morphological features and a panel of antibodies.
31892537	chr10	102103573	102105573	LDB1	Our structural and biochemical data provide a much-anticipated structural basis for understanding how LDB1 and the LDB1/SSBP interactions form the structural core of diverse complexes mediating cell choice decisions and long-range enhancer-promoter interactions.	human	blood	High+Lowthroughput	Crystal structure of human LDB1 in complex with SSBP2	否			erythrocyte	E_01_0103	pull-down	Our structural and biochemical data provide a much-anticipated structural basis for understanding how LDB1 and the LDB1/SSBP interactions form the structural core of diverse complexes mediating cell choice decisions and long-range enhancer-promoter interactions.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Our structural and biochemical data provide a much-anticipated structural basis for understanding how LDB1 and the LDB1/SSBP interactions form the structural core of diverse complexes mediating cell choice decisions and long-range enhancer-promoter interactions.	Immunohistochemical staining	Our structural and biochemical data provide a much-anticipated structural basis for understanding how LDB1 and the LDB1/SSBP interactions form the structural core of diverse complexes mediating cell choice decisions and long-range enhancer-promoter interactions.		pull-down			LDB1		Our structural and biochemical data provide a much-anticipated structural basis for understanding how LDB1 and the LDB1/SSBP interactions form the structural core of diverse complexes mediating cell choice decisions and long-range enhancer-promoter interactions.	
31891591	chr7	148804482	148806482	EZH2	A systems approach identifies Enhancer of Zeste Homolog 2 (EZH2) as a protective factor in epilepsy	human		High+Lowthroughput	A systems approach identifies Enhancer of Zeste Homolog 2 (EZH2) as a protective factor in epilepsy	否		epilepsy		E_01_0104	Western blot，qRT-PCR，LC-MS	A systems approach identifies Enhancer of Zeste Homolog 2 (EZH2) as a protective factor in epilepsy	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		A systems approach identifies Enhancer of Zeste Homolog 2 (EZH2) as a protective factor in epilepsy	Immunohistochemical staining	A systems approach identifies Enhancer of Zeste Homolog 2 (EZH2) as a protective factor in epilepsy		Western blot，qRT-PCR，LC-MS				EZH2		A systems approach identifies Enhancer of Zeste Homolog 2 (EZH2) as a protective factor in epilepsy
31890812	chr2	60447611	60449611	BCL11A	Expression analysis data of BCL11A and γ-globin genes in KU812 and KG-1 cell lines after CRISPR/Cas9-mediated BCL11A enhancer deletion.	human	Kidney, peripheral blood, bone marrow	High+Lowthroughput	Expression analysis data of BCL11A and γ-globin genes in KU812 and KG-1 cell lines after CRISPR/Cas9-mediated BCL11A enhancer deletion	否		β- Thalassemia disorders	HEK293T cell， KU812 cell，KG-1 cell	E_01_0105	Agarose gel electrophoresis, QRT PCR	Expression analysis data of BCL11A and γ-globin genes in KU812 and KG-1 cell lines after CRISPR/Cas9-mediated BCL11A enhancer deletion.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Expression analysis data of BCL11A and γ-globin genes in KU812 and KG-1 cell lines after CRISPR/Cas9-mediated BCL11A enhancer deletion.	Immunohistochemical staining	Expression analysis data of BCL11A and γ-globin genes in KU812 and KG-1 cell lines after CRISPR/Cas9-mediated BCL11A enhancer deletion.		琼脂糖凝胶电泳， qRT-PCR			BCL11A		Expression analysis data of BCL11A and γ-globin genes in KU812 and KG-1 cell lines after CRISPR/Cas9-mediated BCL11A enhancer deletion.	
31888703	chr3	12284215	12286215	PPARG	Enhancer polymorphism rs10865710 associated with traumatic sepsis is a regulator of PPARG gene expression	human		High+Lowthroughput	Enhancer polymorphism rs10865710 associated with traumatic sepsis is a regulator of PPARG gene expression	是	rs10865710	Traumatic sepsis		E_01_0106	Western blot, dual luciferase gene reporter	Enhancer polymorphism rs10865710 associated with traumatic sepsis is a regulator of PPARG gene expression	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Enhancer polymorphism rs10865710 associated with traumatic sepsis is a regulator of PPARG gene expression	Immunohistochemical staining	Enhancer polymorphism rs10865710 associated with traumatic sepsis is a regulator of PPARG gene expression		Western blot，双荧光素酶基因报告				PPARG		Enhancer polymorphism rs10865710 associated with traumatic sepsis is a regulator of PPARG gene expression
31886719	chr11	100684149	100686149	ARHGAP42	First, RBPJ and TEAD1 converge at an intronic enhancer to regulate ARHGAP42 expression in SMCs. Second, TEAD1 and RBPJ interact physically and bind cooperatively to the ARHGAP42 enhancer. Third, miR505 interacts with the ARHGAP42 3'-UTR to facilitate its degradation. Finally, LncRNA, AK124326, inhibits ARHGAP42 transcription.	human	Aortic smooth muscle, bronchial smooth muscle	High+Lowthroughput	Transcriptional and posttranscriptional regulation of the SMC-selective blood pressure-associated gene, ARHGAP42	是	rs604723	Blood pressure regulation	HUAOSMC cell，HUBRSMC cell	E_01_0107	Luciferase assay, immunoprecipitation, QRT PCR, chromatin immunoprecipitation assay, Western blot, electrophoretic mobility shift assay, immunofluorescence	First, RBPJ and TEAD1 converge at an intronic enhancer to regulate ARHGAP42 expression in SMCs. Second, TEAD1 and RBPJ interact physically and bind cooperatively to the ARHGAP42 enhancer. Third, miR505 interacts with the ARHGAP42 3'-UTR to facilitate its degradation. Finally, LncRNA, AK124326, inhibits ARHGAP42 transcription.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		First, RBPJ and TEAD1 converge at an intronic enhancer to regulate ARHGAP42 expression in SMCs. Second, TEAD1 and RBPJ interact physically and bind cooperatively to the ARHGAP42 enhancer. Third, miR505 interacts with the ARHGAP42 3'-UTR to facilitate its degradation. Finally, LncRNA, AK124326, inhibits ARHGAP42 transcription.	Immunohistochemical staining	First, RBPJ and TEAD1 converge at an intronic enhancer to regulate ARHGAP42 expression in SMCs. Second, TEAD1 and RBPJ interact physically and bind cooperatively to the ARHGAP42 enhancer. Third, miR505 interacts with the ARHGAP42 3'-UTR to facilitate its degradation. Finally, LncRNA, AK124326, inhibits ARHGAP42 transcription.		荧光素酶分析，免疫沉淀，qRT-PCR，染色质免疫沉淀实验，Western blot，电泳迁移率分析，免疫荧光			ARHGAP42		First, RBPJ and TEAD1 converge at an intronic enhancer to regulate ARHGAP42 expression in SMCs. Second, TEAD1 and RBPJ interact physically and bind cooperatively to the ARHGAP42 enhancer. Third, miR505 interacts with the ARHGAP42 3'-UTR to facilitate its degradation. Finally, LncRNA, AK124326, inhibits ARHGAP42 transcription.	
31886200	chr7	148804829	148806829	EZH2	Our results suggest a scale of measure for EZH2 expression in pediatric MDS, where aberrant EZH2 expression may be a potential biomarker of disease evolution.	human	bone marrow	High+Lowthroughput	Aberrant Expression of EZH2 in Pediatric Patients with Myelodysplastic Syndrome: A Potential Biomarker of Leukemic Evolution	否		Pediatric myelodysplastic syndrome	bone marrow cell	E_01_0108	qRT–PCR	Our results suggest a scale of measure for EZH2 expression in pediatric MDS, where aberrant EZH2 expression may be a potential biomarker of disease evolution.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Our results suggest a scale of measure for EZH2 expression in pediatric MDS, where aberrant EZH2 expression may be a potential biomarker of disease evolution.	Immunohistochemical staining	Our results suggest a scale of measure for EZH2 expression in pediatric MDS, where aberrant EZH2 expression may be a potential biomarker of disease evolution.		qRT–PCR				EZH2		Our results suggest a scale of measure for EZH2 expression in pediatric MDS, where aberrant EZH2 expression may be a potential biomarker of disease evolution.
31882553	chr19	15232668	15234668	BRD4	Since bromodomain-containing protein 4 (BRD4) facilitates the transcription of genes important for neoplastic cells in a cancer-type specific manner, BRD4-regulated molecules may also include therapeutic targets for mantle cell lymphoma (MCL), a treatment-refractory subtype of malignant lymphoma.	human	lymph	High+Lowthroughput	BRD4-Regulated Molecular Targets in Mantle Cell Lymphoma: Insights into Targeted Therapeutic Approach	否		Mantle cell lymphoma	JVM-2 cell，MINO cell，Z138 cell，KPUM-YY1 cell	E_01_0109	Cell viability assay, Western blot, QRT PCR, chromatin immunoprecipitation	Since bromodomain-containing protein 4 (BRD4) facilitates the transcription of genes important for neoplastic cells in a cancer-type specific manner, BRD4-regulated molecules may also include therapeutic targets for mantle cell lymphoma (MCL), a treatment-refractory subtype of malignant lymphoma.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Since bromodomain-containing protein 4 (BRD4) facilitates the transcription of genes important for neoplastic cells in a cancer-type specific manner, BRD4-regulated molecules may also include therapeutic targets for mantle cell lymphoma (MCL), a treatment-refractory subtype of malignant lymphoma.	Immunohistochemical staining	Since bromodomain-containing protein 4 (BRD4) facilitates the transcription of genes important for neoplastic cells in a cancer-type specific manner, BRD4-regulated molecules may also include therapeutic targets for mantle cell lymphoma (MCL), a treatment-refractory subtype of malignant lymphoma.		细胞活力检测，Western blot，qRT-PCR，染色质免疫沉淀				BRD4		Since bromodomain-containing protein 4 (BRD4) facilitates the transcription of genes important for neoplastic cells in a cancer-type specific manner, BRD4-regulated molecules may also include therapeutic targets for mantle cell lymphoma (MCL), a treatment-refractory subtype of malignant lymphoma.
31878072	chr1	153659104	153661104	ILF2	Therefore, we present a distinct mechanism by which EV71 antagonizes ILF2-mediated antiviral effects by inhibiting ILF2 expression and promoting ILF2 translocation from the nucleus to the cytoplasm through its 2B protein.	human	Kidney, peripheral blood	High+Lowthroughput	Enterovirus 71 Represses Interleukin Enhancer-Binding Factor 2 Production and Nucleus Translocation to Antagonize ILF2 Antiviral Effects	否		antiviral	HEK293T cell、Vero cell、RD cell，thp-1 cell	E_01_0110	RT qPCR, Western blot, CO immunoprecipitation, immunofluorescence	Therefore, we present a distinct mechanism by which EV71 antagonizes ILF2-mediated antiviral effects by inhibiting ILF2 expression and promoting ILF2 translocation from the nucleus to the cytoplasm through its 2B protein.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Therefore, we present a distinct mechanism by which EV71 antagonizes ILF2-mediated antiviral effects by inhibiting ILF2 expression and promoting ILF2 translocation from the nucleus to the cytoplasm through its 2B protein.	Immunohistochemical staining	Therefore, we present a distinct mechanism by which EV71 antagonizes ILF2-mediated antiviral effects by inhibiting ILF2 expression and promoting ILF2 translocation from the nucleus to the cytoplasm through its 2B protein.		RT-qPCR，Western blot，免疫共沉淀，免疫荧光			ILF2		Therefore, we present a distinct mechanism by which EV71 antagonizes ILF2-mediated antiviral effects by inhibiting ILF2 expression and promoting ILF2 translocation from the nucleus to the cytoplasm through its 2B protein.	
31866294	chr7	148804551	148806551	EZH2	Structural Basis of the Interaction Between Ubiquitin Specific Protease 7 and Enhancer of Zeste Homolog 2.	human	colon	High+Lowthroughput	Structural Basis of the Interaction Between Ubiquitin Specific Protease 7 and Enhancer of Zeste Homolog 2	否		tumour	HCT116 cell	E_01_0111	Fluorescence polarization assay, Western blot, CO immunoprecipitation	Structural Basis of the Interaction Between Ubiquitin Specific Protease 7 and Enhancer of Zeste Homolog 2.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Structural Basis of the Interaction Between Ubiquitin Specific Protease 7 and Enhancer of Zeste Homolog 2.	Immunohistochemical staining	Structural Basis of the Interaction Between Ubiquitin Specific Protease 7 and Enhancer of Zeste Homolog 2.		荧光偏振分析，Western Blot，共免疫沉淀				EZH2		Structural Basis of the Interaction Between Ubiquitin Specific Protease 7 and Enhancer of Zeste Homolog 2.
31866047	chr20	59860441	59862441	SYCP2	SYCP2 Translocation-Mediated Dysregulation and Frameshift Variants Cause Human Male Infertility	human	lymph	High+Lowthroughput	SYCP2 Translocation-Mediated Dysregulation and Frameshift Variants Cause Human Male Infertility	是	rs568645874,rs199662252,rs45568532,rs551180067,rs11549332		Lymphoblast	E_01_0112	QRT PCR, Western blot, Sanger sequencing, PAS staining, hematoxylin staining	SYCP2 Translocation-Mediated Dysregulation and Frameshift Variants Cause Human Male Infertility	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		SYCP2 Translocation-Mediated Dysregulation and Frameshift Variants Cause Human Male Infertility	Immunohistochemical staining	SYCP2 Translocation-Mediated Dysregulation and Frameshift Variants Cause Human Male Infertility		qRT-PCR，Western Blot，Sanger测序，PAS染色，苏木精染色			SYCP2		SYCP2 Translocation-Mediated Dysregulation and Frameshift Variants Cause Human Male Infertility	
31864713	chr7	44101569	44103569	AEBP1	Adipocyte enhancer binding protein 1 (AEBP1) knockdown suppresses human glioma cell proliferation, invasion and induces early apoptosis	human	brain	High+Lowthroughput	Adipocyte enhancer binding protein 1 (AEBP1) knockdown suppresses human glioma cell proliferation, invasion and induces early apoptosis	否		Gliomas	U87MG cell，U251 MG cell	E_01_0113	Western blot, immunohistochemistry, QRT PCR, cell viability assay, Transwell, immunofluorescence, flow cytometry	Adipocyte enhancer binding protein 1 (AEBP1) knockdown suppresses human glioma cell proliferation, invasion and induces early apoptosis	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Adipocyte enhancer binding protein 1 (AEBP1) knockdown suppresses human glioma cell proliferation, invasion and induces early apoptosis	Immunohistochemical staining	Adipocyte enhancer binding protein 1 (AEBP1) knockdown suppresses human glioma cell proliferation, invasion and induces early apoptosis		Western-blot，免疫组化，qRT-PCR，细胞活力检测，Transwell，免疫荧光，流式细胞术			AEBP1		Adipocyte enhancer binding protein 1 (AEBP1) knockdown suppresses human glioma cell proliferation, invasion and induces early apoptosis	
31861475	chr9	36570240	36572240	MELK	Inhibition of MELK Protooncogene as an Innovative Treatment for Intrahepatic Cholangiocarcinoma	human	bile duct	High+Lowthroughput	Inhibition of MELK Protooncogene as an Innovative Treatment for Intrahepatic Cholangiocarcinoma	否		Intrahepatic cholangiocarcinoma	iCCA cell	E_01_0114	RT-PCR, immunohistochemistry	Inhibition of MELK Protooncogene as an Innovative Treatment for Intrahepatic Cholangiocarcinoma	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Inhibition of MELK Protooncogene as an Innovative Treatment for Intrahepatic Cholangiocarcinoma	Immunohistochemical staining	Inhibition of MELK Protooncogene as an Innovative Treatment for Intrahepatic Cholangiocarcinoma		RT-PCR，免疫组织化学			MELK		Inhibition of MELK Protooncogene as an Innovative Treatment for Intrahepatic Cholangiocarcinoma	
31860165	chr4	52709533	52711533	DANCR	The long non-coding RNA DANCR regulates the inflammatory phenotype of breast cancer cells and promotes breast cancer progression via EZH2-dependent suppression of SOCS3 transcription	human	breast	High+Lowthroughput	The long non-coding RNA DANCR regulates the inflammatory phenotype of breast cancer cells and promotes breast cancer progression via EZH2-dependent suppression of SOCS3 transcription	否		mammary cancer	breast cancer cells，mammary gland epithelial cell	E_01_0115	QRT PCR, cell viability assay, ELISA, Western blot, RNA immunoprecipitation, chromatin immunoprecipitation, Transwell	The long non-coding RNA DANCR regulates the inflammatory phenotype of breast cancer cells and promotes breast cancer progression via EZH2-dependent suppression of SOCS3 transcription	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The long non-coding RNA DANCR regulates the inflammatory phenotype of breast cancer cells and promotes breast cancer progression via EZH2-dependent suppression of SOCS3 transcription	Immunohistochemical staining	The long non-coding RNA DANCR regulates the inflammatory phenotype of breast cancer cells and promotes breast cancer progression via EZH2-dependent suppression of SOCS3 transcription		qRT-PCR，细胞活力检测，ELISA，Western blot，RNA免疫沉淀，染色质免疫沉淀，Transwell			DANCR		The long non-coding RNA DANCR regulates the inflammatory phenotype of breast cancer cells and promotes breast cancer progression via EZH2-dependent suppression of SOCS3 transcription	
31858557	chr15	42735912	42737912	TTBK2	Circ-TTBK2/miR-520b/EZH2 axis modulated cell proliferation, apoptosis, and invasion in glioma cell lines, and might serve as potential targets for glioma diagnosis and therapy.	human	brain	High+Lowthroughput	Circular RNA TTBK2 promotes the development of human glioma cells via miR-520b/EZH2 axis	否		Gliomas	A172 cell，U251 cell，astrocyte cell	E_01_0116	Transfection, QRT PCR, Western blot, flow cytometry, Transwell, dual luciferase reporter assay	Circ-TTBK2/miR-520b/EZH2 axis modulated cell proliferation, apoptosis, and invasion in glioma cell lines, and might serve as potential targets for glioma diagnosis and therapy.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Circ-TTBK2/miR-520b/EZH2 axis modulated cell proliferation, apoptosis, and invasion in glioma cell lines, and might serve as potential targets for glioma diagnosis and therapy.	Immunohistochemical staining	Circ-TTBK2/miR-520b/EZH2 axis modulated cell proliferation, apoptosis, and invasion in glioma cell lines, and might serve as potential targets for glioma diagnosis and therapy.		转染，qRT-PCR，Western Blot，流式细胞术，Transwell，双荧光素酶报告分析				TTBK2		Circ-TTBK2/miR-520b/EZH2 axis modulated cell proliferation, apoptosis, and invasion in glioma cell lines, and might serve as potential targets for glioma diagnosis and therapy.
31856860	chr20	50188118	50190118	CEBPB	 Analysis of transcription factor targets showed in both CS and SS patients, an enrichment of CCAAT-enhancer-binding protein beta (CEBPB) targets in genes downregulated over time and an enrichment of E2F targets in genes with an increasing expression trend.	human		High+Lowthroughput	A longitudinal study highlights shared aspects of the transcriptomic response to cardiogenic and septic shock	否		Cardiogenic and septic shock		E_01_0117	RNA sequencing	 Analysis of transcription factor targets showed in both CS and SS patients, an enrichment of CCAAT-enhancer-binding protein beta (CEBPB) targets in genes downregulated over time and an enrichment of E2F targets in genes with an increasing expression trend.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		 Analysis of transcription factor targets showed in both CS and SS patients, an enrichment of CCAAT-enhancer-binding protein beta (CEBPB) targets in genes downregulated over time and an enrichment of E2F targets in genes with an increasing expression trend.	Immunohistochemical staining	 Analysis of transcription factor targets showed in both CS and SS patients, an enrichment of CCAAT-enhancer-binding protein beta (CEBPB) targets in genes downregulated over time and an enrichment of E2F targets in genes with an increasing expression trend.		RNA测序				CEBPB		 Analysis of transcription factor targets showed in both CS and SS patients, an enrichment of CCAAT-enhancer-binding protein beta (CEBPB) targets in genes downregulated over time and an enrichment of E2F targets in genes with an increasing expression trend.
31851943	chr19	1606379	1608379	TCF3	Loss-of-function studies of TCF3 confirm the role of TCF3 in mediating condition-specific enhancer-promoter interactions and gene regulation in fetal HSCs.	human	bone marrow	High+Lowthroughput	Spatial Genome Re-organization between Fetal and Adult Hematopoietic Stem Cells	否			HPC-7 cell	E_01_0118	Dna-fish, Western blot, flow cytometry	Loss-of-function studies of TCF3 confirm the role of TCF3 in mediating condition-specific enhancer-promoter interactions and gene regulation in fetal HSCs.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Loss-of-function studies of TCF3 confirm the role of TCF3 in mediating condition-specific enhancer-promoter interactions and gene regulation in fetal HSCs.	Immunohistochemical staining	Loss-of-function studies of TCF3 confirm the role of TCF3 in mediating condition-specific enhancer-promoter interactions and gene regulation in fetal HSCs.		DNA-FISH， Western blot，流式细胞术				TCF7L1		Loss-of-function studies of TCF3 confirm the role of TCF3 in mediating condition-specific enhancer-promoter interactions and gene regulation in fetal HSCs.
31845224	chr2	26345405	26347405	Notch1	Taken together, these data suggest that Notch1 drives ICC formation and proliferation; downregulation of Notch1 induces apoptosis in ICC cells; Notch1 signaling may serve as a novel therapeutic target for the treatment of ICC.	mouse	gallbladder	High+Lowthroughput	Notch1 Drives the Formation and Proliferation of Intrahepatic Cholangiocarcinoma	否		Intrahepatic cholangiocarcinoma	BC-939 cell，RBE cell	E_01_0119	Western blot, flow cytometry, Western blot, immunohistochemistry, immunofluorescence, QRT PCR	Taken together, these data suggest that Notch1 drives ICC formation and proliferation; downregulation of Notch1 induces apoptosis in ICC cells; Notch1 signaling may serve as a novel therapeutic target for the treatment of ICC.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Taken together, these data suggest that Notch1 drives ICC formation and proliferation; downregulation of Notch1 induces apoptosis in ICC cells; Notch1 signaling may serve as a novel therapeutic target for the treatment of ICC.	Immunohistochemical staining	Taken together, these data suggest that Notch1 drives ICC formation and proliferation; downregulation of Notch1 induces apoptosis in ICC cells; Notch1 signaling may serve as a novel therapeutic target for the treatment of ICC.		Western blot， 流式细胞术，Western Blot，免疫组化，免疫荧光，qRT-PCR			Notch1		Taken together, these data suggest that Notch1 drives ICC formation and proliferation; downregulation of Notch1 induces apoptosis in ICC cells; Notch1 signaling may serve as a novel therapeutic target for the treatment of ICC.	
31843716	chr18	55219904	55221904	TCF4	3D-microenvironments initiate TCF4 expression rescuing nuclear β-catenin activity in MCF-7 breast cancer cells	human	breast	High+Lowthroughput	3D-microenvironments initiate TCF4 expression rescuing nuclear β-catenin activity in MCF-7 breast cancer cells	否		mammary cancer	MCF-7 cell，MDA-MB-231 cell	E_01_0120	Flow cytometry, immunofluorescence, Western blot	3D-microenvironments initiate TCF4 expression rescuing nuclear β-catenin activity in MCF-7 breast cancer cells	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		3D-microenvironments initiate TCF4 expression rescuing nuclear β-catenin activity in MCF-7 breast cancer cells	Immunohistochemical staining	3D-microenvironments initiate TCF4 expression rescuing nuclear β-catenin activity in MCF-7 breast cancer cells		流式细胞术，免疫荧光，Western blot				TCF4		3D-microenvironments initiate TCF4 expression rescuing nuclear β-catenin activity in MCF-7 breast cancer cells
31843273	chr7	148804648	148806648	EZH2	Our results confirm the differential expression of EZH2 in uterine cancers compared to normal tissues.	human		High+Lowthroughput	Overexpression of enhance of Zeste homolog 2 (EZH2) in endometrial carcinoma: An NRG Oncology/Gynecologic Oncology Group Study	否		Endometrial cancer		E_01_0121	RT-PCR，Western blot	Our results confirm the differential expression of EZH2 in uterine cancers compared to normal tissues.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Our results confirm the differential expression of EZH2 in uterine cancers compared to normal tissues.	Immunohistochemical staining	Our results confirm the differential expression of EZH2 in uterine cancers compared to normal tissues.		RT-PCR，Western blot				EZH2		Our results confirm the differential expression of EZH2 in uterine cancers compared to normal tissues.
31836590	chr1	145918614	145920614	RBM8A	Thrombocytopenia-absent radii (TAR) syndrome, characterized by neonatal thrombocytopenia and bilateral radial aplasia with thumbs present, is typically caused by the inheritance of a 1q21.1 deletion and a single-nucelotide polymorphism in RBM8A on the nondeleted allele. 	human		High+Lowthroughput	1q21.1 deletion and a rare functional polymorphism in siblings with thrombocytopenia-absent radius-like phenotypes	是	rs61746197	Thrombocytopenia, radial hypoplasia		E_01_0122	Western blot	Thrombocytopenia-absent radii (TAR) syndrome, characterized by neonatal thrombocytopenia and bilateral radial aplasia with thumbs present, is typically caused by the inheritance of a 1q21.1 deletion and a single-nucelotide polymorphism in RBM8A on the nondeleted allele. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Thrombocytopenia-absent radii (TAR) syndrome, characterized by neonatal thrombocytopenia and bilateral radial aplasia with thumbs present, is typically caused by the inheritance of a 1q21.1 deletion and a single-nucelotide polymorphism in RBM8A on the nondeleted allele. 	Immunohistochemical staining	Thrombocytopenia-absent radii (TAR) syndrome, characterized by neonatal thrombocytopenia and bilateral radial aplasia with thumbs present, is typically caused by the inheritance of a 1q21.1 deletion and a single-nucelotide polymorphism in RBM8A on the nondeleted allele. 		Western blot			RBM8A		Thrombocytopenia-absent radii (TAR) syndrome, characterized by neonatal thrombocytopenia and bilateral radial aplasia with thumbs present, is typically caused by the inheritance of a 1q21.1 deletion and a single-nucelotide polymorphism in RBM8A on the nondeleted allele. 	
31831267	chr7	148804596	148806596	EZH2	UNC6852 degrades both wild-type and mutant EZH2, and additionally displays anti-proliferative effects in this cancer model system.	human	Cervix, lymph, kidney	High+Lowthroughput	Degradation of Polycomb Repressive Complex 2 with an EED-Targeted Bivalent Chemical Degrader	否		cancer	Hela cell，DB cell，Pfeiffer cell，293T Cell 	E_01_0123	Western blot, cell viability assay	UNC6852 degrades both wild-type and mutant EZH2, and additionally displays anti-proliferative effects in this cancer model system.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		UNC6852 degrades both wild-type and mutant EZH2, and additionally displays anti-proliferative effects in this cancer model system.	Immunohistochemical staining	UNC6852 degrades both wild-type and mutant EZH2, and additionally displays anti-proliferative effects in this cancer model system.		Western Blot，细胞活力检测				EZH2		UNC6852 degrades both wild-type and mutant EZH2, and additionally displays anti-proliferative effects in this cancer model system.
31827084	chrX	113613674	113615674	XACT	This ERV was hijacked by younger hominoid-specific ERVs that gave rise to the promoter of XACT, thus wiring its expression to the pluripotency network. This work illustrates how retroviral-derived sequences may intervene in species-specific regulatory pathways.	human	embryo	High+Lowthroughput	A primate-specific retroviral enhancer wires the XACT lncRNA into the core pluripotency network in humans	否			embryonic stem cell	E_01_0124	Rna-fish, RT qPCR, chromatin immunoprecipitation, Western blot,	This ERV was hijacked by younger hominoid-specific ERVs that gave rise to the promoter of XACT, thus wiring its expression to the pluripotency network. This work illustrates how retroviral-derived sequences may intervene in species-specific regulatory pathways.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		This ERV was hijacked by younger hominoid-specific ERVs that gave rise to the promoter of XACT, thus wiring its expression to the pluripotency network. This work illustrates how retroviral-derived sequences may intervene in species-specific regulatory pathways.	Immunohistochemical staining	This ERV was hijacked by younger hominoid-specific ERVs that gave rise to the promoter of XACT, thus wiring its expression to the pluripotency network. This work illustrates how retroviral-derived sequences may intervene in species-specific regulatory pathways.		RNA-FISH，RT-qPCR，染色质免疫沉淀，western blot，			XACT		This ERV was hijacked by younger hominoid-specific ERVs that gave rise to the promoter of XACT, thus wiring its expression to the pluripotency network. This work illustrates how retroviral-derived sequences may intervene in species-specific regulatory pathways.	
31826955	chr14	37586693	37588693	FOXA1	Our study has uncovered high FOXA1-induced enhancer reprogramming and HIF-2α-dependent transcriptional programs as vulnerable targets for treating endocrine-resistant and metastatic breast cancer.	human	breast	High+Lowthroughput	FOXA1 upregulation promotes enhancer and transcriptional reprogramming in endocrine-resistant breast cancer	否		mammary cancer	MCF7L cell，T47D cell，600MPE cell	E_01_0125	Western blot, immunohistochemistry, QRT PCR	Our study has uncovered high FOXA1-induced enhancer reprogramming and HIF-2α-dependent transcriptional programs as vulnerable targets for treating endocrine-resistant and metastatic breast cancer.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Our study has uncovered high FOXA1-induced enhancer reprogramming and HIF-2α-dependent transcriptional programs as vulnerable targets for treating endocrine-resistant and metastatic breast cancer.	Immunohistochemical staining	Our study has uncovered high FOXA1-induced enhancer reprogramming and HIF-2α-dependent transcriptional programs as vulnerable targets for treating endocrine-resistant and metastatic breast cancer.		Western blot，免疫组化，qRT-PCR				FOXA1		Our study has uncovered high FOXA1-induced enhancer reprogramming and HIF-2α-dependent transcriptional programs as vulnerable targets for treating endocrine-resistant and metastatic breast cancer.
31825847	chr20	64045290	64047290	SOX18	The SOX18 transcription factor (TF) coincided with a HGSOC-specific SE, and ectopic overexpression of SOX18 in FTSECs caused epithelial-to-mesenchymal transition, indicating that SOX18 plays a role in establishing the mesenchymal signature of fallopian-derived HGSOCs.	human	ovary	High+Lowthroughput	A Study of High-Grade Serous Ovarian Cancer Origins Implicates the SOX18 Transcription Factor in Tumor Development	否		oophoroma	FT246，FT282，FT318，CaOV3，COV318，EFO21，Kuramochi，FUOV1，OAW28，OV177，OVSAHO，TykNu，UWB1.289 cell	E_01_0126	western blot，qRT-PCR	The SOX18 transcription factor (TF) coincided with a HGSOC-specific SE, and ectopic overexpression of SOX18 in FTSECs caused epithelial-to-mesenchymal transition, indicating that SOX18 plays a role in establishing the mesenchymal signature of fallopian-derived HGSOCs.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The SOX18 transcription factor (TF) coincided with a HGSOC-specific SE, and ectopic overexpression of SOX18 in FTSECs caused epithelial-to-mesenchymal transition, indicating that SOX18 plays a role in establishing the mesenchymal signature of fallopian-derived HGSOCs.	Immunohistochemical staining	The SOX18 transcription factor (TF) coincided with a HGSOC-specific SE, and ectopic overexpression of SOX18 in FTSECs caused epithelial-to-mesenchymal transition, indicating that SOX18 plays a role in establishing the mesenchymal signature of fallopian-derived HGSOCs.		western blot，qRT-PCR				SOX18		The SOX18 transcription factor (TF) coincided with a HGSOC-specific SE, and ectopic overexpression of SOX18 in FTSECs caused epithelial-to-mesenchymal transition, indicating that SOX18 plays a role in establishing the mesenchymal signature of fallopian-derived HGSOCs.
31819273	chr7	148804439	148806439	EZH2	Using a hydrophobic tagging approach, we generated MS1943, a first-in-class EZH2 selective degrader that effectively reduces EZH2 levels in cells. Importantly, MS1943 has a profound cytotoxic effect in multiple TNBC cells, while sparing normal cells, and is efficacious in vivo, suggesting that pharmacologic degradation of EZH2 can be advantageous for treating the cancers that are dependent on EZH2.	human	breast	High+Lowthroughput	Discovery of a first-in-class EZH2 selective degrader	否		cancer	MDA-MB-231，MDA-MB-468，BT549	E_01_0127	Western blot, cell viability assay, crystal violet staining, QRT PCR	Using a hydrophobic tagging approach, we generated MS1943, a first-in-class EZH2 selective degrader that effectively reduces EZH2 levels in cells. Importantly, MS1943 has a profound cytotoxic effect in multiple TNBC cells, while sparing normal cells, and is efficacious in vivo, suggesting that pharmacologic degradation of EZH2 can be advantageous for treating the cancers that are dependent on EZH2.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Using a hydrophobic tagging approach, we generated MS1943, a first-in-class EZH2 selective degrader that effectively reduces EZH2 levels in cells. Importantly, MS1943 has a profound cytotoxic effect in multiple TNBC cells, while sparing normal cells, and is efficacious in vivo, suggesting that pharmacologic degradation of EZH2 can be advantageous for treating the cancers that are dependent on EZH2.	Immunohistochemical staining	Using a hydrophobic tagging approach, we generated MS1943, a first-in-class EZH2 selective degrader that effectively reduces EZH2 levels in cells. Importantly, MS1943 has a profound cytotoxic effect in multiple TNBC cells, while sparing normal cells, and is efficacious in vivo, suggesting that pharmacologic degradation of EZH2 can be advantageous for treating the cancers that are dependent on EZH2.		western blot，细胞活力检测，结晶紫染色，qRT-PCR				EZH2		Using a hydrophobic tagging approach, we generated MS1943, a first-in-class EZH2 selective degrader that effectively reduces EZH2 levels in cells. Importantly, MS1943 has a profound cytotoxic effect in multiple TNBC cells, while sparing normal cells, and is efficacious in vivo, suggesting that pharmacologic degradation of EZH2 can be advantageous for treating the cancers that are dependent on EZH2.
31817839	chr1	115283204	115285204	NGF	NGF-Enhanced Vasculogenic Properties of Epithelial Ovarian Cancer Cells Is Reduced by Inhibition of the COX-2/PGE 2 Signaling Axis	human	ovary	High+Lowthroughput	NGF-Enhanced Vasculogenic Properties of Epithelial Ovarian Cancer Cells Is Reduced by Inhibition of the COX-2/PGE 2 Signaling Axis	否		Epithelial ovarian cancer	HOSE cell，A2780 cell，SKOV3 cell，OV90 cell，NIH-OVCAR3 cell	E_01_0128	Immunohistochemistry, immunocytochemistry, Western blot, QRT PCR, ELISA	NGF-Enhanced Vasculogenic Properties of Epithelial Ovarian Cancer Cells Is Reduced by Inhibition of the COX-2/PGE 2 Signaling Axis	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		NGF-Enhanced Vasculogenic Properties of Epithelial Ovarian Cancer Cells Is Reduced by Inhibition of the COX-2/PGE 2 Signaling Axis	Immunohistochemical staining	NGF-Enhanced Vasculogenic Properties of Epithelial Ovarian Cancer Cells Is Reduced by Inhibition of the COX-2/PGE 2 Signaling Axis		免疫组织化学，免疫细胞化学，Western Blot，qRT-PCR， ELISA			NGF		NGF-Enhanced Vasculogenic Properties of Epithelial Ovarian Cancer Cells Is Reduced by Inhibition of the COX-2/PGE 2 Signaling Axis	
31804013	chr5	151027281	151029281	TNIP1	 Hypomorphic TNIP1 expression results from the combined concordant and opposing effects of multiple risk variants carried on the TNIP1 risk haplotype, with the strongest regulatory effect in B lymphoid lineage cells.	human	Peripheral blood	High+Lowthroughput	Role of Systemic Lupus Erythematosus Risk Variants With Opposing Functional Effects as a Driver of Hypomorphic Expression of TNIP1 and Other Genes Within a Three-Dimensional Chromatin Network	否		Systemic lupus erythematosus	Jurkat cell，THP-1cell	E_01_0129	Dual luciferase reporter assay, electrophoretic mobility shift assay, QRT PCR, Western blot, and pulldown	 Hypomorphic TNIP1 expression results from the combined concordant and opposing effects of multiple risk variants carried on the TNIP1 risk haplotype, with the strongest regulatory effect in B lymphoid lineage cells.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		 Hypomorphic TNIP1 expression results from the combined concordant and opposing effects of multiple risk variants carried on the TNIP1 risk haplotype, with the strongest regulatory effect in B lymphoid lineage cells.	Immunohistochemical staining	 Hypomorphic TNIP1 expression results from the combined concordant and opposing effects of multiple risk variants carried on the TNIP1 risk haplotype, with the strongest regulatory effect in B lymphoid lineage cells.		双荧光素酶报告分析，电泳迁移率分析，qRT-PCR，Western blot，pulldown 				TNIP1		 Hypomorphic TNIP1 expression results from the combined concordant and opposing effects of multiple risk variants carried on the TNIP1 risk haplotype, with the strongest regulatory effect in B lymphoid lineage cells.
31799674	chr12	53959218	53961218	HOTAIR	LncRNA HOTAIR activates the expression of NF-κB in myeloma cells and promotes the proliferation of myeloma cells.	human	bone marrow	High+Lowthroughput	Effects of lncRNA HOTAIR on proliferation and apoptosis of myeloma cells through NF-κB pathway	否		Myeloma	Myeloma cell	E_01_0130	QRT PCR, flow cytometry, Western blot, cell viability assay, transfection	LncRNA HOTAIR activates the expression of NF-κB in myeloma cells and promotes the proliferation of myeloma cells.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		LncRNA HOTAIR activates the expression of NF-κB in myeloma cells and promotes the proliferation of myeloma cells.	Immunohistochemical staining	LncRNA HOTAIR activates the expression of NF-κB in myeloma cells and promotes the proliferation of myeloma cells.		qRT-PCR，流式细胞术，Western blot，细胞活力检测，转染				HOTAIR		LncRNA HOTAIR activates the expression of NF-κB in myeloma cells and promotes the proliferation of myeloma cells.
29861296	chr18	26013138	26015138	SS18	These results establish a global hijacking mechanism for SS18-SSX on chromatin, and define the distinct contributions of two concurrent BAF complex perturbations.	human	Synovial sarcoma	High+Lowthroughput	The SS18-SSX Fusion Oncoprotein Hijacks BAF Complex Targeting and Function to Drive Synovial Sarcoma	否		Synovial sarcoma (SS)	HEK293T LentiX cell	E_01_0131	Gene Knockdown,Western Blot,Immunoprecipitations,CRISPR/Cas9,Cell Proliferation Assay,Immunohistochemistry,Chromatin Immunoprecipitation (ChIP),RNA Isolation,RNA-seq,Assay for Transposase-Accessible Chromatin Sequencing (ATAC-seq),ChIP-Seq ,CHIP,Whole Exome Sequencing of Tumors	These results establish a global hijacking mechanism for SS18-SSX on chromatin, and define the distinct contributions of two concurrent BAF complex perturbations.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		These results establish a global hijacking mechanism for SS18-SSX on chromatin, and define the distinct contributions of two concurrent BAF complex perturbations.	Immunohistochemical staining	These results establish a global hijacking mechanism for SS18-SSX on chromatin, and define the distinct contributions of two concurrent BAF complex perturbations.		Gene Knockdown,Western Blot,Immunoprecipitations,CRISPR/Cas9,Cell Proliferation Assay,Immunohistochemistry,Chromatin Immunoprecipitation (ChIP),RNA Isolation,RNA-seq,Assay for Transposase-Accessible Chromatin Sequencing (ATAC-seq),ChIP-Seq ,CHIP,Whole Exome Sequencing of Tumors			SS18,SMARCB1		These results establish a global hijacking mechanism for SS18-SSX on chromatin, and define the distinct contributions of two concurrent BAF complex perturbations.;These results establish a global hijacking mechanism for SS18-SSX on chromatin, and define the distinct contributions of two concurrent BAF complex perturbations.	
29859124	chr1	11009935	11011935	TARDBP	Our study establishes possible mechanisms behind paraspeckle hyper-assembly in ALS and suggests their utility as therapeutic targets in ALS and other diseases with abnormal metabolism of microRNA and dsRNA.	human	Nervous	High+Lowthroughput	Protective paraspeckle hyper-assembly downstream of TDP-43 loss of function in amyotrophic lateral sclerosis	否		Amyotrophic lateral sclerosis (ALS)	SH-SY5Y neuroblastoma cell	E_01_0132	Immunocytochemistry,RNA-FISH,RIP,PCR,Western blot,qRT-PCR,Real-time qPCR,transfection,Cell Viability Assay	Our study establishes possible mechanisms behind paraspeckle hyper-assembly in ALS and suggests their utility as therapeutic targets in ALS and other diseases with abnormal metabolism of microRNA and dsRNA.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Our study establishes possible mechanisms behind paraspeckle hyper-assembly in ALS and suggests their utility as therapeutic targets in ALS and other diseases with abnormal metabolism of microRNA and dsRNA.	Immunohistochemical staining	Our study establishes possible mechanisms behind paraspeckle hyper-assembly in ALS and suggests their utility as therapeutic targets in ALS and other diseases with abnormal metabolism of microRNA and dsRNA.		Immunocytochemistry,RNA-FISH,RIP,PCR,Western blot,qRT-PCR,Real-time qPCR,transfection,Cell Viability Assay			TARDBP		Our study establishes possible mechanisms behind paraspeckle hyper-assembly in ALS and suggests their utility as therapeutic targets in ALS and other diseases with abnormal metabolism of microRNA and dsRNA.	
32517740	chr4	153777966	153779966	SFRP2	We investigated the SFRP2 methylation in peripheral blood mononuclear cells (PBMCs), visceral adipose tissue (VAT), CRC tumor tissue, and adjacent tumor-free area. We also determined the relationship between SFRP2 methylation and methylation of carcinogenic and adipogenic genes.	human		High+Lowthroughput	Association between variation of circulating 25-OH vitamin D and methylation of secreted frizzled-related protein 2 in colorectal cancer	否		Colorectal cancer	Human colorectal carcinoma cell	E_01_0133	PCR	We investigated the SFRP2 methylation in peripheral blood mononuclear cells (PBMCs), visceral adipose tissue (VAT), CRC tumor tissue, and adjacent tumor-free area. We also determined the relationship between SFRP2 methylation and methylation of carcinogenic and adipogenic genes.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We investigated the SFRP2 methylation in peripheral blood mononuclear cells (PBMCs), visceral adipose tissue (VAT), CRC tumor tissue, and adjacent tumor-free area. We also determined the relationship between SFRP2 methylation and methylation of carcinogenic and adipogenic genes.	Immunohistochemical staining	We investigated the SFRP2 methylation in peripheral blood mononuclear cells (PBMCs), visceral adipose tissue (VAT), CRC tumor tissue, and adjacent tumor-free area. We also determined the relationship between SFRP2 methylation and methylation of carcinogenic and adipogenic genes.		PCR			SFRP2		We investigated the SFRP2 methylation in peripheral blood mononuclear cells (PBMCs), visceral adipose tissue (VAT), CRC tumor tissue, and adjacent tumor-free area. We also determined the relationship between SFRP2 methylation and methylation of carcinogenic and adipogenic genes.	
32517078	chr10	112947720	112949720	TCF7L2	We report here that TCF7L2 transcription factor expression was found to be correlated to blast cell numbers during the progression of the disease.	human		High+Lowthroughput	Embryonic Program Activated during Blast Crisis of Chronic Myelogenous Leukemia (CML) Implicates a TCF7L2 and MYC Cooperative Chromatin Binding	否		Chronic Myelogenous Leukemia	K562 cell	E_01_0134	QRT-PCR，	We report here that TCF7L2 transcription factor expression was found to be correlated to blast cell numbers during the progression of the disease.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We report here that TCF7L2 transcription factor expression was found to be correlated to blast cell numbers during the progression of the disease.	Immunohistochemical staining	We report here that TCF7L2 transcription factor expression was found to be correlated to blast cell numbers during the progression of the disease.		QRT-PCR，				TCF7L2		We report here that TCF7L2 transcription factor expression was found to be correlated to blast cell numbers during the progression of the disease.
32514254	chr12	56749082	56751082	HSD17B6	HSD17B6 inhibited tumor cell proliferation, migration and invasion in liver cancer cells and low expression of HSD17B6 correlated with high immune cells infltration, relative reduction of immune responses and multiple immune checkpoint genes expression in HCC, probably by regulating the expression of TGFB1.	human		High+Lowthroughput	Downexpression of HSD17B6 correlates with clinical prognosis and tumor immune infiltrates in hepatocellular carcinoma	否		Hepatocellular carcinoma	HCC cell	E_01_0135	Gene set enrichment analysis，RT‑qPCR，Western blot	HSD17B6 inhibited tumor cell proliferation, migration and invasion in liver cancer cells and low expression of HSD17B6 correlated with high immune cells infltration, relative reduction of immune responses and multiple immune checkpoint genes expression in HCC, probably by regulating the expression of TGFB1.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		HSD17B6 inhibited tumor cell proliferation, migration and invasion in liver cancer cells and low expression of HSD17B6 correlated with high immune cells infltration, relative reduction of immune responses and multiple immune checkpoint genes expression in HCC, probably by regulating the expression of TGFB1.	Immunohistochemical staining	HSD17B6 inhibited tumor cell proliferation, migration and invasion in liver cancer cells and low expression of HSD17B6 correlated with high immune cells infltration, relative reduction of immune responses and multiple immune checkpoint genes expression in HCC, probably by regulating the expression of TGFB1.		Gene set enrichment analysis，RT‑qPCR，Western blot			HSD17B6		HSD17B6 inhibited tumor cell proliferation, migration and invasion in liver cancer cells and low expression of HSD17B6 correlated with high immune cells infltration, relative reduction of immune responses and multiple immune checkpoint genes expression in HCC, probably by regulating the expression of TGFB1.	
29945888	chr11	120233455	120235455	POU2F3	An analysis of human SCLC specimens revealed that POU2F3 is expressed exclusively in variant SCLC tumors that lack expression of neuroendocrine markers and instead express markers of a chemosensory lineage known as tuft cells. Moreover, we show that most SCLC tumors can be classified into one of three lineages based on the expression of POU2F3, ASCL1, or NEUROD1. Experiments in genetically engineered mice suggest a pulmonary neuroendocrine cell of origin for SCLC (Semenova et al. 2015), which is supported by the expression of neuroendocrine differentiation markers chromogranin A (CHGA) and insulinoma-associated protein 1 (INSM1) in human SCLC tumors (Gazdar et al. 2017).	human		High+Lowthroughput	POU2F3 is a master regulator of a tuft cell-like variant of small cell lung cancer	否		Small cell lung cancer (SCLC)	SCLC cell	E_01_0136	Rna-fish, human SCLC immunohistochemistry, Western blot, RNA SEQ, GSEA, chip SEQ, immunofluorescence staining	An analysis of human SCLC specimens revealed that POU2F3 is expressed exclusively in variant SCLC tumors that lack expression of neuroendocrine markers and instead express markers of a chemosensory lineage known as tuft cells. Moreover, we show that most SCLC tumors can be classified into one of three lineages based on the expression of POU2F3, ASCL1, or NEUROD1. Experiments in genetically engineered mice suggest a pulmonary neuroendocrine cell of origin for SCLC (Semenova et al. 2015), which is supported by the expression of neuroendocrine differentiation markers chromogranin A (CHGA) and insulinoma-associated protein 1 (INSM1) in human SCLC tumors (Gazdar et al. 2017).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		An analysis of human SCLC specimens revealed that POU2F3 is expressed exclusively in variant SCLC tumors that lack expression of neuroendocrine markers and instead express markers of a chemosensory lineage known as tuft cells. Moreover, we show that most SCLC tumors can be classified into one of three lineages based on the expression of POU2F3, ASCL1, or NEUROD1. Experiments in genetically engineered mice suggest a pulmonary neuroendocrine cell of origin for SCLC (Semenova et al. 2015), which is supported by the expression of neuroendocrine differentiation markers chromogranin A (CHGA) and insulinoma-associated protein 1 (INSM1) in human SCLC tumors (Gazdar et al. 2017).	Immunohistochemical staining	An analysis of human SCLC specimens revealed that POU2F3 is expressed exclusively in variant SCLC tumors that lack expression of neuroendocrine markers and instead express markers of a chemosensory lineage known as tuft cells. Moreover, we show that most SCLC tumors can be classified into one of three lineages based on the expression of POU2F3, ASCL1, or NEUROD1. Experiments in genetically engineered mice suggest a pulmonary neuroendocrine cell of origin for SCLC (Semenova et al. 2015), which is supported by the expression of neuroendocrine differentiation markers chromogranin A (CHGA) and insulinoma-associated protein 1 (INSM1) in human SCLC tumors (Gazdar et al. 2017).		RNA-FISH,Human SCLC immunohistochemistry,Western blot,RNA-seq,GSEA,ChIP-seq,免疫荧光染色				POU2F3,ASCL1,NEUROD1,INSM1		An analysis of human SCLC specimens revealed that POU2F3 is expressed exclusively in variant SCLC tumors that lack expression of neuroendocrine markers and instead express markers of a chemosensory lineage known as tuft cells. Moreover, we show that most SCLC tumors can be classified into one of three lineages based on the expression of POU2F3, ASCL1, or NEUROD1. Experiments in genetically engineered mice suggest a pulmonary neuroendocrine cell of origin for SCLC (Semenova et al. 2015), which is supported by the expression of neuroendocrine differentiation markers chromogranin A (CHGA) and insulinoma-associated protein 1 (INSM1) in human SCLC tumors (Gazdar et al. 2017).;An analysis of human SCLC specimens revealed that POU2F3 is expressed exclusively in variant SCLC tumors that lack expression of neuroendocrine markers and instead express markers of a chemosensory lineage known as tuft cells. Moreover, we show that most SCLC tumors can be classified into one of three lineages based on the expression of POU2F3, ASCL1, or NEUROD1. Experiments in genetically engineered mice suggest a pulmonary neuroendocrine cell of origin for SCLC (Semenova et al. 2015), which is supported by the expression of neuroendocrine differentiation markers chromogranin A (CHGA) and insulinoma-associated protein 1 (INSM1) in human SCLC tumors (Gazdar et al. 2017).;An analysis of human SCLC specimens revealed that POU2F3 is expressed exclusively in variant SCLC tumors that lack expression of neuroendocrine markers and instead express markers of a chemosensory lineage known as tuft cells. Moreover, we show that most SCLC tumors can be classified into one of three lineages based on the expression of POU2F3, ASCL1, or NEUROD1. Experiments in genetically engineered mice suggest a pulmonary neuroendocrine cell of origin for SCLC (Semenova et al. 2015), which is supported by the expression of neuroendocrine differentiation markers chromogranin A (CHGA) and insulinoma-associated protein 1 (INSM1) in human SCLC tumors (Gazdar et al. 2017).;An analysis of human SCLC specimens revealed that POU2F3 is expressed exclusively in variant SCLC tumors that lack expression of neuroendocrine markers and instead express markers of a chemosensory lineage known as tuft cells. Moreover, we show that most SCLC tumors can be classified into one of three lineages based on the expression of POU2F3, ASCL1, or NEUROD1. Experiments in genetically engineered mice suggest a pulmonary neuroendocrine cell of origin for SCLC (Semenova et al. 2015), which is supported by the expression of neuroendocrine differentiation markers chromogranin A (CHGA) and insulinoma-associated protein 1 (INSM1) in human SCLC tumors (Gazdar et al. 2017).
29580634	chr5	173229639	173231639	NKX2-5	NKX2-5 is a homeobox transcription factor required for the formation of the heart and vessels during development, with significant postnatal downregulation and reactivation in disease states characterised by vascular remodelling.	human	Vascular	High+Lowthroughput	Molecular Basis for Dysregulated Activation of NKX2-5 in the Vascular Remodeling of Systemic Sclerosis	是	rs3095870	scleroderma associated pulmonary hypertensio	smooth muscle cell of the pulmonary artery	E_01_0137	Western blot,qPCR	NKX2-5 is a homeobox transcription factor required for the formation of the heart and vessels during development, with significant postnatal downregulation and reactivation in disease states characterised by vascular remodelling.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		NKX2-5 is a homeobox transcription factor required for the formation of the heart and vessels during development, with significant postnatal downregulation and reactivation in disease states characterised by vascular remodelling.	Immunohistochemical staining	NKX2-5 is a homeobox transcription factor required for the formation of the heart and vessels during development, with significant postnatal downregulation and reactivation in disease states characterised by vascular remodelling.		Western blot,qPCR				NKX2-5		NKX2-5 is a homeobox transcription factor required for the formation of the heart and vessels during development, with significant postnatal downregulation and reactivation in disease states characterised by vascular remodelling.
29579222	chr11	12671903	12673903	TEAD1	TEAD1 is a member of TEA/ATTS domain family transcription regulators with distinct and important roles in VSMC differentiation and in cardiovascular disease	human	Vascular	High+Lowthroughput	Molecular Basis for Dysregulated Activation of NKX2-5 in the Vascular Remodeling of Systemic Sclerosis	是	rs3095870	scleroderma associated pulmonary hypertensio	smooth muscle cell of the pulmonary artery	E_01_0138	Western blot,qPCR	TEAD1 is a member of TEA/ATTS domain family transcription regulators with distinct and important roles in VSMC differentiation and in cardiovascular disease	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		TEAD1 is a member of TEA/ATTS domain family transcription regulators with distinct and important roles in VSMC differentiation and in cardiovascular disease	Immunohistochemical staining	TEAD1 is a member of TEA/ATTS domain family transcription regulators with distinct and important roles in VSMC differentiation and in cardiovascular disease		Western blot,qPCR				TEAD1		TEAD1 is a member of TEA/ATTS domain family transcription regulators with distinct and important roles in VSMC differentiation and in cardiovascular disease
29576612	chr17	42310573	42312573	STAT3	Protein kinase A-mediated phosphorylation regulates STAT3 activation and oncogenic EZH2 activity	human		High+Lowthroughput	Protein kinase A-mediated phosphorylation regulates STAT3 activation and oncogenic EZH2 activity	否				E_01_0139	 EZH2 	Protein kinase A-mediated phosphorylation regulates STAT3 activation and oncogenic EZH2 activity	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Protein kinase A-mediated phosphorylation regulates STAT3 activation and oncogenic EZH2 activity	Immunohistochemical staining	Protein kinase A-mediated phosphorylation regulates STAT3 activation and oncogenic EZH2 activity		 EZH2 				STAT3		Protein kinase A-mediated phosphorylation regulates STAT3 activation and oncogenic EZH2 activity
29572261	chr12	54030375	54032375	HOXC5	Deregulation of HOXC5 and mir-615-3p expression may contribute to the activation of hTERT in human cancers.	human	Somatic	High+Lowthroughput	HoxC5 and miR-615-3p target newly evolved genomic regions to repress hTERT and inhibit tumorigenesis	否		Tumor	somatic cell	E_01_0140	Luciferase reporter assay,Western blot,ChIP-Seq,qRT-PCR,3C-qPCR	Deregulation of HOXC5 and mir-615-3p expression may contribute to the activation of hTERT in human cancers.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Deregulation of HOXC5 and mir-615-3p expression may contribute to the activation of hTERT in human cancers.	Immunohistochemical staining	Deregulation of HOXC5 and mir-615-3p expression may contribute to the activation of hTERT in human cancers.		Luciferase reporter assay,Western blot,ChIP-Seq,qRT-PCR,3C-qPCR				HOXC5		Deregulation of HOXC5 and mir-615-3p expression may contribute to the activation of hTERT in human cancers.
29570423	chr19	19143043	19145043	MEF2B	Myocyte enhancer binding factor 2B (MEF2B) is a transcriptional activator of the BCL6 proto-oncogene in normal germinal center (GC) B-cells.	human	Lymphoid	High+Lowthroughput	Comparison of Myocyte Enhancer Factor 2B Versus Other Germinal Center-associated Antigens in the Differential Diagnosis of B-Cell Non-Hodgkin Lymphomas	否		Lymphomas	B cell	E_01_0141	Immunohistochemical Staining	Myocyte enhancer binding factor 2B (MEF2B) is a transcriptional activator of the BCL6 proto-oncogene in normal germinal center (GC) B-cells.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Myocyte enhancer binding factor 2B (MEF2B) is a transcriptional activator of the BCL6 proto-oncogene in normal germinal center (GC) B-cells.	Immunohistochemical staining	Myocyte enhancer binding factor 2B (MEF2B) is a transcriptional activator of the BCL6 proto-oncogene in normal germinal center (GC) B-cells.		Immunohistochemical Staining			MEF2B		Myocyte enhancer binding factor 2B (MEF2B) is a transcriptional activator of the BCL6 proto-oncogene in normal germinal center (GC) B-cells.	
29569934	chr17	43751254	43753254	SOST	The SOST gene encodes sclerostin, a C-terminal cysteine knot-like domain containing key negative regulator of osteoblastic bone formation that inhibits LRP5/6-mediated canonical Wnt signaling.	human	Bone	High+Lowthroughput	Computational and functional characterization of four SNPs in the SOST locus associated with osteoporosis	是	rs1230399,rs7220711,rs1107748,rs75901553	osteoporosis	Germinal center B-cells	E_01_0142	Luciferase reporter assay,ChIP,qPCR	The SOST gene encodes sclerostin, a C-terminal cysteine knot-like domain containing key negative regulator of osteoblastic bone formation that inhibits LRP5/6-mediated canonical Wnt signaling.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The SOST gene encodes sclerostin, a C-terminal cysteine knot-like domain containing key negative regulator of osteoblastic bone formation that inhibits LRP5/6-mediated canonical Wnt signaling.	Immunohistochemical staining	The SOST gene encodes sclerostin, a C-terminal cysteine knot-like domain containing key negative regulator of osteoblastic bone formation that inhibits LRP5/6-mediated canonical Wnt signaling.		Luciferase reporter assay,ChIP,qPCR			SOST		The SOST gene encodes sclerostin, a C-terminal cysteine knot-like domain containing key negative regulator of osteoblastic bone formation that inhibits LRP5/6-mediated canonical Wnt signaling.	
29563873	chr14	100892224	100894224	MEG8	Our findings indicate that MEG8 lncRNA significantly contributes to epigenetic EMT induction and increase our understanding of the lncRNA-mediated regulatory mechanisms involved in malignant progression of cancer.	human		High+Lowthroughput	MEG8 long noncoding RNA contributes to epigenetic progression of the epithelial-mesenchymal transition of lung and pancreatic cancer cells	否		Lung and pancreatic cancer	A549 cell， LC-2/ad cell，Panc1 cell	E_01_0143	Quantitative PCR，Cell migration assay，Chromatin immunoprecipitation (ChIP) assays，RNA immunoprecipitation (RIP)，Chromatin isolation by RNA purification (ChIRP) assays	Our findings indicate that MEG8 lncRNA significantly contributes to epigenetic EMT induction and increase our understanding of the lncRNA-mediated regulatory mechanisms involved in malignant progression of cancer.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Our findings indicate that MEG8 lncRNA significantly contributes to epigenetic EMT induction and increase our understanding of the lncRNA-mediated regulatory mechanisms involved in malignant progression of cancer.	Immunohistochemical staining	Our findings indicate that MEG8 lncRNA significantly contributes to epigenetic EMT induction and increase our understanding of the lncRNA-mediated regulatory mechanisms involved in malignant progression of cancer.		Quantitative PCR，Cell migration assay，Chromatin immunoprecipitation (ChIP) assays，RNA immunoprecipitation (RIP)，Chromatin isolation by RNA purification (ChIRP) assays			MEG8		Our findings indicate that MEG8 lncRNA significantly contributes to epigenetic EMT induction and increase our understanding of the lncRNA-mediated regulatory mechanisms involved in malignant progression of cancer.	
29563767	chr12	55740444	55742444	GDF11	Additionally, the activation of nuclear NF-κB (nuclear factor κ-light-chainenhancer of activated B cells) signaling pathway was repressed by GDF11 treatment. Collectively, GDF11 may represent a promising molecular target for the prevention and treatment of psoriasis-like skin inflammation. 	human		High+Lowthroughput	GDF11 Antagonizes Psoriasis-like Skin Inflammation via Suppression of NF-κB Signaling Pathway	否		Psoriasiform skin inflammation	Mouse leukemic monocyte macrophages	E_01_0144	miRNA transfection，Real-Time PCR,Western Blot,Immunofluorescence,ELISA Assays	Additionally, the activation of nuclear NF-κB (nuclear factor κ-light-chainenhancer of activated B cells) signaling pathway was repressed by GDF11 treatment. Collectively, GDF11 may represent a promising molecular target for the prevention and treatment of psoriasis-like skin inflammation. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Additionally, the activation of nuclear NF-κB (nuclear factor κ-light-chainenhancer of activated B cells) signaling pathway was repressed by GDF11 treatment. Collectively, GDF11 may represent a promising molecular target for the prevention and treatment of psoriasis-like skin inflammation. 	Immunohistochemical staining	Additionally, the activation of nuclear NF-κB (nuclear factor κ-light-chainenhancer of activated B cells) signaling pathway was repressed by GDF11 treatment. Collectively, GDF11 may represent a promising molecular target for the prevention and treatment of psoriasis-like skin inflammation. 		miRNA transfection，Real-Time PCR,Western Blot,Immunofluorescence,ELISA Assays				GDF11		Additionally, the activation of nuclear NF-κB (nuclear factor κ-light-chainenhancer of activated B cells) signaling pathway was repressed by GDF11 treatment. Collectively, GDF11 may represent a promising molecular target for the prevention and treatment of psoriasis-like skin inflammation. 
29563503	chr8	127077409	127079409	PRNCR1	Taken all together, we confirmed that lncRNA PRNCR1 upregulates HEY2 to promote tumor progression in NSCLC by competitively binding miR-448. 	human		High+Lowthroughput	LncRNA PRNCR1 interacts with HEY2 to abolish miR-448-mediated growth inhibition in non-small cell lung cancer	否		Non small cell lung cancer	A549 cell, SK-MES-1 cell, Calu-3 cell，H1299 cell，NHBE cell	E_01_0145	Cell transfection,RNA isolation,qRT-PCR analysi, Cell proliferation assays, Transwell assays,Luciferase reporter analysis,RIP assay, Western blot assay	Taken all together, we confirmed that lncRNA PRNCR1 upregulates HEY2 to promote tumor progression in NSCLC by competitively binding miR-448. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Taken all together, we confirmed that lncRNA PRNCR1 upregulates HEY2 to promote tumor progression in NSCLC by competitively binding miR-448. 	Immunohistochemical staining	Taken all together, we confirmed that lncRNA PRNCR1 upregulates HEY2 to promote tumor progression in NSCLC by competitively binding miR-448. 		Cell transfection,RNA isolation,qRT-PCR analysi, Cell proliferation assays, Transwell assays,Luciferase reporter analysis,RIP assay, Western blot assay			PRNCR1	HEY2	Taken all together, we confirmed that lncRNA PRNCR1 upregulates HEY2 to promote tumor progression in NSCLC by competitively binding miR-448. 	Taken all together, we confirmed that lncRNA PRNCR1 upregulates HEY2 to promote tumor progression in NSCLC by competitively binding miR-448. 
29563176	chr16	67559907	67561907	CTCF	These first en_x0002_hancers maintain more Hi-C interactions with other en_x0002_hancers and promoters, are more enriched for the loop factors CCCTC-binding factor (CTCF) and cohesin, and commonly overlap with the boundaries of chromatin loops.	human	blood	High+Lowthroughput	The first enhancer in an enhancer chain safeguards subsequent enhancer-promoter contacts from a distance	否			K562 cell	E_01_0146	PCR	These first en_x0002_hancers maintain more Hi-C interactions with other en_x0002_hancers and promoters, are more enriched for the loop factors CCCTC-binding factor (CTCF) and cohesin, and commonly overlap with the boundaries of chromatin loops.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		These first en_x0002_hancers maintain more Hi-C interactions with other en_x0002_hancers and promoters, are more enriched for the loop factors CCCTC-binding factor (CTCF) and cohesin, and commonly overlap with the boundaries of chromatin loops.	Immunohistochemical staining	These first en_x0002_hancers maintain more Hi-C interactions with other en_x0002_hancers and promoters, are more enriched for the loop factors CCCTC-binding factor (CTCF) and cohesin, and commonly overlap with the boundaries of chromatin loops.		PCR				CTCF		These first en_x0002_hancers maintain more Hi-C interactions with other en_x0002_hancers and promoters, are more enriched for the loop factors CCCTC-binding factor (CTCF) and cohesin, and commonly overlap with the boundaries of chromatin loops.
29563122	chr9	21074270	21076270	IFNB1	We constructed IFNB1 luciferase reporter plasmids composed of IFNB1 immediate promoter followed by these enhancers (Figure S6D).	human	uterus	High+Lowthroughput	The Nuclear Matrix Protein SAFA Surveils Viral RNA and Facilitates Immunity by Activating Antiviral Enhancers and Super-enhancers	否			HeLa cell	E_01_0147	PCR, Western blot, flow cytometry, immunofluorescence staining	We constructed IFNB1 luciferase reporter plasmids composed of IFNB1 immediate promoter followed by these enhancers (Figure S6D).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We constructed IFNB1 luciferase reporter plasmids composed of IFNB1 immediate promoter followed by these enhancers (Figure S6D).	Immunohistochemical staining	We constructed IFNB1 luciferase reporter plasmids composed of IFNB1 immediate promoter followed by these enhancers (Figure S6D).		PCR,Western blot,Flow cytometry,免疫荧光染色				IFNB1		We constructed IFNB1 luciferase reporter plasmids composed of IFNB1 immediate promoter followed by these enhancers (Figure S6D).
29559957	chr7	99754049	99756049	CYP3A4	The expression and activity of CYP3A4 vary among individuals. With the development of epigenetics, it is now possible to elucidate interindividual differences in drug-metabolizing enzymes.	human		High+Lowthroughput	DNA methylation determines the regulation of pregnane X receptor on CYP3A4 expression	否			HepG2 cell	E_01_0148	Plasmid construction，In vitro methylation，Luciferase reporter assay，Transfection and rifampicin induction，RNA isolation and real-time quantitative polymerase chain reaction (RT-qPCR) ，ChIP assay	The expression and activity of CYP3A4 vary among individuals. With the development of epigenetics, it is now possible to elucidate interindividual differences in drug-metabolizing enzymes.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The expression and activity of CYP3A4 vary among individuals. With the development of epigenetics, it is now possible to elucidate interindividual differences in drug-metabolizing enzymes.	Immunohistochemical staining	The expression and activity of CYP3A4 vary among individuals. With the development of epigenetics, it is now possible to elucidate interindividual differences in drug-metabolizing enzymes.		Plasmid construction，In vitro methylation，Luciferase reporter assay，Transfection and rifampicin induction，RNA isolation and real-time quantitative polymerase chain reaction (RT-qPCR) ，ChIP assay			CYP3A4		The expression and activity of CYP3A4 vary among individuals. With the development of epigenetics, it is now possible to elucidate interindividual differences in drug-metabolizing enzymes.	
29557377	chr1	156460952	156462952	MEF2D	We identified a rare regulatory variant rs200395694:G > T located in intron 4 of the MEF2D gene encoding the myocyte-specific enhancer factor 2D transcription factor and associated with SLE in Swedish cohorts (504 SLE patients and 839 healthy controls, p = 0.014, CI = 1.1 10). 	human		High+Lowthroughput	A rare regulatory variant in the MEF2D gene affects gene regulation and splicing and is associated with a SLE sub-phenotype in Swedish cohorts	否			T, B, NK cell	E_01_0149	Gene array capture，Seq,Gene array capture	We identified a rare regulatory variant rs200395694:G > T located in intron 4 of the MEF2D gene encoding the myocyte-specific enhancer factor 2D transcription factor and associated with SLE in Swedish cohorts (504 SLE patients and 839 healthy controls, p = 0.014, CI = 1.1 10). 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We identified a rare regulatory variant rs200395694:G > T located in intron 4 of the MEF2D gene encoding the myocyte-specific enhancer factor 2D transcription factor and associated with SLE in Swedish cohorts (504 SLE patients and 839 healthy controls, p = 0.014, CI = 1.1 10). 	Immunohistochemical staining	We identified a rare regulatory variant rs200395694:G > T located in intron 4 of the MEF2D gene encoding the myocyte-specific enhancer factor 2D transcription factor and associated with SLE in Swedish cohorts (504 SLE patients and 839 healthy controls, p = 0.014, CI = 1.1 10). 		Gene array capture，Seq,Gene array capture			MEF2D		We identified a rare regulatory variant rs200395694:G > T located in intron 4 of the MEF2D gene encoding the myocyte-specific enhancer factor 2D transcription factor and associated with SLE in Swedish cohorts (504 SLE patients and 839 healthy controls, p = 0.014, CI = 1.1 10). 	
29556082	chr11	65494664	65496664	MALAT1	MALAT1, HYMAI, LOC730101, KIAA1656, and LOC339803 were found differentially expressed in human atherosclerotic lesions, compared to normal vascular tissue, and may thus serve as potential biomarkers for lesion hypoxia. 	human		High+Lowthroughput	Transcriptional Profiling of Hypoxia-Regulated Non-coding RNAs in Human Primary Endothelial Cells	否			 Primary endothelial cell	E_01_0150	GRO-Seq and RNA-Seq,	MALAT1, HYMAI, LOC730101, KIAA1656, and LOC339803 were found differentially expressed in human atherosclerotic lesions, compared to normal vascular tissue, and may thus serve as potential biomarkers for lesion hypoxia. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		MALAT1, HYMAI, LOC730101, KIAA1656, and LOC339803 were found differentially expressed in human atherosclerotic lesions, compared to normal vascular tissue, and may thus serve as potential biomarkers for lesion hypoxia. 	Immunohistochemical staining	MALAT1, HYMAI, LOC730101, KIAA1656, and LOC339803 were found differentially expressed in human atherosclerotic lesions, compared to normal vascular tissue, and may thus serve as potential biomarkers for lesion hypoxia. 		GRO-Seq and RNA-Seq,				MALAT1		MALAT1, HYMAI, LOC730101, KIAA1656, and LOC339803 were found differentially expressed in human atherosclerotic lesions, compared to normal vascular tissue, and may thus serve as potential biomarkers for lesion hypoxia. 
29554889	chr3	133743314	133745314	TF	Background Homeodomain (HD) transcription factor (TF) NKX2 1 critical for the regional specification of the medial ganglionic eminence (MGE) as well as promoting the GABAergic and cholinergic neuron fates via the induction of TFs such as LHX6 and LHX8.	human		High+Lowthroughput	Genomic analysis of transcriptional networks directing progression of cell states during MGE development.	否				E_01_0151	RT qPCR, in situ hybridization analysis, gene knockdown, chip SEQ, immunofluorescence staining	Background Homeodomain (HD) transcription factor (TF) NKX2 1 critical for the regional specification of the medial ganglionic eminence (MGE) as well as promoting the GABAergic and cholinergic neuron fates via the induction of TFs such as LHX6 and LHX8.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Background Homeodomain (HD) transcription factor (TF) NKX2 1 critical for the regional specification of the medial ganglionic eminence (MGE) as well as promoting the GABAergic and cholinergic neuron fates via the induction of TFs such as LHX6 and LHX8.	Immunohistochemical staining	Background Homeodomain (HD) transcription factor (TF) NKX2 1 critical for the regional specification of the medial ganglionic eminence (MGE) as well as promoting the GABAergic and cholinergic neuron fates via the induction of TFs such as LHX6 and LHX8.		RT-qPCR,原位杂交分析,基因敲降,ChIP-seq ,免疫荧光染色			TF,LHX6,LHX8		Background Homeodomain (HD) transcription factor (TF) NKX2 1 critical for the regional specification of the medial ganglionic eminence (MGE) as well as promoting the GABAergic and cholinergic neuron fates via the induction of TFs such as LHX6 and LHX8.;Background Homeodomain (HD) transcription factor (TF) NKX2 1 critical for the regional specification of the medial ganglionic eminence (MGE) as well as promoting the GABAergic and cholinergic neuron fates via the induction of TFs such as LHX6 and LHX8.;Background Homeodomain (HD) transcription factor (TF) NKX2 1 critical for the regional specification of the medial ganglionic eminence (MGE) as well as promoting the GABAergic and cholinergic neuron fates via the induction of TFs such as LHX6 and LHX8.	
29549111	chr14	21495511	21497511	METTL3	The deletion of m6A writer protein methyltransferaselike (METTL)3 in porcine BMSCs (pBMSCs) could promote adipogenesis and janus kinase (JAK)1 protein expressionvia anm6 A-dependent way. Knockdown ofMETTL3 decreasedmRNAm6 A levels of JAK1, leading to enhanced YTH m6 A RNA binding protein 2 (YTHDF2)-dependent JAK1 mRNA stability. We further demonstrated that JAK1 activated signal transducer and activator of transcription (STAT) 5 through regulation of its phosphorylation to bind to the promoter of CCAAT/enhancer binding protein (C/EBP) b, which could ultimately lead to a modulated adipogenic process. 	human		High+Lowthroughput	Disrupting the three-dimensional regulatory topology of the Pitx1 locus results in overtly normal development	否			Bone marrow stem cell	E_01_0152	flow cytometry ，Real-time quantitative PCR ， staining ，Protein extraction ，Western blot ，Cell transfection ，Immunofluorescence assay ，Quantitative analysis ，Chromatin immunoprecipitation assay ，Luciferase reporter assay	The deletion of m6A writer protein methyltransferaselike (METTL)3 in porcine BMSCs (pBMSCs) could promote adipogenesis and janus kinase (JAK)1 protein expressionvia anm6 A-dependent way. Knockdown ofMETTL3 decreasedmRNAm6 A levels of JAK1, leading to enhanced YTH m6 A RNA binding protein 2 (YTHDF2)-dependent JAK1 mRNA stability. We further demonstrated that JAK1 activated signal transducer and activator of transcription (STAT) 5 through regulation of its phosphorylation to bind to the promoter of CCAAT/enhancer binding protein (C/EBP) b, which could ultimately lead to a modulated adipogenic process. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The deletion of m6A writer protein methyltransferaselike (METTL)3 in porcine BMSCs (pBMSCs) could promote adipogenesis and janus kinase (JAK)1 protein expressionvia anm6 A-dependent way. Knockdown ofMETTL3 decreasedmRNAm6 A levels of JAK1, leading to enhanced YTH m6 A RNA binding protein 2 (YTHDF2)-dependent JAK1 mRNA stability. We further demonstrated that JAK1 activated signal transducer and activator of transcription (STAT) 5 through regulation of its phosphorylation to bind to the promoter of CCAAT/enhancer binding protein (C/EBP) b, which could ultimately lead to a modulated adipogenic process. 	Immunohistochemical staining	The deletion of m6A writer protein methyltransferaselike (METTL)3 in porcine BMSCs (pBMSCs) could promote adipogenesis and janus kinase (JAK)1 protein expressionvia anm6 A-dependent way. Knockdown ofMETTL3 decreasedmRNAm6 A levels of JAK1, leading to enhanced YTH m6 A RNA binding protein 2 (YTHDF2)-dependent JAK1 mRNA stability. We further demonstrated that JAK1 activated signal transducer and activator of transcription (STAT) 5 through regulation of its phosphorylation to bind to the promoter of CCAAT/enhancer binding protein (C/EBP) b, which could ultimately lead to a modulated adipogenic process. 		flow cytometry ，Real-time quantitative PCR ， staining ，Protein extraction ，Western blot ，Cell transfection ，Immunofluorescence assay ，Quantitative analysis ，Chromatin immunoprecipitation assay ，Luciferase reporter assay			METTL3		The deletion of m6A writer protein methyltransferaselike (METTL)3 in porcine BMSCs (pBMSCs) could promote adipogenesis and janus kinase (JAK)1 protein expressionvia anm6 A-dependent way. Knockdown ofMETTL3 decreasedmRNAm6 A levels of JAK1, leading to enhanced YTH m6 A RNA binding protein 2 (YTHDF2)-dependent JAK1 mRNA stability. We further demonstrated that JAK1 activated signal transducer and activator of transcription (STAT) 5 through regulation of its phosphorylation to bind to the promoter of CCAAT/enhancer binding protein (C/EBP) b, which could ultimately lead to a modulated adipogenic process. 	
29545900	chr2	226728889	226730889	IRS1	Phosphatidylinositol-3-kinase (PI3K), 74 insulin receptor substrate 1 (IRS1), and glucose transporter 4 (GLUT4) play crucial roles in 75 glucose metabolism and insulin resistance. The mechanism begins with the stimulation of 76 insulin receptor intrinsic kinase activity to activate PI3K signaling. Then, PI3K inhibits the 77 c-Jun N-terminal kinase 1 (JNK1) activity in succession. Moreover, GLUT4, which is 78 regulated by insulin, is able to reduce glucose levels through participating in the IRS/PI3K 79 signaling pathway (Chen et al., 2018). 	human		High+Lowthroughput	Investigating a multigene prognostic assay based on significant pathways for Luminal A breast cancer through gene expression profile analysis	否			HeLa cell	E_01_0153	Nuclear magnetic resonance (NMR) spectroscopy analysis ，RNA extraction and real-time PCR ，Western blot analysis ，Histopathological analysis ,Analysis of glycated hemoglobin and β-cell function	Phosphatidylinositol-3-kinase (PI3K), 74 insulin receptor substrate 1 (IRS1), and glucose transporter 4 (GLUT4) play crucial roles in 75 glucose metabolism and insulin resistance. The mechanism begins with the stimulation of 76 insulin receptor intrinsic kinase activity to activate PI3K signaling. Then, PI3K inhibits the 77 c-Jun N-terminal kinase 1 (JNK1) activity in succession. Moreover, GLUT4, which is 78 regulated by insulin, is able to reduce glucose levels through participating in the IRS/PI3K 79 signaling pathway (Chen et al., 2018). 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Phosphatidylinositol-3-kinase (PI3K), 74 insulin receptor substrate 1 (IRS1), and glucose transporter 4 (GLUT4) play crucial roles in 75 glucose metabolism and insulin resistance. The mechanism begins with the stimulation of 76 insulin receptor intrinsic kinase activity to activate PI3K signaling. Then, PI3K inhibits the 77 c-Jun N-terminal kinase 1 (JNK1) activity in succession. Moreover, GLUT4, which is 78 regulated by insulin, is able to reduce glucose levels through participating in the IRS/PI3K 79 signaling pathway (Chen et al., 2018). 	Immunohistochemical staining	Phosphatidylinositol-3-kinase (PI3K), 74 insulin receptor substrate 1 (IRS1), and glucose transporter 4 (GLUT4) play crucial roles in 75 glucose metabolism and insulin resistance. The mechanism begins with the stimulation of 76 insulin receptor intrinsic kinase activity to activate PI3K signaling. Then, PI3K inhibits the 77 c-Jun N-terminal kinase 1 (JNK1) activity in succession. Moreover, GLUT4, which is 78 regulated by insulin, is able to reduce glucose levels through participating in the IRS/PI3K 79 signaling pathway (Chen et al., 2018). 		Nuclear magnetic resonance (NMR) spectroscopy analysis ，RNA extraction and real-time PCR ，Western blot analysis ，Histopathological analysis ,Analysis of glycated hemoglobin and β-cell function			IRS1		Phosphatidylinositol-3-kinase (PI3K), 74 insulin receptor substrate 1 (IRS1), and glucose transporter 4 (GLUT4) play crucial roles in 75 glucose metabolism and insulin resistance. The mechanism begins with the stimulation of 76 insulin receptor intrinsic kinase activity to activate PI3K signaling. Then, PI3K inhibits the 77 c-Jun N-terminal kinase 1 (JNK1) activity in succession. Moreover, GLUT4, which is 78 regulated by insulin, is able to reduce glucose levels through participating in the IRS/PI3K 79 signaling pathway (Chen et al., 2018). 	
29540468	chr17	66299977	66301977	PRKCA	The PRKCA enhancer contains two common genetic variants and 4 haplotypes;	human		High+Lowthroughput	Genetic Reduction in Left Ventricular Protein Kinase C-α and Adverse Ventricular Remodeling in Human Subjects	是	rs9912468		non-cardiac cell	E_01_0154	PCR	The PRKCA enhancer contains two common genetic variants and 4 haplotypes;	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The PRKCA enhancer contains two common genetic variants and 4 haplotypes;	Immunohistochemical staining	The PRKCA enhancer contains two common genetic variants and 4 haplotypes;		PCR			PRKCA		The PRKCA enhancer contains two common genetic variants and 4 haplotypes;	
29530320	chr3	181709448	181711448	SOX2	Epigenomic Profifiling Discovers Trans-lineage SOX2 Partnerships Driving Tumor Heterogeneity in Lung Squamous Cell Carcinoma	human	lung	High+Lowthroughput	Synthetically Scalable Poly(ampholyte) Which Dramatically Enhances Cellular Cryopreservation	否			Lung squamous cell	E_01_0155	Western blot, chip SEQ, RNA SEQ, flow cytometry, gene knockdown	Epigenomic Profifiling Discovers Trans-lineage SOX2 Partnerships Driving Tumor Heterogeneity in Lung Squamous Cell Carcinoma	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Epigenomic Profifiling Discovers Trans-lineage SOX2 Partnerships Driving Tumor Heterogeneity in Lung Squamous Cell Carcinoma	Immunohistochemical staining	Epigenomic Profifiling Discovers Trans-lineage SOX2 Partnerships Driving Tumor Heterogeneity in Lung Squamous Cell Carcinoma		Western blot,ChIP-seq,RNA-seq,流式细胞术,基因敲降				SOX2		Epigenomic Profifiling Discovers Trans-lineage SOX2 Partnerships Driving Tumor Heterogeneity in Lung Squamous Cell Carcinoma
29526278	chr21	33540351	33542351	SON	Four AONs and a sense oligonucleotide (SON) were designed to block exonic splicing enhancers (ESEs).	human		High+Lowthroughput	Identification and Rescue of Splice Defects Caused by Two Neighboring Deep-Intronic ABCA4 Mutations Underlying Stargardt Disease	否				E_01_0156	RT-PCR	Four AONs and a sense oligonucleotide (SON) were designed to block exonic splicing enhancers (ESEs).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Four AONs and a sense oligonucleotide (SON) were designed to block exonic splicing enhancers (ESEs).	Immunohistochemical staining	Four AONs and a sense oligonucleotide (SON) were designed to block exonic splicing enhancers (ESEs).		RT-PCR			SON		Four AONs and a sense oligonucleotide (SON) were designed to block exonic splicing enhancers (ESEs).	
29524130	chr14	21495467	21497467	METTL3	The deletion of m6A writer protein methyltransferaselike (METTL)3 in porcine BMSCs (pBMSCs) could promote adipogenesis and janus kinase (JAK)1 protein expressionvia anm6 A-dependent way. Knockdown ofMETTL3 decreasedmRNAm6 A levels of JAK1, leading to enhanced YTH m6 A RNA binding protein 2 (YTHDF2)-dependent JAK1 mRNA stability. We further demonstrated that JAK1 activated signal transducer and activator of transcription (STAT) 5 through regulation of its phosphorylation to bind to the promoter of CCAAT/enhancer binding protein (C/EBP) b, which could ultimately lead to a modulated adipogenic process. 	human		High+Lowthroughput	Disrupting the three-dimensional regulatory topology of the Pitx1 locus results in overtly normal development	否			Bone marrow stem cell	E_01_0157	flow cytometry ，Real-time quantitative PCR ， staining ，Protein extraction ，Western blot ，Cell transfection ，Immunofluorescence assay ，Quantitative analysis ，Chromatin immunoprecipitation assay ，Luciferase reporter assay	The deletion of m6A writer protein methyltransferaselike (METTL)3 in porcine BMSCs (pBMSCs) could promote adipogenesis and janus kinase (JAK)1 protein expressionvia anm6 A-dependent way. Knockdown ofMETTL3 decreasedmRNAm6 A levels of JAK1, leading to enhanced YTH m6 A RNA binding protein 2 (YTHDF2)-dependent JAK1 mRNA stability. We further demonstrated that JAK1 activated signal transducer and activator of transcription (STAT) 5 through regulation of its phosphorylation to bind to the promoter of CCAAT/enhancer binding protein (C/EBP) b, which could ultimately lead to a modulated adipogenic process. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The deletion of m6A writer protein methyltransferaselike (METTL)3 in porcine BMSCs (pBMSCs) could promote adipogenesis and janus kinase (JAK)1 protein expressionvia anm6 A-dependent way. Knockdown ofMETTL3 decreasedmRNAm6 A levels of JAK1, leading to enhanced YTH m6 A RNA binding protein 2 (YTHDF2)-dependent JAK1 mRNA stability. We further demonstrated that JAK1 activated signal transducer and activator of transcription (STAT) 5 through regulation of its phosphorylation to bind to the promoter of CCAAT/enhancer binding protein (C/EBP) b, which could ultimately lead to a modulated adipogenic process. 	Immunohistochemical staining	The deletion of m6A writer protein methyltransferaselike (METTL)3 in porcine BMSCs (pBMSCs) could promote adipogenesis and janus kinase (JAK)1 protein expressionvia anm6 A-dependent way. Knockdown ofMETTL3 decreasedmRNAm6 A levels of JAK1, leading to enhanced YTH m6 A RNA binding protein 2 (YTHDF2)-dependent JAK1 mRNA stability. We further demonstrated that JAK1 activated signal transducer and activator of transcription (STAT) 5 through regulation of its phosphorylation to bind to the promoter of CCAAT/enhancer binding protein (C/EBP) b, which could ultimately lead to a modulated adipogenic process. 		flow cytometry ，Real-time quantitative PCR ， staining ，Protein extraction ，Western blot ，Cell transfection ，Immunofluorescence assay ，Quantitative analysis ，Chromatin immunoprecipitation assay ，Luciferase reporter assay			METTL3		The deletion of m6A writer protein methyltransferaselike (METTL)3 in porcine BMSCs (pBMSCs) could promote adipogenesis and janus kinase (JAK)1 protein expressionvia anm6 A-dependent way. Knockdown ofMETTL3 decreasedmRNAm6 A levels of JAK1, leading to enhanced YTH m6 A RNA binding protein 2 (YTHDF2)-dependent JAK1 mRNA stability. We further demonstrated that JAK1 activated signal transducer and activator of transcription (STAT) 5 through regulation of its phosphorylation to bind to the promoter of CCAAT/enhancer binding protein (C/EBP) b, which could ultimately lead to a modulated adipogenic process. 	
29523836	chr2	226728284	226730284	IRS1	Phosphatidylinositol-3-kinase (PI3K), 74 insulin receptor substrate 1 (IRS1), and glucose transporter 4 (GLUT4) play crucial roles in 75 glucose metabolism and insulin resistance. The mechanism begins with the stimulation of 76 insulin receptor intrinsic kinase activity to activate PI3K signaling. Then, PI3K inhibits the 77 c-Jun N-terminal kinase 1 (JNK1) activity in succession. Moreover, GLUT4, which is 78 regulated by insulin, is able to reduce glucose levels through participating in the IRS/PI3K 79 signaling pathway (Chen et al., 2018). 	human		High+Lowthroughput	Investigating a multigene prognostic assay based on significant pathways for Luminal A breast cancer through gene expression profile analysis	否			HeLa cell	E_01_0158	Nuclear magnetic resonance (NMR) spectroscopy analysis ，RNA extraction and real-time PCR ，Western blot analysis ，Histopathological analysis ,Analysis of glycated hemoglobin and β-cell function	Phosphatidylinositol-3-kinase (PI3K), 74 insulin receptor substrate 1 (IRS1), and glucose transporter 4 (GLUT4) play crucial roles in 75 glucose metabolism and insulin resistance. The mechanism begins with the stimulation of 76 insulin receptor intrinsic kinase activity to activate PI3K signaling. Then, PI3K inhibits the 77 c-Jun N-terminal kinase 1 (JNK1) activity in succession. Moreover, GLUT4, which is 78 regulated by insulin, is able to reduce glucose levels through participating in the IRS/PI3K 79 signaling pathway (Chen et al., 2018). 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Phosphatidylinositol-3-kinase (PI3K), 74 insulin receptor substrate 1 (IRS1), and glucose transporter 4 (GLUT4) play crucial roles in 75 glucose metabolism and insulin resistance. The mechanism begins with the stimulation of 76 insulin receptor intrinsic kinase activity to activate PI3K signaling. Then, PI3K inhibits the 77 c-Jun N-terminal kinase 1 (JNK1) activity in succession. Moreover, GLUT4, which is 78 regulated by insulin, is able to reduce glucose levels through participating in the IRS/PI3K 79 signaling pathway (Chen et al., 2018). 	Immunohistochemical staining	Phosphatidylinositol-3-kinase (PI3K), 74 insulin receptor substrate 1 (IRS1), and glucose transporter 4 (GLUT4) play crucial roles in 75 glucose metabolism and insulin resistance. The mechanism begins with the stimulation of 76 insulin receptor intrinsic kinase activity to activate PI3K signaling. Then, PI3K inhibits the 77 c-Jun N-terminal kinase 1 (JNK1) activity in succession. Moreover, GLUT4, which is 78 regulated by insulin, is able to reduce glucose levels through participating in the IRS/PI3K 79 signaling pathway (Chen et al., 2018). 		Nuclear magnetic resonance (NMR) spectroscopy analysis ，RNA extraction and real-time PCR ，Western blot analysis ，Histopathological analysis ,Analysis of glycated hemoglobin and β-cell function			IRS1		Phosphatidylinositol-3-kinase (PI3K), 74 insulin receptor substrate 1 (IRS1), and glucose transporter 4 (GLUT4) play crucial roles in 75 glucose metabolism and insulin resistance. The mechanism begins with the stimulation of 76 insulin receptor intrinsic kinase activity to activate PI3K signaling. Then, PI3K inhibits the 77 c-Jun N-terminal kinase 1 (JNK1) activity in succession. Moreover, GLUT4, which is 78 regulated by insulin, is able to reduce glucose levels through participating in the IRS/PI3K 79 signaling pathway (Chen et al., 2018). 	
31223056	chr16	71843198	71845198	IST1	we demonstrate that MAPT accumulation suppresses IST1 transcription with the mechanisms involving the ANP32A-regulated mask of histone acetylation	human	connective	High+Lowthroughput	MAPT/Tau accumulation represses autophagy flux by disrupting IST1-regulated ESCRT-III complex formation: a vicious cycle in Alzheimer neurodegeneration	否			macrophage	E_01_0159	PCR	we demonstrate that MAPT accumulation suppresses IST1 transcription with the mechanisms involving the ANP32A-regulated mask of histone acetylation	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		we demonstrate that MAPT accumulation suppresses IST1 transcription with the mechanisms involving the ANP32A-regulated mask of histone acetylation	Immunohistochemical staining	we demonstrate that MAPT accumulation suppresses IST1 transcription with the mechanisms involving the ANP32A-regulated mask of histone acetylation		PCR			IST1		we demonstrate that MAPT accumulation suppresses IST1 transcription with the mechanisms involving the ANP32A-regulated mask of histone acetylation	
31219650	chr7	44101654	44103654	AEBP1	In this study, we explored the clinical significance and biological function of AEBP1 in COAD. We observed that AEBP1 was overexpressed in COAD tissues and cells and that the expression of AEBP1 was correlated with tumor size, the level of histologic differentiation, lymph node metastasis, and cancer stage in COAD patients. 	human	Epithelial	High+Lowthroughput	AEBP1, a prognostic indicator, promotes colon adenocarcinoma cell growth and metastasis through the NF-κB pathway	否			colon cancer cell	E_01_0160	PCR	In this study, we explored the clinical significance and biological function of AEBP1 in COAD. We observed that AEBP1 was overexpressed in COAD tissues and cells and that the expression of AEBP1 was correlated with tumor size, the level of histologic differentiation, lymph node metastasis, and cancer stage in COAD patients. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In this study, we explored the clinical significance and biological function of AEBP1 in COAD. We observed that AEBP1 was overexpressed in COAD tissues and cells and that the expression of AEBP1 was correlated with tumor size, the level of histologic differentiation, lymph node metastasis, and cancer stage in COAD patients. 	Immunohistochemical staining	In this study, we explored the clinical significance and biological function of AEBP1 in COAD. We observed that AEBP1 was overexpressed in COAD tissues and cells and that the expression of AEBP1 was correlated with tumor size, the level of histologic differentiation, lymph node metastasis, and cancer stage in COAD patients. 		PCR			AEBP1		In this study, we explored the clinical significance and biological function of AEBP1 in COAD. We observed that AEBP1 was overexpressed in COAD tissues and cells and that the expression of AEBP1 was correlated with tumor size, the level of histologic differentiation, lymph node metastasis, and cancer stage in COAD patients. 	
31219209	chr7	148805028	148807028	EZH2	And lncRNA‐mediated epigenetic inhibition of antitumor gene via binding EZH2 in various cancers has been gradually detected. l	human	connective	High+Lowthroughput	Long noncoding RNA OIP5-AS1 aggravates cell proliferation, migration in gastric cancer by epigenetically silencing NLRP6 expression via binding EZH2	否		Colon cancer	gastric cancer cell	E_01_0161	PCR	And lncRNA‐mediated epigenetic inhibition of antitumor gene via binding EZH2 in various cancers has been gradually detected. l	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		And lncRNA‐mediated epigenetic inhibition of antitumor gene via binding EZH2 in various cancers has been gradually detected. l	Immunohistochemical staining	And lncRNA‐mediated epigenetic inhibition of antitumor gene via binding EZH2 in various cancers has been gradually detected. l		PCR				EZH2		And lncRNA‐mediated epigenetic inhibition of antitumor gene via binding EZH2 in various cancers has been gradually detected. l
31216773	chr13	27958003	27960003	CDX2	It was found by chromatin immunoprecipitation experiments that CDX2 and HNF4α bind to the YAP1 enhancer in Caco-2 cells. These results reveal a previously unknown enhancer of the YAP1 promoter activity in the YAP1 gene, with importance for high expression levels in intestinal epithelial cells.	human	Colon	High+Lowthroughput	HNF4α and CDX2 Regulate Intestinal YAP1 Promoter Activity	否			intestinal cell	E_01_0162	PCR	It was found by chromatin immunoprecipitation experiments that CDX2 and HNF4α bind to the YAP1 enhancer in Caco-2 cells. These results reveal a previously unknown enhancer of the YAP1 promoter activity in the YAP1 gene, with importance for high expression levels in intestinal epithelial cells.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		It was found by chromatin immunoprecipitation experiments that CDX2 and HNF4α bind to the YAP1 enhancer in Caco-2 cells. These results reveal a previously unknown enhancer of the YAP1 promoter activity in the YAP1 gene, with importance for high expression levels in intestinal epithelial cells.	Immunohistochemical staining	It was found by chromatin immunoprecipitation experiments that CDX2 and HNF4α bind to the YAP1 enhancer in Caco-2 cells. These results reveal a previously unknown enhancer of the YAP1 promoter activity in the YAP1 gene, with importance for high expression levels in intestinal epithelial cells.		PCR				CDX2		It was found by chromatin immunoprecipitation experiments that CDX2 and HNF4α bind to the YAP1 enhancer in Caco-2 cells. These results reveal a previously unknown enhancer of the YAP1 promoter activity in the YAP1 gene, with importance for high expression levels in intestinal epithelial cells.
31216559	chr12	49973763	49975763	RACGAP1	Rac GTPase-activating protein 1 (RACGAP1) is as- sociated with cell proliferation, and there is much evidence of its oncogenic role. 	human	connective	High+Lowthroughput	Rac GTPase-Activating Protein 1 (RACGAP1) as an Oncogenic Enhancer in Esophageal Carcinoma	否			cancer cell	E_01_0163	PCR	Rac GTPase-activating protein 1 (RACGAP1) is as- sociated with cell proliferation, and there is much evidence of its oncogenic role. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Rac GTPase-activating protein 1 (RACGAP1) is as- sociated with cell proliferation, and there is much evidence of its oncogenic role. 	Immunohistochemical staining	Rac GTPase-activating protein 1 (RACGAP1) is as- sociated with cell proliferation, and there is much evidence of its oncogenic role. 		PCR				RACGAP1		Rac GTPase-activating protein 1 (RACGAP1) is as- sociated with cell proliferation, and there is much evidence of its oncogenic role. 
31216030	chr19	4171371	4173371	SIRT6	SIRT6 is critical for activating transcription of Nuclear factor (erythroid-derived 2)-like 2 (NRF2) re-sponsive genes during oxidative stress	human	connective	High+Lowthroughput	SIRT6 promotes transcription of a subset of NRF2 targets by mono-ADP-ribosylating BAF170	否			stem cell	E_01_0164	PCR	SIRT6 is critical for activating transcription of Nuclear factor (erythroid-derived 2)-like 2 (NRF2) re-sponsive genes during oxidative stress	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		SIRT6 is critical for activating transcription of Nuclear factor (erythroid-derived 2)-like 2 (NRF2) re-sponsive genes during oxidative stress	Immunohistochemical staining	SIRT6 is critical for activating transcription of Nuclear factor (erythroid-derived 2)-like 2 (NRF2) re-sponsive genes during oxidative stress		PCR			SIRT6		SIRT6 is critical for activating transcription of Nuclear factor (erythroid-derived 2)-like 2 (NRF2) re-sponsive genes during oxidative stress	
31215771	chr20	56626718	56628718	TFAP2C	We found that the cooperations between regulators were much closer in lung‐metastatic cells. Moreover,regulators such as TFAP2C, GTF2I and LMO4 were found to have potential prognostic value for lung metastasis free (LMF) survival of breast cancer. 	human	connective	High+Lowthroughput	Comprehensive epigenetic analyses reveal master regulators driving lung metastasis of breast cancer	否		mammary cancer	breast cancer cell	E_01_0165	PCR	We found that the cooperations between regulators were much closer in lung‐metastatic cells. Moreover,regulators such as TFAP2C, GTF2I and LMO4 were found to have potential prognostic value for lung metastasis free (LMF) survival of breast cancer. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We found that the cooperations between regulators were much closer in lung‐metastatic cells. Moreover,regulators such as TFAP2C, GTF2I and LMO4 were found to have potential prognostic value for lung metastasis free (LMF) survival of breast cancer. 	Immunohistochemical staining	We found that the cooperations between regulators were much closer in lung‐metastatic cells. Moreover,regulators such as TFAP2C, GTF2I and LMO4 were found to have potential prognostic value for lung metastasis free (LMF) survival of breast cancer. 		PCR				TFAP2C		We found that the cooperations between regulators were much closer in lung‐metastatic cells. Moreover,regulators such as TFAP2C, GTF2I and LMO4 were found to have potential prognostic value for lung metastasis free (LMF) survival of breast cancer. 
31213123	chr7	148804377	148806377	EZH2	Accumulating data demonstrated that Enhancer of zeste homolog 2 (EZH2) as an oncogenic pr otein is over-expressed in various human cancers, including PC.	human	connective	High+Lowthroughput	Diosgenin exhibits tumor suppressive function via down-regulation of EZH2 in pancreatic cancer cells	否		tumour	tumor cell	E_01_0166	PCR	Accumulating data demonstrated that Enhancer of zeste homolog 2 (EZH2) as an oncogenic pr otein is over-expressed in various human cancers, including PC.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Accumulating data demonstrated that Enhancer of zeste homolog 2 (EZH2) as an oncogenic pr otein is over-expressed in various human cancers, including PC.	Immunohistochemical staining	Accumulating data demonstrated that Enhancer of zeste homolog 2 (EZH2) as an oncogenic pr otein is over-expressed in various human cancers, including PC.		PCR				EZH2		Accumulating data demonstrated that Enhancer of zeste homolog 2 (EZH2) as an oncogenic pr otein is over-expressed in various human cancers, including PC.
31189106	chrX	137563628	137565628	ZIC3	Our data therefore place ZIC3 upstream of a set of pro-differentiation transcriptional regulators and provide an important advance in our understanding of the regulatory factors governing the early steps in ESC differentiation	human	connective	High+Lowthroughput	ZIC3 Controls the Transition from Naive to Primed Pluripotency	否			embryonic stem cell	E_01_0167	PCR	Our data therefore place ZIC3 upstream of a set of pro-differentiation transcriptional regulators and provide an important advance in our understanding of the regulatory factors governing the early steps in ESC differentiation	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Our data therefore place ZIC3 upstream of a set of pro-differentiation transcriptional regulators and provide an important advance in our understanding of the regulatory factors governing the early steps in ESC differentiation	Immunohistochemical staining	Our data therefore place ZIC3 upstream of a set of pro-differentiation transcriptional regulators and provide an important advance in our understanding of the regulatory factors governing the early steps in ESC differentiation		PCR			ZIC3		Our data therefore place ZIC3 upstream of a set of pro-differentiation transcriptional regulators and provide an important advance in our understanding of the regulatory factors governing the early steps in ESC differentiation	
31186776	chr1	205594870	205596870	ELK4	In addition, prognostic analysis demonstrated that ETV5 andELK4 expression levels were associated with the survival time of patients with GBM. These results suggested that ELK4 and ETV5 may be prognostic markers for GBM, and that their microRNAs may be candidate therapeutic targets.	human	connective	High+Lowthroughput	ceRNA network analysis reveals prognostic markers for glioblastoma	否		cancer	cancer cell	E_01_0168	PCR	In addition, prognostic analysis demonstrated that ETV5 andELK4 expression levels were associated with the survival time of patients with GBM. These results suggested that ELK4 and ETV5 may be prognostic markers for GBM, and that their microRNAs may be candidate therapeutic targets.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In addition, prognostic analysis demonstrated that ETV5 andELK4 expression levels were associated with the survival time of patients with GBM. These results suggested that ELK4 and ETV5 may be prognostic markers for GBM, and that their microRNAs may be candidate therapeutic targets.	Immunohistochemical staining	In addition, prognostic analysis demonstrated that ETV5 andELK4 expression levels were associated with the survival time of patients with GBM. These results suggested that ELK4 and ETV5 may be prognostic markers for GBM, and that their microRNAs may be candidate therapeutic targets.		PCR				ELK4		In addition, prognostic analysis demonstrated that ETV5 andELK4 expression levels were associated with the survival time of patients with GBM. These results suggested that ELK4 and ETV5 may be prognostic markers for GBM, and that their microRNAs may be candidate therapeutic targets.
31186707	chr20	22578327	22580327	FOXA2	Long non-coding RNA-neighboring enhancer of FOXA2 (lncRNA-NEF) is a recently identified tumor suppressor in hepatocellular carcinoma. T	human	connective	High+Lowthroughput	Long non-coding RNA-neighboring enhancer of FOXA2 inhibits the migration and invasion of small cell lung carcinoma cells by downregulating transforming growth factor-β1	否		lung cancer	Lung cancer cell	E_01_0169	PCR	Long non-coding RNA-neighboring enhancer of FOXA2 (lncRNA-NEF) is a recently identified tumor suppressor in hepatocellular carcinoma. T	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Long non-coding RNA-neighboring enhancer of FOXA2 (lncRNA-NEF) is a recently identified tumor suppressor in hepatocellular carcinoma. T	Immunohistochemical staining	Long non-coding RNA-neighboring enhancer of FOXA2 (lncRNA-NEF) is a recently identified tumor suppressor in hepatocellular carcinoma. T		PCR				FOXA2		Long non-coding RNA-neighboring enhancer of FOXA2 (lncRNA-NEF) is a recently identified tumor suppressor in hepatocellular carcinoma. T
31182783	chr6	31161443	31163443	POU5F1	OCT4, also named POU5F1, is the main regulator of pluripotency in stem cells1 It also has a part in tumorigenesis, cellular stress response, and hence is linked to various diseases from cancer to autoimmune disorders 2–4 .OCT4 possesses several isoforms with different functions at both protein and transcript levels, and their expressions are regulated through different mechanisms and at various biological processes 5,6	human	connective	High+Lowthroughput	lncRNA PSORS1C3 is regulated by glucocorticoids and fine-tunes OCT4 expression in non-pluripotent cells	否			stem cell	E_01_0170	PCR	OCT4, also named POU5F1, is the main regulator of pluripotency in stem cells1 It also has a part in tumorigenesis, cellular stress response, and hence is linked to various diseases from cancer to autoimmune disorders 2–4 .OCT4 possesses several isoforms with different functions at both protein and transcript levels, and their expressions are regulated through different mechanisms and at various biological processes 5,6	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		OCT4, also named POU5F1, is the main regulator of pluripotency in stem cells1 It also has a part in tumorigenesis, cellular stress response, and hence is linked to various diseases from cancer to autoimmune disorders 2–4 .OCT4 possesses several isoforms with different functions at both protein and transcript levels, and their expressions are regulated through different mechanisms and at various biological processes 5,6	Immunohistochemical staining	OCT4, also named POU5F1, is the main regulator of pluripotency in stem cells1 It also has a part in tumorigenesis, cellular stress response, and hence is linked to various diseases from cancer to autoimmune disorders 2–4 .OCT4 possesses several isoforms with different functions at both protein and transcript levels, and their expressions are regulated through different mechanisms and at various biological processes 5,6		PCR				POU5F1		OCT4, also named POU5F1, is the main regulator of pluripotency in stem cells1 It also has a part in tumorigenesis, cellular stress response, and hence is linked to various diseases from cancer to autoimmune disorders 2–4 .OCT4 possesses several isoforms with different functions at both protein and transcript levels, and their expressions are regulated through different mechanisms and at various biological processes 5,6
31174563	chr11	65495199	65497199	MALAT1	Microarray-based analysis initially provided data suggesting that the expression of MALAT1 was up regulated while that of the ABI family member 3 binding protein (ABI3BP) was down-regulated in GBC tissues and cell lines. 	human	connective	High+Lowthroughput	Long noncoding RNA MALAT1 potentiates growth and inhibits senescence by antagonizing ABI3BP in gallbladder cancer cells	否		Gallbladder cancer	Gallbladder cancer cell	E_01_0171	PCR	Microarray-based analysis initially provided data suggesting that the expression of MALAT1 was up regulated while that of the ABI family member 3 binding protein (ABI3BP) was down-regulated in GBC tissues and cell lines. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Microarray-based analysis initially provided data suggesting that the expression of MALAT1 was up regulated while that of the ABI family member 3 binding protein (ABI3BP) was down-regulated in GBC tissues and cell lines. 	Immunohistochemical staining	Microarray-based analysis initially provided data suggesting that the expression of MALAT1 was up regulated while that of the ABI family member 3 binding protein (ABI3BP) was down-regulated in GBC tissues and cell lines. 		PCR				MALAT1		Microarray-based analysis initially provided data suggesting that the expression of MALAT1 was up regulated while that of the ABI family member 3 binding protein (ABI3BP) was down-regulated in GBC tissues and cell lines. 
31171769	chr7	148803892	148805892	EZH2	We revealed that miR-708 was transcriptionally repressed by EZH2 (enhancer of zeste homolog 2)-induced histone H3 lysine 27 trimethylation and promoter methylation. 	human	connective	High+Lowthroughput	Silencing of microRNA-708 promotes cell growth and epithelial-to-mesenchymal transition by activating the SPHK2/AKT/β-catenin pathway in glioma	否		Gliomas	Glioma cell	E_01_0172	PCR	We revealed that miR-708 was transcriptionally repressed by EZH2 (enhancer of zeste homolog 2)-induced histone H3 lysine 27 trimethylation and promoter methylation. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We revealed that miR-708 was transcriptionally repressed by EZH2 (enhancer of zeste homolog 2)-induced histone H3 lysine 27 trimethylation and promoter methylation. 	Immunohistochemical staining	We revealed that miR-708 was transcriptionally repressed by EZH2 (enhancer of zeste homolog 2)-induced histone H3 lysine 27 trimethylation and promoter methylation. 		PCR				EZH2		We revealed that miR-708 was transcriptionally repressed by EZH2 (enhancer of zeste homolog 2)-induced histone H3 lysine 27 trimethylation and promoter methylation. 
31164150	chr16	67559426	67561426	CTCF	Our study suggests an intriguing model where cell type-specific transcription factors such as p63 cooperate with the genomeorganizer CTCF in the three dimensional chromatin space to regulate the transcription program important for the proper cell identity	human	epithelial cells	High+Lowthroughput	p63 cooperates with CTCF to modulate chromatin architecture in skin keratinocytes	否			glial cell	E_01_0173	PCR	Our study suggests an intriguing model where cell type-specific transcription factors such as p63 cooperate with the genomeorganizer CTCF in the three dimensional chromatin space to regulate the transcription program important for the proper cell identity	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Our study suggests an intriguing model where cell type-specific transcription factors such as p63 cooperate with the genomeorganizer CTCF in the three dimensional chromatin space to regulate the transcription program important for the proper cell identity	Immunohistochemical staining	Our study suggests an intriguing model where cell type-specific transcription factors such as p63 cooperate with the genomeorganizer CTCF in the three dimensional chromatin space to regulate the transcription program important for the proper cell identity		PCR				CTCF		Our study suggests an intriguing model where cell type-specific transcription factors such as p63 cooperate with the genomeorganizer CTCF in the three dimensional chromatin space to regulate the transcription program important for the proper cell identity
31162630	chr7	148804276	148806276	EZH2	EZH2 inhibition might be a potential therapeutic target for restenosis.	human	Myotome	High+Lowthroughput	Inhibition of polycomb repressor complex 2 ameliorates neointimal hyperplasia by suppressing trimethylation of H3K27 in vascular smooth muscle cells	否			smooth muscle cell	E_01_0174	PCR	EZH2 inhibition might be a potential therapeutic target for restenosis.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		EZH2 inhibition might be a potential therapeutic target for restenosis.	Immunohistochemical staining	EZH2 inhibition might be a potential therapeutic target for restenosis.		PCR				EZH2		EZH2 inhibition might be a potential therapeutic target for restenosis.
31160593	chr7	148804085	148806085	EZH2	We report that suppressing EZH2 activity ameliorates experimental intestinal inflammation and delayed the onset of colitis-associated cancer. In a	human	connective	High+Lowthroughput	Targeting EZH2 histone methyltransferase activity alleviates experimental intestinal inflammation	否		Colon cancer	colon cancer cell	E_01_0175	PCR	We report that suppressing EZH2 activity ameliorates experimental intestinal inflammation and delayed the onset of colitis-associated cancer. In a	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We report that suppressing EZH2 activity ameliorates experimental intestinal inflammation and delayed the onset of colitis-associated cancer. In a	Immunohistochemical staining	We report that suppressing EZH2 activity ameliorates experimental intestinal inflammation and delayed the onset of colitis-associated cancer. In a		PCR				EZH2		We report that suppressing EZH2 activity ameliorates experimental intestinal inflammation and delayed the onset of colitis-associated cancer. In a
31155838	chr11	69767717	69769717	FGF4	Data suggest that FGF-4 signalling is involved in EWS-Oct-4-mediated tumorigenesis, and that its inhibition impairs tumour growth in vivo significantly	human	connective	High+Lowthroughput	Critical role of the fibroblast growth factor signalling pathway in Ewing's sarcoma octamer-binding transcription factor 4-mediated cell proliferation and tumorigenesis	否		tumour	tumor cell	E_01_0176	PCR	Data suggest that FGF-4 signalling is involved in EWS-Oct-4-mediated tumorigenesis, and that its inhibition impairs tumour growth in vivo significantly	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Data suggest that FGF-4 signalling is involved in EWS-Oct-4-mediated tumorigenesis, and that its inhibition impairs tumour growth in vivo significantly	Immunohistochemical staining	Data suggest that FGF-4 signalling is involved in EWS-Oct-4-mediated tumorigenesis, and that its inhibition impairs tumour growth in vivo significantly		PCR			FGF4		Data suggest that FGF-4 signalling is involved in EWS-Oct-4-mediated tumorigenesis, and that its inhibition impairs tumour growth in vivo significantly	
31081034	chr18	55219304	55221304	TCF4	The psychiatric risk-associated transcription factor 4 (TCF4) is linked to schizophrenia. Rare TCF4 coding variants are found in individuals with PittHopkins syndrome an intellectual disability and autism spectrum disorder.	human	connective	High+Lowthroughput	Structural basis for preferential binding of human TCF4 to DNA containing 5-carboxylcytosine	否			neural cell	E_01_0177	PCR	The psychiatric risk-associated transcription factor 4 (TCF4) is linked to schizophrenia. Rare TCF4 coding variants are found in individuals with PittHopkins syndrome an intellectual disability and autism spectrum disorder.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The psychiatric risk-associated transcription factor 4 (TCF4) is linked to schizophrenia. Rare TCF4 coding variants are found in individuals with PittHopkins syndrome an intellectual disability and autism spectrum disorder.	Immunohistochemical staining	The psychiatric risk-associated transcription factor 4 (TCF4) is linked to schizophrenia. Rare TCF4 coding variants are found in individuals with PittHopkins syndrome an intellectual disability and autism spectrum disorder.		PCR				TCF4		The psychiatric risk-associated transcription factor 4 (TCF4) is linked to schizophrenia. Rare TCF4 coding variants are found in individuals with PittHopkins syndrome an intellectual disability and autism spectrum disorder.
30995827	chr20	22578226	22580226	FOXA2	The role of FOXA2 is different, working as an activator in hepatic cells. As a tumour suppressor, FOXA2 could be responsible for SLC25A13 high expression levels in liver and its downregulation in hepatocellular carcinoma (HCC).	human	connective	High+Lowthroughput	Transcriptional Regulation Factors of the Human Mitochondrial Aspartate/Glutamate Carrier Gene, Isoform 2 (SLC25A13): USF1 as Basal Factor and FOXA2 as Activator in Liver Cells	否			cancer cell	E_01_0178	PCR	The role of FOXA2 is different, working as an activator in hepatic cells. As a tumour suppressor, FOXA2 could be responsible for SLC25A13 high expression levels in liver and its downregulation in hepatocellular carcinoma (HCC).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The role of FOXA2 is different, working as an activator in hepatic cells. As a tumour suppressor, FOXA2 could be responsible for SLC25A13 high expression levels in liver and its downregulation in hepatocellular carcinoma (HCC).	Immunohistochemical staining	The role of FOXA2 is different, working as an activator in hepatic cells. As a tumour suppressor, FOXA2 could be responsible for SLC25A13 high expression levels in liver and its downregulation in hepatocellular carcinoma (HCC).		PCR				FOXA2		The role of FOXA2 is different, working as an activator in hepatic cells. As a tumour suppressor, FOXA2 could be responsible for SLC25A13 high expression levels in liver and its downregulation in hepatocellular carcinoma (HCC).
31127282	chr16	67559749	67561749	CTCF	CTCF is an important regulator of the 3D chromatin ar- chitecture of interphase chromosomes, which guides gene expression (10–13).	human	connective	High+Lowthroughput	Acute depletion of CTCF directly affects MYC regulation through loss of enhancer-promoter looping	否				E_01_0179	PCR	CTCF is an important regulator of the 3D chromatin ar- chitecture of interphase chromosomes, which guides gene expression (10–13).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		CTCF is an important regulator of the 3D chromatin ar- chitecture of interphase chromosomes, which guides gene expression (10–13).	Immunohistochemical staining	CTCF is an important regulator of the 3D chromatin ar- chitecture of interphase chromosomes, which guides gene expression (10–13).		PCR				CTCF		CTCF is an important regulator of the 3D chromatin ar- chitecture of interphase chromosomes, which guides gene expression (10–13).
31053723	chr11	2126891	2128891	IGF2	This work suggests a mechanism for epigenetic regulation of dopamine levels in the brain. Epigenetic misregulation of an enhancer at IGF2 may underlie the dopaminergic abnormalities that drives psychotic symptoms. 	human	connective	High+Lowthroughput	Differential methylation of enhancer at IGF2 is associated with abnormal dopamine synthesis in major psychosis	是			neural cell	E_01_0180	PCR	This work suggests a mechanism for epigenetic regulation of dopamine levels in the brain. Epigenetic misregulation of an enhancer at IGF2 may underlie the dopaminergic abnormalities that drives psychotic symptoms. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		This work suggests a mechanism for epigenetic regulation of dopamine levels in the brain. Epigenetic misregulation of an enhancer at IGF2 may underlie the dopaminergic abnormalities that drives psychotic symptoms. 	Immunohistochemical staining	This work suggests a mechanism for epigenetic regulation of dopamine levels in the brain. Epigenetic misregulation of an enhancer at IGF2 may underlie the dopaminergic abnormalities that drives psychotic symptoms. 		PCR			IGF2		This work suggests a mechanism for epigenetic regulation of dopamine levels in the brain. Epigenetic misregulation of an enhancer at IGF2 may underlie the dopaminergic abnormalities that drives psychotic symptoms. 	
31053176	chrX	153441659	153443659	TREX2	The data highlight a regulatory role of TREX2 DNA methylation for gene expression which might affect incidence and survival of laryngeal cancer. 	human	connective	High+Lowthroughput	DNA methylation at an enhancer of the three prime repair exonuclease 2 gene (TREX2) is linked to gene expression and survival in laryngeal cancer	是			laryngeal carcinoma cell	E_01_0181	PCR	The data highlight a regulatory role of TREX2 DNA methylation for gene expression which might affect incidence and survival of laryngeal cancer. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The data highlight a regulatory role of TREX2 DNA methylation for gene expression which might affect incidence and survival of laryngeal cancer. 	Immunohistochemical staining	The data highlight a regulatory role of TREX2 DNA methylation for gene expression which might affect incidence and survival of laryngeal cancer. 		PCR			TREX2		The data highlight a regulatory role of TREX2 DNA methylation for gene expression which might affect incidence and survival of laryngeal cancer. 	
31721105	chr12	117450290	117452290	KSR2	In order to understand biological roles of TE-derived miR-1269a, we examined expression pattern for miR-1269a and its target gene, KSR2, in various tissues of Sebastes schlegelii.	human	liver	High+Lowthroughput	Expression analysis of LTR-derived miR-1269a and target gene, KSR2 in Sebastes schlegelii	否		liver cancer	HCC cell	E_01_0182		In order to understand biological roles of TE-derived miR-1269a, we examined expression pattern for miR-1269a and its target gene, KSR2, in various tissues of Sebastes schlegelii.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In order to understand biological roles of TE-derived miR-1269a, we examined expression pattern for miR-1269a and its target gene, KSR2, in various tissues of Sebastes schlegelii.	Immunohistochemical staining	In order to understand biological roles of TE-derived miR-1269a, we examined expression pattern for miR-1269a and its target gene, KSR2, in various tissues of Sebastes schlegelii.					KSR2		In order to understand biological roles of TE-derived miR-1269a, we examined expression pattern for miR-1269a and its target gene, KSR2, in various tissues of Sebastes schlegelii.	
31718595	chr7	148804304	148806304	EZH2	Overexpression of EZH2 is positively correlated with tissue pathological grade and stage,metastasis, and poor survival in many types of solid tumors, including lung cancer, breast cancer, gastric cancer, prostate cancer, and melanoma.	human	connective	High+Lowthroughput	EZH2 upregulation by ERα induces proliferation and migration of papillary thyroid carcinoma	否		cancer	Cancer Stem Cell	E_01_0183	PCR, Western blot, immunofluorescence staining	Overexpression of EZH2 is positively correlated with tissue pathological grade and stage,metastasis, and poor survival in many types of solid tumors, including lung cancer, breast cancer, gastric cancer, prostate cancer, and melanoma.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Overexpression of EZH2 is positively correlated with tissue pathological grade and stage,metastasis, and poor survival in many types of solid tumors, including lung cancer, breast cancer, gastric cancer, prostate cancer, and melanoma.	Immunohistochemical staining	Overexpression of EZH2 is positively correlated with tissue pathological grade and stage,metastasis, and poor survival in many types of solid tumors, including lung cancer, breast cancer, gastric cancer, prostate cancer, and melanoma.		PCR、Western blot、免疫荧光染色				EZH2		Overexpression of EZH2 is positively correlated with tissue pathological grade and stage,metastasis, and poor survival in many types of solid tumors, including lung cancer, breast cancer, gastric cancer, prostate cancer, and melanoma.
31698100	chr20	13993019	13995019	MACROD2	Although MACROD2 mutations have not been associated with limb malformation until now, it is located next to KIF16B, which is involved in fibroblast growth factor receptor (FGFR) signaling. 	human		High+Lowthroughput	Split hand/foot malformation associated with 20p12.1 deletion: A case report	是		Split hand / foot malformation		E_01_0184	PCR	Although MACROD2 mutations have not been associated with limb malformation until now, it is located next to KIF16B, which is involved in fibroblast growth factor receptor (FGFR) signaling. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Although MACROD2 mutations have not been associated with limb malformation until now, it is located next to KIF16B, which is involved in fibroblast growth factor receptor (FGFR) signaling. 	Immunohistochemical staining	Although MACROD2 mutations have not been associated with limb malformation until now, it is located next to KIF16B, which is involved in fibroblast growth factor receptor (FGFR) signaling. 		PCR			MACROD2,KIF16B		Although MACROD2 mutations have not been associated with limb malformation until now, it is located next to KIF16B, which is involved in fibroblast growth factor receptor (FGFR) signaling. ;Although MACROD2 mutations have not been associated with limb malformation until now, it is located next to KIF16B, which is involved in fibroblast growth factor receptor (FGFR) signaling. 	
31694013	chr7	148804620	148806620	EZH2	Enhancer of zeste homolog 2 (EZH2) is one central epigenetic silencer of the polycomb repressor complex 2 (PRC2) that is already in clinical use as a novel drug target and is associated with poorer prognosis in several cancer entities	human	intestines	High+Lowthroughput	Oleanolic Acid Acetate Exerts Anti-Inflammatory Activity via IKKα/β Suppression in TLR3-Mediated NF-κB Activation	否		Colon cancer	colon cancer cell	E_01_0185	PCR	Enhancer of zeste homolog 2 (EZH2) is one central epigenetic silencer of the polycomb repressor complex 2 (PRC2) that is already in clinical use as a novel drug target and is associated with poorer prognosis in several cancer entities	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Enhancer of zeste homolog 2 (EZH2) is one central epigenetic silencer of the polycomb repressor complex 2 (PRC2) that is already in clinical use as a novel drug target and is associated with poorer prognosis in several cancer entities	Immunohistochemical staining	Enhancer of zeste homolog 2 (EZH2) is one central epigenetic silencer of the polycomb repressor complex 2 (PRC2) that is already in clinical use as a novel drug target and is associated with poorer prognosis in several cancer entities		PCR				EZH2		Enhancer of zeste homolog 2 (EZH2) is one central epigenetic silencer of the polycomb repressor complex 2 (PRC2) that is already in clinical use as a novel drug target and is associated with poorer prognosis in several cancer entities
31693890	chr7	148804304	148806304	EZH2	The histone methyl transferase enhancer of zeste ho_x0002_molog 2 (EZH2) is a master transcriptional regulatorinvolved in histone H3 lysine 27 trimethylation.	human	breast	High+Lowthroughput	Enhancer of Zeste Homolog 2 in Colorectal Cancer Development and Progression	否		mammary cancer	breast cancer cell	E_01_0186	PCR,Western blot,Flow cytometry	The histone methyl transferase enhancer of zeste ho_x0002_molog 2 (EZH2) is a master transcriptional regulatorinvolved in histone H3 lysine 27 trimethylation.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The histone methyl transferase enhancer of zeste ho_x0002_molog 2 (EZH2) is a master transcriptional regulatorinvolved in histone H3 lysine 27 trimethylation.	Immunohistochemical staining	The histone methyl transferase enhancer of zeste ho_x0002_molog 2 (EZH2) is a master transcriptional regulatorinvolved in histone H3 lysine 27 trimethylation.		PCR,Western blot,Flow cytometry				EZH2		The histone methyl transferase enhancer of zeste ho_x0002_molog 2 (EZH2) is a master transcriptional regulatorinvolved in histone H3 lysine 27 trimethylation.
31693439	chr15	90963083	90965083	PRC1	Four are the main epigenetic pathways involved in this kind of networks and considered in our analysis. The polycomb-repressive complex 1 (PRC1), a transcriptional-repressor complex consisting of several proteins among which an important role is played by the Polycomb group ring finger ones (in particular Bmi-1) and whose action is responsible of the ubiquitylation of H2AK119ub1	human	bone marrow	High+Lowthroughput	Regulation of EZH2 by SMYD2-Mediated Lysine Methylation Is Implicated in Tumorigenesis	否		Myeloma	Myeloma cell	E_01_0187	PCR,Western blot,Flow cytometry	Four are the main epigenetic pathways involved in this kind of networks and considered in our analysis. The polycomb-repressive complex 1 (PRC1), a transcriptional-repressor complex consisting of several proteins among which an important role is played by the Polycomb group ring finger ones (in particular Bmi-1) and whose action is responsible of the ubiquitylation of H2AK119ub1	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Four are the main epigenetic pathways involved in this kind of networks and considered in our analysis. The polycomb-repressive complex 1 (PRC1), a transcriptional-repressor complex consisting of several proteins among which an important role is played by the Polycomb group ring finger ones (in particular Bmi-1) and whose action is responsible of the ubiquitylation of H2AK119ub1	Immunohistochemical staining	Four are the main epigenetic pathways involved in this kind of networks and considered in our analysis. The polycomb-repressive complex 1 (PRC1), a transcriptional-repressor complex consisting of several proteins among which an important role is played by the Polycomb group ring finger ones (in particular Bmi-1) and whose action is responsible of the ubiquitylation of H2AK119ub1		PCR,Western blot,Flow cytometry			PRC1		Four are the main epigenetic pathways involved in this kind of networks and considered in our analysis. The polycomb-repressive complex 1 (PRC1), a transcriptional-repressor complex consisting of several proteins among which an important role is played by the Polycomb group ring finger ones (in particular Bmi-1) and whose action is responsible of the ubiquitylation of H2AK119ub1	
31690584	chr17	72118178	72120178	SOX9	Knockdown of linc02095 results in decreased BC cell proliferation, whereas its overexpression promotes cells proliferation. Linc02095-depleted cells display reduced expression of SOX9 concomitant with reduced RNA polymerase	human	breast	High+Lowthroughput	The hTERT-VNTR2-2(nd) alleles are involved in genomic stability in gastrointestinal cancer	否		mammary cancer	breast cancer cell	E_01_0188	PCR, Western blot, gene knockdown	Knockdown of linc02095 results in decreased BC cell proliferation, whereas its overexpression promotes cells proliferation. Linc02095-depleted cells display reduced expression of SOX9 concomitant with reduced RNA polymerase	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Knockdown of linc02095 results in decreased BC cell proliferation, whereas its overexpression promotes cells proliferation. Linc02095-depleted cells display reduced expression of SOX9 concomitant with reduced RNA polymerase	Immunohistochemical staining	Knockdown of linc02095 results in decreased BC cell proliferation, whereas its overexpression promotes cells proliferation. Linc02095-depleted cells display reduced expression of SOX9 concomitant with reduced RNA polymerase		PCR,Western blot,基因敲降				SOX9		Knockdown of linc02095 results in decreased BC cell proliferation, whereas its overexpression promotes cells proliferation. Linc02095-depleted cells display reduced expression of SOX9 concomitant with reduced RNA polymerase
31682213	chr20	44582166	44584166	ADA	Azodicarbonamide (ADA) is a dough-enhancer, which in Nigeria is an approved replacement for potassium bromate (a dough-enhancer that has been banned in a number of coun_x0002_tries due to its nephrotoxic potential).	human	connective	High+Lowthroughput	An Assessment of the Effects of Azodicarbonamide-containing Diet on Neurobehaviour, Brain Antioxidant Status and Membrane Lipid Peroxidation Status in Rats	否				E_01_0189	PCR	Azodicarbonamide (ADA) is a dough-enhancer, which in Nigeria is an approved replacement for potassium bromate (a dough-enhancer that has been banned in a number of coun_x0002_tries due to its nephrotoxic potential).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Azodicarbonamide (ADA) is a dough-enhancer, which in Nigeria is an approved replacement for potassium bromate (a dough-enhancer that has been banned in a number of coun_x0002_tries due to its nephrotoxic potential).	Immunohistochemical staining	Azodicarbonamide (ADA) is a dough-enhancer, which in Nigeria is an approved replacement for potassium bromate (a dough-enhancer that has been banned in a number of coun_x0002_tries due to its nephrotoxic potential).		PCR			ADA		Azodicarbonamide (ADA) is a dough-enhancer, which in Nigeria is an approved replacement for potassium bromate (a dough-enhancer that has been banned in a number of coun_x0002_tries due to its nephrotoxic potential).	
31680128	chr11	1155000	1157000	MUC5AC	 MUC5AC and MUC5B is a major gel-forming mucin that is linked to increased morbidity and mortality in respiratory diseases	human	Epithelial	High+Lowthroughput	Fipronil upregulates inflammatory cytokines and MUC5AC expression in human nasal epithelial cells	否		airway inflammation 	epithelial cell	E_01_0190	Western blot,PCR	 MUC5AC and MUC5B is a major gel-forming mucin that is linked to increased morbidity and mortality in respiratory diseases	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		 MUC5AC and MUC5B is a major gel-forming mucin that is linked to increased morbidity and mortality in respiratory diseases	Immunohistochemical staining	 MUC5AC and MUC5B is a major gel-forming mucin that is linked to increased morbidity and mortality in respiratory diseases		Western blot,PCR			MUC5AC		 MUC5AC and MUC5B is a major gel-forming mucin that is linked to increased morbidity and mortality in respiratory diseases	
31676868	chr20	40683274	40685274	MAFB	Thus, we took advantage of published ChIP_x0002_seq datasets of islet-specific transcription factors (MAFB, PDX1, FOXA2, NKX6.1 and NKX2.2) mapped in unstimulated human pancreatic islets9 to measure transcription factor occupancy in primed and neo-enhancers before the proinflammatory stimu_x0002_lus.	human	blood	High+Lowthroughput	The impact of proinflammatory cytokines on the β-cell regulatory landscape provides insights into the genetics of type 1 diabetes	是	rs78037977	diabetes	B cell	E_01_0191	Flow cytometry,PCR	Thus, we took advantage of published ChIP_x0002_seq datasets of islet-specific transcription factors (MAFB, PDX1, FOXA2, NKX6.1 and NKX2.2) mapped in unstimulated human pancreatic islets9 to measure transcription factor occupancy in primed and neo-enhancers before the proinflammatory stimu_x0002_lus.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Thus, we took advantage of published ChIP_x0002_seq datasets of islet-specific transcription factors (MAFB, PDX1, FOXA2, NKX6.1 and NKX2.2) mapped in unstimulated human pancreatic islets9 to measure transcription factor occupancy in primed and neo-enhancers before the proinflammatory stimu_x0002_lus.	Immunohistochemical staining	Thus, we took advantage of published ChIP_x0002_seq datasets of islet-specific transcription factors (MAFB, PDX1, FOXA2, NKX6.1 and NKX2.2) mapped in unstimulated human pancreatic islets9 to measure transcription factor occupancy in primed and neo-enhancers before the proinflammatory stimu_x0002_lus.		Flow cytometry,PCR			DEXI	MAFB,SOCS1	The locus includes several upregulated genes (SOCS1, DEXI, CIITA, RMI2) that could represent potential targets of this IRE. Recent research points to DEXI as a T1D candidate gene in immune cells and β cells31,32.	Thus, we took advantage of published ChIP_x0002_seq datasets of islet-specific transcription factors (MAFB, PDX1, FOXA2, NKX6.1 and NKX2.2) mapped in unstimulated human pancreatic islets9 to measure transcription factor occupancy in primed and neo-enhancers before the proinflammatory stimu_x0002_lus.;The locus includes several upregulated genes (SOCS1, DEXI, CIITA, RMI2) that could represent potential targets of this IRE. Recent research points to DEXI as a T1D candidate gene in immune cells and β cells31,32.
31666694	chr11	69983276	69985276	ANO1	By contrast, ANO1 was bi-allelically expressed, suggesting that the biased FGF expression reflected allele_x0002_specific insulator loss. Consistently, in one SDH-deficient tumour with a heterozygous SNP near the CTCF site, we confirmed that only one allele of the FGF insulator was methylated (Extended Data Fig. 4d).	human	Stomach, gut	High+Lowthroughput	Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs	否		Gastrointestinal stromal tumors	GIST-T1 cell	E_01_0192	Flow cytometry	By contrast, ANO1 was bi-allelically expressed, suggesting that the biased FGF expression reflected allele_x0002_specific insulator loss. Consistently, in one SDH-deficient tumour with a heterozygous SNP near the CTCF site, we confirmed that only one allele of the FGF insulator was methylated (Extended Data Fig. 4d).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		By contrast, ANO1 was bi-allelically expressed, suggesting that the biased FGF expression reflected allele_x0002_specific insulator loss. Consistently, in one SDH-deficient tumour with a heterozygous SNP near the CTCF site, we confirmed that only one allele of the FGF insulator was methylated (Extended Data Fig. 4d).	Immunohistochemical staining	By contrast, ANO1 was bi-allelically expressed, suggesting that the biased FGF expression reflected allele_x0002_specific insulator loss. Consistently, in one SDH-deficient tumour with a heterozygous SNP near the CTCF site, we confirmed that only one allele of the FGF insulator was methylated (Extended Data Fig. 4d).		Flow cytometry				ANO1		By contrast, ANO1 was bi-allelically expressed, suggesting that the biased FGF expression reflected allele_x0002_specific insulator loss. Consistently, in one SDH-deficient tumour with a heterozygous SNP near the CTCF site, we confirmed that only one allele of the FGF insulator was methylated (Extended Data Fig. 4d).
31666072	chr17	50181276	50183276	COL1A1	Many mutations associated with these conditions (e.g., col_x0002_lagen [COL1A1] in patients with Ehlers-Danlos syndrome)affect the structural integrity of the vasculature or the abil_x0002_ity of the vessel walls to maintain homeostasis [12, 13].	human	Epithelial	High+Lowthroughput	Epigenetic landscapes suggest that genetic risk for intracranial aneurysm operates on the endothelium	是	rs1333040	inflammation	endothelial cell	E_01_0193	ChIP-Seq	Many mutations associated with these conditions (e.g., col_x0002_lagen [COL1A1] in patients with Ehlers-Danlos syndrome)affect the structural integrity of the vasculature or the abil_x0002_ity of the vessel walls to maintain homeostasis [12, 13].	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Many mutations associated with these conditions (e.g., col_x0002_lagen [COL1A1] in patients with Ehlers-Danlos syndrome)affect the structural integrity of the vasculature or the abil_x0002_ity of the vessel walls to maintain homeostasis [12, 13].	Immunohistochemical staining	Many mutations associated with these conditions (e.g., col_x0002_lagen [COL1A1] in patients with Ehlers-Danlos syndrome)affect the structural integrity of the vasculature or the abil_x0002_ity of the vessel walls to maintain homeostasis [12, 13].		ChIP-Seq				COL1A1		Many mutations associated with these conditions (e.g., col_x0002_lagen [COL1A1] in patients with Ehlers-Danlos syndrome)affect the structural integrity of the vasculature or the abil_x0002_ity of the vessel walls to maintain homeostasis [12, 13].
31665067	chr18	55219450	55221450	TCF4	While pro_x0002_moting the transcription of tumor suppressors genes,RUVBL1 was revealed to promote β-catenin-mediated neoplastic transformation by forming chromatin remod_x0002_eling complex with TIP60 and thus promotes histone H4 acetylation in the promoter region of ITF-2 gene and enhances the transcriptional activity of TCF4 [42].	human	bone	High+Lowthroughput	CircMYO10 promotes osteosarcoma progression by regulating miR-370-3p/RUVBL1 axis to enhance the transcriptional activity of β-catenin/LEF1 complex via effects on chromatin remodeling	否		Osteosarcoma	osteosarcoma cell	E_01_0194	Flow cytometry,PCR,Western blot	While pro_x0002_moting the transcription of tumor suppressors genes,RUVBL1 was revealed to promote β-catenin-mediated neoplastic transformation by forming chromatin remod_x0002_eling complex with TIP60 and thus promotes histone H4 acetylation in the promoter region of ITF-2 gene and enhances the transcriptional activity of TCF4 [42].	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		While pro_x0002_moting the transcription of tumor suppressors genes,RUVBL1 was revealed to promote β-catenin-mediated neoplastic transformation by forming chromatin remod_x0002_eling complex with TIP60 and thus promotes histone H4 acetylation in the promoter region of ITF-2 gene and enhances the transcriptional activity of TCF4 [42].	Immunohistochemical staining	While pro_x0002_moting the transcription of tumor suppressors genes,RUVBL1 was revealed to promote β-catenin-mediated neoplastic transformation by forming chromatin remod_x0002_eling complex with TIP60 and thus promotes histone H4 acetylation in the promoter region of ITF-2 gene and enhances the transcriptional activity of TCF4 [42].		Flow cytometry,PCR,Western blot			MYO10	TCF4	In this study, we identified the oncogenic role of cir_x0002_cMYO10, a circRNA that is upregulated in OS [44].	While pro_x0002_moting the transcription of tumor suppressors genes,RUVBL1 was revealed to promote β-catenin-mediated neoplastic transformation by forming chromatin remod_x0002_eling complex with TIP60 and thus promotes histone H4 acetylation in the promoter region of ITF-2 gene and enhances the transcriptional activity of TCF4 [42].
31664109	chrX	154007840	154009840	IRAK1	IRAK1, IRAK2 and IRAK4 work in concert to stimulate myeloid diferentiation primary response 88 (MyD88) dependent activation of nuclear factor kappa-light-chain enhancer of activated B cells (NFκB) and thus pro-infammatory cytokine production12. 	human	blood	High+Lowthroughput	IRAK3 modulates downstream innate immune signalling through its guanylate cyclase activity	是		inflammation	B cell	E_01_0195	PCR	IRAK1, IRAK2 and IRAK4 work in concert to stimulate myeloid diferentiation primary response 88 (MyD88) dependent activation of nuclear factor kappa-light-chain enhancer of activated B cells (NFκB) and thus pro-infammatory cytokine production12. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		IRAK1, IRAK2 and IRAK4 work in concert to stimulate myeloid diferentiation primary response 88 (MyD88) dependent activation of nuclear factor kappa-light-chain enhancer of activated B cells (NFκB) and thus pro-infammatory cytokine production12. 	Immunohistochemical staining	IRAK1, IRAK2 and IRAK4 work in concert to stimulate myeloid diferentiation primary response 88 (MyD88) dependent activation of nuclear factor kappa-light-chain enhancer of activated B cells (NFκB) and thus pro-infammatory cytokine production12. 		PCR			IRAK1,IRAK4		IRAK1, IRAK2 and IRAK4 work in concert to stimulate myeloid diferentiation primary response 88 (MyD88) dependent activation of nuclear factor kappa-light-chain enhancer of activated B cells (NFκB) and thus pro-infammatory cytokine production12. ;IRAK1, IRAK2 and IRAK4 work in concert to stimulate myeloid diferentiation primary response 88 (MyD88) dependent activation of nuclear factor kappa-light-chain enhancer of activated B cells (NFκB) and thus pro-infammatory cytokine production12. 	
31659808	chr2	237482764	237484764	MLPH	To determine the potential effect of rs13426236 genotypes on MLPH alternative splicing, we performed splicing variant‐specific qPCRs in 87 benign prostate tissues.	human	prostate	High+Lowthroughput	Single-nucleotide polymorphism rs13426236 contributes to an increased prostate cancer risk via regulating MLPH splicing variant 4	是	rs13426236	prostatic cancer	prostate cancer cell	E_01_0196	Flow cytometry,Western blot,PCR	To determine the potential effect of rs13426236 genotypes on MLPH alternative splicing, we performed splicing variant‐specific qPCRs in 87 benign prostate tissues.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		To determine the potential effect of rs13426236 genotypes on MLPH alternative splicing, we performed splicing variant‐specific qPCRs in 87 benign prostate tissues.	Immunohistochemical staining	To determine the potential effect of rs13426236 genotypes on MLPH alternative splicing, we performed splicing variant‐specific qPCRs in 87 benign prostate tissues.		Flow cytometry,Western blot,PCR			MLPH		To determine the potential effect of rs13426236 genotypes on MLPH alternative splicing, we performed splicing variant‐specific qPCRs in 87 benign prostate tissues.	
31659207	chr11	128455802	128457802	ETS1	ETS1 is involved in B cell and T17 cell diferentiation, and an association between rs1128334 and SLE has been reported in Asian SLE cohorts39.	human	blood	High+Lowthroughput	Rare variants in non-coding regulatory regions of the genome that affect gene expression in systemic lupus erythematosus	是	rs9888739	Systemic lupus erythematosus	T cell	E_01_0197	Flow cytometry,PCR	ETS1 is involved in B cell and T17 cell diferentiation, and an association between rs1128334 and SLE has been reported in Asian SLE cohorts39.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		ETS1 is involved in B cell and T17 cell diferentiation, and an association between rs1128334 and SLE has been reported in Asian SLE cohorts39.	Immunohistochemical staining	ETS1 is involved in B cell and T17 cell diferentiation, and an association between rs1128334 and SLE has been reported in Asian SLE cohorts39.		Flow cytometry,PCR			TLR7,TNPO3	ETS1,FOXP3,TNIP1,IRF5	Moreover, mice lacking Gf1 have recently been reported to develop a TLR7-dependent lupus-like phenotype, which the authors showed to involve excess NFκB signaling45.;The IRF5-TNPO3 association with systemic lupus erythematosus has two components that other autoimmune disorders variably share.	ETS1 is involved in B cell and T17 cell diferentiation, and an association between rs1128334 and SLE has been reported in Asian SLE cohorts39.;Te rare variant we identifed at this locus was located in a lower information nucleotide in a FOXP3 motif and was found to increase ETS1 expression via luciferase assay (Fig. 1D and Supplementary Table 1).;We found a rare variant near rs10036748, within the TNIP1 gene, which impaired TNIP1 expression according to a luciferase reporter assay (Fig. 1E and Supplementary Table 1).;We identifed novel variants in the loci of IRF5, ETS1, ITGAM1 and TNIP1, each of which caused alterations in the expression levels of the association genes.
31659164	chr8	11673920	11675920	GATA4	Mapping the chromatin occupancy of transcription factors (TFs) is a key step in deciphering developmental transcriptional programs. Here we use biotinylated knockin alleles of seven key cardiac TFs (GATA4, NKX2-5, MEF2A, MEF2C, SRF, TBX5, TEAD1) to sensitively and reproducibly map their genome-wide occupancy in the fetal and adult mouse heart. 	human	connective	High+Lowthroughput	A reference map of murine cardiac transcription factor chromatin occupancy identifies dynamic and conserved enhancers	否		cancer	stem cell	E_01_0198	PCR,Flow cytometry	Mapping the chromatin occupancy of transcription factors (TFs) is a key step in deciphering developmental transcriptional programs. Here we use biotinylated knockin alleles of seven key cardiac TFs (GATA4, NKX2-5, MEF2A, MEF2C, SRF, TBX5, TEAD1) to sensitively and reproducibly map their genome-wide occupancy in the fetal and adult mouse heart. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Mapping the chromatin occupancy of transcription factors (TFs) is a key step in deciphering developmental transcriptional programs. Here we use biotinylated knockin alleles of seven key cardiac TFs (GATA4, NKX2-5, MEF2A, MEF2C, SRF, TBX5, TEAD1) to sensitively and reproducibly map their genome-wide occupancy in the fetal and adult mouse heart. 	Immunohistochemical staining	Mapping the chromatin occupancy of transcription factors (TFs) is a key step in deciphering developmental transcriptional programs. Here we use biotinylated knockin alleles of seven key cardiac TFs (GATA4, NKX2-5, MEF2A, MEF2C, SRF, TBX5, TEAD1) to sensitively and reproducibly map their genome-wide occupancy in the fetal and adult mouse heart. 		PCR,Flow cytometry				GATA4,NKX2-5,MEF2A		Mapping the chromatin occupancy of transcription factors (TFs) is a key step in deciphering developmental transcriptional programs. Here we use biotinylated knockin alleles of seven key cardiac TFs (GATA4, NKX2-5, MEF2A, MEF2C, SRF, TBX5, TEAD1) to sensitively and reproducibly map their genome-wide occupancy in the fetal and adult mouse heart. ;The development of the heart is orchestrated by intricate transcriptional programs, so that mutations in TFs and epigenetic regulators are important causes of congenital heart disease5. Among the well known cardiac TFs are NKX2-5, TBX5, GATA4,MEF2A, MEF2C, and SRF6–11. ;The development of the heart is orchestrated by intricate transcriptional programs, so that mutations in TFs and epigenetic regulators are important causes of congenital heart disease5. Among the well known cardiac TFs are NKX2-5, TBX5, GATA4,MEF2A, MEF2C, and SRF6–11. 
31652453	chr7	148804156	148806156	EZH2	FBP1 expression in tumor cells is linked to poor patient survival.27,32 Recently, we demonstrated that FBP1 physically interacted with EZH2 in osteosarcoma cells and that GSK343 treatment inhibited the expression of EZH2 and FBP1.23	human	bone	High+Lowthroughput	Ketamine induces endoplasmic reticulum stress in rats and SV-HUC-1 human uroepithelial cells by activating NLRP3/TXNIP aix	否		Osteosarcoma	osteosarcoma cell	E_01_0199	Flow cytometry, Western blot, PCR, immunofluorescence light staining	FBP1 expression in tumor cells is linked to poor patient survival.27,32 Recently, we demonstrated that FBP1 physically interacted with EZH2 in osteosarcoma cells and that GSK343 treatment inhibited the expression of EZH2 and FBP1.23	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		FBP1 expression in tumor cells is linked to poor patient survival.27,32 Recently, we demonstrated that FBP1 physically interacted with EZH2 in osteosarcoma cells and that GSK343 treatment inhibited the expression of EZH2 and FBP1.23	Immunohistochemical staining	FBP1 expression in tumor cells is linked to poor patient survival.27,32 Recently, we demonstrated that FBP1 physically interacted with EZH2 in osteosarcoma cells and that GSK343 treatment inhibited the expression of EZH2 and FBP1.23		Flow cytometry,Western blot,PCR,免疫荧光光染色			FBP1	EZH2	FBP1 expression in tumor cells is linked to poor patient survival.27,32 Recently, we demonstrated that FBP1 physically interacted with EZH2 in osteosarcoma cells and that GSK343 treatment inhibited the expression of EZH2 and FBP1.23	FBP1 expression in tumor cells is linked to poor patient survival.27,32 Recently, we demonstrated that FBP1 physically interacted with EZH2 in osteosarcoma cells and that GSK343 treatment inhibited the expression of EZH2 and FBP1.23
31649059	chr1	8001795	8003795	ERRFI1	As exemplified by the ERRFI1 locus (Fig.3A) and summarized genome-wide for all TSSs (Fig. 3B), both transient and stable transcript TSSs are accurately captured by csRNA-seq. 	human	blood	High+Lowthroughput	Identification and dynamic quantification of regulatory elements using total RNA	否		leukemia	myelogenous leukemia cell	E_01_0200	Flow cytometry	As exemplified by the ERRFI1 locus (Fig.3A) and summarized genome-wide for all TSSs (Fig. 3B), both transient and stable transcript TSSs are accurately captured by csRNA-seq. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		As exemplified by the ERRFI1 locus (Fig.3A) and summarized genome-wide for all TSSs (Fig. 3B), both transient and stable transcript TSSs are accurately captured by csRNA-seq. 	Immunohistochemical staining	As exemplified by the ERRFI1 locus (Fig.3A) and summarized genome-wide for all TSSs (Fig. 3B), both transient and stable transcript TSSs are accurately captured by csRNA-seq. 		Flow cytometry			ERRFI1		As exemplified by the ERRFI1 locus (Fig.3A) and summarized genome-wide for all TSSs (Fig. 3B), both transient and stable transcript TSSs are accurately captured by csRNA-seq. 	
31649055	chr2	47342302	47344302	EPCAM	The significantly differentially expressed genes include common clinical biomarkers for macrophages (CD68 and CD163) and DCIS cells (EPCAM, KRT7, KRT18, and ERBB2 [also known as HER2]) (Fig. 4C; Supplemental File 3). The single-cell samples generally have gene expression profiles similar to the cell type–matched bulk samples. 	human	connective	High+Lowthroughput	FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples	是		leukemia	stromal macrophage cell	E_01_0201	Flow cytometry	The significantly differentially expressed genes include common clinical biomarkers for macrophages (CD68 and CD163) and DCIS cells (EPCAM, KRT7, KRT18, and ERBB2 [also known as HER2]) (Fig. 4C; Supplemental File 3). The single-cell samples generally have gene expression profiles similar to the cell type–matched bulk samples. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The significantly differentially expressed genes include common clinical biomarkers for macrophages (CD68 and CD163) and DCIS cells (EPCAM, KRT7, KRT18, and ERBB2 [also known as HER2]) (Fig. 4C; Supplemental File 3). The single-cell samples generally have gene expression profiles similar to the cell type–matched bulk samples. 	Immunohistochemical staining	The significantly differentially expressed genes include common clinical biomarkers for macrophages (CD68 and CD163) and DCIS cells (EPCAM, KRT7, KRT18, and ERBB2 [also known as HER2]) (Fig. 4C; Supplemental File 3). The single-cell samples generally have gene expression profiles similar to the cell type–matched bulk samples. 		Flow cytometry				EPCAM		The significantly differentially expressed genes include common clinical biomarkers for macrophages (CD68 and CD163) and DCIS cells (EPCAM, KRT7, KRT18, and ERBB2 [also known as HER2]) (Fig. 4C; Supplemental File 3). The single-cell samples generally have gene expression profiles similar to the cell type–matched bulk samples. 
31649032	chr3	66876146	66878146	Shox2	Using mice, here we report that deficiency in short stature homeobox 2 (Shox2), a transcriptional regulator whose expression is restricted to the anterior palatal mesenchyme, leads to a defective palatine process of the maxilla, but does not affect the palatine. 	mouse	connective	High+Lowthroughput	Shox2 regulates osteogenic differentiation and pattern formation during hard palate development in mice	否			mesenchymal cell	E_01_0202	Flow cytometry, PCR, immunofluorescence staining	Using mice, here we report that deficiency in short stature homeobox 2 (Shox2), a transcriptional regulator whose expression is restricted to the anterior palatal mesenchyme, leads to a defective palatine process of the maxilla, but does not affect the palatine. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Using mice, here we report that deficiency in short stature homeobox 2 (Shox2), a transcriptional regulator whose expression is restricted to the anterior palatal mesenchyme, leads to a defective palatine process of the maxilla, but does not affect the palatine. 	Immunohistochemical staining	Using mice, here we report that deficiency in short stature homeobox 2 (Shox2), a transcriptional regulator whose expression is restricted to the anterior palatal mesenchyme, leads to a defective palatine process of the maxilla, but does not affect the palatine. 		Flow cytometry,PCR,免疫荧光染色			Shox2		Using mice, here we report that deficiency in short stature homeobox 2 (Shox2), a transcriptional regulator whose expression is restricted to the anterior palatal mesenchyme, leads to a defective palatine process of the maxilla, but does not affect the palatine. 	
31644352	chr16	28929347	28931347	CD19	Wounds were digested as described above. Single cell suspen_x0002_sions were incubated with fluorescein isothiocyanate–labeled anti-CD3, anti-CD19, and anti-Ly6G (BioLegend) followed by antifluorescein isothiocyanate microbeads (Miltenyi Biotec). 	human	blood	High+Lowthroughput	Sepsis Induces Prolonged Epigenetic Modifications in Bone Marrow and Peripheral Macrophages Impairing Inflammation and Wound Healing	否		septicemia	B cell	E_01_0203	PCR, flow cytometry, immunofluorescence staining	Wounds were digested as described above. Single cell suspen_x0002_sions were incubated with fluorescein isothiocyanate–labeled anti-CD3, anti-CD19, and anti-Ly6G (BioLegend) followed by antifluorescein isothiocyanate microbeads (Miltenyi Biotec). 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Wounds were digested as described above. Single cell suspen_x0002_sions were incubated with fluorescein isothiocyanate–labeled anti-CD3, anti-CD19, and anti-Ly6G (BioLegend) followed by antifluorescein isothiocyanate microbeads (Miltenyi Biotec). 	Immunohistochemical staining	Wounds were digested as described above. Single cell suspen_x0002_sions were incubated with fluorescein isothiocyanate–labeled anti-CD3, anti-CD19, and anti-Ly6G (BioLegend) followed by antifluorescein isothiocyanate microbeads (Miltenyi Biotec). 		PCR,Flow cytometry,免疫荧光染色			CD19		Wounds were digested as described above. Single cell suspen_x0002_sions were incubated with fluorescein isothiocyanate–labeled anti-CD3, anti-CD19, and anti-Ly6G (BioLegend) followed by antifluorescein isothiocyanate microbeads (Miltenyi Biotec). 	
31642979	chr4	184382613	184384613	IRF2	Similarly, IRF2 was predicted to bind to the sequence with the T allele at rs7071351 (Fig. 3d) and IRF2 ChIP-seq peak was also found in the SNP region (Fig. 3b).	human	colon	High+Lowthroughput	Three functional variants were identified to affect RPS24 expression and significantly associated with risk of colorectal cancer	是	rs7071351	Colon cancer	Human colorectal carcinoma cell	E_01_0204	PCR,Flow cytometry	Similarly, IRF2 was predicted to bind to the sequence with the T allele at rs7071351 (Fig. 3d) and IRF2 ChIP-seq peak was also found in the SNP region (Fig. 3b).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Similarly, IRF2 was predicted to bind to the sequence with the T allele at rs7071351 (Fig. 3d) and IRF2 ChIP-seq peak was also found in the SNP region (Fig. 3b).	Immunohistochemical staining	Similarly, IRF2 was predicted to bind to the sequence with the T allele at rs7071351 (Fig. 3d) and IRF2 ChIP-seq peak was also found in the SNP region (Fig. 3b).		PCR,Flow cytometry				IRF2,ZMIZ1		Similarly, IRF2 was predicted to bind to the sequence with the T allele at rs7071351 (Fig. 3d) and IRF2 ChIP-seq peak was also found in the SNP region (Fig. 3b).;However, ZMIZ1-AS1 is a miscellaneous RNA gene with unknown function and both ZMIZ1 and ZMIZ1-AS1 failed to afect cell growth in our functionalinterrogation.
31642363	chr7	148804489	148806489	EZH2	Enhancer of zeste homolog 2 (EZH2), a catalytic component of the polycomb repressive complex 2, acts as a methyltrans_x0002_ferase for H3 lysine 27 trimethylation, mod_x0002_ulates chromatin structure and gene expression, and recruits DNA methyltrans_x0002_ferases for gene silencing.2	human	connective	High+Lowthroughput	Sepsis Induces Prolonged Epigenetic Modifications in Bone Marrow and Peripheral Macrophages Impairing Inflammation and Wound Healing	否			mesenchymal stem cell	E_01_0205	PCR,Western blot	Enhancer of zeste homolog 2 (EZH2), a catalytic component of the polycomb repressive complex 2, acts as a methyltrans_x0002_ferase for H3 lysine 27 trimethylation, mod_x0002_ulates chromatin structure and gene expression, and recruits DNA methyltrans_x0002_ferases for gene silencing.2	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Enhancer of zeste homolog 2 (EZH2), a catalytic component of the polycomb repressive complex 2, acts as a methyltrans_x0002_ferase for H3 lysine 27 trimethylation, mod_x0002_ulates chromatin structure and gene expression, and recruits DNA methyltrans_x0002_ferases for gene silencing.2	Immunohistochemical staining	Enhancer of zeste homolog 2 (EZH2), a catalytic component of the polycomb repressive complex 2, acts as a methyltrans_x0002_ferase for H3 lysine 27 trimethylation, mod_x0002_ulates chromatin structure and gene expression, and recruits DNA methyltrans_x0002_ferases for gene silencing.2		PCR,Western blot				EZH2		Enhancer of zeste homolog 2 (EZH2), a catalytic component of the polycomb repressive complex 2, acts as a methyltrans_x0002_ferase for H3 lysine 27 trimethylation, mod_x0002_ulates chromatin structure and gene expression, and recruits DNA methyltrans_x0002_ferases for gene silencing.2
31641208	chr16	68734197	68736197	CDH1	Here, through comprehensive filtration, we prioritized rs7198799, a common SNP in the second intron of the CDH1, as the putative causal variant. In addition, we found an association of CRC_x0002_risk allele C of rs7198799 with elevated transcript level of biological plausible candidate gene ZFP90 via expression quantitative trait loci analysis.	human	blood	High+Lowthroughput	Enhancer of zeste homolog 2 enhances the migration and chemotaxis of dental mesenchymal stem cells	是	rs7198799	tumour		E_01_0206	PCR,Western blot	Here, through comprehensive filtration, we prioritized rs7198799, a common SNP in the second intron of the CDH1, as the putative causal variant. In addition, we found an association of CRC_x0002_risk allele C of rs7198799 with elevated transcript level of biological plausible candidate gene ZFP90 via expression quantitative trait loci analysis.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Here, through comprehensive filtration, we prioritized rs7198799, a common SNP in the second intron of the CDH1, as the putative causal variant. In addition, we found an association of CRC_x0002_risk allele C of rs7198799 with elevated transcript level of biological plausible candidate gene ZFP90 via expression quantitative trait loci analysis.	Immunohistochemical staining	Here, through comprehensive filtration, we prioritized rs7198799, a common SNP in the second intron of the CDH1, as the putative causal variant. In addition, we found an association of CRC_x0002_risk allele C of rs7198799 with elevated transcript level of biological plausible candidate gene ZFP90 via expression quantitative trait loci analysis.		PCR,Western blot				CDH1		Here, through comprehensive filtration, we prioritized rs7198799, a common SNP in the second intron of the CDH1, as the putative causal variant. In addition, we found an association of CRC_x0002_risk allele C of rs7198799 with elevated transcript level of biological plausible candidate gene ZFP90 via expression quantitative trait loci analysis.
31636473	chr10	67881712	67883712	SIRT1	Sirtuin 1 (SIRT1) is a nicotinamide adenine dinucleotide (NAD+)-dependent protein deacetylase that is involved in various diseases, including cancers, metabolic diseases, and inflammation-associated diseases. However, the role of SIRT1 in ulcerative colitis (UC) is still confusing	human	Epithelial	High+Lowthroughput	Sirtuin 1 alleviates endoplasmic reticulum stress-mediated apoptosis of intestinal epithelial cells in ulcerative colitis	否			epithelial cell	E_01_0207	Flow cytometry,PCR,Western blot	Sirtuin 1 (SIRT1) is a nicotinamide adenine dinucleotide (NAD+)-dependent protein deacetylase that is involved in various diseases, including cancers, metabolic diseases, and inflammation-associated diseases. However, the role of SIRT1 in ulcerative colitis (UC) is still confusing	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Sirtuin 1 (SIRT1) is a nicotinamide adenine dinucleotide (NAD+)-dependent protein deacetylase that is involved in various diseases, including cancers, metabolic diseases, and inflammation-associated diseases. However, the role of SIRT1 in ulcerative colitis (UC) is still confusing	Immunohistochemical staining	Sirtuin 1 (SIRT1) is a nicotinamide adenine dinucleotide (NAD+)-dependent protein deacetylase that is involved in various diseases, including cancers, metabolic diseases, and inflammation-associated diseases. However, the role of SIRT1 in ulcerative colitis (UC) is still confusing		Flow cytometry,PCR,Western blot				SIRT1		Sirtuin 1 (SIRT1) is a nicotinamide adenine dinucleotide (NAD+)-dependent protein deacetylase that is involved in various diseases, including cancers, metabolic diseases, and inflammation-associated diseases. However, the role of SIRT1 in ulcerative colitis (UC) is still confusing
31636429	chr5	70046788	70048788	SMN2	The adenine base was substi_x0002_tuted in the SMN2 mini-gene and the effect of these mutations was evaluated in human cellular models (Fig. 3a).	human	Epithelial	High+Lowthroughput	Structural basis of a small molecule targeting RNA for a specific splicing correction	否		Spinal muscular atrophy	HEK293T	E_01_0208	Western blot	The adenine base was substi_x0002_tuted in the SMN2 mini-gene and the effect of these mutations was evaluated in human cellular models (Fig. 3a).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The adenine base was substi_x0002_tuted in the SMN2 mini-gene and the effect of these mutations was evaluated in human cellular models (Fig. 3a).	Immunohistochemical staining	The adenine base was substi_x0002_tuted in the SMN2 mini-gene and the effect of these mutations was evaluated in human cellular models (Fig. 3a).		Western blot			SMN2		The adenine base was substi_x0002_tuted in the SMN2 mini-gene and the effect of these mutations was evaluated in human cellular models (Fig. 3a).	
31636200	chr4	110614447	110616447	PITX2	Genome-wide association studies found that increased risk for atrial fibrillation (AF), the most common human heart arrhythmia,is associated with noncoding sequence variants located in proxim_x0002_ity to PITX2.	human	connective	High+Lowthroughput	Long-range Pitx2c enhancer-promoter interactions prevent predisposition to atrial fibrillation	是	rs2595104	Atrial fibrillation	embryonic stem cell	E_01_0209	Flow cytometry,PCR,Western blot	Genome-wide association studies found that increased risk for atrial fibrillation (AF), the most common human heart arrhythmia,is associated with noncoding sequence variants located in proxim_x0002_ity to PITX2.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Genome-wide association studies found that increased risk for atrial fibrillation (AF), the most common human heart arrhythmia,is associated with noncoding sequence variants located in proxim_x0002_ity to PITX2.	Immunohistochemical staining	Genome-wide association studies found that increased risk for atrial fibrillation (AF), the most common human heart arrhythmia,is associated with noncoding sequence variants located in proxim_x0002_ity to PITX2.		Flow cytometry,PCR,Western blot				PITX2		Genome-wide association studies found that increased risk for atrial fibrillation (AF), the most common human heart arrhythmia,is associated with noncoding sequence variants located in proxim_x0002_ity to PITX2.
31634421	chr16	92395428	92397428	Runx1	Runx1 is an important haematopoietic transcription factor as stressed by its involve_x0002_ment in a number of haematological malignancies.	mouse	blood	High+Lowthroughput	Gata3 targets Runx1 in the embryonic haematopoietic stem cell niche	否		Hematologic disorders	hematopoietic stem cell	E_01_0210	Flow cytometry,PCR,Western blot	Runx1 is an important haematopoietic transcription factor as stressed by its involve_x0002_ment in a number of haematological malignancies.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Runx1 is an important haematopoietic transcription factor as stressed by its involve_x0002_ment in a number of haematological malignancies.	Immunohistochemical staining	Runx1 is an important haematopoietic transcription factor as stressed by its involve_x0002_ment in a number of haematological malignancies.		Flow cytometry,PCR,Western blot			Runx1		Runx1 is an important haematopoietic transcription factor as stressed by its involve_x0002_ment in a number of haematological malignancies.	
31633376	chr6	84684753	84686753	TBX18	Transcription factor TBX18 is a member of the TBX subfamily of the T-box family, which is involved in the formation and development of sinus node head.	human	Musculature	High+Lowthroughput	Transcription Factor TBX18 Reprograms Vascular Smooth Muscle Cells of Ascending Aorta to Pacemaker-Like Cells	否			smooth muscle cell	E_01_0211	Flow cytometry, PCR, immunofluorescence staining	Transcription factor TBX18 is a member of the TBX subfamily of the T-box family, which is involved in the formation and development of sinus node head.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Transcription factor TBX18 is a member of the TBX subfamily of the T-box family, which is involved in the formation and development of sinus node head.	Immunohistochemical staining	Transcription factor TBX18 is a member of the TBX subfamily of the T-box family, which is involved in the formation and development of sinus node head.		Flow cytometry,PCR,免疫荧光染色				TBX18		Transcription factor TBX18 is a member of the TBX subfamily of the T-box family, which is involved in the formation and development of sinus node head.
31631026	chr1	23017098	23019098	KDM1A	We conduct a CRISPR screen revealing that knockout of KDM1A encoding lysine-specific demethylase 1 (LSD1) sensitizes DIPG cells to histone deacetylase (HDAC) inhibitors. Consistently, Corin, a bifunctional inhibitor of HDACs and LSD1, potently inhibits DIPG growth in vitro and in xenografts.	human	connective	High+Lowthroughput	Re-programing Chromatin with a Bifunctional LSD1/HDAC Inhibitor Induces Therapeutic Differentiation in DIPG	否		Desmosomas	melanoma cells	E_01_0212	Western blot,PCR,Flow cytometry	We conduct a CRISPR screen revealing that knockout of KDM1A encoding lysine-specific demethylase 1 (LSD1) sensitizes DIPG cells to histone deacetylase (HDAC) inhibitors. Consistently, Corin, a bifunctional inhibitor of HDACs and LSD1, potently inhibits DIPG growth in vitro and in xenografts.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We conduct a CRISPR screen revealing that knockout of KDM1A encoding lysine-specific demethylase 1 (LSD1) sensitizes DIPG cells to histone deacetylase (HDAC) inhibitors. Consistently, Corin, a bifunctional inhibitor of HDACs and LSD1, potently inhibits DIPG growth in vitro and in xenografts.	Immunohistochemical staining	We conduct a CRISPR screen revealing that knockout of KDM1A encoding lysine-specific demethylase 1 (LSD1) sensitizes DIPG cells to histone deacetylase (HDAC) inhibitors. Consistently, Corin, a bifunctional inhibitor of HDACs and LSD1, potently inhibits DIPG growth in vitro and in xenografts.		Western blot,PCR,Flow cytometry				KDM1A		We conduct a CRISPR screen revealing that knockout of KDM1A encoding lysine-specific demethylase 1 (LSD1) sensitizes DIPG cells to histone deacetylase (HDAC) inhibitors. Consistently, Corin, a bifunctional inhibitor of HDACs and LSD1, potently inhibits DIPG growth in vitro and in xenografts.
31631012	chr2	209421458	209423458	MAP2	Specif_x0002_ically, examination of potential enhancers within these clusters that are located near neural marker genes, MAP2 (Herzog and Weber, 1978) and ROR2 (Endo et al., 2012), found them to be en_x0002_riched for ATAC-seq signal at 12–24 h, H3K27ac signal at 48–72h, and their expression to peak at 72 h (Figures S2A and S2B).	human	connective	High+Lowthroughput	Identification and Massively Parallel Characterization of Regulatory Elements Driving Neural Induction	是	rs2176546		pluripotent stem cell	E_01_0213	Flow cytometry,PCR	Specif_x0002_ically, examination of potential enhancers within these clusters that are located near neural marker genes, MAP2 (Herzog and Weber, 1978) and ROR2 (Endo et al., 2012), found them to be en_x0002_riched for ATAC-seq signal at 12–24 h, H3K27ac signal at 48–72h, and their expression to peak at 72 h (Figures S2A and S2B).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Specif_x0002_ically, examination of potential enhancers within these clusters that are located near neural marker genes, MAP2 (Herzog and Weber, 1978) and ROR2 (Endo et al., 2012), found them to be en_x0002_riched for ATAC-seq signal at 12–24 h, H3K27ac signal at 48–72h, and their expression to peak at 72 h (Figures S2A and S2B).	Immunohistochemical staining	Specif_x0002_ically, examination of potential enhancers within these clusters that are located near neural marker genes, MAP2 (Herzog and Weber, 1978) and ROR2 (Endo et al., 2012), found them to be en_x0002_riched for ATAC-seq signal at 12–24 h, H3K27ac signal at 48–72h, and their expression to peak at 72 h (Figures S2A and S2B).		Flow cytometry,PCR			MAP2,NANOG,ATF3	ROR2,POU5F1	Specif_x0002_ically, examination of potential enhancers within these clusters that are located near neural marker genes, MAP2 (Herzog and Weber, 1978) and ROR2 (Endo et al., 2012), found them to be en_x0002_riched for ATAC-seq signal at 12–24 h, H3K27ac signal at 48–72h, and their expression to peak at 72 h (Figures S2A and S2B).;Pluripotent markers (NANOG and POU5F1) and direct targets of transforming growth factor b (TGF-b) and bone morphogenetic protein (BMP) signaling(SMAD7, ID1, and LEFTY2) were downregulated, and immediate early genes (ATF3, FOS, FOSB, and EGR1/2/3) were transiently upregulated at 3 h, corresponding to the cell’s stress response against differentiation stimuli.;Pluripotent markers (NANOG and POU5F1) and direct targets of transforming growth factor b (TGF-b) and bone morphogenetic protein (BMP) signaling(SMAD7, ID1, and LEFTY2) were downregulated, and immediate early genes (ATF3, FOS, FOSB, and EGR1/2/3) were transiently upregulated at 3 h, corresponding to the cell’s stress response against differentiation stimuli.	Specif_x0002_ically, examination of potential enhancers within these clusters that are located near neural marker genes, MAP2 (Herzog and Weber, 1978) and ROR2 (Endo et al., 2012), found them to be en_x0002_riched for ATAC-seq signal at 12–24 h, H3K27ac signal at 48–72h, and their expression to peak at 72 h (Figures S2A and S2B).;Pluripotent markers (NANOG and POU5F1) and direct targets of transforming growth factor b (TGF-b) and bone morphogenetic protein (BMP) signaling(SMAD7, ID1, and LEFTY2) were downregulated, and immediate early genes (ATF3, FOS, FOSB, and EGR1/2/3) were transiently upregulated at 3 h, corresponding to the cell’s stress response against differentiation stimuli.
31629814	chrX	47632617	47634617	ELK1	Furthermore, ELK1 supports cell-cycle entry during liver regeneration because Elk1-/- mice show reduced hepatocyte proliferation after PHx.40	human	liver	High+Lowthroughput	The Dynamic Chromatin Architecture of the Regenerating Liver	否		Obesity	hepatocyte	E_01_0214	Flow cytometry,PCR	Furthermore, ELK1 supports cell-cycle entry during liver regeneration because Elk1-/- mice show reduced hepatocyte proliferation after PHx.40	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Furthermore, ELK1 supports cell-cycle entry during liver regeneration because Elk1-/- mice show reduced hepatocyte proliferation after PHx.40	Immunohistochemical staining	Furthermore, ELK1 supports cell-cycle entry during liver regeneration because Elk1-/- mice show reduced hepatocyte proliferation after PHx.40		Flow cytometry,PCR				KCNH4		Furthermore, ELK1 supports cell-cycle entry during liver regeneration because Elk1-/- mice show reduced hepatocyte proliferation after PHx.40
31629687	chr1	35867480	35869480	AGO1	A study showed AGO1 binding with RNA polymerase II and active promoters (Huang et al.,2013), while another report indicated that AGO1 association with active enhancers did not explain the observed widespread changes in gene expression in AGO1 depleted cells	human	liver	High+Lowthroughput	Nuclear AGO1 Regulates Gene Expression by Affecting Chromatin Architecture in Human Cells	否		cancer	HepG2 cell	E_01_0215	Western blot,Flow cytometry,PCR	A study showed AGO1 binding with RNA polymerase II and active promoters (Huang et al.,2013), while another report indicated that AGO1 association with active enhancers did not explain the observed widespread changes in gene expression in AGO1 depleted cells	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		A study showed AGO1 binding with RNA polymerase II and active promoters (Huang et al.,2013), while another report indicated that AGO1 association with active enhancers did not explain the observed widespread changes in gene expression in AGO1 depleted cells	Immunohistochemical staining	A study showed AGO1 binding with RNA polymerase II and active promoters (Huang et al.,2013), while another report indicated that AGO1 association with active enhancers did not explain the observed widespread changes in gene expression in AGO1 depleted cells		Western blot,Flow cytometry,PCR			AGO1		A study showed AGO1 binding with RNA polymerase II and active promoters (Huang et al.,2013), while another report indicated that AGO1 association with active enhancers did not explain the observed widespread changes in gene expression in AGO1 depleted cells	
31628347	chr5	147234799	147236799	Cdx2	We find both prominent TE-specific master TFs (Cdx2, Gata3, and Tead4), and >150 TFs that had not been previously implicated in TE lineage, that are SE-associated.	mouse	connective	High+Lowthroughput	Super-enhancer-guided mapping of regulatory networks controlling mouse trophoblast stem cells	否			Trophoblast stem cell	E_01_0216	Flow cytometry	We find both prominent TE-specific master TFs (Cdx2, Gata3, and Tead4), and >150 TFs that had not been previously implicated in TE lineage, that are SE-associated.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We find both prominent TE-specific master TFs (Cdx2, Gata3, and Tead4), and >150 TFs that had not been previously implicated in TE lineage, that are SE-associated.	Immunohistochemical staining	We find both prominent TE-specific master TFs (Cdx2, Gata3, and Tead4), and >150 TFs that had not been previously implicated in TE lineage, that are SE-associated.		Flow cytometry			Cdx2,Tead4		We find both prominent TE-specific master TFs (Cdx2, Gata3, and Tead4), and >150 TFs that had not been previously implicated in TE lineage, that are SE-associated.;We find both prominent TE-specific master TFs (Cdx2, Gata3, and Tead4), and >150 TFs that had not been previously implicated in TE lineage, that are SE-associated.	
31623059	chr1	998360	1000360	ISG15	However, knockdown of lncRNA ISR had little effect on the expression of several ISGs, including myxovirus resistance protein A (MxA), Interferon-stimulated gene 15 (ISG15) and human 20-50-oligoadenylate synthetase 2 (OAS2) (Figure 3b).	human	blood	High+Lowthroughput	Identification of an Interferon-Stimulated Long Noncoding RNA (LncRNA ISR) Involved in Regulation of Influenza A Virus Replication	否		influenza	B cell	E_01_0217	PCR,Western blot	However, knockdown of lncRNA ISR had little effect on the expression of several ISGs, including myxovirus resistance protein A (MxA), Interferon-stimulated gene 15 (ISG15) and human 20-50-oligoadenylate synthetase 2 (OAS2) (Figure 3b).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		However, knockdown of lncRNA ISR had little effect on the expression of several ISGs, including myxovirus resistance protein A (MxA), Interferon-stimulated gene 15 (ISG15) and human 20-50-oligoadenylate synthetase 2 (OAS2) (Figure 3b).	Immunohistochemical staining	However, knockdown of lncRNA ISR had little effect on the expression of several ISGs, including myxovirus resistance protein A (MxA), Interferon-stimulated gene 15 (ISG15) and human 20-50-oligoadenylate synthetase 2 (OAS2) (Figure 3b).		PCR,Western blot			ISG15		However, knockdown of lncRNA ISR had little effect on the expression of several ISGs, including myxovirus resistance protein A (MxA), Interferon-stimulated gene 15 (ISG15) and human 20-50-oligoadenylate synthetase 2 (OAS2) (Figure 3b).	
31622687	chr3	101825749	101827749	NFKBIZ	No alteration in NFKBIZ mRNA expression was observed in the PBMCs of the psoriatic patients during secukinumab treatment (Fig 3, B).	human	blood	High+Lowthroughput	IκBζ is a key player in the antipsoriatic effects of secukinumab	否		Psoriasis	B cell	E_01_0218	PCR,Western blot	No alteration in NFKBIZ mRNA expression was observed in the PBMCs of the psoriatic patients during secukinumab treatment (Fig 3, B).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		No alteration in NFKBIZ mRNA expression was observed in the PBMCs of the psoriatic patients during secukinumab treatment (Fig 3, B).	Immunohistochemical staining	No alteration in NFKBIZ mRNA expression was observed in the PBMCs of the psoriatic patients during secukinumab treatment (Fig 3, B).		PCR,Western blot			NFKBIZ		No alteration in NFKBIZ mRNA expression was observed in the PBMCs of the psoriatic patients during secukinumab treatment (Fig 3, B).	
31621893	chr12	6531600	6533600	GAPDH	The GAPDH/Gapdh served as an internal control for mRNA expression. The fold change in target mRNA expression was calculated using the equation 2−ΔΔCt .	human	liver	High+Lowthroughput	Costunolide represses hepatic fibrosis through WW domain-containing protein 2-mediated Notch3 degradation	否			hepatic stellate cell	E_01_0219	PCR, Western blot, immunofluorescence staining	The GAPDH/Gapdh served as an internal control for mRNA expression. The fold change in target mRNA expression was calculated using the equation 2−ΔΔCt .	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The GAPDH/Gapdh served as an internal control for mRNA expression. The fold change in target mRNA expression was calculated using the equation 2−ΔΔCt .	Immunohistochemical staining	The GAPDH/Gapdh served as an internal control for mRNA expression. The fold change in target mRNA expression was calculated using the equation 2−ΔΔCt .		PCR,Western blot,免疫荧光染色			Gapdh	GAPDH	The GAPDH/Gapdh served as an internal control for mRNA expression. The fold change in target mRNA expression was calculated using the equation 2−ΔΔCt .	The GAPDH/Gapdh served as an internal control for mRNA expression. The fold change in target mRNA expression was calculated using the equation 2−ΔΔCt .
31621133	chr17	42310525	42312525	STAT3	Via CSF1‐R and CD138, IL‐34 promoted the proliferation and migration of hepatoma cells, and contributed to the activation of ERK and STAT3 pathways and the upregulation of Bcl‐xl and c‐Myc mediated by HBX.	human	liver	High+Lowthroughput	Interleukin-34 mediated by hepatitis B virus X protein via CCAAT/enhancer-binding protein α contributes to the proliferation and migration of hepatoma cells	否		liver cancer	HCC cell	E_01_0220	PCR, gene knockdown, Western blot	Via CSF1‐R and CD138, IL‐34 promoted the proliferation and migration of hepatoma cells, and contributed to the activation of ERK and STAT3 pathways and the upregulation of Bcl‐xl and c‐Myc mediated by HBX.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Via CSF1‐R and CD138, IL‐34 promoted the proliferation and migration of hepatoma cells, and contributed to the activation of ERK and STAT3 pathways and the upregulation of Bcl‐xl and c‐Myc mediated by HBX.	Immunohistochemical staining	Via CSF1‐R and CD138, IL‐34 promoted the proliferation and migration of hepatoma cells, and contributed to the activation of ERK and STAT3 pathways and the upregulation of Bcl‐xl and c‐Myc mediated by HBX.		PCR,基因敲降,Western blot				STAT3		Via CSF1‐R and CD138, IL‐34 promoted the proliferation and migration of hepatoma cells, and contributed to the activation of ERK and STAT3 pathways and the upregulation of Bcl‐xl and c‐Myc mediated by HBX.
31619507	chr4	147635062	147637062	PRMT9	Increased expression of PRMT isoforms, for example, PRMT1, CARM1, PRMT5, PRMT6, and PRMT9, in several tumor types has been correlated with poor overall survival. 	human	lung	High+Lowthroughput	PRMT6 Promotes Lung Tumor Progression via the Alternate Activation of Tumor-Associated Macrophages	否		tumour	NSCLC cell	E_01_0221	PCR, gene knockdown, Western blot	Increased expression of PRMT isoforms, for example, PRMT1, CARM1, PRMT5, PRMT6, and PRMT9, in several tumor types has been correlated with poor overall survival. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Increased expression of PRMT isoforms, for example, PRMT1, CARM1, PRMT5, PRMT6, and PRMT9, in several tumor types has been correlated with poor overall survival. 	Immunohistochemical staining	Increased expression of PRMT isoforms, for example, PRMT1, CARM1, PRMT5, PRMT6, and PRMT9, in several tumor types has been correlated with poor overall survival. 		PCR,基因敲降,Western blot			PRMT9		Increased expression of PRMT isoforms, for example, PRMT1, CARM1, PRMT5, PRMT6, and PRMT9, in several tumor types has been correlated with poor overall survival. 	
31619182	chr7	148804718	148806718	EZH2	In mammals, gain-of-function mutations as well as overexpression of EZH2 have been associated with several tumors, therefore making this subunit a suitable target for the development of selective inhibitors. Indeed, highly specific small-molecule inhibitors of EZH2 have been reported. In plants, mutations in some PRC2 components lead to embryonic lethality, but no trial with any inhibitor has ever been reported.	human	blood	High+Lowthroughput	Inhibition of Polycomb Repressive Complex 2 activity reduces trimethylation of H3K27 and affects development in Arabidopsis seedlings	否		leukemia	leukemic cell	E_01_0222	PCR, Western blot, immunofluorescence staining	In mammals, gain-of-function mutations as well as overexpression of EZH2 have been associated with several tumors, therefore making this subunit a suitable target for the development of selective inhibitors. Indeed, highly specific small-molecule inhibitors of EZH2 have been reported. In plants, mutations in some PRC2 components lead to embryonic lethality, but no trial with any inhibitor has ever been reported.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In mammals, gain-of-function mutations as well as overexpression of EZH2 have been associated with several tumors, therefore making this subunit a suitable target for the development of selective inhibitors. Indeed, highly specific small-molecule inhibitors of EZH2 have been reported. In plants, mutations in some PRC2 components lead to embryonic lethality, but no trial with any inhibitor has ever been reported.	Immunohistochemical staining	In mammals, gain-of-function mutations as well as overexpression of EZH2 have been associated with several tumors, therefore making this subunit a suitable target for the development of selective inhibitors. Indeed, highly specific small-molecule inhibitors of EZH2 have been reported. In plants, mutations in some PRC2 components lead to embryonic lethality, but no trial with any inhibitor has ever been reported.		PCR,Western blot,免疫荧光染色				EZH2		In mammals, gain-of-function mutations as well as overexpression of EZH2 have been associated with several tumors, therefore making this subunit a suitable target for the development of selective inhibitors. Indeed, highly specific small-molecule inhibitors of EZH2 have been reported. In plants, mutations in some PRC2 components lead to embryonic lethality, but no trial with any inhibitor has ever been reported.
31618980	chr10	67881914	67883914	SIRT1	SIRT1 couples the deacetylation of various transcription factors and co- factors to the cleavage of NAD+, an indicator of cellular metabolic status, playing a vital role in metabolism, including fat storage, gluconeogenesis, fatty acid oxidation, lipogenesis, insulin secretion, food intake, circadian rhythm, and inflammation [40].	human	Musculature	High+Lowthroughput	Gynostemma Pentaphyllum Extract Ameliorates High-Fat Diet-Induced Obesity in C57BL/6N Mice by Upregulating SIRT1	否		Obesity	mouse cell of skeletal muscle	E_01_0223	PCR,Western blot	SIRT1 couples the deacetylation of various transcription factors and co- factors to the cleavage of NAD+, an indicator of cellular metabolic status, playing a vital role in metabolism, including fat storage, gluconeogenesis, fatty acid oxidation, lipogenesis, insulin secretion, food intake, circadian rhythm, and inflammation [40].	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		SIRT1 couples the deacetylation of various transcription factors and co- factors to the cleavage of NAD+, an indicator of cellular metabolic status, playing a vital role in metabolism, including fat storage, gluconeogenesis, fatty acid oxidation, lipogenesis, insulin secretion, food intake, circadian rhythm, and inflammation [40].	Immunohistochemical staining	SIRT1 couples the deacetylation of various transcription factors and co- factors to the cleavage of NAD+, an indicator of cellular metabolic status, playing a vital role in metabolism, including fat storage, gluconeogenesis, fatty acid oxidation, lipogenesis, insulin secretion, food intake, circadian rhythm, and inflammation [40].		PCR,Western blot				SIRT1		SIRT1 couples the deacetylation of various transcription factors and co- factors to the cleavage of NAD+, an indicator of cellular metabolic status, playing a vital role in metabolism, including fat storage, gluconeogenesis, fatty acid oxidation, lipogenesis, insulin secretion, food intake, circadian rhythm, and inflammation [40].
31618627	chr12	2956471	2958471	TEAD4	Here, we mapped DSBs at high resolution in cancer and non-tumorigenic cells and found a transcrip_x0002_tion-coupled repair mechanism at oncogeni super_x0002_enhancers. At these super-enhancers the transcrip_x0002_tion factor TEAD4, together with various transcription factors and co-factors, co-localizes with the repair factor RAD51 of the homologous recombination pathway.	human	connective	High+Lowthroughput	Activation of Oncogenic Super-Enhancers Is Coupled with DNA Repair by RAD51	否		cancer		E_01_0224	PCR,Flow cytometry	Here, we mapped DSBs at high resolution in cancer and non-tumorigenic cells and found a transcrip_x0002_tion-coupled repair mechanism at oncogeni super_x0002_enhancers. At these super-enhancers the transcrip_x0002_tion factor TEAD4, together with various transcription factors and co-factors, co-localizes with the repair factor RAD51 of the homologous recombination pathway.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Here, we mapped DSBs at high resolution in cancer and non-tumorigenic cells and found a transcrip_x0002_tion-coupled repair mechanism at oncogeni super_x0002_enhancers. At these super-enhancers the transcrip_x0002_tion factor TEAD4, together with various transcription factors and co-factors, co-localizes with the repair factor RAD51 of the homologous recombination pathway.	Immunohistochemical staining	Here, we mapped DSBs at high resolution in cancer and non-tumorigenic cells and found a transcrip_x0002_tion-coupled repair mechanism at oncogeni super_x0002_enhancers. At these super-enhancers the transcrip_x0002_tion factor TEAD4, together with various transcription factors and co-factors, co-localizes with the repair factor RAD51 of the homologous recombination pathway.		PCR,Flow cytometry				TEAD4		Here, we mapped DSBs at high resolution in cancer and non-tumorigenic cells and found a transcrip_x0002_tion-coupled repair mechanism at oncogeni super_x0002_enhancers. At these super-enhancers the transcrip_x0002_tion factor TEAD4, together with various transcription factors and co-factors, co-localizes with the repair factor RAD51 of the homologous recombination pathway.
31616042	chr16	54280654	54282654	IRX3	The mechanism underlying the link between IRX3 and these conditions was since established using both 4-C and CRISPR-Cas9 based methods, which showed that the SNP in the FTO region de-repressed IRX3 expression, leading to altered energy metabolism and increased lipid storage [18, 19].	human	connective	High+Lowthroughput	Understanding the genetics of neuropsychiatric disorders: the potential role of genomic regulatory blocks	是	rs75059851	tumour	tumor cell	E_01_0225	Flow cytometry	The mechanism underlying the link between IRX3 and these conditions was since established using both 4-C and CRISPR-Cas9 based methods, which showed that the SNP in the FTO region de-repressed IRX3 expression, leading to altered energy metabolism and increased lipid storage [18, 19].	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The mechanism underlying the link between IRX3 and these conditions was since established using both 4-C and CRISPR-Cas9 based methods, which showed that the SNP in the FTO region de-repressed IRX3 expression, leading to altered energy metabolism and increased lipid storage [18, 19].	Immunohistochemical staining	The mechanism underlying the link between IRX3 and these conditions was since established using both 4-C and CRISPR-Cas9 based methods, which showed that the SNP in the FTO region de-repressed IRX3 expression, leading to altered energy metabolism and increased lipid storage [18, 19].		Flow cytometry			IRX3,VRK2		The mechanism underlying the link between IRX3 and these conditions was since established using both 4-C and CRISPR-Cas9 based methods, which showed that the SNP in the FTO region de-repressed IRX3 expression, leading to altered energy metabolism and increased lipid storage [18, 19].;A notable example of an SNP involved in long-range reg_x0002_ulation of gene expression is a locus obtained by merging two SNPs in LD, with two nearby VRK2 and FANCL genes highlighted as putative targets of these variants.	
31615896	chr17	39401537	39403537	MED1	In addition, other TFs and cofactors, such as KLFs, STAT5, PBX1, Krox20, AP1 , ATFs, GATA2/3 , TAF8 , and Mediator subunits (MED1, MED14 and NED23), have been reported to be involved in regulating either adipocyte commitment or differentiation in cell line and/or mouse models.	human	connective	High+Lowthroughput	The transcription factor NKX1-2 promotes adipogenesis and may contribute to a balance between adipocyte and osteoblast differentiation	否		Thyroid cancer	ear mesenchymal stem cell	E_01_0226	Western blot,PCR	In addition, other TFs and cofactors, such as KLFs, STAT5, PBX1, Krox20, AP1 , ATFs, GATA2/3 , TAF8 , and Mediator subunits (MED1, MED14 and NED23), have been reported to be involved in regulating either adipocyte commitment or differentiation in cell line and/or mouse models.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In addition, other TFs and cofactors, such as KLFs, STAT5, PBX1, Krox20, AP1 , ATFs, GATA2/3 , TAF8 , and Mediator subunits (MED1, MED14 and NED23), have been reported to be involved in regulating either adipocyte commitment or differentiation in cell line and/or mouse models.	Immunohistochemical staining	In addition, other TFs and cofactors, such as KLFs, STAT5, PBX1, Krox20, AP1 , ATFs, GATA2/3 , TAF8 , and Mediator subunits (MED1, MED14 and NED23), have been reported to be involved in regulating either adipocyte commitment or differentiation in cell line and/or mouse models.		Western blot,PCR				MED1		In addition, other TFs and cofactors, such as KLFs, STAT5, PBX1, Krox20, AP1 , ATFs, GATA2/3 , TAF8 , and Mediator subunits (MED1, MED14 and NED23), have been reported to be involved in regulating either adipocyte commitment or differentiation in cell line and/or mouse models.
31610176	chr6	131945597	131947597	CCN2	Conversely, fibroblast activation was impaired in mice with a fibroblast-specific deletion of Ccn2, associated with reduced expression of alpha-smooth muscle actin and Sox2.	human	connective	High+Lowthroughput	Insights into Fibroblast Plasticity: Cellular Communication Network 2 Is Required for Activation of Cancer-Associated Fibroblasts in a Murine Model of Melanoma	否		tumour	melanoma cells	E_01_0227	Flow cytometry,PCR,Western blot	Conversely, fibroblast activation was impaired in mice with a fibroblast-specific deletion of Ccn2, associated with reduced expression of alpha-smooth muscle actin and Sox2.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Conversely, fibroblast activation was impaired in mice with a fibroblast-specific deletion of Ccn2, associated with reduced expression of alpha-smooth muscle actin and Sox2.	Immunohistochemical staining	Conversely, fibroblast activation was impaired in mice with a fibroblast-specific deletion of Ccn2, associated with reduced expression of alpha-smooth muscle actin and Sox2.		Flow cytometry,PCR,Western blot			Sox2,ZFHX4	CCN2,BRAF	Conversely, fibroblast activation was impaired in mice with a fibroblast-specific deletion of Ccn2, associated with reduced expression of alpha-smooth muscle actin and Sox2.;This resulted in a 9-gene score composed of the following genes: ZFHX4, DCN, ITGA11, COL6A3, COL1A1, ITGBL1, COL8A1, INHBA, and, MEG3. CAF-specific CCN2 scores were dichotimized with 13 receiver operating characteristics (ROC) curves to determine the optimal cutoff for the endpoint of overall survival censorship.	Conversely, fibroblast activation was impaired in mice with a fibroblast-specific deletion of Ccn2, associated with reduced expression of alpha-smooth muscle actin and Sox2.;Although drugs, including those targeting specific mutations (eg, in BRAF) and checkpoint inhibitors, have been discovered that can retard melanoma progression in some patients, ultimately patients develop resistance to these regimens.
31608710	chr1	173855753	173857753	GAS5	The overexpression vector or short hairpin RNA for GAS5 or enhancer of zeste homolog 2 (EZH2) were transfected into RGCs after in vitro pressurization culture to exam the function of GAS5 in RGC apoptosis.	human	eye	High+Lowthroughput	Silencing of GAS5 Alleviates Glaucoma in Rat Models by Reducing Retinal Ganglion Cell Apoptosis	否		glaucoma	retinal ganglion cell	E_01_0228	PCR, Western blot, immunofluorescence light staining, flow cytometry	The overexpression vector or short hairpin RNA for GAS5 or enhancer of zeste homolog 2 (EZH2) were transfected into RGCs after in vitro pressurization culture to exam the function of GAS5 in RGC apoptosis.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The overexpression vector or short hairpin RNA for GAS5 or enhancer of zeste homolog 2 (EZH2) were transfected into RGCs after in vitro pressurization culture to exam the function of GAS5 in RGC apoptosis.	Immunohistochemical staining	The overexpression vector or short hairpin RNA for GAS5 or enhancer of zeste homolog 2 (EZH2) were transfected into RGCs after in vitro pressurization culture to exam the function of GAS5 in RGC apoptosis.		PCR,Western blot,免疫荧光光染色,Flow cytometry			ABCA1	GAS5,EZH2	In addition, up-regulation of EZH2 promoted trimethylation of lysine 27 on histone H3, therefore suppressing ABCA1 expression, eventually leading to the inhibition of RGC apoptosis.	The overexpression vector or short hairpin RNA for GAS5 or enhancer of zeste homolog 2 (EZH2) were transfected into RGCs after in vitro pressurization culture to exam the function of GAS5 in RGC apoptosis.;The overexpression vector or short hairpin RNA for GAS5 or enhancer of zeste homolog 2 (EZH2) were transfected into RGCs after in vitro pressurization culture to exam the function of GAS5 in RGC apoptosis.
31608546	chr6	88136910	88138910	CNR1	Previous studies have shown that the coding regions of the CNR1 gene, that encodes CB1, lack common non-synonymous polymorphisms that might account for differences in cannabinoid response.	human	connective	High+Lowthroughput	Disease-associated polymorphisms within the conserved ECR1 enhancer differentially regulate the tissue-specific activity of the cannabinoid-1 receptor gene promoter; implications for cannabinoid pharmacogenetics	是	rs2023239	Obesity	SH-SY5Y (human neuroblastoma cell)	E_01_0229	PCR immunofluorescence staining	Previous studies have shown that the coding regions of the CNR1 gene, that encodes CB1, lack common non-synonymous polymorphisms that might account for differences in cannabinoid response.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Previous studies have shown that the coding regions of the CNR1 gene, that encodes CB1, lack common non-synonymous polymorphisms that might account for differences in cannabinoid response.	Immunohistochemical staining	Previous studies have shown that the coding regions of the CNR1 gene, that encodes CB1, lack common non-synonymous polymorphisms that might account for differences in cannabinoid response.		PCR免疫荧光染色			CNR1		Previous studies have shown that the coding regions of the CNR1 gene, that encodes CB1, lack common non-synonymous polymorphisms that might account for differences in cannabinoid response.	
31606247	chr16	30955158	30957158	SETD1A	Our findings advance understanding of how SETD1A mutations predispose to schizophrenia (SCZ) and point to novel therapeutic interventions.	human	Nervous	High+Lowthroughput	Recapitulation and Reversal of Schizophrenia-Related Phenotypes in Setd1a-Deficient Mice	是		Schizophrenia	neural progenitor cell	E_01_0230	Flow cytometry, PCR, immunofluorescence staining, Western blot	Our findings advance understanding of how SETD1A mutations predispose to schizophrenia (SCZ) and point to novel therapeutic interventions.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Our findings advance understanding of how SETD1A mutations predispose to schizophrenia (SCZ) and point to novel therapeutic interventions.	Immunohistochemical staining	Our findings advance understanding of how SETD1A mutations predispose to schizophrenia (SCZ) and point to novel therapeutic interventions.		Flow cytometry,PCR,免疫荧光染色,Western blot			SETD1A		Our findings advance understanding of how SETD1A mutations predispose to schizophrenia (SCZ) and point to novel therapeutic interventions.	
31605138	chr9	21964977	21966977	CDKN2A	The existence of genetic risk factors common to NB and CMM has been suggested by the finding of the loss of function mutation E27X in CDKN2A in melanoma families who display NB (7).	human	blood	High+Lowthroughput	Neural crest-derived tumor neuroblastoma and melanoma share 1p13.2 as susceptibility locus that shows a long-range interaction with the SLC16A1 gene	是	rs2153977	cancer		E_01_0231	Flow cytometry,PCR,Western blot	The existence of genetic risk factors common to NB and CMM has been suggested by the finding of the loss of function mutation E27X in CDKN2A in melanoma families who display NB (7).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The existence of genetic risk factors common to NB and CMM has been suggested by the finding of the loss of function mutation E27X in CDKN2A in melanoma families who display NB (7).	Immunohistochemical staining	The existence of genetic risk factors common to NB and CMM has been suggested by the finding of the loss of function mutation E27X in CDKN2A in melanoma families who display NB (7).		Flow cytometry,PCR,Western blot				CDKN2A		The existence of genetic risk factors common to NB and CMM has been suggested by the finding of the loss of function mutation E27X in CDKN2A in melanoma families who display NB (7).
31599948	chr12	4365800	4367800	FGF23	Fibroblast growth factor 23 (FGF23) is a newly dis_x0002_covered member of the endocrine subfamily of sys_x0002_temic FGF hormones that in humans include FGF19 and FGF21 (1, 2).	human	Epithelial	High+Lowthroughput	A Control Region Near the Fibroblast Growth Factor 23 Gene Mediates Response to Phosphate, 1,25(OH)2D3, and LPS In Vivo	否		cancer	epithelial cell	E_01_0232	PCR 	Fibroblast growth factor 23 (FGF23) is a newly dis_x0002_covered member of the endocrine subfamily of sys_x0002_temic FGF hormones that in humans include FGF19 and FGF21 (1, 2).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Fibroblast growth factor 23 (FGF23) is a newly dis_x0002_covered member of the endocrine subfamily of sys_x0002_temic FGF hormones that in humans include FGF19 and FGF21 (1, 2).	Immunohistochemical staining	Fibroblast growth factor 23 (FGF23) is a newly dis_x0002_covered member of the endocrine subfamily of sys_x0002_temic FGF hormones that in humans include FGF19 and FGF21 (1, 2).		PCR 			FGF23,CYP24A1,Cyp27b1		Fibroblast growth factor 23 (FGF23) is a newly dis_x0002_covered member of the endocrine subfamily of sys_x0002_temic FGF hormones that in humans include FGF19 and FGF21 (1, 2).;Accordingly, FGF23 has been shown to inhibit both the synthesis and se_x0002_cretion of PTH and to suppress CYP27B1 while induc_x0002_ing CYP24A1, the renal enzymes responsible for the synthesis and homeostatic maintenance of circulating 1,25(OH)2D3.;Be_x0002_cause both PTH and 1,25(OH)2D3 also modulate P homeostasis and PTH represents a primary inducer of the Cyp27b1 gene (11, 14, 15), these activities of FGF23 constitute key negative feedback loops that serve to limit the activity of both hormones in the target tissues de_x0002_scribed previously.	
31595632	chr12	6531857	6533857	GAPDH	The RNA concentration was detected by a microplate reader, and RNA was reverse transcribed to cDNA using the QIAGEN miRNA reverse transcription (miScript II RT Kit) and Thermo reverse transcription kits. Using cDNA as a template, the gene expression of U6, miR-326, C/EBPα, PPARγ, and GAPDH was detected by qPCR.	human	connective	High+Lowthroughput	The Role of miR-326 in Adipogenic Differentiation of Human Adipose-Derived Stem Cells by Targeting C/EBPα in vitro	否		Obesity	mesenchymal stem cell	E_01_0233	PCR, Western blot	The RNA concentration was detected by a microplate reader, and RNA was reverse transcribed to cDNA using the QIAGEN miRNA reverse transcription (miScript II RT Kit) and Thermo reverse transcription kits. Using cDNA as a template, the gene expression of U6, miR-326, C/EBPα, PPARγ, and GAPDH was detected by qPCR.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The RNA concentration was detected by a microplate reader, and RNA was reverse transcribed to cDNA using the QIAGEN miRNA reverse transcription (miScript II RT Kit) and Thermo reverse transcription kits. Using cDNA as a template, the gene expression of U6, miR-326, C/EBPα, PPARγ, and GAPDH was detected by qPCR.	Immunohistochemical staining	The RNA concentration was detected by a microplate reader, and RNA was reverse transcribed to cDNA using the QIAGEN miRNA reverse transcription (miScript II RT Kit) and Thermo reverse transcription kits. Using cDNA as a template, the gene expression of U6, miR-326, C/EBPα, PPARγ, and GAPDH was detected by qPCR.		PCR, Western blot				GAPDH		The RNA concentration was detected by a microplate reader, and RNA was reverse transcribed to cDNA using the QIAGEN miRNA reverse transcription (miScript II RT Kit) and Thermo reverse transcription kits. Using cDNA as a template, the gene expression of U6, miR-326, C/EBPα, PPARγ, and GAPDH was detected by qPCR.
31592021	chr10	100370073	100372073	OLMALINC	maturation-associated long intergenic noncoding RNA (OLMALINC) in a statin- and triglyceride (TG)- associated liver co-expression network using liver RNA sequencing (RNA-seq) from 259 Finnish patients who had undergone bariatric surgery.	human	liver	High+Lowthroughput	Novel Lipid Long Intervening Noncoding RNA, Oligodendrocyte Maturation-Associated Long Intergenic Noncoding RNA, Regulates the Liver Steatosis Gene Stearoyl-Coenzyme A Desaturase As an Enhancer RNA	否		liver cancer	HepG2 cell	E_01_0234	Flow cytometry,Western blot	maturation-associated long intergenic noncoding RNA (OLMALINC) in a statin- and triglyceride (TG)- associated liver co-expression network using liver RNA sequencing (RNA-seq) from 259 Finnish patients who had undergone bariatric surgery.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		maturation-associated long intergenic noncoding RNA (OLMALINC) in a statin- and triglyceride (TG)- associated liver co-expression network using liver RNA sequencing (RNA-seq) from 259 Finnish patients who had undergone bariatric surgery.	Immunohistochemical staining	maturation-associated long intergenic noncoding RNA (OLMALINC) in a statin- and triglyceride (TG)- associated liver co-expression network using liver RNA sequencing (RNA-seq) from 259 Finnish patients who had undergone bariatric surgery.		Flow cytometry,Western blot			OLMALINC		maturation-associated long intergenic noncoding RNA (OLMALINC) in a statin- and triglyceride (TG)- associated liver co-expression network using liver RNA sequencing (RNA-seq) from 259 Finnish patients who had undergone bariatric surgery.	
31590652	chr12	7785003	7787003	NANOG	We train our models on p300 co-activator binding sites; H1-specific, transcription factor binding sites (TFBS): NANOG, OCT4, and SOX2; and uncondensed, cleavage sensitive, DNase I Hypersensitivity Regions (DHS); which are all distal to TSS; as positive examples.	human	connective	High+Lowthroughput	AIKYATAN: mapping distal regulatory elements using convolutional learning on GPU	否		cancer	embryonic stem cell	E_01_0235	PCR	We train our models on p300 co-activator binding sites; H1-specific, transcription factor binding sites (TFBS): NANOG, OCT4, and SOX2; and uncondensed, cleavage sensitive, DNase I Hypersensitivity Regions (DHS); which are all distal to TSS; as positive examples.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We train our models on p300 co-activator binding sites; H1-specific, transcription factor binding sites (TFBS): NANOG, OCT4, and SOX2; and uncondensed, cleavage sensitive, DNase I Hypersensitivity Regions (DHS); which are all distal to TSS; as positive examples.	Immunohistochemical staining	We train our models on p300 co-activator binding sites; H1-specific, transcription factor binding sites (TFBS): NANOG, OCT4, and SOX2; and uncondensed, cleavage sensitive, DNase I Hypersensitivity Regions (DHS); which are all distal to TSS; as positive examples.		PCR			NANOG		We train our models on p300 co-activator binding sites; H1-specific, transcription factor binding sites (TFBS): NANOG, OCT4, and SOX2; and uncondensed, cleavage sensitive, DNase I Hypersensitivity Regions (DHS); which are all distal to TSS; as positive examples.	
31589096	chr17	42697169	42699169	EZH1	Furthermore, the treatment of G. glabra root extract was also capable of augmenting the production of EZH1 in C666-1 cells (Figure 3(c)), thereby providing a potential mechanism that AK027294 silencing sup_x0002_presses C666-1 proliferation by increasing EZH1 expression levels.	human	nasopharynx	High+Lowthroughput	Glycyrrhiza glabra suppresses nasopharyngeal carcinoma cell proliferation through inhibiting the expression of lncRNA, AK027294	否		Nasopharyngeal carcinoma	nasopharyngeal carcinoma cell	E_01_0236	Western blot,Flow cytometry,PCR	Furthermore, the treatment of G. glabra root extract was also capable of augmenting the production of EZH1 in C666-1 cells (Figure 3(c)), thereby providing a potential mechanism that AK027294 silencing sup_x0002_presses C666-1 proliferation by increasing EZH1 expression levels.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Furthermore, the treatment of G. glabra root extract was also capable of augmenting the production of EZH1 in C666-1 cells (Figure 3(c)), thereby providing a potential mechanism that AK027294 silencing sup_x0002_presses C666-1 proliferation by increasing EZH1 expression levels.	Immunohistochemical staining	Furthermore, the treatment of G. glabra root extract was also capable of augmenting the production of EZH1 in C666-1 cells (Figure 3(c)), thereby providing a potential mechanism that AK027294 silencing sup_x0002_presses C666-1 proliferation by increasing EZH1 expression levels.		Western blot,Flow cytometry,PCR			EZH1		Furthermore, the treatment of G. glabra root extract was also capable of augmenting the production of EZH1 in C666-1 cells (Figure 3(c)), thereby providing a potential mechanism that AK027294 silencing sup_x0002_presses C666-1 proliferation by increasing EZH1 expression levels.	
31588347	chr5	113018862	113020862	MCC	Mucociliary clearance (MCC) in the respiratory tract acts as the first physical barrier of the innate immune defense mecha_x0002_nism, by which inhaled environmental stimuli, including microbes and irritants.5 MCC depends on two important con_x0002_stituents: mucus production and mucus transport.	human	Epithelial	High+Lowthroughput	Benzisothiazolinone upregulates the MUC5AC expression via ERK1/2, p38, and NF-κB pathways in airway epithelial cells	否		asthma	epithelial cell	E_01_0237	PCR,Western blot 	Mucociliary clearance (MCC) in the respiratory tract acts as the first physical barrier of the innate immune defense mecha_x0002_nism, by which inhaled environmental stimuli, including microbes and irritants.5 MCC depends on two important con_x0002_stituents: mucus production and mucus transport.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Mucociliary clearance (MCC) in the respiratory tract acts as the first physical barrier of the innate immune defense mecha_x0002_nism, by which inhaled environmental stimuli, including microbes and irritants.5 MCC depends on two important con_x0002_stituents: mucus production and mucus transport.	Immunohistochemical staining	Mucociliary clearance (MCC) in the respiratory tract acts as the first physical barrier of the innate immune defense mecha_x0002_nism, by which inhaled environmental stimuli, including microbes and irritants.5 MCC depends on two important con_x0002_stituents: mucus production and mucus transport.		PCR,Western blot 			MCC		Mucociliary clearance (MCC) in the respiratory tract acts as the first physical barrier of the innate immune defense mecha_x0002_nism, by which inhaled environmental stimuli, including microbes and irritants.5 MCC depends on two important con_x0002_stituents: mucus production and mucus transport.	
31588046	chr12	7785776	7787776	NANOG	After 48 h of TGF-bi treatment, the transcriptional downre_x0002_gulation of key pluripotency genes, including NANOG, OCT4 (POU5F1), and PRDM14 was evident (Figure S1A)	human	connective	High+Lowthroughput	The RNA Helicase DDX6 Controls Cellular Plasticity by Modulating P-Body Homeostasis	否		cancer	cancer cell	E_01_0238	Flow cytometry, PCR, immunofluorescence staining	After 48 h of TGF-bi treatment, the transcriptional downre_x0002_gulation of key pluripotency genes, including NANOG, OCT4 (POU5F1), and PRDM14 was evident (Figure S1A)	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		After 48 h of TGF-bi treatment, the transcriptional downre_x0002_gulation of key pluripotency genes, including NANOG, OCT4 (POU5F1), and PRDM14 was evident (Figure S1A)	Immunohistochemical staining	After 48 h of TGF-bi treatment, the transcriptional downre_x0002_gulation of key pluripotency genes, including NANOG, OCT4 (POU5F1), and PRDM14 was evident (Figure S1A)		Flow cytometry,PCR,免疫荧光染色			NANOG		After 48 h of TGF-bi treatment, the transcriptional downre_x0002_gulation of key pluripotency genes, including NANOG, OCT4 (POU5F1), and PRDM14 was evident (Figure S1A)	
31588023	chr1	170660059	170662059	PRRX1	Motifs for the SE-associated TFs PRRX1, NFIC, and NFIX were enriched in both H3K27M sub_x0002_groups over normal pons (Figure 2D)	human	connective	High+Lowthroughput	Histone Variant and Cell Context Determine H3K27M Reprogramming of the Enhancer Landscape and Oncogenic State	否		Malignancy	immune cell	E_01_0239	Flow cytometry, PCR, immunofluorescence staining	Motifs for the SE-associated TFs PRRX1, NFIC, and NFIX were enriched in both H3K27M sub_x0002_groups over normal pons (Figure 2D)	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Motifs for the SE-associated TFs PRRX1, NFIC, and NFIX were enriched in both H3K27M sub_x0002_groups over normal pons (Figure 2D)	Immunohistochemical staining	Motifs for the SE-associated TFs PRRX1, NFIC, and NFIX were enriched in both H3K27M sub_x0002_groups over normal pons (Figure 2D)		Flow cytometry,PCR,免疫荧光染色			PRRX1		Motifs for the SE-associated TFs PRRX1, NFIC, and NFIX were enriched in both H3K27M sub_x0002_groups over normal pons (Figure 2D)	
31586130	chr3	194133931	194135931	HES1	Furthermore, NRARP overexpression blocked NOTCH transcriptional activity as shown by the overall decreased expression of NOTCH1 downstream tar_x0002_gets HES1 and DTX1 in NRARP-overexpressing cells (Fig. 1f).	human	blood	High+Lowthroughput	NRARP displays either pro- or anti-tumoral roles in T-cell acute lymphoblastic leukemia depending on Notch and Wnt signaling	否		Acute lymphoblastic leukemia	T cell	E_01_0240	PCR,Western blot	Furthermore, NRARP overexpression blocked NOTCH transcriptional activity as shown by the overall decreased expression of NOTCH1 downstream tar_x0002_gets HES1 and DTX1 in NRARP-overexpressing cells (Fig. 1f).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Furthermore, NRARP overexpression blocked NOTCH transcriptional activity as shown by the overall decreased expression of NOTCH1 downstream tar_x0002_gets HES1 and DTX1 in NRARP-overexpressing cells (Fig. 1f).	Immunohistochemical staining	Furthermore, NRARP overexpression blocked NOTCH transcriptional activity as shown by the overall decreased expression of NOTCH1 downstream tar_x0002_gets HES1 and DTX1 in NRARP-overexpressing cells (Fig. 1f).		PCR,Western blot				HES1		Furthermore, NRARP overexpression blocked NOTCH transcriptional activity as shown by the overall decreased expression of NOTCH1 downstream tar_x0002_gets HES1 and DTX1 in NRARP-overexpressing cells (Fig. 1f).
31584754	chr3	41191952	41193952	CTNNB1	It is well established that the central genetic event in the tumorigenesis of SPN is a gain-of-function mutation within the CTNNB1 gene that prevents β-catenin phos_x0002_phorylation and its subsequent proteasomal degradation through ubiquitination.1	human	tumour	High+Lowthroughput	The usefulness of lymphoid enhancer-binding factor 1 and androgen receptor in diagnosing solid pseudopapillary neoplasm of the pancreas on cytopathology	否		tumour	tumor cell	E_01_0241	Immunohistochemistry	It is well established that the central genetic event in the tumorigenesis of SPN is a gain-of-function mutation within the CTNNB1 gene that prevents β-catenin phos_x0002_phorylation and its subsequent proteasomal degradation through ubiquitination.1	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		It is well established that the central genetic event in the tumorigenesis of SPN is a gain-of-function mutation within the CTNNB1 gene that prevents β-catenin phos_x0002_phorylation and its subsequent proteasomal degradation through ubiquitination.1	Immunohistochemical staining	It is well established that the central genetic event in the tumorigenesis of SPN is a gain-of-function mutation within the CTNNB1 gene that prevents β-catenin phos_x0002_phorylation and its subsequent proteasomal degradation through ubiquitination.1		免疫组化				CTNNB1		It is well established that the central genetic event in the tumorigenesis of SPN is a gain-of-function mutation within the CTNNB1 gene that prevents β-catenin phos_x0002_phorylation and its subsequent proteasomal degradation through ubiquitination.1
31583122	chr11	35136216	35138216	CD44	It has been suggested that the expression of stem cell-associated markers, such as CD44 and Oct4, may support their roles in therapy evasion, tumor recur_x0002_rence, and metastasis11.	human	lung	High+Lowthroughput	Targeting Wnt/EZH2/microRNA-708 signaling pathway inhibits neuroendocrine differentiation in prostate cancer	否		Lung adenocarcinoma	adenocarcinoma cell	E_01_0242	PCR,Western blot	It has been suggested that the expression of stem cell-associated markers, such as CD44 and Oct4, may support their roles in therapy evasion, tumor recur_x0002_rence, and metastasis11.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		It has been suggested that the expression of stem cell-associated markers, such as CD44 and Oct4, may support their roles in therapy evasion, tumor recur_x0002_rence, and metastasis11.	Immunohistochemical staining	It has been suggested that the expression of stem cell-associated markers, such as CD44 and Oct4, may support their roles in therapy evasion, tumor recur_x0002_rence, and metastasis11.		PCR,Western blot			CD44		It has been suggested that the expression of stem cell-associated markers, such as CD44 and Oct4, may support their roles in therapy evasion, tumor recur_x0002_rence, and metastasis11.	
31582835	chr7	148804794	148806794	EZH2	Histone 3 trimethylated on lysine 27 (H3K27me3), a marker of silent chromatin conformation is present at the ADGRB1 promoter, and inhibition of EZH2, the catalytic component of the Polycomb Repressive complex 2 (PRC2) that methylates H3K27, switches the gene into an active chromatin status and reactivates BAI1 expression.	human	tumour	High+Lowthroughput	EZH2 targeting reduces medulloblastoma growth through epigenetic reactivation of the BAI1/p53 tumor suppressor pathway	否		Medulloblastoma	Medulloblastoma cell	E_01_0243	PCR,Western blot	Histone 3 trimethylated on lysine 27 (H3K27me3), a marker of silent chromatin conformation is present at the ADGRB1 promoter, and inhibition of EZH2, the catalytic component of the Polycomb Repressive complex 2 (PRC2) that methylates H3K27, switches the gene into an active chromatin status and reactivates BAI1 expression.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Histone 3 trimethylated on lysine 27 (H3K27me3), a marker of silent chromatin conformation is present at the ADGRB1 promoter, and inhibition of EZH2, the catalytic component of the Polycomb Repressive complex 2 (PRC2) that methylates H3K27, switches the gene into an active chromatin status and reactivates BAI1 expression.	Immunohistochemical staining	Histone 3 trimethylated on lysine 27 (H3K27me3), a marker of silent chromatin conformation is present at the ADGRB1 promoter, and inhibition of EZH2, the catalytic component of the Polycomb Repressive complex 2 (PRC2) that methylates H3K27, switches the gene into an active chromatin status and reactivates BAI1 expression.		PCR,Western blot				EZH2		Histone 3 trimethylated on lysine 27 (H3K27me3), a marker of silent chromatin conformation is present at the ADGRB1 promoter, and inhibition of EZH2, the catalytic component of the Polycomb Repressive complex 2 (PRC2) that methylates H3K27, switches the gene into an active chromatin status and reactivates BAI1 expression.
31581708	chr17	39726151	39728151	MIEN1	Migration and invasion enhancer 1 (MIEN1) is a membrane-anchored protein and exists in various cancerous tissues. However, the roles of MIEN1 in prostate cancer have not yet been clearly addressed.	human	prostate	High+Lowthroughput	Migration and Invasion Enhancer 1 Is an NF-?B-Inducing Gene Enhancing the Cell Proliferation and Invasion Ability of Human Prostate Carcinoma Cells In Vitro and In Vivo	否		prostatic cancer	prostate cancer cell	E_01_0244	PCR,Western blot,Flow cytometry	Migration and invasion enhancer 1 (MIEN1) is a membrane-anchored protein and exists in various cancerous tissues. However, the roles of MIEN1 in prostate cancer have not yet been clearly addressed.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Migration and invasion enhancer 1 (MIEN1) is a membrane-anchored protein and exists in various cancerous tissues. However, the roles of MIEN1 in prostate cancer have not yet been clearly addressed.	Immunohistochemical staining	Migration and invasion enhancer 1 (MIEN1) is a membrane-anchored protein and exists in various cancerous tissues. However, the roles of MIEN1 in prostate cancer have not yet been clearly addressed.		PCR,Western blot,Flow cytometry			MIEN1,NDRG1		Migration and invasion enhancer 1 (MIEN1) is a membrane-anchored protein and exists in various cancerous tissues. However, the roles of MIEN1 in prostate cancer have not yet been clearly addressed.;Interleukin-6 (IL-6), a pluripotency cytokine, is involved in the malignant progression of prostate cancer [15,16], while N_x0002_myc downstream regulated 1 (NDRG1) is a tumor suppressor gene in numerous cancer cells [17], including prostate [18,19].	
31581661	chr8	127733019	127735019	MYC	Our findings also established that MYC Proto-Oncogene, basic helix-loop-helix (bHLH) Transcription Factor (MYC) signaling was down-regulated in curcumin-treated cell lines.	human	prostate	High+Lowthroughput	Curcumin-Gene Expression Response in Hormone Dependent and Independent Metastatic Prostate Cancer Cells	否		prostatic cancer	prostate cancer cell	E_01_0245	PCR 	Our findings also established that MYC Proto-Oncogene, basic helix-loop-helix (bHLH) Transcription Factor (MYC) signaling was down-regulated in curcumin-treated cell lines.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Our findings also established that MYC Proto-Oncogene, basic helix-loop-helix (bHLH) Transcription Factor (MYC) signaling was down-regulated in curcumin-treated cell lines.	Immunohistochemical staining	Our findings also established that MYC Proto-Oncogene, basic helix-loop-helix (bHLH) Transcription Factor (MYC) signaling was down-regulated in curcumin-treated cell lines.		PCR 				MYC		Our findings also established that MYC Proto-Oncogene, basic helix-loop-helix (bHLH) Transcription Factor (MYC) signaling was down-regulated in curcumin-treated cell lines.
31579913	chr20	63192571	63194571	YTHDF1	After excluding genes located on the X chromosome, the resultant twenty related autosomal chromosome genes involved in the m6A modification of methylated RNA were obtained. Briefly, we included seven literatures (14,19,34-38), which described the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), YTH N6-methyladenosine RNA binding protein 3 (YTHDF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTH domain-containing 1 (YTHDC1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), eukaryotic translation initiation factor 3 subunit A (EIF3A), and	human	colon	High+Lowthroughput	Genetic variants in m6A modification genes are associated with colorectal cancer risk	是	rs118049207	Colon cancer	Human colorectal carcinoma cell	E_01_0246	PCR	After excluding genes located on the X chromosome, the resultant twenty related autosomal chromosome genes involved in the m6A modification of methylated RNA were obtained. Briefly, we included seven literatures (14,19,34-38), which described the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), YTH N6-methyladenosine RNA binding protein 3 (YTHDF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTH domain-containing 1 (YTHDC1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), eukaryotic translation initiation factor 3 subunit A (EIF3A), and	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		After excluding genes located on the X chromosome, the resultant twenty related autosomal chromosome genes involved in the m6A modification of methylated RNA were obtained. Briefly, we included seven literatures (14,19,34-38), which described the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), YTH N6-methyladenosine RNA binding protein 3 (YTHDF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTH domain-containing 1 (YTHDC1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), eukaryotic translation initiation factor 3 subunit A (EIF3A), and	Immunohistochemical staining	After excluding genes located on the X chromosome, the resultant twenty related autosomal chromosome genes involved in the m6A modification of methylated RNA were obtained. Briefly, we included seven literatures (14,19,34-38), which described the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), YTH N6-methyladenosine RNA binding protein 3 (YTHDF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTH domain-containing 1 (YTHDC1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), eukaryotic translation initiation factor 3 subunit A (EIF3A), and		PCR			YTHDF1,YTHDF3,YTHDF2,EIF3A		After excluding genes located on the X chromosome, the resultant twenty related autosomal chromosome genes involved in the m6A modification of methylated RNA were obtained. Briefly, we included seven literatures (14,19,34-38), which described the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), YTH N6-methyladenosine RNA binding protein 3 (YTHDF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTH domain-containing 1 (YTHDC1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), eukaryotic translation initiation factor 3 subunit A (EIF3A), and;After excluding genes located on the X chromosome, the resultant twenty related autosomal chromosome genes involved in the m6A modification of methylated RNA were obtained. Briefly, we included seven literatures (14,19,34-38), which described the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), YTH N6-methyladenosine RNA binding protein 3 (YTHDF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTH domain-containing 1 (YTHDC1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), eukaryotic translation initiation factor 3 subunit A (EIF3A), and;After excluding genes located on the X chromosome, the resultant twenty related autosomal chromosome genes involved in the m6A modification of methylated RNA were obtained. Briefly, we included seven literatures (14,19,34-38), which described the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), YTH N6-methyladenosine RNA binding protein 3 (YTHDF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTH domain-containing 1 (YTHDC1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), eukaryotic translation initiation factor 3 subunit A (EIF3A), and;After excluding genes located on the X chromosome, the resultant twenty related autosomal chromosome genes involved in the m6A modification of methylated RNA were obtained. Briefly, we included seven literatures (14,19,34-38), which described the YTH N6-methyladenosine RNA binding protein 1 (YTHDF1), YTH N6-methyladenosine RNA binding protein 3 (YTHDF3), YTH N6-methyladenosine RNA binding protein 2 (YTHDF2), YTH domain-containing 1 (YTHDC1), heterogeneous nuclear ribonucleoprotein C (HNRNPC), eukaryotic translation initiation factor 3 subunit A (EIF3A), and	
31579098	chr7	148804077	148806077	EZH2	The results demonstrated that different concen_x0002_trations of DZNep could inhibit the expression of enhancer of zeste homolog 2 (EZH2) protein, decrease the RNA and protein expression levels of Hif-1α, total β-catenin and phosphorylated-β-catenin and increase the expression levels of non-phosphorylated-β-catenin to different degrees.	human	tumour	High+Lowthroughput	DZNep inhibits Hif-1α and Wnt signalling molecules to attenuate the proliferation and invasion of BGC-823 gastric cancer cells	否		tumour	tumor cell	E_01_0247	PCR,Western blot,Flow cytometry	The results demonstrated that different concen_x0002_trations of DZNep could inhibit the expression of enhancer of zeste homolog 2 (EZH2) protein, decrease the RNA and protein expression levels of Hif-1α, total β-catenin and phosphorylated-β-catenin and increase the expression levels of non-phosphorylated-β-catenin to different degrees.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The results demonstrated that different concen_x0002_trations of DZNep could inhibit the expression of enhancer of zeste homolog 2 (EZH2) protein, decrease the RNA and protein expression levels of Hif-1α, total β-catenin and phosphorylated-β-catenin and increase the expression levels of non-phosphorylated-β-catenin to different degrees.	Immunohistochemical staining	The results demonstrated that different concen_x0002_trations of DZNep could inhibit the expression of enhancer of zeste homolog 2 (EZH2) protein, decrease the RNA and protein expression levels of Hif-1α, total β-catenin and phosphorylated-β-catenin and increase the expression levels of non-phosphorylated-β-catenin to different degrees.		PCR,Western blot,Flow cytometry				EZH2		The results demonstrated that different concen_x0002_trations of DZNep could inhibit the expression of enhancer of zeste homolog 2 (EZH2) protein, decrease the RNA and protein expression levels of Hif-1α, total β-catenin and phosphorylated-β-catenin and increase the expression levels of non-phosphorylated-β-catenin to different degrees.
31573688	chr12	16545165	16547165	LMO3	LIM domain only 3 (LMO3), a member of the LIM_x0002_only protein group, enhances adipogenesis of human adipose-derived stromal cells by enhancing peroxisome proliferator-activated receptor γ (PPARG) transcriptional activity, and LMO3 is a specific regulator of human adipogenesis, but not of mouse, whose white adipocytes lack LMO3 expression. Moreover, LMO3 is upregulated in a tissue-specific manner in human obese visceral fat, and is an attractive target for interfering with human visceral obe_x0002_sity (Lindroos et al., 2013).	human	connective	High+Lowthroughput	Resveratrol Inhibits Human Visceral Preadipocyte Proliferation and Differentiation in vitro	否		diabetes	3T3-L1 cell	E_01_0248	PCR,Western blot	LIM domain only 3 (LMO3), a member of the LIM_x0002_only protein group, enhances adipogenesis of human adipose-derived stromal cells by enhancing peroxisome proliferator-activated receptor γ (PPARG) transcriptional activity, and LMO3 is a specific regulator of human adipogenesis, but not of mouse, whose white adipocytes lack LMO3 expression. Moreover, LMO3 is upregulated in a tissue-specific manner in human obese visceral fat, and is an attractive target for interfering with human visceral obe_x0002_sity (Lindroos et al., 2013).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		LIM domain only 3 (LMO3), a member of the LIM_x0002_only protein group, enhances adipogenesis of human adipose-derived stromal cells by enhancing peroxisome proliferator-activated receptor γ (PPARG) transcriptional activity, and LMO3 is a specific regulator of human adipogenesis, but not of mouse, whose white adipocytes lack LMO3 expression. Moreover, LMO3 is upregulated in a tissue-specific manner in human obese visceral fat, and is an attractive target for interfering with human visceral obe_x0002_sity (Lindroos et al., 2013).	Immunohistochemical staining	LIM domain only 3 (LMO3), a member of the LIM_x0002_only protein group, enhances adipogenesis of human adipose-derived stromal cells by enhancing peroxisome proliferator-activated receptor γ (PPARG) transcriptional activity, and LMO3 is a specific regulator of human adipogenesis, but not of mouse, whose white adipocytes lack LMO3 expression. Moreover, LMO3 is upregulated in a tissue-specific manner in human obese visceral fat, and is an attractive target for interfering with human visceral obe_x0002_sity (Lindroos et al., 2013).		PCR,Western blot			LMO3		LIM domain only 3 (LMO3), a member of the LIM_x0002_only protein group, enhances adipogenesis of human adipose-derived stromal cells by enhancing peroxisome proliferator-activated receptor γ (PPARG) transcriptional activity, and LMO3 is a specific regulator of human adipogenesis, but not of mouse, whose white adipocytes lack LMO3 expression. Moreover, LMO3 is upregulated in a tissue-specific manner in human obese visceral fat, and is an attractive target for interfering with human visceral obe_x0002_sity (Lindroos et al., 2013).	
31572429	chr22	41558440	41560440	CSDC2	Furthermore, the targeting sequences located in E-cadherin, cold-shock domain-containing protein C2 (CSDC2), and PDE4D genes could interact with miR-373 in MCF-7 cells rather than HeLa cells, which is consistent with our data that these three genes can be regulated by miR_x0002_373 in MCF-7 cells while not in HeLa cells.	human	breast	High+Lowthroughput	Purification and Identification of miRNA Target Sites in Genome Using DNA Affinity Precipitation	否		mammary cancer	MCF-7 cell	E_01_0249		Furthermore, the targeting sequences located in E-cadherin, cold-shock domain-containing protein C2 (CSDC2), and PDE4D genes could interact with miR-373 in MCF-7 cells rather than HeLa cells, which is consistent with our data that these three genes can be regulated by miR_x0002_373 in MCF-7 cells while not in HeLa cells.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Furthermore, the targeting sequences located in E-cadherin, cold-shock domain-containing protein C2 (CSDC2), and PDE4D genes could interact with miR-373 in MCF-7 cells rather than HeLa cells, which is consistent with our data that these three genes can be regulated by miR_x0002_373 in MCF-7 cells while not in HeLa cells.	Immunohistochemical staining	Furthermore, the targeting sequences located in E-cadherin, cold-shock domain-containing protein C2 (CSDC2), and PDE4D genes could interact with miR-373 in MCF-7 cells rather than HeLa cells, which is consistent with our data that these three genes can be regulated by miR_x0002_373 in MCF-7 cells while not in HeLa cells.					CSDC2		Furthermore, the targeting sequences located in E-cadherin, cold-shock domain-containing protein C2 (CSDC2), and PDE4D genes could interact with miR-373 in MCF-7 cells rather than HeLa cells, which is consistent with our data that these three genes can be regulated by miR_x0002_373 in MCF-7 cells while not in HeLa cells.	
31571902	chr22	15781801	15783801	DUXAP8	Dysregulated DUXAP8, LINC01116, LINC01138, and PCAT6 are significantly associated with HCC patients' poor outcomes.	human	liver	High+Lowthroughput	Up-regulated long non-coding RNA DUXAP8 promotes cell growth through repressing Krüppel-like factor 2 expression in human hepatocellular carcinoma	否		liver cancer	hepatocellular carcinoma cell	E_01_0250	PCR	Dysregulated DUXAP8, LINC01116, LINC01138, and PCAT6 are significantly associated with HCC patients' poor outcomes.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Dysregulated DUXAP8, LINC01116, LINC01138, and PCAT6 are significantly associated with HCC patients' poor outcomes.	Immunohistochemical staining	Dysregulated DUXAP8, LINC01116, LINC01138, and PCAT6 are significantly associated with HCC patients' poor outcomes.		PCR			DUXAP8		Dysregulated DUXAP8, LINC01116, LINC01138, and PCAT6 are significantly associated with HCC patients' poor outcomes.	
31570750	chr1	10633990	10635990	CASZ1	This study demonstrates that the CASZ1 gene associated C-allele of rs11121615 has a signifcant, reproducible, association with CVD (CEAP C≥2 meta-odds ratio 1.31, 95% CI 1.27–1.34, P=1×10−98, PHet=0.25), but not with non-varicose vein (CEAP C1, telangiectasia or reticular veins) forms of venous disease.	human	kidney	High+Lowthroughput	A variant of the castor zinc finger 1 (CASZ1) gene is differentially associated with the clinical classification of chronic venous disease	是	rs11121615	Chronic venous disease	HEK293 cell	E_01_0251	PCR,Flow cytometry	This study demonstrates that the CASZ1 gene associated C-allele of rs11121615 has a signifcant, reproducible, association with CVD (CEAP C≥2 meta-odds ratio 1.31, 95% CI 1.27–1.34, P=1×10−98, PHet=0.25), but not with non-varicose vein (CEAP C1, telangiectasia or reticular veins) forms of venous disease.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		This study demonstrates that the CASZ1 gene associated C-allele of rs11121615 has a signifcant, reproducible, association with CVD (CEAP C≥2 meta-odds ratio 1.31, 95% CI 1.27–1.34, P=1×10−98, PHet=0.25), but not with non-varicose vein (CEAP C1, telangiectasia or reticular veins) forms of venous disease.	Immunohistochemical staining	This study demonstrates that the CASZ1 gene associated C-allele of rs11121615 has a signifcant, reproducible, association with CVD (CEAP C≥2 meta-odds ratio 1.31, 95% CI 1.27–1.34, P=1×10−98, PHet=0.25), but not with non-varicose vein (CEAP C1, telangiectasia or reticular veins) forms of venous disease.		PCR,Flow cytometry			CASZ1		This study demonstrates that the CASZ1 gene associated C-allele of rs11121615 has a signifcant, reproducible, association with CVD (CEAP C≥2 meta-odds ratio 1.31, 95% CI 1.27–1.34, P=1×10−98, PHet=0.25), but not with non-varicose vein (CEAP C1, telangiectasia or reticular veins) forms of venous disease.	
31570746	chr13	40553093	40555093	FOXO1	Lastly, point mutations were induced in the binding sites of FOXO1 and HFH-3, enabling the exclusion of all the identifed and selected TFBSs. In this instance, enhancer activity was further downregulated	human	connective	High+Lowthroughput	Characterization of the Long Terminal Repeat of the Endogenous Retrovirus-derived microRNAs in the Olive Flounder	否		cancer	cancer cell	E_01_0252	PCR	Lastly, point mutations were induced in the binding sites of FOXO1 and HFH-3, enabling the exclusion of all the identifed and selected TFBSs. In this instance, enhancer activity was further downregulated	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Lastly, point mutations were induced in the binding sites of FOXO1 and HFH-3, enabling the exclusion of all the identifed and selected TFBSs. In this instance, enhancer activity was further downregulated	Immunohistochemical staining	Lastly, point mutations were induced in the binding sites of FOXO1 and HFH-3, enabling the exclusion of all the identifed and selected TFBSs. In this instance, enhancer activity was further downregulated		PCR				FOXO1		Lastly, point mutations were induced in the binding sites of FOXO1 and HFH-3, enabling the exclusion of all the identifed and selected TFBSs. In this instance, enhancer activity was further downregulated
31563853	chr3	186840138	186842138	ADIPOQ	Relative to untreated control cells, T-brites had increased mRNA expression of PPARγ target genes (ADIPOQ, FABP3, FABP4, and RXRA) and brite/beige marker genes (PGC1α/β, PRDM16, CEBPβ, CIDEA, and ELOVL3), without expression changes in lipogenic genes (FASN and SCD1) (Figure S4a and S4b)	human	Fat	High+Lowthroughput	CIDEA Transcriptionally Regulates UCP1 for Britening and Thermogenesis in Human Fat Cells	否			fat cell	E_01_0253	Western blot, flow cytometry, PCR, immunofluorescence staining	Relative to untreated control cells, T-brites had increased mRNA expression of PPARγ target genes (ADIPOQ, FABP3, FABP4, and RXRA) and brite/beige marker genes (PGC1α/β, PRDM16, CEBPβ, CIDEA, and ELOVL3), without expression changes in lipogenic genes (FASN and SCD1) (Figure S4a and S4b)	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Relative to untreated control cells, T-brites had increased mRNA expression of PPARγ target genes (ADIPOQ, FABP3, FABP4, and RXRA) and brite/beige marker genes (PGC1α/β, PRDM16, CEBPβ, CIDEA, and ELOVL3), without expression changes in lipogenic genes (FASN and SCD1) (Figure S4a and S4b)	Immunohistochemical staining	Relative to untreated control cells, T-brites had increased mRNA expression of PPARγ target genes (ADIPOQ, FABP3, FABP4, and RXRA) and brite/beige marker genes (PGC1α/β, PRDM16, CEBPβ, CIDEA, and ELOVL3), without expression changes in lipogenic genes (FASN and SCD1) (Figure S4a and S4b)		Western blot,Flow cytometry,PCR,免疫荧光染色			ADIPOQ		Relative to untreated control cells, T-brites had increased mRNA expression of PPARγ target genes (ADIPOQ, FABP3, FABP4, and RXRA) and brite/beige marker genes (PGC1α/β, PRDM16, CEBPβ, CIDEA, and ELOVL3), without expression changes in lipogenic genes (FASN and SCD1) (Figure S4a and S4b)	
31563432	chr4	154747879	154749879	Actrt2	Neither wild-type nor mutant b-catenin factors were found to occupy the typical enhancers of Actrt2 and Fam168b (Fig_x0002_ure S5B).	mouse	colon	High+Lowthroughput	Mediator Condensates Localize Signaling Factors to Key Cell Identity Genes	否		Colon cancer	HCT116 cells	E_01_0254	Immunofluorescence light staining, flow cytometry, PCR	Neither wild-type nor mutant b-catenin factors were found to occupy the typical enhancers of Actrt2 and Fam168b (Fig_x0002_ure S5B).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Neither wild-type nor mutant b-catenin factors were found to occupy the typical enhancers of Actrt2 and Fam168b (Fig_x0002_ure S5B).	Immunohistochemical staining	Neither wild-type nor mutant b-catenin factors were found to occupy the typical enhancers of Actrt2 and Fam168b (Fig_x0002_ure S5B).		免疫荧光光染色,Flow cytometry,PCR			Actrt2	STAT3	Neither wild-type nor mutant b-catenin factors were found to occupy the typical enhancers of Actrt2 and Fam168b (Fig_x0002_ure S5B).	Recent studies have shown that TFs and Mediator form phase_x0002_separated condensates at super-enhancers (Boija et al., 2018; Cho et al., 2018; Sabari et al., 2018), and the terminal signaling factors of the WNT, JAK/STAT, and TGF-b pathways (b-catenin, STAT3, and SMAD3, respectively) have been shown to preferen_x0002_tially occupy super-enhancers (Hnisz et al., 2015).
31561451	chr7	55016281	55018281	EGFR	In vitro, we did not find a significant difference in nanoparticle binding to EGFR overexpressing head and neck cancer cells between EGFR-targeted and untargeted FITC-SiO2-NPs.	human	connective	High+Lowthroughput	Fluorescein- and EGFR-Antibody Conjugated Silica Nanoparticles for Enhancement of Real-time Tumor Border Definition Using Confocal Laser Endomicroscopy in Squamous Cell Carcinoma of the Head and Neck	否		tumour	squamous cell	E_01_0255	PCR, Western blot, immunofluorescence staining	In vitro, we did not find a significant difference in nanoparticle binding to EGFR overexpressing head and neck cancer cells between EGFR-targeted and untargeted FITC-SiO2-NPs.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In vitro, we did not find a significant difference in nanoparticle binding to EGFR overexpressing head and neck cancer cells between EGFR-targeted and untargeted FITC-SiO2-NPs.	Immunohistochemical staining	In vitro, we did not find a significant difference in nanoparticle binding to EGFR overexpressing head and neck cancer cells between EGFR-targeted and untargeted FITC-SiO2-NPs.		PCR,Western blot,免疫荧光染色				EGFR		In vitro, we did not find a significant difference in nanoparticle binding to EGFR overexpressing head and neck cancer cells between EGFR-targeted and untargeted FITC-SiO2-NPs.
31561366	chr11	47463063	47465063	CELF1	The DASHR overlap analysis found only one sncRNA overlap, where the variant rs4543938 in the CELF1 region overlapped the piRNA piR-56133.	human	blood	High+Lowthroughput	Fluorescein- and EGFR-Antibody Conjugated Silica Nanoparticles for Enhancement of Real-time Tumor Border Definition Using Confocal Laser Endomicroscopy in Squamous Cell Carcinoma of the Head and Neck	是	rs8093731	Chronic myeloid leukemia	K562 cells	E_01_0256	PCR,Flow cytometry	The DASHR overlap analysis found only one sncRNA overlap, where the variant rs4543938 in the CELF1 region overlapped the piRNA piR-56133.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The DASHR overlap analysis found only one sncRNA overlap, where the variant rs4543938 in the CELF1 region overlapped the piRNA piR-56133.	Immunohistochemical staining	The DASHR overlap analysis found only one sncRNA overlap, where the variant rs4543938 in the CELF1 region overlapped the piRNA piR-56133.		PCR,Flow cytometry			CELF1,FERMT2		The DASHR overlap analysis found only one sncRNA overlap, where the variant rs4543938 in the CELF1 region overlapped the piRNA piR-56133.;Analysis of miRNA seed disruption found that 46 variants across 5 tag regions (CELF1, FERMT2, INPP5D, MS4A6A, and ZCWPW1) overlapped binding sites for 40 miRNAs in 11 target genes (Supplementary Table 2).	
31560287	chr11	116832779	116834779	APOA1	Apolipoprotein A5 (ApoA5) has been shown as a vital regulator of lipid metabolism. Human APOA5 gene is located on the long arm of chromosome 11 adjacent to APOA1/APOC3/APOA4 gene clusters [7].	human	Fat	High+Lowthroughput	New Insights into Apolipoprotein A5 and the Modulation of Human Adipose-derived Mesenchymal Stem Cells Adipogenesis	是		Obesity	adipose-derived mesenchymal stem cells	E_01_0257	PCR,Western blot	Apolipoprotein A5 (ApoA5) has been shown as a vital regulator of lipid metabolism. Human APOA5 gene is located on the long arm of chromosome 11 adjacent to APOA1/APOC3/APOA4 gene clusters [7].	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Apolipoprotein A5 (ApoA5) has been shown as a vital regulator of lipid metabolism. Human APOA5 gene is located on the long arm of chromosome 11 adjacent to APOA1/APOC3/APOA4 gene clusters [7].	Immunohistochemical staining	Apolipoprotein A5 (ApoA5) has been shown as a vital regulator of lipid metabolism. Human APOA5 gene is located on the long arm of chromosome 11 adjacent to APOA1/APOC3/APOA4 gene clusters [7].		PCR,Western blot			APOA1		Apolipoprotein A5 (ApoA5) has been shown as a vital regulator of lipid metabolism. Human APOA5 gene is located on the long arm of chromosome 11 adjacent to APOA1/APOC3/APOA4 gene clusters [7].	
31557715	chr7	25947403	25949403	MIR148A	Physical map of the region showing the position of annotated genes, MIR148A and genetic polymorphisms (SNPs, annotated with their rs identifiers) associated with obesity and other related phenotypes	human	connective	High+Lowthroughput	Detailed Functional Characterization of a Waist-Hip Ratio Locus in 7p15.2 Defines an Enhancer Controlling Adipocyte Differentiation	是	rs1055144	liver cancer	mesenchymal stem cell	E_01_0258	PCR, flow cytometry, immunofluorescence staining	Physical map of the region showing the position of annotated genes, MIR148A and genetic polymorphisms (SNPs, annotated with their rs identifiers) associated with obesity and other related phenotypes	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Physical map of the region showing the position of annotated genes, MIR148A and genetic polymorphisms (SNPs, annotated with their rs identifiers) associated with obesity and other related phenotypes	Immunohistochemical staining	Physical map of the region showing the position of annotated genes, MIR148A and genetic polymorphisms (SNPs, annotated with their rs identifiers) associated with obesity and other related phenotypes		PCR,Flow cytometry,免疫荧光染色			MIR148A,SNX10,CHI3L1		Physical map of the region showing the position of annotated genes, MIR148A and genetic polymorphisms (SNPs, annotated with their rs identifiers) associated with obesity and other related phenotypes;The region is delimited by the distal gene NPVF and the proximal gene SNX10.;RNA-sequencing of cells with disrupted enhancer showed reduced expression of established adipocyte markers, such as ADIPOQ and LPL, and identified CHI3L1 on chromosome 1 as a potential gene involved in adipocyte differentiation. In conclusion, we identified and characterized an enhancer in the SNX10 locus, outlined its plausible mechanisms of action and downstream targets.	
31554806	chr1	37806934	37808934	MTF1	PSIONIC-predicted activity for MTF1 in cell line models correlates with sensitivity to MTF1 inhibition, showing the potential of our approach for personalized therapy. Many identified TFs are significantly associated with survival outcome	human	breast	High+Lowthroughput	Chromatin-informed inference of transcriptional programs in gynecologic and basal breast cancers	否		mammary cancer	breast cancer cell	E_01_0259	Flow cytometry	PSIONIC-predicted activity for MTF1 in cell line models correlates with sensitivity to MTF1 inhibition, showing the potential of our approach for personalized therapy. Many identified TFs are significantly associated with survival outcome	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		PSIONIC-predicted activity for MTF1 in cell line models correlates with sensitivity to MTF1 inhibition, showing the potential of our approach for personalized therapy. Many identified TFs are significantly associated with survival outcome	Immunohistochemical staining	PSIONIC-predicted activity for MTF1 in cell line models correlates with sensitivity to MTF1 inhibition, showing the potential of our approach for personalized therapy. Many identified TFs are significantly associated with survival outcome		Flow cytometry			MTF1		PSIONIC-predicted activity for MTF1 in cell line models correlates with sensitivity to MTF1 inhibition, showing the potential of our approach for personalized therapy. Many identified TFs are significantly associated with survival outcome	
31551335	chr12	55963742	55965742	CDK2	HEAL-FUS complex binds the HIV promoter and enhances recruit_x0002_ment of the histone acetyltransferase p300, which positively regulates HIV transcrip_x0002_tion by increasing histone H3K27 acetylation and P-TEFb enrichment on the HIV promoter, and (ii) HEAL-FUS complex is enriched at the promoter of the cyclin_x0002_dependent kinase 2 gene, CDK2, to enhance CDK2 expression.	human	blood	High+Lowthroughput	The Long Noncoding RNA HEAL Regulates HIV-1 Replication through Epigenetic Regulation of the HIV-1 Promoter	否		AIDS	blood mononuclear cells	E_01_0260	Western blot,PCR	HEAL-FUS complex binds the HIV promoter and enhances recruit_x0002_ment of the histone acetyltransferase p300, which positively regulates HIV transcrip_x0002_tion by increasing histone H3K27 acetylation and P-TEFb enrichment on the HIV promoter, and (ii) HEAL-FUS complex is enriched at the promoter of the cyclin_x0002_dependent kinase 2 gene, CDK2, to enhance CDK2 expression.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		HEAL-FUS complex binds the HIV promoter and enhances recruit_x0002_ment of the histone acetyltransferase p300, which positively regulates HIV transcrip_x0002_tion by increasing histone H3K27 acetylation and P-TEFb enrichment on the HIV promoter, and (ii) HEAL-FUS complex is enriched at the promoter of the cyclin_x0002_dependent kinase 2 gene, CDK2, to enhance CDK2 expression.	Immunohistochemical staining	HEAL-FUS complex binds the HIV promoter and enhances recruit_x0002_ment of the histone acetyltransferase p300, which positively regulates HIV transcrip_x0002_tion by increasing histone H3K27 acetylation and P-TEFb enrichment on the HIV promoter, and (ii) HEAL-FUS complex is enriched at the promoter of the cyclin_x0002_dependent kinase 2 gene, CDK2, to enhance CDK2 expression.		Western blot,PCR			CDK2,NEAT1		HEAL-FUS complex binds the HIV promoter and enhances recruit_x0002_ment of the histone acetyltransferase p300, which positively regulates HIV transcrip_x0002_tion by increasing histone H3K27 acetylation and P-TEFb enrichment on the HIV promoter, and (ii) HEAL-FUS complex is enriched at the promoter of the cyclin_x0002_dependent kinase 2 gene, CDK2, to enhance CDK2 expression.;The first evidence that lncRNAs might be involved in HIV-1 replication came from experiments in the Jurkat T cell line, in which knockdown (KD) of NEAT1 increased viral production by enhancing the nuclear export of Rev-dependent instability element (INS)-containing HIV-1 mRNAs	
31551256	chr9	134027777	134029777	BRD3	BRD3 is recruited to and controls the activity of a subset ERa transcriptional enhancers, providing a therapeu_x0002_tic opportunity to target BRD3 with BET inhibitors in ERa_x0002_positive breast cancers.	human	breast	High+Lowthroughput	Distinct Roles for BET Family Members in Estrogen Receptor α Enhancer Function and Gene Regulation in Breast Cancer Cells	否		mammary cancer	breast cancer cell	E_01_0261	Western blot,PCR,Flow cytometry	BRD3 is recruited to and controls the activity of a subset ERa transcriptional enhancers, providing a therapeu_x0002_tic opportunity to target BRD3 with BET inhibitors in ERa_x0002_positive breast cancers.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		BRD3 is recruited to and controls the activity of a subset ERa transcriptional enhancers, providing a therapeu_x0002_tic opportunity to target BRD3 with BET inhibitors in ERa_x0002_positive breast cancers.	Immunohistochemical staining	BRD3 is recruited to and controls the activity of a subset ERa transcriptional enhancers, providing a therapeu_x0002_tic opportunity to target BRD3 with BET inhibitors in ERa_x0002_positive breast cancers.		Western blot,PCR,Flow cytometry			BRD3		BRD3 is recruited to and controls the activity of a subset ERa transcriptional enhancers, providing a therapeu_x0002_tic opportunity to target BRD3 with BET inhibitors in ERa_x0002_positive breast cancers.	
31551012	chr7	148804569	148806569	EZH2	Additionally, HOXD-AS1 epigenetically silenced PDCD4 through binding to the histone methyltransferase enhancer of zeste homologue 2 (EZH2) on the promoter of PDCD4, thus increasing H3K27me3. More importantly, PDCD4 silencing coun_x0002_teracted HOXD-AS1 knockdown-mediated enhancement of DDP sensitivity in DDP-resistant gastric cancer cells	human	stomach	High+Lowthroughput	HOXD-AS1 confers cisplatin resistance in gastric cancer through epigenetically silencing PDCD4 via recruiting EZH2	否		gastric cancer	gastric cancer cell	E_01_0262	Western blot,PCR	Additionally, HOXD-AS1 epigenetically silenced PDCD4 through binding to the histone methyltransferase enhancer of zeste homologue 2 (EZH2) on the promoter of PDCD4, thus increasing H3K27me3. More importantly, PDCD4 silencing coun_x0002_teracted HOXD-AS1 knockdown-mediated enhancement of DDP sensitivity in DDP-resistant gastric cancer cells	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Additionally, HOXD-AS1 epigenetically silenced PDCD4 through binding to the histone methyltransferase enhancer of zeste homologue 2 (EZH2) on the promoter of PDCD4, thus increasing H3K27me3. More importantly, PDCD4 silencing coun_x0002_teracted HOXD-AS1 knockdown-mediated enhancement of DDP sensitivity in DDP-resistant gastric cancer cells	Immunohistochemical staining	Additionally, HOXD-AS1 epigenetically silenced PDCD4 through binding to the histone methyltransferase enhancer of zeste homologue 2 (EZH2) on the promoter of PDCD4, thus increasing H3K27me3. More importantly, PDCD4 silencing coun_x0002_teracted HOXD-AS1 knockdown-mediated enhancement of DDP sensitivity in DDP-resistant gastric cancer cells		Western blot,PCR			PDCD4	EZH2	Additionally, HOXD-AS1 epigenetically silenced PDCD4 through binding to the histone methyltransferase enhancer of zeste homologue 2 (EZH2) on the promoter of PDCD4, thus increasing H3K27me3. More importantly, PDCD4 silencing coun_x0002_teracted HOXD-AS1 knockdown-mediated enhancement of DDP sensitivity in DDP-resistant gastric cancer cells	Additionally, HOXD-AS1 epigenetically silenced PDCD4 through binding to the histone methyltransferase enhancer of zeste homologue 2 (EZH2) on the promoter of PDCD4, thus increasing H3K27me3. More importantly, PDCD4 silencing coun_x0002_teracted HOXD-AS1 knockdown-mediated enhancement of DDP sensitivity in DDP-resistant gastric cancer cells
31547883	chr16	67559930	67561930	CTCF	In the lysates from starved cells, the recip_x0002_rocal pull-down of CTCF and CGGBP1 was very weak. In lysates from stimulated cells, however, using CGGBP1 antibody we could pull down a major fraction of CTCF (Fig. 2b).	human	kidney	High+Lowthroughput	CGGBP1 regulates CTCF occupancy at repeats	否			HEK293T	E_01_0263	Flow cytometry,PCR	In the lysates from starved cells, the recip_x0002_rocal pull-down of CTCF and CGGBP1 was very weak. In lysates from stimulated cells, however, using CGGBP1 antibody we could pull down a major fraction of CTCF (Fig. 2b).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In the lysates from starved cells, the recip_x0002_rocal pull-down of CTCF and CGGBP1 was very weak. In lysates from stimulated cells, however, using CGGBP1 antibody we could pull down a major fraction of CTCF (Fig. 2b).	Immunohistochemical staining	In the lysates from starved cells, the recip_x0002_rocal pull-down of CTCF and CGGBP1 was very weak. In lysates from stimulated cells, however, using CGGBP1 antibody we could pull down a major fraction of CTCF (Fig. 2b).		Flow cytometry,PCR				CTCF		In the lysates from starved cells, the recip_x0002_rocal pull-down of CTCF and CGGBP1 was very weak. In lysates from stimulated cells, however, using CGGBP1 antibody we could pull down a major fraction of CTCF (Fig. 2b).
31545422	chr7	148804556	148806556	EZH2	In this study, we found that inhibition of enhancer of zeste homolog 2 (EZH2) resulted in suppressed EMT in HNSCC in vitro and in vivo.	human	neck	High+Lowthroughput	Targeting of EZH2 inhibits epithelial?mesenchymal transition in head and neck squamous cell carcinoma via regulating the STAT3/VEGFR2 axis	否		cancer	neck squamous cell	E_01_0264	PCR, Western blot, immunofluorescence staining	In this study, we found that inhibition of enhancer of zeste homolog 2 (EZH2) resulted in suppressed EMT in HNSCC in vitro and in vivo.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In this study, we found that inhibition of enhancer of zeste homolog 2 (EZH2) resulted in suppressed EMT in HNSCC in vitro and in vivo.	Immunohistochemical staining	In this study, we found that inhibition of enhancer of zeste homolog 2 (EZH2) resulted in suppressed EMT in HNSCC in vitro and in vivo.		PCR,Western blot,免疫荧光染色				EZH2,STAT3		In this study, we found that inhibition of enhancer of zeste homolog 2 (EZH2) resulted in suppressed EMT in HNSCC in vitro and in vivo.;We reported that signal transducer and activator of transcription factor 3 (STAT3)/vascular endothelial growth factor receptor 2 (VEGFR2) axis served as the downstream signaling of EZH2 and mediated EMT in HNSCC.
31542774	chr19	29809345	29811345	CCNE1	By integrating SVs associated with acetylated chro_x0002_matin identified by paired-end NanoChIP-seq (PeNChIP-seq) with whole-genome sequencing (WGS) analysis of a large GC cohort, we observed enhancer hijacking events in GC targeting CCNE1, IGF2 and CCND1.	human	blood	High+Lowthroughput	Integrated paired-end enhancer profiling and whole-genome sequencing reveals recurrent CCNE1 and IGF2 enhancer hijacking in primary gastric adenocarcinoma	否		gastric cancer	B cell	E_01_0265	PCR,Flow cytometry	By integrating SVs associated with acetylated chro_x0002_matin identified by paired-end NanoChIP-seq (PeNChIP-seq) with whole-genome sequencing (WGS) analysis of a large GC cohort, we observed enhancer hijacking events in GC targeting CCNE1, IGF2 and CCND1.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		By integrating SVs associated with acetylated chro_x0002_matin identified by paired-end NanoChIP-seq (PeNChIP-seq) with whole-genome sequencing (WGS) analysis of a large GC cohort, we observed enhancer hijacking events in GC targeting CCNE1, IGF2 and CCND1.	Immunohistochemical staining	By integrating SVs associated with acetylated chro_x0002_matin identified by paired-end NanoChIP-seq (PeNChIP-seq) with whole-genome sequencing (WGS) analysis of a large GC cohort, we observed enhancer hijacking events in GC targeting CCNE1, IGF2 and CCND1.		PCR,Flow cytometry				CCNE1		By integrating SVs associated with acetylated chro_x0002_matin identified by paired-end NanoChIP-seq (PeNChIP-seq) with whole-genome sequencing (WGS) analysis of a large GC cohort, we observed enhancer hijacking events in GC targeting CCNE1, IGF2 and CCND1.
31541592	chr6	35570844	35572844	FKBP5	We then carried out qRT‐PCR using primers of APP and FKBP5, a representative AR target gene, to evaluate their expression at the mRNA level.	human	bone	High+Lowthroughput	Amyloid precursor protein, an androgen-regulated gene, is targeted by RNA-binding protein PSF/SFPQ in neuronal cells	否		Osteoma	SH‐SY5Y cells	E_01_0266	PCR,Western blot	We then carried out qRT‐PCR using primers of APP and FKBP5, a representative AR target gene, to evaluate their expression at the mRNA level.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We then carried out qRT‐PCR using primers of APP and FKBP5, a representative AR target gene, to evaluate their expression at the mRNA level.	Immunohistochemical staining	We then carried out qRT‐PCR using primers of APP and FKBP5, a representative AR target gene, to evaluate their expression at the mRNA level.		PCR,Western blot			FKBP5		We then carried out qRT‐PCR using primers of APP and FKBP5, a representative AR target gene, to evaluate their expression at the mRNA level.	
31538139	chr3	186839743	186841743	ADIPOQ	The 50,336 ATAC-seq peaks that were more accessible in primary human adipocytes (‘adipocyte accessible’) included the promoters of the ADIPOQ and PPARGC1A genes with known adipocyte-spe_x0002_cific expression (Fig. 1c,d), providing evidence that we successfully differentiated adipocytes in vitro.	human	Fat	High+Lowthroughput	Reverse gene-environment interaction approach to identify variants influencing body-mass index in humans	是	rs10788522		fat cell	E_01_0267	PCR,Flow cytometry	The 50,336 ATAC-seq peaks that were more accessible in primary human adipocytes (‘adipocyte accessible’) included the promoters of the ADIPOQ and PPARGC1A genes with known adipocyte-spe_x0002_cific expression (Fig. 1c,d), providing evidence that we successfully differentiated adipocytes in vitro.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The 50,336 ATAC-seq peaks that were more accessible in primary human adipocytes (‘adipocyte accessible’) included the promoters of the ADIPOQ and PPARGC1A genes with known adipocyte-spe_x0002_cific expression (Fig. 1c,d), providing evidence that we successfully differentiated adipocytes in vitro.	Immunohistochemical staining	The 50,336 ATAC-seq peaks that were more accessible in primary human adipocytes (‘adipocyte accessible’) included the promoters of the ADIPOQ and PPARGC1A genes with known adipocyte-spe_x0002_cific expression (Fig. 1c,d), providing evidence that we successfully differentiated adipocytes in vitro.		PCR,Flow cytometry			ADIPOQ		The 50,336 ATAC-seq peaks that were more accessible in primary human adipocytes (‘adipocyte accessible’) included the promoters of the ADIPOQ and PPARGC1A genes with known adipocyte-spe_x0002_cific expression (Fig. 1c,d), providing evidence that we successfully differentiated adipocytes in vitro.	
31534142	chr16	67559649	67561649	CTCF	To evaluate the specificity of epigenome editing systematically, we used ChIP-seq to map H3K9me3 and CTCF genome-wide in HEK293 cells after CTCF disruption by dCas9-KRAB (Fig. 1d, e).	human	kidney	High+Lowthroughput	Epigenome editing strategies for the functional annotation of CTCF insulators	否		tumour	HEK293 cell	E_01_0268	PCR,Flow cytometry	To evaluate the specificity of epigenome editing systematically, we used ChIP-seq to map H3K9me3 and CTCF genome-wide in HEK293 cells after CTCF disruption by dCas9-KRAB (Fig. 1d, e).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		To evaluate the specificity of epigenome editing systematically, we used ChIP-seq to map H3K9me3 and CTCF genome-wide in HEK293 cells after CTCF disruption by dCas9-KRAB (Fig. 1d, e).	Immunohistochemical staining	To evaluate the specificity of epigenome editing systematically, we used ChIP-seq to map H3K9me3 and CTCF genome-wide in HEK293 cells after CTCF disruption by dCas9-KRAB (Fig. 1d, e).		PCR,Flow cytometry			GSX2	CTCF,PDGFRA	We found that the interaction between the GSX2 promoter and the PDGFRA insulator was reduced by disruption of the latter, albeit to a lesser extent than that observed for the PDGFRA promoter viewpoint.	To evaluate the specificity of epigenome editing systematically, we used ChIP-seq to map H3K9me3 and CTCF genome-wide in HEK293 cells after CTCF disruption by dCas9-KRAB (Fig. 1d, e).;We found that the interaction between the GSX2 promoter and the PDGFRA insulator was reduced by disruption of the latter, albeit to a lesser extent than that observed for the PDGFRA promoter viewpoint.
31533028	chr21	34785012	34787012	RUNX1	The t(8;21) (q22;q22) translocation generates the RUNX1-ETO fusion protein, which interferes with the hematopoiet_x0002_ic master regulator RUNX1.	human	blood	High+Lowthroughput	RUNX1-ETO Depletion in t(8;21) AML Leads to C/EBPα- and AP-1-Mediated Alterations in Enhancer-Promoter Interaction	否		leukemia	hematopoietic stem cell	E_01_0269	PCR,Flow cytometry	The t(8;21) (q22;q22) translocation generates the RUNX1-ETO fusion protein, which interferes with the hematopoiet_x0002_ic master regulator RUNX1.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The t(8;21) (q22;q22) translocation generates the RUNX1-ETO fusion protein, which interferes with the hematopoiet_x0002_ic master regulator RUNX1.	Immunohistochemical staining	The t(8;21) (q22;q22) translocation generates the RUNX1-ETO fusion protein, which interferes with the hematopoiet_x0002_ic master regulator RUNX1.		PCR,Flow cytometry			CCND2	RUNX1	Figure 2F shows an example of interactions at the upregulated CCND2 gene, which shows changes in interactions between its promoter and two up_x0002_stream distal elements (depicted in red).	The t(8;21) (q22;q22) translocation generates the RUNX1-ETO fusion protein, which interferes with the hematopoiet_x0002_ic master regulator RUNX1.
31531679	chr16	86564387	86566387	FOXC2	FOXC2 is a transcription factor essential for inducing podocyte diferentiation, development and maturation, and is considered to be the earliest podocyte marker.	human	Epithelial	High+Lowthroughput	Evidence for miR-548c-5p regulation of FOXC2 transcription through a distal genomic target site in human podocytes	否			epithelial cell	E_01_0270	PCR, Western blot, immunofluorescence staining	FOXC2 is a transcription factor essential for inducing podocyte diferentiation, development and maturation, and is considered to be the earliest podocyte marker.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		FOXC2 is a transcription factor essential for inducing podocyte diferentiation, development and maturation, and is considered to be the earliest podocyte marker.	Immunohistochemical staining	FOXC2 is a transcription factor essential for inducing podocyte diferentiation, development and maturation, and is considered to be the earliest podocyte marker.		PCR,Western blot,免疫荧光染色			NPHS2,MTHFSD	FOXC2	As the earliest podocyte marker, it has a prominent role in the diferen_x0002_tiation, development and maturation of podocytes, through the transcriptional regulation of a variety of diferent genes, such as podocin (NPHS2) [20, 22].;Schematic alignment of human vs mouse synteny of the miRNA target region. Head-to-head arrangement of MTHFSD and FOXC2 in mouse chromosome 8 corresponds to (or is syntenic to) human chromosome 16.	FOXC2 is a transcription factor essential for inducing podocyte diferentiation, development and maturation, and is considered to be the earliest podocyte marker.
31530818	chr8	127732403	127734403	MYC	FitHiChIP also captures previously validated enhancer interactions for several genes including MYC, TP53, and NMU.	human	blood	High+Lowthroughput	Identification of significant chromatin contacts from HiChIP data by FitHiChIP	否		leukemia	T cell	E_01_0271	Flow cytometry	FitHiChIP also captures previously validated enhancer interactions for several genes including MYC, TP53, and NMU.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		FitHiChIP also captures previously validated enhancer interactions for several genes including MYC, TP53, and NMU.	Immunohistochemical staining	FitHiChIP also captures previously validated enhancer interactions for several genes including MYC, TP53, and NMU.		Flow cytometry				MYC,TP53		FitHiChIP also captures previously validated enhancer interactions for several genes including MYC, TP53, and NMU.;FitHiChIP also captures previously validated enhancer interactions for several genes including MYC, TP53, and NMU.
31530812	chr2	24200308	24202308	ITSN2	In the PFC, according to the published transcriptome data of 16 PFC layers and the adjacent white matter48, the expression of ITSN2 is significantly lower in humans and chimpanzees than in rhesus macaques, consistent with their reduced H3K27Ac signals (an indication of enhancer activity) owing to the ASSV that disrupts an ADE in ITSN2 (Fig. 5c, d, g).	human	Nervous	High+Lowthroughput	Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants	是			neuronal cell	E_01_0272	Flow cytometry,Western blot	In the PFC, according to the published transcriptome data of 16 PFC layers and the adjacent white matter48, the expression of ITSN2 is significantly lower in humans and chimpanzees than in rhesus macaques, consistent with their reduced H3K27Ac signals (an indication of enhancer activity) owing to the ASSV that disrupts an ADE in ITSN2 (Fig. 5c, d, g).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In the PFC, according to the published transcriptome data of 16 PFC layers and the adjacent white matter48, the expression of ITSN2 is significantly lower in humans and chimpanzees than in rhesus macaques, consistent with their reduced H3K27Ac signals (an indication of enhancer activity) owing to the ASSV that disrupts an ADE in ITSN2 (Fig. 5c, d, g).	Immunohistochemical staining	In the PFC, according to the published transcriptome data of 16 PFC layers and the adjacent white matter48, the expression of ITSN2 is significantly lower in humans and chimpanzees than in rhesus macaques, consistent with their reduced H3K27Ac signals (an indication of enhancer activity) owing to the ASSV that disrupts an ADE in ITSN2 (Fig. 5c, d, g).		Flow cytometry,Western blot			ITSN2,NEDD9		In the PFC, according to the published transcriptome data of 16 PFC layers and the adjacent white matter48, the expression of ITSN2 is significantly lower in humans and chimpanzees than in rhesus macaques, consistent with their reduced H3K27Ac signals (an indication of enhancer activity) owing to the ASSV that disrupts an ADE in ITSN2 (Fig. 5c, d, g).;Gene expression data of cerebellum in NHPs are not available to check its effect on NEDD9 expression	
31530225	chr16	53698982	53700982	FTO	FTO encodes an ortholog to the AlkB family of enzymes that demethylate nucleic acids	human	connective	High+Lowthroughput	Functional genomic characterization of the FTO locus in African Americans	是	rs9927317	Obesity	mesenchymal stem cell	E_01_0273	Flow cytometry	FTO encodes an ortholog to the AlkB family of enzymes that demethylate nucleic acids	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		FTO encodes an ortholog to the AlkB family of enzymes that demethylate nucleic acids	Immunohistochemical staining	FTO encodes an ortholog to the AlkB family of enzymes that demethylate nucleic acids		Flow cytometry			FTO,RPGRIP1L,IRX3,IRX5	CUX1	FTO encodes an ortholog to the AlkB family of enzymes that demethylate nucleic acids;The first intronic region of FTO is less than 100 bp 3’ from the transcriptional start site of the gene Retinitis Pigmentosa GTPase Regulator-Interacting Protein-1 Like (RPGRIP1L), a ciliary gene (24, 56) that is transcribed in the 5’ direction.;Other groups have shown that rs9930506 is associated with expression of IRX3 in the brain (39), as well as expression of both IRX3 and IRX5 in adipose tissue (7), with apparent biological relevance conveyed by physical interactions (chromosome conformation) with these genes’ promoters, although the resolution of this chromatin interaction data was not sufficient to detect (or rule out) interactions with RPGRIP1L.;Other groups have shown that rs9930506 is associated with expression of IRX3 in the brain (39), as well as expression of both IRX3 and IRX5 in adipose tissue (7), with apparent biological relevance conveyed by physical interactions (chromosome conformation) with these genes’ promoters, although the resolution of this chromatin interaction data was not sufficient to detect (or rule out) interactions with RPGRIP1L.	We previously showed that rs8050136 resides within a putative binding site for the transcription factor Cut-like Homeobox 1 (CUX1) (46), which regulates expression of FTO and RPGRIP1L (43, 44).
31529763	chr17	43041465	43043465	BRCA1	Here we study how the N-terminal plastic region of Myc folds in complex with Max in the absence and presence of an E_x0002_box DNA fragment, and another intrinsically disordered binding partner, BRCA1.	human		High+Lowthroughput	(19) F?NMR Spectroscopy Tagging and Paramagnetic Relaxation Enhancement-Based Conformation Analysis of Intrinsically Disordered Protein Complexes	否		tumour	E-coli cell	E_01_0274	Flow cytometry	Here we study how the N-terminal plastic region of Myc folds in complex with Max in the absence and presence of an E_x0002_box DNA fragment, and another intrinsically disordered binding partner, BRCA1.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Here we study how the N-terminal plastic region of Myc folds in complex with Max in the absence and presence of an E_x0002_box DNA fragment, and another intrinsically disordered binding partner, BRCA1.	Immunohistochemical staining	Here we study how the N-terminal plastic region of Myc folds in complex with Max in the absence and presence of an E_x0002_box DNA fragment, and another intrinsically disordered binding partner, BRCA1.		Flow cytometry				BRCA1		Here we study how the N-terminal plastic region of Myc folds in complex with Max in the absence and presence of an E_x0002_box DNA fragment, and another intrinsically disordered binding partner, BRCA1.
31525599	chr11	10302280	10304280	ADM	ADMs were cut into disks with different diameters (4 mm and 8 mm) using a puncher, placed in a 24-well plate (Corning Costar) and ster_x0002_ilized with water (Millipore) containing 0.1 (v/v) peracetic acid and 4% (v/v) ethanol and incubated for 2 h at room temperature.	human		High+Lowthroughput	Tracing upconversion nanoparticle penetration in human skin	否				E_01_0275	PCR, immunofluorescence staining	ADMs were cut into disks with different diameters (4 mm and 8 mm) using a puncher, placed in a 24-well plate (Corning Costar) and ster_x0002_ilized with water (Millipore) containing 0.1 (v/v) peracetic acid and 4% (v/v) ethanol and incubated for 2 h at room temperature.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		ADMs were cut into disks with different diameters (4 mm and 8 mm) using a puncher, placed in a 24-well plate (Corning Costar) and ster_x0002_ilized with water (Millipore) containing 0.1 (v/v) peracetic acid and 4% (v/v) ethanol and incubated for 2 h at room temperature.	Immunohistochemical staining	ADMs were cut into disks with different diameters (4 mm and 8 mm) using a puncher, placed in a 24-well plate (Corning Costar) and ster_x0002_ilized with water (Millipore) containing 0.1 (v/v) peracetic acid and 4% (v/v) ethanol and incubated for 2 h at room temperature.		PCR,免疫荧光染色			ADM		ADMs were cut into disks with different diameters (4 mm and 8 mm) using a puncher, placed in a 24-well plate (Corning Costar) and ster_x0002_ilized with water (Millipore) containing 0.1 (v/v) peracetic acid and 4% (v/v) ethanol and incubated for 2 h at room temperature.	
31521883	chr18	63120882	63122882	BCL2	In experiment 4, the effect of trehalose treatment on the mRNA expression of lysosome-associated membrane protein 2 (LAMP2), porcine autophagy-related 5 (pATG5), LC3, BCL2 antagonist/ killer (Bak), BCL2 associated X (Bax), and B-cell lymphoma 2 (Bcl2) in cumulus cells and blastocysts were analyzed.	human	blood	High+Lowthroughput	Trehalose supplementation during porcine oocytes in?vitro maturation improves the developmental capacity of parthenotes	否			B cell	E_01_0276	PCR, immunofluorescence staining	In experiment 4, the effect of trehalose treatment on the mRNA expression of lysosome-associated membrane protein 2 (LAMP2), porcine autophagy-related 5 (pATG5), LC3, BCL2 antagonist/ killer (Bak), BCL2 associated X (Bax), and B-cell lymphoma 2 (Bcl2) in cumulus cells and blastocysts were analyzed.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In experiment 4, the effect of trehalose treatment on the mRNA expression of lysosome-associated membrane protein 2 (LAMP2), porcine autophagy-related 5 (pATG5), LC3, BCL2 antagonist/ killer (Bak), BCL2 associated X (Bax), and B-cell lymphoma 2 (Bcl2) in cumulus cells and blastocysts were analyzed.	Immunohistochemical staining	In experiment 4, the effect of trehalose treatment on the mRNA expression of lysosome-associated membrane protein 2 (LAMP2), porcine autophagy-related 5 (pATG5), LC3, BCL2 antagonist/ killer (Bak), BCL2 associated X (Bax), and B-cell lymphoma 2 (Bcl2) in cumulus cells and blastocysts were analyzed.		PCR,免疫荧光染色				BCL2		In experiment 4, the effect of trehalose treatment on the mRNA expression of lysosome-associated membrane protein 2 (LAMP2), porcine autophagy-related 5 (pATG5), LC3, BCL2 antagonist/ killer (Bak), BCL2 associated X (Bax), and B-cell lymphoma 2 (Bcl2) in cumulus cells and blastocysts were analyzed.
31519749	chr3	142303842	142305842	XRN1	Insect-borne flaviviruses produce a 300- 500 base long noncoding RNA, termed subgenomic flavivirus RNA (sfRNA), by stalling the cellular 5’-3’ exoribonuclease 1 (XRN1) via structures located in their 3’ UTRs.	human		High+Lowthroughput	Zika virus noncoding sfRNAs sequester multiple host-derived RNA-binding proteins and modulate mRNA decay and splicing during infection	否		Villous carcinoma	choriocarcinoma cells	E_01_0277	PCR,Western blot	Insect-borne flaviviruses produce a 300- 500 base long noncoding RNA, termed subgenomic flavivirus RNA (sfRNA), by stalling the cellular 5’-3’ exoribonuclease 1 (XRN1) via structures located in their 3’ UTRs.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Insect-borne flaviviruses produce a 300- 500 base long noncoding RNA, termed subgenomic flavivirus RNA (sfRNA), by stalling the cellular 5’-3’ exoribonuclease 1 (XRN1) via structures located in their 3’ UTRs.	Immunohistochemical staining	Insect-borne flaviviruses produce a 300- 500 base long noncoding RNA, termed subgenomic flavivirus RNA (sfRNA), by stalling the cellular 5’-3’ exoribonuclease 1 (XRN1) via structures located in their 3’ UTRs.		PCR,Western blot			XRN1		Insect-borne flaviviruses produce a 300- 500 base long noncoding RNA, termed subgenomic flavivirus RNA (sfRNA), by stalling the cellular 5’-3’ exoribonuclease 1 (XRN1) via structures located in their 3’ UTRs.	
31515496	chr16	67559926	67561926	CTCF	By combining the in situ Hi-C data with active and repressive histone marks, CTCF binding sites, nucleosome-depleted regions, and tran_x0002_scriptome profiling, we identify topologically associating domains (TADs) that change in size and epigenetic states between normal and prostate cancer cells.	human	prostate	High+Lowthroughput	A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome	是		prostatic cancer	prostate cancer cell	E_01_0278	PCR,Flow cytometry	By combining the in situ Hi-C data with active and repressive histone marks, CTCF binding sites, nucleosome-depleted regions, and tran_x0002_scriptome profiling, we identify topologically associating domains (TADs) that change in size and epigenetic states between normal and prostate cancer cells.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		By combining the in situ Hi-C data with active and repressive histone marks, CTCF binding sites, nucleosome-depleted regions, and tran_x0002_scriptome profiling, we identify topologically associating domains (TADs) that change in size and epigenetic states between normal and prostate cancer cells.	Immunohistochemical staining	By combining the in situ Hi-C data with active and repressive histone marks, CTCF binding sites, nucleosome-depleted regions, and tran_x0002_scriptome profiling, we identify topologically associating domains (TADs) that change in size and epigenetic states between normal and prostate cancer cells.		PCR,Flow cytometry			PRMT6,GABRB3	CTCF,FOXA1,TBX3	Examples of genes that belong to this cate_x0002_gory are TBX3 and PRMT6, which are known to be involved in prostate cancers23,24.;Moreover, we found that the size change of a TAD can be related to gene expression changes. For example, in normal cells, there is one large TAD at chromosome 15q12 containing the GABRB3 gene, which is not expressed in RWPE1.	By combining the in situ Hi-C data with active and repressive histone marks, CTCF binding sites, nucleosome-depleted regions, and tran_x0002_scriptome profiling, we identify topologically associating domains (TADs) that change in size and epigenetic states between normal and prostate cancer cells.;Moreover, we identify normal and prostate cancer-specific enhancer-promoter loops and involved transcription factors. For example, we show that FOXA1 is enriched in prostate cancer-specific enhancer_x0002_promoter loop anchors.;Examples of genes that belong to this cate_x0002_gory are TBX3 and PRMT6, which are known to be involved in prostate cancers23,24.
31514731	chr16	67559877	67561877	CTCF	These first en_x0002_hancers maintain more Hi-C interactions with other en_x0002_hancers and promoters, are more enriched for the loop factors CCCTC-binding factor (CTCF) and cohesin, and commonly overlap with the boundaries of chromatin loops.	human	blood	High+Lowthroughput	The first enhancer in an enhancer chain safeguards subsequent enhancer-promoter contacts from a distance	是		leukemia	K562 cell	E_01_0279	PCR	These first en_x0002_hancers maintain more Hi-C interactions with other en_x0002_hancers and promoters, are more enriched for the loop factors CCCTC-binding factor (CTCF) and cohesin, and commonly overlap with the boundaries of chromatin loops.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		These first en_x0002_hancers maintain more Hi-C interactions with other en_x0002_hancers and promoters, are more enriched for the loop factors CCCTC-binding factor (CTCF) and cohesin, and commonly overlap with the boundaries of chromatin loops.	Immunohistochemical staining	These first en_x0002_hancers maintain more Hi-C interactions with other en_x0002_hancers and promoters, are more enriched for the loop factors CCCTC-binding factor (CTCF) and cohesin, and commonly overlap with the boundaries of chromatin loops.		PCR				CTCF		These first en_x0002_hancers maintain more Hi-C interactions with other en_x0002_hancers and promoters, are more enriched for the loop factors CCCTC-binding factor (CTCF) and cohesin, and commonly overlap with the boundaries of chromatin loops.
31513772	chr9	21074265	21076265	IFNB1	We constructed IFNB1 luciferase reporter plasmids composed of IFNB1 immediate promoter followed by these enhancers (Figure S6D).	human	uterus	High+Lowthroughput	The Nuclear Matrix Protein SAFA Surveils Viral RNA and Facilitates Immunity by Activating Antiviral Enhancers and Super-enhancers	否		cervical carcinoma	HeLa cell	E_01_0280	PCR, Western blot, flow cytometry, immunofluorescence staining	We constructed IFNB1 luciferase reporter plasmids composed of IFNB1 immediate promoter followed by these enhancers (Figure S6D).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We constructed IFNB1 luciferase reporter plasmids composed of IFNB1 immediate promoter followed by these enhancers (Figure S6D).	Immunohistochemical staining	We constructed IFNB1 luciferase reporter plasmids composed of IFNB1 immediate promoter followed by these enhancers (Figure S6D).		PCR,Western blot,Flow cytometry,免疫荧光染色				IFNB1		We constructed IFNB1 luciferase reporter plasmids composed of IFNB1 immediate promoter followed by these enhancers (Figure S6D).
31509720	chr10	121475640	121477640	FGFR2	Fibroblast growth factor receptor 2 (FGFR2) in craniofacial bones mediates osteoprogenitor proliferation, differentiation, and apoptosis.	human	bone	High+Lowthroughput	Genetic Polymorphisms in FGFR2 Underlie Skeletal Malocclusion	是	rs2162540	Osteosarcoma	MG-63 cell	E_01_0281	Western blot,PCR,Flow cytometry	Fibroblast growth factor receptor 2 (FGFR2) in craniofacial bones mediates osteoprogenitor proliferation, differentiation, and apoptosis.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Fibroblast growth factor receptor 2 (FGFR2) in craniofacial bones mediates osteoprogenitor proliferation, differentiation, and apoptosis.	Immunohistochemical staining	Fibroblast growth factor receptor 2 (FGFR2) in craniofacial bones mediates osteoprogenitor proliferation, differentiation, and apoptosis.		Western blot,PCR,Flow cytometry				FGFR2,RUNX2,SMAD4		Fibroblast growth factor receptor 2 (FGFR2) in craniofacial bones mediates osteoprogenitor proliferation, differentiation, and apoptosis.;That is, rs2162540 was significantly associated with skeletal class II malocclusion, while others were associated with skeletal class III malocclusion. Electrophoretic mobility shift assay and chromatin immunoprecipitation analysis showed that the common genotypes of rs2981578 and rs10736303 contained the binding sites of RUNX2 and SMAD4.;That is, rs2162540 was significantly associated with skeletal class II malocclusion, while others were associated with skeletal class III malocclusion. Electrophoretic mobility shift assay and chromatin immunoprecipitation analysis showed that the common genotypes of rs2981578 and rs10736303 contained the binding sites of RUNX2 and SMAD4.
31507631	chr11	65877171	65879171	CTSW	This paper presents evidence that the breast_x0002_cancer-associated variant rs3903072 may regulate the expression of CTSW in tumor_x0002_infiltrating lymphocytes.	human	connective	High+Lowthroughput	The Cancer-Associated Genetic Variant Rs3903072 Modulates Immune Cells in the Tumor Microenvironment	是	rs3903072	cancer	immune cell	E_01_0282	Flow cytometry,PCR	This paper presents evidence that the breast_x0002_cancer-associated variant rs3903072 may regulate the expression of CTSW in tumor_x0002_infiltrating lymphocytes.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		This paper presents evidence that the breast_x0002_cancer-associated variant rs3903072 may regulate the expression of CTSW in tumor_x0002_infiltrating lymphocytes.	Immunohistochemical staining	This paper presents evidence that the breast_x0002_cancer-associated variant rs3903072 may regulate the expression of CTSW in tumor_x0002_infiltrating lymphocytes.		Flow cytometry,PCR			CTSW		This paper presents evidence that the breast_x0002_cancer-associated variant rs3903072 may regulate the expression of CTSW in tumor_x0002_infiltrating lymphocytes.	
31504407	chr6	151653980	151655980	ESR1	We observed ESR1 mRNA and ER protein down_x0002_regulation in BC cells treated with conditioned media (CM) from patient-derived, cancer-activated bone marrow stromal cells (BMSCs) and the BMSC cell line HS5.	human	breast	High+Lowthroughput	Bone Marrow Stromal Cells Transcriptionally Repress ESR1 but Cannot Overcome Constitutive ESR1 Mutant Activity	否		mammary cancer	MCF7 cell	E_01_0283	PCR, Western blot, immunofluorescence staining	We observed ESR1 mRNA and ER protein down_x0002_regulation in BC cells treated with conditioned media (CM) from patient-derived, cancer-activated bone marrow stromal cells (BMSCs) and the BMSC cell line HS5.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We observed ESR1 mRNA and ER protein down_x0002_regulation in BC cells treated with conditioned media (CM) from patient-derived, cancer-activated bone marrow stromal cells (BMSCs) and the BMSC cell line HS5.	Immunohistochemical staining	We observed ESR1 mRNA and ER protein down_x0002_regulation in BC cells treated with conditioned media (CM) from patient-derived, cancer-activated bone marrow stromal cells (BMSCs) and the BMSC cell line HS5.		PCR,Western blot,免疫荧光染色				ESR1		We observed ESR1 mRNA and ER protein down_x0002_regulation in BC cells treated with conditioned media (CM) from patient-derived, cancer-activated bone marrow stromal cells (BMSCs) and the BMSC cell line HS5.
31503357	chrX	119233203	119235203	PGRMC1	Expression of PGRMC1 and HSD17B4 was knocked down and subsequent studies were performed to analyze cell proliferation, migration, invasion, and apoptosis. Mechanistic studies that explored the epidermal growth factor receptor (EGFR) pathway were performed by Western blot	human	prostate	High+Lowthroughput	Functional validation of metabolic genes that distinguish Gleason 3 from Gleason 4 prostate cancer foci	否		prostatic cancer	prostate cancer cell	E_01_0284	PCR,Western blot 	Expression of PGRMC1 and HSD17B4 was knocked down and subsequent studies were performed to analyze cell proliferation, migration, invasion, and apoptosis. Mechanistic studies that explored the epidermal growth factor receptor (EGFR) pathway were performed by Western blot	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Expression of PGRMC1 and HSD17B4 was knocked down and subsequent studies were performed to analyze cell proliferation, migration, invasion, and apoptosis. Mechanistic studies that explored the epidermal growth factor receptor (EGFR) pathway were performed by Western blot	Immunohistochemical staining	Expression of PGRMC1 and HSD17B4 was knocked down and subsequent studies were performed to analyze cell proliferation, migration, invasion, and apoptosis. Mechanistic studies that explored the epidermal growth factor receptor (EGFR) pathway were performed by Western blot		PCR,Western blot 			PGRMC1		Expression of PGRMC1 and HSD17B4 was knocked down and subsequent studies were performed to analyze cell proliferation, migration, invasion, and apoptosis. Mechanistic studies that explored the epidermal growth factor receptor (EGFR) pathway were performed by Western blot	
31501538	chr8	95534429	95536429	Ccl17	We observed robust upregulation of immune marker genes associated with myeloid-derived suppressor cells (MDSCs) (Il10, Ifng, Csf1, Il6, Ptgs2 and Nfkb1), tumour-associ_x0002_ated macrophages (TAMs) (Ccl17, Ccl22, Il1r1, Il1a, Cxcl10 and Tnf) and tumour-associated neutrophils (TANs) (Cxcl1, Cxcl2, Cxcl5, Tnf and Il17a) (Supplementary Table 4) in colonic tumours from P. anaerobius-treated ApcMin/+.	mouse	colon	High+Lowthroughput	Peptostreptococcus anaerobius promotes colorectal carcinogenesis and modulates tumour immunity	否		Colon cancer		E_01_0285	Western blot,PCR	We observed robust upregulation of immune marker genes associated with myeloid-derived suppressor cells (MDSCs) (Il10, Ifng, Csf1, Il6, Ptgs2 and Nfkb1), tumour-associ_x0002_ated macrophages (TAMs) (Ccl17, Ccl22, Il1r1, Il1a, Cxcl10 and Tnf) and tumour-associated neutrophils (TANs) (Cxcl1, Cxcl2, Cxcl5, Tnf and Il17a) (Supplementary Table 4) in colonic tumours from P. anaerobius-treated ApcMin/+.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We observed robust upregulation of immune marker genes associated with myeloid-derived suppressor cells (MDSCs) (Il10, Ifng, Csf1, Il6, Ptgs2 and Nfkb1), tumour-associ_x0002_ated macrophages (TAMs) (Ccl17, Ccl22, Il1r1, Il1a, Cxcl10 and Tnf) and tumour-associated neutrophils (TANs) (Cxcl1, Cxcl2, Cxcl5, Tnf and Il17a) (Supplementary Table 4) in colonic tumours from P. anaerobius-treated ApcMin/+.	Immunohistochemical staining	We observed robust upregulation of immune marker genes associated with myeloid-derived suppressor cells (MDSCs) (Il10, Ifng, Csf1, Il6, Ptgs2 and Nfkb1), tumour-associ_x0002_ated macrophages (TAMs) (Ccl17, Ccl22, Il1r1, Il1a, Cxcl10 and Tnf) and tumour-associated neutrophils (TANs) (Cxcl1, Cxcl2, Cxcl5, Tnf and Il17a) (Supplementary Table 4) in colonic tumours from P. anaerobius-treated ApcMin/+.		Western blot,PCR			Ccl17		We observed robust upregulation of immune marker genes associated with myeloid-derived suppressor cells (MDSCs) (Il10, Ifng, Csf1, Il6, Ptgs2 and Nfkb1), tumour-associ_x0002_ated macrophages (TAMs) (Ccl17, Ccl22, Il1r1, Il1a, Cxcl10 and Tnf) and tumour-associated neutrophils (TANs) (Cxcl1, Cxcl2, Cxcl5, Tnf and Il17a) (Supplementary Table 4) in colonic tumours from P. anaerobius-treated ApcMin/+.	
31501517	chr19	46644863	46646863	DACT3	For instance, strong chromatin interactions were found between the DACT3 and AP2S1 promoter regions, and one significant eQTL, rs78730097 (NC_000019) for DACT3 was located in the AP2S1 promoter in the dorsolateral prefrontal cortex (Supplementary Fig. 10a)	human	connective	High+Lowthroughput	A compendium of promoter-centered long-range chromatin interactions in the human genome	是			embryonic cell 	E_01_0286	Flow cytometry,PCR	For instance, strong chromatin interactions were found between the DACT3 and AP2S1 promoter regions, and one significant eQTL, rs78730097 (NC_000019) for DACT3 was located in the AP2S1 promoter in the dorsolateral prefrontal cortex (Supplementary Fig. 10a)	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		For instance, strong chromatin interactions were found between the DACT3 and AP2S1 promoter regions, and one significant eQTL, rs78730097 (NC_000019) for DACT3 was located in the AP2S1 promoter in the dorsolateral prefrontal cortex (Supplementary Fig. 10a)	Immunohistochemical staining	For instance, strong chromatin interactions were found between the DACT3 and AP2S1 promoter regions, and one significant eQTL, rs78730097 (NC_000019) for DACT3 was located in the AP2S1 promoter in the dorsolateral prefrontal cortex (Supplementary Fig. 10a)		Flow cytometry,PCR			DACT3		For instance, strong chromatin interactions were found between the DACT3 and AP2S1 promoter regions, and one significant eQTL, rs78730097 (NC_000019) for DACT3 was located in the AP2S1 promoter in the dorsolateral prefrontal cortex (Supplementary Fig. 10a)	
31500558	chr7	18084316	18086316	HDAC9	Targeted resequencing of the HDAC9 locus in patients with atherosclerotic stroke and controls supported candidacy of rs2107595 as the causative single nucleotide polymorphism. A proteomic search for nuclear binding partners revealed preferential binding of the E2F3/TFDP1/Rb1 complex (E2F transcription factor 3/transcription factor Dp-1/Retinoblastoma 1) to the rs2107595 common allele, consistent with the disruption of an E2F3 consensus site by the risk allele.	human	connective	High+Lowthroughput	The Atherosclerosis Risk Variant rs2107595 Mediates Allele-Specific Transcriptional Regulation of HDAC9 via E2F3 and Rb1	是	rs2107595	atherosclerosis	immune cell	E_01_0287	Flow cytometry,PCR	Targeted resequencing of the HDAC9 locus in patients with atherosclerotic stroke and controls supported candidacy of rs2107595 as the causative single nucleotide polymorphism. A proteomic search for nuclear binding partners revealed preferential binding of the E2F3/TFDP1/Rb1 complex (E2F transcription factor 3/transcription factor Dp-1/Retinoblastoma 1) to the rs2107595 common allele, consistent with the disruption of an E2F3 consensus site by the risk allele.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Targeted resequencing of the HDAC9 locus in patients with atherosclerotic stroke and controls supported candidacy of rs2107595 as the causative single nucleotide polymorphism. A proteomic search for nuclear binding partners revealed preferential binding of the E2F3/TFDP1/Rb1 complex (E2F transcription factor 3/transcription factor Dp-1/Retinoblastoma 1) to the rs2107595 common allele, consistent with the disruption of an E2F3 consensus site by the risk allele.	Immunohistochemical staining	Targeted resequencing of the HDAC9 locus in patients with atherosclerotic stroke and controls supported candidacy of rs2107595 as the causative single nucleotide polymorphism. A proteomic search for nuclear binding partners revealed preferential binding of the E2F3/TFDP1/Rb1 complex (E2F transcription factor 3/transcription factor Dp-1/Retinoblastoma 1) to the rs2107595 common allele, consistent with the disruption of an E2F3 consensus site by the risk allele.		Flow cytometry,PCR			HDAC9		Targeted resequencing of the HDAC9 locus in patients with atherosclerotic stroke and controls supported candidacy of rs2107595 as the causative single nucleotide polymorphism. A proteomic search for nuclear binding partners revealed preferential binding of the E2F3/TFDP1/Rb1 complex (E2F transcription factor 3/transcription factor Dp-1/Retinoblastoma 1) to the rs2107595 common allele, consistent with the disruption of an E2F3 consensus site by the risk allele.	
31491956	chr7	55015564	55017564	EGFR	ROS are known to activate the epidermal growth factor receptor (EGFR), which causes the activation of the Ras/mitogen-activated protein kinases (MAPKs)pathway.	human	stomach	High+Lowthroughput	Lycopene Inhibits Activation of Epidermal Growth Factor Receptor and Expression of Cyclooxygenase-2 in Gastric Cancer Cells	否		gastric cancer	gastric cancer cell	E_01_0288	PCR,Western blot,Flow cytometry	ROS are known to activate the epidermal growth factor receptor (EGFR), which causes the activation of the Ras/mitogen-activated protein kinases (MAPKs)pathway.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		ROS are known to activate the epidermal growth factor receptor (EGFR), which causes the activation of the Ras/mitogen-activated protein kinases (MAPKs)pathway.	Immunohistochemical staining	ROS are known to activate the epidermal growth factor receptor (EGFR), which causes the activation of the Ras/mitogen-activated protein kinases (MAPKs)pathway.		PCR,Western blot,Flow cytometry				EGFR		ROS are known to activate the epidermal growth factor receptor (EGFR), which causes the activation of the Ras/mitogen-activated protein kinases (MAPKs)pathway.
31481468	chr9	6410546	6412546	UHRF2	In mammals, SRA domains are found in only two proteins (15), the DNA methylation maintenance factor UHRF1 and the structurally related, but functionally distinct, UHRF2 (16, 17).	human	colon	High+Lowthroughput	The finger loop of the SRA domain in the E3 ligase UHRF1 is a regulator of ubiquitin targeting and is required for the maintenance of DNA methylation	否		Colon cancer	colon cancer cell	E_01_0289	Western blot	In mammals, SRA domains are found in only two proteins (15), the DNA methylation maintenance factor UHRF1 and the structurally related, but functionally distinct, UHRF2 (16, 17).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In mammals, SRA domains are found in only two proteins (15), the DNA methylation maintenance factor UHRF1 and the structurally related, but functionally distinct, UHRF2 (16, 17).	Immunohistochemical staining	In mammals, SRA domains are found in only two proteins (15), the DNA methylation maintenance factor UHRF1 and the structurally related, but functionally distinct, UHRF2 (16, 17).		Western blot				UHRF2		In mammals, SRA domains are found in only two proteins (15), the DNA methylation maintenance factor UHRF1 and the structurally related, but functionally distinct, UHRF2 (16, 17).
31478258	chr7	148803962	148805962	EZH2	In addition, PCAT‐1 epigenetically silenced PTEN through binding to the histone methyltransferase enhancer of zeste homolog 2 (EZH2), thus increasing H3K27me3.	human	stomach	High+Lowthroughput	PCAT-1 contributes to cisplatin resistance in gastric cancer through epigenetically silencing PTEN via recruiting EZH2	否		gastric cancer	gastric cancer cell	E_01_0290	Western blot, PCR,Flow cytometry	In addition, PCAT‐1 epigenetically silenced PTEN through binding to the histone methyltransferase enhancer of zeste homolog 2 (EZH2), thus increasing H3K27me3.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In addition, PCAT‐1 epigenetically silenced PTEN through binding to the histone methyltransferase enhancer of zeste homolog 2 (EZH2), thus increasing H3K27me3.	Immunohistochemical staining	In addition, PCAT‐1 epigenetically silenced PTEN through binding to the histone methyltransferase enhancer of zeste homolog 2 (EZH2), thus increasing H3K27me3.		Western blot, PCR,Flow cytometry				EZH2		In addition, PCAT‐1 epigenetically silenced PTEN through binding to the histone methyltransferase enhancer of zeste homolog 2 (EZH2), thus increasing H3K27me3.
30700785	chr17	31933934	31935934	SUZ12	PRC2 is composed of four main subunits; Suppressor of Zeste 12 (SUZ12), Retinoblastoma-Associated Protein 46/48 (RbAp46/48)	human		High+Lowthroughput	The EZH2 SANT1 domain is a histone reader providing sensitivity to the modification state of the H4 tail	否			eukaryotic,HeLa,E. coli Rosetta2 (DE3) pLysS cell	E_01_0291	ChIP-seq,Gateway Recombination cloning,EMSAs,HADDOCK Modeling	PRC2 is composed of four main subunits; Suppressor of Zeste 12 (SUZ12), Retinoblastoma-Associated Protein 46/48 (RbAp46/48)	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		PRC2 is composed of four main subunits; Suppressor of Zeste 12 (SUZ12), Retinoblastoma-Associated Protein 46/48 (RbAp46/48)	Immunohistochemical staining	PRC2 is composed of four main subunits; Suppressor of Zeste 12 (SUZ12), Retinoblastoma-Associated Protein 46/48 (RbAp46/48)		ChIP-seq,Gateway Recombination cloning,EMSAs,HADDOCK Modeling				SUZ12		PRC2 is composed of four main subunits; Suppressor of Zeste 12 (SUZ12), Retinoblastoma-Associated Protein 46/48 (RbAp46/48)
30696717	chr4	71738822	71740822	GC	Our classifiers also indicate that there are functionally relevant differences in enhancer and promoter GC content beyond the influence of CpG islands	human	Liver	High+Lowthroughput	Sequence Characteristics Distinguish Transcribed Enhancers from Promoters and Predict Their Breadth of Activity	否		common metabolic disorders		E_01_0292	Western blot,Immunostaining,RT-PCR	Our classifiers also indicate that there are functionally relevant differences in enhancer and promoter GC content beyond the influence of CpG islands	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Our classifiers also indicate that there are functionally relevant differences in enhancer and promoter GC content beyond the influence of CpG islands	Immunohistochemical staining	Our classifiers also indicate that there are functionally relevant differences in enhancer and promoter GC content beyond the influence of CpG islands		Western blot,Immunostaining,RT-PCR			GC		Our classifiers also indicate that there are functionally relevant differences in enhancer and promoter GC content beyond the influence of CpG islands	
30692044	chr10	100732827	100734827	PAX2	To generate the recombinant lentivirus, lentiviral pLKO-shAR/pLKO-Scr with pMD2.G packaging and psPAX2 envelope plasmids	human	prostate	High+Lowthroughput	Preclinical study using androgen receptor (AR) degradation enhancer to increase radiotherapy efficacy via targeting radiation-increased AR to better suppress prostate cancer progression			Prostate cancer		E_01_0293	PCR,Western blot	To generate the recombinant lentivirus, lentiviral pLKO-shAR/pLKO-Scr with pMD2.G packaging and psPAX2 envelope plasmids	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		To generate the recombinant lentivirus, lentiviral pLKO-shAR/pLKO-Scr with pMD2.G packaging and psPAX2 envelope plasmids	Immunohistochemical staining	To generate the recombinant lentivirus, lentiviral pLKO-shAR/pLKO-Scr with pMD2.G packaging and psPAX2 envelope plasmids		PCR,Western blot				PAX2		To generate the recombinant lentivirus, lentiviral pLKO-shAR/pLKO-Scr with pMD2.G packaging and psPAX2 envelope plasmids
33147208	chr9	21074558	21076558	IFNB1	This variant prevents binding of the C/EBP-β transcription factor, and is associated with decreased expression of IFNB1 in activated monocytes.	human	Epithelial	High+Lowthroughput	A genetic variant controls interferon-尾 gene expression in human myeloid cells by preventing C/EBP-尾 binding on a conserved enhancer	是			monocyte cells	E_01_0294	Flow cytometry	This variant prevents binding of the C/EBP-β transcription factor, and is associated with decreased expression of IFNB1 in activated monocytes.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		This variant prevents binding of the C/EBP-β transcription factor, and is associated with decreased expression of IFNB1 in activated monocytes.	Immunohistochemical staining	This variant prevents binding of the C/EBP-β transcription factor, and is associated with decreased expression of IFNB1 in activated monocytes.		流式细胞术				IFNB1		This variant prevents binding of the C/EBP-β transcription factor, and is associated with decreased expression of IFNB1 in activated monocytes.
30688289	chr4	73737463	73739463	CXCL8	Quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot were performed to determine the expressions of inflammatory cytokines including interleukin (IL)-1β, IL-6, tumor necrosis factor-α (TNF-α), apoptosis-related genes, and the downstream target genes of NF-κB signaling pathway, including NFKBIA, CXCL8, and cyclin D1.	human	Kidney	High+Lowthroughput	The Effect of Overexpression of the Enhancer of Zeste Homolog 1 (EZH1) Gene on Aristolochic Acid-Induced Injury in HK-2 Human Kidney Proximal Tubule Cells In Vitro			Acute kidney injury	Human Kidney Proximal Tubule cell	E_01_0295	PCR, Western blots, sequencing technology	Quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot were performed to determine the expressions of inflammatory cytokines including interleukin (IL)-1β, IL-6, tumor necrosis factor-α (TNF-α), apoptosis-related genes, and the downstream target genes of NF-κB signaling pathway, including NFKBIA, CXCL8, and cyclin D1.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot were performed to determine the expressions of inflammatory cytokines including interleukin (IL)-1β, IL-6, tumor necrosis factor-α (TNF-α), apoptosis-related genes, and the downstream target genes of NF-κB signaling pathway, including NFKBIA, CXCL8, and cyclin D1.	Immunohistochemical staining	Quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot were performed to determine the expressions of inflammatory cytokines including interleukin (IL)-1β, IL-6, tumor necrosis factor-α (TNF-α), apoptosis-related genes, and the downstream target genes of NF-κB signaling pathway, including NFKBIA, CXCL8, and cyclin D1.		PCR，Western blots,测序技术				CXCL8		Quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot were performed to determine the expressions of inflammatory cytokines including interleukin (IL)-1β, IL-6, tumor necrosis factor-α (TNF-α), apoptosis-related genes, and the downstream target genes of NF-κB signaling pathway, including NFKBIA, CXCL8, and cyclin D1.
30683753	chr3	133743339	133745339	TF	This higher tissue specificity is strongly associated with having less complex transcription factor (TF) motif profiles at the core promoter.	human	Liver	High+Lowthroughput	High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity			common metabolic disorders		E_01_0296	Western blot,Immunostaining,RT-PCR	This higher tissue specificity is strongly associated with having less complex transcription factor (TF) motif profiles at the core promoter.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		This higher tissue specificity is strongly associated with having less complex transcription factor (TF) motif profiles at the core promoter.	Immunohistochemical staining	This higher tissue specificity is strongly associated with having less complex transcription factor (TF) motif profiles at the core promoter.		Western blot,Immunostaining,RT-PCR			TF		This higher tissue specificity is strongly associated with having less complex transcription factor (TF) motif profiles at the core promoter.	
30683142	chr17	43041963	43043963	BRCA1	o provide insights into alternative classification and potential therapeutic targeting strategies of BRCA1-like hormone-receptor-positive tumors we developed and applied a novel copy number classifier to identify BRCA1-like hormone-receptor-positive tumors and their characteristic somatic alteration profiles.	human	Breast	High+Lowthroughput	Molecular and epigenetic profiles of BRCA1-like hormone-receptor-positive breast tumors identified with development and application of a copy-number-based classifier			mammary cancer	breast cancer cell	E_01_0297	PCR, sequencing technology	o provide insights into alternative classification and potential therapeutic targeting strategies of BRCA1-like hormone-receptor-positive tumors we developed and applied a novel copy number classifier to identify BRCA1-like hormone-receptor-positive tumors and their characteristic somatic alteration profiles.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		o provide insights into alternative classification and potential therapeutic targeting strategies of BRCA1-like hormone-receptor-positive tumors we developed and applied a novel copy number classifier to identify BRCA1-like hormone-receptor-positive tumors and their characteristic somatic alteration profiles.	Immunohistochemical staining	o provide insights into alternative classification and potential therapeutic targeting strategies of BRCA1-like hormone-receptor-positive tumors we developed and applied a novel copy number classifier to identify BRCA1-like hormone-receptor-positive tumors and their characteristic somatic alteration profiles.		PCR，测序技术				BRCA1		o provide insights into alternative classification and potential therapeutic targeting strategies of BRCA1-like hormone-receptor-positive tumors we developed and applied a novel copy number classifier to identify BRCA1-like hormone-receptor-positive tumors and their characteristic somatic alteration profiles.
30682089	chr15	72964799	72966799	Ago2	One strand then incorporates with Argonaute (Ago2) proteins into the RNA Inducing Silencing Complex (RISC)	mouse	lymph	High+Lowthroughput	HIV-1 infection increases microRNAs that inhibit Dicer1, HRB and HIV-EP2, thereby reducing viral replication			AIDS	Sup-T1 cell，HeLa-MAGI cell	E_01_0298	PCR, Western blot, sequencing technology	One strand then incorporates with Argonaute (Ago2) proteins into the RNA Inducing Silencing Complex (RISC)	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		One strand then incorporates with Argonaute (Ago2) proteins into the RNA Inducing Silencing Complex (RISC)	Immunohistochemical staining	One strand then incorporates with Argonaute (Ago2) proteins into the RNA Inducing Silencing Complex (RISC)		PCR，Western blot，测序技术			Ago2		One strand then incorporates with Argonaute (Ago2) proteins into the RNA Inducing Silencing Complex (RISC)	
30678091	chr15	99562775	99564775	MEF2A	The strongest effect visible in three distinct cell types was observed for rs12946510 that is predicted to alter MEF2A/C and FOXO1 binding sites.	human	lymph	High+Lowthroughput	Functional SNPs in the Human Autoimmunity-Associated Locus 17q12-21			mammary cancer	immune cell	E_01_0299	PCR，Western blot，ChIP-seq	The strongest effect visible in three distinct cell types was observed for rs12946510 that is predicted to alter MEF2A/C and FOXO1 binding sites.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The strongest effect visible in three distinct cell types was observed for rs12946510 that is predicted to alter MEF2A/C and FOXO1 binding sites.	Immunohistochemical staining	The strongest effect visible in three distinct cell types was observed for rs12946510 that is predicted to alter MEF2A/C and FOXO1 binding sites.		PCR，Western blot，ChIP-seq				MEF2A		The strongest effect visible in three distinct cell types was observed for rs12946510 that is predicted to alter MEF2A/C and FOXO1 binding sites.
30676242	chr14	64081786	64083786	ESR2	They were also more likely to be in ARNT and ESR2 transcription factor binding sites	human	lymph	High+Lowthroughput	Exposure to polybrominated biphenyl (PBB) associates with genome-wide DNA methylation differences in peripheral blood			Autoimmune diseases	B cell	E_01_0300	ChIP-seq	They were also more likely to be in ARNT and ESR2 transcription factor binding sites	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		They were also more likely to be in ARNT and ESR2 transcription factor binding sites	Immunohistochemical staining	They were also more likely to be in ARNT and ESR2 transcription factor binding sites		ChIP-seq				ESR2		They were also more likely to be in ARNT and ESR2 transcription factor binding sites
30675263	chr13	73052370	73054370	KLF5	In addition, the expression levels of tumor invasion-associated proteins, including Kruppel-like factor 5 (KLF5), matrix metallopeptidase (MMP)-2, MMP-9, and E-cadherin (ECD) were detected subsequent to transfection.	human	lymph	High+Lowthroughput	Association of the invasiveness of colon cancer with the expression of C/EBPα			Colon cancer	SW480 cell，CC cell	E_01_0301	PCR，ChIP-Seq	In addition, the expression levels of tumor invasion-associated proteins, including Kruppel-like factor 5 (KLF5), matrix metallopeptidase (MMP)-2, MMP-9, and E-cadherin (ECD) were detected subsequent to transfection.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In addition, the expression levels of tumor invasion-associated proteins, including Kruppel-like factor 5 (KLF5), matrix metallopeptidase (MMP)-2, MMP-9, and E-cadherin (ECD) were detected subsequent to transfection.	Immunohistochemical staining	In addition, the expression levels of tumor invasion-associated proteins, including Kruppel-like factor 5 (KLF5), matrix metallopeptidase (MMP)-2, MMP-9, and E-cadherin (ECD) were detected subsequent to transfection.		PCR，ChIP-Seq			KLF5		In addition, the expression levels of tumor invasion-associated proteins, including Kruppel-like factor 5 (KLF5), matrix metallopeptidase (MMP)-2, MMP-9, and E-cadherin (ECD) were detected subsequent to transfection.	
30672466	chr11	114255412	114257412	NNMT	Subsequently, PLZF was recruited to osteogenic enhancers, influencing H3K27 acetylation and expression of nearby genes important for osteogenic function. Furthermore, we identified a latent enhancer within the ZBTB16/PLZF locus itself that became active, gained PLZF, p300 and Mediator binding and looped to the promoter of the nicotinamide N-methyltransferase (NNMT) gene.	human	bone	High+Lowthroughput	PLZF targets developmental enhancers for activation during osteogenic differentiation of human mesenchymal stem cells					E_01_0302	PCR，Western blot，ChIP-seq	Subsequently, PLZF was recruited to osteogenic enhancers, influencing H3K27 acetylation and expression of nearby genes important for osteogenic function. Furthermore, we identified a latent enhancer within the ZBTB16/PLZF locus itself that became active, gained PLZF, p300 and Mediator binding and looped to the promoter of the nicotinamide N-methyltransferase (NNMT) gene.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Subsequently, PLZF was recruited to osteogenic enhancers, influencing H3K27 acetylation and expression of nearby genes important for osteogenic function. Furthermore, we identified a latent enhancer within the ZBTB16/PLZF locus itself that became active, gained PLZF, p300 and Mediator binding and looped to the promoter of the nicotinamide N-methyltransferase (NNMT) gene.	Immunohistochemical staining	Subsequently, PLZF was recruited to osteogenic enhancers, influencing H3K27 acetylation and expression of nearby genes important for osteogenic function. Furthermore, we identified a latent enhancer within the ZBTB16/PLZF locus itself that became active, gained PLZF, p300 and Mediator binding and looped to the promoter of the nicotinamide N-methyltransferase (NNMT) gene.		PCR，Western blot，ChIP-seq			NNMT		Subsequently, PLZF was recruited to osteogenic enhancers, influencing H3K27 acetylation and expression of nearby genes important for osteogenic function. Furthermore, we identified a latent enhancer within the ZBTB16/PLZF locus itself that became active, gained PLZF, p300 and Mediator binding and looped to the promoter of the nicotinamide N-methyltransferase (NNMT) gene.	
34529725	chr7	128935299	128937299	IRF5	Here, we performed a comprehensive integrated post-GWAS analysis of T1D to identify functional regulatory variants in enhancers and their cognate target genes. Starting with 1,817 candidate T1D SNPs defined from the GWAS catalog and LDlink databases	human	Renal	High+Lowthroughput	A comprehensive integrated post-GWAS analysis of Type 1 diabetes reveals enhancer_x005f_x005f_x005f_x005f_x005f_x005f_x005f_x005f_x005f_x005f_x005f_x0002_based immune dysregulation	有		Type 1 diabetes		E_01_0303	Gel electrophoresis Western blot flow cytometry chip	Here, we performed a comprehensive integrated post-GWAS analysis of T1D to identify functional regulatory variants in enhancers and their cognate target genes. Starting with 1,817 candidate T1D SNPs defined from the GWAS catalog and LDlink databases	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Here, we performed a comprehensive integrated post-GWAS analysis of T1D to identify functional regulatory variants in enhancers and their cognate target genes. Starting with 1,817 candidate T1D SNPs defined from the GWAS catalog and LDlink databases	Immunohistochemical staining	Here, we performed a comprehensive integrated post-GWAS analysis of T1D to identify functional regulatory variants in enhancers and their cognate target genes. Starting with 1,817 candidate T1D SNPs defined from the GWAS catalog and LDlink databases		凝胶电泳 Western blot 流式细胞术 CHIP				IRF5		Here, we performed a comprehensive integrated post-GWAS analysis of T1D to identify functional regulatory variants in enhancers and their cognate target genes. Starting with 1,817 candidate T1D SNPs defined from the GWAS catalog and LDlink databases
30670628	chr6	43767278	43769278	VEGFA	Integration of gene expression, dynamic enhancer, and transcription factor occupancy changes induced by VEGFA yielded a VEGFA-regulated transcriptional regulatory network	human	endothelial	High+Lowthroughput	A dynamic and integrated epigenetic program at distal regions orchestrates transcriptional responses to VEGFA				endothelial cell	E_01_0304	PCR，Western blot，ChIP-seq	Integration of gene expression, dynamic enhancer, and transcription factor occupancy changes induced by VEGFA yielded a VEGFA-regulated transcriptional regulatory network	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Integration of gene expression, dynamic enhancer, and transcription factor occupancy changes induced by VEGFA yielded a VEGFA-regulated transcriptional regulatory network	Immunohistochemical staining	Integration of gene expression, dynamic enhancer, and transcription factor occupancy changes induced by VEGFA yielded a VEGFA-regulated transcriptional regulatory network		PCR，Western blot，ChIP-seq				VEGFA		Integration of gene expression, dynamic enhancer, and transcription factor occupancy changes induced by VEGFA yielded a VEGFA-regulated transcriptional regulatory network
30670569	chrX	55006658	55008658	ALAS2	we first generated mutant mice by disrupting the GATA-1 binding motif at the intron 1 enhancer of the ALAS2 gene	human	blood	High+Lowthroughput	Generation and Molecular Characterization of Human Ring Sideroblasts: a Key Role of Ferrous Iron in Terminal Erythroid Differentiation and Ring Sideroblast Formation			anemia		E_01_0305	PCR，Western blot，ChIP-seq	we first generated mutant mice by disrupting the GATA-1 binding motif at the intron 1 enhancer of the ALAS2 gene	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		we first generated mutant mice by disrupting the GATA-1 binding motif at the intron 1 enhancer of the ALAS2 gene	Immunohistochemical staining	we first generated mutant mice by disrupting the GATA-1 binding motif at the intron 1 enhancer of the ALAS2 gene		PCR，Western blot，ChIP-seq			ALAS2		we first generated mutant mice by disrupting the GATA-1 binding motif at the intron 1 enhancer of the ALAS2 gene	
30664779	chr5	69231799	69233799	CDK7	These systematic approaches reveal that the developmental transcription factor T (brachyury; TBXT) is the top selectively essential gene in chordoma, and that transcriptional cyclin-dependent kinase (CDK) inhibitors targeting CDK7/12/13 and CDK9 potently suppress chordoma cell proliferation.	human	bone	High+Lowthroughput	Small-molecule targeting of brachyury transcription factor addiction in chordoma			chordoma	chordoma cell	E_01_0306	PCR，ChIP-seq	These systematic approaches reveal that the developmental transcription factor T (brachyury; TBXT) is the top selectively essential gene in chordoma, and that transcriptional cyclin-dependent kinase (CDK) inhibitors targeting CDK7/12/13 and CDK9 potently suppress chordoma cell proliferation.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		These systematic approaches reveal that the developmental transcription factor T (brachyury; TBXT) is the top selectively essential gene in chordoma, and that transcriptional cyclin-dependent kinase (CDK) inhibitors targeting CDK7/12/13 and CDK9 potently suppress chordoma cell proliferation.	Immunohistochemical staining	These systematic approaches reveal that the developmental transcription factor T (brachyury; TBXT) is the top selectively essential gene in chordoma, and that transcriptional cyclin-dependent kinase (CDK) inhibitors targeting CDK7/12/13 and CDK9 potently suppress chordoma cell proliferation.		PCR，ChIP-seq			CDK7		These systematic approaches reveal that the developmental transcription factor T (brachyury; TBXT) is the top selectively essential gene in chordoma, and that transcriptional cyclin-dependent kinase (CDK) inhibitors targeting CDK7/12/13 and CDK9 potently suppress chordoma cell proliferation.	
30664211	chr1	153387368	153389368	S100A8	The reporter assay demonstrated that the upregulatory effect of S100A8 induced by IL‑1α was dependent on the S100A8 promoter specific region	human	epithelial	High+Lowthroughput	Expression of S100A8 is induced by interleukin?1α in TR146 epithelial cells through a mechanism involving CCAAT/enhancer binding protein β			Infection of mucosal epithelial cells	TR146 epithelial cell	E_01_0307	PCR, Western blot, chip SEQ bioinformatic prediction	The reporter assay demonstrated that the upregulatory effect of S100A8 induced by IL‑1α was dependent on the S100A8 promoter specific region	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The reporter assay demonstrated that the upregulatory effect of S100A8 induced by IL‑1α was dependent on the S100A8 promoter specific region	Immunohistochemical staining	The reporter assay demonstrated that the upregulatory effect of S100A8 induced by IL‑1α was dependent on the S100A8 promoter specific region		PCR，Western blot，ChIP-seq生物信息预测			S100A8		The reporter assay demonstrated that the upregulatory effect of S100A8 induced by IL‑1α was dependent on the S100A8 promoter specific region	
30664173	chr9	117701433	117703433	TLR4	The cell proliferation rate and inflammatory cytokine expression of PBMCs treated with the FimA fusion protein with or without transfection with toll‑like receptor 4 (TLR4) small interfering (si)RNA were detected by CCK‑8 assays and ELISAs, respectively.	human	blood	High+Lowthroughput	Recombinant fimbriae protein of Porphyromonas gingivalis induces an inflammatory response via the TLR4/NF?κB signaling pathway in human peripheral blood mononuclear cells			Periodontal disease	peripheral blood mononuclear cell	E_01_0308	PCR, Western blot, sequencing technology	The cell proliferation rate and inflammatory cytokine expression of PBMCs treated with the FimA fusion protein with or without transfection with toll‑like receptor 4 (TLR4) small interfering (si)RNA were detected by CCK‑8 assays and ELISAs, respectively.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The cell proliferation rate and inflammatory cytokine expression of PBMCs treated with the FimA fusion protein with or without transfection with toll‑like receptor 4 (TLR4) small interfering (si)RNA were detected by CCK‑8 assays and ELISAs, respectively.	Immunohistochemical staining	The cell proliferation rate and inflammatory cytokine expression of PBMCs treated with the FimA fusion protein with or without transfection with toll‑like receptor 4 (TLR4) small interfering (si)RNA were detected by CCK‑8 assays and ELISAs, respectively.		PCR，Western blot，测序技术				TLR4		The cell proliferation rate and inflammatory cytokine expression of PBMCs treated with the FimA fusion protein with or without transfection with toll‑like receptor 4 (TLR4) small interfering (si)RNA were detected by CCK‑8 assays and ELISAs, respectively.
30662920	chr6	137864227	137866227	TNFAIP3	The TNFAIP3 gene encodes the A20 protein essential for the development and functional performance of dendritic, B and T cells and macrophages as well as an important negative feedback regulator of the NF-κB pathway	human	lymph	High+Lowthroughput	TNFAIP3 F127C Coding Variation in Greek Primary Sjogren's Syndrome Patients			Periodontal disease	peripheral blood mononuclear cell	E_01_0309	PCR	The TNFAIP3 gene encodes the A20 protein essential for the development and functional performance of dendritic, B and T cells and macrophages as well as an important negative feedback regulator of the NF-κB pathway	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The TNFAIP3 gene encodes the A20 protein essential for the development and functional performance of dendritic, B and T cells and macrophages as well as an important negative feedback regulator of the NF-κB pathway	Immunohistochemical staining	The TNFAIP3 gene encodes the A20 protein essential for the development and functional performance of dendritic, B and T cells and macrophages as well as an important negative feedback regulator of the NF-κB pathway		PCR				TNFAIP3		The TNFAIP3 gene encodes the A20 protein essential for the development and functional performance of dendritic, B and T cells and macrophages as well as an important negative feedback regulator of the NF-κB pathway
30662804	chr6	11180709	11182709	NEDD9	Human enhancer of filamentation 1 (HEF1, also known as CasL and NEDD9) is a non-catalytic scaffolding protein belonging to CAS (Crk-associated substrate) protein family that interacts with multiple signaling cascades.	human	bladder	High+Lowthroughput	SPAG9 regulates HEF1 expression and drives EMT in bladder transitional cell carcinoma via rac1 signaling pathway			Transitional cell carcinoma of the urinary bladder	bladder cancer cell	E_01_0310	PCR, Western blot, sequencing technology	Human enhancer of filamentation 1 (HEF1, also known as CasL and NEDD9) is a non-catalytic scaffolding protein belonging to CAS (Crk-associated substrate) protein family that interacts with multiple signaling cascades.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Human enhancer of filamentation 1 (HEF1, also known as CasL and NEDD9) is a non-catalytic scaffolding protein belonging to CAS (Crk-associated substrate) protein family that interacts with multiple signaling cascades.	Immunohistochemical staining	Human enhancer of filamentation 1 (HEF1, also known as CasL and NEDD9) is a non-catalytic scaffolding protein belonging to CAS (Crk-associated substrate) protein family that interacts with multiple signaling cascades.		PCR，Western blot，测序技术			NEDD9		Human enhancer of filamentation 1 (HEF1, also known as CasL and NEDD9) is a non-catalytic scaffolding protein belonging to CAS (Crk-associated substrate) protein family that interacts with multiple signaling cascades.	
30662285	chr11	102517572	102519572	MMP7	Notch3 may affect the invasiveness and metastasis of osteosarcoma cells by regulating the downstream target gene Hes1 and its effector protein, MMP7.	human	bone	High+Lowthroughput	Overexpression of Notch3 is associated with metastasis and poor prognosis in osteosarcoma patients			Osteosarcoma	osteosarcoma cell	E_01_0311	Lentiviral transfection, gene knockdown, PCR, Western blot	Notch3 may affect the invasiveness and metastasis of osteosarcoma cells by regulating the downstream target gene Hes1 and its effector protein, MMP7.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Notch3 may affect the invasiveness and metastasis of osteosarcoma cells by regulating the downstream target gene Hes1 and its effector protein, MMP7.	Immunohistochemical staining	Notch3 may affect the invasiveness and metastasis of osteosarcoma cells by regulating the downstream target gene Hes1 and its effector protein, MMP7.		慢病毒转染，基因敲除，PCR，Western blot				MMP7		Notch3 may affect the invasiveness and metastasis of osteosarcoma cells by regulating the downstream target gene Hes1 and its effector protein, MMP7.
30659980	chrX	154538337	154540337	IKBKG	IKBKG loss-of-function mutation causes incontinentia pigmenti (IP), a rare X-linked disease featuring linear hypopigmentation, alopecia, hypodontia, and immunodeficiency.	human	bone	High+Lowthroughput	Absence of an osteopetrosis phenotype in IKBKG (NEMO) mutation-positive women: A case-control study			Osteosclerosis	B cell， Oc precursor cell	E_01_0312	PCR，Bone marrow aspiration，Histomorphometry	IKBKG loss-of-function mutation causes incontinentia pigmenti (IP), a rare X-linked disease featuring linear hypopigmentation, alopecia, hypodontia, and immunodeficiency.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		IKBKG loss-of-function mutation causes incontinentia pigmenti (IP), a rare X-linked disease featuring linear hypopigmentation, alopecia, hypodontia, and immunodeficiency.	Immunohistochemical staining	IKBKG loss-of-function mutation causes incontinentia pigmenti (IP), a rare X-linked disease featuring linear hypopigmentation, alopecia, hypodontia, and immunodeficiency.		PCR，Bone marrow aspiration，Histomorphometry			IKBKG		IKBKG loss-of-function mutation causes incontinentia pigmenti (IP), a rare X-linked disease featuring linear hypopigmentation, alopecia, hypodontia, and immunodeficiency.	
30659195	chr19	15232704	15234704	BRD4	Conversely, deletion of this enhancer via CRISPR/Cas9 reduces C/EBPβ expression and its genome-wide co-occupancy with BRD4 at H3K27ac-marked enhancers and super-enhancers	human	liver	High+Lowthroughput	Aberrant enhancer hypomethylation contributes to hepatic carcinogenesis through global transcriptional reprogramming			liver cancer	HCC cell	E_01_0313	PCR，Western blot，ChIP-seq	Conversely, deletion of this enhancer via CRISPR/Cas9 reduces C/EBPβ expression and its genome-wide co-occupancy with BRD4 at H3K27ac-marked enhancers and super-enhancers	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Conversely, deletion of this enhancer via CRISPR/Cas9 reduces C/EBPβ expression and its genome-wide co-occupancy with BRD4 at H3K27ac-marked enhancers and super-enhancers	Immunohistochemical staining	Conversely, deletion of this enhancer via CRISPR/Cas9 reduces C/EBPβ expression and its genome-wide co-occupancy with BRD4 at H3K27ac-marked enhancers and super-enhancers		PCR，Western blot，ChIP-seq				BRD4		Conversely, deletion of this enhancer via CRISPR/Cas9 reduces C/EBPβ expression and its genome-wide co-occupancy with BRD4 at H3K27ac-marked enhancers and super-enhancers
30659153	chr16	67560054	67562054	CTCF	chromHMM chromatin states from Roadmap (32), cross-tissue gene expression for TSSs from GTEx (33), TAD boundaries from high-resolution Hi-C data, called using an arrowhead score (34), and binding clusters for the insulator protein CTCF from ENCODE	human		High+Lowthroughput	Chromatin features constrain structural variation across evolutionary timescales					E_01_0314	Western blot，ChIP-seq	chromHMM chromatin states from Roadmap (32), cross-tissue gene expression for TSSs from GTEx (33), TAD boundaries from high-resolution Hi-C data, called using an arrowhead score (34), and binding clusters for the insulator protein CTCF from ENCODE	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		chromHMM chromatin states from Roadmap (32), cross-tissue gene expression for TSSs from GTEx (33), TAD boundaries from high-resolution Hi-C data, called using an arrowhead score (34), and binding clusters for the insulator protein CTCF from ENCODE	Immunohistochemical staining	chromHMM chromatin states from Roadmap (32), cross-tissue gene expression for TSSs from GTEx (33), TAD boundaries from high-resolution Hi-C data, called using an arrowhead score (34), and binding clusters for the insulator protein CTCF from ENCODE		Western blot，ChIP-seq				CTCF		chromHMM chromatin states from Roadmap (32), cross-tissue gene expression for TSSs from GTEx (33), TAD boundaries from high-resolution Hi-C data, called using an arrowhead score (34), and binding clusters for the insulator protein CTCF from ENCODE
30657937	chr16	85896547	85898547	IRF8	We analyze binding of PU.1/SPI1 and IRF8 from human monocytes, delineate DNA-sequence determinants for their cooperativity	human		High+Lowthroughput	NextPBM: a platform to study cell-specific transcription factor binding and cooperativity					E_01_0315	HT nextPBM	We analyze binding of PU.1/SPI1 and IRF8 from human monocytes, delineate DNA-sequence determinants for their cooperativity	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We analyze binding of PU.1/SPI1 and IRF8 from human monocytes, delineate DNA-sequence determinants for their cooperativity	Immunohistochemical staining	We analyze binding of PU.1/SPI1 and IRF8 from human monocytes, delineate DNA-sequence determinants for their cooperativity		HT nextPBM				IRF8		We analyze binding of PU.1/SPI1 and IRF8 from human monocytes, delineate DNA-sequence determinants for their cooperativity
30655550	chr19	17400341	17402341	BST2	CBX6 induced significant downregulation of bone marrow stromal cell antigen-2 (BST2), a potential therapeutic target, via interactions with its promoter region. Our collective findings support a tumor suppressor role of CBX6 in breast cancer.	human	breast	High+Lowthroughput	CBX6 is negatively regulated by EZH2 and plays a potential tumor suppressor role in breast cancer			mammary cancer	breast cancer cell	E_01_0316	PCR，Western blot，ChIP-seq	CBX6 induced significant downregulation of bone marrow stromal cell antigen-2 (BST2), a potential therapeutic target, via interactions with its promoter region. Our collective findings support a tumor suppressor role of CBX6 in breast cancer.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		CBX6 induced significant downregulation of bone marrow stromal cell antigen-2 (BST2), a potential therapeutic target, via interactions with its promoter region. Our collective findings support a tumor suppressor role of CBX6 in breast cancer.	Immunohistochemical staining	CBX6 induced significant downregulation of bone marrow stromal cell antigen-2 (BST2), a potential therapeutic target, via interactions with its promoter region. Our collective findings support a tumor suppressor role of CBX6 in breast cancer.		PCR，Western blot，ChIP-seq			BST2		CBX6 induced significant downregulation of bone marrow stromal cell antigen-2 (BST2), a potential therapeutic target, via interactions with its promoter region. Our collective findings support a tumor suppressor role of CBX6 in breast cancer.	
30655376	chr14	68785051	68787051	ZFP36L1	In vitro reporter assay and 5'-azacitidine treatment confirmed the functional relevance of hyper-methylation of ZFP36L1 enhancer.	human	bone	High+Lowthroughput	Epigenomic profiling of myelofibrosis reveals widespread DNA methylation changes in enhancer elements and ZFP36L1 as a potential tumor suppressor gene that is epigenetically regulated			Myelofibrosis	bone marrow cell	E_01_0317	PCR，Western blot	In vitro reporter assay and 5'-azacitidine treatment confirmed the functional relevance of hyper-methylation of ZFP36L1 enhancer.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In vitro reporter assay and 5'-azacitidine treatment confirmed the functional relevance of hyper-methylation of ZFP36L1 enhancer.	Immunohistochemical staining	In vitro reporter assay and 5'-azacitidine treatment confirmed the functional relevance of hyper-methylation of ZFP36L1 enhancer.		PCR，Western blot			ZFP36L1		In vitro reporter assay and 5'-azacitidine treatment confirmed the functional relevance of hyper-methylation of ZFP36L1 enhancer.	
30654703	chr12	57092847	57094847	STAT6	The overexpression vectors of NEAT1 and ITCH, and siRNA targeting NEAT1, EZH2 (enhancer of zeste homolog 2) and STAT6 (signal transducer and activator of transcription 6) were transfected into CD4+T cells.	human	lymph	High+Lowthroughput	NEAT1 regulates Th2 cell development by targeting STAT6 for degradation				Th2 cell	E_01_0318	PCR, Western blot, chip SEQ, RNA immunoprecipitation, cell transfection	The overexpression vectors of NEAT1 and ITCH, and siRNA targeting NEAT1, EZH2 (enhancer of zeste homolog 2) and STAT6 (signal transducer and activator of transcription 6) were transfected into CD4+T cells.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The overexpression vectors of NEAT1 and ITCH, and siRNA targeting NEAT1, EZH2 (enhancer of zeste homolog 2) and STAT6 (signal transducer and activator of transcription 6) were transfected into CD4+T cells.	Immunohistochemical staining	The overexpression vectors of NEAT1 and ITCH, and siRNA targeting NEAT1, EZH2 (enhancer of zeste homolog 2) and STAT6 (signal transducer and activator of transcription 6) were transfected into CD4+T cells.		PCR，Western blot，ChIP-seq，RNA免疫沉淀，细胞转染				STAT6		The overexpression vectors of NEAT1 and ITCH, and siRNA targeting NEAT1, EZH2 (enhancer of zeste homolog 2) and STAT6 (signal transducer and activator of transcription 6) were transfected into CD4+T cells.
30653446	chr3	11269697	11271697	ATG7	Specifically, deletion of ATG7 in retinal vascular ECs of db/db mice and cultured HUVECs indicated a detrimental role of autophagy in hyperglycemia-induced endothelial dysfunction. Pretreatment with GANT61, a Hh pathway inhibitor, abolished the metformin-mediated downregulation of autophagy and endothelial protective action	human	kidney	High+Lowthroughput	Metformin alleviates hyperglycemia-induced endothelial impairment by downregulating autophagy via the Hedgehog pathway			diabetes	endothelial cell	E_01_0319	PCR	Specifically, deletion of ATG7 in retinal vascular ECs of db/db mice and cultured HUVECs indicated a detrimental role of autophagy in hyperglycemia-induced endothelial dysfunction. Pretreatment with GANT61, a Hh pathway inhibitor, abolished the metformin-mediated downregulation of autophagy and endothelial protective action	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Specifically, deletion of ATG7 in retinal vascular ECs of db/db mice and cultured HUVECs indicated a detrimental role of autophagy in hyperglycemia-induced endothelial dysfunction. Pretreatment with GANT61, a Hh pathway inhibitor, abolished the metformin-mediated downregulation of autophagy and endothelial protective action	Immunohistochemical staining	Specifically, deletion of ATG7 in retinal vascular ECs of db/db mice and cultured HUVECs indicated a detrimental role of autophagy in hyperglycemia-induced endothelial dysfunction. Pretreatment with GANT61, a Hh pathway inhibitor, abolished the metformin-mediated downregulation of autophagy and endothelial protective action		PCR			ATG7,BNIP3		Specifically, deletion of ATG7 in retinal vascular ECs of db/db mice and cultured HUVECs indicated a detrimental role of autophagy in hyperglycemia-induced endothelial dysfunction. Pretreatment with GANT61, a Hh pathway inhibitor, abolished the metformin-mediated downregulation of autophagy and endothelial protective action;Mechanistically, GLI1 knockdown-triggered autophagy was related to upregulation of BNIP3, which subsequently disrupted the association of BECN1/Beclin 1 and BCL2.	
30651971	chr9	117701165	117703165	TLR4	Furthermore, defciency of TLR4 receptor resulted in disappeared of the autophagy activation by treatment with IL-33 or EBSS (Fig. 6).	human	lymph	High+Lowthroughput	IL-33 ameliorates experimental colitis involving regulation of autophagy of macrophages in mice			colitis	macrophage	E_01_0320	Western blot, immunofluorescence staining	Furthermore, defciency of TLR4 receptor resulted in disappeared of the autophagy activation by treatment with IL-33 or EBSS (Fig. 6).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Furthermore, defciency of TLR4 receptor resulted in disappeared of the autophagy activation by treatment with IL-33 or EBSS (Fig. 6).	Immunohistochemical staining	Furthermore, defciency of TLR4 receptor resulted in disappeared of the autophagy activation by treatment with IL-33 or EBSS (Fig. 6).		Western blot，免疫荧光染色法				TLR4		Furthermore, defciency of TLR4 receptor resulted in disappeared of the autophagy activation by treatment with IL-33 or EBSS (Fig. 6).
30651597	chr3	69736856	69738856	MITF	Thus, MITF ensures the rapid resumption of transcription after completion of strand repair and maintains transcriptional output, which is indispensable for survival of the melanocytic lineage including melanoma in vitro and in vivo.	human	kidney	High+Lowthroughput	Lineage-specific control of TFIIH by MITF determines transcriptional homeostasis and DNA repair				Renal cell	E_01_0321	PCR, Western blot, chip SEQ, lentiviral infection, Clontech	Thus, MITF ensures the rapid resumption of transcription after completion of strand repair and maintains transcriptional output, which is indispensable for survival of the melanocytic lineage including melanoma in vitro and in vivo.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Thus, MITF ensures the rapid resumption of transcription after completion of strand repair and maintains transcriptional output, which is indispensable for survival of the melanocytic lineage including melanoma in vitro and in vivo.	Immunohistochemical staining	Thus, MITF ensures the rapid resumption of transcription after completion of strand repair and maintains transcriptional output, which is indispensable for survival of the melanocytic lineage including melanoma in vitro and in vivo.		PCR，Western blot，ChIP-seq，慢病毒感染，克隆技术			CDK7	MITF,MYC	Moreover, MITF controls cMYC implicated in general transcription by transactivation of far upstream binding protein 2 (FUBP2/KSHRP), which induces c-MYC pulse regulation through TFIIH, and experimental depletion of MITF results in consecutive loss of CDK7 in the TFIIH-CAK subcomplex	Thus, MITF ensures the rapid resumption of transcription after completion of strand repair and maintains transcriptional output, which is indispensable for survival of the melanocytic lineage including melanoma in vitro and in vivo.;Moreover, MITF controls cMYC implicated in general transcription by transactivation of far upstream binding protein 2 (FUBP2/KSHRP), which induces c-MYC pulse regulation through TFIIH, and experimental depletion of MITF results in consecutive loss of CDK7 in the TFIIH-CAK subcomplex
30649550	chr2	86437792	86439792	KDM3A	In the current study, using a FBSinducing model following serum starvation, we identified KDM3A, a demethylase of histone H3K9me1/2, as a positive regulator for hippo target genes.	human	lymph	High+Lowthroughput	Histone demethylase KDM3A is required for enhancer activation of hippo target genes in colorectal cancer			colorectal cancer 	HCT116 cell	E_01_0322	PCR，Western blot，ChIP-seq	In the current study, using a FBSinducing model following serum starvation, we identified KDM3A, a demethylase of histone H3K9me1/2, as a positive regulator for hippo target genes.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In the current study, using a FBSinducing model following serum starvation, we identified KDM3A, a demethylase of histone H3K9me1/2, as a positive regulator for hippo target genes.	Immunohistochemical staining	In the current study, using a FBSinducing model following serum starvation, we identified KDM3A, a demethylase of histone H3K9me1/2, as a positive regulator for hippo target genes.		PCR，Western blot，ChIP-seq			KDM3A		In the current study, using a FBSinducing model following serum starvation, we identified KDM3A, a demethylase of histone H3K9me1/2, as a positive regulator for hippo target genes.	
30644437	chr22	30922640	30924640	MORC2	Here, we found that MORC2 interacted with TE-III domain of C/EBPα, and the overexpression of MORC2 promoted wild-type C/EBPα sumoylation and its subsequent degradation, which didn’t significantly observe in mutant C/EBPα-K161R.	human	lymph	High+Lowthroughput	MORC2 regulates C/EBPα-mediated cell differentiation via sumoylation				C2C12 cell	E_01_0323	PCR，Western blot	Here, we found that MORC2 interacted with TE-III domain of C/EBPα, and the overexpression of MORC2 promoted wild-type C/EBPα sumoylation and its subsequent degradation, which didn’t significantly observe in mutant C/EBPα-K161R.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Here, we found that MORC2 interacted with TE-III domain of C/EBPα, and the overexpression of MORC2 promoted wild-type C/EBPα sumoylation and its subsequent degradation, which didn’t significantly observe in mutant C/EBPα-K161R.	Immunohistochemical staining	Here, we found that MORC2 interacted with TE-III domain of C/EBPα, and the overexpression of MORC2 promoted wild-type C/EBPα sumoylation and its subsequent degradation, which didn’t significantly observe in mutant C/EBPα-K161R.		PCR，Western blot			MORC2		Here, we found that MORC2 interacted with TE-III domain of C/EBPα, and the overexpression of MORC2 promoted wild-type C/EBPα sumoylation and its subsequent degradation, which didn’t significantly observe in mutant C/EBPα-K161R.	
30643424	chr17	42310283	42312283	STAT3	Zhang et al’s29 research showed that pancreatic cancer stem cells developed chemoresistance toward GEM through the NAPDH oxidase/ROS (Nox/ROS)/NF-κB/STAT 3 signaling pathway (STAT3).	human	tongue	High+Lowthroughput	Evodiamine inactivates NF-κB and potentiates the antitumor effects of gemcitabine on tongue cancer both in vitro and in vivo			tongue cancer	tongue cancer cell，Tca8113 cell	E_01_0324	PCR, sequencing technology	Zhang et al’s29 research showed that pancreatic cancer stem cells developed chemoresistance toward GEM through the NAPDH oxidase/ROS (Nox/ROS)/NF-κB/STAT 3 signaling pathway (STAT3).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Zhang et al’s29 research showed that pancreatic cancer stem cells developed chemoresistance toward GEM through the NAPDH oxidase/ROS (Nox/ROS)/NF-κB/STAT 3 signaling pathway (STAT3).	Immunohistochemical staining	Zhang et al’s29 research showed that pancreatic cancer stem cells developed chemoresistance toward GEM through the NAPDH oxidase/ROS (Nox/ROS)/NF-κB/STAT 3 signaling pathway (STAT3).		PCR，测序技术				STAT3		Zhang et al’s29 research showed that pancreatic cancer stem cells developed chemoresistance toward GEM through the NAPDH oxidase/ROS (Nox/ROS)/NF-κB/STAT 3 signaling pathway (STAT3).
30642336	chr18	76976527	76978527	MBP	ScFv antibody proteins without any tag and with different fusion tags such as 6xHis, GST and MBP, were expressed in E. coli in diferent growth condition.	human	lymph	High+Lowthroughput	Evaluation of scFv protein recovery from E. coli by in vitro refolding and mild solubilization process					E_01_0325	In vitro refolding and gentle lysis method	ScFv antibody proteins without any tag and with different fusion tags such as 6xHis, GST and MBP, were expressed in E. coli in diferent growth condition.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		ScFv antibody proteins without any tag and with different fusion tags such as 6xHis, GST and MBP, were expressed in E. coli in diferent growth condition.	Immunohistochemical staining	ScFv antibody proteins without any tag and with different fusion tags such as 6xHis, GST and MBP, were expressed in E. coli in diferent growth condition.		体外重折叠和温和溶解法			MBP		ScFv antibody proteins without any tag and with different fusion tags such as 6xHis, GST and MBP, were expressed in E. coli in diferent growth condition.	
30642251	chr17	7658541	7660541	TP53	If gene symbols are used that do not occur in the downloaded annotation data, as can be the case if an invalid or outdated symbol is used (e.g., P53 instead of the official gene symbol TP53), GOPHER will issue a warning and report a list of unmappable symbols that can be used to search for the current correct symbols.	human	adipose	High+Lowthroughput	GOPHER: Generator Of Probes for capture Hi-C Experiments at high Resolution				IWAT cell	E_01_0326	Hi-C，PCR，Western blot，ChIP-seq	If gene symbols are used that do not occur in the downloaded annotation data, as can be the case if an invalid or outdated symbol is used (e.g., P53 instead of the official gene symbol TP53), GOPHER will issue a warning and report a list of unmappable symbols that can be used to search for the current correct symbols.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		If gene symbols are used that do not occur in the downloaded annotation data, as can be the case if an invalid or outdated symbol is used (e.g., P53 instead of the official gene symbol TP53), GOPHER will issue a warning and report a list of unmappable symbols that can be used to search for the current correct symbols.	Immunohistochemical staining	If gene symbols are used that do not occur in the downloaded annotation data, as can be the case if an invalid or outdated symbol is used (e.g., P53 instead of the official gene symbol TP53), GOPHER will issue a warning and report a list of unmappable symbols that can be used to search for the current correct symbols.		Hi-C，PCR，Western blot，ChIP-seq				TP53		If gene symbols are used that do not occur in the downloaded annotation data, as can be the case if an invalid or outdated symbol is used (e.g., P53 instead of the official gene symbol TP53), GOPHER will issue a warning and report a list of unmappable symbols that can be used to search for the current correct symbols.
30639323	chr16	86507633	86509633	FOXF1	In contrast to ACDMPV caused by loss-of-function (LoF) of FOXF1 (MIM: 601089),20,21 the molecular etiology of AcDys and CAD is largely unknown.	human	Lung	High+Lowthroughput	Complex Compound Inheritance of Lethal Lung Developmental Disorders Due to Disruption of the TBX-FGF Pathway			Pulmonary hypoplasia	IMR-90 ，NHLF cell	E_01_0327	PCR, chip SEQ, variant enrichment analysis, bioinformatics prediction	In contrast to ACDMPV caused by loss-of-function (LoF) of FOXF1 (MIM: 601089),20,21 the molecular etiology of AcDys and CAD is largely unknown.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In contrast to ACDMPV caused by loss-of-function (LoF) of FOXF1 (MIM: 601089),20,21 the molecular etiology of AcDys and CAD is largely unknown.	Immunohistochemical staining	In contrast to ACDMPV caused by loss-of-function (LoF) of FOXF1 (MIM: 601089),20,21 the molecular etiology of AcDys and CAD is largely unknown.		PCR，ChIP-seq，变体富集分析，生物信息学预测				FOXF1		In contrast to ACDMPV caused by loss-of-function (LoF) of FOXF1 (MIM: 601089),20,21 the molecular etiology of AcDys and CAD is largely unknown.
30632221	chr8	127732390	127734390	MYC	MYC is known to cause increased expression of EZH2 in prostate cancer, both directly and through downregulation of miR-26a and miR-26b, which are known to inhibit EZH2.5	human	brain	High+Lowthroughput	Inhibition of enhancer of zest homologue 2 is a potential therapeutic target for high-MYC medulloblastoma			Medulloblastoma		E_01_0328	PCR，Western blot	MYC is known to cause increased expression of EZH2 in prostate cancer, both directly and through downregulation of miR-26a and miR-26b, which are known to inhibit EZH2.5	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		MYC is known to cause increased expression of EZH2 in prostate cancer, both directly and through downregulation of miR-26a and miR-26b, which are known to inhibit EZH2.5	Immunohistochemical staining	MYC is known to cause increased expression of EZH2 in prostate cancer, both directly and through downregulation of miR-26a and miR-26b, which are known to inhibit EZH2.5		PCR，Western blot				MYC,EZH2		MYC is known to cause increased expression of EZH2 in prostate cancer, both directly and through downregulation of miR-26a and miR-26b, which are known to inhibit EZH2.5;MYC is known to cause increased expression of EZH2 in prostate cancer, both directly and through downregulation of miR-26a and miR-26b, which are known to inhibit EZH2.5
30631044	chr13	27957842	27959842	CDX2	Caudal-related homeobox transcription factor 2 (CDX2), an intestine-specific nuclear transcription factor, has been strongly implicated in the tumourigenesis of various human cancers.	human	lymph	High+Lowthroughput	CDX2 inhibits the proliferation and tumor formation of colon cancer cells by suppressing Wnt/β-catenin signaling via transactivation of GSK-3β and Axin2 expression			Colon cancer	colon cancer cell	E_01_0329	Immunohistochemistry, PCR, Western blot, chip seq	Caudal-related homeobox transcription factor 2 (CDX2), an intestine-specific nuclear transcription factor, has been strongly implicated in the tumourigenesis of various human cancers.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Caudal-related homeobox transcription factor 2 (CDX2), an intestine-specific nuclear transcription factor, has been strongly implicated in the tumourigenesis of various human cancers.	Immunohistochemical staining	Caudal-related homeobox transcription factor 2 (CDX2), an intestine-specific nuclear transcription factor, has been strongly implicated in the tumourigenesis of various human cancers.		免疫组化检测，PCR，Western blot，ChIP-seq				CDX2		Caudal-related homeobox transcription factor 2 (CDX2), an intestine-specific nuclear transcription factor, has been strongly implicated in the tumourigenesis of various human cancers.
30628724	chr7	148804584	148806584	EZH2	Polycomb group proteins are important epigenetic regulators for cell proliferation and differentiation, organ development, as well as initiation and progression of lethal diseases, including cancer. Upregulated Polycomb group proteins, including Enhancer of zeste homolog 2 (EZH2), promote proliferation, migration, invasion and metastasis of cancer cells, as well as self-renewal of cancer stem cells.	human	prostate	High+Lowthroughput	Polycomb group proteins EZH2 and EED directly regulate androgen receptor in advanced prostate cancer			prostatic cancer	Cancer Stem Cell	E_01_0330	Immunoprecipitation, RNA SEQ, PCR, Western blot	Polycomb group proteins are important epigenetic regulators for cell proliferation and differentiation, organ development, as well as initiation and progression of lethal diseases, including cancer. Upregulated Polycomb group proteins, including Enhancer of zeste homolog 2 (EZH2), promote proliferation, migration, invasion and metastasis of cancer cells, as well as self-renewal of cancer stem cells.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Polycomb group proteins are important epigenetic regulators for cell proliferation and differentiation, organ development, as well as initiation and progression of lethal diseases, including cancer. Upregulated Polycomb group proteins, including Enhancer of zeste homolog 2 (EZH2), promote proliferation, migration, invasion and metastasis of cancer cells, as well as self-renewal of cancer stem cells.	Immunohistochemical staining	Polycomb group proteins are important epigenetic regulators for cell proliferation and differentiation, organ development, as well as initiation and progression of lethal diseases, including cancer. Upregulated Polycomb group proteins, including Enhancer of zeste homolog 2 (EZH2), promote proliferation, migration, invasion and metastasis of cancer cells, as well as self-renewal of cancer stem cells.		免疫沉淀法，RNA-seq，PCR，Western blot				EZH2		Polycomb group proteins are important epigenetic regulators for cell proliferation and differentiation, organ development, as well as initiation and progression of lethal diseases, including cancer. Upregulated Polycomb group proteins, including Enhancer of zeste homolog 2 (EZH2), promote proliferation, migration, invasion and metastasis of cancer cells, as well as self-renewal of cancer stem cells.
30628655	chr11	1155242	1157242	MUC5AC	P300 decreases the protein expression level of MUC5AC. The empty vector, untransfected control, the P300 expression plasmid and P300 siRNA, together with their control plasmids, were transfected into A549 cells. Immunofluorescence was then performed to detect the protein expression of MUC5AC in each group.	human	Lung	High+Lowthroughput	Characterization of the human mucin 5AC promoter and its regulation by the histone acetyltransferase P300			asthma	A549 cell	E_01_0331	Transient transfection, luciferase assay, immunoprecipitation, PCR, Western blot	P300 decreases the protein expression level of MUC5AC. The empty vector, untransfected control, the P300 expression plasmid and P300 siRNA, together with their control plasmids, were transfected into A549 cells. Immunofluorescence was then performed to detect the protein expression of MUC5AC in each group.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		P300 decreases the protein expression level of MUC5AC. The empty vector, untransfected control, the P300 expression plasmid and P300 siRNA, together with their control plasmids, were transfected into A549 cells. Immunofluorescence was then performed to detect the protein expression of MUC5AC in each group.	Immunohistochemical staining	P300 decreases the protein expression level of MUC5AC. The empty vector, untransfected control, the P300 expression plasmid and P300 siRNA, together with their control plasmids, were transfected into A549 cells. Immunofluorescence was then performed to detect the protein expression of MUC5AC in each group.		瞬时转染，荧光素酶检测，免疫沉淀法，PCR，Western blot			MUC5AC		P300 decreases the protein expression level of MUC5AC. The empty vector, untransfected control, the P300 expression plasmid and P300 siRNA, together with their control plasmids, were transfected into A549 cells. Immunofluorescence was then performed to detect the protein expression of MUC5AC in each group.	
30626398	chr17	48604528	48606528	HOXB7	Finally, we performed both technical and experimental bisulfte pyrosequencing validations of three of the CpGs found at the HOXB7 (cg07547765), SOCS3 (cg11047325) and ZFPM2 (cg03830443) genes (Fig. 5, see Additional fle 13: Table S7 for full data).	human	blood	High+Lowthroughput	Longitudinal genome-wide DNA methylation analysis uncovers persistent early-life DNA methylation changes					E_01_0332	Bisulfite pyrosequencing	Finally, we performed both technical and experimental bisulfte pyrosequencing validations of three of the CpGs found at the HOXB7 (cg07547765), SOCS3 (cg11047325) and ZFPM2 (cg03830443) genes (Fig. 5, see Additional fle 13: Table S7 for full data).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Finally, we performed both technical and experimental bisulfte pyrosequencing validations of three of the CpGs found at the HOXB7 (cg07547765), SOCS3 (cg11047325) and ZFPM2 (cg03830443) genes (Fig. 5, see Additional fle 13: Table S7 for full data).	Immunohistochemical staining	Finally, we performed both technical and experimental bisulfte pyrosequencing validations of three of the CpGs found at the HOXB7 (cg07547765), SOCS3 (cg11047325) and ZFPM2 (cg03830443) genes (Fig. 5, see Additional fle 13: Table S7 for full data).		亚硫酸氢盐焦磷酸测序				HOXB7		Finally, we performed both technical and experimental bisulfte pyrosequencing validations of three of the CpGs found at the HOXB7 (cg07547765), SOCS3 (cg11047325) and ZFPM2 (cg03830443) genes (Fig. 5, see Additional fle 13: Table S7 for full data).
30622230	chr12	95513693	95515693	USP44	Here, we found that enhancer of zeste homolog 2 (EZH2), a histone H3 lysine 27 methyltransferase, is regulated by USP44.	human	prostate	High+Lowthroughput	USP44 Promotes the Tumorigenesis of Prostate Cancer Cells through EZH2 Protein Stabilization			prostatic cancer	prostate cancer cell	E_01_0333	PCR, immunofluorescence staining	Here, we found that enhancer of zeste homolog 2 (EZH2), a histone H3 lysine 27 methyltransferase, is regulated by USP44.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Here, we found that enhancer of zeste homolog 2 (EZH2), a histone H3 lysine 27 methyltransferase, is regulated by USP44.	Immunohistochemical staining	Here, we found that enhancer of zeste homolog 2 (EZH2), a histone H3 lysine 27 methyltransferase, is regulated by USP44.		PCR，免疫荧光染色法			USP44		Here, we found that enhancer of zeste homolog 2 (EZH2), a histone H3 lysine 27 methyltransferase, is regulated by USP44.	
30621608	chr3	190319460	190321460	CLDN16	This rare disease is caused by mutations in CLDN16 that encodes claudin-16, a tight-junction protein involved in paracellular reabsorption of magnesium and calcium in the renal tubule. Most of these variants are located in exons and have been classified as missense mutations.	human	kidney	High+Lowthroughput	Exonic CLDN16 mutations associated with familial hypomagnesemia with hypercalciuria and nephrocalcinosis can induce deleterious mRNA alterations			Familial hypomagnesemia, hypercalciuria, and nephrocalcinosis	COS7 cells	E_01_0334	PCR	This rare disease is caused by mutations in CLDN16 that encodes claudin-16, a tight-junction protein involved in paracellular reabsorption of magnesium and calcium in the renal tubule. Most of these variants are located in exons and have been classified as missense mutations.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		This rare disease is caused by mutations in CLDN16 that encodes claudin-16, a tight-junction protein involved in paracellular reabsorption of magnesium and calcium in the renal tubule. Most of these variants are located in exons and have been classified as missense mutations.	Immunohistochemical staining	This rare disease is caused by mutations in CLDN16 that encodes claudin-16, a tight-junction protein involved in paracellular reabsorption of magnesium and calcium in the renal tubule. Most of these variants are located in exons and have been classified as missense mutations.		PCR			CLDN16		This rare disease is caused by mutations in CLDN16 that encodes claudin-16, a tight-junction protein involved in paracellular reabsorption of magnesium and calcium in the renal tubule. Most of these variants are located in exons and have been classified as missense mutations.	
30620726	chr3	128476298	128478298	GATA2	GATA-binding protein 2 (GATA2) mutations cause GATA-2 deficiency syndrome involving immunodeficiency, myelodysplastic syndrome, and acute myeloid leukemia.	human	blood	High+Lowthroughput	Single-nucleotide human disease mutation inactivates a blood-regenerative GATA2 enhancer			Acute myeloid leukemia	progenitor cell	E_01_0335	PCR，ChIP-seq	GATA-binding protein 2 (GATA2) mutations cause GATA-2 deficiency syndrome involving immunodeficiency, myelodysplastic syndrome, and acute myeloid leukemia.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		GATA-binding protein 2 (GATA2) mutations cause GATA-2 deficiency syndrome involving immunodeficiency, myelodysplastic syndrome, and acute myeloid leukemia.	Immunohistochemical staining	GATA-binding protein 2 (GATA2) mutations cause GATA-2 deficiency syndrome involving immunodeficiency, myelodysplastic syndrome, and acute myeloid leukemia.		PCR，ChIP-seq				GATA2		GATA-binding protein 2 (GATA2) mutations cause GATA-2 deficiency syndrome involving immunodeficiency, myelodysplastic syndrome, and acute myeloid leukemia.
30619471	chr17	42310619	42312619	STAT3	As a proof of concept of a possible functional relevance of this observation, we experimentally verified that the expression levels of a circRNA derived from an MS-associated locus, i.e., hsa_circ_0043813 from the STAT3 gene, can be modulated by the three genotypes at the disease-associated SNP.	human	nerve	High+Lowthroughput	Interpreting Non-coding Genetic Variation in Multiple Sclerosis Genome-Wide Associated Regions			Multiple sclerosis	SH-SY5Y， Jurkat cell	E_01_0336	RNA sequencing, PCR	As a proof of concept of a possible functional relevance of this observation, we experimentally verified that the expression levels of a circRNA derived from an MS-associated locus, i.e., hsa_circ_0043813 from the STAT3 gene, can be modulated by the three genotypes at the disease-associated SNP.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		As a proof of concept of a possible functional relevance of this observation, we experimentally verified that the expression levels of a circRNA derived from an MS-associated locus, i.e., hsa_circ_0043813 from the STAT3 gene, can be modulated by the three genotypes at the disease-associated SNP.	Immunohistochemical staining	As a proof of concept of a possible functional relevance of this observation, we experimentally verified that the expression levels of a circRNA derived from an MS-associated locus, i.e., hsa_circ_0043813 from the STAT3 gene, can be modulated by the three genotypes at the disease-associated SNP.		RNA测序，PCR				STAT3		As a proof of concept of a possible functional relevance of this observation, we experimentally verified that the expression levels of a circRNA derived from an MS-associated locus, i.e., hsa_circ_0043813 from the STAT3 gene, can be modulated by the three genotypes at the disease-associated SNP.
30618413	chr4	153681347	153683347	TLR2	Lipopolysaccharide-stimulated RWPE-1 cells expressed higher levels of TLR2, TLR10, high mobility group box 1 (HMGB1), phospho-nuclear factor kappa-light-chain-enhancer of activated B-cells P65 (phospho-NF-κB P65)	human	prostate	High+Lowthroughput	Toll-like receptor 10 (TLR10) exhibits suppressive effects on inflammation of prostate epithelial cells			prostatitis	prostate epithelial cell	E_01_0337	PCR，Western blot，ChIP-seq	Lipopolysaccharide-stimulated RWPE-1 cells expressed higher levels of TLR2, TLR10, high mobility group box 1 (HMGB1), phospho-nuclear factor kappa-light-chain-enhancer of activated B-cells P65 (phospho-NF-κB P65)	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Lipopolysaccharide-stimulated RWPE-1 cells expressed higher levels of TLR2, TLR10, high mobility group box 1 (HMGB1), phospho-nuclear factor kappa-light-chain-enhancer of activated B-cells P65 (phospho-NF-κB P65)	Immunohistochemical staining	Lipopolysaccharide-stimulated RWPE-1 cells expressed higher levels of TLR2, TLR10, high mobility group box 1 (HMGB1), phospho-nuclear factor kappa-light-chain-enhancer of activated B-cells P65 (phospho-NF-κB P65)		PCR，Western blot，ChIP-seq				TLR2		Lipopolysaccharide-stimulated RWPE-1 cells expressed higher levels of TLR2, TLR10, high mobility group box 1 (HMGB1), phospho-nuclear factor kappa-light-chain-enhancer of activated B-cells P65 (phospho-NF-κB P65)
30610059	chr10	70594223	70596223	PRF1	H3K9me3 was enriched in the promoters of GZMB, PRF1, FASLG, and IFNG in quiescent T cells.	human	colorectum	High+Lowthroughput	SUV39H1 Represses the Expression of Cytotoxic T-Lymphocyte Effector Genes to Promote Colon Tumor Immune Evasion			Colon neoplasms	T cell	E_01_0338	Immunohistochemical staining, flow cytometry, PCR, Western blot, chip seq	H3K9me3 was enriched in the promoters of GZMB, PRF1, FASLG, and IFNG in quiescent T cells.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		H3K9me3 was enriched in the promoters of GZMB, PRF1, FASLG, and IFNG in quiescent T cells.	Immunohistochemical staining	H3K9me3 was enriched in the promoters of GZMB, PRF1, FASLG, and IFNG in quiescent T cells.		免疫组织化学染色法，流式细胞术，PCR，Western blot，ChIP-seq				ZNF395		H3K9me3 was enriched in the promoters of GZMB, PRF1, FASLG, and IFNG in quiescent T cells.
30606720	chr3	181709342	181711342	SOX2	In several triple-negative breast cancer (TNBC) models, Six2 enhanced the expression of genes associated with embryonic stem cell programs. Six2 directly bound the Sox2 Srr2 enhancer	human	breast	High+Lowthroughput	SIX2 Mediates Late-Stage Metastasis via Direct Regulation of SOX2 and Induction of a Cancer Stem Cell Program			mammary cancer	Cancer Stem Cell	E_01_0339	PCR，Western blot，RNA-seq	In several triple-negative breast cancer (TNBC) models, Six2 enhanced the expression of genes associated with embryonic stem cell programs. Six2 directly bound the Sox2 Srr2 enhancer	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In several triple-negative breast cancer (TNBC) models, Six2 enhanced the expression of genes associated with embryonic stem cell programs. Six2 directly bound the Sox2 Srr2 enhancer	Immunohistochemical staining	In several triple-negative breast cancer (TNBC) models, Six2 enhanced the expression of genes associated with embryonic stem cell programs. Six2 directly bound the Sox2 Srr2 enhancer		PCR，Western blot，RNA-seq				SOX2		In several triple-negative breast cancer (TNBC) models, Six2 enhanced the expression of genes associated with embryonic stem cell programs. Six2 directly bound the Sox2 Srr2 enhancer
30605688	chr2	69455371	69457371	AAK1	Here, using a gain-of-function screen of the human kinome, we report that the AP2 associated kinase 1 (AAK1), a known CME enhancer	human		High+Lowthroughput	WNT Activates the AAK1 Kinase to Promote Clathrin-Mediated Endocytosis of LRP6 and Establish a Negative Feedback Loop				HEK293T	E_01_0340	PCR，Western blot	Here, using a gain-of-function screen of the human kinome, we report that the AP2 associated kinase 1 (AAK1), a known CME enhancer	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Here, using a gain-of-function screen of the human kinome, we report that the AP2 associated kinase 1 (AAK1), a known CME enhancer	Immunohistochemical staining	Here, using a gain-of-function screen of the human kinome, we report that the AP2 associated kinase 1 (AAK1), a known CME enhancer		PCR，Western blot			AAK1		Here, using a gain-of-function screen of the human kinome, we report that the AP2 associated kinase 1 (AAK1), a known CME enhancer	
30603559	chr7	148804645	148806645	EZH2	Western blot determined the expression levels of enhancer of zeste homolog 2 (EZH2)	human	Hair	High+Lowthroughput	MiR-214 Regulates the Human Hair Follicle Stem Cell Proliferation and Differentiation by Targeting EZH2 and Wnt/β-Catenin Signaling Way In Vitro				Hair Follicle Stem Cell	E_01_0341	Immunofluorescence, DAPI staining, PCR	Western blot determined the expression levels of enhancer of zeste homolog 2 (EZH2)	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Western blot determined the expression levels of enhancer of zeste homolog 2 (EZH2)	Immunohistochemical staining	Western blot determined the expression levels of enhancer of zeste homolog 2 (EZH2)		免疫荧光法，DAPI染色，PCR				EZH2		Western blot determined the expression levels of enhancer of zeste homolog 2 (EZH2)
30596070	chr19	10130616	10132616	DNMT1	Our previous studies showed that HOTAIR modulated HOXA1 DNA methylation by reducing DNMT1 and DNMT3b expression in drug-resistant small cell lung cancer (SCLC).	human	Lung	High+Lowthroughput	H3K27me3 induces multidrug resistance in small cell lung cancer by affecting HOXA1 DNA methylation via regulation of the lncRNA HOTAIR			lung cancer	NSCLC cell	E_01_0342	Flow cytometry, cell transfection techniques, immunohistochemical staining, PCR, Western blot, chip seq	Our previous studies showed that HOTAIR modulated HOXA1 DNA methylation by reducing DNMT1 and DNMT3b expression in drug-resistant small cell lung cancer (SCLC).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Our previous studies showed that HOTAIR modulated HOXA1 DNA methylation by reducing DNMT1 and DNMT3b expression in drug-resistant small cell lung cancer (SCLC).	Immunohistochemical staining	Our previous studies showed that HOTAIR modulated HOXA1 DNA methylation by reducing DNMT1 and DNMT3b expression in drug-resistant small cell lung cancer (SCLC).		流式细胞术，细胞转染技术，免疫组织化学染色，PCR，Western blot，ChIP-seq				DNMT1		Our previous studies showed that HOTAIR modulated HOXA1 DNA methylation by reducing DNMT1 and DNMT3b expression in drug-resistant small cell lung cancer (SCLC).
30594152	chr22	37967907	37969907	SOX10	Two inhibitory activity regions were found in the - 1409 bp to - 1381 bp and - 1196 bp to - 1124 bp fragments, which might be bound to the GATA or SOX10 transcription factors as predicted by the JASPAR software.	human	nerve	High+Lowthroughput	Characterization and functional analyses of the human HTR1A gene: 5' regulatory region modulates gene expression in vitro			Schizophrenia	SK-N-SH cell	E_01_0343	Cell transfection	Two inhibitory activity regions were found in the - 1409 bp to - 1381 bp and - 1196 bp to - 1124 bp fragments, which might be bound to the GATA or SOX10 transcription factors as predicted by the JASPAR software.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Two inhibitory activity regions were found in the - 1409 bp to - 1381 bp and - 1196 bp to - 1124 bp fragments, which might be bound to the GATA or SOX10 transcription factors as predicted by the JASPAR software.	Immunohistochemical staining	Two inhibitory activity regions were found in the - 1409 bp to - 1381 bp and - 1196 bp to - 1124 bp fragments, which might be bound to the GATA or SOX10 transcription factors as predicted by the JASPAR software.		细胞转染				SOX10		Two inhibitory activity regions were found in the - 1409 bp to - 1381 bp and - 1196 bp to - 1124 bp fragments, which might be bound to the GATA or SOX10 transcription factors as predicted by the JASPAR software.
30590588	chr2	144361789	144363789	ZEB2	The spatiotemporal regulation of ZEB2 is complex and involves various regulatory elements, including alternative promoters and specific enhancers that contribute to the multifactorial function of this transcription factor	human	nerve	High+Lowthroughput	Functional characterization of the ZEB2 regulatory landscape				neural crest cell	E_01_0344	Hi-C，PCR，Western blot，ChIP-seq	The spatiotemporal regulation of ZEB2 is complex and involves various regulatory elements, including alternative promoters and specific enhancers that contribute to the multifactorial function of this transcription factor	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The spatiotemporal regulation of ZEB2 is complex and involves various regulatory elements, including alternative promoters and specific enhancers that contribute to the multifactorial function of this transcription factor	Immunohistochemical staining	The spatiotemporal regulation of ZEB2 is complex and involves various regulatory elements, including alternative promoters and specific enhancers that contribute to the multifactorial function of this transcription factor		Hi-C，PCR，Western blot，ChIP-seq				ZEB2		The spatiotemporal regulation of ZEB2 is complex and involves various regulatory elements, including alternative promoters and specific enhancers that contribute to the multifactorial function of this transcription factor
30590042	chr20	33672756	33674756	E2F1	We found that the transcription factor E2F1 and its heterodimerization partner DP1 represent a dependency in multiple myeloma cells.	human	bone	High+Lowthroughput	Non-overlapping Control of Transcriptome by Promoter- and Super-Enhancer-Associated Dependencies in Multiple Myeloma			Multiple myeloma	multiple myeloma cell	E_01_0345	PCR，Western blot，ChIP-seq	We found that the transcription factor E2F1 and its heterodimerization partner DP1 represent a dependency in multiple myeloma cells.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We found that the transcription factor E2F1 and its heterodimerization partner DP1 represent a dependency in multiple myeloma cells.	Immunohistochemical staining	We found that the transcription factor E2F1 and its heterodimerization partner DP1 represent a dependency in multiple myeloma cells.		PCR，Western blot，ChIP-seq				E2F1		We found that the transcription factor E2F1 and its heterodimerization partner DP1 represent a dependency in multiple myeloma cells.
30563971	chr3	189628751	189630751	TP63	We further identified that the TP63 gene was repressed by this precision-guided machinery of TRPS1-CHD4/NuRD(MTA2) complex, which decommissions its enhancer leading to a decrease in ΔNp63 and enhancing the metastatic ability of breast cancer cells.	human	breast	High+Lowthroughput	Atypical GATA transcription factor TRPS1 represses gene expression by recruiting CHD4/NuRD(MTA2) and suppresses cell migration and invasion by repressing TP63 expression			mammary cancer	T47D cell	E_01_0346	PCR，Western blot，ChIP-seq	We further identified that the TP63 gene was repressed by this precision-guided machinery of TRPS1-CHD4/NuRD(MTA2) complex, which decommissions its enhancer leading to a decrease in ΔNp63 and enhancing the metastatic ability of breast cancer cells.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We further identified that the TP63 gene was repressed by this precision-guided machinery of TRPS1-CHD4/NuRD(MTA2) complex, which decommissions its enhancer leading to a decrease in ΔNp63 and enhancing the metastatic ability of breast cancer cells.	Immunohistochemical staining	We further identified that the TP63 gene was repressed by this precision-guided machinery of TRPS1-CHD4/NuRD(MTA2) complex, which decommissions its enhancer leading to a decrease in ΔNp63 and enhancing the metastatic ability of breast cancer cells.		PCR，Western blot，ChIP-seq				TP63		We further identified that the TP63 gene was repressed by this precision-guided machinery of TRPS1-CHD4/NuRD(MTA2) complex, which decommissions its enhancer leading to a decrease in ΔNp63 and enhancing the metastatic ability of breast cancer cells.
30559760	chr7	151553558	151555558	PRKAG2	we analyzed a whole genome case-control expression profiles in human CKD to investigate whether the susceptibility gene PRKAG2 is differently expressed in CKD cases compared with control samples.	human	kidney	High+Lowthroughput	Functional Prediction of Chronic Kidney Disease Susceptibility Gene PRKAG2 by Comprehensively Bioinformatics Analysis			Chronic kidney disease	Caco2 cell	E_01_0347	ChIP-seq	we analyzed a whole genome case-control expression profiles in human CKD to investigate whether the susceptibility gene PRKAG2 is differently expressed in CKD cases compared with control samples.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		we analyzed a whole genome case-control expression profiles in human CKD to investigate whether the susceptibility gene PRKAG2 is differently expressed in CKD cases compared with control samples.	Immunohistochemical staining	we analyzed a whole genome case-control expression profiles in human CKD to investigate whether the susceptibility gene PRKAG2 is differently expressed in CKD cases compared with control samples.		ChIP-seq			PRKAG2		we analyzed a whole genome case-control expression profiles in human CKD to investigate whether the susceptibility gene PRKAG2 is differently expressed in CKD cases compared with control samples.	
30552336	chr17	72118256	72120256	SOX9	In a recent independent but complementary study on Sox9 regulation in the mouse by Gonen and colleagues, an orthologous mouse enhancer (Enh13) showing 80% sequence conservation with eSR-A was identified13 .	human	epithelial	High+Lowthroughput	Human sex reversal is caused by duplication or deletion of core enhancers upstream of SOX9				COS7 cells	E_01_0348	PCR，ChIP-seq	In a recent independent but complementary study on Sox9 regulation in the mouse by Gonen and colleagues, an orthologous mouse enhancer (Enh13) showing 80% sequence conservation with eSR-A was identified13 .	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In a recent independent but complementary study on Sox9 regulation in the mouse by Gonen and colleagues, an orthologous mouse enhancer (Enh13) showing 80% sequence conservation with eSR-A was identified13 .	Immunohistochemical staining	In a recent independent but complementary study on Sox9 regulation in the mouse by Gonen and colleagues, an orthologous mouse enhancer (Enh13) showing 80% sequence conservation with eSR-A was identified13 .		PCR，ChIP-seq				SOX9		In a recent independent but complementary study on Sox9 regulation in the mouse by Gonen and colleagues, an orthologous mouse enhancer (Enh13) showing 80% sequence conservation with eSR-A was identified13 .
30544224	chr14	73133812	73135812	PSEN1	Thirty-four unique mutations in patients with HS have been found in three genes encoding the γ-secretase complex: nicastrin (NCSTN), presenilin 1 (PSEN1), presenilin enhancer 2 (PSENEN) and in POGLUT1, an endoplasmic reticulum O-glucosyltransferase involved in Notch signaling.	human	lymph	High+Lowthroughput	Analysis of hidradenitis suppurativa-linked mutations in four genes and the effects of PSEN1-P242LfsX11 on cytokine and chemokine expression in macrophages			Hidradenitis suppurativa	THP-1 cells	E_01_0349	PCR，Western blot	Thirty-four unique mutations in patients with HS have been found in three genes encoding the γ-secretase complex: nicastrin (NCSTN), presenilin 1 (PSEN1), presenilin enhancer 2 (PSENEN) and in POGLUT1, an endoplasmic reticulum O-glucosyltransferase involved in Notch signaling.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Thirty-four unique mutations in patients with HS have been found in three genes encoding the γ-secretase complex: nicastrin (NCSTN), presenilin 1 (PSEN1), presenilin enhancer 2 (PSENEN) and in POGLUT1, an endoplasmic reticulum O-glucosyltransferase involved in Notch signaling.	Immunohistochemical staining	Thirty-four unique mutations in patients with HS have been found in three genes encoding the γ-secretase complex: nicastrin (NCSTN), presenilin 1 (PSEN1), presenilin enhancer 2 (PSENEN) and in POGLUT1, an endoplasmic reticulum O-glucosyltransferase involved in Notch signaling.		PCR，Western blot				PSEN1		Thirty-four unique mutations in patients with HS have been found in three genes encoding the γ-secretase complex: nicastrin (NCSTN), presenilin 1 (PSEN1), presenilin enhancer 2 (PSENEN) and in POGLUT1, an endoplasmic reticulum O-glucosyltransferase involved in Notch signaling.
30538561	chr7	100799729	100801729	EPHB4	We also found that Notch signaling pathway was abnormally activated and treatment of Notch signaling ligand human Jagged1 peptide downregulated EPHB2 and upregulated EPHB4 in the SW620 cells, as well as promoted the chromatin modification protein Jumonji domain-containing protein-3 (JMJD3) cytonuclear trans-localization with the NICD, which indicated that NICD brought JMJD3 to the EPHB4 enhancer region to decrease the H3K27me3 level.	human	colorectum	High+Lowthroughput	Notch signaling promotes serrated neoplasia pathway in colorectal cancer through epigenetic modification of EPHB2 and EPHB4			colorectal cancer 	SW620 cell	E_01_0350	PCR, Western blot, chip SEQ, immunoblotting	We also found that Notch signaling pathway was abnormally activated and treatment of Notch signaling ligand human Jagged1 peptide downregulated EPHB2 and upregulated EPHB4 in the SW620 cells, as well as promoted the chromatin modification protein Jumonji domain-containing protein-3 (JMJD3) cytonuclear trans-localization with the NICD, which indicated that NICD brought JMJD3 to the EPHB4 enhancer region to decrease the H3K27me3 level.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We also found that Notch signaling pathway was abnormally activated and treatment of Notch signaling ligand human Jagged1 peptide downregulated EPHB2 and upregulated EPHB4 in the SW620 cells, as well as promoted the chromatin modification protein Jumonji domain-containing protein-3 (JMJD3) cytonuclear trans-localization with the NICD, which indicated that NICD brought JMJD3 to the EPHB4 enhancer region to decrease the H3K27me3 level.	Immunohistochemical staining	We also found that Notch signaling pathway was abnormally activated and treatment of Notch signaling ligand human Jagged1 peptide downregulated EPHB2 and upregulated EPHB4 in the SW620 cells, as well as promoted the chromatin modification protein Jumonji domain-containing protein-3 (JMJD3) cytonuclear trans-localization with the NICD, which indicated that NICD brought JMJD3 to the EPHB4 enhancer region to decrease the H3K27me3 level.		PCR，Western blot，ChIP-seq，免疫印迹法			EPHB4		We also found that Notch signaling pathway was abnormally activated and treatment of Notch signaling ligand human Jagged1 peptide downregulated EPHB2 and upregulated EPHB4 in the SW620 cells, as well as promoted the chromatin modification protein Jumonji domain-containing protein-3 (JMJD3) cytonuclear trans-localization with the NICD, which indicated that NICD brought JMJD3 to the EPHB4 enhancer region to decrease the H3K27me3 level.	
30531861	chr4	121814031	121816031	CCNA2	Here, we identify a hepatocellular carcinoma (HCC) subgroup exhibiting cyclin activation through various mechanisms including hepatitis B virus (HBV) and adeno-associated virus type 2 (AAV2) insertions, enhancer hijacking and recurrent CCNA2 fusions.	human	liver	High+Lowthroughput	Cyclin A2/E1 activation defines a hepatocellular carcinoma subclass with a rearrangement signature of replication stress			Hepatocellular carcinoma		E_01_0351	PCR，Western blot，ChIP-seq	Here, we identify a hepatocellular carcinoma (HCC) subgroup exhibiting cyclin activation through various mechanisms including hepatitis B virus (HBV) and adeno-associated virus type 2 (AAV2) insertions, enhancer hijacking and recurrent CCNA2 fusions.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Here, we identify a hepatocellular carcinoma (HCC) subgroup exhibiting cyclin activation through various mechanisms including hepatitis B virus (HBV) and adeno-associated virus type 2 (AAV2) insertions, enhancer hijacking and recurrent CCNA2 fusions.	Immunohistochemical staining	Here, we identify a hepatocellular carcinoma (HCC) subgroup exhibiting cyclin activation through various mechanisms including hepatitis B virus (HBV) and adeno-associated virus type 2 (AAV2) insertions, enhancer hijacking and recurrent CCNA2 fusions.		PCR，Western blot，ChIP-seq			CCNA2		Here, we identify a hepatocellular carcinoma (HCC) subgroup exhibiting cyclin activation through various mechanisms including hepatitis B virus (HBV) and adeno-associated virus type 2 (AAV2) insertions, enhancer hijacking and recurrent CCNA2 fusions.	
30529831	chr6	84684707	84686707	TBX18	Our analyses also suggest a role in atherosclerosis for developmental transcription factor genes having little or no previous association with atherosclerosis, such as NR2F2 (COUP-TFII) and TBX18.	human	blood	High+Lowthroughput	Atherosclerosis-associated differentially methylated regions can reflect the disease phenotype and are often at enhancers			atherosclerosis		E_01_0352	Differentially methylated region method	Our analyses also suggest a role in atherosclerosis for developmental transcription factor genes having little or no previous association with atherosclerosis, such as NR2F2 (COUP-TFII) and TBX18.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Our analyses also suggest a role in atherosclerosis for developmental transcription factor genes having little or no previous association with atherosclerosis, such as NR2F2 (COUP-TFII) and TBX18.	Immunohistochemical staining	Our analyses also suggest a role in atherosclerosis for developmental transcription factor genes having little or no previous association with atherosclerosis, such as NR2F2 (COUP-TFII) and TBX18.		差异甲基化区域法				TBX18		Our analyses also suggest a role in atherosclerosis for developmental transcription factor genes having little or no previous association with atherosclerosis, such as NR2F2 (COUP-TFII) and TBX18.
30975980	chr7	19018300	19020300	TWIST1	SC66 also attenuated expression of TWIST1 and Mcl-1, factors important in cell invasiveness and anti-apoptosis, respectively. 	human	Epithelial	High+Lowthroughput	Akt inhibitor SC66 promotes cell sensitivity to cisplatin in chemoresistant ovarian cancer cells through inhibition of COL11A1 expression	否		Epithelial ovarian carcinoma 		E_01_0353	Gene knockdown, cell transfection techniques, Western blot	SC66 also attenuated expression of TWIST1 and Mcl-1, factors important in cell invasiveness and anti-apoptosis, respectively. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		SC66 also attenuated expression of TWIST1 and Mcl-1, factors important in cell invasiveness and anti-apoptosis, respectively. 	Immunohistochemical staining	SC66 also attenuated expression of TWIST1 and Mcl-1, factors important in cell invasiveness and anti-apoptosis, respectively. 		基因敲降、细胞转染技术、Western blot			TWIST2	TWIST1	SC66 also attenuated expression of TWIST1 and Mcl-2, factors important in cell invasiveness and anti-apoptosis, respectively. 	SC66 also attenuated expression of TWIST1 and Mcl-1, factors important in cell invasiveness and anti-apoptosis, respectively. 
30970615	chr4	41253337	41255337	UCHL1	UCHL1 was associated with growth breast cancer [61]. The loss of tumor suppressor UCHL1 was responsible for the inactivation of apoptosis, as well as cisplatin resistance, in EOC 	human		High+Lowthroughput	Mining Featured Biomarkers Linked with Epithelial Ovarian CancerBased on Bioinformatics	否		Epithelial Ovarian CancerBased	ovarian cell	E_01_0354	Immunofluorescence staining	UCHL1 was associated with growth breast cancer [61]. The loss of tumor suppressor UCHL1 was responsible for the inactivation of apoptosis, as well as cisplatin resistance, in EOC 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		UCHL1 was associated with growth breast cancer [61]. The loss of tumor suppressor UCHL1 was responsible for the inactivation of apoptosis, as well as cisplatin resistance, in EOC 	Immunohistochemical staining	UCHL1 was associated with growth breast cancer [61]. The loss of tumor suppressor UCHL1 was responsible for the inactivation of apoptosis, as well as cisplatin resistance, in EOC 		免疫荧光染色			UCHL1		UCHL1 was associated with growth breast cancer [61]. The loss of tumor suppressor UCHL1 was responsible for the inactivation of apoptosis, as well as cisplatin resistance, in EOC 	
30967505	chr7	148804534	148806534	EZH2	Enhancer of Zeste Homolog 2 (EZH2) is the catalytic subunit of Polycomb Repressor Complex 2 (PRC2), the enzyme that catalyzes monomethylation, dimethylation, and trimethylation of lysine 27 on histone H3 (H3K27).	human	Ovarian	High+Lowthroughput	Histone H3 tail binds a unique sensing pocket in EZH2 to activate the PRC2 methyltransferase	否		cancer		E_01_0355	gel electrophoresis	Enhancer of Zeste Homolog 2 (EZH2) is the catalytic subunit of Polycomb Repressor Complex 2 (PRC2), the enzyme that catalyzes monomethylation, dimethylation, and trimethylation of lysine 27 on histone H3 (H3K27).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Enhancer of Zeste Homolog 2 (EZH2) is the catalytic subunit of Polycomb Repressor Complex 2 (PRC2), the enzyme that catalyzes monomethylation, dimethylation, and trimethylation of lysine 27 on histone H3 (H3K27).	Immunohistochemical staining	Enhancer of Zeste Homolog 2 (EZH2) is the catalytic subunit of Polycomb Repressor Complex 2 (PRC2), the enzyme that catalyzes monomethylation, dimethylation, and trimethylation of lysine 27 on histone H3 (H3K27).		凝胶电泳				EZH2		Enhancer of Zeste Homolog 2 (EZH2) is the catalytic subunit of Polycomb Repressor Complex 2 (PRC2), the enzyme that catalyzes monomethylation, dimethylation, and trimethylation of lysine 27 on histone H3 (H3K27).
30955885	chr16	67559978	67561978	CTCF	Uncoupling DNA demethylation from antisense transcription by Tet3 overexpression in mouse olfactory neurons promotes CTCF binding to all Pcdhα promoters, resulting in proximity-biased DNA looping of the HS5-1 enhancer. 	human	epithelial cells	High+Lowthroughput	Antisense lncRNA Transcription Mediates DNA Demethylation to Drive Stochastic Protocadherin α Promoter Choice	否				E_01_0356	Immunofluorescence staining	Uncoupling DNA demethylation from antisense transcription by Tet3 overexpression in mouse olfactory neurons promotes CTCF binding to all Pcdhα promoters, resulting in proximity-biased DNA looping of the HS5-1 enhancer. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Uncoupling DNA demethylation from antisense transcription by Tet3 overexpression in mouse olfactory neurons promotes CTCF binding to all Pcdhα promoters, resulting in proximity-biased DNA looping of the HS5-1 enhancer. 	Immunohistochemical staining	Uncoupling DNA demethylation from antisense transcription by Tet3 overexpression in mouse olfactory neurons promotes CTCF binding to all Pcdhα promoters, resulting in proximity-biased DNA looping of the HS5-1 enhancer. 		免疫荧光染色				CTCF		Uncoupling DNA demethylation from antisense transcription by Tet3 overexpression in mouse olfactory neurons promotes CTCF binding to all Pcdhα promoters, resulting in proximity-biased DNA looping of the HS5-1 enhancer. 
30952976	chr3	194133551	194135551	HES1	We identify transcriptional repressor - hairy and enhancer of split-1 (HES1) - as a mediator of the OGT inhibition response in the TNBC cells. 	human		High+Lowthroughput	O-GlcNAc Transferase Inhibition Differentially Affects Breast Cancer Subtypes	否		Affects Breast Cancer		E_01_0357	Western blot, gene knockdown	We identify transcriptional repressor - hairy and enhancer of split-1 (HES1) - as a mediator of the OGT inhibition response in the TNBC cells. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We identify transcriptional repressor - hairy and enhancer of split-1 (HES1) - as a mediator of the OGT inhibition response in the TNBC cells. 	Immunohistochemical staining	We identify transcriptional repressor - hairy and enhancer of split-1 (HES1) - as a mediator of the OGT inhibition response in the TNBC cells. 		Western blot、基因敲降				HES1		We identify transcriptional repressor - hairy and enhancer of split-1 (HES1) - as a mediator of the OGT inhibition response in the TNBC cells. 
30948729	chr1	27662995	27664995	IFI6	Taken together, this study reveals a non-canonical function for CTCF-s that antagonizes the genomic binding of canonical CTCF and cohesin, and that modulates chromatin looping and causes apoptosis by stimulating IFI6 expression.	human	Epithelial	High+Lowthroughput	An alternative CTCF isoform antagonizes canonical CTCF occupancy and changes chromatin architecture to promote apoptosis	否				E_01_0358	QRT PCR, Western blot, immunofluorescence staining, gel electrophoresis, chip SEQ, RNA seq	Taken together, this study reveals a non-canonical function for CTCF-s that antagonizes the genomic binding of canonical CTCF and cohesin, and that modulates chromatin looping and causes apoptosis by stimulating IFI6 expression.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Taken together, this study reveals a non-canonical function for CTCF-s that antagonizes the genomic binding of canonical CTCF and cohesin, and that modulates chromatin looping and causes apoptosis by stimulating IFI6 expression.	Immunohistochemical staining	Taken together, this study reveals a non-canonical function for CTCF-s that antagonizes the genomic binding of canonical CTCF and cohesin, and that modulates chromatin looping and causes apoptosis by stimulating IFI6 expression.		qRT-PCR、Western blot、免疫荧光染色、凝胶电泳、ChIP-seq、RNA-seq 			IFI6		Taken together, this study reveals a non-canonical function for CTCF-s that antagonizes the genomic binding of canonical CTCF and cohesin, and that modulates chromatin looping and causes apoptosis by stimulating IFI6 expression.	
30945396	chr20	50187983	50189983	CEBPB	Mechanically, PGC1α binds to CCAAT/enhancer binding protein β (CEBPB), a member of the transcription factor family of CEBP, to promote CPT1A transcription, resulting in activation of FAO. 	human	epithelial cells	High+Lowthroughput	PGC1α/CEBPB/CPT1A axis promotes radiation resistance of nasopharyngeal carcinoma through activating fatty acid oxidation	否		nasopharyngeal carcinoma		E_01_0359	Western blot, immunohistochemistry	Mechanically, PGC1α binds to CCAAT/enhancer binding protein β (CEBPB), a member of the transcription factor family of CEBP, to promote CPT1A transcription, resulting in activation of FAO. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Mechanically, PGC1α binds to CCAAT/enhancer binding protein β (CEBPB), a member of the transcription factor family of CEBP, to promote CPT1A transcription, resulting in activation of FAO. 	Immunohistochemical staining	Mechanically, PGC1α binds to CCAAT/enhancer binding protein β (CEBPB), a member of the transcription factor family of CEBP, to promote CPT1A transcription, resulting in activation of FAO. 		Western blot、免疫组化				CEBPB		Mechanically, PGC1α binds to CCAAT/enhancer binding protein β (CEBPB), a member of the transcription factor family of CEBP, to promote CPT1A transcription, resulting in activation of FAO. 
30910956	chr17	40306219	40308219	RARA	Among them, rs10772119 and rs883868 disrupt the binding of retinoic acid receptor α (RARA) and Yin and Yang 1 (YY1), respectively.	human		High+Lowthroughput	Risk variants disrupting enhancers of T(H)1 and T(REG) cells in type 2 diabetes	是		type 2 diabetes	islet cell	E_01_0360	ChIP-Seq	Among them, rs10772119 and rs883868 disrupt the binding of retinoic acid receptor α (RARA) and Yin and Yang 1 (YY1), respectively.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Among them, rs10772119 and rs883868 disrupt the binding of retinoic acid receptor α (RARA) and Yin and Yang 1 (YY1), respectively.	Immunohistochemical staining	Among them, rs10772119 and rs883868 disrupt the binding of retinoic acid receptor α (RARA) and Yin and Yang 1 (YY1), respectively.		ChIP-Seq				RARA,YY1		Among them, rs10772119 and rs883868 disrupt the binding of retinoic acid receptor α (RARA) and Yin and Yang 1 (YY1), respectively.;Among them, rs10772119 and rs883868 disrupt the binding of retinoic acid receptor α (RARA) and Yin and Yang 1 (YY1), respectively.
30905509	chr3	133743290	133745290	TF	This process is important to understand because induced pluripotency in somatic cells represents reversal of ontogeny and transcription factor (TF)- based reprogramming can leave vestiges of the original cell lineage.	human	Epithelial	High+Lowthroughput	Extensive Recovery of Embryonic Enhancer and Gene Memory Stored in Hypomethylated Enhancer DNA	否			enterocyte of epithelium of intestinal vi	E_01_0361	ChIP-seq	This process is important to understand because induced pluripotency in somatic cells represents reversal of ontogeny and transcription factor (TF)- based reprogramming can leave vestiges of the original cell lineage.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		This process is important to understand because induced pluripotency in somatic cells represents reversal of ontogeny and transcription factor (TF)- based reprogramming can leave vestiges of the original cell lineage.	Immunohistochemical staining	This process is important to understand because induced pluripotency in somatic cells represents reversal of ontogeny and transcription factor (TF)- based reprogramming can leave vestiges of the original cell lineage.		ChIP-seq			TF		This process is important to understand because induced pluripotency in somatic cells represents reversal of ontogeny and transcription factor (TF)- based reprogramming can leave vestiges of the original cell lineage.	
30903020	chr7	148804044	148806044	EZH2	Robust expression of EZH2 in endocervical neoplastic lesions.	human		High+Lowthroughput	Bromodomain and extraterminal proteins foster the core transcriptional regulatory programs and confer vulnerability in liposarcoma	否			fat cell	E_01_0362	Chip SEQ, QRT PCR, Western blot test	Robust expression of EZH2 in endocervical neoplastic lesions.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Robust expression of EZH2 in endocervical neoplastic lesions.	Immunohistochemical staining	Robust expression of EZH2 in endocervical neoplastic lesions.		ChIP-seq、qRT-PCR、免疫印迹测试				EZH2		Robust expression of EZH2 in endocervical neoplastic lesions.
30901906	chr2	28389918	28391918	FOSL2	We identify a bromodomain and extraterminal (BET) protein-cooperated FUS-DDIT3 function in myxoid LPS and a BET protein-dependent core transcriptional regulatory circuitry consisting of FOSL2, MYC, and RUNX1 in de-differentiated LPS.	human	connective	High+Lowthroughput	WNT3a and WNT5a Transported by Exosomes Activate WNT Signaling Pathways in Human Cardiac Fibroblasts	否				E_01_0363	Immunofluorescence staining, Western blot RT PCR	We identify a bromodomain and extraterminal (BET) protein-cooperated FUS-DDIT3 function in myxoid LPS and a BET protein-dependent core transcriptional regulatory circuitry consisting of FOSL2, MYC, and RUNX1 in de-differentiated LPS.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We identify a bromodomain and extraterminal (BET) protein-cooperated FUS-DDIT3 function in myxoid LPS and a BET protein-dependent core transcriptional regulatory circuitry consisting of FOSL2, MYC, and RUNX1 in de-differentiated LPS.	Immunohistochemical staining	We identify a bromodomain and extraterminal (BET) protein-cooperated FUS-DDIT3 function in myxoid LPS and a BET protein-dependent core transcriptional regulatory circuitry consisting of FOSL2, MYC, and RUNX1 in de-differentiated LPS.		免疫荧光染色、Western blotRT-PCR				FOSL2,MYC,RUNX1		We identify a bromodomain and extraterminal (BET) protein-cooperated FUS-DDIT3 function in myxoid LPS and a BET protein-dependent core transcriptional regulatory circuitry consisting of FOSL2, MYC, and RUNX1 in de-differentiated LPS.;We identify a bromodomain and extraterminal (BET) protein-cooperated FUS-DDIT3 function in myxoid LPS and a BET protein-dependent core transcriptional regulatory circuitry consisting of FOSL2, MYC, and RUNX1 in de-differentiated LPS.;We identify a bromodomain and extraterminal (BET) protein-cooperated FUS-DDIT3 function in myxoid LPS and a BET protein-dependent core transcriptional regulatory circuitry consisting of FOSL2, MYC, and RUNX1 in de-differentiated LPS.
30899425	chr12	55722375	55724375	CD63	Obtained exosomes showed size ranging between 20⁻150 nm and expressed exosomal markers ALG-2-interacting protein X (ALIX) and CD63.	human		High+Lowthroughput	Super-enhancers: novel target for pancreatic ductal adenocarcinoma	否		pancreatic ductal adenocarcinoma		E_01_0364	Chip SEQ, Western blot, PCR, immunohistochemistry, immunofluorescence staining	Obtained exosomes showed size ranging between 20⁻150 nm and expressed exosomal markers ALG-2-interacting protein X (ALIX) and CD63.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Obtained exosomes showed size ranging between 20⁻150 nm and expressed exosomal markers ALG-2-interacting protein X (ALIX) and CD63.	Immunohistochemical staining	Obtained exosomes showed size ranging between 20⁻150 nm and expressed exosomal markers ALG-2-interacting protein X (ALIX) and CD63.		ChIP-Seq、Western blot、PCR、免疫组化、免疫荧光染色			CD63		Obtained exosomes showed size ranging between 20⁻150 nm and expressed exosomal markers ALG-2-interacting protein X (ALIX) and CD63.	
30898391	chr17	39401325	39403325	MED1	Differential H3K27AC marks were identified at enhancer regions of genes including c-MYC, MED1, OCT-4, NANOG, and SOX2 that can act as SE in non-cancerous, cancerous and metastatic PDAC cell lines.	human	Kidney	High+Lowthroughput	Genome-wide association studies identify susceptibility loci for epithelial ovarian cancer in east Asian women	是		epithelial ovarian cancer		E_01_0365	Bioinformatic prediction	Differential H3K27AC marks were identified at enhancer regions of genes including c-MYC, MED1, OCT-4, NANOG, and SOX2 that can act as SE in non-cancerous, cancerous and metastatic PDAC cell lines.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Differential H3K27AC marks were identified at enhancer regions of genes including c-MYC, MED1, OCT-4, NANOG, and SOX2 that can act as SE in non-cancerous, cancerous and metastatic PDAC cell lines.	Immunohistochemical staining	Differential H3K27AC marks were identified at enhancer regions of genes including c-MYC, MED1, OCT-4, NANOG, and SOX2 that can act as SE in non-cancerous, cancerous and metastatic PDAC cell lines.		生物信息学预测			NANOG,ESPNL	MED1,SOX2	Differential H3K27AC marks were identified at enhancer regions of genes including c-MYC, MED1, OCT-4, NANOG, and SOX2 that can act as SE in non-cancerous, cancerous and metastatic PDAC cell lines.;At 2q37.3, expression quantitative trait locus analysis in 404 HGSOC tissues identified ESPNL as a putative candidate susceptibility gene .	Differential H3K27AC marks were identified at enhancer regions of genes including c-MYC, MED1, OCT-4, NANOG, and SOX2 that can act as SE in non-cancerous, cancerous and metastatic PDAC cell lines.;Differential H3K27AC marks were identified at enhancer regions of genes including c-MYC, MED1, OCT-4, NANOG, and SOX2 that can act as SE in non-cancerous, cancerous and metastatic PDAC cell lines.
30894209	chr12	52484679	52486679	KRT6A	This study aimed to study the mechanisms of ectopic keratin 6A (KRT6A) in NPC.	human		High+Lowthroughput	Hypoxia-induced miR-191-C/EBPβ signaling regulates cell proliferation and apoptosis of fibroblast-like synoviocytes from patients with rheumatoid arthritis	否		rheumatoid arthritis		E_01_0366	RT-PCR, cell transfection techniques, Western blot	This study aimed to study the mechanisms of ectopic keratin 6A (KRT6A) in NPC.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		This study aimed to study the mechanisms of ectopic keratin 6A (KRT6A) in NPC.	Immunohistochemical staining	This study aimed to study the mechanisms of ectopic keratin 6A (KRT6A) in NPC.		RT-PCR、细胞转染技术、Western blot			KRT6A		This study aimed to study the mechanisms of ectopic keratin 6A (KRT6A) in NPC.	
30892634	chr19	16322108	16324108	KLF2	KLF2 (kruppel-like factor 2 [lung]) regulates osteoclastogenesis by modulating autophagy.	human		High+Lowthroughput	PLZF limits enhancer activity during hematopoietic progenitor aging	否				E_01_0367	RT qPCR, immunofluorescence staining, Western blot, ATAC seq	KLF2 (kruppel-like factor 2 [lung]) regulates osteoclastogenesis by modulating autophagy.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		KLF2 (kruppel-like factor 2 [lung]) regulates osteoclastogenesis by modulating autophagy.	Immunohistochemical staining	KLF2 (kruppel-like factor 2 [lung]) regulates osteoclastogenesis by modulating autophagy.		RT-qPCR、免疫荧光染色、Western blot、ATAC-seq				KLF2		KLF2 (kruppel-like factor 2 [lung]) regulates osteoclastogenesis by modulating autophagy.
30892142	chr3	108040340	108042340	CD47	CD47 enhancer-FIREFLY vec_x0002_tor was generated from the previously described construct CD47-E5.	human		High+Lowthroughput	The Transcription Factor ERG Regulates Super-Enhancers Associated With an Endothelial-Specific Gene Expression Program	是				E_01_0368	ChIP-seq	CD47 enhancer-FIREFLY vec_x0002_tor was generated from the previously described construct CD47-E5.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		CD47 enhancer-FIREFLY vec_x0002_tor was generated from the previously described construct CD47-E5.	Immunohistochemical staining	CD47 enhancer-FIREFLY vec_x0002_tor was generated from the previously described construct CD47-E5.		ChIP-seq				CD47		CD47 enhancer-FIREFLY vec_x0002_tor was generated from the previously described construct CD47-E5.
30888859	chr3	10139527	10141527	VHL	Renal cell carcinoma (RCC) is the major cause of death among patients with von Hippel-Lindau (VHL) disease.	human		High+Lowthroughput	AMPK and PPARβ positive feedback loop regulates endurance exercise training-mediated GLUT4 expression in skeletal muscle	否				E_01_0369	Western blot, immunofluorescence staining	Renal cell carcinoma (RCC) is the major cause of death among patients with von Hippel-Lindau (VHL) disease.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Renal cell carcinoma (RCC) is the major cause of death among patients with von Hippel-Lindau (VHL) disease.	Immunohistochemical staining	Renal cell carcinoma (RCC) is the major cause of death among patients with von Hippel-Lindau (VHL) disease.		Western blot、免疫荧光染色				VHL		Renal cell carcinoma (RCC) is the major cause of death among patients with von Hippel-Lindau (VHL) disease.
30886108	chr15	99562658	99564658	MEF2A	We discovered that AMPK activation increases PPARβ via myocyte enhancer factor 2A (MEF2A), which acted as a transcription factor for PPARβ.	human		High+Lowthroughput	Gene activation precedes DNA demethylation in response to infection in human dendritic cells	否				E_01_0370	Gene knockdown	We discovered that AMPK activation increases PPARβ via myocyte enhancer factor 2A (MEF2A), which acted as a transcription factor for PPARβ.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We discovered that AMPK activation increases PPARβ via myocyte enhancer factor 2A (MEF2A), which acted as a transcription factor for PPARβ.	Immunohistochemical staining	We discovered that AMPK activation increases PPARβ via myocyte enhancer factor 2A (MEF2A), which acted as a transcription factor for PPARβ.		基因敲降			KRT6A	MEF2A	KRT6A levels, metastasis‑associated factors and the Wnt/β‑catenin pathway were measured using RT‑qPCR and western blotting.	We discovered that AMPK activation increases PPARβ via myocyte enhancer factor 2A (MEF2A), which acted as a transcription factor for PPARβ.
30884312	chr15	99563063	99565063	MEF2A	MEF2A alters the proliferation, inflammation-related gene expression profiles and its silencing induces cellular senescence in human coronary endothelial cells.	human	Cancer	High+Lowthroughput	PRISMA: Protein Interaction Screen on Peptide Matrix Reveals Interaction Footprints and Modifications- Dependent Interactome of Intrinsically Disordered C/EBPβ	否		preeclampsia		E_01_0371	Bioinformatic predictions	MEF2A alters the proliferation, inflammation-related gene expression profiles and its silencing induces cellular senescence in human coronary endothelial cells.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		MEF2A alters the proliferation, inflammation-related gene expression profiles and its silencing induces cellular senescence in human coronary endothelial cells.	Immunohistochemical staining	MEF2A alters the proliferation, inflammation-related gene expression profiles and its silencing induces cellular senescence in human coronary endothelial cells.		生物药信息学预测				MEF2A		MEF2A alters the proliferation, inflammation-related gene expression profiles and its silencing induces cellular senescence in human coronary endothelial cells.
30881868	chr16	56426207	56428207	NUDT21	The role of NUDT21 in microRNA-binging sites of EZH2 gene increases the of risk preeclampsia.	human		High+Lowthroughput	ILF2 Directly Binds and Stabilizes CREB to Stimulate Malignant Phenotypes of Liver Cancer Cells	否				E_01_0372	Immunohistochemistry, immunofluorescence staining, Western blot	The role of NUDT21 in microRNA-binging sites of EZH2 gene increases the of risk preeclampsia.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The role of NUDT21 in microRNA-binging sites of EZH2 gene increases the of risk preeclampsia.	Immunohistochemical staining	The role of NUDT21 in microRNA-binging sites of EZH2 gene increases the of risk preeclampsia.		免疫组化、免疫荧光染色、Western blot			NUDT21	EZH2	The role of NUDT21 in microRNA-binging sites of EZH2 gene increases the of risk preeclampsia.	The role of NUDT21 in microRNA-binging sites of EZH2 gene increases the of risk preeclampsia.
30881490	chr1	153658951	153660951	ILF2	ILF2 Directly Binds and Stabilizes CREB to Stimulate Malignant Phenotypes of Liver Cancer Cells.	human		High+Lowthroughput	The oncogenic role of Wnt10a in colorectal cancer through activation of canonical Wnt/β-catenin signaling	否		CRC		E_01_0373	RT qPCR, Western blot / cell transfection	ILF2 Directly Binds and Stabilizes CREB to Stimulate Malignant Phenotypes of Liver Cancer Cells.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		ILF2 Directly Binds and Stabilizes CREB to Stimulate Malignant Phenotypes of Liver Cancer Cells.	Immunohistochemical staining	ILF2 Directly Binds and Stabilizes CREB to Stimulate Malignant Phenotypes of Liver Cancer Cells.		RT-qPCR、Western blot/细胞转染技术			ILF2		ILF2 Directly Binds and Stabilizes CREB to Stimulate Malignant Phenotypes of Liver Cancer Cells.	
30879360	chr7	148804532	148806532	EZH2	EZH2 Inhibition in Ewing Sarcoma Upregulates G(D2) Expression for Targeting with Gene-Modified T Cells.	human		High+Lowthroughput	Retinoic Acid Is a Negative Regulator of sFLT1 Expression in Decidual Stromal Cells, and Its Levels Are Reduced in Preeclamptic Decidua	否				E_01_0374	PCR, Western blot, immunofluorescence staining	EZH2 Inhibition in Ewing Sarcoma Upregulates G(D2) Expression for Targeting with Gene-Modified T Cells.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		EZH2 Inhibition in Ewing Sarcoma Upregulates G(D2) Expression for Targeting with Gene-Modified T Cells.	Immunohistochemical staining	EZH2 Inhibition in Ewing Sarcoma Upregulates G(D2) Expression for Targeting with Gene-Modified T Cells.		PCR、Western blot、免疫荧光染色				EZH2		EZH2 Inhibition in Ewing Sarcoma Upregulates G(D2) Expression for Targeting with Gene-Modified T Cells.
33124415	chr9	70381888	70383888	KLF9	Genomic determinants implicated in the glucocorticoid-mediated induction of KLF9 in pulmonary epithelial cells.	human		High+Lowthroughput	Mass Spectrometry-Based Metabolic Fingerprinting Contributes to Unveil the Role of RSUME in Renal Cell Carcinoma Cell Metabolism.	否		Clear cell renal cell carcinoma	Renal cell	E_01_0375	Cell transfection techniques, PCR	Genomic determinants implicated in the glucocorticoid-mediated induction of KLF9 in pulmonary epithelial cells.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Genomic determinants implicated in the glucocorticoid-mediated induction of KLF9 in pulmonary epithelial cells.	Immunohistochemical staining	Genomic determinants implicated in the glucocorticoid-mediated induction of KLF9 in pulmonary epithelial cells.		细胞转染技术、PCR				KLF9		Genomic determinants implicated in the glucocorticoid-mediated induction of KLF9 in pulmonary epithelial cells.
32602275	chr3	10138986	10140986	VHL	Clear cell renal cell carcinoma (ccRCC) is a heterogeneous disease with 50-80% patients exhibiting mutations in the von Hippel-Lindau (VHL) gene.	human	Epithelial	High+Lowthroughput	Enhancer-Gene Interaction Analyses Identified the Epidermal Growth Factor Receptor as a Susceptibility Gene for Type 2 Diabetes Mellitus.	是		type 2 diabetes	islet cell	E_01_0376	Bioinformatic prediction	Clear cell renal cell carcinoma (ccRCC) is a heterogeneous disease with 50-80% patients exhibiting mutations in the von Hippel-Lindau (VHL) gene.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Clear cell renal cell carcinoma (ccRCC) is a heterogeneous disease with 50-80% patients exhibiting mutations in the von Hippel-Lindau (VHL) gene.	Immunohistochemical staining	Clear cell renal cell carcinoma (ccRCC) is a heterogeneous disease with 50-80% patients exhibiting mutations in the von Hippel-Lindau (VHL) gene.		生物信息学预测				VHL,EGFR		Clear cell renal cell carcinoma (ccRCC) is a heterogeneous disease with 50-80% patients exhibiting mutations in the von Hippel-Lindau (VHL) gene.;The SNP rs4947941 was annotated as an enhancer, and rs7785013 was located in the epidermal growth factor receptor (EGFR) gene.
31733305	chr4	152317572	152319572	FBXW7	FBXW7 promotes pathological cardiac hypertrophy by targeting EZH2-SIX1 signaling.	human	Endothelial	High+Lowthroughput	The novel axis of YAP1, transcription enhancer factor 3 and Down Syndrome Candidate Region 1 isoform 1L is a common signaling pathway downstream of several angiogenic factors.	否			endothelial cell	E_01_0377	PCR, gel electrophoresis, gene knockdown, immunofluorescence staining	FBXW7 promotes pathological cardiac hypertrophy by targeting EZH2-SIX1 signaling.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		FBXW7 promotes pathological cardiac hypertrophy by targeting EZH2-SIX1 signaling.	Immunohistochemical staining	FBXW7 promotes pathological cardiac hypertrophy by targeting EZH2-SIX1 signaling.		PCR、凝胶电泳、基因敲降、免疫荧光染色			SIX1	FBXW7,EZH2	FBXW7 promotes pathological cardiac hypertrophy by targeting EZH2-SIX1 signaling.	FBXW7 promotes pathological cardiac hypertrophy by targeting EZH2-SIX1 signaling.;FBXW7 promotes pathological cardiac hypertrophy by targeting EZH2-SIX1 signaling.
32408759	chr15	99562918	99564918	MEF2A	MEF2A alters the proliferation, inflammation-related gene expression profiles and its silencing induces cellular senescence in human coronary endothelial cells.	human	Embryonic	High+Lowthroughput	Variants in miRNA regulome and their association with the risk of nonsyndromi corofacial clefts	否		nonsyndromic orofacial clefts	embryonic cell 	E_01_0378	PCR	MEF2A alters the proliferation, inflammation-related gene expression profiles and its silencing induces cellular senescence in human coronary endothelial cells.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		MEF2A alters the proliferation, inflammation-related gene expression profiles and its silencing induces cellular senescence in human coronary endothelial cells.	Immunohistochemical staining	MEF2A alters the proliferation, inflammation-related gene expression profiles and its silencing induces cellular senescence in human coronary endothelial cells.		PCR				MEF2A		MEF2A alters the proliferation, inflammation-related gene expression profiles and its silencing induces cellular senescence in human coronary endothelial cells.
33009960	chr17	76373734	76375734	SPHK1	Transcription of the proto-oncogene SPHK1 is regulated by KHPS1, an antisense RNA that activates SPHK1 expression by forming a triple-helical RNA-DNA-DNA structure at the SPHK1 enhancer.	human	Immunohistochem	High+Lowthroughput	Cereblon Promotes the Ubiquitination and Proteasomal Degradation of Interleukin Enhancer-Binding Factor 2	否			leukocyte	E_01_0379	gel electrophoresis	Transcription of the proto-oncogene SPHK1 is regulated by KHPS1, an antisense RNA that activates SPHK1 expression by forming a triple-helical RNA-DNA-DNA structure at the SPHK1 enhancer.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Transcription of the proto-oncogene SPHK1 is regulated by KHPS1, an antisense RNA that activates SPHK1 expression by forming a triple-helical RNA-DNA-DNA structure at the SPHK1 enhancer.	Immunohistochemical staining	Transcription of the proto-oncogene SPHK1 is regulated by KHPS1, an antisense RNA that activates SPHK1 expression by forming a triple-helical RNA-DNA-DNA structure at the SPHK1 enhancer.		凝胶电泳			SPHK1		Transcription of the proto-oncogene SPHK1 is regulated by KHPS1, an antisense RNA that activates SPHK1 expression by forming a triple-helical RNA-DNA-DNA structure at the SPHK1 enhancer.	
32094355	chr1	153658363	153660363	ILF2	Interleukin enhancer-binding factor 2 (ILF2) forms a heterodimer with interleukin enhancer-binding factor 3 (ILF3) via double-stranded RNA-binding motif and zinc finger associated domain and thus regulates gene expression and cancer cell growth.	human	Epithelial	High+Lowthroughput	Altered chromatin landscape and enhancer engagement underlie transcriptional dysregulation in MED12 mutant uterine leiomyomas	否		uterine leiomyomas	uterine smooth muscle cell	E_01_0380	PCR	Interleukin enhancer-binding factor 2 (ILF2) forms a heterodimer with interleukin enhancer-binding factor 3 (ILF3) via double-stranded RNA-binding motif and zinc finger associated domain and thus regulates gene expression and cancer cell growth.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Interleukin enhancer-binding factor 2 (ILF2) forms a heterodimer with interleukin enhancer-binding factor 3 (ILF3) via double-stranded RNA-binding motif and zinc finger associated domain and thus regulates gene expression and cancer cell growth.	Immunohistochemical staining	Interleukin enhancer-binding factor 2 (ILF2) forms a heterodimer with interleukin enhancer-binding factor 3 (ILF3) via double-stranded RNA-binding motif and zinc finger associated domain and thus regulates gene expression and cancer cell growth.		PCR			ILF2		Interleukin enhancer-binding factor 2 (ILF2) forms a heterodimer with interleukin enhancer-binding factor 3 (ILF3) via double-stranded RNA-binding motif and zinc finger associated domain and thus regulates gene expression and cancer cell growth.	
32736380	chrX	71115647	71117647	MED12	Altered chromatin landscape and enhancer engagement underlie transcriptional dysregulation in MED12 mutant uterine leiomyomas.	human		High+Lowthroughput	Constructing and deconstructing GATA2-regulated cell fate programs to establish developmental trajectories	否			stem cell	E_01_0381	PCR	Altered chromatin landscape and enhancer engagement underlie transcriptional dysregulation in MED12 mutant uterine leiomyomas.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Altered chromatin landscape and enhancer engagement underlie transcriptional dysregulation in MED12 mutant uterine leiomyomas.	Immunohistochemical staining	Altered chromatin landscape and enhancer engagement underlie transcriptional dysregulation in MED12 mutant uterine leiomyomas.		PCR			MED12		Altered chromatin landscape and enhancer engagement underlie transcriptional dysregulation in MED12 mutant uterine leiomyomas.	
33203992	chr3	128476653	128478653	GATA2	Constructing and deconstructing GATA2-regulated cell fate programs to establish developmental trajectories.	human	Thyroid	High+Lowthroughput	Characterizing the function of EPB41L4A in the predisposition to papillary thyroid carcinoma	是		papillary thyroid carcinoma	thyroid gland cell	E_01_0382	PCR	Constructing and deconstructing GATA2-regulated cell fate programs to establish developmental trajectories.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Constructing and deconstructing GATA2-regulated cell fate programs to establish developmental trajectories.	Immunohistochemical staining	Constructing and deconstructing GATA2-regulated cell fate programs to establish developmental trajectories.		PCR			EPB41L4A	GATA2	Characterizing the function of EPB41L4A in the predisposition to papillary thyroid carcinoma.	Constructing and deconstructing GATA2-regulated cell fate programs to establish developmental trajectories.
31411680	chr7	148804636	148806636	EZH2	A systems approach identifies Enhancer of Zeste Homolog 2 (EZH2) as a protective factor in epilepsy .	human	Brain	High+Lowthroughput	[Noncoding Polymorphism rs6832152 Is an Attractive Candidate for Genome Editing Aimed at Finding New Molecular Mechanisms of Autoimmune Diseases].	否			brain cell 	E_01_0383	Single cell sequencing	A systems approach identifies Enhancer of Zeste Homolog 2 (EZH2) as a protective factor in epilepsy .	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		A systems approach identifies Enhancer of Zeste Homolog 2 (EZH2) as a protective factor in epilepsy .	Immunohistochemical staining	A systems approach identifies Enhancer of Zeste Homolog 2 (EZH2) as a protective factor in epilepsy .		单细胞测序				EZH2		A systems approach identifies Enhancer of Zeste Homolog 2 (EZH2) as a protective factor in epilepsy .
30896882	chr1	95231641	95233641	RWDD3	Previously we have described that RWDD3 or RSUME (RWD domain-containing protein SUMO Enhancer) sumoylates and binds VHL protein and negatively regulates HIF degradation, leading to xenograft RCC tumor growth in mice.	human		High+Lowthroughput		否		 nasopharyngeal carcinoma		E_01_0384	RT qPCR, Western blot, cell transfection	Previously we have described that RWDD3 or RSUME (RWD domain-containing protein SUMO Enhancer) sumoylates and binds VHL protein and negatively regulates HIF degradation, leading to xenograft RCC tumor growth in mice.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Previously we have described that RWDD3 or RSUME (RWD domain-containing protein SUMO Enhancer) sumoylates and binds VHL protein and negatively regulates HIF degradation, leading to xenograft RCC tumor growth in mice.	Immunohistochemical staining	Previously we have described that RWDD3 or RSUME (RWD domain-containing protein SUMO Enhancer) sumoylates and binds VHL protein and negatively regulates HIF degradation, leading to xenograft RCC tumor growth in mice.		RT-qPCR、Western blot、细胞转染技术			RWDD3		Previously we have described that RWDD3 or RSUME (RWD domain-containing protein SUMO Enhancer) sumoylates and binds VHL protein and negatively regulates HIF degradation, leading to xenograft RCC tumor growth in mice.	
34531368	chrX	67540972	67542972	AR	The androgen receptor (AR) is commonly known as a key transcription factor in prostate cancer development, progression and therapy resistance.	human	Immune cells	High+Lowthroughput	Androgen receptor enhancer usage and the chromatin regulatory landscape in human prostate cancers.	否		genomically silent childhood cancer	EwS cell	E_01_0385	PCR	The androgen receptor (AR) is commonly known as a key transcription factor in prostate cancer development, progression and therapy resistance.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The androgen receptor (AR) is commonly known as a key transcription factor in prostate cancer development, progression and therapy resistance.	Immunohistochemical staining	The androgen receptor (AR) is commonly known as a key transcription factor in prostate cancer development, progression and therapy resistance.		PCR				AR		The androgen receptor (AR) is commonly known as a key transcription factor in prostate cancer development, progression and therapy resistance.
34294917	chr16	23675330	23677330	PLK1	Therapeutic targeting of the PLK1-PRC1-axis triggers cell death in genomically silent childhood cancer .	human		High+Lowthroughput	Therapeutic targeting of the PLK1-PRC1-axis triggers cell death in genomically silent childhood cancer.	否			brain cell 	E_01_0386	RNA SEQ, gel electrophoresis	Therapeutic targeting of the PLK1-PRC1-axis triggers cell death in genomically silent childhood cancer .	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Therapeutic targeting of the PLK1-PRC1-axis triggers cell death in genomically silent childhood cancer .	Immunohistochemical staining	Therapeutic targeting of the PLK1-PRC1-axis triggers cell death in genomically silent childhood cancer .		RNA-seq、凝胶电泳			PLK1		Therapeutic targeting of the PLK1-PRC1-axis triggers cell death in genomically silent childhood cancer .	
33704060	chr6	1607232	1609232	FOXC1	Superenhancer distribution revealed a group of potential TFs in core regulatory circuits in human glomerulus cells, including FOXC1/2, WT1, and LMX1B.	human	Epithelial	High+Lowthroughput	Super-Enhancer-Associated Transcription Factors Maintain Transcriptional Regulation in Mature Podocytes.	否			epithelial cell	E_01_0387	Gel electrophoresis, PCR	Superenhancer distribution revealed a group of potential TFs in core regulatory circuits in human glomerulus cells, including FOXC1/2, WT1, and LMX1B.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Superenhancer distribution revealed a group of potential TFs in core regulatory circuits in human glomerulus cells, including FOXC1/2, WT1, and LMX1B.	Immunohistochemical staining	Superenhancer distribution revealed a group of potential TFs in core regulatory circuits in human glomerulus cells, including FOXC1/2, WT1, and LMX1B.		凝胶电泳、PCR			WT1,LMX1B	FOXC1,FOXC2	Superenhancer distribution revealed a group of potential TFs in core regulatory circuits in human glomerulus cells, including FOXC1/2, WT1, and LMX1B.;Superenhancer distribution revealed a group of potential TFs in core regulatory circuits in human glomerulus cells, including FOXC1/2, WT1, and LMX1B.	Superenhancer distribution revealed a group of potential TFs in core regulatory circuits in human glomerulus cells, including FOXC1/2, WT1, and LMX1B.;Superenhancer distribution revealed a group of potential TFs in core regulatory circuits in human glomerulus cells, including FOXC1/2, WT1, and LMX1B.
29941091	chr16	67559331	67561331	CTCF	The altered chromosomal looping and consequent effects on host genome transcription depend on the proviral integration site and the presence of nearby CTCF-BS, and so differ in each infected T-cell clone. The changes in chromatin structure caused by HTLV-1 might not only create novel loops but also destroy pre-existing CTCF-dependent loops that are present in uninfected cells. Further work is needed to investigate the impact of altered looping and transcription on the persistence, infectivity and oncogenic potential of the infected T-cell clones.	human	lymphoid	High+Lowthroughput	The human leukemia virus HTLV-1 alters the structure and transcription of host chromatin in cis	是		leukemia	T lymphocyte	E_01_0388	q4C,CRISPR/Cas9,RNA-seq,ChIP-seq,WGS,	The altered chromosomal looping and consequent effects on host genome transcription depend on the proviral integration site and the presence of nearby CTCF-BS, and so differ in each infected T-cell clone. The changes in chromatin structure caused by HTLV-1 might not only create novel loops but also destroy pre-existing CTCF-dependent loops that are present in uninfected cells. Further work is needed to investigate the impact of altered looping and transcription on the persistence, infectivity and oncogenic potential of the infected T-cell clones.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The altered chromosomal looping and consequent effects on host genome transcription depend on the proviral integration site and the presence of nearby CTCF-BS, and so differ in each infected T-cell clone. The changes in chromatin structure caused by HTLV-1 might not only create novel loops but also destroy pre-existing CTCF-dependent loops that are present in uninfected cells. Further work is needed to investigate the impact of altered looping and transcription on the persistence, infectivity and oncogenic potential of the infected T-cell clones.	Immunohistochemical staining	The altered chromosomal looping and consequent effects on host genome transcription depend on the proviral integration site and the presence of nearby CTCF-BS, and so differ in each infected T-cell clone. The changes in chromatin structure caused by HTLV-1 might not only create novel loops but also destroy pre-existing CTCF-dependent loops that are present in uninfected cells. Further work is needed to investigate the impact of altered looping and transcription on the persistence, infectivity and oncogenic potential of the infected T-cell clones.		q4C,CRISPR/Cas9,RNA-seq,ChIP-seq,WGS,			PRC1	CTCF,YY1	The altered chromosomal looping and consequent effects on host genome transcription depend on the proviral integration site and the presence of nearby CTCF-BS, and so differ in each infected T-cell clone. The changes in chromatin structure caused by HTLV-1 might not only create novel loops but also destroy pre-existing CTCF-dependent loops that are present in uninfected cells. Further work is needed to investigate the impact of altered looping and transcription on the persistence, infectivity and oncogenic potential of the infected T-cell clones.	The altered chromosomal looping and consequent effects on host genome transcription depend on the proviral integration site and the presence of nearby CTCF-BS, and so differ in each infected T-cell clone. The changes in chromatin structure caused by HTLV-1 might not only create novel loops but also destroy pre-existing CTCF-dependent loops that are present in uninfected cells. Further work is needed to investigate the impact of altered looping and transcription on the persistence, infectivity and oncogenic potential of the infected T-cell clones.;The altered chromosomal looping and consequent effects on host genome transcription depend on the proviral integration site and the presence of nearby CTCF-BS, and so differ in each infected T-cell clone. The changes in chromatin structure caused by HTLV-1 might not only create novel loops but also destroy pre-existing CTCF-dependent loops that are present in uninfected cells. Further work is needed to investigate the impact of altered looping and transcription on the persistence, infectivity and oncogenic potential of the infected T-cell clones.
29940916	chr7	148804605	148806605	EZH2	We found a negative correlation between estrogen-related receptors and Enhancer of Zeste Homolog 2, aglobal repressor gene. Immunohistochemistry in primary breast tumors of different grades showed a correlated expression of estrogen-related receptors and EZH2. Their correlated expression was further validated using online MERAV expression dataset where a negative correlation of variable strengths was observed in breast cancer. Ectopic expression of EZH2 in low EZH2-expressing normal breast epithelial cells abrogated their expression and at the same time, its silencing enhanced the expression of estrogen-related receptors in cancerous cells. Global occupancy of EZH2 on ERRα and ERRβ was observed in-vivo.	human	Mammary	High+Lowthroughput	Estrogen-related receptors alpha, beta and gamma expression and function is associated with transcriptional repressor EZH2 in breast carcinoma	否		mammary cancer	epithelial cell	E_01_0389	Immunohistochemistry,transfection,Western blot,CHIP,qRT-PCR,CHIP-qPCR,	We found a negative correlation between estrogen-related receptors and Enhancer of Zeste Homolog 2, aglobal repressor gene. Immunohistochemistry in primary breast tumors of different grades showed a correlated expression of estrogen-related receptors and EZH2. Their correlated expression was further validated using online MERAV expression dataset where a negative correlation of variable strengths was observed in breast cancer. Ectopic expression of EZH2 in low EZH2-expressing normal breast epithelial cells abrogated their expression and at the same time, its silencing enhanced the expression of estrogen-related receptors in cancerous cells. Global occupancy of EZH2 on ERRα and ERRβ was observed in-vivo.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We found a negative correlation between estrogen-related receptors and Enhancer of Zeste Homolog 2, aglobal repressor gene. Immunohistochemistry in primary breast tumors of different grades showed a correlated expression of estrogen-related receptors and EZH2. Their correlated expression was further validated using online MERAV expression dataset where a negative correlation of variable strengths was observed in breast cancer. Ectopic expression of EZH2 in low EZH2-expressing normal breast epithelial cells abrogated their expression and at the same time, its silencing enhanced the expression of estrogen-related receptors in cancerous cells. Global occupancy of EZH2 on ERRα and ERRβ was observed in-vivo.	Immunohistochemical staining	We found a negative correlation between estrogen-related receptors and Enhancer of Zeste Homolog 2, aglobal repressor gene. Immunohistochemistry in primary breast tumors of different grades showed a correlated expression of estrogen-related receptors and EZH2. Their correlated expression was further validated using online MERAV expression dataset where a negative correlation of variable strengths was observed in breast cancer. Ectopic expression of EZH2 in low EZH2-expressing normal breast epithelial cells abrogated their expression and at the same time, its silencing enhanced the expression of estrogen-related receptors in cancerous cells. Global occupancy of EZH2 on ERRα and ERRβ was observed in-vivo.		Immunohistochemistry,transfection,Western blot,CHIP,qRT-PCR,CHIP-qPCR,				EZH2		We found a negative correlation between estrogen-related receptors and Enhancer of Zeste Homolog 2, aglobal repressor gene. Immunohistochemistry in primary breast tumors of different grades showed a correlated expression of estrogen-related receptors and EZH2. Their correlated expression was further validated using online MERAV expression dataset where a negative correlation of variable strengths was observed in breast cancer. Ectopic expression of EZH2 in low EZH2-expressing normal breast epithelial cells abrogated their expression and at the same time, its silencing enhanced the expression of estrogen-related receptors in cancerous cells. Global occupancy of EZH2 on ERRα and ERRβ was observed in-vivo.
29940792	chr16	87381402	87383402	MAP1LC3B	These findings indicated that cancer cell autophagy is regulated by a collaborative interaction between tumor and immune cell components in distinct HCC microenvironments, thus allowing the inflammatory monocytes to be rerouted in a tumor-promoting direction.	human	Liver	High+Lowthroughput	Peritumoral monocytes induce cancer cell autophagy to facilitate the progression of human hepatocellular carcinoma	否		Hepatocellular carcinoma	monocyte cells	E_01_0390	Immunofluorescence,Immunohistochemical Staining,qRT-PCR,Immunoblotting,Transmission electron microscopy,ELISA,RNA interference,	These findings indicated that cancer cell autophagy is regulated by a collaborative interaction between tumor and immune cell components in distinct HCC microenvironments, thus allowing the inflammatory monocytes to be rerouted in a tumor-promoting direction.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		These findings indicated that cancer cell autophagy is regulated by a collaborative interaction between tumor and immune cell components in distinct HCC microenvironments, thus allowing the inflammatory monocytes to be rerouted in a tumor-promoting direction.	Immunohistochemical staining	These findings indicated that cancer cell autophagy is regulated by a collaborative interaction between tumor and immune cell components in distinct HCC microenvironments, thus allowing the inflammatory monocytes to be rerouted in a tumor-promoting direction.		Immunofluorescence,Immunohistochemical Staining,qRT-PCR,Immunoblotting,Transmission electron microscopy,ELISA,RNA interference,			MAP1LC3B	TNF,IL1B,SNAI1	These findings indicated that cancer cell autophagy is regulated by a collaborative interaction between tumor and immune cell components in distinct HCC microenvironments, thus allowing the inflammatory monocytes to be rerouted in a tumor-promoting direction.	These findings indicated that cancer cell autophagy is regulated by a collaborative interaction between tumor and immune cell components in distinct HCC microenvironments, thus allowing the inflammatory monocytes to be rerouted in a tumor-promoting direction.;These findings indicated that cancer cell autophagy is regulated by a collaborative interaction between tumor and immune cell components in distinct HCC microenvironments, thus allowing the inflammatory monocytes to be rerouted in a tumor-promoting direction.;These findings indicated that cancer cell autophagy is regulated by a collaborative interaction between tumor and immune cell components in distinct HCC microenvironments, thus allowing the inflammatory monocytes to be rerouted in a tumor-promoting direction.
29934339	chr16	53698968	53700968	FTO	We employed in vitro adipogenesis models to investigate molecular mechanisms by which Fto affects adipocyte development and function. Fto expression is upregulated during adipogenesis, and is required for the maintenance of CEBPB and Cebpd/CEBPD expression in murine and human adipocytes in vitro. Fto knockdown decreases both the number of 3T3-L1 cells that differentiate into adipocytes as well as the amount of lipid per mature adipocyte. This effect on adipocyte programming is conveyed, in part, by modulation of C/ebpβ-regulated transcription. We find that Fto also affects Cebpd transcription by demethylating DNA N6-methyldeoxyadenosine in the Cebpd promoter. Fto is permissive for adipogenesis and promotes maintenance of lipid content in mature adipocytes by enabling C/ebpβ-driven transcription and expression of Cebpd. These findings are consistent with the loss of fat mass in mice segregating for a dominant-negative Fto allele. 	human	adipose	High+Lowthroughput	FTO mediates cell-autonomous effects on adipogenesis and adipocyte lipid content by regulating gene expression via 6mA DNA modifications	是	rs9939609,rs8050136,rs1421085	Diabetes mellitus, obesity	fat cell	E_01_0391	transfection,RNA expression studies, RNA-Seq,m6A-RIP,6mA DNA Immunoprecipitation,Lipid Staining,Quantitative real time PCR,ChIP,Western blot,	We employed in vitro adipogenesis models to investigate molecular mechanisms by which Fto affects adipocyte development and function. Fto expression is upregulated during adipogenesis, and is required for the maintenance of CEBPB and Cebpd/CEBPD expression in murine and human adipocytes in vitro. Fto knockdown decreases both the number of 3T3-L1 cells that differentiate into adipocytes as well as the amount of lipid per mature adipocyte. This effect on adipocyte programming is conveyed, in part, by modulation of C/ebpβ-regulated transcription. We find that Fto also affects Cebpd transcription by demethylating DNA N6-methyldeoxyadenosine in the Cebpd promoter. Fto is permissive for adipogenesis and promotes maintenance of lipid content in mature adipocytes by enabling C/ebpβ-driven transcription and expression of Cebpd. These findings are consistent with the loss of fat mass in mice segregating for a dominant-negative Fto allele. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We employed in vitro adipogenesis models to investigate molecular mechanisms by which Fto affects adipocyte development and function. Fto expression is upregulated during adipogenesis, and is required for the maintenance of CEBPB and Cebpd/CEBPD expression in murine and human adipocytes in vitro. Fto knockdown decreases both the number of 3T3-L1 cells that differentiate into adipocytes as well as the amount of lipid per mature adipocyte. This effect on adipocyte programming is conveyed, in part, by modulation of C/ebpβ-regulated transcription. We find that Fto also affects Cebpd transcription by demethylating DNA N6-methyldeoxyadenosine in the Cebpd promoter. Fto is permissive for adipogenesis and promotes maintenance of lipid content in mature adipocytes by enabling C/ebpβ-driven transcription and expression of Cebpd. These findings are consistent with the loss of fat mass in mice segregating for a dominant-negative Fto allele. 	Immunohistochemical staining	We employed in vitro adipogenesis models to investigate molecular mechanisms by which Fto affects adipocyte development and function. Fto expression is upregulated during adipogenesis, and is required for the maintenance of CEBPB and Cebpd/CEBPD expression in murine and human adipocytes in vitro. Fto knockdown decreases both the number of 3T3-L1 cells that differentiate into adipocytes as well as the amount of lipid per mature adipocyte. This effect on adipocyte programming is conveyed, in part, by modulation of C/ebpβ-regulated transcription. We find that Fto also affects Cebpd transcription by demethylating DNA N6-methyldeoxyadenosine in the Cebpd promoter. Fto is permissive for adipogenesis and promotes maintenance of lipid content in mature adipocytes by enabling C/ebpβ-driven transcription and expression of Cebpd. These findings are consistent with the loss of fat mass in mice segregating for a dominant-negative Fto allele. 		transfection,RNA expression studies, RNA-Seq,m6A-RIP,6mA DNA Immunoprecipitation,Lipid Staining,Quantitative real time PCR,ChIP,Western blot,			FTO	CEBPB	We employed in vitro adipogenesis models to investigate molecular mechanisms by which Fto affects adipocyte development and function. Fto expression is upregulated during adipogenesis, and is required for the maintenance of CEBPB and Cebpd/CEBPD expression in murine and human adipocytes in vitro. Fto knockdown decreases both the number of 3T3-L1 cells that differentiate into adipocytes as well as the amount of lipid per mature adipocyte. This effect on adipocyte programming is conveyed, in part, by modulation of C/ebpβ-regulated transcription. We find that Fto also affects Cebpd transcription by demethylating DNA N6-methyldeoxyadenosine in the Cebpd promoter. Fto is permissive for adipogenesis and promotes maintenance of lipid content in mature adipocytes by enabling C/ebpβ-driven transcription and expression of Cebpd. These findings are consistent with the loss of fat mass in mice segregating for a dominant-negative Fto allele. 	We employed in vitro adipogenesis models to investigate molecular mechanisms by which Fto affects adipocyte development and function. Fto expression is upregulated during adipogenesis, and is required for the maintenance of CEBPB and Cebpd/CEBPD expression in murine and human adipocytes in vitro. Fto knockdown decreases both the number of 3T3-L1 cells that differentiate into adipocytes as well as the amount of lipid per mature adipocyte. This effect on adipocyte programming is conveyed, in part, by modulation of C/ebpβ-regulated transcription. We find that Fto also affects Cebpd transcription by demethylating DNA N6-methyldeoxyadenosine in the Cebpd promoter. Fto is permissive for adipogenesis and promotes maintenance of lipid content in mature adipocytes by enabling C/ebpβ-driven transcription and expression of Cebpd. These findings are consistent with the loss of fat mass in mice segregating for a dominant-negative Fto allele. 
29932212	chr21	34784999	34786999	RUNX1	CSF3R mutations are uncommon in AML; however, when they occur, they are often associated with core-binding factor gene abnormalities and CEBPAdm. An in-depth understanding of the interaction between these genetic alterations could facilitate a clearer understanding of the role of CSF3R mutations in AML development and may be used for disease classification, prognosis, and the development of targeted therapy.	human	Nervous	High+Lowthroughput	CSF3R Mutations are frequently associated with abnormalities of RUNX1, CBFB, CEBPA, and NPM1 genes in acute myeloid leukemia	否		Acute myeloid leukemia	neutrophils	E_01_0392	DNA-Seq,RT-PCR,Mutation Analysis,	CSF3R mutations are uncommon in AML; however, when they occur, they are often associated with core-binding factor gene abnormalities and CEBPAdm. An in-depth understanding of the interaction between these genetic alterations could facilitate a clearer understanding of the role of CSF3R mutations in AML development and may be used for disease classification, prognosis, and the development of targeted therapy.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		CSF3R mutations are uncommon in AML; however, when they occur, they are often associated with core-binding factor gene abnormalities and CEBPAdm. An in-depth understanding of the interaction between these genetic alterations could facilitate a clearer understanding of the role of CSF3R mutations in AML development and may be used for disease classification, prognosis, and the development of targeted therapy.	Immunohistochemical staining	CSF3R mutations are uncommon in AML; however, when they occur, they are often associated with core-binding factor gene abnormalities and CEBPAdm. An in-depth understanding of the interaction between these genetic alterations could facilitate a clearer understanding of the role of CSF3R mutations in AML development and may be used for disease classification, prognosis, and the development of targeted therapy.		DNA-Seq,RT-PCR,Mutation Analysis,			NPM1,CSF3R	RUNX1,CBFB,CEBPA	CSF3R mutations are uncommon in AML; however, when they occur, they are often associated with core-binding factor gene abnormalities and CEBPAdm. An in-depth understanding of the interaction between these genetic alterations could facilitate a clearer understanding of the role of CSF3R mutations in AML development and may be used for disease classification, prognosis, and the development of targeted therapy.;CSF3R mutations are uncommon in AML; however, when they occur, they are often associated with core-binding factor gene abnormalities and CEBPAdm. An in-depth understanding of the interaction between these genetic alterations could facilitate a clearer understanding of the role of CSF3R mutations in AML development and may be used for disease classification, prognosis, and the development of targeted therapy.	CSF3R mutations are uncommon in AML; however, when they occur, they are often associated with core-binding factor gene abnormalities and CEBPAdm. An in-depth understanding of the interaction between these genetic alterations could facilitate a clearer understanding of the role of CSF3R mutations in AML development and may be used for disease classification, prognosis, and the development of targeted therapy.;CSF3R mutations are uncommon in AML; however, when they occur, they are often associated with core-binding factor gene abnormalities and CEBPAdm. An in-depth understanding of the interaction between these genetic alterations could facilitate a clearer understanding of the role of CSF3R mutations in AML development and may be used for disease classification, prognosis, and the development of targeted therapy.;CSF3R mutations are uncommon in AML; however, when they occur, they are often associated with core-binding factor gene abnormalities and CEBPAdm. An in-depth understanding of the interaction between these genetic alterations could facilitate a clearer understanding of the role of CSF3R mutations in AML development and may be used for disease classification, prognosis, and the development of targeted therapy.
29929436	chr1	45508017	45510017	PRDX1	Additionally, migration and invasion abilities of PRDX1KD MDA-MB-231 and PRDX1KD SK-HEP-1 cancer cells were significantly enhanced compared to those of control cancer cells. Taken together, these results suggest that PRDX1 negatively regulates TLR4 signaling for NFKB activation and autophagy functions such as bactericidal activity, cancer cell migration, and cancer cell invasion by inhibiting TRAF6 ubiquitin-ligase activity.	human	Epithelial	High+Lowthroughput	Inhibition of TRAF6 ubiquitin-ligase activity by PRDX1 leads to inhibition of NFKB activation and autophagy activation	否		Other	THP-1	E_01_0393	Luciferase reporter assay,Western blot,Immunoprecipitation (IP),qRT-PCR,Immunofluorescence microscopy,Salmonella Infection Assay,transwell migration assay,	Additionally, migration and invasion abilities of PRDX1KD MDA-MB-231 and PRDX1KD SK-HEP-1 cancer cells were significantly enhanced compared to those of control cancer cells. Taken together, these results suggest that PRDX1 negatively regulates TLR4 signaling for NFKB activation and autophagy functions such as bactericidal activity, cancer cell migration, and cancer cell invasion by inhibiting TRAF6 ubiquitin-ligase activity.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Additionally, migration and invasion abilities of PRDX1KD MDA-MB-231 and PRDX1KD SK-HEP-1 cancer cells were significantly enhanced compared to those of control cancer cells. Taken together, these results suggest that PRDX1 negatively regulates TLR4 signaling for NFKB activation and autophagy functions such as bactericidal activity, cancer cell migration, and cancer cell invasion by inhibiting TRAF6 ubiquitin-ligase activity.	Immunohistochemical staining	Additionally, migration and invasion abilities of PRDX1KD MDA-MB-231 and PRDX1KD SK-HEP-1 cancer cells were significantly enhanced compared to those of control cancer cells. Taken together, these results suggest that PRDX1 negatively regulates TLR4 signaling for NFKB activation and autophagy functions such as bactericidal activity, cancer cell migration, and cancer cell invasion by inhibiting TRAF6 ubiquitin-ligase activity.		Luciferase reporter assay,Western blot,Immunoprecipitation (IP),qRT-PCR,Immunofluorescence microscopy,Salmonella Infection Assay,transwell migration assay,			PRDX1,TRAF6,BECN1	TLR4	Additionally, migration and invasion abilities of PRDX1KD MDA-MB-231 and PRDX1KD SK-HEP-1 cancer cells were significantly enhanced compared to those of control cancer cells. Taken together, these results suggest that PRDX1 negatively regulates TLR4 signaling for NFKB activation and autophagy functions such as bactericidal activity, cancer cell migration, and cancer cell invasion by inhibiting TRAF6 ubiquitin-ligase activity.;Additionally, migration and invasion abilities of PRDX1KD MDA-MB-231 and PRDX1KD SK-HEP-1 cancer cells were significantly enhanced compared to those of control cancer cells. Taken together, these results suggest that PRDX1 negatively regulates TLR4 signaling for NFKB activation and autophagy functions such as bactericidal activity, cancer cell migration, and cancer cell invasion by inhibiting TRAF6 ubiquitin-ligase activity.;Additionally, migration and invasion abilities of PRDX1KD MDA-MB-231 and PRDX1KD SK-HEP-1 cancer cells were significantly enhanced compared to those of control cancer cells. Taken together, these results suggest that PRDX1 negatively regulates TLR4 signaling for NFKB activation and autophagy functions such as bactericidal activity, cancer cell migration, and cancer cell invasion by inhibiting TRAF6 ubiquitin-ligase activity.	Additionally, migration and invasion abilities of PRDX1KD MDA-MB-231 and PRDX1KD SK-HEP-1 cancer cells were significantly enhanced compared to those of control cancer cells. Taken together, these results suggest that PRDX1 negatively regulates TLR4 signaling for NFKB activation and autophagy functions such as bactericidal activity, cancer cell migration, and cancer cell invasion by inhibiting TRAF6 ubiquitin-ligase activity.
29928592	chr8	19898949	19900949	LPL	TBBPA did not influence osteoblast differentiation, but TCDD suppressed ALP staining and activity, calcium deposition, and osteoblast-related mRNA levels. In a mixture of TBBPA and TCDD, TBBPA inhibited TCDD suppression of adipocyte and osteoblast differentiation in a dose-dependent manner. Interestingly, we observed lipid droplets in TBBPA-treated cells differentiated into osteoblasts. These results suggest that TBBPA and TCDD disrupted differentiation into adipocytes and osteoblasts and contributes to a more complete toxicological understanding of exposure to these chemical substances.	human	Nervous	High+Lowthroughput	Complex toxicity as disruption of adipocyte or osteoblast differentiation in human mesenchymal stem cells under the mixed condition of TBBPA and TCDD	否			mesenchymal stem cell	E_01_0394	RT-qPCR,oil red O staining,ALP activity assay,cell matrix ALP staining, alizarin red S staining,	TBBPA did not influence osteoblast differentiation, but TCDD suppressed ALP staining and activity, calcium deposition, and osteoblast-related mRNA levels. In a mixture of TBBPA and TCDD, TBBPA inhibited TCDD suppression of adipocyte and osteoblast differentiation in a dose-dependent manner. Interestingly, we observed lipid droplets in TBBPA-treated cells differentiated into osteoblasts. These results suggest that TBBPA and TCDD disrupted differentiation into adipocytes and osteoblasts and contributes to a more complete toxicological understanding of exposure to these chemical substances.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		TBBPA did not influence osteoblast differentiation, but TCDD suppressed ALP staining and activity, calcium deposition, and osteoblast-related mRNA levels. In a mixture of TBBPA and TCDD, TBBPA inhibited TCDD suppression of adipocyte and osteoblast differentiation in a dose-dependent manner. Interestingly, we observed lipid droplets in TBBPA-treated cells differentiated into osteoblasts. These results suggest that TBBPA and TCDD disrupted differentiation into adipocytes and osteoblasts and contributes to a more complete toxicological understanding of exposure to these chemical substances.	Immunohistochemical staining	TBBPA did not influence osteoblast differentiation, but TCDD suppressed ALP staining and activity, calcium deposition, and osteoblast-related mRNA levels. In a mixture of TBBPA and TCDD, TBBPA inhibited TCDD suppression of adipocyte and osteoblast differentiation in a dose-dependent manner. Interestingly, we observed lipid droplets in TBBPA-treated cells differentiated into osteoblasts. These results suggest that TBBPA and TCDD disrupted differentiation into adipocytes and osteoblasts and contributes to a more complete toxicological understanding of exposure to these chemical substances.		RT-qPCR,oil red O staining,ALP activity assay,cell matrix ALP staining, alizarin red S staining,				LPL		TBBPA did not influence osteoblast differentiation, but TCDD suppressed ALP staining and activity, calcium deposition, and osteoblast-related mRNA levels. In a mixture of TBBPA and TCDD, TBBPA inhibited TCDD suppression of adipocyte and osteoblast differentiation in a dose-dependent manner. Interestingly, we observed lipid droplets in TBBPA-treated cells differentiated into osteoblasts. These results suggest that TBBPA and TCDD disrupted differentiation into adipocytes and osteoblasts and contributes to a more complete toxicological understanding of exposure to these chemical substances.
29928447	chr2	15937740	15939740	MYCN	The CTC-specific mutations were enhancer of zeste polycomb repressive complex 2 subunit, notch 1, AT-rich interaction domain 1A, serine/threonine kinase 11, fms related tyrosine kinase 3, MYCN proto-oncogene, bHLH transcription factor, APC, WNT signaling pathway regulator, and phosphatase and tensin homolog. The technique used by the present study was demonstrated to be effective at isolating CTCs at a sufficiently high purity for genomic analysis, and supported the use of comprehensive cancer panel analysis as a potential application for precision medicine.	human		High+Lowthroughput	Cancer panel analysis of circulating tumor cells in patients with breast cancer	否		mammary cancer	NCI-H358	E_01_0395	Immunofluorescent staining,Whole genome amplification,CCP,	The CTC-specific mutations were enhancer of zeste polycomb repressive complex 2 subunit, notch 1, AT-rich interaction domain 1A, serine/threonine kinase 11, fms related tyrosine kinase 3, MYCN proto-oncogene, bHLH transcription factor, APC, WNT signaling pathway regulator, and phosphatase and tensin homolog. The technique used by the present study was demonstrated to be effective at isolating CTCs at a sufficiently high purity for genomic analysis, and supported the use of comprehensive cancer panel analysis as a potential application for precision medicine.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The CTC-specific mutations were enhancer of zeste polycomb repressive complex 2 subunit, notch 1, AT-rich interaction domain 1A, serine/threonine kinase 11, fms related tyrosine kinase 3, MYCN proto-oncogene, bHLH transcription factor, APC, WNT signaling pathway regulator, and phosphatase and tensin homolog. The technique used by the present study was demonstrated to be effective at isolating CTCs at a sufficiently high purity for genomic analysis, and supported the use of comprehensive cancer panel analysis as a potential application for precision medicine.	Immunohistochemical staining	The CTC-specific mutations were enhancer of zeste polycomb repressive complex 2 subunit, notch 1, AT-rich interaction domain 1A, serine/threonine kinase 11, fms related tyrosine kinase 3, MYCN proto-oncogene, bHLH transcription factor, APC, WNT signaling pathway regulator, and phosphatase and tensin homolog. The technique used by the present study was demonstrated to be effective at isolating CTCs at a sufficiently high purity for genomic analysis, and supported the use of comprehensive cancer panel analysis as a potential application for precision medicine.		Immunofluorescent staining,Whole genome amplification,CCP,				MYCN,APC		The CTC-specific mutations were enhancer of zeste polycomb repressive complex 2 subunit, notch 1, AT-rich interaction domain 1A, serine/threonine kinase 11, fms related tyrosine kinase 3, MYCN proto-oncogene, bHLH transcription factor, APC, WNT signaling pathway regulator, and phosphatase and tensin homolog. The technique used by the present study was demonstrated to be effective at isolating CTCs at a sufficiently high purity for genomic analysis, and supported the use of comprehensive cancer panel analysis as a potential application for precision medicine.;The CTC-specific mutations were enhancer of zeste polycomb repressive complex 2 subunit, notch 1, AT-rich interaction domain 1A, serine/threonine kinase 11, fms related tyrosine kinase 3, MYCN proto-oncogene, bHLH transcription factor, APC, WNT signaling pathway regulator, and phosphatase and tensin homolog. The technique used by the present study was demonstrated to be effective at isolating CTCs at a sufficiently high purity for genomic analysis, and supported the use of comprehensive cancer panel analysis as a potential application for precision medicine.
29928394	chr10	52311539	52313539	DKK1	In the present study, DNase I hypersensitive sites and histone modifications of DKK1 were investigated in the A549 lung cancer cell line using the UCSC Genome Browser. A set of cis-acting enhancer elements were identified by a dual-luciferase reporter gene assay system to increase activity of the DKK1 promoter with lung cancer specificity. To the best of our knowledge, these data provide the first insight into the role of the DKK1 locus in lung cancer, and confirm the contribution of intronic cis-acting elements to the regulation of DKK1 expression, providing a new insight into gene regulation in lung cancer, which could inform the development of targeted therapy.	human	Lung cancer	High+Lowthroughput	Prediction and identification of transcriptional regulatory elements at the lung cancer-specific DKK1 locus	否		lung cancer		E_01_0396	PCR,Plasmid transfection,Firefly/Renilla luciferase quantification,	In the present study, DNase I hypersensitive sites and histone modifications of DKK1 were investigated in the A549 lung cancer cell line using the UCSC Genome Browser. A set of cis-acting enhancer elements were identified by a dual-luciferase reporter gene assay system to increase activity of the DKK1 promoter with lung cancer specificity. To the best of our knowledge, these data provide the first insight into the role of the DKK1 locus in lung cancer, and confirm the contribution of intronic cis-acting elements to the regulation of DKK1 expression, providing a new insight into gene regulation in lung cancer, which could inform the development of targeted therapy.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In the present study, DNase I hypersensitive sites and histone modifications of DKK1 were investigated in the A549 lung cancer cell line using the UCSC Genome Browser. A set of cis-acting enhancer elements were identified by a dual-luciferase reporter gene assay system to increase activity of the DKK1 promoter with lung cancer specificity. To the best of our knowledge, these data provide the first insight into the role of the DKK1 locus in lung cancer, and confirm the contribution of intronic cis-acting elements to the regulation of DKK1 expression, providing a new insight into gene regulation in lung cancer, which could inform the development of targeted therapy.	Immunohistochemical staining	In the present study, DNase I hypersensitive sites and histone modifications of DKK1 were investigated in the A549 lung cancer cell line using the UCSC Genome Browser. A set of cis-acting enhancer elements were identified by a dual-luciferase reporter gene assay system to increase activity of the DKK1 promoter with lung cancer specificity. To the best of our knowledge, these data provide the first insight into the role of the DKK1 locus in lung cancer, and confirm the contribution of intronic cis-acting elements to the regulation of DKK1 expression, providing a new insight into gene regulation in lung cancer, which could inform the development of targeted therapy.		PCR,Plasmid transfection,Firefly/Renilla luciferase quantification,			DKK1		In the present study, DNase I hypersensitive sites and histone modifications of DKK1 were investigated in the A549 lung cancer cell line using the UCSC Genome Browser. A set of cis-acting enhancer elements were identified by a dual-luciferase reporter gene assay system to increase activity of the DKK1 promoter with lung cancer specificity. To the best of our knowledge, these data provide the first insight into the role of the DKK1 locus in lung cancer, and confirm the contribution of intronic cis-acting elements to the regulation of DKK1 expression, providing a new insight into gene regulation in lung cancer, which could inform the development of targeted therapy.	
29927026	chr4	108044908	108046908	LEF1	Our results showed a novel LEF1‐CYGB axis in OS lung metastasis and may provide a new way of developing therapeutic strategies to prevent OS lung metastasis	human	Skeletal	High+Lowthroughput	Novel lymphoid enhancer-binding factor 1-cytoglobin axis promotes extravasation of osteosarcoma cells into the lungs	否		Osteosarcoma (OS)	LM8-C3H	E_01_0397	Histology analysis,Western blot,Cell‐proliferation assay,Extravasation assay,Cell‐adhesion assay,Transmigration assay,Genomewide meta‐analysis,Reverse transcription‐PCR,qPCR,CRISPR‐Cas9 ,	Our results showed a novel LEF1‐CYGB axis in OS lung metastasis and may provide a new way of developing therapeutic strategies to prevent OS lung metastasis	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Our results showed a novel LEF1‐CYGB axis in OS lung metastasis and may provide a new way of developing therapeutic strategies to prevent OS lung metastasis	Immunohistochemical staining	Our results showed a novel LEF1‐CYGB axis in OS lung metastasis and may provide a new way of developing therapeutic strategies to prevent OS lung metastasis		Histology analysis,Western blot,Cell‐proliferation assay,Extravasation assay,Cell‐adhesion assay,Transmigration assay,Genomewide meta‐analysis,Reverse transcription‐PCR,qPCR,CRISPR‐Cas9 ,			Cygb,CYGB	LEF1	Our results showed a novel LEF1‐CYGB axis in OS lung metastasis and may provide a new way of developing therapeutic strategies to prevent OS lung metastasis;Our results showed a novel LEF1‐CYGB axis in OS lung metastasis and may provide a new way of developing therapeutic strategies to prevent OS lung metastasis	Our results showed a novel LEF1‐CYGB axis in OS lung metastasis and may provide a new way of developing therapeutic strategies to prevent OS lung metastasis
29925637	chr3	185640391	185642391	IGF2BP2	We demonstrated that linc-ADAL interacts with heterogeneous nuclear ribonucleoprotein U (hnRNPU) and insulin-like growth factor 2 mRNA binding protein 2 (IGF2BP2) at distinct subcellular locations to regulate adipocyte differentiation and lipogenesis.	human	adipose	High+Lowthroughput	Interrogation of nonconserved human adipose lincRNAs identifies a regulatory role of linc-ADAL in adipocyte metabolism	否		Other	fat cell	E_01_0398	RNA knockdown,RNA-seq,ChIP-seq,Western blot, immunoblot, CLIP-seq,	We demonstrated that linc-ADAL interacts with heterogeneous nuclear ribonucleoprotein U (hnRNPU) and insulin-like growth factor 2 mRNA binding protein 2 (IGF2BP2) at distinct subcellular locations to regulate adipocyte differentiation and lipogenesis.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We demonstrated that linc-ADAL interacts with heterogeneous nuclear ribonucleoprotein U (hnRNPU) and insulin-like growth factor 2 mRNA binding protein 2 (IGF2BP2) at distinct subcellular locations to regulate adipocyte differentiation and lipogenesis.	Immunohistochemical staining	We demonstrated that linc-ADAL interacts with heterogeneous nuclear ribonucleoprotein U (hnRNPU) and insulin-like growth factor 2 mRNA binding protein 2 (IGF2BP2) at distinct subcellular locations to regulate adipocyte differentiation and lipogenesis.		RNA knockdown,RNA-seq,ChIP-seq,Western blot, immunoblot, CLIP-seq,				IGF2BP2		We demonstrated that linc-ADAL interacts with heterogeneous nuclear ribonucleoprotein U (hnRNPU) and insulin-like growth factor 2 mRNA binding protein 2 (IGF2BP2) at distinct subcellular locations to regulate adipocyte differentiation and lipogenesis.
29923177	chr10	22317950	22319950	BMI1	At PIP4K2A, we identified rs4748812 (Pmeta=1.3x10-15), which alters a RUNX1 binding motif and demonstrated chromosomal looping to the PIP4K2A promoter. Fine-mapping chromosome 10p12 in a multi-ethnic ALL GWAS confirmed independent associations and identified putative functional variants upstream of BMI1 and at PIP4K2A.	human	lymphoid	High+Lowthroughput	BMI1 enhancer polymorphism underlies chromosome 10p12.31 association with childhood acute lymphoblastic leukemia	是	rs11591377,rs4748812	Childhood acute lymphoblastic leukaemia (all)		E_01_0399	CHIP-seq,GWS,Enhancer assay,H3k27ac HiChIP data analysis,MethylC-Seq Analysis,Transcription factor binding analysis,	At PIP4K2A, we identified rs4748812 (Pmeta=1.3x10-15), which alters a RUNX1 binding motif and demonstrated chromosomal looping to the PIP4K2A promoter. Fine-mapping chromosome 10p12 in a multi-ethnic ALL GWAS confirmed independent associations and identified putative functional variants upstream of BMI1 and at PIP4K2A.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		At PIP4K2A, we identified rs4748812 (Pmeta=1.3x10-15), which alters a RUNX1 binding motif and demonstrated chromosomal looping to the PIP4K2A promoter. Fine-mapping chromosome 10p12 in a multi-ethnic ALL GWAS confirmed independent associations and identified putative functional variants upstream of BMI1 and at PIP4K2A.	Immunohistochemical staining	At PIP4K2A, we identified rs4748812 (Pmeta=1.3x10-15), which alters a RUNX1 binding motif and demonstrated chromosomal looping to the PIP4K2A promoter. Fine-mapping chromosome 10p12 in a multi-ethnic ALL GWAS confirmed independent associations and identified putative functional variants upstream of BMI1 and at PIP4K2A.		CHIP-seq,GWS,Enhancer assay,H3k27ac HiChIP data analysis,MethylC-Seq Analysis,Transcription factor binding analysis,			PIP4K2A	BMI1,MYBL2,RUNX1,ARID5B,IKZF1,CEBPE,GATA3	At PIP4K2A, we identified rs4748812 (Pmeta=1.3x10-15), which alters a RUNX1 binding motif and demonstrated chromosomal looping to the PIP4K2A promoter. Fine-mapping chromosome 10p12 in a multi-ethnic ALL GWAS confirmed independent associations and identified putative functional variants upstream of BMI1 and at PIP4K2A.	At PIP4K2A, we identified rs4748812 (Pmeta=1.3x10-15), which alters a RUNX1 binding motif and demonstrated chromosomal looping to the PIP4K2A promoter. Fine-mapping chromosome 10p12 in a multi-ethnic ALL GWAS confirmed independent associations and identified putative functional variants upstream of BMI1 and at PIP4K2A.;At PIP4K2A, we identified rs4748812 (Pmeta=1.3x10-15), which alters a RUNX1 binding motif and demonstrated chromosomal looping to the PIP4K2A promoter. Fine-mapping chromosome 10p12 in a multi-ethnic ALL GWAS confirmed independent associations and identified putative functional variants upstream of BMI1 and at PIP4K2A.;At PIP4K2A, we identified rs4748812 (Pmeta=1.3x10-15), which alters a RUNX1 binding motif and demonstrated chromosomal looping to the PIP4K2A promoter. Fine-mapping chromosome 10p12 in a multi-ethnic ALL GWAS confirmed independent associations and identified putative functional variants upstream of BMI1 and at PIP4K2A.;At PIP4K2A, we identified rs4748812 (Pmeta=1.3x10-15), which alters a RUNX1 binding motif and demonstrated chromosomal looping to the PIP4K2A promoter. Fine-mapping chromosome 10p12 in a multi-ethnic ALL GWAS confirmed independent associations and identified putative functional variants upstream of BMI1 and at PIP4K2A.;At PIP4K2A, we identified rs4748812 (Pmeta=1.3x10-15), which alters a RUNX1 binding motif and demonstrated chromosomal looping to the PIP4K2A promoter. Fine-mapping chromosome 10p12 in a multi-ethnic ALL GWAS confirmed independent associations and identified putative functional variants upstream of BMI1 and at PIP4K2A.;At PIP4K2A, we identified rs4748812 (Pmeta=1.3x10-15), which alters a RUNX1 binding motif and demonstrated chromosomal looping to the PIP4K2A promoter. Fine-mapping chromosome 10p12 in a multi-ethnic ALL GWAS confirmed independent associations and identified putative functional variants upstream of BMI1 and at PIP4K2A.;At PIP4K2A, we identified rs4748812 (Pmeta=1.3x10-15), which alters a RUNX1 binding motif and demonstrated chromosomal looping to the PIP4K2A promoter. Fine-mapping chromosome 10p12 in a multi-ethnic ALL GWAS confirmed independent associations and identified putative functional variants upstream of BMI1 and at PIP4K2A.
29916899	chr11	65495083	65497083	MALAT1	MALAT1 could affect EMT and metastasis of EC cells through Ezh2-Notch1 signaling pathway. This study can give deeper understandings of the role of MALAT1 in EC and may provide some new directions for treatment of patients with EC.	human	Esophageal	High+Lowthroughput	LncRNA MALAT1 promotes epithelial-to-mesenchymal transition of esophageal cancer through Ezh2-Notch1 signaling pathway	否		Esophageal cancer (EC)	TE-1	E_01_0400	transfection,RT-PCR,Western blot,	MALAT1 could affect EMT and metastasis of EC cells through Ezh2-Notch1 signaling pathway. This study can give deeper understandings of the role of MALAT1 in EC and may provide some new directions for treatment of patients with EC.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		MALAT1 could affect EMT and metastasis of EC cells through Ezh2-Notch1 signaling pathway. This study can give deeper understandings of the role of MALAT1 in EC and may provide some new directions for treatment of patients with EC.	Immunohistochemical staining	MALAT1 could affect EMT and metastasis of EC cells through Ezh2-Notch1 signaling pathway. This study can give deeper understandings of the role of MALAT1 in EC and may provide some new directions for treatment of patients with EC.		transfection,RT-PCR,Western blot,			Ezh2,Notch1,Hes1	MALAT1	MALAT1 could affect EMT and metastasis of EC cells through Ezh2-Notch1 signaling pathway. This study can give deeper understandings of the role of MALAT1 in EC and may provide some new directions for treatment of patients with EC.;MALAT1 could affect EMT and metastasis of EC cells through Ezh2-Notch1 signaling pathway. This study can give deeper understandings of the role of MALAT1 in EC and may provide some new directions for treatment of patients with EC.;MALAT1 could affect EMT and metastasis of EC cells through Ezh2-Notch1 signaling pathway. This study can give deeper understandings of the role of MALAT1 in EC and may provide some new directions for treatment of patients with EC.	MALAT1 could affect EMT and metastasis of EC cells through Ezh2-Notch1 signaling pathway. This study can give deeper understandings of the role of MALAT1 in EC and may provide some new directions for treatment of patients with EC.
29915186	chr4	108045032	108047032	LEF1	Altogether, we provide evidence that BMP signalling is an important regulator for the neuronal fate specification of AH-NSPCs cultures and we show that it significantly cooperates with the previously described master regulator of adult hippocampal neurogenesis, the WNT signalling pathway.	human	Nervous	High+Lowthroughput	BMP and WNT signalling cooperate through LEF1 in the neuronal specification of adult hippocampal neural stem and progenitor cells	否		Hippocampal dentate gyrus		E_01_0401	Immunostaining,Gene Expression analysis,Western blot,ChIP,	Altogether, we provide evidence that BMP signalling is an important regulator for the neuronal fate specification of AH-NSPCs cultures and we show that it significantly cooperates with the previously described master regulator of adult hippocampal neurogenesis, the WNT signalling pathway.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Altogether, we provide evidence that BMP signalling is an important regulator for the neuronal fate specification of AH-NSPCs cultures and we show that it significantly cooperates with the previously described master regulator of adult hippocampal neurogenesis, the WNT signalling pathway.	Immunohistochemical staining	Altogether, we provide evidence that BMP signalling is an important regulator for the neuronal fate specification of AH-NSPCs cultures and we show that it significantly cooperates with the previously described master regulator of adult hippocampal neurogenesis, the WNT signalling pathway.		Immunostaining,Gene Expression analysis,Western blot,ChIP,				LEF1		Altogether, we provide evidence that BMP signalling is an important regulator for the neuronal fate specification of AH-NSPCs cultures and we show that it significantly cooperates with the previously described master regulator of adult hippocampal neurogenesis, the WNT signalling pathway.
29914089	chr5	17983939	17985939	Cd36	Gene analysis identified a Gamma interferon activation site (GAS) element in the CD36 gene promoter that acts as a STAT3 binding site, an interaction that was confirmed by ChIP assay. STAT3 interacts with nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), suggesting that nobiletin also acts through the CD36/ (STAT3)/NF-κB signaling axis. Nobiletin inhibited CD36-dependent breast cancer cell migration and invasion as well as CD36-mediated tumor sphere formation. Taken together, these results suggest that nobiletin inhibits cancer stem cells in multiple ways.	mouse	Epithelial	High+Lowthroughput	Nobiletin Inhibits CD36-Dependent Tumor Angiogenesis, Migration, Invasion, and Sphere Formation Through the Cd36/Stat3/Nf-Κb Signaling Axis	否		cancer	MCF-7	E_01_0402	Reverse Transcription-PCR,Western Blot,EMSA,Wound Healing Assay,Matrigel Invasion Assay,siRNA Analysis,In vitro Angiogenesis Assay,Molecular Docking,	Gene analysis identified a Gamma interferon activation site (GAS) element in the CD36 gene promoter that acts as a STAT3 binding site, an interaction that was confirmed by ChIP assay. STAT3 interacts with nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), suggesting that nobiletin also acts through the CD36/ (STAT3)/NF-κB signaling axis. Nobiletin inhibited CD36-dependent breast cancer cell migration and invasion as well as CD36-mediated tumor sphere formation. Taken together, these results suggest that nobiletin inhibits cancer stem cells in multiple ways.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Gene analysis identified a Gamma interferon activation site (GAS) element in the CD36 gene promoter that acts as a STAT3 binding site, an interaction that was confirmed by ChIP assay. STAT3 interacts with nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), suggesting that nobiletin also acts through the CD36/ (STAT3)/NF-κB signaling axis. Nobiletin inhibited CD36-dependent breast cancer cell migration and invasion as well as CD36-mediated tumor sphere formation. Taken together, these results suggest that nobiletin inhibits cancer stem cells in multiple ways.	Immunohistochemical staining	Gene analysis identified a Gamma interferon activation site (GAS) element in the CD36 gene promoter that acts as a STAT3 binding site, an interaction that was confirmed by ChIP assay. STAT3 interacts with nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), suggesting that nobiletin also acts through the CD36/ (STAT3)/NF-κB signaling axis. Nobiletin inhibited CD36-dependent breast cancer cell migration and invasion as well as CD36-mediated tumor sphere formation. Taken together, these results suggest that nobiletin inhibits cancer stem cells in multiple ways.		Reverse Transcription-PCR,Western Blot,EMSA,Wound Healing Assay,Matrigel Invasion Assay,siRNA Analysis,In vitro Angiogenesis Assay,Molecular Docking,			Cd36,Stat3		Gene analysis identified a Gamma interferon activation site (GAS) element in the CD36 gene promoter that acts as a STAT3 binding site, an interaction that was confirmed by ChIP assay. STAT3 interacts with nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), suggesting that nobiletin also acts through the CD36/ (STAT3)/NF-κB signaling axis. Nobiletin inhibited CD36-dependent breast cancer cell migration and invasion as well as CD36-mediated tumor sphere formation. Taken together, these results suggest that nobiletin inhibits cancer stem cells in multiple ways.;Gene analysis identified a Gamma interferon activation site (GAS) element in the CD36 gene promoter that acts as a STAT3 binding site, an interaction that was confirmed by ChIP assay. STAT3 interacts with nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), suggesting that nobiletin also acts through the CD36/ (STAT3)/NF-κB signaling axis. Nobiletin inhibited CD36-dependent breast cancer cell migration and invasion as well as CD36-mediated tumor sphere formation. Taken together, these results suggest that nobiletin inhibits cancer stem cells in multiple ways.	
29913133	chr1	209782740	209784740	IRF6	Therefore, we conclude that IRF6 and TFAP2A are part of a genetic regulatory network that is critical in epithelial development, with implications for both orofacial and cutaneous tissues. Our work provides in vivo, functional data to explain the relationship between AP2A protein binding and the MCS9.7 enhancer in orofacial clefting. This work is important because the MCS9.7 enhancer element contains a variant that abrogates AP2A protein binding and increases risk for orofacial clefting worldwide.	human	Epithelial	High+Lowthroughput	IRF6 and AP2A Interaction Regulates Epidermal Development	否	rs642961	Van der Woude syndrome (cleft lip / palate), popliteal pterygium syndrome (eye disease)	epidermal cell	E_01_0403	Western blot,	Therefore, we conclude that IRF6 and TFAP2A are part of a genetic regulatory network that is critical in epithelial development, with implications for both orofacial and cutaneous tissues. Our work provides in vivo, functional data to explain the relationship between AP2A protein binding and the MCS9.7 enhancer in orofacial clefting. This work is important because the MCS9.7 enhancer element contains a variant that abrogates AP2A protein binding and increases risk for orofacial clefting worldwide.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Therefore, we conclude that IRF6 and TFAP2A are part of a genetic regulatory network that is critical in epithelial development, with implications for both orofacial and cutaneous tissues. Our work provides in vivo, functional data to explain the relationship between AP2A protein binding and the MCS9.7 enhancer in orofacial clefting. This work is important because the MCS9.7 enhancer element contains a variant that abrogates AP2A protein binding and increases risk for orofacial clefting worldwide.	Immunohistochemical staining	Therefore, we conclude that IRF6 and TFAP2A are part of a genetic regulatory network that is critical in epithelial development, with implications for both orofacial and cutaneous tissues. Our work provides in vivo, functional data to explain the relationship between AP2A protein binding and the MCS9.7 enhancer in orofacial clefting. This work is important because the MCS9.7 enhancer element contains a variant that abrogates AP2A protein binding and increases risk for orofacial clefting worldwide.		Western blot,			Tfap2c,Tfap2a,Irf6	IRF6,TP63,GRHL3	Therefore, we conclude that IRF6 and TFAP2A are part of a genetic regulatory network that is critical in epithelial development, with implications for both orofacial and cutaneous tissues. Our work provides in vivo, functional data to explain the relationship between AP2A protein binding and the MCS9.7 enhancer in orofacial clefting. This work is important because the MCS9.7 enhancer element contains a variant that abrogates AP2A protein binding and increases risk for orofacial clefting worldwide.;Therefore, we conclude that IRF6 and TFAP2A are part of a genetic regulatory network that is critical in epithelial development, with implications for both orofacial and cutaneous tissues. Our work provides in vivo, functional data to explain the relationship between AP2A protein binding and the MCS9.7 enhancer in orofacial clefting. This work is important because the MCS9.7 enhancer element contains a variant that abrogates AP2A protein binding and increases risk for orofacial clefting worldwide.;Therefore, we conclude that IRF6 and TFAP2A are part of a genetic regulatory network that is critical in epithelial development, with implications for both orofacial and cutaneous tissues. Our work provides in vivo, functional data to explain the relationship between AP2A protein binding and the MCS9.7 enhancer in orofacial clefting. This work is important because the MCS9.7 enhancer element contains a variant that abrogates AP2A protein binding and increases risk for orofacial clefting worldwide.	Therefore, we conclude that IRF6 and TFAP2A are part of a genetic regulatory network that is critical in epithelial development, with implications for both orofacial and cutaneous tissues. Our work provides in vivo, functional data to explain the relationship between AP2A protein binding and the MCS9.7 enhancer in orofacial clefting. This work is important because the MCS9.7 enhancer element contains a variant that abrogates AP2A protein binding and increases risk for orofacial clefting worldwide.;Therefore, we conclude that IRF6 and TFAP2A are part of a genetic regulatory network that is critical in epithelial development, with implications for both orofacial and cutaneous tissues. Our work provides in vivo, functional data to explain the relationship between AP2A protein binding and the MCS9.7 enhancer in orofacial clefting. This work is important because the MCS9.7 enhancer element contains a variant that abrogates AP2A protein binding and increases risk for orofacial clefting worldwide.;Therefore, we conclude that IRF6 and TFAP2A are part of a genetic regulatory network that is critical in epithelial development, with implications for both orofacial and cutaneous tissues. Our work provides in vivo, functional data to explain the relationship between AP2A protein binding and the MCS9.7 enhancer in orofacial clefting. This work is important because the MCS9.7 enhancer element contains a variant that abrogates AP2A protein binding and increases risk for orofacial clefting worldwide.
29911120	chr13	40552875	40554875	FOXO1	Increasing of the apoptotic ratio was linked to miR-182-5p inhibition in the LNA-anti-miR group rather than other groups. Similarly, the necrotic ratio in the LNA-anti-miR group was higher.Our results supported the hypothesis that miR-182-5p inhibition can reduce the cell viability predominantly due to induces apoptosis and necrosis. The present results can apply in translational medicine for investigation of antisense therapy and drug development in leukemia.	human	Nervous	High+Lowthroughput	Apoptosis induction in acute promyelocytic leukemia cells through upregulation of CEBPα by miR-182 blockage	否		Acute promyelocytic leukemia	HL-60	E_01_0404	Cell transfection,Reverse transcriptase microRNA real-time PCR,qRT-PCR,Cell viability assay,	Increasing of the apoptotic ratio was linked to miR-182-5p inhibition in the LNA-anti-miR group rather than other groups. Similarly, the necrotic ratio in the LNA-anti-miR group was higher.Our results supported the hypothesis that miR-182-5p inhibition can reduce the cell viability predominantly due to induces apoptosis and necrosis. The present results can apply in translational medicine for investigation of antisense therapy and drug development in leukemia.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Increasing of the apoptotic ratio was linked to miR-182-5p inhibition in the LNA-anti-miR group rather than other groups. Similarly, the necrotic ratio in the LNA-anti-miR group was higher.Our results supported the hypothesis that miR-182-5p inhibition can reduce the cell viability predominantly due to induces apoptosis and necrosis. The present results can apply in translational medicine for investigation of antisense therapy and drug development in leukemia.	Immunohistochemical staining	Increasing of the apoptotic ratio was linked to miR-182-5p inhibition in the LNA-anti-miR group rather than other groups. Similarly, the necrotic ratio in the LNA-anti-miR group was higher.Our results supported the hypothesis that miR-182-5p inhibition can reduce the cell viability predominantly due to induces apoptosis and necrosis. The present results can apply in translational medicine for investigation of antisense therapy and drug development in leukemia.		Cell transfection,Reverse transcriptase microRNA real-time PCR,qRT-PCR,Cell viability assay,				FOXO1		Increasing of the apoptotic ratio was linked to miR-182-5p inhibition in the LNA-anti-miR group rather than other groups. Similarly, the necrotic ratio in the LNA-anti-miR group was higher.Our results supported the hypothesis that miR-182-5p inhibition can reduce the cell viability predominantly due to induces apoptosis and necrosis. The present results can apply in translational medicine for investigation of antisense therapy and drug development in leukemia.
29909987	chrX	67541571	67543571	AR	Collectively, these observations underscore the importance of epigenomic profiling in primary specimens and the value of deploying genome editing to functionally characterize noncoding elements. More broadly, this work identifies a therapeutic vulnerability for targeting the AR and emphasizes the importance of regulatory elements as highly recurrent oncogenic drivers.	human	connective	High+Lowthroughput	A Somatically Acquired Enhancer of the Androgen Receptor Is a Noncoding Driver in Advanced Prostate Cancer	否		prostatic cancer		E_01_0405	PCR,CRISPR/Cas9,Proliferation Assays,Competition Experiments,Quantitative RT-PCR,Immunoblotting,Cloning,Chromosome Conformation Capture(3C),Crystal Violet Proliferation Assays,ChIP-seq,ChIP,ChIP-qPCR,Whole-Genome Bisulfite Sequencing analysis(WGBS),	Collectively, these observations underscore the importance of epigenomic profiling in primary specimens and the value of deploying genome editing to functionally characterize noncoding elements. More broadly, this work identifies a therapeutic vulnerability for targeting the AR and emphasizes the importance of regulatory elements as highly recurrent oncogenic drivers.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Collectively, these observations underscore the importance of epigenomic profiling in primary specimens and the value of deploying genome editing to functionally characterize noncoding elements. More broadly, this work identifies a therapeutic vulnerability for targeting the AR and emphasizes the importance of regulatory elements as highly recurrent oncogenic drivers.	Immunohistochemical staining	Collectively, these observations underscore the importance of epigenomic profiling in primary specimens and the value of deploying genome editing to functionally characterize noncoding elements. More broadly, this work identifies a therapeutic vulnerability for targeting the AR and emphasizes the importance of regulatory elements as highly recurrent oncogenic drivers.		PCR,CRISPR/Cas9,Proliferation Assays,Competition Experiments,Quantitative RT-PCR,Immunoblotting,Cloning,Chromosome Conformation Capture(3C),Crystal Violet Proliferation Assays,ChIP-seq,ChIP,ChIP-qPCR,Whole-Genome Bisulfite Sequencing analysis(WGBS),			EIF4A3,SF3B3,RPL23	AR	Collectively, these observations underscore the importance of epigenomic profiling in primary specimens and the value of deploying genome editing to functionally characterize noncoding elements. More broadly, this work identifies a therapeutic vulnerability for targeting the AR and emphasizes the importance of regulatory elements as highly recurrent oncogenic drivers.;Collectively, these observations underscore the importance of epigenomic profiling in primary specimens and the value of deploying genome editing to functionally characterize noncoding elements. More broadly, this work identifies a therapeutic vulnerability for targeting the AR and emphasizes the importance of regulatory elements as highly recurrent oncogenic drivers.;Collectively, these observations underscore the importance of epigenomic profiling in primary specimens and the value of deploying genome editing to functionally characterize noncoding elements. More broadly, this work identifies a therapeutic vulnerability for targeting the AR and emphasizes the importance of regulatory elements as highly recurrent oncogenic drivers.	Collectively, these observations underscore the importance of epigenomic profiling in primary specimens and the value of deploying genome editing to functionally characterize noncoding elements. More broadly, this work identifies a therapeutic vulnerability for targeting the AR and emphasizes the importance of regulatory elements as highly recurrent oncogenic drivers.
29909985	chrX	67541233	67543233	AR	A subset of cases displayed AR or MYC enhancer duplication in the context of a genome-wide tandem duplicator phenotype associated with CDK12 inactivation. Our findings highlight the complex genomic structure of mCRPC, nominate alterations that may inform prostate cancer treatment, and suggest that additional recurrent events in the non-coding mCRPC genome remain to be discovered.	human	Myotome	High+Lowthroughput	Structural Alterations Driving Castration-Resistant Prostate Cancer Revealed by Linked-Read Genome Sequencing	否		Metastatic castration resistant prostate cancer (mcrpc)	LNCaP	E_01_0406	WGS,qPCR,Hi-C,CHIP,DNA seq,	A subset of cases displayed AR or MYC enhancer duplication in the context of a genome-wide tandem duplicator phenotype associated with CDK12 inactivation. Our findings highlight the complex genomic structure of mCRPC, nominate alterations that may inform prostate cancer treatment, and suggest that additional recurrent events in the non-coding mCRPC genome remain to be discovered.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		A subset of cases displayed AR or MYC enhancer duplication in the context of a genome-wide tandem duplicator phenotype associated with CDK12 inactivation. Our findings highlight the complex genomic structure of mCRPC, nominate alterations that may inform prostate cancer treatment, and suggest that additional recurrent events in the non-coding mCRPC genome remain to be discovered.	Immunohistochemical staining	A subset of cases displayed AR or MYC enhancer duplication in the context of a genome-wide tandem duplicator phenotype associated with CDK12 inactivation. Our findings highlight the complex genomic structure of mCRPC, nominate alterations that may inform prostate cancer treatment, and suggest that additional recurrent events in the non-coding mCRPC genome remain to be discovered.		WGS,qPCR,Hi-C,CHIP,DNA seq,			CDK12	AR,MYC	A subset of cases displayed AR or MYC enhancer duplication in the context of a genome-wide tandem duplicator phenotype associated with CDK12 inactivation. Our findings highlight the complex genomic structure of mCRPC, nominate alterations that may inform prostate cancer treatment, and suggest that additional recurrent events in the non-coding mCRPC genome remain to be discovered.	A subset of cases displayed AR or MYC enhancer duplication in the context of a genome-wide tandem duplicator phenotype associated with CDK12 inactivation. Our findings highlight the complex genomic structure of mCRPC, nominate alterations that may inform prostate cancer treatment, and suggest that additional recurrent events in the non-coding mCRPC genome remain to be discovered.;A subset of cases displayed AR or MYC enhancer duplication in the context of a genome-wide tandem duplicator phenotype associated with CDK12 inactivation. Our findings highlight the complex genomic structure of mCRPC, nominate alterations that may inform prostate cancer treatment, and suggest that additional recurrent events in the non-coding mCRPC genome remain to be discovered.
29909962	chr8	11792732	11794732	FDFT1	Whole-exome sequencing was used to identify recessive disease-causing variants in FDFT1. Functional characterization of one variant demonstrated a partial splicing defect and altered promoter and/or enhancer activity, reflecting essential mechanisms for regulating cholesterol biosynthesis/uptake in steady state.	human	connective	High+Lowthroughput	Squalene Synthase Deficiency: Clinical, Biochemical, and Molecular Characterization of a Defect in Cholesterol Biosynthesis	否		Squalene synthase deficiency	fibroblast	E_01_0407	PCR,WES,Western blot,	Whole-exome sequencing was used to identify recessive disease-causing variants in FDFT1. Functional characterization of one variant demonstrated a partial splicing defect and altered promoter and/or enhancer activity, reflecting essential mechanisms for regulating cholesterol biosynthesis/uptake in steady state.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Whole-exome sequencing was used to identify recessive disease-causing variants in FDFT1. Functional characterization of one variant demonstrated a partial splicing defect and altered promoter and/or enhancer activity, reflecting essential mechanisms for regulating cholesterol biosynthesis/uptake in steady state.	Immunohistochemical staining	Whole-exome sequencing was used to identify recessive disease-causing variants in FDFT1. Functional characterization of one variant demonstrated a partial splicing defect and altered promoter and/or enhancer activity, reflecting essential mechanisms for regulating cholesterol biosynthesis/uptake in steady state.		PCR,WES,Western blot,			FDFT1		Whole-exome sequencing was used to identify recessive disease-causing variants in FDFT1. Functional characterization of one variant demonstrated a partial splicing defect and altered promoter and/or enhancer activity, reflecting essential mechanisms for regulating cholesterol biosynthesis/uptake in steady state.	
29908199	chrX	55006337	55008337	ALAS2	These results suggest that the induction of mitochondrial ferritin expression might be essential for, but not the primary cause of, ring sideroblast formation. Our results also suggest that the insufficient supply of protoporphyrin IX due to ALAS2 deficiency in combination with increased iron import into mitochondria during erythroid differentiation results in the formation of ring sideroblasts. Furthermore, HA2low cells are a useful tool for characterizing ring sideroblasts in vitro.	human	connective	High+Lowthroughput	Establishment of a cell model of X-linked sideroblastic anemia using genome editing	否		X-linked sideroblastic anemia		E_01_0408	Quantitative real-time polymerase chain reaction,Western blot,Electron microscopy,Flow cytometry,Staining,	These results suggest that the induction of mitochondrial ferritin expression might be essential for, but not the primary cause of, ring sideroblast formation. Our results also suggest that the insufficient supply of protoporphyrin IX due to ALAS2 deficiency in combination with increased iron import into mitochondria during erythroid differentiation results in the formation of ring sideroblasts. Furthermore, HA2low cells are a useful tool for characterizing ring sideroblasts in vitro.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		These results suggest that the induction of mitochondrial ferritin expression might be essential for, but not the primary cause of, ring sideroblast formation. Our results also suggest that the insufficient supply of protoporphyrin IX due to ALAS2 deficiency in combination with increased iron import into mitochondria during erythroid differentiation results in the formation of ring sideroblasts. Furthermore, HA2low cells are a useful tool for characterizing ring sideroblasts in vitro.	Immunohistochemical staining	These results suggest that the induction of mitochondrial ferritin expression might be essential for, but not the primary cause of, ring sideroblast formation. Our results also suggest that the insufficient supply of protoporphyrin IX due to ALAS2 deficiency in combination with increased iron import into mitochondria during erythroid differentiation results in the formation of ring sideroblasts. Furthermore, HA2low cells are a useful tool for characterizing ring sideroblasts in vitro.		Quantitative real-time polymerase chain reaction,Western blot,Electron microscopy,Flow cytometry,Staining,			ALAS2		These results suggest that the induction of mitochondrial ferritin expression might be essential for, but not the primary cause of, ring sideroblast formation. Our results also suggest that the insufficient supply of protoporphyrin IX due to ALAS2 deficiency in combination with increased iron import into mitochondria during erythroid differentiation results in the formation of ring sideroblasts. Furthermore, HA2low cells are a useful tool for characterizing ring sideroblasts in vitro.	
29907596	chr17	44074243	44076243	HDAC5	In vivo, endotoxemia in MEF2-reporter mice induced upregulation of PGE2 and MEF2 activation. Our findings provide an unexpected new link between inflammation and cardiac remodeling by de-repression of MEF2 through HDAC5 inactivation, which has potential implications for new strategies to treat inflammatory cardiomyopathies.	human	Nervous	High+Lowthroughput	Inflammation leads through PGE/EP(3) signaling to HDAC5/MEF2-dependent transcription in cardiac myocytes	否		Inflammatory cardiomyopathy	nrvm	E_01_0409	Luciferase reporter assay,Immunoblotting,Immunostaining,RNA analysis,Western Blot	In vivo, endotoxemia in MEF2-reporter mice induced upregulation of PGE2 and MEF2 activation. Our findings provide an unexpected new link between inflammation and cardiac remodeling by de-repression of MEF2 through HDAC5 inactivation, which has potential implications for new strategies to treat inflammatory cardiomyopathies.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In vivo, endotoxemia in MEF2-reporter mice induced upregulation of PGE2 and MEF2 activation. Our findings provide an unexpected new link between inflammation and cardiac remodeling by de-repression of MEF2 through HDAC5 inactivation, which has potential implications for new strategies to treat inflammatory cardiomyopathies.	Immunohistochemical staining	In vivo, endotoxemia in MEF2-reporter mice induced upregulation of PGE2 and MEF2 activation. Our findings provide an unexpected new link between inflammation and cardiac remodeling by de-repression of MEF2 through HDAC5 inactivation, which has potential implications for new strategies to treat inflammatory cardiomyopathies.		Luciferase reporter assay,Immunoblotting,Immunostaining,RNA analysis,Western Blot			HDAC5		In vivo, endotoxemia in MEF2-reporter mice induced upregulation of PGE2 and MEF2 activation. Our findings provide an unexpected new link between inflammation and cardiac remodeling by de-repression of MEF2 through HDAC5 inactivation, which has potential implications for new strategies to treat inflammatory cardiomyopathies.	
29906314	chr6	38673142	38675142	GLO1	We show GR extract and shikonin dose-dependently inhibited glycation and enhanced oxidative defenses through nuclear factor erythroid 2-related factor 2 (Nrf2)/antioxidant response element activation. Inflammatory targets, nuclear factor kappa-light-chain-enhancer of activated B cells (NFκB) and tumor necrosis factor alpha, were suppressed by GR extract and shikonin. Glyoxalase 1 (GLO1) and glutathione synthesis genes were significantly upregulated by GR extract and shikonin. GR extract boosted higher wavelength UV absorption in select cosmetic matrices. Rationale for the use of GR extract and shikonin are supported by our research. By inhibiting glycation, modulating oxidative stress, suppressing inflammation and UV-absorptive properties, GR extract and shikonin potentially offer multiple skin benefits.	human	connective	High+Lowthroughput	Gromwell (Lithospermum erythrorhizon) root extract protects against glycation and related inflammatory and oxidative stress while offering UV absorption capability	否		Glycosylation	HepG2 cell	E_01_0410	qRT-PCR,qPCR	We show GR extract and shikonin dose-dependently inhibited glycation and enhanced oxidative defenses through nuclear factor erythroid 2-related factor 2 (Nrf2)/antioxidant response element activation. Inflammatory targets, nuclear factor kappa-light-chain-enhancer of activated B cells (NFκB) and tumor necrosis factor alpha, were suppressed by GR extract and shikonin. Glyoxalase 1 (GLO1) and glutathione synthesis genes were significantly upregulated by GR extract and shikonin. GR extract boosted higher wavelength UV absorption in select cosmetic matrices. Rationale for the use of GR extract and shikonin are supported by our research. By inhibiting glycation, modulating oxidative stress, suppressing inflammation and UV-absorptive properties, GR extract and shikonin potentially offer multiple skin benefits.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We show GR extract and shikonin dose-dependently inhibited glycation and enhanced oxidative defenses through nuclear factor erythroid 2-related factor 2 (Nrf2)/antioxidant response element activation. Inflammatory targets, nuclear factor kappa-light-chain-enhancer of activated B cells (NFκB) and tumor necrosis factor alpha, were suppressed by GR extract and shikonin. Glyoxalase 1 (GLO1) and glutathione synthesis genes were significantly upregulated by GR extract and shikonin. GR extract boosted higher wavelength UV absorption in select cosmetic matrices. Rationale for the use of GR extract and shikonin are supported by our research. By inhibiting glycation, modulating oxidative stress, suppressing inflammation and UV-absorptive properties, GR extract and shikonin potentially offer multiple skin benefits.	Immunohistochemical staining	We show GR extract and shikonin dose-dependently inhibited glycation and enhanced oxidative defenses through nuclear factor erythroid 2-related factor 2 (Nrf2)/antioxidant response element activation. Inflammatory targets, nuclear factor kappa-light-chain-enhancer of activated B cells (NFκB) and tumor necrosis factor alpha, were suppressed by GR extract and shikonin. Glyoxalase 1 (GLO1) and glutathione synthesis genes were significantly upregulated by GR extract and shikonin. GR extract boosted higher wavelength UV absorption in select cosmetic matrices. Rationale for the use of GR extract and shikonin are supported by our research. By inhibiting glycation, modulating oxidative stress, suppressing inflammation and UV-absorptive properties, GR extract and shikonin potentially offer multiple skin benefits.		qRT-PCR,qPCR			GLO1		We show GR extract and shikonin dose-dependently inhibited glycation and enhanced oxidative defenses through nuclear factor erythroid 2-related factor 2 (Nrf2)/antioxidant response element activation. Inflammatory targets, nuclear factor kappa-light-chain-enhancer of activated B cells (NFκB) and tumor necrosis factor alpha, were suppressed by GR extract and shikonin. Glyoxalase 1 (GLO1) and glutathione synthesis genes were significantly upregulated by GR extract and shikonin. GR extract boosted higher wavelength UV absorption in select cosmetic matrices. Rationale for the use of GR extract and shikonin are supported by our research. By inhibiting glycation, modulating oxidative stress, suppressing inflammation and UV-absorptive properties, GR extract and shikonin potentially offer multiple skin benefits.	
29905573	chr7	148804380	148806380	EZH2	Collectively, our data demonstrated that modulating EZH2 expression in T cells can improve antitumor responses elicited by anti-CTLA-4 therapy, which provides a strong rationale for a combination trial of CPI-1205 plus ipilimumab.	human	lymphoid	High+Lowthroughput	Modulation of EZH2 expression in T cells improves efficacy of anti-CTLA-4 therapy	否		tumour	T cell	E_01_0411	RNA-seq	Collectively, our data demonstrated that modulating EZH2 expression in T cells can improve antitumor responses elicited by anti-CTLA-4 therapy, which provides a strong rationale for a combination trial of CPI-1205 plus ipilimumab.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Collectively, our data demonstrated that modulating EZH2 expression in T cells can improve antitumor responses elicited by anti-CTLA-4 therapy, which provides a strong rationale for a combination trial of CPI-1205 plus ipilimumab.	Immunohistochemical staining	Collectively, our data demonstrated that modulating EZH2 expression in T cells can improve antitumor responses elicited by anti-CTLA-4 therapy, which provides a strong rationale for a combination trial of CPI-1205 plus ipilimumab.		RNA-seq				EZH2		Collectively, our data demonstrated that modulating EZH2 expression in T cells can improve antitumor responses elicited by anti-CTLA-4 therapy, which provides a strong rationale for a combination trial of CPI-1205 plus ipilimumab.
29899688	chr21	25877858	25879858	APP	To study the relationship between Mg2+ and TNF-α, we used human- or mouse-derived glial and neuronal cell lines or APP/PS1 transgenic (Tg) mice as in vitro and in vivo experimental models, respectively. Our data demonstrates that magnesium-L-threonate (MgT) can decrease the expression of TNF-α by restoring the levels of Mg2+ in glial cells. In addition, PI3-K/AKT and NF-κB signals play critical roles in mediating the effects of Mg2+ on suppressing the expression of TNF-α. In neurons, Mg2+ elevation showed similar suppressive effects on the expression of presenilin enhancer 2 (PEN2) and nicastrin (NCT) through a PI3-K/AKT and NF-κB-dependent mechanism. As the major components of γ-secretase, overexpression of presenilin 1 (PS1), PEN2 and NCT potentially promote the synthesis of Aβ, which in turn activates TNF-α in glial cells. Reciprocally, TNF-α stimulates the expression of PEN2 and NCT in neurons. The crosstalk between TNF-α and Aβ in glial cells and neurons could ultimately aggravate the development and progression of AD.	human	Nervous	High+Lowthroughput	Magnesium Ions Inhibit the Expression of Tumor Necrosis Factor α and the Activity of γ-Secretase in a β-Amyloid Protein-Dependent Mechanism in APP/PS1 Transgenic Mice	否		Alzheimer's disease (AD)	A172	E_01_0412	transgenic mice,qRT-PCR,SDS-PAGE,Western blot,Immunohistochemistry,	To study the relationship between Mg2+ and TNF-α, we used human- or mouse-derived glial and neuronal cell lines or APP/PS1 transgenic (Tg) mice as in vitro and in vivo experimental models, respectively. Our data demonstrates that magnesium-L-threonate (MgT) can decrease the expression of TNF-α by restoring the levels of Mg2+ in glial cells. In addition, PI3-K/AKT and NF-κB signals play critical roles in mediating the effects of Mg2+ on suppressing the expression of TNF-α. In neurons, Mg2+ elevation showed similar suppressive effects on the expression of presenilin enhancer 2 (PEN2) and nicastrin (NCT) through a PI3-K/AKT and NF-κB-dependent mechanism. As the major components of γ-secretase, overexpression of presenilin 1 (PS1), PEN2 and NCT potentially promote the synthesis of Aβ, which in turn activates TNF-α in glial cells. Reciprocally, TNF-α stimulates the expression of PEN2 and NCT in neurons. The crosstalk between TNF-α and Aβ in glial cells and neurons could ultimately aggravate the development and progression of AD.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		To study the relationship between Mg2+ and TNF-α, we used human- or mouse-derived glial and neuronal cell lines or APP/PS1 transgenic (Tg) mice as in vitro and in vivo experimental models, respectively. Our data demonstrates that magnesium-L-threonate (MgT) can decrease the expression of TNF-α by restoring the levels of Mg2+ in glial cells. In addition, PI3-K/AKT and NF-κB signals play critical roles in mediating the effects of Mg2+ on suppressing the expression of TNF-α. In neurons, Mg2+ elevation showed similar suppressive effects on the expression of presenilin enhancer 2 (PEN2) and nicastrin (NCT) through a PI3-K/AKT and NF-κB-dependent mechanism. As the major components of γ-secretase, overexpression of presenilin 1 (PS1), PEN2 and NCT potentially promote the synthesis of Aβ, which in turn activates TNF-α in glial cells. Reciprocally, TNF-α stimulates the expression of PEN2 and NCT in neurons. The crosstalk between TNF-α and Aβ in glial cells and neurons could ultimately aggravate the development and progression of AD.	Immunohistochemical staining	To study the relationship between Mg2+ and TNF-α, we used human- or mouse-derived glial and neuronal cell lines or APP/PS1 transgenic (Tg) mice as in vitro and in vivo experimental models, respectively. Our data demonstrates that magnesium-L-threonate (MgT) can decrease the expression of TNF-α by restoring the levels of Mg2+ in glial cells. In addition, PI3-K/AKT and NF-κB signals play critical roles in mediating the effects of Mg2+ on suppressing the expression of TNF-α. In neurons, Mg2+ elevation showed similar suppressive effects on the expression of presenilin enhancer 2 (PEN2) and nicastrin (NCT) through a PI3-K/AKT and NF-κB-dependent mechanism. As the major components of γ-secretase, overexpression of presenilin 1 (PS1), PEN2 and NCT potentially promote the synthesis of Aβ, which in turn activates TNF-α in glial cells. Reciprocally, TNF-α stimulates the expression of PEN2 and NCT in neurons. The crosstalk between TNF-α and Aβ in glial cells and neurons could ultimately aggravate the development and progression of AD.		transgenic mice,qRT-PCR,SDS-PAGE,Western blot,Immunohistochemistry,				APP		To study the relationship between Mg2+ and TNF-α, we used human- or mouse-derived glial and neuronal cell lines or APP/PS1 transgenic (Tg) mice as in vitro and in vivo experimental models, respectively. Our data demonstrates that magnesium-L-threonate (MgT) can decrease the expression of TNF-α by restoring the levels of Mg2+ in glial cells. In addition, PI3-K/AKT and NF-κB signals play critical roles in mediating the effects of Mg2+ on suppressing the expression of TNF-α. In neurons, Mg2+ elevation showed similar suppressive effects on the expression of presenilin enhancer 2 (PEN2) and nicastrin (NCT) through a PI3-K/AKT and NF-κB-dependent mechanism. As the major components of γ-secretase, overexpression of presenilin 1 (PS1), PEN2 and NCT potentially promote the synthesis of Aβ, which in turn activates TNF-α in glial cells. Reciprocally, TNF-α stimulates the expression of PEN2 and NCT in neurons. The crosstalk between TNF-α and Aβ in glial cells and neurons could ultimately aggravate the development and progression of AD.
29898397	chr7	148805021	148807021	EZH2	Here, we reveal a mechanism to selectively target and reprogram the function of tumor-infiltrating Tregs (TI-Tregs) by exploiting their dependency on the histone H3K27 methyltransferase enhancer of zeste homolog 2 (EZH2) in tumors. Disruption of EZH2 activity in Tregs, either pharmacologically or genetically, drove the acquisition of pro-inflammatory functions in TI-Tregs, remodeling the tumor microenvironment and enhancing the recruitment and function of CD8 and CD4 effector T cells that eliminate tumors. Moreover, abolishing EZH2 function in Tregs was mechanistically distinct from, more potent than, and less toxic than a generalized Treg depletion approach. This study reveals a strategy to target Tregs in cancer that mitigates autoimmunity by reprogramming their function in tumors to enhance anti-cancer immunity.	human	lymphoid	High+Lowthroughput	Targeting EZH2 Reprograms Intratumoral Regulatory T Cells to Enhance Cancer Immunity	否		cancer	lymphocyte	E_01_0413	Flow Cytometry,Histology, RNA-seq,transgenic mice	Here, we reveal a mechanism to selectively target and reprogram the function of tumor-infiltrating Tregs (TI-Tregs) by exploiting their dependency on the histone H3K27 methyltransferase enhancer of zeste homolog 2 (EZH2) in tumors. Disruption of EZH2 activity in Tregs, either pharmacologically or genetically, drove the acquisition of pro-inflammatory functions in TI-Tregs, remodeling the tumor microenvironment and enhancing the recruitment and function of CD8 and CD4 effector T cells that eliminate tumors. Moreover, abolishing EZH2 function in Tregs was mechanistically distinct from, more potent than, and less toxic than a generalized Treg depletion approach. This study reveals a strategy to target Tregs in cancer that mitigates autoimmunity by reprogramming their function in tumors to enhance anti-cancer immunity.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Here, we reveal a mechanism to selectively target and reprogram the function of tumor-infiltrating Tregs (TI-Tregs) by exploiting their dependency on the histone H3K27 methyltransferase enhancer of zeste homolog 2 (EZH2) in tumors. Disruption of EZH2 activity in Tregs, either pharmacologically or genetically, drove the acquisition of pro-inflammatory functions in TI-Tregs, remodeling the tumor microenvironment and enhancing the recruitment and function of CD8 and CD4 effector T cells that eliminate tumors. Moreover, abolishing EZH2 function in Tregs was mechanistically distinct from, more potent than, and less toxic than a generalized Treg depletion approach. This study reveals a strategy to target Tregs in cancer that mitigates autoimmunity by reprogramming their function in tumors to enhance anti-cancer immunity.	Immunohistochemical staining	Here, we reveal a mechanism to selectively target and reprogram the function of tumor-infiltrating Tregs (TI-Tregs) by exploiting their dependency on the histone H3K27 methyltransferase enhancer of zeste homolog 2 (EZH2) in tumors. Disruption of EZH2 activity in Tregs, either pharmacologically or genetically, drove the acquisition of pro-inflammatory functions in TI-Tregs, remodeling the tumor microenvironment and enhancing the recruitment and function of CD8 and CD4 effector T cells that eliminate tumors. Moreover, abolishing EZH2 function in Tregs was mechanistically distinct from, more potent than, and less toxic than a generalized Treg depletion approach. This study reveals a strategy to target Tregs in cancer that mitigates autoimmunity by reprogramming their function in tumors to enhance anti-cancer immunity.		Flow Cytometry,Histology, RNA-seq,transgenic mice				EZH2,FOXP3		Here, we reveal a mechanism to selectively target and reprogram the function of tumor-infiltrating Tregs (TI-Tregs) by exploiting their dependency on the histone H3K27 methyltransferase enhancer of zeste homolog 2 (EZH2) in tumors. Disruption of EZH2 activity in Tregs, either pharmacologically or genetically, drove the acquisition of pro-inflammatory functions in TI-Tregs, remodeling the tumor microenvironment and enhancing the recruitment and function of CD8 and CD4 effector T cells that eliminate tumors. Moreover, abolishing EZH2 function in Tregs was mechanistically distinct from, more potent than, and less toxic than a generalized Treg depletion approach. This study reveals a strategy to target Tregs in cancer that mitigates autoimmunity by reprogramming their function in tumors to enhance anti-cancer immunity.;Here, we reveal a mechanism to selectively target and reprogram the function of tumor-infiltrating Tregs (TI-Tregs) by exploiting their dependency on the histone H3K27 methyltransferase enhancer of zeste homolog 2 (EZH2) in tumors. Disruption of EZH2 activity in Tregs, either pharmacologically or genetically, drove the acquisition of pro-inflammatory functions in TI-Tregs, remodeling the tumor microenvironment and enhancing the recruitment and function of CD8 and CD4 effector T cells that eliminate tumors. Moreover, abolishing EZH2 function in Tregs was mechanistically distinct from, more potent than, and less toxic than a generalized Treg depletion approach. This study reveals a strategy to target Tregs in cancer that mitigates autoimmunity by reprogramming their function in tumors to enhance anti-cancer immunity.
29896299	chr2	216669551	216671551	IGFBP5	Taken together, our findings reveal that atheroprotective flow reduces H3K27me3 as a chromatin-based mechanism to augment the expression of genes that confer an anti-inflammatory response in the endothelium. Our study exemplifies flow-dependent epigenetic regulation of endothelial gene expression, and also suggests that targeting the EZH2/H3K27me3/IGFBP5 pathway may offer novel therapeutics for inflammatory disorders such as atherosclerosis.	human	Epithelial	High+Lowthroughput	Flow-dependent epigenetic regulation of IGFBP5 expression by H3K27me3 contributes to endothelial anti-inflammatory effects	否		atherosclerosis	HUVECs	E_01_0414	ChIP,RNA-seq,ChIP-qPCR,Western blot ,siRNA,miRNA transfection,Luciferase reporter assay,immunofluorescent staining,	Taken together, our findings reveal that atheroprotective flow reduces H3K27me3 as a chromatin-based mechanism to augment the expression of genes that confer an anti-inflammatory response in the endothelium. Our study exemplifies flow-dependent epigenetic regulation of endothelial gene expression, and also suggests that targeting the EZH2/H3K27me3/IGFBP5 pathway may offer novel therapeutics for inflammatory disorders such as atherosclerosis.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Taken together, our findings reveal that atheroprotective flow reduces H3K27me3 as a chromatin-based mechanism to augment the expression of genes that confer an anti-inflammatory response in the endothelium. Our study exemplifies flow-dependent epigenetic regulation of endothelial gene expression, and also suggests that targeting the EZH2/H3K27me3/IGFBP5 pathway may offer novel therapeutics for inflammatory disorders such as atherosclerosis.	Immunohistochemical staining	Taken together, our findings reveal that atheroprotective flow reduces H3K27me3 as a chromatin-based mechanism to augment the expression of genes that confer an anti-inflammatory response in the endothelium. Our study exemplifies flow-dependent epigenetic regulation of endothelial gene expression, and also suggests that targeting the EZH2/H3K27me3/IGFBP5 pathway may offer novel therapeutics for inflammatory disorders such as atherosclerosis.		ChIP,RNA-seq,ChIP-qPCR,Western blot ,siRNA,miRNA transfection,Luciferase reporter assay,immunofluorescent staining,			IGFBP5	EZH2	Taken together, our findings reveal that atheroprotective flow reduces H3K27me3 as a chromatin-based mechanism to augment the expression of genes that confer an anti-inflammatory response in the endothelium. Our study exemplifies flow-dependent epigenetic regulation of endothelial gene expression, and also suggests that targeting the EZH2/H3K27me3/IGFBP5 pathway may offer novel therapeutics for inflammatory disorders such as atherosclerosis.	Taken together, our findings reveal that atheroprotective flow reduces H3K27me3 as a chromatin-based mechanism to augment the expression of genes that confer an anti-inflammatory response in the endothelium. Our study exemplifies flow-dependent epigenetic regulation of endothelial gene expression, and also suggests that targeting the EZH2/H3K27me3/IGFBP5 pathway may offer novel therapeutics for inflammatory disorders such as atherosclerosis.
29894816	chr2	136111792	136113792	CXCR4	The current results indicate that 4DV3 might serve as a prototype for a new type of dual function ligand, one that acts as a HIV-1 entry inhibitor and a CXCR4 drug delivery targeting ligand.	human	lymphoid	High+Lowthroughput	Design and evaluation of a CXCR4 targeting peptide 4DV3 as an HIV entry inhibitor and a ligand for targeted drug delivery	否		AIDS		E_01_0415	competitive binding assay,MTT assay,luciferase activity	The current results indicate that 4DV3 might serve as a prototype for a new type of dual function ligand, one that acts as a HIV-1 entry inhibitor and a CXCR4 drug delivery targeting ligand.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The current results indicate that 4DV3 might serve as a prototype for a new type of dual function ligand, one that acts as a HIV-1 entry inhibitor and a CXCR4 drug delivery targeting ligand.	Immunohistochemical staining	The current results indicate that 4DV3 might serve as a prototype for a new type of dual function ligand, one that acts as a HIV-1 entry inhibitor and a CXCR4 drug delivery targeting ligand.		competitive binding assay,MTT assay,luciferase activity				CXCR4		The current results indicate that 4DV3 might serve as a prototype for a new type of dual function ligand, one that acts as a HIV-1 entry inhibitor and a CXCR4 drug delivery targeting ligand.
29889836	chr1	169719974	169721974	SELE	In conclusion, everolimus attenuates EC activation via reduced NF-κB p65 translocation causing decreased E-selectin and VCAM-1 expression at transcriptional and post-transcriptional level after DES.	human	Epithelial	High+Lowthroughput	Endothelial cell activation is attenuated by everolimus via transcriptional and post-transcriptional regulatory mechanisms after drug-eluting coronary stenting	否		Other	HCAEC	E_01_0416	RT-qPCR,ELISA,ChIP-seq,Transfection,	In conclusion, everolimus attenuates EC activation via reduced NF-κB p65 translocation causing decreased E-selectin and VCAM-1 expression at transcriptional and post-transcriptional level after DES.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In conclusion, everolimus attenuates EC activation via reduced NF-κB p65 translocation causing decreased E-selectin and VCAM-1 expression at transcriptional and post-transcriptional level after DES.	Immunohistochemical staining	In conclusion, everolimus attenuates EC activation via reduced NF-κB p65 translocation causing decreased E-selectin and VCAM-1 expression at transcriptional and post-transcriptional level after DES.		RT-qPCR,ELISA,ChIP-seq,Transfection,			SELE,VCAM1		In conclusion, everolimus attenuates EC activation via reduced NF-κB p65 translocation causing decreased E-selectin and VCAM-1 expression at transcriptional and post-transcriptional level after DES.;In conclusion, everolimus attenuates EC activation via reduced NF-κB p65 translocation causing decreased E-selectin and VCAM-1 expression at transcriptional and post-transcriptional level after DES.	
29888110	chr4	7751285	7753285	AFAP1-AS1	Here, we identify a lncRNA AFAP1-AS1 that facilitates colorectal cancer, where it is upregulated. AFAP1-AS1 expression was associated with colorectal cancer patient survival. AFAP1-AS1 knockdown inhibited cell proliferation, cell cycle, and tumorigenesis in an subcutaneous mouse xenograft model system. Further data demonstrated that AFAP1-AS1 was associated with enhancer of zeste homolog 2 (EZH2) and that this association was required for the repression of EZH2 target genes. Our findings indicate that AFAP1-AS1 is an oncogenic lncRNA that promotes tumor progression and may be a novel prognostic factor in colorectal cancer. Targeting AFAP1-AS1 might be a potential therapeutic strategy for colorectal cancer treatment.	human	Colon	High+Lowthroughput	Long noncoding RNA AFAP1-AS1 facilitates tumor growth through enhancer of zeste homolog 2 in colorectal cancer	否		colorectal cancer 	LOVO cell	E_01_0417	ChIP-qPCR,RNA pull-down assay,RNA immunoprecipitation,RNA extraction,quantitative RT-PCR,Western blot,	Here, we identify a lncRNA AFAP1-AS1 that facilitates colorectal cancer, where it is upregulated. AFAP1-AS1 expression was associated with colorectal cancer patient survival. AFAP1-AS1 knockdown inhibited cell proliferation, cell cycle, and tumorigenesis in an subcutaneous mouse xenograft model system. Further data demonstrated that AFAP1-AS1 was associated with enhancer of zeste homolog 2 (EZH2) and that this association was required for the repression of EZH2 target genes. Our findings indicate that AFAP1-AS1 is an oncogenic lncRNA that promotes tumor progression and may be a novel prognostic factor in colorectal cancer. Targeting AFAP1-AS1 might be a potential therapeutic strategy for colorectal cancer treatment.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Here, we identify a lncRNA AFAP1-AS1 that facilitates colorectal cancer, where it is upregulated. AFAP1-AS1 expression was associated with colorectal cancer patient survival. AFAP1-AS1 knockdown inhibited cell proliferation, cell cycle, and tumorigenesis in an subcutaneous mouse xenograft model system. Further data demonstrated that AFAP1-AS1 was associated with enhancer of zeste homolog 2 (EZH2) and that this association was required for the repression of EZH2 target genes. Our findings indicate that AFAP1-AS1 is an oncogenic lncRNA that promotes tumor progression and may be a novel prognostic factor in colorectal cancer. Targeting AFAP1-AS1 might be a potential therapeutic strategy for colorectal cancer treatment.	Immunohistochemical staining	Here, we identify a lncRNA AFAP1-AS1 that facilitates colorectal cancer, where it is upregulated. AFAP1-AS1 expression was associated with colorectal cancer patient survival. AFAP1-AS1 knockdown inhibited cell proliferation, cell cycle, and tumorigenesis in an subcutaneous mouse xenograft model system. Further data demonstrated that AFAP1-AS1 was associated with enhancer of zeste homolog 2 (EZH2) and that this association was required for the repression of EZH2 target genes. Our findings indicate that AFAP1-AS1 is an oncogenic lncRNA that promotes tumor progression and may be a novel prognostic factor in colorectal cancer. Targeting AFAP1-AS1 might be a potential therapeutic strategy for colorectal cancer treatment.		ChIP-qPCR,RNA pull-down assay,RNA immunoprecipitation,RNA extraction,quantitative RT-PCR,Western blot,			AFAP1-AS1	EZH2	Here, we identify a lncRNA AFAP1-AS1 that facilitates colorectal cancer, where it is upregulated. AFAP1-AS1 expression was associated with colorectal cancer patient survival. AFAP1-AS1 knockdown inhibited cell proliferation, cell cycle, and tumorigenesis in an subcutaneous mouse xenograft model system. Further data demonstrated that AFAP1-AS1 was associated with enhancer of zeste homolog 2 (EZH2) and that this association was required for the repression of EZH2 target genes. Our findings indicate that AFAP1-AS1 is an oncogenic lncRNA that promotes tumor progression and may be a novel prognostic factor in colorectal cancer. Targeting AFAP1-AS1 might be a potential therapeutic strategy for colorectal cancer treatment.	Here, we identify a lncRNA AFAP1-AS1 that facilitates colorectal cancer, where it is upregulated. AFAP1-AS1 expression was associated with colorectal cancer patient survival. AFAP1-AS1 knockdown inhibited cell proliferation, cell cycle, and tumorigenesis in an subcutaneous mouse xenograft model system. Further data demonstrated that AFAP1-AS1 was associated with enhancer of zeste homolog 2 (EZH2) and that this association was required for the repression of EZH2 target genes. Our findings indicate that AFAP1-AS1 is an oncogenic lncRNA that promotes tumor progression and may be a novel prognostic factor in colorectal cancer. Targeting AFAP1-AS1 might be a potential therapeutic strategy for colorectal cancer treatment.
29887316	chr22	39516355	39518355	ATF4	ATF4 knockdown by siRNA significantly attenuated the suppressive effect of palmitate on EPO production. Studies utilizing inherited super-anemic mice (ISAM) mated with EPO-Cre mice (ISAM-REC mice) for lineage-labeling of REP cells showed that ATF4 activation by palmitate suppressed EPO production in REP cells. Laser capture microdissection confirmed ATF4 activation in the interstitial area of ISAM-REC mice treated with palmitate-conjugated BSA. Thus, endoplasmic reticulum stress induced by palmitate suppressed EPO expression by REP cells in a manner independent of HIF activation. The link between endoplasmic reticulum stress, dyslipidemia, and hypoxia may contribute to development and progression of anemia in CKD.	human	Liver	High+Lowthroughput	Palmitate deranges erythropoietin production via transcription factor ATF4 activation of unfolded protein response	否		Chronic kidney injury	HepG2	E_01_0418	Oil red O staining,Western blot,Luciferase assays,quantitative real-time PCR,Histological analysis,Immunofluorescence analysis,Electron microscopy,Laser microdissection,	ATF4 knockdown by siRNA significantly attenuated the suppressive effect of palmitate on EPO production. Studies utilizing inherited super-anemic mice (ISAM) mated with EPO-Cre mice (ISAM-REC mice) for lineage-labeling of REP cells showed that ATF4 activation by palmitate suppressed EPO production in REP cells. Laser capture microdissection confirmed ATF4 activation in the interstitial area of ISAM-REC mice treated with palmitate-conjugated BSA. Thus, endoplasmic reticulum stress induced by palmitate suppressed EPO expression by REP cells in a manner independent of HIF activation. The link between endoplasmic reticulum stress, dyslipidemia, and hypoxia may contribute to development and progression of anemia in CKD.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		ATF4 knockdown by siRNA significantly attenuated the suppressive effect of palmitate on EPO production. Studies utilizing inherited super-anemic mice (ISAM) mated with EPO-Cre mice (ISAM-REC mice) for lineage-labeling of REP cells showed that ATF4 activation by palmitate suppressed EPO production in REP cells. Laser capture microdissection confirmed ATF4 activation in the interstitial area of ISAM-REC mice treated with palmitate-conjugated BSA. Thus, endoplasmic reticulum stress induced by palmitate suppressed EPO expression by REP cells in a manner independent of HIF activation. The link between endoplasmic reticulum stress, dyslipidemia, and hypoxia may contribute to development and progression of anemia in CKD.	Immunohistochemical staining	ATF4 knockdown by siRNA significantly attenuated the suppressive effect of palmitate on EPO production. Studies utilizing inherited super-anemic mice (ISAM) mated with EPO-Cre mice (ISAM-REC mice) for lineage-labeling of REP cells showed that ATF4 activation by palmitate suppressed EPO production in REP cells. Laser capture microdissection confirmed ATF4 activation in the interstitial area of ISAM-REC mice treated with palmitate-conjugated BSA. Thus, endoplasmic reticulum stress induced by palmitate suppressed EPO expression by REP cells in a manner independent of HIF activation. The link between endoplasmic reticulum stress, dyslipidemia, and hypoxia may contribute to development and progression of anemia in CKD.		Oil red O staining,Western blot,Luciferase assays,quantitative real-time PCR,Histological analysis,Immunofluorescence analysis,Electron microscopy,Laser microdissection,				ATF4,EPO		ATF4 knockdown by siRNA significantly attenuated the suppressive effect of palmitate on EPO production. Studies utilizing inherited super-anemic mice (ISAM) mated with EPO-Cre mice (ISAM-REC mice) for lineage-labeling of REP cells showed that ATF4 activation by palmitate suppressed EPO production in REP cells. Laser capture microdissection confirmed ATF4 activation in the interstitial area of ISAM-REC mice treated with palmitate-conjugated BSA. Thus, endoplasmic reticulum stress induced by palmitate suppressed EPO expression by REP cells in a manner independent of HIF activation. The link between endoplasmic reticulum stress, dyslipidemia, and hypoxia may contribute to development and progression of anemia in CKD.;ATF4 knockdown by siRNA significantly attenuated the suppressive effect of palmitate on EPO production. Studies utilizing inherited super-anemic mice (ISAM) mated with EPO-Cre mice (ISAM-REC mice) for lineage-labeling of REP cells showed that ATF4 activation by palmitate suppressed EPO production in REP cells. Laser capture microdissection confirmed ATF4 activation in the interstitial area of ISAM-REC mice treated with palmitate-conjugated BSA. Thus, endoplasmic reticulum stress induced by palmitate suppressed EPO expression by REP cells in a manner independent of HIF activation. The link between endoplasmic reticulum stress, dyslipidemia, and hypoxia may contribute to development and progression of anemia in CKD.
29885843	chr11	46853631	46855631	LRP4	Thus, the biological role of LRP4 in the thyroid cancer in the present study was investigated using the PTC cell lines TPC1, BCPAP and KTC-1. In these cell lines, the mRNA level of LRP4 was higher than normal thyroid cancer cell named HTORI3. In vitro experiments demonstrated that LRP4 downregulation significantly inhibited the colony formation, proliferation, migration, and invasion of the three PTC cell lines. Knockdown of LRP4 by small interfering RNA (siRNA) in those cell lines decreased the protein expression of N-cadherin, Enhancer of zeste homolog 2 (EZH2), and Zinc finger E-box-binding home-box 1 (ZEB1). Furthermore, LRP4 knockdown significantly reduced the levels of phosphorylated PI3K in the PTC cell lines. In conclusion, the present study indicated that LRP4 is a gene associated with PTC and might become a potential therapeutic target.	human	Parathyroid	High+Lowthroughput	LRP4 promotes proliferation, migration, and invasion in papillary thyroid cancer	否		Thyroid cancer	TPC1	E_01_0419	qRT-PCR,Cell transfection,Cell proliferation assay,Colony formation assay,Cell migration and invasion assays,Western blot,LRP4 siRNA	Thus, the biological role of LRP4 in the thyroid cancer in the present study was investigated using the PTC cell lines TPC1, BCPAP and KTC-1. In these cell lines, the mRNA level of LRP4 was higher than normal thyroid cancer cell named HTORI3. In vitro experiments demonstrated that LRP4 downregulation significantly inhibited the colony formation, proliferation, migration, and invasion of the three PTC cell lines. Knockdown of LRP4 by small interfering RNA (siRNA) in those cell lines decreased the protein expression of N-cadherin, Enhancer of zeste homolog 2 (EZH2), and Zinc finger E-box-binding home-box 1 (ZEB1). Furthermore, LRP4 knockdown significantly reduced the levels of phosphorylated PI3K in the PTC cell lines. In conclusion, the present study indicated that LRP4 is a gene associated with PTC and might become a potential therapeutic target.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Thus, the biological role of LRP4 in the thyroid cancer in the present study was investigated using the PTC cell lines TPC1, BCPAP and KTC-1. In these cell lines, the mRNA level of LRP4 was higher than normal thyroid cancer cell named HTORI3. In vitro experiments demonstrated that LRP4 downregulation significantly inhibited the colony formation, proliferation, migration, and invasion of the three PTC cell lines. Knockdown of LRP4 by small interfering RNA (siRNA) in those cell lines decreased the protein expression of N-cadherin, Enhancer of zeste homolog 2 (EZH2), and Zinc finger E-box-binding home-box 1 (ZEB1). Furthermore, LRP4 knockdown significantly reduced the levels of phosphorylated PI3K in the PTC cell lines. In conclusion, the present study indicated that LRP4 is a gene associated with PTC and might become a potential therapeutic target.	Immunohistochemical staining	Thus, the biological role of LRP4 in the thyroid cancer in the present study was investigated using the PTC cell lines TPC1, BCPAP and KTC-1. In these cell lines, the mRNA level of LRP4 was higher than normal thyroid cancer cell named HTORI3. In vitro experiments demonstrated that LRP4 downregulation significantly inhibited the colony formation, proliferation, migration, and invasion of the three PTC cell lines. Knockdown of LRP4 by small interfering RNA (siRNA) in those cell lines decreased the protein expression of N-cadherin, Enhancer of zeste homolog 2 (EZH2), and Zinc finger E-box-binding home-box 1 (ZEB1). Furthermore, LRP4 knockdown significantly reduced the levels of phosphorylated PI3K in the PTC cell lines. In conclusion, the present study indicated that LRP4 is a gene associated with PTC and might become a potential therapeutic target.		qRT-PCR,Cell transfection,Cell proliferation assay,Colony formation assay,Cell migration and invasion assays,Western blot,LRP4 siRNA			LRP4	EZH2,ZEB1	Thus, the biological role of LRP4 in the thyroid cancer in the present study was investigated using the PTC cell lines TPC1, BCPAP and KTC-1. In these cell lines, the mRNA level of LRP4 was higher than normal thyroid cancer cell named HTORI3. In vitro experiments demonstrated that LRP4 downregulation significantly inhibited the colony formation, proliferation, migration, and invasion of the three PTC cell lines. Knockdown of LRP4 by small interfering RNA (siRNA) in those cell lines decreased the protein expression of N-cadherin, Enhancer of zeste homolog 2 (EZH2), and Zinc finger E-box-binding home-box 1 (ZEB1). Furthermore, LRP4 knockdown significantly reduced the levels of phosphorylated PI3K in the PTC cell lines. In conclusion, the present study indicated that LRP4 is a gene associated with PTC and might become a potential therapeutic target.	Thus, the biological role of LRP4 in the thyroid cancer in the present study was investigated using the PTC cell lines TPC1, BCPAP and KTC-1. In these cell lines, the mRNA level of LRP4 was higher than normal thyroid cancer cell named HTORI3. In vitro experiments demonstrated that LRP4 downregulation significantly inhibited the colony formation, proliferation, migration, and invasion of the three PTC cell lines. Knockdown of LRP4 by small interfering RNA (siRNA) in those cell lines decreased the protein expression of N-cadherin, Enhancer of zeste homolog 2 (EZH2), and Zinc finger E-box-binding home-box 1 (ZEB1). Furthermore, LRP4 knockdown significantly reduced the levels of phosphorylated PI3K in the PTC cell lines. In conclusion, the present study indicated that LRP4 is a gene associated with PTC and might become a potential therapeutic target.;Thus, the biological role of LRP4 in the thyroid cancer in the present study was investigated using the PTC cell lines TPC1, BCPAP and KTC-1. In these cell lines, the mRNA level of LRP4 was higher than normal thyroid cancer cell named HTORI3. In vitro experiments demonstrated that LRP4 downregulation significantly inhibited the colony formation, proliferation, migration, and invasion of the three PTC cell lines. Knockdown of LRP4 by small interfering RNA (siRNA) in those cell lines decreased the protein expression of N-cadherin, Enhancer of zeste homolog 2 (EZH2), and Zinc finger E-box-binding home-box 1 (ZEB1). Furthermore, LRP4 knockdown significantly reduced the levels of phosphorylated PI3K in the PTC cell lines. In conclusion, the present study indicated that LRP4 is a gene associated with PTC and might become a potential therapeutic target.
29885461	chr6	131945329	131947329	CCN2	Loss of CCN2 in CAFs resulted in reduced CAF activation, as detected by staining with anti-α-smooth muscle actin antibodies, and reduced tumor-induced neovascularization, as detected by micro-computed tomography (micro-CT) and staining with anti-CD31 antibodies. CCN2-deficient B16(F10) cells were defective in a tubule formation/vasculogenic mimicry assay in vitro. Mice deleted for CCN2 in CAFs also showed impaired vasculogenic mimicry of subcutaneously-injected B16-F10 cells in vivo. Our results provide new insights into the cross-talk among different cell types in the tumor microenvironment and suggest CAFs play a heretofore unappreciated role by being essential for tumor neovascularization via the production of CCN2. Our data are consistent with the hypothesis that activated CAFs are essential for melanoma metastasis and that, due to its role in this process, CCN2 is a therapeutic target for melanoma.	human	Nervous	High+Lowthroughput	Activation of cancer-associated fibroblasts is required for tumor neovascularization in a murine model of melanoma	否		Metastatic melanoma	B16-F10	E_01_0420	ELISA,Histological analysis,transfection,RNA-seq,immunohistochemistry experiments,	Loss of CCN2 in CAFs resulted in reduced CAF activation, as detected by staining with anti-α-smooth muscle actin antibodies, and reduced tumor-induced neovascularization, as detected by micro-computed tomography (micro-CT) and staining with anti-CD31 antibodies. CCN2-deficient B16(F10) cells were defective in a tubule formation/vasculogenic mimicry assay in vitro. Mice deleted for CCN2 in CAFs also showed impaired vasculogenic mimicry of subcutaneously-injected B16-F10 cells in vivo. Our results provide new insights into the cross-talk among different cell types in the tumor microenvironment and suggest CAFs play a heretofore unappreciated role by being essential for tumor neovascularization via the production of CCN2. Our data are consistent with the hypothesis that activated CAFs are essential for melanoma metastasis and that, due to its role in this process, CCN2 is a therapeutic target for melanoma.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Loss of CCN2 in CAFs resulted in reduced CAF activation, as detected by staining with anti-α-smooth muscle actin antibodies, and reduced tumor-induced neovascularization, as detected by micro-computed tomography (micro-CT) and staining with anti-CD31 antibodies. CCN2-deficient B16(F10) cells were defective in a tubule formation/vasculogenic mimicry assay in vitro. Mice deleted for CCN2 in CAFs also showed impaired vasculogenic mimicry of subcutaneously-injected B16-F10 cells in vivo. Our results provide new insights into the cross-talk among different cell types in the tumor microenvironment and suggest CAFs play a heretofore unappreciated role by being essential for tumor neovascularization via the production of CCN2. Our data are consistent with the hypothesis that activated CAFs are essential for melanoma metastasis and that, due to its role in this process, CCN2 is a therapeutic target for melanoma.	Immunohistochemical staining	Loss of CCN2 in CAFs resulted in reduced CAF activation, as detected by staining with anti-α-smooth muscle actin antibodies, and reduced tumor-induced neovascularization, as detected by micro-computed tomography (micro-CT) and staining with anti-CD31 antibodies. CCN2-deficient B16(F10) cells were defective in a tubule formation/vasculogenic mimicry assay in vitro. Mice deleted for CCN2 in CAFs also showed impaired vasculogenic mimicry of subcutaneously-injected B16-F10 cells in vivo. Our results provide new insights into the cross-talk among different cell types in the tumor microenvironment and suggest CAFs play a heretofore unappreciated role by being essential for tumor neovascularization via the production of CCN2. Our data are consistent with the hypothesis that activated CAFs are essential for melanoma metastasis and that, due to its role in this process, CCN2 is a therapeutic target for melanoma.		ELISA,Histological analysis,transfection,RNA-seq,immunohistochemistry experiments,				CCN2,COL1A2		Loss of CCN2 in CAFs resulted in reduced CAF activation, as detected by staining with anti-α-smooth muscle actin antibodies, and reduced tumor-induced neovascularization, as detected by micro-computed tomography (micro-CT) and staining with anti-CD31 antibodies. CCN2-deficient B16(F10) cells were defective in a tubule formation/vasculogenic mimicry assay in vitro. Mice deleted for CCN2 in CAFs also showed impaired vasculogenic mimicry of subcutaneously-injected B16-F10 cells in vivo. Our results provide new insights into the cross-talk among different cell types in the tumor microenvironment and suggest CAFs play a heretofore unappreciated role by being essential for tumor neovascularization via the production of CCN2. Our data are consistent with the hypothesis that activated CAFs are essential for melanoma metastasis and that, due to its role in this process, CCN2 is a therapeutic target for melanoma.;Loss of CCN2 in CAFs resulted in reduced CAF activation, as detected by staining with anti-α-smooth muscle actin antibodies, and reduced tumor-induced neovascularization, as detected by micro-computed tomography (micro-CT) and staining with anti-CD31 antibodies. CCN2-deficient B16(F10) cells were defective in a tubule formation/vasculogenic mimicry assay in vitro. Mice deleted for CCN2 in CAFs also showed impaired vasculogenic mimicry of subcutaneously-injected B16-F10 cells in vivo. Our results provide new insights into the cross-talk among different cell types in the tumor microenvironment and suggest CAFs play a heretofore unappreciated role by being essential for tumor neovascularization via the production of CCN2. Our data are consistent with the hypothesis that activated CAFs are essential for melanoma metastasis and that, due to its role in this process, CCN2 is a therapeutic target for melanoma.
29885262	chr1	55036580	55038580	PCSK9	We, therefore, studied the effect of PCSK9 on interferon (IFN) β expression. We show that PCSK9 decreases IFNβ promoter/enhancer activity, mRNA and protein levels, and its downstream 2',5'-oligoadenylate synthetase-1 mRNA level. ProPCSK9, but not the cleaved PCSK9, down-regulates IFNβ promoter/enhancer activity. Moreover, PCSK9 decreases IFNβ promoter/enhancer activity through the positive regulatory domain IV region where the activating transcription factor-2 (ATF-2)/c-Jun heterodimer binds. Mechanistically, we demonstrate an interaction between PCSK9 and ATF-2, which reduces ATF-2/c-Jun dimerization and ATF-2/c-Jun binding to the IFNβ enhancer. This novel function of PCSK9 should have important implications in optimizing the clinical use of PCSK9 inhibitors.	human	Liver	High+Lowthroughput	Proprotein convertase subtilisin/kexin type 9 inhibits interferon β expression through interacting with ATF-2	否		cancer	Huh-7 cell	E_01_0421	transcription,luciferase assay,Western blot,RT-qPCR,ELISA,ChIP,	We, therefore, studied the effect of PCSK9 on interferon (IFN) β expression. We show that PCSK9 decreases IFNβ promoter/enhancer activity, mRNA and protein levels, and its downstream 2',5'-oligoadenylate synthetase-1 mRNA level. ProPCSK9, but not the cleaved PCSK9, down-regulates IFNβ promoter/enhancer activity. Moreover, PCSK9 decreases IFNβ promoter/enhancer activity through the positive regulatory domain IV region where the activating transcription factor-2 (ATF-2)/c-Jun heterodimer binds. Mechanistically, we demonstrate an interaction between PCSK9 and ATF-2, which reduces ATF-2/c-Jun dimerization and ATF-2/c-Jun binding to the IFNβ enhancer. This novel function of PCSK9 should have important implications in optimizing the clinical use of PCSK9 inhibitors.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We, therefore, studied the effect of PCSK9 on interferon (IFN) β expression. We show that PCSK9 decreases IFNβ promoter/enhancer activity, mRNA and protein levels, and its downstream 2',5'-oligoadenylate synthetase-1 mRNA level. ProPCSK9, but not the cleaved PCSK9, down-regulates IFNβ promoter/enhancer activity. Moreover, PCSK9 decreases IFNβ promoter/enhancer activity through the positive regulatory domain IV region where the activating transcription factor-2 (ATF-2)/c-Jun heterodimer binds. Mechanistically, we demonstrate an interaction between PCSK9 and ATF-2, which reduces ATF-2/c-Jun dimerization and ATF-2/c-Jun binding to the IFNβ enhancer. This novel function of PCSK9 should have important implications in optimizing the clinical use of PCSK9 inhibitors.	Immunohistochemical staining	We, therefore, studied the effect of PCSK9 on interferon (IFN) β expression. We show that PCSK9 decreases IFNβ promoter/enhancer activity, mRNA and protein levels, and its downstream 2',5'-oligoadenylate synthetase-1 mRNA level. ProPCSK9, but not the cleaved PCSK9, down-regulates IFNβ promoter/enhancer activity. Moreover, PCSK9 decreases IFNβ promoter/enhancer activity through the positive regulatory domain IV region where the activating transcription factor-2 (ATF-2)/c-Jun heterodimer binds. Mechanistically, we demonstrate an interaction between PCSK9 and ATF-2, which reduces ATF-2/c-Jun dimerization and ATF-2/c-Jun binding to the IFNβ enhancer. This novel function of PCSK9 should have important implications in optimizing the clinical use of PCSK9 inhibitors.		transcription,luciferase assay,Western blot,RT-qPCR,ELISA,ChIP,			PCSK9		We, therefore, studied the effect of PCSK9 on interferon (IFN) β expression. We show that PCSK9 decreases IFNβ promoter/enhancer activity, mRNA and protein levels, and its downstream 2',5'-oligoadenylate synthetase-1 mRNA level. ProPCSK9, but not the cleaved PCSK9, down-regulates IFNβ promoter/enhancer activity. Moreover, PCSK9 decreases IFNβ promoter/enhancer activity through the positive regulatory domain IV region where the activating transcription factor-2 (ATF-2)/c-Jun heterodimer binds. Mechanistically, we demonstrate an interaction between PCSK9 and ATF-2, which reduces ATF-2/c-Jun dimerization and ATF-2/c-Jun binding to the IFNβ enhancer. This novel function of PCSK9 should have important implications in optimizing the clinical use of PCSK9 inhibitors.	
29884649	chr13	110709998	110711998	ING1	Correspondingly, GADD45α occupies C/EBPβ/δ-dependent superenhancers and, cooperatively with ING1, promotes local DNA demethylation via long-range chromatin loops to permit C/EBPβ recruitment. The results indicate that enhancer methylation can affect aging and imply that C/EBP proteins play an unexpected role in this process. Our study suggests a causal nexus between DNA demethylation, metabolism, and organismal aging.	human	Nervous	High+Lowthroughput	Impaired DNA demethylation of C/EBP sites causes premature aging	否		Premature ageing	MEF	E_01_0422	WGBS-seq,Oil Red O staining,RNA isolation,cDNA synthesis,qPCR,RNA-seq,RNA expression microarrays,ChIP,ChIP-seq,NG Capture-C,Methylation-sensitive PCR,Hematoxylin and eosin (H&E) staining,SA-β-Gal staining,Luciferase reporter assays,Co-IP,immunoblotting,Immunostaining	Correspondingly, GADD45α occupies C/EBPβ/δ-dependent superenhancers and, cooperatively with ING1, promotes local DNA demethylation via long-range chromatin loops to permit C/EBPβ recruitment. The results indicate that enhancer methylation can affect aging and imply that C/EBP proteins play an unexpected role in this process. Our study suggests a causal nexus between DNA demethylation, metabolism, and organismal aging.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Correspondingly, GADD45α occupies C/EBPβ/δ-dependent superenhancers and, cooperatively with ING1, promotes local DNA demethylation via long-range chromatin loops to permit C/EBPβ recruitment. The results indicate that enhancer methylation can affect aging and imply that C/EBP proteins play an unexpected role in this process. Our study suggests a causal nexus between DNA demethylation, metabolism, and organismal aging.	Immunohistochemical staining	Correspondingly, GADD45α occupies C/EBPβ/δ-dependent superenhancers and, cooperatively with ING1, promotes local DNA demethylation via long-range chromatin loops to permit C/EBPβ recruitment. The results indicate that enhancer methylation can affect aging and imply that C/EBP proteins play an unexpected role in this process. Our study suggests a causal nexus between DNA demethylation, metabolism, and organismal aging.		WGBS-seq,Oil Red O staining,RNA isolation,cDNA synthesis,qPCR,RNA-seq,RNA expression microarrays,ChIP,ChIP-seq,NG Capture-C,Methylation-sensitive PCR,Hematoxylin and eosin (H&E) staining,SA-β-Gal staining,Luciferase reporter assays,Co-IP,immunoblotting,Immunostaining			ING1		Correspondingly, GADD45α occupies C/EBPβ/δ-dependent superenhancers and, cooperatively with ING1, promotes local DNA demethylation via long-range chromatin loops to permit C/EBPβ recruitment. The results indicate that enhancer methylation can affect aging and imply that C/EBP proteins play an unexpected role in this process. Our study suggests a causal nexus between DNA demethylation, metabolism, and organismal aging.	
29883697	chr11	47266314	47268314	MADD	The chromosomal enhancer maps of 6 brain regions were then aligned with the GWAS summary data to obtain the association testing results of enhancer regions for insomnia. Gene prioritization, tissue/cell and pathway enrichment analysis were implemented by Data-driven Expression Prioritized Integration for Complex Traits (DEPICT) tool. We identified multiple cross-brain regions or brain-region specific prioritized genes for insomnia, such as MADD (P = .0013 in angular gyrus), PPP2R3C (P = .0319 in cingulate gyrus), CASP9 (P = .0066 in angular gyrus and P = .0278 in hippocampus middle), PLEKHM2 (P = .0032 in angular gyrus, P = .0052 in anterior caudate, P = .0385 in cingulate gyrus and P = .0011 in inferior temporal lobe). This study also detected a group of insomnia associated biological pathways within multiple or specific brain regions, such as REACTOME_SIGNALING_BY_NOTCH and KEGG_GLYCEROPHOSPHOLIPID_METABOLISM. Our results showed that insomnia associated genes were significantly enriched in neural stem cells. Our results highlight a set of potential points, particularly neural stem cells, for subsequent biological studies for insomnia.	human	Nervous	High+Lowthroughput	Integrative analysis of genome-wide association study and brain region related enhancer maps identifies biological pathways for insomnia	否		insomnia	neuronal stem cell	E_01_0423	GWAS	The chromosomal enhancer maps of 6 brain regions were then aligned with the GWAS summary data to obtain the association testing results of enhancer regions for insomnia. Gene prioritization, tissue/cell and pathway enrichment analysis were implemented by Data-driven Expression Prioritized Integration for Complex Traits (DEPICT) tool. We identified multiple cross-brain regions or brain-region specific prioritized genes for insomnia, such as MADD (P = .0013 in angular gyrus), PPP2R3C (P = .0319 in cingulate gyrus), CASP9 (P = .0066 in angular gyrus and P = .0278 in hippocampus middle), PLEKHM2 (P = .0032 in angular gyrus, P = .0052 in anterior caudate, P = .0385 in cingulate gyrus and P = .0011 in inferior temporal lobe). This study also detected a group of insomnia associated biological pathways within multiple or specific brain regions, such as REACTOME_SIGNALING_BY_NOTCH and KEGG_GLYCEROPHOSPHOLIPID_METABOLISM. Our results showed that insomnia associated genes were significantly enriched in neural stem cells. Our results highlight a set of potential points, particularly neural stem cells, for subsequent biological studies for insomnia.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The chromosomal enhancer maps of 6 brain regions were then aligned with the GWAS summary data to obtain the association testing results of enhancer regions for insomnia. Gene prioritization, tissue/cell and pathway enrichment analysis were implemented by Data-driven Expression Prioritized Integration for Complex Traits (DEPICT) tool. We identified multiple cross-brain regions or brain-region specific prioritized genes for insomnia, such as MADD (P = .0013 in angular gyrus), PPP2R3C (P = .0319 in cingulate gyrus), CASP9 (P = .0066 in angular gyrus and P = .0278 in hippocampus middle), PLEKHM2 (P = .0032 in angular gyrus, P = .0052 in anterior caudate, P = .0385 in cingulate gyrus and P = .0011 in inferior temporal lobe). This study also detected a group of insomnia associated biological pathways within multiple or specific brain regions, such as REACTOME_SIGNALING_BY_NOTCH and KEGG_GLYCEROPHOSPHOLIPID_METABOLISM. Our results showed that insomnia associated genes were significantly enriched in neural stem cells. Our results highlight a set of potential points, particularly neural stem cells, for subsequent biological studies for insomnia.	Immunohistochemical staining	The chromosomal enhancer maps of 6 brain regions were then aligned with the GWAS summary data to obtain the association testing results of enhancer regions for insomnia. Gene prioritization, tissue/cell and pathway enrichment analysis were implemented by Data-driven Expression Prioritized Integration for Complex Traits (DEPICT) tool. We identified multiple cross-brain regions or brain-region specific prioritized genes for insomnia, such as MADD (P = .0013 in angular gyrus), PPP2R3C (P = .0319 in cingulate gyrus), CASP9 (P = .0066 in angular gyrus and P = .0278 in hippocampus middle), PLEKHM2 (P = .0032 in angular gyrus, P = .0052 in anterior caudate, P = .0385 in cingulate gyrus and P = .0011 in inferior temporal lobe). This study also detected a group of insomnia associated biological pathways within multiple or specific brain regions, such as REACTOME_SIGNALING_BY_NOTCH and KEGG_GLYCEROPHOSPHOLIPID_METABOLISM. Our results showed that insomnia associated genes were significantly enriched in neural stem cells. Our results highlight a set of potential points, particularly neural stem cells, for subsequent biological studies for insomnia.		GWAS			MADD,PPP2R3C,CASP9,PLEKHM2		The chromosomal enhancer maps of 6 brain regions were then aligned with the GWAS summary data to obtain the association testing results of enhancer regions for insomnia. Gene prioritization, tissue/cell and pathway enrichment analysis were implemented by Data-driven Expression Prioritized Integration for Complex Traits (DEPICT) tool. We identified multiple cross-brain regions or brain-region specific prioritized genes for insomnia, such as MADD (P = .0013 in angular gyrus), PPP2R3C (P = .0319 in cingulate gyrus), CASP9 (P = .0066 in angular gyrus and P = .0278 in hippocampus middle), PLEKHM2 (P = .0032 in angular gyrus, P = .0052 in anterior caudate, P = .0385 in cingulate gyrus and P = .0011 in inferior temporal lobe). This study also detected a group of insomnia associated biological pathways within multiple or specific brain regions, such as REACTOME_SIGNALING_BY_NOTCH and KEGG_GLYCEROPHOSPHOLIPID_METABOLISM. Our results showed that insomnia associated genes were significantly enriched in neural stem cells. Our results highlight a set of potential points, particularly neural stem cells, for subsequent biological studies for insomnia.;The chromosomal enhancer maps of 6 brain regions were then aligned with the GWAS summary data to obtain the association testing results of enhancer regions for insomnia. Gene prioritization, tissue/cell and pathway enrichment analysis were implemented by Data-driven Expression Prioritized Integration for Complex Traits (DEPICT) tool. We identified multiple cross-brain regions or brain-region specific prioritized genes for insomnia, such as MADD (P = .0013 in angular gyrus), PPP2R3C (P = .0319 in cingulate gyrus), CASP9 (P = .0066 in angular gyrus and P = .0278 in hippocampus middle), PLEKHM2 (P = .0032 in angular gyrus, P = .0052 in anterior caudate, P = .0385 in cingulate gyrus and P = .0011 in inferior temporal lobe). This study also detected a group of insomnia associated biological pathways within multiple or specific brain regions, such as REACTOME_SIGNALING_BY_NOTCH and KEGG_GLYCEROPHOSPHOLIPID_METABOLISM. Our results showed that insomnia associated genes were significantly enriched in neural stem cells. Our results highlight a set of potential points, particularly neural stem cells, for subsequent biological studies for insomnia.;The chromosomal enhancer maps of 6 brain regions were then aligned with the GWAS summary data to obtain the association testing results of enhancer regions for insomnia. Gene prioritization, tissue/cell and pathway enrichment analysis were implemented by Data-driven Expression Prioritized Integration for Complex Traits (DEPICT) tool. We identified multiple cross-brain regions or brain-region specific prioritized genes for insomnia, such as MADD (P = .0013 in angular gyrus), PPP2R3C (P = .0319 in cingulate gyrus), CASP9 (P = .0066 in angular gyrus and P = .0278 in hippocampus middle), PLEKHM2 (P = .0032 in angular gyrus, P = .0052 in anterior caudate, P = .0385 in cingulate gyrus and P = .0011 in inferior temporal lobe). This study also detected a group of insomnia associated biological pathways within multiple or specific brain regions, such as REACTOME_SIGNALING_BY_NOTCH and KEGG_GLYCEROPHOSPHOLIPID_METABOLISM. Our results showed that insomnia associated genes were significantly enriched in neural stem cells. Our results highlight a set of potential points, particularly neural stem cells, for subsequent biological studies for insomnia.;The chromosomal enhancer maps of 6 brain regions were then aligned with the GWAS summary data to obtain the association testing results of enhancer regions for insomnia. Gene prioritization, tissue/cell and pathway enrichment analysis were implemented by Data-driven Expression Prioritized Integration for Complex Traits (DEPICT) tool. We identified multiple cross-brain regions or brain-region specific prioritized genes for insomnia, such as MADD (P = .0013 in angular gyrus), PPP2R3C (P = .0319 in cingulate gyrus), CASP9 (P = .0066 in angular gyrus and P = .0278 in hippocampus middle), PLEKHM2 (P = .0032 in angular gyrus, P = .0052 in anterior caudate, P = .0385 in cingulate gyrus and P = .0011 in inferior temporal lobe). This study also detected a group of insomnia associated biological pathways within multiple or specific brain regions, such as REACTOME_SIGNALING_BY_NOTCH and KEGG_GLYCEROPHOSPHOLIPID_METABOLISM. Our results showed that insomnia associated genes were significantly enriched in neural stem cells. Our results highlight a set of potential points, particularly neural stem cells, for subsequent biological studies for insomnia.	
29882899	chr8	127732924	127734924	MYC	Moreover, we show that in colon carcinoma cells, Wnt-responsive enhancers preferentially upregulate transcription from the P1 promoter using reporter assays and in the context of the endogenous Wnt induction. In addition, multiple enhancer deletions using CRISPR/Cas9 corroborate the regulatory specificity of P1. Finally, we show that preferential activation between Wnt-responsive enhancers and the P1 promoter is influenced by the distinct core promoter elements that are present in the MYC promoters. Taken together, our results provide new insight into how enhancers can specifically target alternative promoters and suggest that formation of these selective interactions could allow more precise combinatorial regulation of transcription initiation.	human	Colon	High+Lowthroughput	Selective Activation of Alternative MYC Core Promoters by Wnt-Responsive Enhancers	否		Other	HCT-116	E_01_0424	PCR,Luciferase Reporter Assay,Real Time qPCR,Genome Editing,ChIP-Seq,	Moreover, we show that in colon carcinoma cells, Wnt-responsive enhancers preferentially upregulate transcription from the P1 promoter using reporter assays and in the context of the endogenous Wnt induction. In addition, multiple enhancer deletions using CRISPR/Cas9 corroborate the regulatory specificity of P1. Finally, we show that preferential activation between Wnt-responsive enhancers and the P1 promoter is influenced by the distinct core promoter elements that are present in the MYC promoters. Taken together, our results provide new insight into how enhancers can specifically target alternative promoters and suggest that formation of these selective interactions could allow more precise combinatorial regulation of transcription initiation.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Moreover, we show that in colon carcinoma cells, Wnt-responsive enhancers preferentially upregulate transcription from the P1 promoter using reporter assays and in the context of the endogenous Wnt induction. In addition, multiple enhancer deletions using CRISPR/Cas9 corroborate the regulatory specificity of P1. Finally, we show that preferential activation between Wnt-responsive enhancers and the P1 promoter is influenced by the distinct core promoter elements that are present in the MYC promoters. Taken together, our results provide new insight into how enhancers can specifically target alternative promoters and suggest that formation of these selective interactions could allow more precise combinatorial regulation of transcription initiation.	Immunohistochemical staining	Moreover, we show that in colon carcinoma cells, Wnt-responsive enhancers preferentially upregulate transcription from the P1 promoter using reporter assays and in the context of the endogenous Wnt induction. In addition, multiple enhancer deletions using CRISPR/Cas9 corroborate the regulatory specificity of P1. Finally, we show that preferential activation between Wnt-responsive enhancers and the P1 promoter is influenced by the distinct core promoter elements that are present in the MYC promoters. Taken together, our results provide new insight into how enhancers can specifically target alternative promoters and suggest that formation of these selective interactions could allow more precise combinatorial regulation of transcription initiation.		PCR,Luciferase Reporter Assay,Real Time qPCR,Genome Editing,ChIP-Seq,				MYC		Moreover, we show that in colon carcinoma cells, Wnt-responsive enhancers preferentially upregulate transcription from the P1 promoter using reporter assays and in the context of the endogenous Wnt induction. In addition, multiple enhancer deletions using CRISPR/Cas9 corroborate the regulatory specificity of P1. Finally, we show that preferential activation between Wnt-responsive enhancers and the P1 promoter is influenced by the distinct core promoter elements that are present in the MYC promoters. Taken together, our results provide new insight into how enhancers can specifically target alternative promoters and suggest that formation of these selective interactions could allow more precise combinatorial regulation of transcription initiation.
29881302	chr7	27736725	27738725	TAX1BP1	We describe a potential mechanism related to failure of A20 to suppress inflammation in CD, characterized by high A20 expression and low A20 protein levels. The dysregulation of A20 is potentially due to alterations in ABIN-1, and infection with E. coli strain LF82 could affect the function and stability of A20. Our study signifies an important finding in A20 regulation in IBD, which prevents it from suppressing inflammation.	human	Colon	High+Lowthroughput	Tumor necrosis factor α-induced protein 3 (A20) is dysregulated in pediatric Crohn disease	否		Pediatric inflammatory bowel disease (IBD)	T-84	E_01_0425	Total RNA extraction,reverse transcription PCR,Cytokine analysis,Immunofluorescence microscopy,ELISA,	We describe a potential mechanism related to failure of A20 to suppress inflammation in CD, characterized by high A20 expression and low A20 protein levels. The dysregulation of A20 is potentially due to alterations in ABIN-1, and infection with E. coli strain LF82 could affect the function and stability of A20. Our study signifies an important finding in A20 regulation in IBD, which prevents it from suppressing inflammation.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We describe a potential mechanism related to failure of A20 to suppress inflammation in CD, characterized by high A20 expression and low A20 protein levels. The dysregulation of A20 is potentially due to alterations in ABIN-1, and infection with E. coli strain LF82 could affect the function and stability of A20. Our study signifies an important finding in A20 regulation in IBD, which prevents it from suppressing inflammation.	Immunohistochemical staining	We describe a potential mechanism related to failure of A20 to suppress inflammation in CD, characterized by high A20 expression and low A20 protein levels. The dysregulation of A20 is potentially due to alterations in ABIN-1, and infection with E. coli strain LF82 could affect the function and stability of A20. Our study signifies an important finding in A20 regulation in IBD, which prevents it from suppressing inflammation.		Total RNA extraction,reverse transcription PCR,Cytokine analysis,Immunofluorescence microscopy,ELISA,			TAX1BP1		We describe a potential mechanism related to failure of A20 to suppress inflammation in CD, characterized by high A20 expression and low A20 protein levels. The dysregulation of A20 is potentially due to alterations in ABIN-1, and infection with E. coli strain LF82 could affect the function and stability of A20. Our study signifies an important finding in A20 regulation in IBD, which prevents it from suppressing inflammation.	
29880601	chr12	7916539	7918539	SLC2A3	Finally, we investigated expression of the SLC2A3 and SLC2A14 genes, adjacently positioned to the eRNA07573 locus,in eRNA07573 KO cells. Here, we show that 145 unstable nuclear RNAs, including enhancer RNAs (eRNAs) and long noncoding RNAs (lncRNAs) such as NEAT1v2, are stabilized upon Salmonella infection in HeLa cells. In uninfected cells, the RNA exosome, aided by the Nuclear EXosome Targeting (NEXT) complex, degrades these labile transcripts. Upon infection, the levels of the exosome/NEXT components, RRP6 and MTR4, dramatically decrease, resulting in transcript stabilization. Depletion of lncRNAs, NEAT1v2, or eRNA07573 in HeLa cells triggers increased susceptibility to Salmonella infection concomitant with the deregulated expression of a distinct class of immunity-related genes, indicating that the accumulation of unstable nuclear RNAs contributes to antibacterial defense. Our results highlight a fundamental role for regulated degradation of nuclear RNA in the response to pathogenic infection.	human	connective	High+Lowthroughput	Diminished nuclear RNA decay upon Salmonella infection upregulates antibacterial noncoding RNAs	否		Salmonella infection	HeLa	E_01_0426	transfection,RT–qPCR,siRNA,Immunoblotting,FISH,immunocytochemistry,Northern blot	Finally, we investigated expression of the SLC2A3 and SLC2A14 genes, adjacently positioned to the eRNA07573 locus,in eRNA07573 KO cells. Here, we show that 145 unstable nuclear RNAs, including enhancer RNAs (eRNAs) and long noncoding RNAs (lncRNAs) such as NEAT1v2, are stabilized upon Salmonella infection in HeLa cells. In uninfected cells, the RNA exosome, aided by the Nuclear EXosome Targeting (NEXT) complex, degrades these labile transcripts. Upon infection, the levels of the exosome/NEXT components, RRP6 and MTR4, dramatically decrease, resulting in transcript stabilization. Depletion of lncRNAs, NEAT1v2, or eRNA07573 in HeLa cells triggers increased susceptibility to Salmonella infection concomitant with the deregulated expression of a distinct class of immunity-related genes, indicating that the accumulation of unstable nuclear RNAs contributes to antibacterial defense. Our results highlight a fundamental role for regulated degradation of nuclear RNA in the response to pathogenic infection.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Finally, we investigated expression of the SLC2A3 and SLC2A14 genes, adjacently positioned to the eRNA07573 locus,in eRNA07573 KO cells. Here, we show that 145 unstable nuclear RNAs, including enhancer RNAs (eRNAs) and long noncoding RNAs (lncRNAs) such as NEAT1v2, are stabilized upon Salmonella infection in HeLa cells. In uninfected cells, the RNA exosome, aided by the Nuclear EXosome Targeting (NEXT) complex, degrades these labile transcripts. Upon infection, the levels of the exosome/NEXT components, RRP6 and MTR4, dramatically decrease, resulting in transcript stabilization. Depletion of lncRNAs, NEAT1v2, or eRNA07573 in HeLa cells triggers increased susceptibility to Salmonella infection concomitant with the deregulated expression of a distinct class of immunity-related genes, indicating that the accumulation of unstable nuclear RNAs contributes to antibacterial defense. Our results highlight a fundamental role for regulated degradation of nuclear RNA in the response to pathogenic infection.	Immunohistochemical staining	Finally, we investigated expression of the SLC2A3 and SLC2A14 genes, adjacently positioned to the eRNA07573 locus,in eRNA07573 KO cells. Here, we show that 145 unstable nuclear RNAs, including enhancer RNAs (eRNAs) and long noncoding RNAs (lncRNAs) such as NEAT1v2, are stabilized upon Salmonella infection in HeLa cells. In uninfected cells, the RNA exosome, aided by the Nuclear EXosome Targeting (NEXT) complex, degrades these labile transcripts. Upon infection, the levels of the exosome/NEXT components, RRP6 and MTR4, dramatically decrease, resulting in transcript stabilization. Depletion of lncRNAs, NEAT1v2, or eRNA07573 in HeLa cells triggers increased susceptibility to Salmonella infection concomitant with the deregulated expression of a distinct class of immunity-related genes, indicating that the accumulation of unstable nuclear RNAs contributes to antibacterial defense. Our results highlight a fundamental role for regulated degradation of nuclear RNA in the response to pathogenic infection.		transfection,RT–qPCR,siRNA,Immunoblotting,FISH,immunocytochemistry,Northern blot			SLC2A3	SOCS3	Finally, we investigated expression of the SLC2A3 and SLC2A14 genes, adjacently positioned to the eRNA07573 locus,in eRNA07573 KO cells. Here, we show that 145 unstable nuclear RNAs, including enhancer RNAs (eRNAs) and long noncoding RNAs (lncRNAs) such as NEAT1v2, are stabilized upon Salmonella infection in HeLa cells. In uninfected cells, the RNA exosome, aided by the Nuclear EXosome Targeting (NEXT) complex, degrades these labile transcripts. Upon infection, the levels of the exosome/NEXT components, RRP6 and MTR4, dramatically decrease, resulting in transcript stabilization. Depletion of lncRNAs, NEAT1v2, or eRNA07573 in HeLa cells triggers increased susceptibility to Salmonella infection concomitant with the deregulated expression of a distinct class of immunity-related genes, indicating that the accumulation of unstable nuclear RNAs contributes to antibacterial defense. Our results highlight a fundamental role for regulated degradation of nuclear RNA in the response to pathogenic infection.	Finally, we investigated expression of the SLC2A3 and SLC2A14 genes, adjacently positioned to the eRNA07573 locus,in eRNA07573 KO cells. Here, we show that 145 unstable nuclear RNAs, including enhancer RNAs (eRNAs) and long noncoding RNAs (lncRNAs) such as NEAT1v2, are stabilized upon Salmonella infection in HeLa cells. In uninfected cells, the RNA exosome, aided by the Nuclear EXosome Targeting (NEXT) complex, degrades these labile transcripts. Upon infection, the levels of the exosome/NEXT components, RRP6 and MTR4, dramatically decrease, resulting in transcript stabilization. Depletion of lncRNAs, NEAT1v2, or eRNA07573 in HeLa cells triggers increased susceptibility to Salmonella infection concomitant with the deregulated expression of a distinct class of immunity-related genes, indicating that the accumulation of unstable nuclear RNAs contributes to antibacterial defense. Our results highlight a fundamental role for regulated degradation of nuclear RNA in the response to pathogenic infection.
29879032	chr14	51429786	51431786	Ang2	Initially, we found that BAY11-7082 inhibited NF-κB expression in a concentration-dependent manner. According to the findings of MTT assay and flow cytometry, we understood that RA-HFLS treated by BAY11-7082 (an inhibitor of NF-κB), the inhibition of NF-κB pathway, suppressed RA-HFLS proliferation and induced RA-HFLS apoptosis in a concentration and time-dependent manner. Furthermore, RA-HFLS treated by BAY11-7082 presented decreased VEGF, Ang1 and Ang2 expressions in a concentration-dependent manner.The study concluded that inhibition of NF-κB pathway induced cell apoptosis and suppressed proliferation and angiogenesis of RA-HFLS, which could serve as a novel target in the treatment of RA.	mouse		High+Lowthroughput	Inhibition of NF-κB signaling pathway induces apoptosis and suppresses proliferation and angiogenesis of human fibroblast-like synovial cells in rheumatoid arthritis	否		Rheumatoid arthritis (RA)	HFLS cell	E_01_0427	MTT,Flow cytometry,Western blot	Initially, we found that BAY11-7082 inhibited NF-κB expression in a concentration-dependent manner. According to the findings of MTT assay and flow cytometry, we understood that RA-HFLS treated by BAY11-7082 (an inhibitor of NF-κB), the inhibition of NF-κB pathway, suppressed RA-HFLS proliferation and induced RA-HFLS apoptosis in a concentration and time-dependent manner. Furthermore, RA-HFLS treated by BAY11-7082 presented decreased VEGF, Ang1 and Ang2 expressions in a concentration-dependent manner.The study concluded that inhibition of NF-κB pathway induced cell apoptosis and suppressed proliferation and angiogenesis of RA-HFLS, which could serve as a novel target in the treatment of RA.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Initially, we found that BAY11-7082 inhibited NF-κB expression in a concentration-dependent manner. According to the findings of MTT assay and flow cytometry, we understood that RA-HFLS treated by BAY11-7082 (an inhibitor of NF-κB), the inhibition of NF-κB pathway, suppressed RA-HFLS proliferation and induced RA-HFLS apoptosis in a concentration and time-dependent manner. Furthermore, RA-HFLS treated by BAY11-7082 presented decreased VEGF, Ang1 and Ang2 expressions in a concentration-dependent manner.The study concluded that inhibition of NF-κB pathway induced cell apoptosis and suppressed proliferation and angiogenesis of RA-HFLS, which could serve as a novel target in the treatment of RA.	Immunohistochemical staining	Initially, we found that BAY11-7082 inhibited NF-κB expression in a concentration-dependent manner. According to the findings of MTT assay and flow cytometry, we understood that RA-HFLS treated by BAY11-7082 (an inhibitor of NF-κB), the inhibition of NF-κB pathway, suppressed RA-HFLS proliferation and induced RA-HFLS apoptosis in a concentration and time-dependent manner. Furthermore, RA-HFLS treated by BAY11-7082 presented decreased VEGF, Ang1 and Ang2 expressions in a concentration-dependent manner.The study concluded that inhibition of NF-κB pathway induced cell apoptosis and suppressed proliferation and angiogenesis of RA-HFLS, which could serve as a novel target in the treatment of RA.		MTT,Flow cytometry,Western blot			Ang2		Initially, we found that BAY11-7082 inhibited NF-κB expression in a concentration-dependent manner. According to the findings of MTT assay and flow cytometry, we understood that RA-HFLS treated by BAY11-7082 (an inhibitor of NF-κB), the inhibition of NF-κB pathway, suppressed RA-HFLS proliferation and induced RA-HFLS apoptosis in a concentration and time-dependent manner. Furthermore, RA-HFLS treated by BAY11-7082 presented decreased VEGF, Ang1 and Ang2 expressions in a concentration-dependent manner.The study concluded that inhibition of NF-κB pathway induced cell apoptosis and suppressed proliferation and angiogenesis of RA-HFLS, which could serve as a novel target in the treatment of RA.	
29877106	chr10	24788525	24790525	Arg1	PCG and luteolin suppress the productions of pro-inflammatory cytokines interlukin-6 (IL-6), interlukin-12 (IL-12) and tumor necrosis factor alpha (TNF-α) in macrophages. Luteolin promotes macrophage M2 polarization by enhancing expressions of arginase (Arg1) and mannose receptor C type 1 (Mrc1). PCG and luteolin suppress nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) activation and interferon regulatory factor 1 (IRF1), interferon regulatory factor 5 (IRF5) expression. PCG together with luteolin relieves chronic pharyngitis by anti-inflammatory via suppressing NF-κB pathway and the polarization of M1 macrophage.	mouse	lymphoid	High+Lowthroughput	Polysaccharides from Citrus grandis associate with luteolin relieves chronic pharyngitis by anti-inflammatory via suppressing NF-κB pathway and the polarization of M1 macrophages	否		chronic pharyngitis	macrophage	E_01_0428	Western blot,Enzyme-linked immunosorbent assay(ELISA),RT-PCR	PCG and luteolin suppress the productions of pro-inflammatory cytokines interlukin-6 (IL-6), interlukin-12 (IL-12) and tumor necrosis factor alpha (TNF-α) in macrophages. Luteolin promotes macrophage M2 polarization by enhancing expressions of arginase (Arg1) and mannose receptor C type 1 (Mrc1). PCG and luteolin suppress nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) activation and interferon regulatory factor 1 (IRF1), interferon regulatory factor 5 (IRF5) expression. PCG together with luteolin relieves chronic pharyngitis by anti-inflammatory via suppressing NF-κB pathway and the polarization of M1 macrophage.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		PCG and luteolin suppress the productions of pro-inflammatory cytokines interlukin-6 (IL-6), interlukin-12 (IL-12) and tumor necrosis factor alpha (TNF-α) in macrophages. Luteolin promotes macrophage M2 polarization by enhancing expressions of arginase (Arg1) and mannose receptor C type 1 (Mrc1). PCG and luteolin suppress nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) activation and interferon regulatory factor 1 (IRF1), interferon regulatory factor 5 (IRF5) expression. PCG together with luteolin relieves chronic pharyngitis by anti-inflammatory via suppressing NF-κB pathway and the polarization of M1 macrophage.	Immunohistochemical staining	PCG and luteolin suppress the productions of pro-inflammatory cytokines interlukin-6 (IL-6), interlukin-12 (IL-12) and tumor necrosis factor alpha (TNF-α) in macrophages. Luteolin promotes macrophage M2 polarization by enhancing expressions of arginase (Arg1) and mannose receptor C type 1 (Mrc1). PCG and luteolin suppress nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) activation and interferon regulatory factor 1 (IRF1), interferon regulatory factor 5 (IRF5) expression. PCG together with luteolin relieves chronic pharyngitis by anti-inflammatory via suppressing NF-κB pathway and the polarization of M1 macrophage.		Western blot,Enzyme-linked immunosorbent assay(ELISA),RT-PCR			Arg1,Mrc1	IRF1,IRF5	PCG and luteolin suppress the productions of pro-inflammatory cytokines interlukin-6 (IL-6), interlukin-12 (IL-12) and tumor necrosis factor alpha (TNF-α) in macrophages. Luteolin promotes macrophage M2 polarization by enhancing expressions of arginase (Arg1) and mannose receptor C type 1 (Mrc1). PCG and luteolin suppress nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) activation and interferon regulatory factor 1 (IRF1), interferon regulatory factor 5 (IRF5) expression. PCG together with luteolin relieves chronic pharyngitis by anti-inflammatory via suppressing NF-κB pathway and the polarization of M1 macrophage.;PCG and luteolin suppress the productions of pro-inflammatory cytokines interlukin-6 (IL-6), interlukin-12 (IL-12) and tumor necrosis factor alpha (TNF-α) in macrophages. Luteolin promotes macrophage M2 polarization by enhancing expressions of arginase (Arg1) and mannose receptor C type 1 (Mrc1). PCG and luteolin suppress nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) activation and interferon regulatory factor 1 (IRF1), interferon regulatory factor 5 (IRF5) expression. PCG together with luteolin relieves chronic pharyngitis by anti-inflammatory via suppressing NF-κB pathway and the polarization of M1 macrophage.	PCG and luteolin suppress the productions of pro-inflammatory cytokines interlukin-6 (IL-6), interlukin-12 (IL-12) and tumor necrosis factor alpha (TNF-α) in macrophages. Luteolin promotes macrophage M2 polarization by enhancing expressions of arginase (Arg1) and mannose receptor C type 1 (Mrc1). PCG and luteolin suppress nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) activation and interferon regulatory factor 1 (IRF1), interferon regulatory factor 5 (IRF5) expression. PCG together with luteolin relieves chronic pharyngitis by anti-inflammatory via suppressing NF-κB pathway and the polarization of M1 macrophage.;PCG and luteolin suppress the productions of pro-inflammatory cytokines interlukin-6 (IL-6), interlukin-12 (IL-12) and tumor necrosis factor alpha (TNF-α) in macrophages. Luteolin promotes macrophage M2 polarization by enhancing expressions of arginase (Arg1) and mannose receptor C type 1 (Mrc1). PCG and luteolin suppress nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) activation and interferon regulatory factor 1 (IRF1), interferon regulatory factor 5 (IRF5) expression. PCG together with luteolin relieves chronic pharyngitis by anti-inflammatory via suppressing NF-κB pathway and the polarization of M1 macrophage.
29876014	chr18	63121048	63123048	BCL2	Here, we analyzed the epigenome of two high-risk APL (hrAPL) patients and compared it to non-high-risk APL cases. Despite the lack of common genetic signatures, we found that human hrAPL blasts from patients with extremely poor prognosis display specific patterns of histone H3 acetylation, specifically hyperacetylation at a common set of enhancer regions. In addition, unique profiles of the repressive marks H3K27me3 and DNA methylation were exposed in high-risk APLs. Epigenetic comparison with low/intermediate-risk APLs and AMLs revealed hrAPL-specific patterns of histone acetylation and DNA methylation, suggesting these could be further developed into markers for clinical identification. The epigenetic drug MC2884, a newly generated general HAT/EZH2 inhibitor, induces apoptosis of high-risk APL blasts and reshapes their epigenomes by targeting both active and repressive marks. Together, our analysis uncovers distinctive epigenome signatures of hrAPL patients, and provides proof of concept for use of epigenome profiling coupled to epigenetic drugs to 'personalize' precision medicine.	human	Nervous	High+Lowthroughput	Multi-omics profiling reveals a distinctive epigenome signature for high-risk acute promyelocytic leukemia	是		Acute promyelocytic leukemia (APL)	promyelocyte	E_01_0429	NGS,ChIP,RNA extraction,RT-PCR,Whole-genome bisulfite sequencing(WGBS),RNA-seq	Here, we analyzed the epigenome of two high-risk APL (hrAPL) patients and compared it to non-high-risk APL cases. Despite the lack of common genetic signatures, we found that human hrAPL blasts from patients with extremely poor prognosis display specific patterns of histone H3 acetylation, specifically hyperacetylation at a common set of enhancer regions. In addition, unique profiles of the repressive marks H3K27me3 and DNA methylation were exposed in high-risk APLs. Epigenetic comparison with low/intermediate-risk APLs and AMLs revealed hrAPL-specific patterns of histone acetylation and DNA methylation, suggesting these could be further developed into markers for clinical identification. The epigenetic drug MC2884, a newly generated general HAT/EZH2 inhibitor, induces apoptosis of high-risk APL blasts and reshapes their epigenomes by targeting both active and repressive marks. Together, our analysis uncovers distinctive epigenome signatures of hrAPL patients, and provides proof of concept for use of epigenome profiling coupled to epigenetic drugs to 'personalize' precision medicine.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Here, we analyzed the epigenome of two high-risk APL (hrAPL) patients and compared it to non-high-risk APL cases. Despite the lack of common genetic signatures, we found that human hrAPL blasts from patients with extremely poor prognosis display specific patterns of histone H3 acetylation, specifically hyperacetylation at a common set of enhancer regions. In addition, unique profiles of the repressive marks H3K27me3 and DNA methylation were exposed in high-risk APLs. Epigenetic comparison with low/intermediate-risk APLs and AMLs revealed hrAPL-specific patterns of histone acetylation and DNA methylation, suggesting these could be further developed into markers for clinical identification. The epigenetic drug MC2884, a newly generated general HAT/EZH2 inhibitor, induces apoptosis of high-risk APL blasts and reshapes their epigenomes by targeting both active and repressive marks. Together, our analysis uncovers distinctive epigenome signatures of hrAPL patients, and provides proof of concept for use of epigenome profiling coupled to epigenetic drugs to 'personalize' precision medicine.	Immunohistochemical staining	Here, we analyzed the epigenome of two high-risk APL (hrAPL) patients and compared it to non-high-risk APL cases. Despite the lack of common genetic signatures, we found that human hrAPL blasts from patients with extremely poor prognosis display specific patterns of histone H3 acetylation, specifically hyperacetylation at a common set of enhancer regions. In addition, unique profiles of the repressive marks H3K27me3 and DNA methylation were exposed in high-risk APLs. Epigenetic comparison with low/intermediate-risk APLs and AMLs revealed hrAPL-specific patterns of histone acetylation and DNA methylation, suggesting these could be further developed into markers for clinical identification. The epigenetic drug MC2884, a newly generated general HAT/EZH2 inhibitor, induces apoptosis of high-risk APL blasts and reshapes their epigenomes by targeting both active and repressive marks. Together, our analysis uncovers distinctive epigenome signatures of hrAPL patients, and provides proof of concept for use of epigenome profiling coupled to epigenetic drugs to 'personalize' precision medicine.		NGS,ChIP,RNA extraction,RT-PCR,Whole-genome bisulfite sequencing(WGBS),RNA-seq			AK2	BCL2	Here, we analyzed the epigenome of two high-risk APL (hrAPL) patients and compared it to non-high-risk APL cases. Despite the lack of common genetic signatures, we found that human hrAPL blasts from patients with extremely poor prognosis display specific patterns of histone H3 acetylation, specifically hyperacetylation at a common set of enhancer regions. In addition, unique profiles of the repressive marks H3K27me3 and DNA methylation were exposed in high-risk APLs. Epigenetic comparison with low/intermediate-risk APLs and AMLs revealed hrAPL-specific patterns of histone acetylation and DNA methylation, suggesting these could be further developed into markers for clinical identification. The epigenetic drug MC2884, a newly generated general HAT/EZH2 inhibitor, induces apoptosis of high-risk APL blasts and reshapes their epigenomes by targeting both active and repressive marks. Together, our analysis uncovers distinctive epigenome signatures of hrAPL patients, and provides proof of concept for use of epigenome profiling coupled to epigenetic drugs to 'personalize' precision medicine.	Here, we analyzed the epigenome of two high-risk APL (hrAPL) patients and compared it to non-high-risk APL cases. Despite the lack of common genetic signatures, we found that human hrAPL blasts from patients with extremely poor prognosis display specific patterns of histone H3 acetylation, specifically hyperacetylation at a common set of enhancer regions. In addition, unique profiles of the repressive marks H3K27me3 and DNA methylation were exposed in high-risk APLs. Epigenetic comparison with low/intermediate-risk APLs and AMLs revealed hrAPL-specific patterns of histone acetylation and DNA methylation, suggesting these could be further developed into markers for clinical identification. The epigenetic drug MC2884, a newly generated general HAT/EZH2 inhibitor, induces apoptosis of high-risk APL blasts and reshapes their epigenomes by targeting both active and repressive marks. Together, our analysis uncovers distinctive epigenome signatures of hrAPL patients, and provides proof of concept for use of epigenome profiling coupled to epigenetic drugs to 'personalize' precision medicine.
29875794	chrX	67541120	67543120	AR	To find relevant epigenetic signatures enriched at the ARA-lincRNAs' transcription start sites (TSSs) we used a machine learning approach and identified that the ARA-lincRNA genomic loci in LNCaP cells are significantly enriched with epigenetic marks that are characteristic of in cis enhancer RNA regulators, and that the H3K27ac mark of active enhancers is conspicuously enriched at the TSS of ARA-lincRNAs adjacent to androgen-activated protein-coding genes. In addition, LNCaP topologically associating domains (TADs) that comprise chromatin regions with ARA-lincRNAs exhibit transcription factor contents, epigenetic marks and gene transcriptional activities that are significantly different from TADs not containing ARA-lincRNAs. This work highlights the possible involvement of hundreds of lincRNAs working in synergy with the AR on the genome-wide androgen-induced gene regulatory program in prostate cells.	human	Myotome	High+Lowthroughput	Chromatin Landscape Distinguishes the Genomic Loci of Hundreds of Androgen-Receptor-Associated LincRNAs From the Loci of Non-associated LincRNAs	否			LNCaP	E_01_0430	RNA-seq,RIP-Seq,RT-qPCR,Reverse Transcription PCR,GSEA,DNAseI Datasets	To find relevant epigenetic signatures enriched at the ARA-lincRNAs' transcription start sites (TSSs) we used a machine learning approach and identified that the ARA-lincRNA genomic loci in LNCaP cells are significantly enriched with epigenetic marks that are characteristic of in cis enhancer RNA regulators, and that the H3K27ac mark of active enhancers is conspicuously enriched at the TSS of ARA-lincRNAs adjacent to androgen-activated protein-coding genes. In addition, LNCaP topologically associating domains (TADs) that comprise chromatin regions with ARA-lincRNAs exhibit transcription factor contents, epigenetic marks and gene transcriptional activities that are significantly different from TADs not containing ARA-lincRNAs. This work highlights the possible involvement of hundreds of lincRNAs working in synergy with the AR on the genome-wide androgen-induced gene regulatory program in prostate cells.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		To find relevant epigenetic signatures enriched at the ARA-lincRNAs' transcription start sites (TSSs) we used a machine learning approach and identified that the ARA-lincRNA genomic loci in LNCaP cells are significantly enriched with epigenetic marks that are characteristic of in cis enhancer RNA regulators, and that the H3K27ac mark of active enhancers is conspicuously enriched at the TSS of ARA-lincRNAs adjacent to androgen-activated protein-coding genes. In addition, LNCaP topologically associating domains (TADs) that comprise chromatin regions with ARA-lincRNAs exhibit transcription factor contents, epigenetic marks and gene transcriptional activities that are significantly different from TADs not containing ARA-lincRNAs. This work highlights the possible involvement of hundreds of lincRNAs working in synergy with the AR on the genome-wide androgen-induced gene regulatory program in prostate cells.	Immunohistochemical staining	To find relevant epigenetic signatures enriched at the ARA-lincRNAs' transcription start sites (TSSs) we used a machine learning approach and identified that the ARA-lincRNA genomic loci in LNCaP cells are significantly enriched with epigenetic marks that are characteristic of in cis enhancer RNA regulators, and that the H3K27ac mark of active enhancers is conspicuously enriched at the TSS of ARA-lincRNAs adjacent to androgen-activated protein-coding genes. In addition, LNCaP topologically associating domains (TADs) that comprise chromatin regions with ARA-lincRNAs exhibit transcription factor contents, epigenetic marks and gene transcriptional activities that are significantly different from TADs not containing ARA-lincRNAs. This work highlights the possible involvement of hundreds of lincRNAs working in synergy with the AR on the genome-wide androgen-induced gene regulatory program in prostate cells.		RNA-seq,RIP-Seq,RT-qPCR,Reverse Transcription PCR,GSEA,DNAseI Datasets			TUBA1C	AR	To find relevant epigenetic signatures enriched at the ARA-lincRNAs' transcription start sites (TSSs) we used a machine learning approach and identified that the ARA-lincRNA genomic loci in LNCaP cells are significantly enriched with epigenetic marks that are characteristic of in cis enhancer RNA regulators, and that the H3K27ac mark of active enhancers is conspicuously enriched at the TSS of ARA-lincRNAs adjacent to androgen-activated protein-coding genes. In addition, LNCaP topologically associating domains (TADs) that comprise chromatin regions with ARA-lincRNAs exhibit transcription factor contents, epigenetic marks and gene transcriptional activities that are significantly different from TADs not containing ARA-lincRNAs. This work highlights the possible involvement of hundreds of lincRNAs working in synergy with the AR on the genome-wide androgen-induced gene regulatory program in prostate cells.	To find relevant epigenetic signatures enriched at the ARA-lincRNAs' transcription start sites (TSSs) we used a machine learning approach and identified that the ARA-lincRNA genomic loci in LNCaP cells are significantly enriched with epigenetic marks that are characteristic of in cis enhancer RNA regulators, and that the H3K27ac mark of active enhancers is conspicuously enriched at the TSS of ARA-lincRNAs adjacent to androgen-activated protein-coding genes. In addition, LNCaP topologically associating domains (TADs) that comprise chromatin regions with ARA-lincRNAs exhibit transcription factor contents, epigenetic marks and gene transcriptional activities that are significantly different from TADs not containing ARA-lincRNAs. This work highlights the possible involvement of hundreds of lincRNAs working in synergy with the AR on the genome-wide androgen-induced gene regulatory program in prostate cells.
29875318	chr19	30520129	30522129	Dkk1	In conclusion, the osteoanabolic effects of Dkk1 inhibition can be realized if sclerostin upregulation is prevented. Anabolic therapies for patients with low bone mass might benefit from a strategy that accounts for the compensatory milieu of WNT inhibitors in bone tissue.	mouse	connective	High+Lowthroughput	Sclerostin neutralization unleashes the osteoanabolic effects of Dkk1 inhibition	否		Osteoporosis	osteocyte	E_01_0431	DXA,μCT,pQCT,Histology,transgenic mice,ELISA,	In conclusion, the osteoanabolic effects of Dkk1 inhibition can be realized if sclerostin upregulation is prevented. Anabolic therapies for patients with low bone mass might benefit from a strategy that accounts for the compensatory milieu of WNT inhibitors in bone tissue.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In conclusion, the osteoanabolic effects of Dkk1 inhibition can be realized if sclerostin upregulation is prevented. Anabolic therapies for patients with low bone mass might benefit from a strategy that accounts for the compensatory milieu of WNT inhibitors in bone tissue.	Immunohistochemical staining	In conclusion, the osteoanabolic effects of Dkk1 inhibition can be realized if sclerostin upregulation is prevented. Anabolic therapies for patients with low bone mass might benefit from a strategy that accounts for the compensatory milieu of WNT inhibitors in bone tissue.		DXA,μCT,pQCT,Histology,transgenic mice,ELISA,			Dkk1,Dmp1,SOST,LRP5		In conclusion, the osteoanabolic effects of Dkk1 inhibition can be realized if sclerostin upregulation is prevented. Anabolic therapies for patients with low bone mass might benefit from a strategy that accounts for the compensatory milieu of WNT inhibitors in bone tissue.;In conclusion, the osteoanabolic effects of Dkk1 inhibition can be realized if sclerostin upregulation is prevented. Anabolic therapies for patients with low bone mass might benefit from a strategy that accounts for the compensatory milieu of WNT inhibitors in bone tissue.;In conclusion, the osteoanabolic effects of Dkk1 inhibition can be realized if sclerostin upregulation is prevented. Anabolic therapies for patients with low bone mass might benefit from a strategy that accounts for the compensatory milieu of WNT inhibitors in bone tissue.;In conclusion, the osteoanabolic effects of Dkk1 inhibition can be realized if sclerostin upregulation is prevented. Anabolic therapies for patients with low bone mass might benefit from a strategy that accounts for the compensatory milieu of WNT inhibitors in bone tissue.	
29874879	chr14	74473514	74475514	NPC2	Our study demonstrated that NPC2-mediated free cholesterol homeostasis controls HSC proliferation and mitochondrial function.	human	connective	High+Lowthroughput	Niemann-Pick Type C2 Protein Regulates Free Cholesterol Accumulation and Influences Hepatic Stellate Cell Proliferation and Mitochondrial Respiration Function	否		hepatic fibrosis 	HSC-T6 cell	E_01_0432	Western Blot,Real-Time PCR,Seahorse Assay	Our study demonstrated that NPC2-mediated free cholesterol homeostasis controls HSC proliferation and mitochondrial function.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Our study demonstrated that NPC2-mediated free cholesterol homeostasis controls HSC proliferation and mitochondrial function.	Immunohistochemical staining	Our study demonstrated that NPC2-mediated free cholesterol homeostasis controls HSC proliferation and mitochondrial function.		Western Blot,Real-Time PCR,Seahorse Assay			NPC2	TLR4	Our study demonstrated that NPC2-mediated free cholesterol homeostasis controls HSC proliferation and mitochondrial function.	Our study demonstrated that NPC2-mediated free cholesterol homeostasis controls HSC proliferation and mitochondrial function.
29871881	chr4	102498539	102500539	NFKB1	Looking at chromatin capture data, we found that the two classes of enhancers were lying in distinct topologically associating domains and chromatin loops. Our results suggest that specific nucleotide compositions encode for classes of enhancers that are functionally distinct and specifically organized in the human genome.	human		High+Lowthroughput	Human Enhancers Harboring Specific Sequence Composition, Activity, and Genome Organization Are Linked to the Immune Response	是		Other		E_01_0433	Hi-C,RELA ChIP-seq, DNA seq	Looking at chromatin capture data, we found that the two classes of enhancers were lying in distinct topologically associating domains and chromatin loops. Our results suggest that specific nucleotide compositions encode for classes of enhancers that are functionally distinct and specifically organized in the human genome.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Looking at chromatin capture data, we found that the two classes of enhancers were lying in distinct topologically associating domains and chromatin loops. Our results suggest that specific nucleotide compositions encode for classes of enhancers that are functionally distinct and specifically organized in the human genome.	Immunohistochemical staining	Looking at chromatin capture data, we found that the two classes of enhancers were lying in distinct topologically associating domains and chromatin loops. Our results suggest that specific nucleotide compositions encode for classes of enhancers that are functionally distinct and specifically organized in the human genome.		Hi-C,RELA ChIP-seq, DNA seq			BACH2	NFKB1,REL,RELA,BPTF	Looking at chromatin capture data, we found that the two classes of enhancers were lying in distinct topologically associating domains and chromatin loops. Our results suggest that specific nucleotide compositions encode for classes of enhancers that are functionally distinct and specifically organized in the human genome.	Looking at chromatin capture data, we found that the two classes of enhancers were lying in distinct topologically associating domains and chromatin loops. Our results suggest that specific nucleotide compositions encode for classes of enhancers that are functionally distinct and specifically organized in the human genome.;Looking at chromatin capture data, we found that the two classes of enhancers were lying in distinct topologically associating domains and chromatin loops. Our results suggest that specific nucleotide compositions encode for classes of enhancers that are functionally distinct and specifically organized in the human genome.;Looking at chromatin capture data, we found that the two classes of enhancers were lying in distinct topologically associating domains and chromatin loops. Our results suggest that specific nucleotide compositions encode for classes of enhancers that are functionally distinct and specifically organized in the human genome.;Looking at chromatin capture data, we found that the two classes of enhancers were lying in distinct topologically associating domains and chromatin loops. Our results suggest that specific nucleotide compositions encode for classes of enhancers that are functionally distinct and specifically organized in the human genome.
29869821	chr2	15587927	15589927	DDX1	These results suggest that LGR5 is a critical effector of DDX1 in colorectal cancer cells. The DDX1-LGR5 axis could be a new drug target for this type of malignant cancer.	human	Colon	High+Lowthroughput	DEAD box protein DDX1 promotes colorectal tumorigenesis through transcriptional activation of the LGR5 gene	否		Colorectal neoplasms	LoVo cell	E_01_0434	CRISPR / Cas9,knockdown,Quantitative RT‐PCR,Western blot,Luciferase reporter assay,Immunohistochemistry, Immunofluorescence analysis,ChIP	These results suggest that LGR5 is a critical effector of DDX1 in colorectal cancer cells. The DDX1-LGR5 axis could be a new drug target for this type of malignant cancer.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		These results suggest that LGR5 is a critical effector of DDX1 in colorectal cancer cells. The DDX1-LGR5 axis could be a new drug target for this type of malignant cancer.	Immunohistochemical staining	These results suggest that LGR5 is a critical effector of DDX1 in colorectal cancer cells. The DDX1-LGR5 axis could be a new drug target for this type of malignant cancer.		CRISPR / Cas9,knockdown,Quantitative RT‐PCR,Western blot,Luciferase reporter assay,Immunohistochemistry, Immunofluorescence analysis,ChIP			DDX1	LGR5,SOX2	These results suggest that LGR5 is a critical effector of DDX1 in colorectal cancer cells. The DDX1-LGR5 axis could be a new drug target for this type of malignant cancer.	These results suggest that LGR5 is a critical effector of DDX1 in colorectal cancer cells. The DDX1-LGR5 axis could be a new drug target for this type of malignant cancer.;These results suggest that LGR5 is a critical effector of DDX1 in colorectal cancer cells. The DDX1-LGR5 axis could be a new drug target for this type of malignant cancer.
29866822	chr4	54654583	54656583	KIT	Utilizing chromatin immunoprecipitation with sequencing of tumor samples and cell lines, we describe the enhancer landscape of GIST, highlighting genes that reinforce and extend our understanding of these neoplasms. A group of core transcription factors can be distinguished from others unique to localized and metastatic disease. The transcription factor HAND1 emerges in metastatic disease, binds to established GIST-associated enhancers, and facilitates GIST cell proliferation and KIT gene expression. The pattern of transcription factor expression in primary tumors is predictive of metastasis-free survival in GIST patients. These results provide insight into the enhancer landscape and transcription factor network underlying GIST, and define a unique strategy for predicting clinical behavior of this disease.	human	Kidney	High+Lowthroughput	Gastrointestinal stromal tumor enhancers support a transcription factor network predictive of clinical outcome	否		Gastrointestinal stromal tumor (GIST)	293FT	E_01_0435	Transfection,RNA-Seq,ATAC-seq,ChIP-Seq,Quantitative RT-PCR,Cloning,CRISPR Assays,Immunoblotting	Utilizing chromatin immunoprecipitation with sequencing of tumor samples and cell lines, we describe the enhancer landscape of GIST, highlighting genes that reinforce and extend our understanding of these neoplasms. A group of core transcription factors can be distinguished from others unique to localized and metastatic disease. The transcription factor HAND1 emerges in metastatic disease, binds to established GIST-associated enhancers, and facilitates GIST cell proliferation and KIT gene expression. The pattern of transcription factor expression in primary tumors is predictive of metastasis-free survival in GIST patients. These results provide insight into the enhancer landscape and transcription factor network underlying GIST, and define a unique strategy for predicting clinical behavior of this disease.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Utilizing chromatin immunoprecipitation with sequencing of tumor samples and cell lines, we describe the enhancer landscape of GIST, highlighting genes that reinforce and extend our understanding of these neoplasms. A group of core transcription factors can be distinguished from others unique to localized and metastatic disease. The transcription factor HAND1 emerges in metastatic disease, binds to established GIST-associated enhancers, and facilitates GIST cell proliferation and KIT gene expression. The pattern of transcription factor expression in primary tumors is predictive of metastasis-free survival in GIST patients. These results provide insight into the enhancer landscape and transcription factor network underlying GIST, and define a unique strategy for predicting clinical behavior of this disease.	Immunohistochemical staining	Utilizing chromatin immunoprecipitation with sequencing of tumor samples and cell lines, we describe the enhancer landscape of GIST, highlighting genes that reinforce and extend our understanding of these neoplasms. A group of core transcription factors can be distinguished from others unique to localized and metastatic disease. The transcription factor HAND1 emerges in metastatic disease, binds to established GIST-associated enhancers, and facilitates GIST cell proliferation and KIT gene expression. The pattern of transcription factor expression in primary tumors is predictive of metastasis-free survival in GIST patients. These results provide insight into the enhancer landscape and transcription factor network underlying GIST, and define a unique strategy for predicting clinical behavior of this disease.		Transfection,RNA-Seq,ATAC-seq,ChIP-Seq,Quantitative RT-PCR,Cloning,CRISPR Assays,Immunoblotting				KIT,PDGFRA,HAND1		Utilizing chromatin immunoprecipitation with sequencing of tumor samples and cell lines, we describe the enhancer landscape of GIST, highlighting genes that reinforce and extend our understanding of these neoplasms. A group of core transcription factors can be distinguished from others unique to localized and metastatic disease. The transcription factor HAND1 emerges in metastatic disease, binds to established GIST-associated enhancers, and facilitates GIST cell proliferation and KIT gene expression. The pattern of transcription factor expression in primary tumors is predictive of metastasis-free survival in GIST patients. These results provide insight into the enhancer landscape and transcription factor network underlying GIST, and define a unique strategy for predicting clinical behavior of this disease.;Utilizing chromatin immunoprecipitation with sequencing of tumor samples and cell lines, we describe the enhancer landscape of GIST, highlighting genes that reinforce and extend our understanding of these neoplasms. A group of core transcription factors can be distinguished from others unique to localized and metastatic disease. The transcription factor HAND1 emerges in metastatic disease, binds to established GIST-associated enhancers, and facilitates GIST cell proliferation and KIT gene expression. The pattern of transcription factor expression in primary tumors is predictive of metastasis-free survival in GIST patients. These results provide insight into the enhancer landscape and transcription factor network underlying GIST, and define a unique strategy for predicting clinical behavior of this disease.;Utilizing chromatin immunoprecipitation with sequencing of tumor samples and cell lines, we describe the enhancer landscape of GIST, highlighting genes that reinforce and extend our understanding of these neoplasms. A group of core transcription factors can be distinguished from others unique to localized and metastatic disease. The transcription factor HAND1 emerges in metastatic disease, binds to established GIST-associated enhancers, and facilitates GIST cell proliferation and KIT gene expression. The pattern of transcription factor expression in primary tumors is predictive of metastasis-free survival in GIST patients. These results provide insight into the enhancer landscape and transcription factor network underlying GIST, and define a unique strategy for predicting clinical behavior of this disease.
29864144	chrX	71530253	71532253	OGT	The results showed that OGT silencing affects EZH2 binding to FOXC1 promoter but the effect is cell-context dependent. Despite the slight decrease in EZH2 protein level in cells with OGT depletion, EZH2 binding to FOXC1 was increased. Moreover, OGT binding to promoter regions of FOXA1 and FOXC1 was increased in cells with knockdown of EZH2. Increased expression of FOXA1 and FOXC1 in cells with OGT deregulation was associated with increased acetylation level of histone H3. The results suggest that OGT is involved in regulation of FOXA1 and FOXC1 expression but its role is not associated with regulation of EZH2 protein stability.	human	Mammary	High+Lowthroughput	Impact of OGT deregulation on EZH2 target genes FOXA1 and FOXC1 expression in breast cancer cells	否		mammary cancer	MCF10A	E_01_0436	RT-PCR,RNA isolation,Western blot,Chromatin immunoprecipitation assay(CHIP),Migration/invasion assay,	The results showed that OGT silencing affects EZH2 binding to FOXC1 promoter but the effect is cell-context dependent. Despite the slight decrease in EZH2 protein level in cells with OGT depletion, EZH2 binding to FOXC1 was increased. Moreover, OGT binding to promoter regions of FOXA1 and FOXC1 was increased in cells with knockdown of EZH2. Increased expression of FOXA1 and FOXC1 in cells with OGT deregulation was associated with increased acetylation level of histone H3. The results suggest that OGT is involved in regulation of FOXA1 and FOXC1 expression but its role is not associated with regulation of EZH2 protein stability.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The results showed that OGT silencing affects EZH2 binding to FOXC1 promoter but the effect is cell-context dependent. Despite the slight decrease in EZH2 protein level in cells with OGT depletion, EZH2 binding to FOXC1 was increased. Moreover, OGT binding to promoter regions of FOXA1 and FOXC1 was increased in cells with knockdown of EZH2. Increased expression of FOXA1 and FOXC1 in cells with OGT deregulation was associated with increased acetylation level of histone H3. The results suggest that OGT is involved in regulation of FOXA1 and FOXC1 expression but its role is not associated with regulation of EZH2 protein stability.	Immunohistochemical staining	The results showed that OGT silencing affects EZH2 binding to FOXC1 promoter but the effect is cell-context dependent. Despite the slight decrease in EZH2 protein level in cells with OGT depletion, EZH2 binding to FOXC1 was increased. Moreover, OGT binding to promoter regions of FOXA1 and FOXC1 was increased in cells with knockdown of EZH2. Increased expression of FOXA1 and FOXC1 in cells with OGT deregulation was associated with increased acetylation level of histone H3. The results suggest that OGT is involved in regulation of FOXA1 and FOXC1 expression but its role is not associated with regulation of EZH2 protein stability.		RT-PCR,RNA isolation,Western blot,Chromatin immunoprecipitation assay(CHIP),Migration/invasion assay,				OGT,EZH2,FOXA1,FOXC1,SUZ12		The results showed that OGT silencing affects EZH2 binding to FOXC1 promoter but the effect is cell-context dependent. Despite the slight decrease in EZH2 protein level in cells with OGT depletion, EZH2 binding to FOXC1 was increased. Moreover, OGT binding to promoter regions of FOXA1 and FOXC1 was increased in cells with knockdown of EZH2. Increased expression of FOXA1 and FOXC1 in cells with OGT deregulation was associated with increased acetylation level of histone H3. The results suggest that OGT is involved in regulation of FOXA1 and FOXC1 expression but its role is not associated with regulation of EZH2 protein stability.;The results showed that OGT silencing affects EZH2 binding to FOXC1 promoter but the effect is cell-context dependent. Despite the slight decrease in EZH2 protein level in cells with OGT depletion, EZH2 binding to FOXC1 was increased. Moreover, OGT binding to promoter regions of FOXA1 and FOXC1 was increased in cells with knockdown of EZH2. Increased expression of FOXA1 and FOXC1 in cells with OGT deregulation was associated with increased acetylation level of histone H3. The results suggest that OGT is involved in regulation of FOXA1 and FOXC1 expression but its role is not associated with regulation of EZH2 protein stability.;The results showed that OGT silencing affects EZH2 binding to FOXC1 promoter but the effect is cell-context dependent. Despite the slight decrease in EZH2 protein level in cells with OGT depletion, EZH2 binding to FOXC1 was increased. Moreover, OGT binding to promoter regions of FOXA1 and FOXC1 was increased in cells with knockdown of EZH2. Increased expression of FOXA1 and FOXC1 in cells with OGT deregulation was associated with increased acetylation level of histone H3. The results suggest that OGT is involved in regulation of FOXA1 and FOXC1 expression but its role is not associated with regulation of EZH2 protein stability.;The results showed that OGT silencing affects EZH2 binding to FOXC1 promoter but the effect is cell-context dependent. Despite the slight decrease in EZH2 protein level in cells with OGT depletion, EZH2 binding to FOXC1 was increased. Moreover, OGT binding to promoter regions of FOXA1 and FOXC1 was increased in cells with knockdown of EZH2. Increased expression of FOXA1 and FOXC1 in cells with OGT deregulation was associated with increased acetylation level of histone H3. The results suggest that OGT is involved in regulation of FOXA1 and FOXC1 expression but its role is not associated with regulation of EZH2 protein stability.;The results showed that OGT silencing affects EZH2 binding to FOXC1 promoter but the effect is cell-context dependent. Despite the slight decrease in EZH2 protein level in cells with OGT depletion, EZH2 binding to FOXC1 was increased. Moreover, OGT binding to promoter regions of FOXA1 and FOXC1 was increased in cells with knockdown of EZH2. Increased expression of FOXA1 and FOXC1 in cells with OGT deregulation was associated with increased acetylation level of histone H3. The results suggest that OGT is involved in regulation of FOXA1 and FOXC1 expression but its role is not associated with regulation of EZH2 protein stability.
29858072	chr5	138462604	138464604	EGR1	Mechanistically, we reveal P62 enhances IGFII transcriptional activity through forming IGFII promoter-enhancer chromatin loop and increasing METTL3 occupancy on IGFII 3' UTR and enhances H-Ras overexpression by harboring inflammation-related factors, e.g., TNFR1, CLYD, EGR1, NFκB, TLR4, and PPARγ. Furthermore, the P62 cooperates with TNF-α to promote malignant transformation of mesenchymal stem cells. These findings, for the first time, provide insight into the positive role that P62 plays in malignant transformation of mesenchymal stem cells and reveal a novel link between P62 and the inflammation factors in mesenchymal stem cells.	human	Nervous	High+Lowthroughput	Inflammatory-Related P62 Triggers Malignant Transformation of Mesenchymal Stem Cells through the Cascade of CUDR-CTCF-IGFII-RAS Signaling	否		Inflammation, tumour	HBMMSCs cell	E_01_0437	Transfection,RT-PCR,Western Blot,GST Pull-Down,Super-EMSA,ChIP,Co-IP,ChIP-3C/ChIP-Loop Assays,Cells Proliferation CCK8 Assay,Soft-Agar Colony Formation Assay,Xenograft Transplantation In Vivo,Histological Analysis	Mechanistically, we reveal P62 enhances IGFII transcriptional activity through forming IGFII promoter-enhancer chromatin loop and increasing METTL3 occupancy on IGFII 3' UTR and enhances H-Ras overexpression by harboring inflammation-related factors, e.g., TNFR1, CLYD, EGR1, NFκB, TLR4, and PPARγ. Furthermore, the P62 cooperates with TNF-α to promote malignant transformation of mesenchymal stem cells. These findings, for the first time, provide insight into the positive role that P62 plays in malignant transformation of mesenchymal stem cells and reveal a novel link between P62 and the inflammation factors in mesenchymal stem cells.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Mechanistically, we reveal P62 enhances IGFII transcriptional activity through forming IGFII promoter-enhancer chromatin loop and increasing METTL3 occupancy on IGFII 3' UTR and enhances H-Ras overexpression by harboring inflammation-related factors, e.g., TNFR1, CLYD, EGR1, NFκB, TLR4, and PPARγ. Furthermore, the P62 cooperates with TNF-α to promote malignant transformation of mesenchymal stem cells. These findings, for the first time, provide insight into the positive role that P62 plays in malignant transformation of mesenchymal stem cells and reveal a novel link between P62 and the inflammation factors in mesenchymal stem cells.	Immunohistochemical staining	Mechanistically, we reveal P62 enhances IGFII transcriptional activity through forming IGFII promoter-enhancer chromatin loop and increasing METTL3 occupancy on IGFII 3' UTR and enhances H-Ras overexpression by harboring inflammation-related factors, e.g., TNFR1, CLYD, EGR1, NFκB, TLR4, and PPARγ. Furthermore, the P62 cooperates with TNF-α to promote malignant transformation of mesenchymal stem cells. These findings, for the first time, provide insight into the positive role that P62 plays in malignant transformation of mesenchymal stem cells and reveal a novel link between P62 and the inflammation factors in mesenchymal stem cells.		Transfection,RT-PCR,Western Blot,GST Pull-Down,Super-EMSA,ChIP,Co-IP,ChIP-3C/ChIP-Loop Assays,Cells Proliferation CCK8 Assay,Soft-Agar Colony Formation Assay,Xenograft Transplantation In Vivo,Histological Analysis				EGR1,TLR4,CTCF		Mechanistically, we reveal P62 enhances IGFII transcriptional activity through forming IGFII promoter-enhancer chromatin loop and increasing METTL3 occupancy on IGFII 3' UTR and enhances H-Ras overexpression by harboring inflammation-related factors, e.g., TNFR1, CLYD, EGR1, NFκB, TLR4, and PPARγ. Furthermore, the P62 cooperates with TNF-α to promote malignant transformation of mesenchymal stem cells. These findings, for the first time, provide insight into the positive role that P62 plays in malignant transformation of mesenchymal stem cells and reveal a novel link between P62 and the inflammation factors in mesenchymal stem cells.;Mechanistically, we reveal P62 enhances IGFII transcriptional activity through forming IGFII promoter-enhancer chromatin loop and increasing METTL3 occupancy on IGFII 3' UTR and enhances H-Ras overexpression by harboring inflammation-related factors, e.g., TNFR1, CLYD, EGR1, NFκB, TLR4, and PPARγ. Furthermore, the P62 cooperates with TNF-α to promote malignant transformation of mesenchymal stem cells. These findings, for the first time, provide insight into the positive role that P62 plays in malignant transformation of mesenchymal stem cells and reveal a novel link between P62 and the inflammation factors in mesenchymal stem cells.;Mechanistically, we reveal P62 enhances IGFII transcriptional activity through forming IGFII promoter-enhancer chromatin loop and increasing METTL3 occupancy on IGFII 3' UTR and enhances H-Ras overexpression by harboring inflammation-related factors, e.g., TNFR1, CLYD, EGR1, NFκB, TLR4, and PPARγ. Furthermore, the P62 cooperates with TNF-α to promote malignant transformation of mesenchymal stem cells. These findings, for the first time, provide insight into the positive role that P62 plays in malignant transformation of mesenchymal stem cells and reveal a novel link between P62 and the inflammation factors in mesenchymal stem cells.
29853604	chr4	186066731	186068731	TLR3	This study characterizes two different poly-I:C-induced signaling pathways in their induction of immunostimulatory and suppressive factors and suggests improved ways to reprogram the TME to enhance the antitumor efficacy of immunotherapies. 	human	connective	High+Lowthroughput	Helicase-Driven Activation of NFκB-COX2 Pathway Mediates the Immunosuppressive Component of dsRNA-Driven Inflammation in the Human Tumor Microenvironment	否		Inflammation, cancer	C0135C	E_01_0438	Western blot,Image flow analysis,Immunofluorescence,Phospho-CREB activation,RT-PCR,ELISA,chemotaxis assays,	This study characterizes two different poly-I:C-induced signaling pathways in their induction of immunostimulatory and suppressive factors and suggests improved ways to reprogram the TME to enhance the antitumor efficacy of immunotherapies. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		This study characterizes two different poly-I:C-induced signaling pathways in their induction of immunostimulatory and suppressive factors and suggests improved ways to reprogram the TME to enhance the antitumor efficacy of immunotherapies. 	Immunohistochemical staining	This study characterizes two different poly-I:C-induced signaling pathways in their induction of immunostimulatory and suppressive factors and suggests improved ways to reprogram the TME to enhance the antitumor efficacy of immunotherapies. 		Western blot,Image flow analysis,Immunofluorescence,Phospho-CREB activation,RT-PCR,ELISA,chemotaxis assays,			TLR3,CCL22,CXCL12	TRAF3,IRF3,CXCL10,IL10	This study characterizes two different poly-I:C-induced signaling pathways in their induction of immunostimulatory and suppressive factors and suggests improved ways to reprogram the TME to enhance the antitumor efficacy of immunotherapies. ;This study characterizes two different poly-I:C-induced signaling pathways in their induction of immunostimulatory and suppressive factors and suggests improved ways to reprogram the TME to enhance the antitumor efficacy of immunotherapies. ;This study characterizes two different poly-I:C-induced signaling pathways in their induction of immunostimulatory and suppressive factors and suggests improved ways to reprogram the TME to enhance the antitumor efficacy of immunotherapies. 	This study characterizes two different poly-I:C-induced signaling pathways in their induction of immunostimulatory and suppressive factors and suggests improved ways to reprogram the TME to enhance the antitumor efficacy of immunotherapies. ;This study characterizes two different poly-I:C-induced signaling pathways in their induction of immunostimulatory and suppressive factors and suggests improved ways to reprogram the TME to enhance the antitumor efficacy of immunotherapies. ;This study characterizes two different poly-I:C-induced signaling pathways in their induction of immunostimulatory and suppressive factors and suggests improved ways to reprogram the TME to enhance the antitumor efficacy of immunotherapies. ;This study characterizes two different poly-I:C-induced signaling pathways in their induction of immunostimulatory and suppressive factors and suggests improved ways to reprogram the TME to enhance the antitumor efficacy of immunotherapies. 
29853569	chr3	97917797	97919797	Notch2	We identified unique protein signatures that represent temporal changes in the vessel wall during neointimal lesion formation in the presence and absence of Notch2. Overall lesion formation was not affected with loss of smooth muscle Notch2, suggesting compensatory pathways. We also validated the regulation of known injury- or Notch-related targets identified in other vascular contexts, providing additional insight into conserved pathways involved in vascular remodeling.	mouse	Myotome	High+Lowthroughput	Notch2 and Proteomic Signatures in Mouse Neointimal Lesion Formation	否		Neointimal lesions	VSMC	E_01_0439	PCR, immunohistochemical staining,Vessel morphometric analysis,immunostaining,Transgenic mice,	We identified unique protein signatures that represent temporal changes in the vessel wall during neointimal lesion formation in the presence and absence of Notch2. Overall lesion formation was not affected with loss of smooth muscle Notch2, suggesting compensatory pathways. We also validated the regulation of known injury- or Notch-related targets identified in other vascular contexts, providing additional insight into conserved pathways involved in vascular remodeling.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We identified unique protein signatures that represent temporal changes in the vessel wall during neointimal lesion formation in the presence and absence of Notch2. Overall lesion formation was not affected with loss of smooth muscle Notch2, suggesting compensatory pathways. We also validated the regulation of known injury- or Notch-related targets identified in other vascular contexts, providing additional insight into conserved pathways involved in vascular remodeling.	Immunohistochemical staining	We identified unique protein signatures that represent temporal changes in the vessel wall during neointimal lesion formation in the presence and absence of Notch2. Overall lesion formation was not affected with loss of smooth muscle Notch2, suggesting compensatory pathways. We also validated the regulation of known injury- or Notch-related targets identified in other vascular contexts, providing additional insight into conserved pathways involved in vascular remodeling.		PCR, immunohistochemical staining,Vessel morphometric analysis,immunostaining,Transgenic mice,			Notch2,Notch1		We identified unique protein signatures that represent temporal changes in the vessel wall during neointimal lesion formation in the presence and absence of Notch2. Overall lesion formation was not affected with loss of smooth muscle Notch2, suggesting compensatory pathways. We also validated the regulation of known injury- or Notch-related targets identified in other vascular contexts, providing additional insight into conserved pathways involved in vascular remodeling.;We identified unique protein signatures that represent temporal changes in the vessel wall during neointimal lesion formation in the presence and absence of Notch2. Overall lesion formation was not affected with loss of smooth muscle Notch2, suggesting compensatory pathways. We also validated the regulation of known injury- or Notch-related targets identified in other vascular contexts, providing additional insight into conserved pathways involved in vascular remodeling.	
29851165	chr11	32385307	32387307	WT1	Our data suggest that the methylation pattern of the WT1 promoter and enhancers in human podocytes are distinctive from those in HK2. Furthermore, TGF-β1 alters the methylation levels of the WT1 promoter and enhancers in human podocytes. This modification may be relevant to the attenuation of WT1 by TGF-β1, which could contribute to podocyte injury.	human		High+Lowthroughput	TGF-β1 alters DNA methylation levels in promoter and enhancer regions of the WT1 gene in human podocytes	否		Wilms tumor 1 (WT1)	AB8/13 	E_01_0440	ChIP-seq,Quantitative methylation-specific PCR,Quantitative methylation-specific PCR,Western blot,	Our data suggest that the methylation pattern of the WT1 promoter and enhancers in human podocytes are distinctive from those in HK2. Furthermore, TGF-β1 alters the methylation levels of the WT1 promoter and enhancers in human podocytes. This modification may be relevant to the attenuation of WT1 by TGF-β1, which could contribute to podocyte injury.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Our data suggest that the methylation pattern of the WT1 promoter and enhancers in human podocytes are distinctive from those in HK2. Furthermore, TGF-β1 alters the methylation levels of the WT1 promoter and enhancers in human podocytes. This modification may be relevant to the attenuation of WT1 by TGF-β1, which could contribute to podocyte injury.	Immunohistochemical staining	Our data suggest that the methylation pattern of the WT1 promoter and enhancers in human podocytes are distinctive from those in HK2. Furthermore, TGF-β1 alters the methylation levels of the WT1 promoter and enhancers in human podocytes. This modification may be relevant to the attenuation of WT1 by TGF-β1, which could contribute to podocyte injury.		ChIP-seq,Quantitative methylation-specific PCR,Quantitative methylation-specific PCR,Western blot,			WT1		Our data suggest that the methylation pattern of the WT1 promoter and enhancers in human podocytes are distinctive from those in HK2. Furthermore, TGF-β1 alters the methylation levels of the WT1 promoter and enhancers in human podocytes. This modification may be relevant to the attenuation of WT1 by TGF-β1, which could contribute to podocyte injury.	
29848731	chr7	148804383	148806383	EZH2	EZH2 was frequently observed in patients with resected SCLC, but no significant associations were found between its expression and the clinicopathological characteristics and postoperative survivals.	human	Lung	High+Lowthroughput	Prevalence of Enhancer of Zeste Homolog 2 in Patients with Resected Small Cell Lung Cancer	否		Small cell lung cancer (SCLC)	NSCC cell	E_01_0441	Immunohistochemical analyses,	EZH2 was frequently observed in patients with resected SCLC, but no significant associations were found between its expression and the clinicopathological characteristics and postoperative survivals.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		EZH2 was frequently observed in patients with resected SCLC, but no significant associations were found between its expression and the clinicopathological characteristics and postoperative survivals.	Immunohistochemical staining	EZH2 was frequently observed in patients with resected SCLC, but no significant associations were found between its expression and the clinicopathological characteristics and postoperative survivals.		Immunohistochemical analyses,				EZH2		EZH2 was frequently observed in patients with resected SCLC, but no significant associations were found between its expression and the clinicopathological characteristics and postoperative survivals.
29845218	chr16	4254258	4256258	TFAP4	In addition, there was a positive correlation between the TFAP4 and TRERNA1 expression level in clinical GC cases, which also indicated that TFAP4 can directly modulate the expression of TRERNA1. In the present study, we provide a novel potential therapeutic target and strategy for GC.	human	Gastric	High+Lowthroughput	Elevated TFAP4 regulates lncRNA TRERNA1 to promote cell migration and invasion in gastric cancer	否		gastric cancer	AGS, SGC‑7901 and BGC‑823	E_01_0442	Reverse transcription‑quantitative PCR (RT‑qPCR),transfection,Cell migration and invasion assays,Luciferase reporter assay,Chromatin immunoprecipitation (ChIP) assay	In addition, there was a positive correlation between the TFAP4 and TRERNA1 expression level in clinical GC cases, which also indicated that TFAP4 can directly modulate the expression of TRERNA1. In the present study, we provide a novel potential therapeutic target and strategy for GC.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In addition, there was a positive correlation between the TFAP4 and TRERNA1 expression level in clinical GC cases, which also indicated that TFAP4 can directly modulate the expression of TRERNA1. In the present study, we provide a novel potential therapeutic target and strategy for GC.	Immunohistochemical staining	In addition, there was a positive correlation between the TFAP4 and TRERNA1 expression level in clinical GC cases, which also indicated that TFAP4 can directly modulate the expression of TRERNA1. In the present study, we provide a novel potential therapeutic target and strategy for GC.		Reverse transcription‑quantitative PCR (RT‑qPCR),transfection,Cell migration and invasion assays,Luciferase reporter assay,Chromatin immunoprecipitation (ChIP) assay			TRERNA1	TFAP4	In addition, there was a positive correlation between the TFAP4 and TRERNA1 expression level in clinical GC cases, which also indicated that TFAP4 can directly modulate the expression of TRERNA1. In the present study, we provide a novel potential therapeutic target and strategy for GC.	In addition, there was a positive correlation between the TFAP4 and TRERNA1 expression level in clinical GC cases, which also indicated that TFAP4 can directly modulate the expression of TRERNA1. In the present study, we provide a novel potential therapeutic target and strategy for GC.
29842805	chr15	99562745	99564745	MEF2A	The results of the present study demonstrated that the binding of histone deacetylase 1 (HDAC1) to the SOD3 promoter region contributed to SOD3 silencing in basal THP-1 cells. On the other hand, the dissociation of HDAC1 from the SOD3 promoter region and the enrichment of p300, a histone acetyltransferase (HAT), within that region were observed in TPA-induced THP-1 cells. Myocyte enhancer factor 2 (MEF2) functions as a scaffold protein that interacts with histone deacetylases (HDAC) or HAT and regulates gene expression. The present results showed that the MEF2A and MEF2D function as mediators for TPA-elicited SOD3 expression by interacting with HDAC or p300. Additionally, the knockdown of MEF2A or MEF2D in human skin fibroblasts suppressed SOD3 expression at the mRNA and protein levels. Our results provide an insight into epigenetic regulation of redox gene expression, and may ultimately contribute to suppressing the progression of tumours and vascular diseases.	human	Epithelial	High+Lowthroughput	The MEF2A and MEF2D function as scaffold proteins that interact with HDAC1 or p300 in SOD3 expression in THP-1 cells	否		Neoplasm, vascular disease	THP-1	E_01_0443	Western blot,Chromatin immunoprecipitation (ChIP) assay,RT-PCR,transfection,Immunoprecipitation (IP),small interfering RNA transfection	The results of the present study demonstrated that the binding of histone deacetylase 1 (HDAC1) to the SOD3 promoter region contributed to SOD3 silencing in basal THP-1 cells. On the other hand, the dissociation of HDAC1 from the SOD3 promoter region and the enrichment of p300, a histone acetyltransferase (HAT), within that region were observed in TPA-induced THP-1 cells. Myocyte enhancer factor 2 (MEF2) functions as a scaffold protein that interacts with histone deacetylases (HDAC) or HAT and regulates gene expression. The present results showed that the MEF2A and MEF2D function as mediators for TPA-elicited SOD3 expression by interacting with HDAC or p300. Additionally, the knockdown of MEF2A or MEF2D in human skin fibroblasts suppressed SOD3 expression at the mRNA and protein levels. Our results provide an insight into epigenetic regulation of redox gene expression, and may ultimately contribute to suppressing the progression of tumours and vascular diseases.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The results of the present study demonstrated that the binding of histone deacetylase 1 (HDAC1) to the SOD3 promoter region contributed to SOD3 silencing in basal THP-1 cells. On the other hand, the dissociation of HDAC1 from the SOD3 promoter region and the enrichment of p300, a histone acetyltransferase (HAT), within that region were observed in TPA-induced THP-1 cells. Myocyte enhancer factor 2 (MEF2) functions as a scaffold protein that interacts with histone deacetylases (HDAC) or HAT and regulates gene expression. The present results showed that the MEF2A and MEF2D function as mediators for TPA-elicited SOD3 expression by interacting with HDAC or p300. Additionally, the knockdown of MEF2A or MEF2D in human skin fibroblasts suppressed SOD3 expression at the mRNA and protein levels. Our results provide an insight into epigenetic regulation of redox gene expression, and may ultimately contribute to suppressing the progression of tumours and vascular diseases.	Immunohistochemical staining	The results of the present study demonstrated that the binding of histone deacetylase 1 (HDAC1) to the SOD3 promoter region contributed to SOD3 silencing in basal THP-1 cells. On the other hand, the dissociation of HDAC1 from the SOD3 promoter region and the enrichment of p300, a histone acetyltransferase (HAT), within that region were observed in TPA-induced THP-1 cells. Myocyte enhancer factor 2 (MEF2) functions as a scaffold protein that interacts with histone deacetylases (HDAC) or HAT and regulates gene expression. The present results showed that the MEF2A and MEF2D function as mediators for TPA-elicited SOD3 expression by interacting with HDAC or p300. Additionally, the knockdown of MEF2A or MEF2D in human skin fibroblasts suppressed SOD3 expression at the mRNA and protein levels. Our results provide an insight into epigenetic regulation of redox gene expression, and may ultimately contribute to suppressing the progression of tumours and vascular diseases.		Western blot,Chromatin immunoprecipitation (ChIP) assay,RT-PCR,transfection,Immunoprecipitation (IP),small interfering RNA transfection			MEF2D,SOD3	MEF2A,HDAC1	The results of the present study demonstrated that the binding of histone deacetylase 1 (HDAC1) to the SOD3 promoter region contributed to SOD3 silencing in basal THP-1 cells. On the other hand, the dissociation of HDAC1 from the SOD3 promoter region and the enrichment of p300, a histone acetyltransferase (HAT), within that region were observed in TPA-induced THP-1 cells. Myocyte enhancer factor 2 (MEF2) functions as a scaffold protein that interacts with histone deacetylases (HDAC) or HAT and regulates gene expression. The present results showed that the MEF2A and MEF2D function as mediators for TPA-elicited SOD3 expression by interacting with HDAC or p300. Additionally, the knockdown of MEF2A or MEF2D in human skin fibroblasts suppressed SOD3 expression at the mRNA and protein levels. Our results provide an insight into epigenetic regulation of redox gene expression, and may ultimately contribute to suppressing the progression of tumours and vascular diseases.;The results of the present study demonstrated that the binding of histone deacetylase 1 (HDAC1) to the SOD3 promoter region contributed to SOD3 silencing in basal THP-1 cells. On the other hand, the dissociation of HDAC1 from the SOD3 promoter region and the enrichment of p300, a histone acetyltransferase (HAT), within that region were observed in TPA-induced THP-1 cells. Myocyte enhancer factor 2 (MEF2) functions as a scaffold protein that interacts with histone deacetylases (HDAC) or HAT and regulates gene expression. The present results showed that the MEF2A and MEF2D function as mediators for TPA-elicited SOD3 expression by interacting with HDAC or p300. Additionally, the knockdown of MEF2A or MEF2D in human skin fibroblasts suppressed SOD3 expression at the mRNA and protein levels. Our results provide an insight into epigenetic regulation of redox gene expression, and may ultimately contribute to suppressing the progression of tumours and vascular diseases.	The results of the present study demonstrated that the binding of histone deacetylase 1 (HDAC1) to the SOD3 promoter region contributed to SOD3 silencing in basal THP-1 cells. On the other hand, the dissociation of HDAC1 from the SOD3 promoter region and the enrichment of p300, a histone acetyltransferase (HAT), within that region were observed in TPA-induced THP-1 cells. Myocyte enhancer factor 2 (MEF2) functions as a scaffold protein that interacts with histone deacetylases (HDAC) or HAT and regulates gene expression. The present results showed that the MEF2A and MEF2D function as mediators for TPA-elicited SOD3 expression by interacting with HDAC or p300. Additionally, the knockdown of MEF2A or MEF2D in human skin fibroblasts suppressed SOD3 expression at the mRNA and protein levels. Our results provide an insight into epigenetic regulation of redox gene expression, and may ultimately contribute to suppressing the progression of tumours and vascular diseases.;The results of the present study demonstrated that the binding of histone deacetylase 1 (HDAC1) to the SOD3 promoter region contributed to SOD3 silencing in basal THP-1 cells. On the other hand, the dissociation of HDAC1 from the SOD3 promoter region and the enrichment of p300, a histone acetyltransferase (HAT), within that region were observed in TPA-induced THP-1 cells. Myocyte enhancer factor 2 (MEF2) functions as a scaffold protein that interacts with histone deacetylases (HDAC) or HAT and regulates gene expression. The present results showed that the MEF2A and MEF2D function as mediators for TPA-elicited SOD3 expression by interacting with HDAC or p300. Additionally, the knockdown of MEF2A or MEF2D in human skin fibroblasts suppressed SOD3 expression at the mRNA and protein levels. Our results provide an insight into epigenetic regulation of redox gene expression, and may ultimately contribute to suppressing the progression of tumours and vascular diseases.
29813070	chr10	80968670	80970670	Zbtb7a	Moreover, the presence of prebound Zbtb7a can specify promoters that are amenable to TF-induced changes in accessibility. Therefore, Zbtb7a represents a widely used promoter factor that transduces signals from other TFs to enable control of accessibility and regulation of gene expression.	mouse	Nervous	High+Lowthroughput	Zbtb7a is a transducer for the control of promoter accessibility by NF-kappa B and multiple other transcription factors	否		Other	3T3	E_01_0444	Zbtb7a knockdown,quantitative real-time PCR,ChIP,ChIP-seq,DHS sequencing,Reporter assays,BiFC,GST pull-down,MS,Analysis of genomic datasets	Moreover, the presence of prebound Zbtb7a can specify promoters that are amenable to TF-induced changes in accessibility. Therefore, Zbtb7a represents a widely used promoter factor that transduces signals from other TFs to enable control of accessibility and regulation of gene expression.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Moreover, the presence of prebound Zbtb7a can specify promoters that are amenable to TF-induced changes in accessibility. Therefore, Zbtb7a represents a widely used promoter factor that transduces signals from other TFs to enable control of accessibility and regulation of gene expression.	Immunohistochemical staining	Moreover, the presence of prebound Zbtb7a can specify promoters that are amenable to TF-induced changes in accessibility. Therefore, Zbtb7a represents a widely used promoter factor that transduces signals from other TFs to enable control of accessibility and regulation of gene expression.		Zbtb7a knockdown,quantitative real-time PCR,ChIP,ChIP-seq,DHS sequencing,Reporter assays,BiFC,GST pull-down,MS,Analysis of genomic datasets			Zbtb7a		Moreover, the presence of prebound Zbtb7a can specify promoters that are amenable to TF-induced changes in accessibility. Therefore, Zbtb7a represents a widely used promoter factor that transduces signals from other TFs to enable control of accessibility and regulation of gene expression.	
29808619	chr17	34252611	34254611	CCL2	AR signaling in CAF-like cells decreased expression of multiple cytokines; most notably CCL2 and CXCL8 and both cytokines increased migration of PCa cells. These results suggest direct paracrine regulation of PCa cell migration by CAFs through AR signaling.	human	Prostate	High+Lowthroughput	Loss of androgen receptor signaling in prostate cancer-associated fibroblasts (CAFs) promotes CCL2- and CXCL8-mediated cancer cell migration	否		Prostate cancer (PCA)	LNCaPs、cwr1	E_01_0445	ChiP-seq,ChIP-seq,western blot,immunohistochemistry (IHC)	AR signaling in CAF-like cells decreased expression of multiple cytokines; most notably CCL2 and CXCL8 and both cytokines increased migration of PCa cells. These results suggest direct paracrine regulation of PCa cell migration by CAFs through AR signaling.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		AR signaling in CAF-like cells decreased expression of multiple cytokines; most notably CCL2 and CXCL8 and both cytokines increased migration of PCa cells. These results suggest direct paracrine regulation of PCa cell migration by CAFs through AR signaling.	Immunohistochemical staining	AR signaling in CAF-like cells decreased expression of multiple cytokines; most notably CCL2 and CXCL8 and both cytokines increased migration of PCa cells. These results suggest direct paracrine regulation of PCa cell migration by CAFs through AR signaling.		ChiP-seq,ChIP-seq,western blot,immunohistochemistry (IHC)				CCL2,CXCL8,AR		AR signaling in CAF-like cells decreased expression of multiple cytokines; most notably CCL2 and CXCL8 and both cytokines increased migration of PCa cells. These results suggest direct paracrine regulation of PCa cell migration by CAFs through AR signaling.;AR signaling in CAF-like cells decreased expression of multiple cytokines; most notably CCL2 and CXCL8 and both cytokines increased migration of PCa cells. These results suggest direct paracrine regulation of PCa cell migration by CAFs through AR signaling.;AR signaling in CAF-like cells decreased expression of multiple cytokines; most notably CCL2 and CXCL8 and both cytokines increased migration of PCa cells. These results suggest direct paracrine regulation of PCa cell migration by CAFs through AR signaling.
29806631	chr4	106918996	106920996	DKK2	In NF-κB signaling pathway, the mRNA levels of C-C Motif Chemokine Ligand 4 (CCL4) and C-C Motif Chemokine Ligand 4 Like 2 (CCL4L2) were increased, while the mRNA levels of BCL2 Related Protein A1 were decreased. These results suggest that Wnt and NF-κB signaling may be altered in the process of facet joint cartilage degeneration. The present study will expand our understanding of the molecular bases underlying facet joint osteoarthritis.	human	Facet joint	High+Lowthroughput	Altered Wnt and NF-κB Signaling in Facet Joint Osteoarthritis: Insights from RNA Deep Sequencing	否		Facet joint osteoarthritis, lumbar spine osteoarthritis	mutant lymphoma cell	E_01_0446	RNA-seq,Bioinformatic analysis,qRT-PCR,	In NF-κB signaling pathway, the mRNA levels of C-C Motif Chemokine Ligand 4 (CCL4) and C-C Motif Chemokine Ligand 4 Like 2 (CCL4L2) were increased, while the mRNA levels of BCL2 Related Protein A1 were decreased. These results suggest that Wnt and NF-κB signaling may be altered in the process of facet joint cartilage degeneration. The present study will expand our understanding of the molecular bases underlying facet joint osteoarthritis.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In NF-κB signaling pathway, the mRNA levels of C-C Motif Chemokine Ligand 4 (CCL4) and C-C Motif Chemokine Ligand 4 Like 2 (CCL4L2) were increased, while the mRNA levels of BCL2 Related Protein A1 were decreased. These results suggest that Wnt and NF-κB signaling may be altered in the process of facet joint cartilage degeneration. The present study will expand our understanding of the molecular bases underlying facet joint osteoarthritis.	Immunohistochemical staining	In NF-κB signaling pathway, the mRNA levels of C-C Motif Chemokine Ligand 4 (CCL4) and C-C Motif Chemokine Ligand 4 Like 2 (CCL4L2) were increased, while the mRNA levels of BCL2 Related Protein A1 were decreased. These results suggest that Wnt and NF-κB signaling may be altered in the process of facet joint cartilage degeneration. The present study will expand our understanding of the molecular bases underlying facet joint osteoarthritis.		RNA-seq,Bioinformatic analysis,qRT-PCR,			DKK2,TCF7,CCL4,CCL4L2	SOX17,MYC,CAMK2A,LEF1	In NF-κB signaling pathway, the mRNA levels of C-C Motif Chemokine Ligand 4 (CCL4) and C-C Motif Chemokine Ligand 4 Like 2 (CCL4L2) were increased, while the mRNA levels of BCL2 Related Protein A1 were decreased. These results suggest that Wnt and NF-κB signaling may be altered in the process of facet joint cartilage degeneration. The present study will expand our understanding of the molecular bases underlying facet joint osteoarthritis.;In NF-κB signaling pathway, the mRNA levels of C-C Motif Chemokine Ligand 4 (CCL4) and C-C Motif Chemokine Ligand 4 Like 2 (CCL4L2) were increased, while the mRNA levels of BCL2 Related Protein A1 were decreased. These results suggest that Wnt and NF-κB signaling may be altered in the process of facet joint cartilage degeneration. The present study will expand our understanding of the molecular bases underlying facet joint osteoarthritis.;In NF-κB signaling pathway, the mRNA levels of C-C Motif Chemokine Ligand 4 (CCL4) and C-C Motif Chemokine Ligand 4 Like 2 (CCL4L2) were increased, while the mRNA levels of BCL2 Related Protein A1 were decreased. These results suggest that Wnt and NF-κB signaling may be altered in the process of facet joint cartilage degeneration. The present study will expand our understanding of the molecular bases underlying facet joint osteoarthritis.;In NF-κB signaling pathway, the mRNA levels of C-C Motif Chemokine Ligand 4 (CCL4) and C-C Motif Chemokine Ligand 4 Like 2 (CCL4L2) were increased, while the mRNA levels of BCL2 Related Protein A1 were decreased. These results suggest that Wnt and NF-κB signaling may be altered in the process of facet joint cartilage degeneration. The present study will expand our understanding of the molecular bases underlying facet joint osteoarthritis.	In NF-κB signaling pathway, the mRNA levels of C-C Motif Chemokine Ligand 4 (CCL4) and C-C Motif Chemokine Ligand 4 Like 2 (CCL4L2) were increased, while the mRNA levels of BCL2 Related Protein A1 were decreased. These results suggest that Wnt and NF-κB signaling may be altered in the process of facet joint cartilage degeneration. The present study will expand our understanding of the molecular bases underlying facet joint osteoarthritis.;In NF-κB signaling pathway, the mRNA levels of C-C Motif Chemokine Ligand 4 (CCL4) and C-C Motif Chemokine Ligand 4 Like 2 (CCL4L2) were increased, while the mRNA levels of BCL2 Related Protein A1 were decreased. These results suggest that Wnt and NF-κB signaling may be altered in the process of facet joint cartilage degeneration. The present study will expand our understanding of the molecular bases underlying facet joint osteoarthritis.;In NF-κB signaling pathway, the mRNA levels of C-C Motif Chemokine Ligand 4 (CCL4) and C-C Motif Chemokine Ligand 4 Like 2 (CCL4L2) were increased, while the mRNA levels of BCL2 Related Protein A1 were decreased. These results suggest that Wnt and NF-κB signaling may be altered in the process of facet joint cartilage degeneration. The present study will expand our understanding of the molecular bases underlying facet joint osteoarthritis.;In NF-κB signaling pathway, the mRNA levels of C-C Motif Chemokine Ligand 4 (CCL4) and C-C Motif Chemokine Ligand 4 Like 2 (CCL4L2) were increased, while the mRNA levels of BCL2 Related Protein A1 were decreased. These results suggest that Wnt and NF-κB signaling may be altered in the process of facet joint cartilage degeneration. The present study will expand our understanding of the molecular bases underlying facet joint osteoarthritis.
29805666	chr7	148804346	148806346	EZH2	Collectively, these data demonstrate that EZH2 is frequently overexpressed in EC cells and its overexpression is associated with promoting the proliferation and invasion and decreasing the apoptosis of EC cells, suggesting that EZH2 may provide potential therapeutic targets for treatment of endometrial carcinoma.	human	Endometrial cancer	High+Lowthroughput	Enhancer of zeste homolog 2 blockade by RNA interference is implicated with inhibited proliferation, invasion and promoted apoptosis in endometrial carcinoma	否		Endometrial cancer (EC)	monoblast	E_01_0447	Western blot,EZH2 small interfering (si)RNA transfection,Quantitative reverse transcription‑polymerase chain reaction (RT‑qPCR) analysis,In vitro cell proliferation assay,Annexin V/propidium iodide (PI) staining,Matrigel invasion assay,immunohistochemical analysis 	Collectively, these data demonstrate that EZH2 is frequently overexpressed in EC cells and its overexpression is associated with promoting the proliferation and invasion and decreasing the apoptosis of EC cells, suggesting that EZH2 may provide potential therapeutic targets for treatment of endometrial carcinoma.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Collectively, these data demonstrate that EZH2 is frequently overexpressed in EC cells and its overexpression is associated with promoting the proliferation and invasion and decreasing the apoptosis of EC cells, suggesting that EZH2 may provide potential therapeutic targets for treatment of endometrial carcinoma.	Immunohistochemical staining	Collectively, these data demonstrate that EZH2 is frequently overexpressed in EC cells and its overexpression is associated with promoting the proliferation and invasion and decreasing the apoptosis of EC cells, suggesting that EZH2 may provide potential therapeutic targets for treatment of endometrial carcinoma.		Western blot,EZH2 small interfering (si)RNA transfection,Quantitative reverse transcription‑polymerase chain reaction (RT‑qPCR) analysis,In vitro cell proliferation assay,Annexin V/propidium iodide (PI) staining,Matrigel invasion assay,immunohistochemical analysis 				EZH2,BCL2		Collectively, these data demonstrate that EZH2 is frequently overexpressed in EC cells and its overexpression is associated with promoting the proliferation and invasion and decreasing the apoptosis of EC cells, suggesting that EZH2 may provide potential therapeutic targets for treatment of endometrial carcinoma.;Collectively, these data demonstrate that EZH2 is frequently overexpressed in EC cells and its overexpression is associated with promoting the proliferation and invasion and decreasing the apoptosis of EC cells, suggesting that EZH2 may provide potential therapeutic targets for treatment of endometrial carcinoma.
29805099	chr20	50188232	50190232	CEBPB	Collectively, tumor glycolysis orchestrates a molecular network of the AMPK-ULK1, autophagy, and CEBPB pathways to affect MDSCs and maintain tumor immunosuppression.	human	Mammary	High+Lowthroughput	Aerobic Glycolysis Controls Myeloid-Derived Suppressor Cells and Tumor Immunity via a Specific CEBPB Isoform in Triple-Negative Breast Cancer	否		Triple negative breast cancer (TNBC)	4T1	E_01_0448	Short Pairpin RNAs (shRNA),Small Interfering RNA (siRNA),Genetic Knockout,Western Blot,RNA Extraction,Reverse Transcription,Real-Time Polymerase Chain Reaction,Flow Cytometry Analysis (FACS),Immunofluorescence Staining,Metabolic Assay,Bioinformatics Analysis	Collectively, tumor glycolysis orchestrates a molecular network of the AMPK-ULK1, autophagy, and CEBPB pathways to affect MDSCs and maintain tumor immunosuppression.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Collectively, tumor glycolysis orchestrates a molecular network of the AMPK-ULK1, autophagy, and CEBPB pathways to affect MDSCs and maintain tumor immunosuppression.	Immunohistochemical staining	Collectively, tumor glycolysis orchestrates a molecular network of the AMPK-ULK1, autophagy, and CEBPB pathways to affect MDSCs and maintain tumor immunosuppression.		Short Pairpin RNAs (shRNA),Small Interfering RNA (siRNA),Genetic Knockout,Western Blot,RNA Extraction,Reverse Transcription,Real-Time Polymerase Chain Reaction,Flow Cytometry Analysis (FACS),Immunofluorescence Staining,Metabolic Assay,Bioinformatics Analysis				CEBPB		Collectively, tumor glycolysis orchestrates a molecular network of the AMPK-ULK1, autophagy, and CEBPB pathways to affect MDSCs and maintain tumor immunosuppression.
29802990	chr15	102311121	102313121	Sp1	We identified two alternative nine-SNPs haplotypes strictly linked to the allele *1 and *2 of hs1.2, that could be used as markers to further investigate the region and associations to pathology. Finally, we identified two haplotypes, namely E2A1 and E2A2, that strongly support the hypothesis of a relevant effect of the rs35216181 in the onset of Psoriasis when the *2 allele is present.	mouse	lymphoid	High+Lowthroughput	Association between Psoriasis and haplotypes of the IgH 3' Regulatory Region 1	是	rs35216181,rs373084296	Autoimmune disease, psoriasis	T cell	E_01_0449	nested-PCR	We identified two alternative nine-SNPs haplotypes strictly linked to the allele *1 and *2 of hs1.2, that could be used as markers to further investigate the region and associations to pathology. Finally, we identified two haplotypes, namely E2A1 and E2A2, that strongly support the hypothesis of a relevant effect of the rs35216181 in the onset of Psoriasis when the *2 allele is present.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We identified two alternative nine-SNPs haplotypes strictly linked to the allele *1 and *2 of hs1.2, that could be used as markers to further investigate the region and associations to pathology. Finally, we identified two haplotypes, namely E2A1 and E2A2, that strongly support the hypothesis of a relevant effect of the rs35216181 in the onset of Psoriasis when the *2 allele is present.	Immunohistochemical staining	We identified two alternative nine-SNPs haplotypes strictly linked to the allele *1 and *2 of hs1.2, that could be used as markers to further investigate the region and associations to pathology. Finally, we identified two haplotypes, namely E2A1 and E2A2, that strongly support the hypothesis of a relevant effect of the rs35216181 in the onset of Psoriasis when the *2 allele is present.		nested-PCR			Sp1		We identified two alternative nine-SNPs haplotypes strictly linked to the allele *1 and *2 of hs1.2, that could be used as markers to further investigate the region and associations to pathology. Finally, we identified two haplotypes, namely E2A1 and E2A2, that strongly support the hypothesis of a relevant effect of the rs35216181 in the onset of Psoriasis when the *2 allele is present.	
29799396	chr12	6784343	6786343	CD4	Employing a combined phenotypic and transcriptomic approach we disclosed a Th1/Th17 phenotype as well as innate and adaptive functions of CD4+CD8+ double-positive T-cells in GPA.	human	connective	High+Lowthroughput	Circulating CD4+CD8+ double-positive T-cells display features of innate and adaptive immune function in granulomatosis with polyangiitis	否		Granulomatosis with polyangiitis (GPA)	whole blood cell	E_01_0450	Flow cytometric analysis,Transcriptome,biological database analysis	Employing a combined phenotypic and transcriptomic approach we disclosed a Th1/Th17 phenotype as well as innate and adaptive functions of CD4+CD8+ double-positive T-cells in GPA.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Employing a combined phenotypic and transcriptomic approach we disclosed a Th1/Th17 phenotype as well as innate and adaptive functions of CD4+CD8+ double-positive T-cells in GPA.	Immunohistochemical staining	Employing a combined phenotypic and transcriptomic approach we disclosed a Th1/Th17 phenotype as well as innate and adaptive functions of CD4+CD8+ double-positive T-cells in GPA.		Flow cytometric analysis,Transcriptome,biological database analysis			CD4		Employing a combined phenotypic and transcriptomic approach we disclosed a Th1/Th17 phenotype as well as innate and adaptive functions of CD4+CD8+ double-positive T-cells in GPA.	
29797095	chr3	133743341	133745341	TF	We present a workflow, integrating epigenomics and topologically associating domain data, aimed at discovering trait-associated SNP pairs from GWAS where neither SNP achieved independent genome-wide significance. Each analyzed SNP pair consists of one SNP in a putative active enhancer and another SNP in a putative physically interacting gene promoter in a trait-relevant tissue. As a proof-of-principle case study, we used this approach to identify focused collections of SNP pairs that we analyzed in three independent Type 2 diabetes (T2D) GWAS. This approach led us to discover 35 significant SNP pairs, encompassing both novel signals and signals for which we have found orthogonal support from other sources. Nine of these pairs are consistent with eQTL results, two are consistent with our own capture C experiments, and seven involve signals supported by recent T2D literature.	human	Liver	High+Lowthroughput	Leveraging epigenomics and contactomics data to investigate SNP pairs in GWAS	是	rs76024800,rs7577213	Type 2 diabetes (T2D)	HEPG2	E_01_0451	GWAS,DNase-Seq,ATAC-Seq,	We present a workflow, integrating epigenomics and topologically associating domain data, aimed at discovering trait-associated SNP pairs from GWAS where neither SNP achieved independent genome-wide significance. Each analyzed SNP pair consists of one SNP in a putative active enhancer and another SNP in a putative physically interacting gene promoter in a trait-relevant tissue. As a proof-of-principle case study, we used this approach to identify focused collections of SNP pairs that we analyzed in three independent Type 2 diabetes (T2D) GWAS. This approach led us to discover 35 significant SNP pairs, encompassing both novel signals and signals for which we have found orthogonal support from other sources. Nine of these pairs are consistent with eQTL results, two are consistent with our own capture C experiments, and seven involve signals supported by recent T2D literature.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We present a workflow, integrating epigenomics and topologically associating domain data, aimed at discovering trait-associated SNP pairs from GWAS where neither SNP achieved independent genome-wide significance. Each analyzed SNP pair consists of one SNP in a putative active enhancer and another SNP in a putative physically interacting gene promoter in a trait-relevant tissue. As a proof-of-principle case study, we used this approach to identify focused collections of SNP pairs that we analyzed in three independent Type 2 diabetes (T2D) GWAS. This approach led us to discover 35 significant SNP pairs, encompassing both novel signals and signals for which we have found orthogonal support from other sources. Nine of these pairs are consistent with eQTL results, two are consistent with our own capture C experiments, and seven involve signals supported by recent T2D literature.	Immunohistochemical staining	We present a workflow, integrating epigenomics and topologically associating domain data, aimed at discovering trait-associated SNP pairs from GWAS where neither SNP achieved independent genome-wide significance. Each analyzed SNP pair consists of one SNP in a putative active enhancer and another SNP in a putative physically interacting gene promoter in a trait-relevant tissue. As a proof-of-principle case study, we used this approach to identify focused collections of SNP pairs that we analyzed in three independent Type 2 diabetes (T2D) GWAS. This approach led us to discover 35 significant SNP pairs, encompassing both novel signals and signals for which we have found orthogonal support from other sources. Nine of these pairs are consistent with eQTL results, two are consistent with our own capture C experiments, and seven involve signals supported by recent T2D literature.		GWAS,DNase-Seq,ATAC-Seq,			TF		We present a workflow, integrating epigenomics and topologically associating domain data, aimed at discovering trait-associated SNP pairs from GWAS where neither SNP achieved independent genome-wide significance. Each analyzed SNP pair consists of one SNP in a putative active enhancer and another SNP in a putative physically interacting gene promoter in a trait-relevant tissue. As a proof-of-principle case study, we used this approach to identify focused collections of SNP pairs that we analyzed in three independent Type 2 diabetes (T2D) GWAS. This approach led us to discover 35 significant SNP pairs, encompassing both novel signals and signals for which we have found orthogonal support from other sources. Nine of these pairs are consistent with eQTL results, two are consistent with our own capture C experiments, and seven involve signals supported by recent T2D literature.	
29794985	chr17	17678780	17680780	RAI1	These results suggest a likely contribution of RAI1, either alone or in combination of other factors, to social behavior and reinforce the RAI1 gene as a candidate gene in patients with autistic manifestations or social behavioral abnormalities.	human	Nervous	High+Lowthroughput	A Rare De Novo RAI1 Gene Mutation Affecting BDNF-Enhancer-Driven Transcription Activity Associated with Autism and Atypical Smith-Magenis Syndrome Presentation	是		Autism, atypical Smith Magenis syndrome	Neuro-2a	E_01_0452	AMPure,PCR,Western Blot,Immunofluorescence Analysis,Reporter Gene Assays,RNA-Seq,transfection of Neuro-2a cells	These results suggest a likely contribution of RAI1, either alone or in combination of other factors, to social behavior and reinforce the RAI1 gene as a candidate gene in patients with autistic manifestations or social behavioral abnormalities.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		These results suggest a likely contribution of RAI1, either alone or in combination of other factors, to social behavior and reinforce the RAI1 gene as a candidate gene in patients with autistic manifestations or social behavioral abnormalities.	Immunohistochemical staining	These results suggest a likely contribution of RAI1, either alone or in combination of other factors, to social behavior and reinforce the RAI1 gene as a candidate gene in patients with autistic manifestations or social behavioral abnormalities.		AMPure,PCR,Western Blot,Immunofluorescence Analysis,Reporter Gene Assays,RNA-Seq,transfection of Neuro-2a cells			RAI1	BDNF	These results suggest a likely contribution of RAI1, either alone or in combination of other factors, to social behavior and reinforce the RAI1 gene as a candidate gene in patients with autistic manifestations or social behavioral abnormalities.	These results suggest a likely contribution of RAI1, either alone or in combination of other factors, to social behavior and reinforce the RAI1 gene as a candidate gene in patients with autistic manifestations or social behavioral abnormalities.
29794473	chr8	19899275	19901275	LPL	During the adipogenic differentiation of hASCs, miR-27b expression decreased, and LPL expression increased. The abnormal expression of miR-27b and LPL effectively regulated the adipogenic differentiation of hASCs.	human	adipose	High+Lowthroughput	MiR-27b Impairs Adipocyte Differentiation of Human Adipose Tissue-Derived Mesenchymal Stem Cells by Targeting LPL	否		Other	hASCs	E_01_0453	Double Dual Luciferase Reporter Assay,qRT-PCR,western blot,cellular immunofluorescence,oil red O staining assay,Cell transfection	During the adipogenic differentiation of hASCs, miR-27b expression decreased, and LPL expression increased. The abnormal expression of miR-27b and LPL effectively regulated the adipogenic differentiation of hASCs.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		During the adipogenic differentiation of hASCs, miR-27b expression decreased, and LPL expression increased. The abnormal expression of miR-27b and LPL effectively regulated the adipogenic differentiation of hASCs.	Immunohistochemical staining	During the adipogenic differentiation of hASCs, miR-27b expression decreased, and LPL expression increased. The abnormal expression of miR-27b and LPL effectively regulated the adipogenic differentiation of hASCs.		Double Dual Luciferase Reporter Assay,qRT-PCR,western blot,cellular immunofluorescence,oil red O staining assay,Cell transfection				LPL		During the adipogenic differentiation of hASCs, miR-27b expression decreased, and LPL expression increased. The abnormal expression of miR-27b and LPL effectively regulated the adipogenic differentiation of hASCs.
29792826	chr4	56905265	56907265	REST	Using CRISPR/Cas9, we further functionally validated an enhancer on chr8p23.1 as activator counteracting REST, a master regulator known to be a transcriptional suppressor of Alzheimer disease. Our results suggest an evolutionary origin of aging-related diseases: the side effects of human-specific, neural-tissue expressed enhancers. Thus, adaptive molecular changes in human macroevolution may introduce vulnerabilities to disease development in modern populations.	human		High+Lowthroughput	Fast-Evolving Human-Specific Neural Enhancers Are Associated with Aging-Related Diseases	是		Alzheimer's disease, aging	HEK293T	E_01_0454	CRISPR/Cas9,chromatin immunoprecipitation sequencing,qRT-PCR,PCR, RNA-seq,transfection	Using CRISPR/Cas9, we further functionally validated an enhancer on chr8p23.1 as activator counteracting REST, a master regulator known to be a transcriptional suppressor of Alzheimer disease. Our results suggest an evolutionary origin of aging-related diseases: the side effects of human-specific, neural-tissue expressed enhancers. Thus, adaptive molecular changes in human macroevolution may introduce vulnerabilities to disease development in modern populations.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Using CRISPR/Cas9, we further functionally validated an enhancer on chr8p23.1 as activator counteracting REST, a master regulator known to be a transcriptional suppressor of Alzheimer disease. Our results suggest an evolutionary origin of aging-related diseases: the side effects of human-specific, neural-tissue expressed enhancers. Thus, adaptive molecular changes in human macroevolution may introduce vulnerabilities to disease development in modern populations.	Immunohistochemical staining	Using CRISPR/Cas9, we further functionally validated an enhancer on chr8p23.1 as activator counteracting REST, a master regulator known to be a transcriptional suppressor of Alzheimer disease. Our results suggest an evolutionary origin of aging-related diseases: the side effects of human-specific, neural-tissue expressed enhancers. Thus, adaptive molecular changes in human macroevolution may introduce vulnerabilities to disease development in modern populations.		CRISPR/Cas9,chromatin immunoprecipitation sequencing,qRT-PCR,PCR, RNA-seq,transfection				REST		Using CRISPR/Cas9, we further functionally validated an enhancer on chr8p23.1 as activator counteracting REST, a master regulator known to be a transcriptional suppressor of Alzheimer disease. Our results suggest an evolutionary origin of aging-related diseases: the side effects of human-specific, neural-tissue expressed enhancers. Thus, adaptive molecular changes in human macroevolution may introduce vulnerabilities to disease development in modern populations.
29790264	chr11	32384629	32386629	WT1	These results demonstrated several TAAs may be promising for immunotherapy for cholangiocarcinoma, and patients with high lymphocyte counts may benefit more from immunotherapy.	human	lymphoid	High+Lowthroughput	Immune responses against tumour-associated antigen-derived cytotoxic T lymphocyte epitopes in cholangiocarcinoma patients	否		Cholangiocarcinoma	TILs	E_01_0455	ELISPOT,PCR,real-time PCR,Immunotherapy	These results demonstrated several TAAs may be promising for immunotherapy for cholangiocarcinoma, and patients with high lymphocyte counts may benefit more from immunotherapy.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		These results demonstrated several TAAs may be promising for immunotherapy for cholangiocarcinoma, and patients with high lymphocyte counts may benefit more from immunotherapy.	Immunohistochemical staining	These results demonstrated several TAAs may be promising for immunotherapy for cholangiocarcinoma, and patients with high lymphocyte counts may benefit more from immunotherapy.		ELISPOT,PCR,real-time PCR,Immunotherapy			WT1,MUC5AC,GPC3,KIF20A	EZH2	These results demonstrated several TAAs may be promising for immunotherapy for cholangiocarcinoma, and patients with high lymphocyte counts may benefit more from immunotherapy.;These results demonstrated several TAAs may be promising for immunotherapy for cholangiocarcinoma, and patients with high lymphocyte counts may benefit more from immunotherapy.;These results demonstrated several TAAs may be promising for immunotherapy for cholangiocarcinoma, and patients with high lymphocyte counts may benefit more from immunotherapy.;These results demonstrated several TAAs may be promising for immunotherapy for cholangiocarcinoma, and patients with high lymphocyte counts may benefit more from immunotherapy.	These results demonstrated several TAAs may be promising for immunotherapy for cholangiocarcinoma, and patients with high lymphocyte counts may benefit more from immunotherapy.
29789713	chr1	47429569	47431569	FOXD2-AS1	Mechanically, FOXD2-AS1 promoted GC tumorigenesis partly through EZH2 and LSD1 mediated EphB3 downregulation. The present results revealed that FOXD2-AS1 acted as a tumor inducer in GC partly through EphB3 inhibition by direct interaction with EZH2 and LSD1, and may prove to be a potential biomarker of carcinogenesis.	human		High+Lowthroughput	Upregulation of the long noncoding RNA FOXD2-AS1 promotes carcinogenesis by epigenetically silencing EphB3 through EZH2 and LSD1, and predicts poor prognosis in gastric cancer	否		Gastric cancer (GC)	BGC823	E_01_0456	GSEA,quantitative real-time PCR,transfection,Flow cytometry,Western blot,Immunohistochemistry(IHC),ChIRP,RIP,RNA pull-down assay,Cell proliferation assays,chromatin immunoprecipitation (ChIP)	Mechanically, FOXD2-AS1 promoted GC tumorigenesis partly through EZH2 and LSD1 mediated EphB3 downregulation. The present results revealed that FOXD2-AS1 acted as a tumor inducer in GC partly through EphB3 inhibition by direct interaction with EZH2 and LSD1, and may prove to be a potential biomarker of carcinogenesis.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Mechanically, FOXD2-AS1 promoted GC tumorigenesis partly through EZH2 and LSD1 mediated EphB3 downregulation. The present results revealed that FOXD2-AS1 acted as a tumor inducer in GC partly through EphB3 inhibition by direct interaction with EZH2 and LSD1, and may prove to be a potential biomarker of carcinogenesis.	Immunohistochemical staining	Mechanically, FOXD2-AS1 promoted GC tumorigenesis partly through EZH2 and LSD1 mediated EphB3 downregulation. The present results revealed that FOXD2-AS1 acted as a tumor inducer in GC partly through EphB3 inhibition by direct interaction with EZH2 and LSD1, and may prove to be a potential biomarker of carcinogenesis.		GSEA,quantitative real-time PCR,transfection,Flow cytometry,Western blot,Immunohistochemistry(IHC),ChIRP,RIP,RNA pull-down assay,Cell proliferation assays,chromatin immunoprecipitation (ChIP)			FOXD2-AS1	EZH2	Mechanically, FOXD2-AS1 promoted GC tumorigenesis partly through EZH2 and LSD1 mediated EphB3 downregulation. The present results revealed that FOXD2-AS1 acted as a tumor inducer in GC partly through EphB3 inhibition by direct interaction with EZH2 and LSD1, and may prove to be a potential biomarker of carcinogenesis.	Mechanically, FOXD2-AS1 promoted GC tumorigenesis partly through EZH2 and LSD1 mediated EphB3 downregulation. The present results revealed that FOXD2-AS1 acted as a tumor inducer in GC partly through EphB3 inhibition by direct interaction with EZH2 and LSD1, and may prove to be a potential biomarker of carcinogenesis.
29789597	chr6	31572755	31574755	TNF	In conclusion, EZH2 and H3K27me3 contributed to the pathogenesis of liver failure via triggering TNF and other indispensable proinflammatory cytokines. EZH2 was to modify H3K27me3 enrichment, as well as, activation of the downstream NF-κB and Akt signalling pathways.	human	lymphoid	High+Lowthroughput	Enhancer of zeste homolog 2-catalysed H3K27 trimethylation plays a key role in acute-on-chronic liver failure via TNF-mediated pathway	否		Acute phase chronic liver failure	PBMC	E_01_0457	Western blot,reverse transcription-PCR,cytokine analysis,Immunostaining,Histological analysis,Chromatin immunoprecipitation (ChIP) assays	In conclusion, EZH2 and H3K27me3 contributed to the pathogenesis of liver failure via triggering TNF and other indispensable proinflammatory cytokines. EZH2 was to modify H3K27me3 enrichment, as well as, activation of the downstream NF-κB and Akt signalling pathways.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In conclusion, EZH2 and H3K27me3 contributed to the pathogenesis of liver failure via triggering TNF and other indispensable proinflammatory cytokines. EZH2 was to modify H3K27me3 enrichment, as well as, activation of the downstream NF-κB and Akt signalling pathways.	Immunohistochemical staining	In conclusion, EZH2 and H3K27me3 contributed to the pathogenesis of liver failure via triggering TNF and other indispensable proinflammatory cytokines. EZH2 was to modify H3K27me3 enrichment, as well as, activation of the downstream NF-κB and Akt signalling pathways.		Western blot,reverse transcription-PCR,cytokine analysis,Immunostaining,Histological analysis,Chromatin immunoprecipitation (ChIP) assays			CD68	TNF,EZH2	In conclusion, EZH2 and H3K27me3 contributed to the pathogenesis of liver failure via triggering TNF and other indispensable proinflammatory cytokines. EZH2 was to modify H3K27me3 enrichment, as well as, activation of the downstream NF-κB and Akt signalling pathways.	In conclusion, EZH2 and H3K27me3 contributed to the pathogenesis of liver failure via triggering TNF and other indispensable proinflammatory cytokines. EZH2 was to modify H3K27me3 enrichment, as well as, activation of the downstream NF-κB and Akt signalling pathways.;In conclusion, EZH2 and H3K27me3 contributed to the pathogenesis of liver failure via triggering TNF and other indispensable proinflammatory cytokines. EZH2 was to modify H3K27me3 enrichment, as well as, activation of the downstream NF-κB and Akt signalling pathways.
29789579	chr14	75276080	75278080	FOS	Taken together, we resolve the long-standing controversy and uncertainty in the field, and reveal a fundamental role of OCT4A protein in regulating FOS/AP-1 signaling-centered genes that mediate the adhesion, migration, and propagation of somatic cancer cells.	human	Nervous	High+Lowthroughput	Endogenous authentic OCT4A proteins directly regulate FOS/AP-1 transcription in somatic cancer cells	否		Other	293T	E_01_0458	CRISPR\Cas9,PCR,western blot,qRT-PCR,immunoprecipitation(IP),Immunostaining,immunoblotting,ChIP assays,ChIP-PCR,MS analysis,RNA-Seq,western blotting (WB) analysis	Taken together, we resolve the long-standing controversy and uncertainty in the field, and reveal a fundamental role of OCT4A protein in regulating FOS/AP-1 signaling-centered genes that mediate the adhesion, migration, and propagation of somatic cancer cells.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Taken together, we resolve the long-standing controversy and uncertainty in the field, and reveal a fundamental role of OCT4A protein in regulating FOS/AP-1 signaling-centered genes that mediate the adhesion, migration, and propagation of somatic cancer cells.	Immunohistochemical staining	Taken together, we resolve the long-standing controversy and uncertainty in the field, and reveal a fundamental role of OCT4A protein in regulating FOS/AP-1 signaling-centered genes that mediate the adhesion, migration, and propagation of somatic cancer cells.		CRISPR\Cas9,PCR,western blot,qRT-PCR,immunoprecipitation(IP),Immunostaining,immunoblotting,ChIP assays,ChIP-PCR,MS analysis,RNA-Seq,western blotting (WB) analysis				FOS,POU5F1		Taken together, we resolve the long-standing controversy and uncertainty in the field, and reveal a fundamental role of OCT4A protein in regulating FOS/AP-1 signaling-centered genes that mediate the adhesion, migration, and propagation of somatic cancer cells.;Taken together, we resolve the long-standing controversy and uncertainty in the field, and reveal a fundamental role of OCT4A protein in regulating FOS/AP-1 signaling-centered genes that mediate the adhesion, migration, and propagation of somatic cancer cells.
29789508	chr17	82075550	82077550	FASN	Taken together, these findings demonstrate that the effect of metformin on adipocyte differentiation is biphasic and dose-dependent. Lower concentrations of metformin induce adipogenesis, which could be mediated in an AMPK-independent manner, while higher concentrations of metformin inhibit adipogenesis via AMPK activation.	human	adipose	High+Lowthroughput	Dual Effects of Metformin on Adipogenic Differentiation of 3T3-L1 Preadipocyte in AMPK-Dependent and Independent Manners	否		Type 2 diabetes (T2D)	3T3-L1	E_01_0459	Oil Red O Staining,MTT assay,Quantitative Real-Time PCR,Western Blot	Taken together, these findings demonstrate that the effect of metformin on adipocyte differentiation is biphasic and dose-dependent. Lower concentrations of metformin induce adipogenesis, which could be mediated in an AMPK-independent manner, while higher concentrations of metformin inhibit adipogenesis via AMPK activation.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Taken together, these findings demonstrate that the effect of metformin on adipocyte differentiation is biphasic and dose-dependent. Lower concentrations of metformin induce adipogenesis, which could be mediated in an AMPK-independent manner, while higher concentrations of metformin inhibit adipogenesis via AMPK activation.	Immunohistochemical staining	Taken together, these findings demonstrate that the effect of metformin on adipocyte differentiation is biphasic and dose-dependent. Lower concentrations of metformin induce adipogenesis, which could be mediated in an AMPK-independent manner, while higher concentrations of metformin inhibit adipogenesis via AMPK activation.		Oil Red O Staining,MTT assay,Quantitative Real-Time PCR,Western Blot			FASN		Taken together, these findings demonstrate that the effect of metformin on adipocyte differentiation is biphasic and dose-dependent. Lower concentrations of metformin induce adipogenesis, which could be mediated in an AMPK-independent manner, while higher concentrations of metformin inhibit adipogenesis via AMPK activation.	
29785964	chr6	170551706	170553706	TBP	In contrast, TBP-TFIIB and TBP-BRF2 complexes were not recruited unless a TATA box was present, which allowed selective and efficient recruitment of the TBP-BRF2 complex. Thus, TBP both prevented BRF2 recruitment to Pol II promoters and enhanced BRF2 recruitment to Pol III promoters. On Pol II promoters, TBP recruitment was separate from TFIIB recruitment and enhanced by TFIIA. Our results provide a model for specific Pol recruitment at SNAPc-dependent promoters.	human		High+Lowthroughput	Mechanism of selective recruitment of RNA polymerases II and III to snRNA gene promoters	否		Other	293 cell	E_01_0460	transfection,immunoblots,DNase I footprinting,EMSAs,In vitro transcription assay,ChIPs,Pull-down assay,ChIP-seq,ChIP-qPCRs	In contrast, TBP-TFIIB and TBP-BRF2 complexes were not recruited unless a TATA box was present, which allowed selective and efficient recruitment of the TBP-BRF2 complex. Thus, TBP both prevented BRF2 recruitment to Pol II promoters and enhanced BRF2 recruitment to Pol III promoters. On Pol II promoters, TBP recruitment was separate from TFIIB recruitment and enhanced by TFIIA. Our results provide a model for specific Pol recruitment at SNAPc-dependent promoters.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In contrast, TBP-TFIIB and TBP-BRF2 complexes were not recruited unless a TATA box was present, which allowed selective and efficient recruitment of the TBP-BRF2 complex. Thus, TBP both prevented BRF2 recruitment to Pol II promoters and enhanced BRF2 recruitment to Pol III promoters. On Pol II promoters, TBP recruitment was separate from TFIIB recruitment and enhanced by TFIIA. Our results provide a model for specific Pol recruitment at SNAPc-dependent promoters.	Immunohistochemical staining	In contrast, TBP-TFIIB and TBP-BRF2 complexes were not recruited unless a TATA box was present, which allowed selective and efficient recruitment of the TBP-BRF2 complex. Thus, TBP both prevented BRF2 recruitment to Pol II promoters and enhanced BRF2 recruitment to Pol III promoters. On Pol II promoters, TBP recruitment was separate from TFIIB recruitment and enhanced by TFIIA. Our results provide a model for specific Pol recruitment at SNAPc-dependent promoters.		transfection,immunoblots,DNase I footprinting,EMSAs,In vitro transcription assay,ChIPs,Pull-down assay,ChIP-seq,ChIP-qPCRs			BRF2	TBP	In contrast, TBP-TFIIB and TBP-BRF2 complexes were not recruited unless a TATA box was present, which allowed selective and efficient recruitment of the TBP-BRF2 complex. Thus, TBP both prevented BRF2 recruitment to Pol II promoters and enhanced BRF2 recruitment to Pol III promoters. On Pol II promoters, TBP recruitment was separate from TFIIB recruitment and enhanced by TFIIA. Our results provide a model for specific Pol recruitment at SNAPc-dependent promoters.	In contrast, TBP-TFIIB and TBP-BRF2 complexes were not recruited unless a TATA box was present, which allowed selective and efficient recruitment of the TBP-BRF2 complex. Thus, TBP both prevented BRF2 recruitment to Pol II promoters and enhanced BRF2 recruitment to Pol III promoters. On Pol II promoters, TBP recruitment was separate from TFIIB recruitment and enhanced by TFIIA. Our results provide a model for specific Pol recruitment at SNAPc-dependent promoters.
29783071	chr15	99562489	99564489	MEF2A	Finally, the results of ChIP indicated that MEF2A occupied the promoter region of the Capn3 gene in rat denervated gastrocnemius muscle tissue. Based on these results, we proposed that MEF2A is a transcriptional regulator for Capn3 gene expression.	human	Gastrocnemius muscle	High+Lowthroughput	MEF2A regulates Calpain 3 expression in L6 myoblasts	否		Muscle wasting after reversible sciatic nerve injury	L6 cell	E_01_0461	Luciferase reporter assay,EMSA,PCR,Western Blot,qRT-PCR,immunocytochemistry,ChIP,siRNA treatment,Bioinformatics analysis,plasmid construction	Finally, the results of ChIP indicated that MEF2A occupied the promoter region of the Capn3 gene in rat denervated gastrocnemius muscle tissue. Based on these results, we proposed that MEF2A is a transcriptional regulator for Capn3 gene expression.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Finally, the results of ChIP indicated that MEF2A occupied the promoter region of the Capn3 gene in rat denervated gastrocnemius muscle tissue. Based on these results, we proposed that MEF2A is a transcriptional regulator for Capn3 gene expression.	Immunohistochemical staining	Finally, the results of ChIP indicated that MEF2A occupied the promoter region of the Capn3 gene in rat denervated gastrocnemius muscle tissue. Based on these results, we proposed that MEF2A is a transcriptional regulator for Capn3 gene expression.		Luciferase reporter assay,EMSA,PCR,Western Blot,qRT-PCR,immunocytochemistry,ChIP,siRNA treatment,Bioinformatics analysis,plasmid construction			Capn3	MEF2A	Finally, the results of ChIP indicated that MEF2A occupied the promoter region of the Capn3 gene in rat denervated gastrocnemius muscle tissue. Based on these results, we proposed that MEF2A is a transcriptional regulator for Capn3 gene expression.	Finally, the results of ChIP indicated that MEF2A occupied the promoter region of the Capn3 gene in rat denervated gastrocnemius muscle tissue. Based on these results, we proposed that MEF2A is a transcriptional regulator for Capn3 gene expression.
29779941	chr1	3066245	3068245	PRDM16	These findings provide insights into how epigenetic control of transcriptional enhancers in radial glial determines the organization of the mammalian cerebral cortex.	human	Nervous	High+Lowthroughput	The Epigenetic State of PRDM16-Regulated Enhancers in Radial Glia Controls Cortical Neuron Position	否		Other	HEK293	E_01_0462	RNA,Chromatin Immunoprecipitation,Native Chromatin Immunoprecipitation,Prdm16 and Pdzrn3 Knockdown,RNaseq Analysis,ChIP-Seq,Binding and Expression Target Analysis (BETA),	These findings provide insights into how epigenetic control of transcriptional enhancers in radial glial determines the organization of the mammalian cerebral cortex.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		These findings provide insights into how epigenetic control of transcriptional enhancers in radial glial determines the organization of the mammalian cerebral cortex.	Immunohistochemical staining	These findings provide insights into how epigenetic control of transcriptional enhancers in radial glial determines the organization of the mammalian cerebral cortex.		RNA,Chromatin Immunoprecipitation,Native Chromatin Immunoprecipitation,Prdm16 and Pdzrn3 Knockdown,RNaseq Analysis,ChIP-Seq,Binding and Expression Target Analysis (BETA),			PRDM16,PDZRN3		These findings provide insights into how epigenetic control of transcriptional enhancers in radial glial determines the organization of the mammalian cerebral cortex.;These findings provide insights into how epigenetic control of transcriptional enhancers in radial glial determines the organization of the mammalian cerebral cortex.	
29779861	chr19	42504265	42506265	CEACAM1		human	Epithelial	High+Lowthroughput	HopQ impacts the integrin α5β1-independent NF-κB activation by Helicobacter pylori in CEACAM expressing cells	否		Peptic ulcer disease, gastric cancer	HeLa cell	E_01_0463	siRNA transfection,Immunofluorescence (IF),immunoblotting,immunoprecipitation,PCR		Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq			Immunohistochemical staining			siRNA transfection,Immunofluorescence (IF),immunoblotting,immunoprecipitation,PCR			CEACAM1			
29777912	chr19	15233026	15235026	BRD4	Our result reveals a novel molecular mechanism by which a super-enhancer around the second intron regulates the expression of Regnase-1, and in turn maintains a desired level of Regnase-1.	human	connective	High+Lowthroughput	A super-enhancer maintains homeostatic expression of Regnase-1	否		Autoimmune diseases, cancer	HEK293T	E_01_0464	transfection,Quantitative RT-PCR,Western blot,CRISPR/Cas9	Our result reveals a novel molecular mechanism by which a super-enhancer around the second intron regulates the expression of Regnase-1, and in turn maintains a desired level of Regnase-1.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Our result reveals a novel molecular mechanism by which a super-enhancer around the second intron regulates the expression of Regnase-1, and in turn maintains a desired level of Regnase-1.	Immunohistochemical staining	Our result reveals a novel molecular mechanism by which a super-enhancer around the second intron regulates the expression of Regnase-1, and in turn maintains a desired level of Regnase-1.		transfection,Quantitative RT-PCR,Western blot,CRISPR/Cas9			ZC3H12A	BRD4,MED1	Our result reveals a novel molecular mechanism by which a super-enhancer around the second intron regulates the expression of Regnase-1, and in turn maintains a desired level of Regnase-1.	Our result reveals a novel molecular mechanism by which a super-enhancer around the second intron regulates the expression of Regnase-1, and in turn maintains a desired level of Regnase-1.;Our result reveals a novel molecular mechanism by which a super-enhancer around the second intron regulates the expression of Regnase-1, and in turn maintains a desired level of Regnase-1.
29775615	chr4	87647723	87649723	DMP1	This study provides a new understanding of DMP1's function in regulation of osteogenesis: not only an enhancer of bone formation, but also a negative regulator of MSCs differentiation in bone.	human	connective	High+Lowthroughput	Extracellular matrix protein DMP1 suppresses osteogenic differentiation of Mesenchymal Stem Cells	否		Other	mouse bone marrow cell	E_01_0465	Immunofluorescence staining,Real-time PCR,Western blot,Analysis of histology	This study provides a new understanding of DMP1's function in regulation of osteogenesis: not only an enhancer of bone formation, but also a negative regulator of MSCs differentiation in bone.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		This study provides a new understanding of DMP1's function in regulation of osteogenesis: not only an enhancer of bone formation, but also a negative regulator of MSCs differentiation in bone.	Immunohistochemical staining	This study provides a new understanding of DMP1's function in regulation of osteogenesis: not only an enhancer of bone formation, but also a negative regulator of MSCs differentiation in bone.		Immunofluorescence staining,Real-time PCR,Western blot,Analysis of histology			DMP1		This study provides a new understanding of DMP1's function in regulation of osteogenesis: not only an enhancer of bone formation, but also a negative regulator of MSCs differentiation in bone.	
29775582	chr2	11479885	11481885	GREB1	"Collectively, these data suggest that the enhancer and promoter remain ""poised"" for transcription via their contacts with GBS1 and GBS2. Upon E2 induction, GBS1 and GBS2 disengage from the enhancer, allowing direct EPC for active transcription."	human	Epithelial	High+Lowthroughput	SRC-3 Coactivator Governs Dynamic Estrogen-Induced Chromatin Looping Interactions during Transcription	否		Other	HeLa S3	E_01_0466	3C,Immunoblotting,Chromatin Reconstitution,Immunodepletion,3C-qPCR,qPCR	"Collectively, these data suggest that the enhancer and promoter remain ""poised"" for transcription via their contacts with GBS1 and GBS2. Upon E2 induction, GBS1 and GBS2 disengage from the enhancer, allowing direct EPC for active transcription."	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		"Collectively, these data suggest that the enhancer and promoter remain ""poised"" for transcription via their contacts with GBS1 and GBS2. Upon E2 induction, GBS1 and GBS2 disengage from the enhancer, allowing direct EPC for active transcription."	Immunohistochemical staining	"Collectively, these data suggest that the enhancer and promoter remain ""poised"" for transcription via their contacts with GBS1 and GBS2. Upon E2 induction, GBS1 and GBS2 disengage from the enhancer, allowing direct EPC for active transcription."		3C,Immunoblotting,Chromatin Reconstitution,Immunodepletion,3C-qPCR,qPCR			GREB1		"Collectively, these data suggest that the enhancer and promoter remain ""poised"" for transcription via their contacts with GBS1 and GBS2. Upon E2 induction, GBS1 and GBS2 disengage from the enhancer, allowing direct EPC for active transcription."	
29774079	chr19	15825440	15827440	UCA1	These findings uncover for the first time that AC026904.1 and UCA1 could cooperatively upregulate Slug expression at both transcriptional and post-transcriptional levels, exerting critical roles in TGF-β-induced EMT. The present work provides new evidence that lncRNAs function as key regulators of EMT and hold great promise to be used as novel biomarkers and therapeutic targets for metastatic breast cancer.	human	Mammary	High+Lowthroughput	"Long non-coding RNAs AC026904.1 and UCA1: a ""one-two punch"" for TGF-β-induced SNAI2 activation and epithelial-mesenchymal transition in breast cancer"	否		mammary cancer	MDA-MB-231-luc-D3H2LN	E_01_0467	ChIRP,microarray analysis,qPCR,Kaplan-Meier survival analysis,confocal laser microscopy,Western blot,chromosome conformation capture (3C),RNA purification (ChIRP), ChIP,luciferase reporter assay,transwell migration assay	These findings uncover for the first time that AC026904.1 and UCA1 could cooperatively upregulate Slug expression at both transcriptional and post-transcriptional levels, exerting critical roles in TGF-β-induced EMT. The present work provides new evidence that lncRNAs function as key regulators of EMT and hold great promise to be used as novel biomarkers and therapeutic targets for metastatic breast cancer.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		These findings uncover for the first time that AC026904.1 and UCA1 could cooperatively upregulate Slug expression at both transcriptional and post-transcriptional levels, exerting critical roles in TGF-β-induced EMT. The present work provides new evidence that lncRNAs function as key regulators of EMT and hold great promise to be used as novel biomarkers and therapeutic targets for metastatic breast cancer.	Immunohistochemical staining	These findings uncover for the first time that AC026904.1 and UCA1 could cooperatively upregulate Slug expression at both transcriptional and post-transcriptional levels, exerting critical roles in TGF-β-induced EMT. The present work provides new evidence that lncRNAs function as key regulators of EMT and hold great promise to be used as novel biomarkers and therapeutic targets for metastatic breast cancer.		ChIRP,microarray analysis,qPCR,Kaplan-Meier survival analysis,confocal laser microscopy,Western blot,chromosome conformation capture (3C),RNA purification (ChIRP), ChIP,luciferase reporter assay,transwell migration assay			UCA1	SNAI2	These findings uncover for the first time that AC026904.1 and UCA1 could cooperatively upregulate Slug expression at both transcriptional and post-transcriptional levels, exerting critical roles in TGF-β-induced EMT. The present work provides new evidence that lncRNAs function as key regulators of EMT and hold great promise to be used as novel biomarkers and therapeutic targets for metastatic breast cancer.	These findings uncover for the first time that AC026904.1 and UCA1 could cooperatively upregulate Slug expression at both transcriptional and post-transcriptional levels, exerting critical roles in TGF-β-induced EMT. The present work provides new evidence that lncRNAs function as key regulators of EMT and hold great promise to be used as novel biomarkers and therapeutic targets for metastatic breast cancer.
29773854	chr12	102393392	102395392	IGF1	Our analysis demonstrates the utility of haplotype association analyses in discovering and characterizing PBC susceptibility loci.	human	Epithelial	High+Lowthroughput	Genome-wide haplotype association analysis of primary biliary cholangitis risk in Japanese	是		Primary biliary cholangitis (PBC)	epithelial cell	E_01_0468	ChIP-seq	Our analysis demonstrates the utility of haplotype association analyses in discovering and characterizing PBC susceptibility loci.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Our analysis demonstrates the utility of haplotype association analyses in discovering and characterizing PBC susceptibility loci.	Immunohistochemical staining	Our analysis demonstrates the utility of haplotype association analyses in discovering and characterizing PBC susceptibility loci.		ChIP-seq			UMAD1,TNFSF15	IGF1	Our analysis demonstrates the utility of haplotype association analyses in discovering and characterizing PBC susceptibility loci.;Our analysis demonstrates the utility of haplotype association analyses in discovering and characterizing PBC susceptibility loci.	Our analysis demonstrates the utility of haplotype association analyses in discovering and characterizing PBC susceptibility loci.
29773832	chr3	133743689	133745689	TF	Thus, our study provides new insight into the epigenetic landscapes associated with the heterogeneity of PDAC, thereby increasing our mechanistic understanding of this disease, as well as offering potential new markers and therapeutic targets.	human	Epithelial	High+Lowthroughput	Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes	否		Pancreatic ductal adenocarcinoma (PDAC) subtype	epithelial cell	E_01_0469	RNA extraction,RNA-seq,ChIP-seq,SNP arrays analysis,siRNA transfection,qPCR	Thus, our study provides new insight into the epigenetic landscapes associated with the heterogeneity of PDAC, thereby increasing our mechanistic understanding of this disease, as well as offering potential new markers and therapeutic targets.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Thus, our study provides new insight into the epigenetic landscapes associated with the heterogeneity of PDAC, thereby increasing our mechanistic understanding of this disease, as well as offering potential new markers and therapeutic targets.	Immunohistochemical staining	Thus, our study provides new insight into the epigenetic landscapes associated with the heterogeneity of PDAC, thereby increasing our mechanistic understanding of this disease, as well as offering potential new markers and therapeutic targets.		RNA extraction,RNA-seq,ChIP-seq,SNP arrays analysis,siRNA transfection,qPCR			TF	IL6	Thus, our study provides new insight into the epigenetic landscapes associated with the heterogeneity of PDAC, thereby increasing our mechanistic understanding of this disease, as well as offering potential new markers and therapeutic targets.	Thus, our study provides new insight into the epigenetic landscapes associated with the heterogeneity of PDAC, thereby increasing our mechanistic understanding of this disease, as well as offering potential new markers and therapeutic targets.
29772677	chrX	123856883	123858883	XIAP	Overall, these findings suggest that lambertianic acid enhances TRAIL-induced apoptosis via inhibition of XIAP/NF-κB in TRAIL resistant NSCLCs.	human	Lung	High+Lowthroughput	Lambertianic Acid Sensitizes Non-Small Cell Lung Cancers to TRAIL-Induced Apoptosis via Inhibition of XIAP/NF-κB and Activation of Caspases and Death Receptor 4	否			A549	E_01_0470	Western Blot,Co-Immunoprecipitation,Cell Cycle Analysis,Crystal Violet Assay,Cytotoxicity Assay,flow cytometry	Overall, these findings suggest that lambertianic acid enhances TRAIL-induced apoptosis via inhibition of XIAP/NF-κB in TRAIL resistant NSCLCs.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Overall, these findings suggest that lambertianic acid enhances TRAIL-induced apoptosis via inhibition of XIAP/NF-κB in TRAIL resistant NSCLCs.	Immunohistochemical staining	Overall, these findings suggest that lambertianic acid enhances TRAIL-induced apoptosis via inhibition of XIAP/NF-κB in TRAIL resistant NSCLCs.		Western Blot,Co-Immunoprecipitation,Cell Cycle Analysis,Crystal Violet Assay,Cytotoxicity Assay,flow cytometry				XIAP		Overall, these findings suggest that lambertianic acid enhances TRAIL-induced apoptosis via inhibition of XIAP/NF-κB in TRAIL resistant NSCLCs.
29771329	chr17	15227161	15229161	PMP22	In this study, we have utilized genome editing to create a deletion of this super-enhancer to determine its role in Pmp22 regulation. Our data show a significant decrease in Pmp22 transcript expression using allele-specific internal controls. Moreover, the P2 promoter of the Pmp22 gene, which is used in other cell types, is affected, but we find that the Schwann cell-specific P1 promoter is disproportionately more sensitive to loss of the super-enhancer. These data show for the first time the requirement of these upstream enhancers for full Pmp22 expression.	human	connective	High+Lowthroughput	Regulation of the neuropathy-associated Pmp22 gene by a distal super-enhancer	否		Inherited peripheral neuropathies		E_01_0471	CRISPR/Cas9,siRNA treatment,RT-qPCR,Spectral karyotyping	In this study, we have utilized genome editing to create a deletion of this super-enhancer to determine its role in Pmp22 regulation. Our data show a significant decrease in Pmp22 transcript expression using allele-specific internal controls. Moreover, the P2 promoter of the Pmp22 gene, which is used in other cell types, is affected, but we find that the Schwann cell-specific P1 promoter is disproportionately more sensitive to loss of the super-enhancer. These data show for the first time the requirement of these upstream enhancers for full Pmp22 expression.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In this study, we have utilized genome editing to create a deletion of this super-enhancer to determine its role in Pmp22 regulation. Our data show a significant decrease in Pmp22 transcript expression using allele-specific internal controls. Moreover, the P2 promoter of the Pmp22 gene, which is used in other cell types, is affected, but we find that the Schwann cell-specific P1 promoter is disproportionately more sensitive to loss of the super-enhancer. These data show for the first time the requirement of these upstream enhancers for full Pmp22 expression.	Immunohistochemical staining	In this study, we have utilized genome editing to create a deletion of this super-enhancer to determine its role in Pmp22 regulation. Our data show a significant decrease in Pmp22 transcript expression using allele-specific internal controls. Moreover, the P2 promoter of the Pmp22 gene, which is used in other cell types, is affected, but we find that the Schwann cell-specific P1 promoter is disproportionately more sensitive to loss of the super-enhancer. These data show for the first time the requirement of these upstream enhancers for full Pmp22 expression.		CRISPR/Cas9,siRNA treatment,RT-qPCR,Spectral karyotyping			PMP22,Pmp22		In this study, we have utilized genome editing to create a deletion of this super-enhancer to determine its role in Pmp22 regulation. Our data show a significant decrease in Pmp22 transcript expression using allele-specific internal controls. Moreover, the P2 promoter of the Pmp22 gene, which is used in other cell types, is affected, but we find that the Schwann cell-specific P1 promoter is disproportionately more sensitive to loss of the super-enhancer. These data show for the first time the requirement of these upstream enhancers for full Pmp22 expression.;In this study, we have utilized genome editing to create a deletion of this super-enhancer to determine its role in Pmp22 regulation. Our data show a significant decrease in Pmp22 transcript expression using allele-specific internal controls. Moreover, the P2 promoter of the Pmp22 gene, which is used in other cell types, is affected, but we find that the Schwann cell-specific P1 promoter is disproportionately more sensitive to loss of the super-enhancer. These data show for the first time the requirement of these upstream enhancers for full Pmp22 expression.	
29769415	chr3	41191924	41193924	CTNNB1	Our results show that miR-340 was expressed a higher level in normal tissue than OS tissue. Expression of Notch, CTNNB1, hairy and enhancer of split 1 (Hes1), Bcl-2, Runt-related transcription factor 2 (Runx2), and osteocalcin increased and that of miR-340, Bcl-2 interacting mediator of cell death (BIM), and Bcl-2 associated protein X (Bax) decreased in OS tissues. U-2OS cell line had the highest miR-340 expression. We also found that the up-regulation of miR-340 had increased expression of miR-340, BIM, and Bax but decreased expression of Notch, CTNNB1, Hes1, Bcl-2, Runx2, and osteocalcin. Up-regulation of miR-340p lead to increased cell apoptosis, suppressed cell proliferation, migration, and invasion. Our study demonstrates that overexpression of miR-340 could suppress OS cell proliferation, migration, and invasion as well as promoting OS cell apoptosis by inactivating the Notch signaling pathway via down-regulating CTNNB1. Functional miR-340 overexpression might be a future therapeutic strategy for OS.	human	Osteosarcoma	High+Lowthroughput	Up-regulation of microRNA-340 promotes osteosarcoma cell apoptosis while suppressing proliferation, migration, and invasion by inactivating the CTNNB1-mediated Notch signaling pathway	否		Osteosarcoma (OS)		E_01_0472	Luciferase reporter assay,Western Blot,RT-QPCR,immunohistochemistry,in situ hybridization(ISH),transfection,MTT,flow cytometry,scratch test,transwell assay	Our results show that miR-340 was expressed a higher level in normal tissue than OS tissue. Expression of Notch, CTNNB1, hairy and enhancer of split 1 (Hes1), Bcl-2, Runt-related transcription factor 2 (Runx2), and osteocalcin increased and that of miR-340, Bcl-2 interacting mediator of cell death (BIM), and Bcl-2 associated protein X (Bax) decreased in OS tissues. U-2OS cell line had the highest miR-340 expression. We also found that the up-regulation of miR-340 had increased expression of miR-340, BIM, and Bax but decreased expression of Notch, CTNNB1, Hes1, Bcl-2, Runx2, and osteocalcin. Up-regulation of miR-340p lead to increased cell apoptosis, suppressed cell proliferation, migration, and invasion. Our study demonstrates that overexpression of miR-340 could suppress OS cell proliferation, migration, and invasion as well as promoting OS cell apoptosis by inactivating the Notch signaling pathway via down-regulating CTNNB1. Functional miR-340 overexpression might be a future therapeutic strategy for OS.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Our results show that miR-340 was expressed a higher level in normal tissue than OS tissue. Expression of Notch, CTNNB1, hairy and enhancer of split 1 (Hes1), Bcl-2, Runt-related transcription factor 2 (Runx2), and osteocalcin increased and that of miR-340, Bcl-2 interacting mediator of cell death (BIM), and Bcl-2 associated protein X (Bax) decreased in OS tissues. U-2OS cell line had the highest miR-340 expression. We also found that the up-regulation of miR-340 had increased expression of miR-340, BIM, and Bax but decreased expression of Notch, CTNNB1, Hes1, Bcl-2, Runx2, and osteocalcin. Up-regulation of miR-340p lead to increased cell apoptosis, suppressed cell proliferation, migration, and invasion. Our study demonstrates that overexpression of miR-340 could suppress OS cell proliferation, migration, and invasion as well as promoting OS cell apoptosis by inactivating the Notch signaling pathway via down-regulating CTNNB1. Functional miR-340 overexpression might be a future therapeutic strategy for OS.	Immunohistochemical staining	Our results show that miR-340 was expressed a higher level in normal tissue than OS tissue. Expression of Notch, CTNNB1, hairy and enhancer of split 1 (Hes1), Bcl-2, Runt-related transcription factor 2 (Runx2), and osteocalcin increased and that of miR-340, Bcl-2 interacting mediator of cell death (BIM), and Bcl-2 associated protein X (Bax) decreased in OS tissues. U-2OS cell line had the highest miR-340 expression. We also found that the up-regulation of miR-340 had increased expression of miR-340, BIM, and Bax but decreased expression of Notch, CTNNB1, Hes1, Bcl-2, Runx2, and osteocalcin. Up-regulation of miR-340p lead to increased cell apoptosis, suppressed cell proliferation, migration, and invasion. Our study demonstrates that overexpression of miR-340 could suppress OS cell proliferation, migration, and invasion as well as promoting OS cell apoptosis by inactivating the Notch signaling pathway via down-regulating CTNNB1. Functional miR-340 overexpression might be a future therapeutic strategy for OS.		Luciferase reporter assay,Western Blot,RT-QPCR,immunohistochemistry,in situ hybridization(ISH),transfection,MTT,flow cytometry,scratch test,transwell assay			Hes1,Runx2,Bax	CTNNB1	Our results show that miR-340 was expressed a higher level in normal tissue than OS tissue. Expression of Notch, CTNNB1, hairy and enhancer of split 1 (Hes1), Bcl-2, Runt-related transcription factor 2 (Runx2), and osteocalcin increased and that of miR-340, Bcl-2 interacting mediator of cell death (BIM), and Bcl-2 associated protein X (Bax) decreased in OS tissues. U-2OS cell line had the highest miR-340 expression. We also found that the up-regulation of miR-340 had increased expression of miR-340, BIM, and Bax but decreased expression of Notch, CTNNB1, Hes1, Bcl-2, Runx2, and osteocalcin. Up-regulation of miR-340p lead to increased cell apoptosis, suppressed cell proliferation, migration, and invasion. Our study demonstrates that overexpression of miR-340 could suppress OS cell proliferation, migration, and invasion as well as promoting OS cell apoptosis by inactivating the Notch signaling pathway via down-regulating CTNNB1. Functional miR-340 overexpression might be a future therapeutic strategy for OS.;Our results show that miR-340 was expressed a higher level in normal tissue than OS tissue. Expression of Notch, CTNNB1, hairy and enhancer of split 1 (Hes1), Bcl-2, Runt-related transcription factor 2 (Runx2), and osteocalcin increased and that of miR-340, Bcl-2 interacting mediator of cell death (BIM), and Bcl-2 associated protein X (Bax) decreased in OS tissues. U-2OS cell line had the highest miR-340 expression. We also found that the up-regulation of miR-340 had increased expression of miR-340, BIM, and Bax but decreased expression of Notch, CTNNB1, Hes1, Bcl-2, Runx2, and osteocalcin. Up-regulation of miR-340p lead to increased cell apoptosis, suppressed cell proliferation, migration, and invasion. Our study demonstrates that overexpression of miR-340 could suppress OS cell proliferation, migration, and invasion as well as promoting OS cell apoptosis by inactivating the Notch signaling pathway via down-regulating CTNNB1. Functional miR-340 overexpression might be a future therapeutic strategy for OS.;Our results show that miR-340 was expressed a higher level in normal tissue than OS tissue. Expression of Notch, CTNNB1, hairy and enhancer of split 1 (Hes1), Bcl-2, Runt-related transcription factor 2 (Runx2), and osteocalcin increased and that of miR-340, Bcl-2 interacting mediator of cell death (BIM), and Bcl-2 associated protein X (Bax) decreased in OS tissues. U-2OS cell line had the highest miR-340 expression. We also found that the up-regulation of miR-340 had increased expression of miR-340, BIM, and Bax but decreased expression of Notch, CTNNB1, Hes1, Bcl-2, Runx2, and osteocalcin. Up-regulation of miR-340p lead to increased cell apoptosis, suppressed cell proliferation, migration, and invasion. Our study demonstrates that overexpression of miR-340 could suppress OS cell proliferation, migration, and invasion as well as promoting OS cell apoptosis by inactivating the Notch signaling pathway via down-regulating CTNNB1. Functional miR-340 overexpression might be a future therapeutic strategy for OS.	Our results show that miR-340 was expressed a higher level in normal tissue than OS tissue. Expression of Notch, CTNNB1, hairy and enhancer of split 1 (Hes1), Bcl-2, Runt-related transcription factor 2 (Runx2), and osteocalcin increased and that of miR-340, Bcl-2 interacting mediator of cell death (BIM), and Bcl-2 associated protein X (Bax) decreased in OS tissues. U-2OS cell line had the highest miR-340 expression. We also found that the up-regulation of miR-340 had increased expression of miR-340, BIM, and Bax but decreased expression of Notch, CTNNB1, Hes1, Bcl-2, Runx2, and osteocalcin. Up-regulation of miR-340p lead to increased cell apoptosis, suppressed cell proliferation, migration, and invasion. Our study demonstrates that overexpression of miR-340 could suppress OS cell proliferation, migration, and invasion as well as promoting OS cell apoptosis by inactivating the Notch signaling pathway via down-regulating CTNNB1. Functional miR-340 overexpression might be a future therapeutic strategy for OS.
29769310	chr17	57998205	58000205	SRSF1	Gene expression profiling by RNA-seq revealed that E12A acts distinctly from HNRPLL and regulates a set of growth-related genes, such as cyclin CCND1 and growth factor receptor TGFBR1 Accordingly, silencing E12A expression leads to impaired clonogenic ability and enhanced sensitivity to doxorubicin, thus highlighting the significance of this alternative isoform in tumor cell survival. In summary, we present the interplay of RNA editing and splicing as a regulatory mechanism of gene expression and also its physiological relevance. These findings extend our understanding of transcriptional dynamics and provide a mechanistic explanation to the link of RNA editors to tumorigenesis.	human	Epithelial	High+Lowthroughput	Tumor-associated intronic editing of HNRPLL generates a novel splicing variant linked to cell proliferation	否		tumour	HeLa cell	E_01_0473	gene knockdown,RT-PCR,qPCR,RNA-immunoprecipitation (RNA-IP) experiment,RNC-mRNA,Splicing luciferase reporter assay,RNA-seq,Gene expression analysis,Chromatin immunoprecipitation assay (ChIP)	Gene expression profiling by RNA-seq revealed that E12A acts distinctly from HNRPLL and regulates a set of growth-related genes, such as cyclin CCND1 and growth factor receptor TGFBR1 Accordingly, silencing E12A expression leads to impaired clonogenic ability and enhanced sensitivity to doxorubicin, thus highlighting the significance of this alternative isoform in tumor cell survival. In summary, we present the interplay of RNA editing and splicing as a regulatory mechanism of gene expression and also its physiological relevance. These findings extend our understanding of transcriptional dynamics and provide a mechanistic explanation to the link of RNA editors to tumorigenesis.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Gene expression profiling by RNA-seq revealed that E12A acts distinctly from HNRPLL and regulates a set of growth-related genes, such as cyclin CCND1 and growth factor receptor TGFBR1 Accordingly, silencing E12A expression leads to impaired clonogenic ability and enhanced sensitivity to doxorubicin, thus highlighting the significance of this alternative isoform in tumor cell survival. In summary, we present the interplay of RNA editing and splicing as a regulatory mechanism of gene expression and also its physiological relevance. These findings extend our understanding of transcriptional dynamics and provide a mechanistic explanation to the link of RNA editors to tumorigenesis.	Immunohistochemical staining	Gene expression profiling by RNA-seq revealed that E12A acts distinctly from HNRPLL and regulates a set of growth-related genes, such as cyclin CCND1 and growth factor receptor TGFBR1 Accordingly, silencing E12A expression leads to impaired clonogenic ability and enhanced sensitivity to doxorubicin, thus highlighting the significance of this alternative isoform in tumor cell survival. In summary, we present the interplay of RNA editing and splicing as a regulatory mechanism of gene expression and also its physiological relevance. These findings extend our understanding of transcriptional dynamics and provide a mechanistic explanation to the link of RNA editors to tumorigenesis.		gene knockdown,RT-PCR,qPCR,RNA-immunoprecipitation (RNA-IP) experiment,RNC-mRNA,Splicing luciferase reporter assay,RNA-seq,Gene expression analysis,Chromatin immunoprecipitation assay (ChIP)			SRSF1,ADAR,TGFBR1	CCND1	Gene expression profiling by RNA-seq revealed that E12A acts distinctly from HNRPLL and regulates a set of growth-related genes, such as cyclin CCND1 and growth factor receptor TGFBR1 Accordingly, silencing E12A expression leads to impaired clonogenic ability and enhanced sensitivity to doxorubicin, thus highlighting the significance of this alternative isoform in tumor cell survival. In summary, we present the interplay of RNA editing and splicing as a regulatory mechanism of gene expression and also its physiological relevance. These findings extend our understanding of transcriptional dynamics and provide a mechanistic explanation to the link of RNA editors to tumorigenesis.;Gene expression profiling by RNA-seq revealed that E12A acts distinctly from HNRPLL and regulates a set of growth-related genes, such as cyclin CCND1 and growth factor receptor TGFBR1 Accordingly, silencing E12A expression leads to impaired clonogenic ability and enhanced sensitivity to doxorubicin, thus highlighting the significance of this alternative isoform in tumor cell survival. In summary, we present the interplay of RNA editing and splicing as a regulatory mechanism of gene expression and also its physiological relevance. These findings extend our understanding of transcriptional dynamics and provide a mechanistic explanation to the link of RNA editors to tumorigenesis.;Gene expression profiling by RNA-seq revealed that E12A acts distinctly from HNRPLL and regulates a set of growth-related genes, such as cyclin CCND1 and growth factor receptor TGFBR1 Accordingly, silencing E12A expression leads to impaired clonogenic ability and enhanced sensitivity to doxorubicin, thus highlighting the significance of this alternative isoform in tumor cell survival. In summary, we present the interplay of RNA editing and splicing as a regulatory mechanism of gene expression and also its physiological relevance. These findings extend our understanding of transcriptional dynamics and provide a mechanistic explanation to the link of RNA editors to tumorigenesis.	Gene expression profiling by RNA-seq revealed that E12A acts distinctly from HNRPLL and regulates a set of growth-related genes, such as cyclin CCND1 and growth factor receptor TGFBR1 Accordingly, silencing E12A expression leads to impaired clonogenic ability and enhanced sensitivity to doxorubicin, thus highlighting the significance of this alternative isoform in tumor cell survival. In summary, we present the interplay of RNA editing and splicing as a regulatory mechanism of gene expression and also its physiological relevance. These findings extend our understanding of transcriptional dynamics and provide a mechanistic explanation to the link of RNA editors to tumorigenesis.
29768655	chr7	148804347	148806347	EZH2	More importantly, we revealed that siEZH2 down-regulated NF-κB p65 within the nucleus. These findings indicate that the let-7e/EZH2/H3K27me3/NF-κB p65 pathway is a novel regulatory axis of TNFα expression. In addition, we determined the protein differences between siEZH2 and siEZH2-NC by iTRAQ and found a number of proteins that might be associated with TNFα.	human	connective	High+Lowthroughput	Let-7e inhibits TNF-α expression by targeting the methyl transferase EZH2 in DENV2-infected THP-1 cells	否		Other	THP-1 cells	E_01_0474	Western blot,Immunofluorescence assay,qRT-PCR,ELISA,Luciferase reporter assay,iTRAQ,miRNA or siRNA transfection,EZH2 knockdown,Smad3 knockdown	More importantly, we revealed that siEZH2 down-regulated NF-κB p65 within the nucleus. These findings indicate that the let-7e/EZH2/H3K27me3/NF-κB p65 pathway is a novel regulatory axis of TNFα expression. In addition, we determined the protein differences between siEZH2 and siEZH2-NC by iTRAQ and found a number of proteins that might be associated with TNFα.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		More importantly, we revealed that siEZH2 down-regulated NF-κB p65 within the nucleus. These findings indicate that the let-7e/EZH2/H3K27me3/NF-κB p65 pathway is a novel regulatory axis of TNFα expression. In addition, we determined the protein differences between siEZH2 and siEZH2-NC by iTRAQ and found a number of proteins that might be associated with TNFα.	Immunohistochemical staining	More importantly, we revealed that siEZH2 down-regulated NF-κB p65 within the nucleus. These findings indicate that the let-7e/EZH2/H3K27me3/NF-κB p65 pathway is a novel regulatory axis of TNFα expression. In addition, we determined the protein differences between siEZH2 and siEZH2-NC by iTRAQ and found a number of proteins that might be associated with TNFα.		Western blot,Immunofluorescence assay,qRT-PCR,ELISA,Luciferase reporter assay,iTRAQ,miRNA or siRNA transfection,EZH2 knockdown,Smad3 knockdown			Smad3	EZH2	More importantly, we revealed that siEZH2 down-regulated NF-κB p65 within the nucleus. These findings indicate that the let-7e/EZH2/H3K27me3/NF-κB p65 pathway is a novel regulatory axis of TNFα expression. In addition, we determined the protein differences between siEZH2 and siEZH2-NC by iTRAQ and found a number of proteins that might be associated with TNFα.	More importantly, we revealed that siEZH2 down-regulated NF-κB p65 within the nucleus. These findings indicate that the let-7e/EZH2/H3K27me3/NF-κB p65 pathway is a novel regulatory axis of TNFα expression. In addition, we determined the protein differences between siEZH2 and siEZH2-NC by iTRAQ and found a number of proteins that might be associated with TNFα.
29768212	chr1	186669486	186671486	PTGS2	mTOR pathway activation is associated with decreased NF-κB-mediated gene expression (e.g., PTGS2, IL-6, and IL-8) but increased STAT1-dependent gene expression (e.g., CXCL11 and TNFSF13B). We further demonstrate how metabolic inputs, such as amino acids, impinge on TNF-mTORC1 signaling to differentially regulate pro-inflammatory signaling circuits. Our results define a critical role for mTOR in the regulation of the pro-inflammatory response in FLSs and unfold its pathogenic involvement in TNF-driven diseases, such as rheumatoid arthritis (RA).	human	Synovial	High+Lowthroughput	mTOR Senses Environmental Cues to Shape the Fibroblast-like Synoviocyte Response to Inflammation	否		Inflammation, rheumatoid arthritis (RA)		E_01_0475	Immunohistochemistry,Western Blot,qPCR,ELISA,EMSA,siRNA-Mediated Knockdown,Immunofluorescence Staining,Automated Imaging	mTOR pathway activation is associated with decreased NF-κB-mediated gene expression (e.g., PTGS2, IL-6, and IL-8) but increased STAT1-dependent gene expression (e.g., CXCL11 and TNFSF13B). We further demonstrate how metabolic inputs, such as amino acids, impinge on TNF-mTORC1 signaling to differentially regulate pro-inflammatory signaling circuits. Our results define a critical role for mTOR in the regulation of the pro-inflammatory response in FLSs and unfold its pathogenic involvement in TNF-driven diseases, such as rheumatoid arthritis (RA).	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		mTOR pathway activation is associated with decreased NF-κB-mediated gene expression (e.g., PTGS2, IL-6, and IL-8) but increased STAT1-dependent gene expression (e.g., CXCL11 and TNFSF13B). We further demonstrate how metabolic inputs, such as amino acids, impinge on TNF-mTORC1 signaling to differentially regulate pro-inflammatory signaling circuits. Our results define a critical role for mTOR in the regulation of the pro-inflammatory response in FLSs and unfold its pathogenic involvement in TNF-driven diseases, such as rheumatoid arthritis (RA).	Immunohistochemical staining	mTOR pathway activation is associated with decreased NF-κB-mediated gene expression (e.g., PTGS2, IL-6, and IL-8) but increased STAT1-dependent gene expression (e.g., CXCL11 and TNFSF13B). We further demonstrate how metabolic inputs, such as amino acids, impinge on TNF-mTORC1 signaling to differentially regulate pro-inflammatory signaling circuits. Our results define a critical role for mTOR in the regulation of the pro-inflammatory response in FLSs and unfold its pathogenic involvement in TNF-driven diseases, such as rheumatoid arthritis (RA).		Immunohistochemistry,Western Blot,qPCR,ELISA,EMSA,siRNA-Mediated Knockdown,Immunofluorescence Staining,Automated Imaging			CXCL11,TNFSF13B	PTGS2,STAT1	mTOR pathway activation is associated with decreased NF-κB-mediated gene expression (e.g., PTGS2, IL-6, and IL-8) but increased STAT1-dependent gene expression (e.g., CXCL11 and TNFSF13B). We further demonstrate how metabolic inputs, such as amino acids, impinge on TNF-mTORC1 signaling to differentially regulate pro-inflammatory signaling circuits. Our results define a critical role for mTOR in the regulation of the pro-inflammatory response in FLSs and unfold its pathogenic involvement in TNF-driven diseases, such as rheumatoid arthritis (RA).;mTOR pathway activation is associated with decreased NF-κB-mediated gene expression (e.g., PTGS2, IL-6, and IL-8) but increased STAT1-dependent gene expression (e.g., CXCL11 and TNFSF13B). We further demonstrate how metabolic inputs, such as amino acids, impinge on TNF-mTORC1 signaling to differentially regulate pro-inflammatory signaling circuits. Our results define a critical role for mTOR in the regulation of the pro-inflammatory response in FLSs and unfold its pathogenic involvement in TNF-driven diseases, such as rheumatoid arthritis (RA).	mTOR pathway activation is associated with decreased NF-κB-mediated gene expression (e.g., PTGS2, IL-6, and IL-8) but increased STAT1-dependent gene expression (e.g., CXCL11 and TNFSF13B). We further demonstrate how metabolic inputs, such as amino acids, impinge on TNF-mTORC1 signaling to differentially regulate pro-inflammatory signaling circuits. Our results define a critical role for mTOR in the regulation of the pro-inflammatory response in FLSs and unfold its pathogenic involvement in TNF-driven diseases, such as rheumatoid arthritis (RA).;mTOR pathway activation is associated with decreased NF-κB-mediated gene expression (e.g., PTGS2, IL-6, and IL-8) but increased STAT1-dependent gene expression (e.g., CXCL11 and TNFSF13B). We further demonstrate how metabolic inputs, such as amino acids, impinge on TNF-mTORC1 signaling to differentially regulate pro-inflammatory signaling circuits. Our results define a critical role for mTOR in the regulation of the pro-inflammatory response in FLSs and unfold its pathogenic involvement in TNF-driven diseases, such as rheumatoid arthritis (RA).
29768199	chr14	21382478	21384478	CHD8		human	adipose	High+Lowthroughput	The Autism-Related Protein CHD8 Cooperates with C/EBPβ to Regulate Adipogenesis	否		Autism spectrum disorder (ASD)	preadipocyte	E_01_0476	transgenic mice,RNA Interference,Luciferase Assay,RT-PCR,Real-Time PCR Analysis,Transfection,Immunoblot Analysis,Immunoprecipitation,ChIP,FAIRE,ChIP-Seq,RNA-Seq,Histopathology		Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq			Immunohistochemical staining			transgenic mice,RNA Interference,Luciferase Assay,RT-PCR,Real-Time PCR Analysis,Transfection,Immunoblot Analysis,Immunoprecipitation,ChIP,FAIRE,ChIP-Seq,RNA-Seq,Histopathology			CHD8			
29765957	chr16	67559780	67561780	CTCF	The prevalence of four SNPs (rs1324192, rs7019262, rs518054, and rs571221) risk alleles haplotype in this region was significantly higher (compared with other haplotypes) in frail older adults compared with non-frail older adults (29.7 vs. 20.8%, p = 0.0005, respectively). Functional analyses using in silico approaches placed rs518054 in the CTCF binding site as well as DNase hypersensitive region. Furthermore, rs518054 was found to be in an enhancer site of NFIB gene located downstream. NFIB is a transcription factor that promotes cell differentiation during development, has antiapoptotic effect, maintains stem cell populations in adult tissues, and also acts as epigenetic regulators. Our study found novel association of SNPs in the regulatory region in the 9p21-23 region with the frailty phenotype; signifying the importance of this locus in aging.	human	Epithelial	High+Lowthroughput	Genetic Insights Into Frailty: Association of 9p21-23 Locus With Frailty	是	rs1324192,rs7019262,rs518054,rs571221	Frailty, aging		E_01_0477	WGS	The prevalence of four SNPs (rs1324192, rs7019262, rs518054, and rs571221) risk alleles haplotype in this region was significantly higher (compared with other haplotypes) in frail older adults compared with non-frail older adults (29.7 vs. 20.8%, p = 0.0005, respectively). Functional analyses using in silico approaches placed rs518054 in the CTCF binding site as well as DNase hypersensitive region. Furthermore, rs518054 was found to be in an enhancer site of NFIB gene located downstream. NFIB is a transcription factor that promotes cell differentiation during development, has antiapoptotic effect, maintains stem cell populations in adult tissues, and also acts as epigenetic regulators. Our study found novel association of SNPs in the regulatory region in the 9p21-23 region with the frailty phenotype; signifying the importance of this locus in aging.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The prevalence of four SNPs (rs1324192, rs7019262, rs518054, and rs571221) risk alleles haplotype in this region was significantly higher (compared with other haplotypes) in frail older adults compared with non-frail older adults (29.7 vs. 20.8%, p = 0.0005, respectively). Functional analyses using in silico approaches placed rs518054 in the CTCF binding site as well as DNase hypersensitive region. Furthermore, rs518054 was found to be in an enhancer site of NFIB gene located downstream. NFIB is a transcription factor that promotes cell differentiation during development, has antiapoptotic effect, maintains stem cell populations in adult tissues, and also acts as epigenetic regulators. Our study found novel association of SNPs in the regulatory region in the 9p21-23 region with the frailty phenotype; signifying the importance of this locus in aging.	Immunohistochemical staining	The prevalence of four SNPs (rs1324192, rs7019262, rs518054, and rs571221) risk alleles haplotype in this region was significantly higher (compared with other haplotypes) in frail older adults compared with non-frail older adults (29.7 vs. 20.8%, p = 0.0005, respectively). Functional analyses using in silico approaches placed rs518054 in the CTCF binding site as well as DNase hypersensitive region. Furthermore, rs518054 was found to be in an enhancer site of NFIB gene located downstream. NFIB is a transcription factor that promotes cell differentiation during development, has antiapoptotic effect, maintains stem cell populations in adult tissues, and also acts as epigenetic regulators. Our study found novel association of SNPs in the regulatory region in the 9p21-23 region with the frailty phenotype; signifying the importance of this locus in aging.		WGS			NFIB	CTCF	The prevalence of four SNPs (rs1324192, rs7019262, rs518054, and rs571221) risk alleles haplotype in this region was significantly higher (compared with other haplotypes) in frail older adults compared with non-frail older adults (29.7 vs. 20.8%, p = 0.0005, respectively). Functional analyses using in silico approaches placed rs518054 in the CTCF binding site as well as DNase hypersensitive region. Furthermore, rs518054 was found to be in an enhancer site of NFIB gene located downstream. NFIB is a transcription factor that promotes cell differentiation during development, has antiapoptotic effect, maintains stem cell populations in adult tissues, and also acts as epigenetic regulators. Our study found novel association of SNPs in the regulatory region in the 9p21-23 region with the frailty phenotype; signifying the importance of this locus in aging.	The prevalence of four SNPs (rs1324192, rs7019262, rs518054, and rs571221) risk alleles haplotype in this region was significantly higher (compared with other haplotypes) in frail older adults compared with non-frail older adults (29.7 vs. 20.8%, p = 0.0005, respectively). Functional analyses using in silico approaches placed rs518054 in the CTCF binding site as well as DNase hypersensitive region. Furthermore, rs518054 was found to be in an enhancer site of NFIB gene located downstream. NFIB is a transcription factor that promotes cell differentiation during development, has antiapoptotic effect, maintains stem cell populations in adult tissues, and also acts as epigenetic regulators. Our study found novel association of SNPs in the regulatory region in the 9p21-23 region with the frailty phenotype; signifying the importance of this locus in aging.
29763375	chr12	56268405	56270405	CS	Thus, pre-pregnancy maternal obesity disrupts the placental hGH/CS gene locus chromosomal architecture. However, based on data from obese women who develop GDM, insulin treatment partially recapitulates the chromosomal architecture seen in lean women and positively affects hCS production, presumably facilitating prolactin receptor-related signaling by hCS.	human	Placental	High+Lowthroughput	Chromosomal architecture and placental expression of the human growth hormone gene family are targeted by pre-pregnancy maternal obesity	否		Obesity		E_01_0478	Real-time reverse transcription-polymerase chain reaction,protein immunoblotting,Enzyme-linked immunosorbent assay (ELISA),Chromosome conformation capture (3C) assay,Amplicon sequencing,bioinformatics, Chromatin immunoprecipitation (ChIP) assay	Thus, pre-pregnancy maternal obesity disrupts the placental hGH/CS gene locus chromosomal architecture. However, based on data from obese women who develop GDM, insulin treatment partially recapitulates the chromosomal architecture seen in lean women and positively affects hCS production, presumably facilitating prolactin receptor-related signaling by hCS.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Thus, pre-pregnancy maternal obesity disrupts the placental hGH/CS gene locus chromosomal architecture. However, based on data from obese women who develop GDM, insulin treatment partially recapitulates the chromosomal architecture seen in lean women and positively affects hCS production, presumably facilitating prolactin receptor-related signaling by hCS.	Immunohistochemical staining	Thus, pre-pregnancy maternal obesity disrupts the placental hGH/CS gene locus chromosomal architecture. However, based on data from obese women who develop GDM, insulin treatment partially recapitulates the chromosomal architecture seen in lean women and positively affects hCS production, presumably facilitating prolactin receptor-related signaling by hCS.		Real-time reverse transcription-polymerase chain reaction,protein immunoblotting,Enzyme-linked immunosorbent assay (ELISA),Chromosome conformation capture (3C) assay,Amplicon sequencing,bioinformatics, Chromatin immunoprecipitation (ChIP) assay			CS		Thus, pre-pregnancy maternal obesity disrupts the placental hGH/CS gene locus chromosomal architecture. However, based on data from obese women who develop GDM, insulin treatment partially recapitulates the chromosomal architecture seen in lean women and positively affects hCS production, presumably facilitating prolactin receptor-related signaling by hCS.	
29762844	chr9	117701608	117703608	TLR4	TLR4 mediates FFAs induced inflammatory responses in HUVECs. TLR4 interference in HUVECs significantly reduces the inflammatory cytokines expression, decreases the cell apoptosis rate and increases cell viability.	human	connective	High+Lowthroughput	Free fatty acids mediates human umbilical vein endothelial cells inflammation through toll-like receptor-4	否		Inflammation in HUVECs	HEK293 cell	E_01_0479	Flow Cytometry,ELISA,qPCR,Western Blot,Cell Apoptosis Assay,Viability Assay	TLR4 mediates FFAs induced inflammatory responses in HUVECs. TLR4 interference in HUVECs significantly reduces the inflammatory cytokines expression, decreases the cell apoptosis rate and increases cell viability.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		TLR4 mediates FFAs induced inflammatory responses in HUVECs. TLR4 interference in HUVECs significantly reduces the inflammatory cytokines expression, decreases the cell apoptosis rate and increases cell viability.	Immunohistochemical staining	TLR4 mediates FFAs induced inflammatory responses in HUVECs. TLR4 interference in HUVECs significantly reduces the inflammatory cytokines expression, decreases the cell apoptosis rate and increases cell viability.		Flow Cytometry,ELISA,qPCR,Western Blot,Cell Apoptosis Assay,Viability Assay				TLR4,CCL5,CXCL10		TLR4 mediates FFAs induced inflammatory responses in HUVECs. TLR4 interference in HUVECs significantly reduces the inflammatory cytokines expression, decreases the cell apoptosis rate and increases cell viability.;TLR4 mediates FFAs induced inflammatory responses in HUVECs. TLR4 interference in HUVECs significantly reduces the inflammatory cytokines expression, decreases the cell apoptosis rate and increases cell viability.;TLR4 mediates FFAs induced inflammatory responses in HUVECs. TLR4 interference in HUVECs significantly reduces the inflammatory cytokines expression, decreases the cell apoptosis rate and increases cell viability.
29761425	chr3	133743127	133745127	TF	All the results suggested that genistein has the function of alleviating and treating LPS-induced DIC by anti-inflammatory and anticoagulation effects. We tentatively propose that genistein is a potential drug for auxiliary treatment of DIC.	human	lymphoid	High+Lowthroughput	Genistein has the function of alleviating and treating disseminated intravascular coagulation caused by lipopolysaccharide	否		Disseminated intravascular coagulation (DIC)	 RAW 264.7	E_01_0480	Western blot, H&E staining,PTAH staining,MTT	All the results suggested that genistein has the function of alleviating and treating LPS-induced DIC by anti-inflammatory and anticoagulation effects. We tentatively propose that genistein is a potential drug for auxiliary treatment of DIC.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		All the results suggested that genistein has the function of alleviating and treating LPS-induced DIC by anti-inflammatory and anticoagulation effects. We tentatively propose that genistein is a potential drug for auxiliary treatment of DIC.	Immunohistochemical staining	All the results suggested that genistein has the function of alleviating and treating LPS-induced DIC by anti-inflammatory and anticoagulation effects. We tentatively propose that genistein is a potential drug for auxiliary treatment of DIC.		Western blot, H&E staining,PTAH staining,MTT			TF		All the results suggested that genistein has the function of alleviating and treating LPS-induced DIC by anti-inflammatory and anticoagulation effects. We tentatively propose that genistein is a potential drug for auxiliary treatment of DIC.	
29761173	chr20	22578409	22580409	FOXA2	HNF4α and other members of the LETFs appear to be important regulators of hepatocyte function in patients with chronic hepatic failure. 	human	Liver	High+Lowthroughput	Liver-enriched transcription factor expression relates to chronic hepatic failure in humans	否		Liver metastasis, primary hepatocellular carcinoma, decompensated cirrhosis	hepatocyte	E_01_0481	qRT-PCR,immunohistochemistry	HNF4α and other members of the LETFs appear to be important regulators of hepatocyte function in patients with chronic hepatic failure. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		HNF4α and other members of the LETFs appear to be important regulators of hepatocyte function in patients with chronic hepatic failure. 	Immunohistochemical staining	HNF4α and other members of the LETFs appear to be important regulators of hepatocyte function in patients with chronic hepatic failure. 		qRT-PCR,immunohistochemistry			OTC,CYP3A4,F7,LRP1	FOXA2	HNF4α and other members of the LETFs appear to be important regulators of hepatocyte function in patients with chronic hepatic failure. ;HNF4α and other members of the LETFs appear to be important regulators of hepatocyte function in patients with chronic hepatic failure. ;HNF4α and other members of the LETFs appear to be important regulators of hepatocyte function in patients with chronic hepatic failure. ;HNF4α and other members of the LETFs appear to be important regulators of hepatocyte function in patients with chronic hepatic failure. 	HNF4α and other members of the LETFs appear to be important regulators of hepatocyte function in patients with chronic hepatic failure. 
29760797	chr11	8221840	8223840	LMO1	In summary, the current study confirmed that the potentially functional LMO1 rs2168101 G>T and rs3750952 G>C polymorphisms were associated with neuroblastoma susceptibility. This research requires further validation with larger sample sizes and inclusion of different ethnicities.	human	lymphoid	High+Lowthroughput	LMO1 super-enhancer polymorphism rs2168101 G>T correlates with decreased neuroblastoma risk in Chinese children	是	rs2168101,rs3750952	Neuroblastoma	lymphocyte	E_01_0482	RNA-seq	In summary, the current study confirmed that the potentially functional LMO1 rs2168101 G>T and rs3750952 G>C polymorphisms were associated with neuroblastoma susceptibility. This research requires further validation with larger sample sizes and inclusion of different ethnicities.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In summary, the current study confirmed that the potentially functional LMO1 rs2168101 G>T and rs3750952 G>C polymorphisms were associated with neuroblastoma susceptibility. This research requires further validation with larger sample sizes and inclusion of different ethnicities.	Immunohistochemical staining	In summary, the current study confirmed that the potentially functional LMO1 rs2168101 G>T and rs3750952 G>C polymorphisms were associated with neuroblastoma susceptibility. This research requires further validation with larger sample sizes and inclusion of different ethnicities.		RNA-seq				LMO1,FAS		In summary, the current study confirmed that the potentially functional LMO1 rs2168101 G>T and rs3750952 G>C polymorphisms were associated with neuroblastoma susceptibility. This research requires further validation with larger sample sizes and inclusion of different ethnicities.;In summary, the current study confirmed that the potentially functional LMO1 rs2168101 G>T and rs3750952 G>C polymorphisms were associated with neuroblastoma susceptibility. This research requires further validation with larger sample sizes and inclusion of different ethnicities.
29760402	chr15	39606417	39608417	Dcstamp	Furthermore, osteoclast differentiation was impaired by targeted deletion of bidirectional eRNA regions. The combined results show that eRNAs play important roles in osteoclastogenic gene regulation, and may therefore provide novel insights to elucidate the transcriptional mechanisms that control osteoclast differentiation.	mouse	Nervous	High+Lowthroughput	Roles of Enhancer RNAs in RANKL-induced Osteoclast Differentiation Identified by Genome-wide Cap-analysis of Gene Expression using CRISPR/Cas9	否		Other		E_01_0483	qRT-PCR,TRAP staining,CRISPR/Cas9,Retroviral gene transfer,shRNA transfection,CAGE,	Furthermore, osteoclast differentiation was impaired by targeted deletion of bidirectional eRNA regions. The combined results show that eRNAs play important roles in osteoclastogenic gene regulation, and may therefore provide novel insights to elucidate the transcriptional mechanisms that control osteoclast differentiation.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Furthermore, osteoclast differentiation was impaired by targeted deletion of bidirectional eRNA regions. The combined results show that eRNAs play important roles in osteoclastogenic gene regulation, and may therefore provide novel insights to elucidate the transcriptional mechanisms that control osteoclast differentiation.	Immunohistochemical staining	Furthermore, osteoclast differentiation was impaired by targeted deletion of bidirectional eRNA regions. The combined results show that eRNAs play important roles in osteoclastogenic gene regulation, and may therefore provide novel insights to elucidate the transcriptional mechanisms that control osteoclast differentiation.		qRT-PCR,TRAP staining,CRISPR/Cas9,Retroviral gene transfer,shRNA transfection,CAGE,			Dcstamp,Nfatc1,Nrp2		Furthermore, osteoclast differentiation was impaired by targeted deletion of bidirectional eRNA regions. The combined results show that eRNAs play important roles in osteoclastogenic gene regulation, and may therefore provide novel insights to elucidate the transcriptional mechanisms that control osteoclast differentiation.;Furthermore, osteoclast differentiation was impaired by targeted deletion of bidirectional eRNA regions. The combined results show that eRNAs play important roles in osteoclastogenic gene regulation, and may therefore provide novel insights to elucidate the transcriptional mechanisms that control osteoclast differentiation.;Furthermore, osteoclast differentiation was impaired by targeted deletion of bidirectional eRNA regions. The combined results show that eRNAs play important roles in osteoclastogenic gene regulation, and may therefore provide novel insights to elucidate the transcriptional mechanisms that control osteoclast differentiation.	
29760161	chr16	67559664	67561664	CTCF	Thus, the CTCF boundary constrains the normal gene-expression program, as well as plays a role in maintaining the oncogenic transcription program for leukemic transformation. The CTCF boundaries may serve as novel therapeutic targets for the treatment of myeloid malignancies.	human	connective	High+Lowthroughput	CTCF boundary remodels chromatin domain and drives aberrant HOX gene transcription in acute myeloid leukemia	否		Acute myeloid leukemia (AML)	AML cell lines	E_01_0484	RNA,qRT-PCR,RNA-seq,ChIP,ChIP-seq,ATAC-seq,4C-seq,CRISPR/Cas9,	Thus, the CTCF boundary constrains the normal gene-expression program, as well as plays a role in maintaining the oncogenic transcription program for leukemic transformation. The CTCF boundaries may serve as novel therapeutic targets for the treatment of myeloid malignancies.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Thus, the CTCF boundary constrains the normal gene-expression program, as well as plays a role in maintaining the oncogenic transcription program for leukemic transformation. The CTCF boundaries may serve as novel therapeutic targets for the treatment of myeloid malignancies.	Immunohistochemical staining	Thus, the CTCF boundary constrains the normal gene-expression program, as well as plays a role in maintaining the oncogenic transcription program for leukemic transformation. The CTCF boundaries may serve as novel therapeutic targets for the treatment of myeloid malignancies.		RNA,qRT-PCR,RNA-seq,ChIP,ChIP-seq,ATAC-seq,4C-seq,CRISPR/Cas9,				CTCF,HOXA7,HOXA9,HOXA13		Thus, the CTCF boundary constrains the normal gene-expression program, as well as plays a role in maintaining the oncogenic transcription program for leukemic transformation. The CTCF boundaries may serve as novel therapeutic targets for the treatment of myeloid malignancies.;Thus, the CTCF boundary constrains the normal gene-expression program, as well as plays a role in maintaining the oncogenic transcription program for leukemic transformation. The CTCF boundaries may serve as novel therapeutic targets for the treatment of myeloid malignancies.;Thus, the CTCF boundary constrains the normal gene-expression program, as well as plays a role in maintaining the oncogenic transcription program for leukemic transformation. The CTCF boundaries may serve as novel therapeutic targets for the treatment of myeloid malignancies.;Thus, the CTCF boundary constrains the normal gene-expression program, as well as plays a role in maintaining the oncogenic transcription program for leukemic transformation. The CTCF boundaries may serve as novel therapeutic targets for the treatment of myeloid malignancies.
29759640	chr7	148804547	148806547	EZH2	The current study demonstrated that high EZH2 expression was associated with activation of tumor angiogenesis, and activation of the EZH2-mediated angiogenesis pathway predicted the prognosis of patients with ICC.	human	Epithelial	High+Lowthroughput	Enhancer of zeste homolog 2 (EZH2) regulates tumor angiogenesis and predicts recurrence and prognosis of intrahepatic cholangiocarcinoma	否		Intrahepatic cholangiocarcinoma (ICC)	cholangiocarcinoma RBE cell	E_01_0485	Immunohistochemical staining and scoring,qRT-PCR,small interfering RNAs (siRNAs),qRT-PCR,Western blot,Bioinformatics analysis,	The current study demonstrated that high EZH2 expression was associated with activation of tumor angiogenesis, and activation of the EZH2-mediated angiogenesis pathway predicted the prognosis of patients with ICC.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The current study demonstrated that high EZH2 expression was associated with activation of tumor angiogenesis, and activation of the EZH2-mediated angiogenesis pathway predicted the prognosis of patients with ICC.	Immunohistochemical staining	The current study demonstrated that high EZH2 expression was associated with activation of tumor angiogenesis, and activation of the EZH2-mediated angiogenesis pathway predicted the prognosis of patients with ICC.		Immunohistochemical staining and scoring,qRT-PCR,small interfering RNAs (siRNAs),qRT-PCR,Western blot,Bioinformatics analysis,			VASH1	EZH2	The current study demonstrated that high EZH2 expression was associated with activation of tumor angiogenesis, and activation of the EZH2-mediated angiogenesis pathway predicted the prognosis of patients with ICC.	The current study demonstrated that high EZH2 expression was associated with activation of tumor angiogenesis, and activation of the EZH2-mediated angiogenesis pathway predicted the prognosis of patients with ICC.
29758293	chr9	81580468	81582468	TLE1	Using trio-based exome sequencing, we identified a homozygous missense mutation in the Transducin-like enhancer of split-1 (TLE1) gene, encoding for a non DNA-binding transcriptional corepressor, highly expressed in the postnatal brain. The regulation of the post-mitotic neural survival activity of TLE1 depends critically on an interaction with FOXG1, a gene shown to be involved in a postnatal microcephaly syndrome. Functional analysis on affected dermal fibroblasts showed a significant decrease in mitotic and proliferative index, indicating a lengthening of the cell cycle and a delay in mitosis, supporting that this gene could be a new candidate for postnatal microcephaly.	human	Nervous	High+Lowthroughput	TLE1, a key player in neurogenesis, a new candidate gene for autosomal recessive postnatal microcephaly	是	rs201140985	Postnatal microcephaly	neural progenitor cell	E_01_0486	Immunostaining	Using trio-based exome sequencing, we identified a homozygous missense mutation in the Transducin-like enhancer of split-1 (TLE1) gene, encoding for a non DNA-binding transcriptional corepressor, highly expressed in the postnatal brain. The regulation of the post-mitotic neural survival activity of TLE1 depends critically on an interaction with FOXG1, a gene shown to be involved in a postnatal microcephaly syndrome. Functional analysis on affected dermal fibroblasts showed a significant decrease in mitotic and proliferative index, indicating a lengthening of the cell cycle and a delay in mitosis, supporting that this gene could be a new candidate for postnatal microcephaly.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Using trio-based exome sequencing, we identified a homozygous missense mutation in the Transducin-like enhancer of split-1 (TLE1) gene, encoding for a non DNA-binding transcriptional corepressor, highly expressed in the postnatal brain. The regulation of the post-mitotic neural survival activity of TLE1 depends critically on an interaction with FOXG1, a gene shown to be involved in a postnatal microcephaly syndrome. Functional analysis on affected dermal fibroblasts showed a significant decrease in mitotic and proliferative index, indicating a lengthening of the cell cycle and a delay in mitosis, supporting that this gene could be a new candidate for postnatal microcephaly.	Immunohistochemical staining	Using trio-based exome sequencing, we identified a homozygous missense mutation in the Transducin-like enhancer of split-1 (TLE1) gene, encoding for a non DNA-binding transcriptional corepressor, highly expressed in the postnatal brain. The regulation of the post-mitotic neural survival activity of TLE1 depends critically on an interaction with FOXG1, a gene shown to be involved in a postnatal microcephaly syndrome. Functional analysis on affected dermal fibroblasts showed a significant decrease in mitotic and proliferative index, indicating a lengthening of the cell cycle and a delay in mitosis, supporting that this gene could be a new candidate for postnatal microcephaly.		Immunostaining			FOXG1	TLE1	Using trio-based exome sequencing, we identified a homozygous missense mutation in the Transducin-like enhancer of split-1 (TLE1) gene, encoding for a non DNA-binding transcriptional corepressor, highly expressed in the postnatal brain. The regulation of the post-mitotic neural survival activity of TLE1 depends critically on an interaction with FOXG1, a gene shown to be involved in a postnatal microcephaly syndrome. Functional analysis on affected dermal fibroblasts showed a significant decrease in mitotic and proliferative index, indicating a lengthening of the cell cycle and a delay in mitosis, supporting that this gene could be a new candidate for postnatal microcephaly.	Using trio-based exome sequencing, we identified a homozygous missense mutation in the Transducin-like enhancer of split-1 (TLE1) gene, encoding for a non DNA-binding transcriptional corepressor, highly expressed in the postnatal brain. The regulation of the post-mitotic neural survival activity of TLE1 depends critically on an interaction with FOXG1, a gene shown to be involved in a postnatal microcephaly syndrome. Functional analysis on affected dermal fibroblasts showed a significant decrease in mitotic and proliferative index, indicating a lengthening of the cell cycle and a delay in mitosis, supporting that this gene could be a new candidate for postnatal microcephaly.
29755131	chr7	152132016	152134016	KMT2C	From a therapeutic standpoint, KMT2C-depleted cells that develop hormone-independence retain their dependence on ERα, displaying ongoing sensitivity to ERα antagonists. We conclude that KMT2C is a key regulator of ERα activity whose loss uncouples breast cancer proliferation from hormone abundance.	human	Epithelial	High+Lowthroughput	KMT2C mediates the estrogen dependence of breast cancer through regulation of ERα enhancer function	否		mammary cancer	SKBR3 cell	E_01_0487	CRISPR/Cas9,next-generation sequencing (IMPACT) assay,Proliferation assays,Immunoblotting,Lentiviral Infections,Quantitative RT-PCR,Chromatin Immunoprecipitation,Immunohistochemistry,Rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME),Chromatin Immunoprecipitation followed by sequencing,	From a therapeutic standpoint, KMT2C-depleted cells that develop hormone-independence retain their dependence on ERα, displaying ongoing sensitivity to ERα antagonists. We conclude that KMT2C is a key regulator of ERα activity whose loss uncouples breast cancer proliferation from hormone abundance.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		From a therapeutic standpoint, KMT2C-depleted cells that develop hormone-independence retain their dependence on ERα, displaying ongoing sensitivity to ERα antagonists. We conclude that KMT2C is a key regulator of ERα activity whose loss uncouples breast cancer proliferation from hormone abundance.	Immunohistochemical staining	From a therapeutic standpoint, KMT2C-depleted cells that develop hormone-independence retain their dependence on ERα, displaying ongoing sensitivity to ERα antagonists. We conclude that KMT2C is a key regulator of ERα activity whose loss uncouples breast cancer proliferation from hormone abundance.		CRISPR/Cas9,next-generation sequencing (IMPACT) assay,Proliferation assays,Immunoblotting,Lentiviral Infections,Quantitative RT-PCR,Chromatin Immunoprecipitation,Immunohistochemistry,Rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME),Chromatin Immunoprecipitation followed by sequencing,				KMT2C,FOXA1		From a therapeutic standpoint, KMT2C-depleted cells that develop hormone-independence retain their dependence on ERα, displaying ongoing sensitivity to ERα antagonists. We conclude that KMT2C is a key regulator of ERα activity whose loss uncouples breast cancer proliferation from hormone abundance.;From a therapeutic standpoint, KMT2C-depleted cells that develop hormone-independence retain their dependence on ERα, displaying ongoing sensitivity to ERα antagonists. We conclude that KMT2C is a key regulator of ERα activity whose loss uncouples breast cancer proliferation from hormone abundance.
29755129	chr13	27063070	27065070	USP12	Consequently, USP12 levels are predictive not only of cancer development but also of patient's therapy resistance, relapse and survival. Therefore, our findings suggest that USP12 could serve as a promising therapeutic target in currently incurable castrate-resistant prostate cancer.	human	connective	High+Lowthroughput	Molecular mechanism of the TP53-MDM2-AR-AKT signalling network regulation by USP12	否		prostatic cancer	LNCaP	E_01_0488	transfection,siRNA gene silencing,Immunoprecipitation (IP),Immunohistochemistry,Colony formation,Chromatin immunoprecipitation (ChIP),qPCR,	Consequently, USP12 levels are predictive not only of cancer development but also of patient's therapy resistance, relapse and survival. Therefore, our findings suggest that USP12 could serve as a promising therapeutic target in currently incurable castrate-resistant prostate cancer.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Consequently, USP12 levels are predictive not only of cancer development but also of patient's therapy resistance, relapse and survival. Therefore, our findings suggest that USP12 could serve as a promising therapeutic target in currently incurable castrate-resistant prostate cancer.	Immunohistochemical staining	Consequently, USP12 levels are predictive not only of cancer development but also of patient's therapy resistance, relapse and survival. Therefore, our findings suggest that USP12 could serve as a promising therapeutic target in currently incurable castrate-resistant prostate cancer.		transfection,siRNA gene silencing,Immunoprecipitation (IP),Immunohistochemistry,Colony formation,Chromatin immunoprecipitation (ChIP),qPCR,			USP12	TP53	Consequently, USP12 levels are predictive not only of cancer development but also of patient's therapy resistance, relapse and survival. Therefore, our findings suggest that USP12 could serve as a promising therapeutic target in currently incurable castrate-resistant prostate cancer.	Consequently, USP12 levels are predictive not only of cancer development but also of patient's therapy resistance, relapse and survival. Therefore, our findings suggest that USP12 could serve as a promising therapeutic target in currently incurable castrate-resistant prostate cancer.
29754817	chr12	47838311	47840311	VDR	Mechanistically, ligand promotes VDR association with PBAF to effect genome-wide changes in chromatin accessibility and enhancer landscape, resulting in an anti-inflammatory response. Importantly, pharmacological inhibition of BRD9 promotes PBAF-VDR association to restore β cell function and ameliorate hyperglycemia in murine T2D models. These studies reveal an unrecognized VDR-dependent transcriptional program underpinning β cell survival and identifies the VDR:PBAF/BAF association as a potential therapeutic target for T2D.	human	connective	High+Lowthroughput	Vitamin D Switches BAF Complexes to Protect β Cells	否		Type 2 diabetes (T2D)	INS1 cell	E_01_0489	CRISPR screening,RNA-Seq,qPCR,H&E staining,Immunohistochemistry,immunofluorescence,Immunoprecipitation,siRNA knockdown,transfection,shRNA knockdown,FACS analysis,ELISA,Chromatin Immunoprecipitation,ChIP-Seq,ATAC-Seq,Transmission electronic microscopy,LC-MS Analysis,	Mechanistically, ligand promotes VDR association with PBAF to effect genome-wide changes in chromatin accessibility and enhancer landscape, resulting in an anti-inflammatory response. Importantly, pharmacological inhibition of BRD9 promotes PBAF-VDR association to restore β cell function and ameliorate hyperglycemia in murine T2D models. These studies reveal an unrecognized VDR-dependent transcriptional program underpinning β cell survival and identifies the VDR:PBAF/BAF association as a potential therapeutic target for T2D.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Mechanistically, ligand promotes VDR association with PBAF to effect genome-wide changes in chromatin accessibility and enhancer landscape, resulting in an anti-inflammatory response. Importantly, pharmacological inhibition of BRD9 promotes PBAF-VDR association to restore β cell function and ameliorate hyperglycemia in murine T2D models. These studies reveal an unrecognized VDR-dependent transcriptional program underpinning β cell survival and identifies the VDR:PBAF/BAF association as a potential therapeutic target for T2D.	Immunohistochemical staining	Mechanistically, ligand promotes VDR association with PBAF to effect genome-wide changes in chromatin accessibility and enhancer landscape, resulting in an anti-inflammatory response. Importantly, pharmacological inhibition of BRD9 promotes PBAF-VDR association to restore β cell function and ameliorate hyperglycemia in murine T2D models. These studies reveal an unrecognized VDR-dependent transcriptional program underpinning β cell survival and identifies the VDR:PBAF/BAF association as a potential therapeutic target for T2D.		CRISPR screening,RNA-Seq,qPCR,H&E staining,Immunohistochemistry,immunofluorescence,Immunoprecipitation,siRNA knockdown,transfection,shRNA knockdown,FACS analysis,ELISA,Chromatin Immunoprecipitation,ChIP-Seq,ATAC-Seq,Transmission electronic microscopy,LC-MS Analysis,			BRD7,BRD9	CYP27B1	Mechanistically, ligand promotes VDR association with PBAF to effect genome-wide changes in chromatin accessibility and enhancer landscape, resulting in an anti-inflammatory response. Importantly, pharmacological inhibition of BRD9 promotes PBAF-VDR association to restore β cell function and ameliorate hyperglycemia in murine T2D models. These studies reveal an unrecognized VDR-dependent transcriptional program underpinning β cell survival and identifies the VDR:PBAF/BAF association as a potential therapeutic target for T2D.;Mechanistically, ligand promotes VDR association with PBAF to effect genome-wide changes in chromatin accessibility and enhancer landscape, resulting in an anti-inflammatory response. Importantly, pharmacological inhibition of BRD9 promotes PBAF-VDR association to restore β cell function and ameliorate hyperglycemia in murine T2D models. These studies reveal an unrecognized VDR-dependent transcriptional program underpinning β cell survival and identifies the VDR:PBAF/BAF association as a potential therapeutic target for T2D.	Mechanistically, ligand promotes VDR association with PBAF to effect genome-wide changes in chromatin accessibility and enhancer landscape, resulting in an anti-inflammatory response. Importantly, pharmacological inhibition of BRD9 promotes PBAF-VDR association to restore β cell function and ameliorate hyperglycemia in murine T2D models. These studies reveal an unrecognized VDR-dependent transcriptional program underpinning β cell survival and identifies the VDR:PBAF/BAF association as a potential therapeutic target for T2D.
29754779	chr9	134132377	134134377	WDR5	In summary, linc1405 mediates a Eomes/WDR5/GCN5 complex that contributes to cardiogenesis, highlighting the critical roles of lincRNA-based complexes in the epigenetic regulation of cardiogenesis in vitro and in vivo.	human	Epithelial	High+Lowthroughput	A Linc1405/Eomes Complex Promotes Cardiac Mesoderm Specification and Cardiogenesis	否		Other	embryonic stem cell	E_01_0490	PCR,CRISPR,Fluorescence activated cell sorter analysis,Microarray analysis,Chromatin immunoprecipitation,Fluorescent in situ hybridization,Quantitative RT-PCR,Western blot,Immunostaining,RIP assay,RNA immunoprecipitation,Luciferase reporter assay,Co-immunoprecipitation,Echocardiography analysis,Hematoxylin and Eeosin staining,	In summary, linc1405 mediates a Eomes/WDR5/GCN5 complex that contributes to cardiogenesis, highlighting the critical roles of lincRNA-based complexes in the epigenetic regulation of cardiogenesis in vitro and in vivo.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In summary, linc1405 mediates a Eomes/WDR5/GCN5 complex that contributes to cardiogenesis, highlighting the critical roles of lincRNA-based complexes in the epigenetic regulation of cardiogenesis in vitro and in vivo.	Immunohistochemical staining	In summary, linc1405 mediates a Eomes/WDR5/GCN5 complex that contributes to cardiogenesis, highlighting the critical roles of lincRNA-based complexes in the epigenetic regulation of cardiogenesis in vitro and in vivo.		PCR,CRISPR,Fluorescence activated cell sorter analysis,Microarray analysis,Chromatin immunoprecipitation,Fluorescent in situ hybridization,Quantitative RT-PCR,Western blot,Immunostaining,RIP assay,RNA immunoprecipitation,Luciferase reporter assay,Co-immunoprecipitation,Echocardiography analysis,Hematoxylin and Eeosin staining,			WDR5,Mesp1,Eomes		In summary, linc1405 mediates a Eomes/WDR5/GCN5 complex that contributes to cardiogenesis, highlighting the critical roles of lincRNA-based complexes in the epigenetic regulation of cardiogenesis in vitro and in vivo.;In summary, linc1405 mediates a Eomes/WDR5/GCN5 complex that contributes to cardiogenesis, highlighting the critical roles of lincRNA-based complexes in the epigenetic regulation of cardiogenesis in vitro and in vivo.;In summary, linc1405 mediates a Eomes/WDR5/GCN5 complex that contributes to cardiogenesis, highlighting the critical roles of lincRNA-based complexes in the epigenetic regulation of cardiogenesis in vitro and in vivo.	
29754769	chr2	45385835	45387835	SRBD1	It also supports meta-analysis of multiple DNM studies, while adjusting for study-specific technical effects. We applied TADA-A to WGS data of _x0001_300 autism-affected family trios across five studies and discovered several autism risk genes.The software is freely available for all research uses.	human	/	High+Lowthroughput	A Statistical Framework for Mapping Risk Genes from De Novo Mutations in Whole-Genome-Sequencing Studies	否		autism		E_01_0491	WES,WGS,TADA-Annotations(TADA-A),	It also supports meta-analysis of multiple DNM studies, while adjusting for study-specific technical effects. We applied TADA-A to WGS data of _x0001_300 autism-affected family trios across five studies and discovered several autism risk genes.The software is freely available for all research uses.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		It also supports meta-analysis of multiple DNM studies, while adjusting for study-specific technical effects. We applied TADA-A to WGS data of _x0001_300 autism-affected family trios across five studies and discovered several autism risk genes.The software is freely available for all research uses.	Immunohistochemical staining	It also supports meta-analysis of multiple DNM studies, while adjusting for study-specific technical effects. We applied TADA-A to WGS data of _x0001_300 autism-affected family trios across five studies and discovered several autism risk genes.The software is freely available for all research uses.		WES,WGS,TADA-Annotations(TADA-A),			SRBD1		It also supports meta-analysis of multiple DNM studies, while adjusting for study-specific technical effects. We applied TADA-A to WGS data of _x0001_300 autism-affected family trios across five studies and discovered several autism risk genes.The software is freely available for all research uses.	
29751043	chr7	45108269	45110269	Bax	In addition, TUDCA suppressed gentamicin-induced endoplasmic reticulum stress as reflected by inversing the expression levels of Binding immunoglobulin protein (Bip), CCAAT/-enhancer-binding protein homologous protein (CHOP) and Caspase 3. TUDCA attenuated gentamicin-induced hair cell death by inhibiting protein nitration activation and ER stress, providing new insights into the new potential therapies for sensorineural deafness.	mouse	connective	High+Lowthroughput	Tauroursodeoxycholic acid attenuates gentamicin-induced cochlear hair cell death in vitro	否		Other	HEI-OC1 cell	E_01_0492	Quantitative real-time PCR,ELISA,Western blot,Cochlear hair cell staining,	In addition, TUDCA suppressed gentamicin-induced endoplasmic reticulum stress as reflected by inversing the expression levels of Binding immunoglobulin protein (Bip), CCAAT/-enhancer-binding protein homologous protein (CHOP) and Caspase 3. TUDCA attenuated gentamicin-induced hair cell death by inhibiting protein nitration activation and ER stress, providing new insights into the new potential therapies for sensorineural deafness.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In addition, TUDCA suppressed gentamicin-induced endoplasmic reticulum stress as reflected by inversing the expression levels of Binding immunoglobulin protein (Bip), CCAAT/-enhancer-binding protein homologous protein (CHOP) and Caspase 3. TUDCA attenuated gentamicin-induced hair cell death by inhibiting protein nitration activation and ER stress, providing new insights into the new potential therapies for sensorineural deafness.	Immunohistochemical staining	In addition, TUDCA suppressed gentamicin-induced endoplasmic reticulum stress as reflected by inversing the expression levels of Binding immunoglobulin protein (Bip), CCAAT/-enhancer-binding protein homologous protein (CHOP) and Caspase 3. TUDCA attenuated gentamicin-induced hair cell death by inhibiting protein nitration activation and ER stress, providing new insights into the new potential therapies for sensorineural deafness.		Quantitative real-time PCR,ELISA,Western blot,Cochlear hair cell staining,			Bax,Bcl2		In addition, TUDCA suppressed gentamicin-induced endoplasmic reticulum stress as reflected by inversing the expression levels of Binding immunoglobulin protein (Bip), CCAAT/-enhancer-binding protein homologous protein (CHOP) and Caspase 3. TUDCA attenuated gentamicin-induced hair cell death by inhibiting protein nitration activation and ER stress, providing new insights into the new potential therapies for sensorineural deafness.;In addition, TUDCA suppressed gentamicin-induced endoplasmic reticulum stress as reflected by inversing the expression levels of Binding immunoglobulin protein (Bip), CCAAT/-enhancer-binding protein homologous protein (CHOP) and Caspase 3. TUDCA attenuated gentamicin-induced hair cell death by inhibiting protein nitration activation and ER stress, providing new insights into the new potential therapies for sensorineural deafness.	
29750193	chr3	10290270	10292270	SEC13	mEAK-7 knockdown decreases cell proliferation and migration, whereas overexpression of mEAK-7 enhances these cellular effects. Constitutively activated S6K rescues mTOR signaling in mEAK-7-knocked down cells. Thus, mEAK-7 activates an alternative mTOR signaling pathway through S6K2 and 4E-BP1 to regulate cell proliferation and migration.	human	connective	High+Lowthroughput	Mammalian EAK-7 activates alternative mTOR signaling to regulate cell proliferation and migration	否		Other	H1299 cell	E_01_0493	siRNA,transfection,Immunoprecipitation analysis,mmunoblotting,immunofluorescence,	mEAK-7 knockdown decreases cell proliferation and migration, whereas overexpression of mEAK-7 enhances these cellular effects. Constitutively activated S6K rescues mTOR signaling in mEAK-7-knocked down cells. Thus, mEAK-7 activates an alternative mTOR signaling pathway through S6K2 and 4E-BP1 to regulate cell proliferation and migration.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		mEAK-7 knockdown decreases cell proliferation and migration, whereas overexpression of mEAK-7 enhances these cellular effects. Constitutively activated S6K rescues mTOR signaling in mEAK-7-knocked down cells. Thus, mEAK-7 activates an alternative mTOR signaling pathway through S6K2 and 4E-BP1 to regulate cell proliferation and migration.	Immunohistochemical staining	mEAK-7 knockdown decreases cell proliferation and migration, whereas overexpression of mEAK-7 enhances these cellular effects. Constitutively activated S6K rescues mTOR signaling in mEAK-7-knocked down cells. Thus, mEAK-7 activates an alternative mTOR signaling pathway through S6K2 and 4E-BP1 to regulate cell proliferation and migration.		siRNA,transfection,Immunoprecipitation analysis,mmunoblotting,immunofluorescence,			SEC13		mEAK-7 knockdown decreases cell proliferation and migration, whereas overexpression of mEAK-7 enhances these cellular effects. Constitutively activated S6K rescues mTOR signaling in mEAK-7-knocked down cells. Thus, mEAK-7 activates an alternative mTOR signaling pathway through S6K2 and 4E-BP1 to regulate cell proliferation and migration.	
29749927	chr9	63857441	63859441	Smad6	Functional experiments prototypically validated the strongly epigenetically regulated inhibitors of TGFβ family signaling SMAD6 and SMAD7 as regulators of EC quiescence. These data establish the transcriptional and epigenetic landscape of vascular quiescence that will serve as a foundation for further mechanistic studies of vascular homeostasis and disease-associated activation.	mouse	Lung	High+Lowthroughput	The transcriptomic and epigenetic map of vascular quiescence in the continuous lung endothelium	否		Other	HUVECs cell 	E_01_0494	FACS,Immunofluorescence staining,Elisa,Immunoblot,qPCR,RNA-seq,T-WGBS,MassARRAY,Interactome analysis,	Functional experiments prototypically validated the strongly epigenetically regulated inhibitors of TGFβ family signaling SMAD6 and SMAD7 as regulators of EC quiescence. These data establish the transcriptional and epigenetic landscape of vascular quiescence that will serve as a foundation for further mechanistic studies of vascular homeostasis and disease-associated activation.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Functional experiments prototypically validated the strongly epigenetically regulated inhibitors of TGFβ family signaling SMAD6 and SMAD7 as regulators of EC quiescence. These data establish the transcriptional and epigenetic landscape of vascular quiescence that will serve as a foundation for further mechanistic studies of vascular homeostasis and disease-associated activation.	Immunohistochemical staining	Functional experiments prototypically validated the strongly epigenetically regulated inhibitors of TGFβ family signaling SMAD6 and SMAD7 as regulators of EC quiescence. These data establish the transcriptional and epigenetic landscape of vascular quiescence that will serve as a foundation for further mechanistic studies of vascular homeostasis and disease-associated activation.		FACS,Immunofluorescence staining,Elisa,Immunoblot,qPCR,RNA-seq,T-WGBS,MassARRAY,Interactome analysis,			Smad6,Smad7		Functional experiments prototypically validated the strongly epigenetically regulated inhibitors of TGFβ family signaling SMAD6 and SMAD7 as regulators of EC quiescence. These data establish the transcriptional and epigenetic landscape of vascular quiescence that will serve as a foundation for further mechanistic studies of vascular homeostasis and disease-associated activation.;Functional experiments prototypically validated the strongly epigenetically regulated inhibitors of TGFβ family signaling SMAD6 and SMAD7 as regulators of EC quiescence. These data establish the transcriptional and epigenetic landscape of vascular quiescence that will serve as a foundation for further mechanistic studies of vascular homeostasis and disease-associated activation.	
29749529	chr17	44900352	44902352	GFAP	In addition, Golgi fragmentation was observed in the process. On the other hand, it was also demonstrated, in a primary neuronal‑astroglial co‑culture system, that the overexpression of α‑syn significantly decreased the levels of glia‑derived neurotrophic factor (GDNF) and partly inhibited neurite outgrowth. Although direct evidence is currently lacking, it was proposed that dysfunction of the ER‑Golgi compartment in astrocytes overexpressing α‑syn may lead to a decline of GDNF levels, which in turn would suppress neurite outgrowth. Taken together, the results of the present study offer further insights into the pathogenesis of PD from the perspective of astrocytes, which may provide novel strategies for the diagnosis and treatment of PD in the future.	human	connective	High+Lowthroughput	α?synuclein induces apoptosis of astrocytes by causing dysfunction of the endoplasmic reticulum?Golgi compartment	否		Parkinson's disease (PD)	 293FT	E_01_0495	Immunofluorescence,Immunoassay,Western blot, CHOP Knockdown,transfection,Immunostaining,flow cytometry,RNA-seq,siRNA,	In addition, Golgi fragmentation was observed in the process. On the other hand, it was also demonstrated, in a primary neuronal‑astroglial co‑culture system, that the overexpression of α‑syn significantly decreased the levels of glia‑derived neurotrophic factor (GDNF) and partly inhibited neurite outgrowth. Although direct evidence is currently lacking, it was proposed that dysfunction of the ER‑Golgi compartment in astrocytes overexpressing α‑syn may lead to a decline of GDNF levels, which in turn would suppress neurite outgrowth. Taken together, the results of the present study offer further insights into the pathogenesis of PD from the perspective of astrocytes, which may provide novel strategies for the diagnosis and treatment of PD in the future.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In addition, Golgi fragmentation was observed in the process. On the other hand, it was also demonstrated, in a primary neuronal‑astroglial co‑culture system, that the overexpression of α‑syn significantly decreased the levels of glia‑derived neurotrophic factor (GDNF) and partly inhibited neurite outgrowth. Although direct evidence is currently lacking, it was proposed that dysfunction of the ER‑Golgi compartment in astrocytes overexpressing α‑syn may lead to a decline of GDNF levels, which in turn would suppress neurite outgrowth. Taken together, the results of the present study offer further insights into the pathogenesis of PD from the perspective of astrocytes, which may provide novel strategies for the diagnosis and treatment of PD in the future.	Immunohistochemical staining	In addition, Golgi fragmentation was observed in the process. On the other hand, it was also demonstrated, in a primary neuronal‑astroglial co‑culture system, that the overexpression of α‑syn significantly decreased the levels of glia‑derived neurotrophic factor (GDNF) and partly inhibited neurite outgrowth. Although direct evidence is currently lacking, it was proposed that dysfunction of the ER‑Golgi compartment in astrocytes overexpressing α‑syn may lead to a decline of GDNF levels, which in turn would suppress neurite outgrowth. Taken together, the results of the present study offer further insights into the pathogenesis of PD from the perspective of astrocytes, which may provide novel strategies for the diagnosis and treatment of PD in the future.		Immunofluorescence,Immunoassay,Western blot, CHOP Knockdown,transfection,Immunostaining,flow cytometry,RNA-seq,siRNA,			MAP2	GFAP,GDNF	In addition, Golgi fragmentation was observed in the process. On the other hand, it was also demonstrated, in a primary neuronal‑astroglial co‑culture system, that the overexpression of α‑syn significantly decreased the levels of glia‑derived neurotrophic factor (GDNF) and partly inhibited neurite outgrowth. Although direct evidence is currently lacking, it was proposed that dysfunction of the ER‑Golgi compartment in astrocytes overexpressing α‑syn may lead to a decline of GDNF levels, which in turn would suppress neurite outgrowth. Taken together, the results of the present study offer further insights into the pathogenesis of PD from the perspective of astrocytes, which may provide novel strategies for the diagnosis and treatment of PD in the future.	In addition, Golgi fragmentation was observed in the process. On the other hand, it was also demonstrated, in a primary neuronal‑astroglial co‑culture system, that the overexpression of α‑syn significantly decreased the levels of glia‑derived neurotrophic factor (GDNF) and partly inhibited neurite outgrowth. Although direct evidence is currently lacking, it was proposed that dysfunction of the ER‑Golgi compartment in astrocytes overexpressing α‑syn may lead to a decline of GDNF levels, which in turn would suppress neurite outgrowth. Taken together, the results of the present study offer further insights into the pathogenesis of PD from the perspective of astrocytes, which may provide novel strategies for the diagnosis and treatment of PD in the future.;In addition, Golgi fragmentation was observed in the process. On the other hand, it was also demonstrated, in a primary neuronal‑astroglial co‑culture system, that the overexpression of α‑syn significantly decreased the levels of glia‑derived neurotrophic factor (GDNF) and partly inhibited neurite outgrowth. Although direct evidence is currently lacking, it was proposed that dysfunction of the ER‑Golgi compartment in astrocytes overexpressing α‑syn may lead to a decline of GDNF levels, which in turn would suppress neurite outgrowth. Taken together, the results of the present study offer further insights into the pathogenesis of PD from the perspective of astrocytes, which may provide novel strategies for the diagnosis and treatment of PD in the future.
29749465	chrY	2784042	2786042	SRY	In addition, the current findings indicate that there is crosstalk between SOX18 and nuclear factor κ-light-chain-enhancer of activated B cells, which was demonstrated to contribute to MDA-MB231/lymph endothelial intravasation. The present data demonstrate that the endothelial-specific and lymph endothelial-specific transcription factors SOX18 and PROX1 contribute to LEC retraction.	human	Mammary	High+Lowthroughput	12(S)-HETE induces lymph endothelial cell retraction in?vitro by upregulation of SOX18	否		mammary cancer	MDA-MB231 breast cancer cell	E_01_0496	CCID assay,Transfection,RT-qPCR,Western blot,immunofluorescence,	In addition, the current findings indicate that there is crosstalk between SOX18 and nuclear factor κ-light-chain-enhancer of activated B cells, which was demonstrated to contribute to MDA-MB231/lymph endothelial intravasation. The present data demonstrate that the endothelial-specific and lymph endothelial-specific transcription factors SOX18 and PROX1 contribute to LEC retraction.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In addition, the current findings indicate that there is crosstalk between SOX18 and nuclear factor κ-light-chain-enhancer of activated B cells, which was demonstrated to contribute to MDA-MB231/lymph endothelial intravasation. The present data demonstrate that the endothelial-specific and lymph endothelial-specific transcription factors SOX18 and PROX1 contribute to LEC retraction.	Immunohistochemical staining	In addition, the current findings indicate that there is crosstalk between SOX18 and nuclear factor κ-light-chain-enhancer of activated B cells, which was demonstrated to contribute to MDA-MB231/lymph endothelial intravasation. The present data demonstrate that the endothelial-specific and lymph endothelial-specific transcription factors SOX18 and PROX1 contribute to LEC retraction.		CCID assay,Transfection,RT-qPCR,Western blot,immunofluorescence,			PROX1	SRY,SOX18	In addition, the current findings indicate that there is crosstalk between SOX18 and nuclear factor κ-light-chain-enhancer of activated B cells, which was demonstrated to contribute to MDA-MB231/lymph endothelial intravasation. The present data demonstrate that the endothelial-specific and lymph endothelial-specific transcription factors SOX18 and PROX1 contribute to LEC retraction.	In addition, the current findings indicate that there is crosstalk between SOX18 and nuclear factor κ-light-chain-enhancer of activated B cells, which was demonstrated to contribute to MDA-MB231/lymph endothelial intravasation. The present data demonstrate that the endothelial-specific and lymph endothelial-specific transcription factors SOX18 and PROX1 contribute to LEC retraction.;In addition, the current findings indicate that there is crosstalk between SOX18 and nuclear factor κ-light-chain-enhancer of activated B cells, which was demonstrated to contribute to MDA-MB231/lymph endothelial intravasation. The present data demonstrate that the endothelial-specific and lymph endothelial-specific transcription factors SOX18 and PROX1 contribute to LEC retraction.
29749460	chr6	7878754	7880754	TXNDC5	These findings suggested that TXNDC5 functions as an important stress survival factor to maintain tumorigenesis of CRC cells under hypoxia by regulating hypoxia‑induced ROS/ER stress signaling. The present study provided novel insights into the role of TXNDC5 in the tumorigenesis of CRC.	human	Colon	High+Lowthroughput	Role of TXNDC5 in tumorigenesis of colorectal cancer cells: In vivo and in vitro evidence	否		Colorectal cancer (CRC)	rKo cell	E_01_0497	Western blot,RT‑qPCR,Immunohistochemistry,MTT cell proliferation assay,Colony formation assay,Cell apoptosis assay,Transient transfection of small interfering (si)RNA,	These findings suggested that TXNDC5 functions as an important stress survival factor to maintain tumorigenesis of CRC cells under hypoxia by regulating hypoxia‑induced ROS/ER stress signaling. The present study provided novel insights into the role of TXNDC5 in the tumorigenesis of CRC.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		These findings suggested that TXNDC5 functions as an important stress survival factor to maintain tumorigenesis of CRC cells under hypoxia by regulating hypoxia‑induced ROS/ER stress signaling. The present study provided novel insights into the role of TXNDC5 in the tumorigenesis of CRC.	Immunohistochemical staining	These findings suggested that TXNDC5 functions as an important stress survival factor to maintain tumorigenesis of CRC cells under hypoxia by regulating hypoxia‑induced ROS/ER stress signaling. The present study provided novel insights into the role of TXNDC5 in the tumorigenesis of CRC.		Western blot,RT‑qPCR,Immunohistochemistry,MTT cell proliferation assay,Colony formation assay,Cell apoptosis assay,Transient transfection of small interfering (si)RNA,			TXNDC5	ATF4	These findings suggested that TXNDC5 functions as an important stress survival factor to maintain tumorigenesis of CRC cells under hypoxia by regulating hypoxia‑induced ROS/ER stress signaling. The present study provided novel insights into the role of TXNDC5 in the tumorigenesis of CRC.	These findings suggested that TXNDC5 functions as an important stress survival factor to maintain tumorigenesis of CRC cells under hypoxia by regulating hypoxia‑induced ROS/ER stress signaling. The present study provided novel insights into the role of TXNDC5 in the tumorigenesis of CRC.
29749452	chr2	192746411	192748411	PCGEM1	In conclusion, the present study demonstrated a positive regulatory association between MEF2 and PCGEM1, and a reciprocal negative regulatory association between PCGEM1 and miR‑148a that controls cell apoptosis. The present study, therefore, provides new insights into the mechanism of PCGEM1 function in prostate cancer development.	human	Prostate cancer	High+Lowthroughput	MEF2?activated long non?coding RNA PCGEM1 promotes cell proliferation in hormone?refractory prostate cancer through downregulation of miR?148a	否		prostatic cancer	LNCaP	E_01_0498	RT‑qPCR,Western blot,Cell transfection,luciferase reporter assay,Chromatin immunoprecipitation (ChIP) assay,Apoptosis assay,flow cytometry,siRNA,	In conclusion, the present study demonstrated a positive regulatory association between MEF2 and PCGEM1, and a reciprocal negative regulatory association between PCGEM1 and miR‑148a that controls cell apoptosis. The present study, therefore, provides new insights into the mechanism of PCGEM1 function in prostate cancer development.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In conclusion, the present study demonstrated a positive regulatory association between MEF2 and PCGEM1, and a reciprocal negative regulatory association between PCGEM1 and miR‑148a that controls cell apoptosis. The present study, therefore, provides new insights into the mechanism of PCGEM1 function in prostate cancer development.	Immunohistochemical staining	In conclusion, the present study demonstrated a positive regulatory association between MEF2 and PCGEM1, and a reciprocal negative regulatory association between PCGEM1 and miR‑148a that controls cell apoptosis. The present study, therefore, provides new insights into the mechanism of PCGEM1 function in prostate cancer development.		RT‑qPCR,Western blot,Cell transfection,luciferase reporter assay,Chromatin immunoprecipitation (ChIP) assay,Apoptosis assay,flow cytometry,siRNA,			PCGEM1		In conclusion, the present study demonstrated a positive regulatory association between MEF2 and PCGEM1, and a reciprocal negative regulatory association between PCGEM1 and miR‑148a that controls cell apoptosis. The present study, therefore, provides new insights into the mechanism of PCGEM1 function in prostate cancer development.	
29748386	chr5	132437549	132439549	IRF1	In conclusion, although IRF1 can trigger enhanceosome formation independently of STAT1, its ability to do so depends on local chromatin cues.	human	Adrenal	High+Lowthroughput	Frequent interferon regulatory factor 1 (IRF1) binding at remote elements without histone modification	否		Other	SW13 cell	E_01_0499	ChIP–qPCR,qPCR,ChIP,ChIP-chip assays,	In conclusion, although IRF1 can trigger enhanceosome formation independently of STAT1, its ability to do so depends on local chromatin cues.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In conclusion, although IRF1 can trigger enhanceosome formation independently of STAT1, its ability to do so depends on local chromatin cues.	Immunohistochemical staining	In conclusion, although IRF1 can trigger enhanceosome formation independently of STAT1, its ability to do so depends on local chromatin cues.		ChIP–qPCR,qPCR,ChIP,ChIP-chip assays,				IRF1,STAT1,SMARCA4		In conclusion, although IRF1 can trigger enhanceosome formation independently of STAT1, its ability to do so depends on local chromatin cues.;In conclusion, although IRF1 can trigger enhanceosome formation independently of STAT1, its ability to do so depends on local chromatin cues.;In conclusion, although IRF1 can trigger enhanceosome formation independently of STAT1, its ability to do so depends on local chromatin cues.
29748098	chr7	148804691	148806691	EZH2	Increased EZH2 expression is associated with adverse pathologic features and inferior oncologic outcomes in patients with high-grade UTUC. The role of EZH2 biology in UTUC pathogenesis remains to be further elucidated.	human	Epithelial	High+Lowthroughput	Multi-institutional evaluation of the prognostic significance of EZH2 expression in high-grade upper tract urothelial carcinoma	否		Upper urothelial carcinoma (utuc)	epithelial cell	E_01_0500	immunohistochemical staining (IHC),	Increased EZH2 expression is associated with adverse pathologic features and inferior oncologic outcomes in patients with high-grade UTUC. The role of EZH2 biology in UTUC pathogenesis remains to be further elucidated.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Increased EZH2 expression is associated with adverse pathologic features and inferior oncologic outcomes in patients with high-grade UTUC. The role of EZH2 biology in UTUC pathogenesis remains to be further elucidated.	Immunohistochemical staining	Increased EZH2 expression is associated with adverse pathologic features and inferior oncologic outcomes in patients with high-grade UTUC. The role of EZH2 biology in UTUC pathogenesis remains to be further elucidated.		immunohistochemical staining (IHC),				EZH2		Increased EZH2 expression is associated with adverse pathologic features and inferior oncologic outcomes in patients with high-grade UTUC. The role of EZH2 biology in UTUC pathogenesis remains to be further elucidated.
29743187	chr12	100470925	100472925	NR1H4	In summary, NAFLD was characterized by an imbalance in arachidonate metabolism. FXR activation reprogramed arachidonate metabolism by inducing P450 epoxygenase expression and EET production. In vitro, FXR-mediated NF-kB inhibition required active P450 epoxygenases.	human	Liver	High+Lowthroughput	Effects of Farnesoid X Receptor Activation on Arachidonic Acid Metabolism, NF-kB Signaling, and Hepatic Inflammation	否		Non alcoholic fatty liver disease (NAFLD), inflammation	THP-1 cells	E_01_0501	Migration assay,Transient transfection,gene expression analysis,immunostaining,	In summary, NAFLD was characterized by an imbalance in arachidonate metabolism. FXR activation reprogramed arachidonate metabolism by inducing P450 epoxygenase expression and EET production. In vitro, FXR-mediated NF-kB inhibition required active P450 epoxygenases.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In summary, NAFLD was characterized by an imbalance in arachidonate metabolism. FXR activation reprogramed arachidonate metabolism by inducing P450 epoxygenase expression and EET production. In vitro, FXR-mediated NF-kB inhibition required active P450 epoxygenases.	Immunohistochemical staining	In summary, NAFLD was characterized by an imbalance in arachidonate metabolism. FXR activation reprogramed arachidonate metabolism by inducing P450 epoxygenase expression and EET production. In vitro, FXR-mediated NF-kB inhibition required active P450 epoxygenases.		Migration assay,Transient transfection,gene expression analysis,immunostaining,			LTB	NR1H4	In summary, NAFLD was characterized by an imbalance in arachidonate metabolism. FXR activation reprogramed arachidonate metabolism by inducing P450 epoxygenase expression and EET production. In vitro, FXR-mediated NF-kB inhibition required active P450 epoxygenases.	In summary, NAFLD was characterized by an imbalance in arachidonate metabolism. FXR activation reprogramed arachidonate metabolism by inducing P450 epoxygenase expression and EET production. In vitro, FXR-mediated NF-kB inhibition required active P450 epoxygenases.
29742982	chr9	21137636	21139636	Keap1	Nrf2 exerts pleiotropic roles in the thyroid gland to couple cell stress defense mechanisms to iodide metabolism and the thyroid hormone synthesis machinery, both under basal conditions and in response to excess iodide.	mouse	Epithelial	High+Lowthroughput	NFE2-Related Transcription Factor 2 Coordinates Antioxidant Defense with Thyroglobulin Production and Iodination in the Thyroid Gland	否		Other	PCCL3 cell	E_01_0502	real-time PCR,Protein isolation,Western immunoblotting,immunohistochemistry,analysis of protein oxidation,RNA interference,Chromatin immunoprecip,Cell transfections,reporter assay,CRISPR/Cas9,	Nrf2 exerts pleiotropic roles in the thyroid gland to couple cell stress defense mechanisms to iodide metabolism and the thyroid hormone synthesis machinery, both under basal conditions and in response to excess iodide.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Nrf2 exerts pleiotropic roles in the thyroid gland to couple cell stress defense mechanisms to iodide metabolism and the thyroid hormone synthesis machinery, both under basal conditions and in response to excess iodide.	Immunohistochemical staining	Nrf2 exerts pleiotropic roles in the thyroid gland to couple cell stress defense mechanisms to iodide metabolism and the thyroid hormone synthesis machinery, both under basal conditions and in response to excess iodide.		real-time PCR,Protein isolation,Western immunoblotting,immunohistochemistry,analysis of protein oxidation,RNA interference,Chromatin immunoprecip,Cell transfections,reporter assay,CRISPR/Cas9,			Keap1,Tg	NFE2	Nrf2 exerts pleiotropic roles in the thyroid gland to couple cell stress defense mechanisms to iodide metabolism and the thyroid hormone synthesis machinery, both under basal conditions and in response to excess iodide.;Nrf2 exerts pleiotropic roles in the thyroid gland to couple cell stress defense mechanisms to iodide metabolism and the thyroid hormone synthesis machinery, both under basal conditions and in response to excess iodide.	Nrf2 exerts pleiotropic roles in the thyroid gland to couple cell stress defense mechanisms to iodide metabolism and the thyroid hormone synthesis machinery, both under basal conditions and in response to excess iodide.
29740349	chr22	28791734	28793734	XBP1	The levels of p-PI3K(Ser191), p-PI3K(Ser262), p-AKT(Ser473), and p-mTOR were decreased postburn, suggesting that autophagy-related PI3K/AKT/mTOR pathway is involved in the intestinal epithelial barrier dysfunction following severe burn. In summary, severe burn injury induces the ER stress and autophagy in intestinal epithelia, leading to the disruption of intestinal barrier.	human	Epithelial	High+Lowthroughput	Severe Burn-Induced Intestinal Epithelial Barrier Dysfunction Is Associated With Endoplasmic Reticulum Stress and Autophagy in Mice	否		Intestinal barrier dysfunction	epithelial cell	E_01_0503	histological,immunofluorescent,Western blot,Immunofluorescent Staining,Microscopy,Image Analysis,	The levels of p-PI3K(Ser191), p-PI3K(Ser262), p-AKT(Ser473), and p-mTOR were decreased postburn, suggesting that autophagy-related PI3K/AKT/mTOR pathway is involved in the intestinal epithelial barrier dysfunction following severe burn. In summary, severe burn injury induces the ER stress and autophagy in intestinal epithelia, leading to the disruption of intestinal barrier.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The levels of p-PI3K(Ser191), p-PI3K(Ser262), p-AKT(Ser473), and p-mTOR were decreased postburn, suggesting that autophagy-related PI3K/AKT/mTOR pathway is involved in the intestinal epithelial barrier dysfunction following severe burn. In summary, severe burn injury induces the ER stress and autophagy in intestinal epithelia, leading to the disruption of intestinal barrier.	Immunohistochemical staining	The levels of p-PI3K(Ser191), p-PI3K(Ser262), p-AKT(Ser473), and p-mTOR were decreased postburn, suggesting that autophagy-related PI3K/AKT/mTOR pathway is involved in the intestinal epithelial barrier dysfunction following severe burn. In summary, severe burn injury induces the ER stress and autophagy in intestinal epithelia, leading to the disruption of intestinal barrier.		histological,immunofluorescent,Western blot,Immunofluorescent Staining,Microscopy,Image Analysis,			ATG5	XBP1	The levels of p-PI3K(Ser191), p-PI3K(Ser262), p-AKT(Ser473), and p-mTOR were decreased postburn, suggesting that autophagy-related PI3K/AKT/mTOR pathway is involved in the intestinal epithelial barrier dysfunction following severe burn. In summary, severe burn injury induces the ER stress and autophagy in intestinal epithelia, leading to the disruption of intestinal barrier.	The levels of p-PI3K(Ser191), p-PI3K(Ser262), p-AKT(Ser473), and p-mTOR were decreased postburn, suggesting that autophagy-related PI3K/AKT/mTOR pathway is involved in the intestinal epithelial barrier dysfunction following severe burn. In summary, severe burn injury induces the ER stress and autophagy in intestinal epithelia, leading to the disruption of intestinal barrier.
29740122	chr1	150643764	150645764	GOLPH3L	Furthermore, we identify genetic variants affecting expression of 927 enhancers, which we refer to as enhancer expression quantitative loci or eeQTLs. Enhancer expression patterns are consistent across studies, including differentially expressed eRNAs and eeQTLs. Combining eeQTLs with a genome-wide association study of schizophrenia identifies a genetic variant that alters enhancer function and expression of its target gene, GOLPH3L. Our novel approach to analyzing enhancer transcription is adaptable to other large-scale, non-poly-A depleted, RNA-seq studies.	human	Nervous	High+Lowthroughput	Differential activity of transcribed enhancers in the prefrontal cortex of 537 cases with schizophrenia and controls	否		Schizophrenia	neuronal cell	E_01_0504	RNA-seq,Gene co-expression analyses,ATACseq,	Furthermore, we identify genetic variants affecting expression of 927 enhancers, which we refer to as enhancer expression quantitative loci or eeQTLs. Enhancer expression patterns are consistent across studies, including differentially expressed eRNAs and eeQTLs. Combining eeQTLs with a genome-wide association study of schizophrenia identifies a genetic variant that alters enhancer function and expression of its target gene, GOLPH3L. Our novel approach to analyzing enhancer transcription is adaptable to other large-scale, non-poly-A depleted, RNA-seq studies.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Furthermore, we identify genetic variants affecting expression of 927 enhancers, which we refer to as enhancer expression quantitative loci or eeQTLs. Enhancer expression patterns are consistent across studies, including differentially expressed eRNAs and eeQTLs. Combining eeQTLs with a genome-wide association study of schizophrenia identifies a genetic variant that alters enhancer function and expression of its target gene, GOLPH3L. Our novel approach to analyzing enhancer transcription is adaptable to other large-scale, non-poly-A depleted, RNA-seq studies.	Immunohistochemical staining	Furthermore, we identify genetic variants affecting expression of 927 enhancers, which we refer to as enhancer expression quantitative loci or eeQTLs. Enhancer expression patterns are consistent across studies, including differentially expressed eRNAs and eeQTLs. Combining eeQTLs with a genome-wide association study of schizophrenia identifies a genetic variant that alters enhancer function and expression of its target gene, GOLPH3L. Our novel approach to analyzing enhancer transcription is adaptable to other large-scale, non-poly-A depleted, RNA-seq studies.		RNA-seq,Gene co-expression analyses,ATACseq,			GOLPH3L		Furthermore, we identify genetic variants affecting expression of 927 enhancers, which we refer to as enhancer expression quantitative loci or eeQTLs. Enhancer expression patterns are consistent across studies, including differentially expressed eRNAs and eeQTLs. Combining eeQTLs with a genome-wide association study of schizophrenia identifies a genetic variant that alters enhancer function and expression of its target gene, GOLPH3L. Our novel approach to analyzing enhancer transcription is adaptable to other large-scale, non-poly-A depleted, RNA-seq studies.	
29739060	chr1	206764791	206766791	IL10	Our findings suggested a potential role of miR-10a in the inflammatory process underlying atherosclerosis; however, more studies are needed to support these finding.	human	Nervous	High+Lowthroughput	Lower Expression of miR-10a in Coronary Artery Disease and its Association with Pro/Anti-Inflammatory Cytokines	否		Coronary artery disease (CAD), atherosclerosis	peripheral blood mononuclear cell	E_01_0505	Quantitative real-time PCR,ELISA,	Our findings suggested a potential role of miR-10a in the inflammatory process underlying atherosclerosis; however, more studies are needed to support these finding.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Our findings suggested a potential role of miR-10a in the inflammatory process underlying atherosclerosis; however, more studies are needed to support these finding.	Immunohistochemical staining	Our findings suggested a potential role of miR-10a in the inflammatory process underlying atherosclerosis; however, more studies are needed to support these finding.		Quantitative real-time PCR,ELISA,				IL10		Our findings suggested a potential role of miR-10a in the inflammatory process underlying atherosclerosis; however, more studies are needed to support these finding.
29738565	chr4	71739247	71741247	GC	Here we show genome-wide that blocked GBR generally require CHD9 and BRM for GR occupancy in contrast to GBR that are not blocked by Hic-5. Hic-5 blocked GBR are enriched near Hic-5 blocked GR target genes but not near GR target genes that are not blocked by Hic-5. Furthermore blocked GBR are in a closed conformation prior to Hic-5 depletion, and require Hic-5 depletion and glucocorticoid treatment to create an open conformation necessary for GR occupancy. A transcription factor binding motif characteristic of the ETS family was enriched near blocked GBR and blocked genes but not near non-blocked GBR or non-blocked GR target genes. Thus, we identify specific differences in chromatin conformation, chromatin remodeler requirements, and local DNA sequence motifs that contribute to gene-specific actions of transcription factors and coregulators. These findings shed light on mechanisms that contribute to binding site selection by transcription factors, which vary in a cell type-specific manner.	human	Osteosarcoma	High+Lowthroughput	Different chromatin and DNA sequence characteristics define glucocorticoid receptor binding sites that are blocked or not blocked by coregulator Hic-5	否		Other	U2OS osteosarcoma cells 	E_01_0506	siRNA transfection,ChIP,Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq),	Here we show genome-wide that blocked GBR generally require CHD9 and BRM for GR occupancy in contrast to GBR that are not blocked by Hic-5. Hic-5 blocked GBR are enriched near Hic-5 blocked GR target genes but not near GR target genes that are not blocked by Hic-5. Furthermore blocked GBR are in a closed conformation prior to Hic-5 depletion, and require Hic-5 depletion and glucocorticoid treatment to create an open conformation necessary for GR occupancy. A transcription factor binding motif characteristic of the ETS family was enriched near blocked GBR and blocked genes but not near non-blocked GBR or non-blocked GR target genes. Thus, we identify specific differences in chromatin conformation, chromatin remodeler requirements, and local DNA sequence motifs that contribute to gene-specific actions of transcription factors and coregulators. These findings shed light on mechanisms that contribute to binding site selection by transcription factors, which vary in a cell type-specific manner.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Here we show genome-wide that blocked GBR generally require CHD9 and BRM for GR occupancy in contrast to GBR that are not blocked by Hic-5. Hic-5 blocked GBR are enriched near Hic-5 blocked GR target genes but not near GR target genes that are not blocked by Hic-5. Furthermore blocked GBR are in a closed conformation prior to Hic-5 depletion, and require Hic-5 depletion and glucocorticoid treatment to create an open conformation necessary for GR occupancy. A transcription factor binding motif characteristic of the ETS family was enriched near blocked GBR and blocked genes but not near non-blocked GBR or non-blocked GR target genes. Thus, we identify specific differences in chromatin conformation, chromatin remodeler requirements, and local DNA sequence motifs that contribute to gene-specific actions of transcription factors and coregulators. These findings shed light on mechanisms that contribute to binding site selection by transcription factors, which vary in a cell type-specific manner.	Immunohistochemical staining	Here we show genome-wide that blocked GBR generally require CHD9 and BRM for GR occupancy in contrast to GBR that are not blocked by Hic-5. Hic-5 blocked GBR are enriched near Hic-5 blocked GR target genes but not near GR target genes that are not blocked by Hic-5. Furthermore blocked GBR are in a closed conformation prior to Hic-5 depletion, and require Hic-5 depletion and glucocorticoid treatment to create an open conformation necessary for GR occupancy. A transcription factor binding motif characteristic of the ETS family was enriched near blocked GBR and blocked genes but not near non-blocked GBR or non-blocked GR target genes. Thus, we identify specific differences in chromatin conformation, chromatin remodeler requirements, and local DNA sequence motifs that contribute to gene-specific actions of transcription factors and coregulators. These findings shed light on mechanisms that contribute to binding site selection by transcription factors, which vary in a cell type-specific manner.		siRNA transfection,ChIP,Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq),			GC,CHD9		Here we show genome-wide that blocked GBR generally require CHD9 and BRM for GR occupancy in contrast to GBR that are not blocked by Hic-5. Hic-5 blocked GBR are enriched near Hic-5 blocked GR target genes but not near GR target genes that are not blocked by Hic-5. Furthermore blocked GBR are in a closed conformation prior to Hic-5 depletion, and require Hic-5 depletion and glucocorticoid treatment to create an open conformation necessary for GR occupancy. A transcription factor binding motif characteristic of the ETS family was enriched near blocked GBR and blocked genes but not near non-blocked GBR or non-blocked GR target genes. Thus, we identify specific differences in chromatin conformation, chromatin remodeler requirements, and local DNA sequence motifs that contribute to gene-specific actions of transcription factors and coregulators. These findings shed light on mechanisms that contribute to binding site selection by transcription factors, which vary in a cell type-specific manner.;Here we show genome-wide that blocked GBR generally require CHD9 and BRM for GR occupancy in contrast to GBR that are not blocked by Hic-5. Hic-5 blocked GBR are enriched near Hic-5 blocked GR target genes but not near GR target genes that are not blocked by Hic-5. Furthermore blocked GBR are in a closed conformation prior to Hic-5 depletion, and require Hic-5 depletion and glucocorticoid treatment to create an open conformation necessary for GR occupancy. A transcription factor binding motif characteristic of the ETS family was enriched near blocked GBR and blocked genes but not near non-blocked GBR or non-blocked GR target genes. Thus, we identify specific differences in chromatin conformation, chromatin remodeler requirements, and local DNA sequence motifs that contribute to gene-specific actions of transcription factors and coregulators. These findings shed light on mechanisms that contribute to binding site selection by transcription factors, which vary in a cell type-specific manner.	
29738494	chr19	41216765	41218765	AXL	Using the first X-ray structure of the hYAP50⁻71-hTEAD1209⁻426 complex (PDB 3KYS) published in 2010, a protein-protein interaction inhibitors-enriched library (175,000 chemical compounds) was screened against this hydrophobic pocket of TEAD. Four different chemical families have been identified and evaluated using biophysical techniques (thermal shift assay, microscale thermophoresis) and in cellulo assays (luciferase activity in transfected HEK293 cells, RTqPCR in MDA-MB231 cells). A first promising hit with micromolar inhibition in the luciferase gene reporter assay was discovered. This hit also decreased mRNA levels of TEAD target genes.	human	connective	High+Lowthroughput	Toward the Discovery of a Novel Class of YAP?TEAD Interaction Inhibitors by Virtual Screening Approach Targeting YAP?TEAD Protein?Protein Interface	否		cancer	HEK293 cell	E_01_0507	RT-qPCR,luciferase gene reporter assay,Microscale Thermophoresis,	Using the first X-ray structure of the hYAP50⁻71-hTEAD1209⁻426 complex (PDB 3KYS) published in 2010, a protein-protein interaction inhibitors-enriched library (175,000 chemical compounds) was screened against this hydrophobic pocket of TEAD. Four different chemical families have been identified and evaluated using biophysical techniques (thermal shift assay, microscale thermophoresis) and in cellulo assays (luciferase activity in transfected HEK293 cells, RTqPCR in MDA-MB231 cells). A first promising hit with micromolar inhibition in the luciferase gene reporter assay was discovered. This hit also decreased mRNA levels of TEAD target genes.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Using the first X-ray structure of the hYAP50⁻71-hTEAD1209⁻426 complex (PDB 3KYS) published in 2010, a protein-protein interaction inhibitors-enriched library (175,000 chemical compounds) was screened against this hydrophobic pocket of TEAD. Four different chemical families have been identified and evaluated using biophysical techniques (thermal shift assay, microscale thermophoresis) and in cellulo assays (luciferase activity in transfected HEK293 cells, RTqPCR in MDA-MB231 cells). A first promising hit with micromolar inhibition in the luciferase gene reporter assay was discovered. This hit also decreased mRNA levels of TEAD target genes.	Immunohistochemical staining	Using the first X-ray structure of the hYAP50⁻71-hTEAD1209⁻426 complex (PDB 3KYS) published in 2010, a protein-protein interaction inhibitors-enriched library (175,000 chemical compounds) was screened against this hydrophobic pocket of TEAD. Four different chemical families have been identified and evaluated using biophysical techniques (thermal shift assay, microscale thermophoresis) and in cellulo assays (luciferase activity in transfected HEK293 cells, RTqPCR in MDA-MB231 cells). A first promising hit with micromolar inhibition in the luciferase gene reporter assay was discovered. This hit also decreased mRNA levels of TEAD target genes.		RT-qPCR,luciferase gene reporter assay,Microscale Thermophoresis,			AXL		Using the first X-ray structure of the hYAP50⁻71-hTEAD1209⁻426 complex (PDB 3KYS) published in 2010, a protein-protein interaction inhibitors-enriched library (175,000 chemical compounds) was screened against this hydrophobic pocket of TEAD. Four different chemical families have been identified and evaluated using biophysical techniques (thermal shift assay, microscale thermophoresis) and in cellulo assays (luciferase activity in transfected HEK293 cells, RTqPCR in MDA-MB231 cells). A first promising hit with micromolar inhibition in the luciferase gene reporter assay was discovered. This hit also decreased mRNA levels of TEAD target genes.	
29737550	chr7	45108306	45110306	Bax	In-silico analysis revealed new enhancer and silencer motifs for mutant alleles of CASP-3rs4647602 and rs4647610 polymorphisms. In conclusion, placental CASP-3rs4647602 and rs4647610 polymorphisms were not associated with PE. Further studies with higher sample size are necessary to confirm or refute these findings.	mouse	Placental	High+Lowthroughput	The association of the placental CASPASE-3 gene polymorphisms and preeclampsia susceptibility and in-silico analysis	是	rs4647602,rs4647610	Preeclampsia		E_01_0508	PCR-RFLP,Bioinformatics analysis,	In-silico analysis revealed new enhancer and silencer motifs for mutant alleles of CASP-3rs4647602 and rs4647610 polymorphisms. In conclusion, placental CASP-3rs4647602 and rs4647610 polymorphisms were not associated with PE. Further studies with higher sample size are necessary to confirm or refute these findings.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In-silico analysis revealed new enhancer and silencer motifs for mutant alleles of CASP-3rs4647602 and rs4647610 polymorphisms. In conclusion, placental CASP-3rs4647602 and rs4647610 polymorphisms were not associated with PE. Further studies with higher sample size are necessary to confirm or refute these findings.	Immunohistochemical staining	In-silico analysis revealed new enhancer and silencer motifs for mutant alleles of CASP-3rs4647602 and rs4647610 polymorphisms. In conclusion, placental CASP-3rs4647602 and rs4647610 polymorphisms were not associated with PE. Further studies with higher sample size are necessary to confirm or refute these findings.		PCR-RFLP,Bioinformatics analysis,			Bax		In-silico analysis revealed new enhancer and silencer motifs for mutant alleles of CASP-3rs4647602 and rs4647610 polymorphisms. In conclusion, placental CASP-3rs4647602 and rs4647610 polymorphisms were not associated with PE. Further studies with higher sample size are necessary to confirm or refute these findings.	
29736797	chr3	41192441	41194441	CTNNB1	We examined three SN-GPCs by immunohistochemistry and CTNNB1 mutation analysis. All cases expressed nuclear β-catenin. We identified CTNNB1 exon 3 mutations in two analyzable cases. Lymphoid enhancer-binding factor 1 (LEF1), a protein downstream from β-catenin, was also expressed in all cases. Our results further characterized the activation of the Wnt signaling pathway caused by CTNNB1 exon 3 mutation and suggest the utility of LEF1 immunohistochemistry in the differential diagnosis of SN-GPC.	human	/	High+Lowthroughput	β-catenin (CTNNB1) mutation and LEF1 expression in sinonasal glomangiopericytoma (sinonasal-type hemangiopericytoma)	否		Sinonasal tubular cell tumor (sn-gpc)		E_01_0509	Immunohistochemistry,PCR,Sanger sequencing,	We examined three SN-GPCs by immunohistochemistry and CTNNB1 mutation analysis. All cases expressed nuclear β-catenin. We identified CTNNB1 exon 3 mutations in two analyzable cases. Lymphoid enhancer-binding factor 1 (LEF1), a protein downstream from β-catenin, was also expressed in all cases. Our results further characterized the activation of the Wnt signaling pathway caused by CTNNB1 exon 3 mutation and suggest the utility of LEF1 immunohistochemistry in the differential diagnosis of SN-GPC.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We examined three SN-GPCs by immunohistochemistry and CTNNB1 mutation analysis. All cases expressed nuclear β-catenin. We identified CTNNB1 exon 3 mutations in two analyzable cases. Lymphoid enhancer-binding factor 1 (LEF1), a protein downstream from β-catenin, was also expressed in all cases. Our results further characterized the activation of the Wnt signaling pathway caused by CTNNB1 exon 3 mutation and suggest the utility of LEF1 immunohistochemistry in the differential diagnosis of SN-GPC.	Immunohistochemical staining	We examined three SN-GPCs by immunohistochemistry and CTNNB1 mutation analysis. All cases expressed nuclear β-catenin. We identified CTNNB1 exon 3 mutations in two analyzable cases. Lymphoid enhancer-binding factor 1 (LEF1), a protein downstream from β-catenin, was also expressed in all cases. Our results further characterized the activation of the Wnt signaling pathway caused by CTNNB1 exon 3 mutation and suggest the utility of LEF1 immunohistochemistry in the differential diagnosis of SN-GPC.		Immunohistochemistry,PCR,Sanger sequencing,				CTNNB1,LEF1		We examined three SN-GPCs by immunohistochemistry and CTNNB1 mutation analysis. All cases expressed nuclear β-catenin. We identified CTNNB1 exon 3 mutations in two analyzable cases. Lymphoid enhancer-binding factor 1 (LEF1), a protein downstream from β-catenin, was also expressed in all cases. Our results further characterized the activation of the Wnt signaling pathway caused by CTNNB1 exon 3 mutation and suggest the utility of LEF1 immunohistochemistry in the differential diagnosis of SN-GPC.;We examined three SN-GPCs by immunohistochemistry and CTNNB1 mutation analysis. All cases expressed nuclear β-catenin. We identified CTNNB1 exon 3 mutations in two analyzable cases. Lymphoid enhancer-binding factor 1 (LEF1), a protein downstream from β-catenin, was also expressed in all cases. Our results further characterized the activation of the Wnt signaling pathway caused by CTNNB1 exon 3 mutation and suggest the utility of LEF1 immunohistochemistry in the differential diagnosis of SN-GPC.
29736028	chr1	205825403	205827403	PM20D1	We find that PM20D1 is a methylation and expression quantitative trait locus coupled to an AD-risk associated haplotype, which displays enhancer-like characteristics and contacts the PM20D1 promoter via a haplotype-dependent, CCCTC-binding-factor-mediated chromatin loop. Furthermore, PM20D1 is increased following AD-related neurotoxic insults at symptomatic stages in the APP/PS1 mouse model of AD and in human patients with AD who are carriers of the non-risk haplotype. In line, genetically increasing or decreasing the expression of PM20D1 reduces and aggravates AD-related pathologies, respectively. These findings suggest that in a particular genetic background, PM20D1 contributes to neuroprotection against AD.	human	lymphoid	High+Lowthroughput	PM20D1 is a?quantitative trait locus associated with Alzheimer's disease	是	rs708727	Alzheimer's disease (AD)	Immortalized B cells	E_01_0510	GWAS,EWAS,RT–PCR,quantitative real-time PCR,DNA methylation,RNA expression,Chromatin conformation capture (3C) protocol,Chromatin immunoprecipitation (ChIP) assays,Cloning,Immunohistochemistry (IHC),Western blot,Luciferase assays,Cell viability assays,Lentivirus production,Amyloid plaques,Amyloid-β assays,	We find that PM20D1 is a methylation and expression quantitative trait locus coupled to an AD-risk associated haplotype, which displays enhancer-like characteristics and contacts the PM20D1 promoter via a haplotype-dependent, CCCTC-binding-factor-mediated chromatin loop. Furthermore, PM20D1 is increased following AD-related neurotoxic insults at symptomatic stages in the APP/PS1 mouse model of AD and in human patients with AD who are carriers of the non-risk haplotype. In line, genetically increasing or decreasing the expression of PM20D1 reduces and aggravates AD-related pathologies, respectively. These findings suggest that in a particular genetic background, PM20D1 contributes to neuroprotection against AD.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We find that PM20D1 is a methylation and expression quantitative trait locus coupled to an AD-risk associated haplotype, which displays enhancer-like characteristics and contacts the PM20D1 promoter via a haplotype-dependent, CCCTC-binding-factor-mediated chromatin loop. Furthermore, PM20D1 is increased following AD-related neurotoxic insults at symptomatic stages in the APP/PS1 mouse model of AD and in human patients with AD who are carriers of the non-risk haplotype. In line, genetically increasing or decreasing the expression of PM20D1 reduces and aggravates AD-related pathologies, respectively. These findings suggest that in a particular genetic background, PM20D1 contributes to neuroprotection against AD.	Immunohistochemical staining	We find that PM20D1 is a methylation and expression quantitative trait locus coupled to an AD-risk associated haplotype, which displays enhancer-like characteristics and contacts the PM20D1 promoter via a haplotype-dependent, CCCTC-binding-factor-mediated chromatin loop. Furthermore, PM20D1 is increased following AD-related neurotoxic insults at symptomatic stages in the APP/PS1 mouse model of AD and in human patients with AD who are carriers of the non-risk haplotype. In line, genetically increasing or decreasing the expression of PM20D1 reduces and aggravates AD-related pathologies, respectively. These findings suggest that in a particular genetic background, PM20D1 contributes to neuroprotection against AD.		GWAS,EWAS,RT–PCR,quantitative real-time PCR,DNA methylation,RNA expression,Chromatin conformation capture (3C) protocol,Chromatin immunoprecipitation (ChIP) assays,Cloning,Immunohistochemistry (IHC),Western blot,Luciferase assays,Cell viability assays,Lentivirus production,Amyloid plaques,Amyloid-β assays,			PM20D1		We find that PM20D1 is a methylation and expression quantitative trait locus coupled to an AD-risk associated haplotype, which displays enhancer-like characteristics and contacts the PM20D1 promoter via a haplotype-dependent, CCCTC-binding-factor-mediated chromatin loop. Furthermore, PM20D1 is increased following AD-related neurotoxic insults at symptomatic stages in the APP/PS1 mouse model of AD and in human patients with AD who are carriers of the non-risk haplotype. In line, genetically increasing or decreasing the expression of PM20D1 reduces and aggravates AD-related pathologies, respectively. These findings suggest that in a particular genetic background, PM20D1 contributes to neuroprotection against AD.	
29736013	chrX	44870832	44872832	KDM6A	Collectively, our findings identify a dual role for UTX in suppressing acute myeloid leukemia via repression of oncogenic ETS and upregulation of tumor-suppressive GATA programs.	human	connective	High+Lowthroughput	UTX-mediated enhancer and chromatin remodeling suppresses myeloid leukemogenesis through noncatalytic inverse regulation of ETS and GATA programs	否		Acute myeloid leukemia		E_01_0511	PCR,qRT–PCR,cDNA synthesis,Flow cytometry,Protein extraction,immunoblotting,coimmunoprecipitation,Proliferation assays,Plasmids,cloning,Histological analysis of mouse tissue,RNA extraction,RNA-seq,ChIP–seq,ChIP–qPCR,ATAC–seq,Chip–seq,motif analysis,GSEA,data visualization,LC–MS/MS analysis,Exome sequencing,Exome data analysis,	Collectively, our findings identify a dual role for UTX in suppressing acute myeloid leukemia via repression of oncogenic ETS and upregulation of tumor-suppressive GATA programs.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Collectively, our findings identify a dual role for UTX in suppressing acute myeloid leukemia via repression of oncogenic ETS and upregulation of tumor-suppressive GATA programs.	Immunohistochemical staining	Collectively, our findings identify a dual role for UTX in suppressing acute myeloid leukemia via repression of oncogenic ETS and upregulation of tumor-suppressive GATA programs.		PCR,qRT–PCR,cDNA synthesis,Flow cytometry,Protein extraction,immunoblotting,coimmunoprecipitation,Proliferation assays,Plasmids,cloning,Histological analysis of mouse tissue,RNA extraction,RNA-seq,ChIP–seq,ChIP–qPCR,ATAC–seq,Chip–seq,motif analysis,GSEA,data visualization,LC–MS/MS analysis,Exome sequencing,Exome data analysis,			KDM6A		Collectively, our findings identify a dual role for UTX in suppressing acute myeloid leukemia via repression of oncogenic ETS and upregulation of tumor-suppressive GATA programs.	
29735004	chr13	40553262	40555262	FOXO1	EPAC2 knockdown markedly reduced Phe-stimulated C/EBPβ and C/EBPδ mRNA levels, as well as forkhead box O1 (FOXO1) protein levels. These results suggest that EPAC signalling enhances PKA-mediated dPRL expression in ESCs by acting on C/EBP response elements in the promoter region of the gene.	human	Epithelial	High+Lowthroughput	Exchange protein directly activated by cAMP (EPAC) promotes transcriptional activation of the decidual prolactin gene via CCAAT/enhancer-binding protein in human endometrial stromal cells	否		Other	endometrial stromal cell	E_01_0512	Luciferase assay,Treatment with siRNAs,RT-qPCR,Immunoblotting,Immunofluorescence,transfection,	EPAC2 knockdown markedly reduced Phe-stimulated C/EBPβ and C/EBPδ mRNA levels, as well as forkhead box O1 (FOXO1) protein levels. These results suggest that EPAC signalling enhances PKA-mediated dPRL expression in ESCs by acting on C/EBP response elements in the promoter region of the gene.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		EPAC2 knockdown markedly reduced Phe-stimulated C/EBPβ and C/EBPδ mRNA levels, as well as forkhead box O1 (FOXO1) protein levels. These results suggest that EPAC signalling enhances PKA-mediated dPRL expression in ESCs by acting on C/EBP response elements in the promoter region of the gene.	Immunohistochemical staining	EPAC2 knockdown markedly reduced Phe-stimulated C/EBPβ and C/EBPδ mRNA levels, as well as forkhead box O1 (FOXO1) protein levels. These results suggest that EPAC signalling enhances PKA-mediated dPRL expression in ESCs by acting on C/EBP response elements in the promoter region of the gene.		Luciferase assay,Treatment with siRNAs,RT-qPCR,Immunoblotting,Immunofluorescence,transfection,				FOXO1		EPAC2 knockdown markedly reduced Phe-stimulated C/EBPβ and C/EBPδ mRNA levels, as well as forkhead box O1 (FOXO1) protein levels. These results suggest that EPAC signalling enhances PKA-mediated dPRL expression in ESCs by acting on C/EBP response elements in the promoter region of the gene.
29733381	chr6	108557419	108559419	FOXO3	Our functional studies highlighted the importance of the HSF1-FOXO3-SOD2/CAT/GADD45A cascade in cellular stress response and survival by promoting ROS detoxification, redox balance and DNA repair. Our findings suggest the existence of an HSF1-FOXO3 axis in human cells that could be involved in stress response pathways functionally regulating lifespan and disease susceptibility.	human	connective	High+Lowthroughput	The longevity SNP rs2802292 uncovered: HSF1 activates stress-dependent expression of FOXO3 through an intronic enhancer	是	rs2802292	Other		E_01_0513	CRISPR/Cas9,Quantitative real-time PCR,Immunoblotting,Cell transfection,RNA interference,Cloning,ChIP,Luciferase assay,ChIP-loop assay,Cellular glutathione assay,DNA damage assay,Cell proliferation assay,	Our functional studies highlighted the importance of the HSF1-FOXO3-SOD2/CAT/GADD45A cascade in cellular stress response and survival by promoting ROS detoxification, redox balance and DNA repair. Our findings suggest the existence of an HSF1-FOXO3 axis in human cells that could be involved in stress response pathways functionally regulating lifespan and disease susceptibility.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Our functional studies highlighted the importance of the HSF1-FOXO3-SOD2/CAT/GADD45A cascade in cellular stress response and survival by promoting ROS detoxification, redox balance and DNA repair. Our findings suggest the existence of an HSF1-FOXO3 axis in human cells that could be involved in stress response pathways functionally regulating lifespan and disease susceptibility.	Immunohistochemical staining	Our functional studies highlighted the importance of the HSF1-FOXO3-SOD2/CAT/GADD45A cascade in cellular stress response and survival by promoting ROS detoxification, redox balance and DNA repair. Our findings suggest the existence of an HSF1-FOXO3 axis in human cells that could be involved in stress response pathways functionally regulating lifespan and disease susceptibility.		CRISPR/Cas9,Quantitative real-time PCR,Immunoblotting,Cell transfection,RNA interference,Cloning,ChIP,Luciferase assay,ChIP-loop assay,Cellular glutathione assay,DNA damage assay,Cell proliferation assay,			SOD2	FOXO3,HSF1,GADD45A	Our functional studies highlighted the importance of the HSF1-FOXO3-SOD2/CAT/GADD45A cascade in cellular stress response and survival by promoting ROS detoxification, redox balance and DNA repair. Our findings suggest the existence of an HSF1-FOXO3 axis in human cells that could be involved in stress response pathways functionally regulating lifespan and disease susceptibility.	Our functional studies highlighted the importance of the HSF1-FOXO3-SOD2/CAT/GADD45A cascade in cellular stress response and survival by promoting ROS detoxification, redox balance and DNA repair. Our findings suggest the existence of an HSF1-FOXO3 axis in human cells that could be involved in stress response pathways functionally regulating lifespan and disease susceptibility.;Our functional studies highlighted the importance of the HSF1-FOXO3-SOD2/CAT/GADD45A cascade in cellular stress response and survival by promoting ROS detoxification, redox balance and DNA repair. Our findings suggest the existence of an HSF1-FOXO3 axis in human cells that could be involved in stress response pathways functionally regulating lifespan and disease susceptibility.;Our functional studies highlighted the importance of the HSF1-FOXO3-SOD2/CAT/GADD45A cascade in cellular stress response and survival by promoting ROS detoxification, redox balance and DNA repair. Our findings suggest the existence of an HSF1-FOXO3 axis in human cells that could be involved in stress response pathways functionally regulating lifespan and disease susceptibility.
29732557	chr7	148804423	148806423	EZH2	Our results indicate that elevated levels of EZH2 are relevant to CM tumourigenesis and progression, and that EZH2 may become a potential therapeutic target for patients with CM.	human	connective	High+Lowthroughput	Overexpression of EZH2 in conjunctival melanoma offers a new therapeutic target	否		Conjunctival malignant melanoma (CM)		E_01_0514	Immunohistochemistry (IHC) staining,Immunoblotting,Cell proliferation,colony assay,Flow cytometry,RNA isolation,cDNA synthesis,quantitative PCR,	Our results indicate that elevated levels of EZH2 are relevant to CM tumourigenesis and progression, and that EZH2 may become a potential therapeutic target for patients with CM.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Our results indicate that elevated levels of EZH2 are relevant to CM tumourigenesis and progression, and that EZH2 may become a potential therapeutic target for patients with CM.	Immunohistochemical staining	Our results indicate that elevated levels of EZH2 are relevant to CM tumourigenesis and progression, and that EZH2 may become a potential therapeutic target for patients with CM.		Immunohistochemistry (IHC) staining,Immunoblotting,Cell proliferation,colony assay,Flow cytometry,RNA isolation,cDNA synthesis,quantitative PCR,				EZH2,CDKN1A		Our results indicate that elevated levels of EZH2 are relevant to CM tumourigenesis and progression, and that EZH2 may become a potential therapeutic target for patients with CM.;Our results indicate that elevated levels of EZH2 are relevant to CM tumourigenesis and progression, and that EZH2 may become a potential therapeutic target for patients with CM.
29731896	chr20	10635162	10637162	JAG1	Together, these results indicated that miR-124 suppressed gastric cancer progression, partly through inhibiting JAG1 and EZH2. Thus, lentivirus-mediated overexpression of miR-124 may be a potential therapeutic strategy against gastric cancer.	human	Gastric cancer	High+Lowthroughput	Lentivirus-mediated overexpression of miR-124 suppresses growth and invasion by targeting JAG1 and EZH2 in gastric cancer	否		gastric cancer	GC cell	E_01_0515	siRNA transfection,RT‑qPCR,Methylation analysis,Cell proliferation assay,Western blot,Cell migration,cell invasion assays,	Together, these results indicated that miR-124 suppressed gastric cancer progression, partly through inhibiting JAG1 and EZH2. Thus, lentivirus-mediated overexpression of miR-124 may be a potential therapeutic strategy against gastric cancer.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Together, these results indicated that miR-124 suppressed gastric cancer progression, partly through inhibiting JAG1 and EZH2. Thus, lentivirus-mediated overexpression of miR-124 may be a potential therapeutic strategy against gastric cancer.	Immunohistochemical staining	Together, these results indicated that miR-124 suppressed gastric cancer progression, partly through inhibiting JAG1 and EZH2. Thus, lentivirus-mediated overexpression of miR-124 may be a potential therapeutic strategy against gastric cancer.		siRNA transfection,RT‑qPCR,Methylation analysis,Cell proliferation assay,Western blot,Cell migration,cell invasion assays,			JAG1	EZH2	Together, these results indicated that miR-124 suppressed gastric cancer progression, partly through inhibiting JAG1 and EZH2. Thus, lentivirus-mediated overexpression of miR-124 may be a potential therapeutic strategy against gastric cancer.	Together, these results indicated that miR-124 suppressed gastric cancer progression, partly through inhibiting JAG1 and EZH2. Thus, lentivirus-mediated overexpression of miR-124 may be a potential therapeutic strategy against gastric cancer.
29731168	chr8	127791607	127793607	PVT1	Cancer genome sequencing identifies recurrent mutations encompassing the human PVT1 promoter, and genome editing verified that PVT1 promoter mutation promotes cancer cell growth. These results highlight regulatory sequences of lncRNA genes as potential disease-associated DNA elements.	human	connective	High+Lowthroughput	Promoter of lncRNA Gene PVT1 Is a Tumor-Suppressor DNA Boundary Element	否		mammary cancer	HEK293T	E_01_0516	RNA-seq,Rearrangement analysis,Hi-ChIP,UMI-4C,4C-Seq,Luciferase reporter assay,CRISPR/Cas9,4sU-labeling,JQ1 treatment,ChIP,ATAC-seq,Northern blot,Cell growth competition assay,Western blot,qRT-PCR,siRNA,ASO,	Cancer genome sequencing identifies recurrent mutations encompassing the human PVT1 promoter, and genome editing verified that PVT1 promoter mutation promotes cancer cell growth. These results highlight regulatory sequences of lncRNA genes as potential disease-associated DNA elements.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Cancer genome sequencing identifies recurrent mutations encompassing the human PVT1 promoter, and genome editing verified that PVT1 promoter mutation promotes cancer cell growth. These results highlight regulatory sequences of lncRNA genes as potential disease-associated DNA elements.	Immunohistochemical staining	Cancer genome sequencing identifies recurrent mutations encompassing the human PVT1 promoter, and genome editing verified that PVT1 promoter mutation promotes cancer cell growth. These results highlight regulatory sequences of lncRNA genes as potential disease-associated DNA elements.		RNA-seq,Rearrangement analysis,Hi-ChIP,UMI-4C,4C-Seq,Luciferase reporter assay,CRISPR/Cas9,4sU-labeling,JQ1 treatment,ChIP,ATAC-seq,Northern blot,Cell growth competition assay,Western blot,qRT-PCR,siRNA,ASO,			PVT1		Cancer genome sequencing identifies recurrent mutations encompassing the human PVT1 promoter, and genome editing verified that PVT1 promoter mutation promotes cancer cell growth. These results highlight regulatory sequences of lncRNA genes as potential disease-associated DNA elements.	
29730385	chr19	6658582	6660582	TNFSF14	To explore signaling in melanocytes treated with TNFSF14, we performed RNA-seq and found that nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) signaling is activated by TNFSF14. Further, we observed that inhibition of NF-kB effectively blocks the hypopigmentation induced by TNFSF14. We conclude that TNFSF14 inhibits melanogenesis in melanocytes via NF-κB signaling and could be applied in the treatment of cutaneous pigment disorders.	human	Epithelial	High+Lowthroughput	TNFSF14 inhibits melanogenesis via NF-kB signaling in melanocytes	否		Skin pigmentation disturbances	Normal human epidermal melanocytes	E_01_0517	RNA-seq,transfection,RT-qPCR,Cell proliferation assay,Western blot,	To explore signaling in melanocytes treated with TNFSF14, we performed RNA-seq and found that nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) signaling is activated by TNFSF14. Further, we observed that inhibition of NF-kB effectively blocks the hypopigmentation induced by TNFSF14. We conclude that TNFSF14 inhibits melanogenesis in melanocytes via NF-κB signaling and could be applied in the treatment of cutaneous pigment disorders.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		To explore signaling in melanocytes treated with TNFSF14, we performed RNA-seq and found that nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) signaling is activated by TNFSF14. Further, we observed that inhibition of NF-kB effectively blocks the hypopigmentation induced by TNFSF14. We conclude that TNFSF14 inhibits melanogenesis in melanocytes via NF-κB signaling and could be applied in the treatment of cutaneous pigment disorders.	Immunohistochemical staining	To explore signaling in melanocytes treated with TNFSF14, we performed RNA-seq and found that nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) signaling is activated by TNFSF14. Further, we observed that inhibition of NF-kB effectively blocks the hypopigmentation induced by TNFSF14. We conclude that TNFSF14 inhibits melanogenesis in melanocytes via NF-κB signaling and could be applied in the treatment of cutaneous pigment disorders.		RNA-seq,transfection,RT-qPCR,Cell proliferation assay,Western blot,			TNFSF14		To explore signaling in melanocytes treated with TNFSF14, we performed RNA-seq and found that nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) signaling is activated by TNFSF14. Further, we observed that inhibition of NF-kB effectively blocks the hypopigmentation induced by TNFSF14. We conclude that TNFSF14 inhibits melanogenesis in melanocytes via NF-κB signaling and could be applied in the treatment of cutaneous pigment disorders.	
29728367	chr6	43180135	43182135	CUL9	We conclude that our proposed method is potentially useful and is complementary to TWAS and other standard gene- and pathway-based methods.	human		High+Lowthroughput	Integration of Enhancer-Promoter Interactions with GWAS Summary Results Identifies Novel Schizophrenia-Associated Genes and Pathways	是		Schizophrenia (SCZ)	MCF-7 cell	E_01_0518	ChIA-PET,RNA-seq,GWAS,TWAS,	We conclude that our proposed method is potentially useful and is complementary to TWAS and other standard gene- and pathway-based methods.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We conclude that our proposed method is potentially useful and is complementary to TWAS and other standard gene- and pathway-based methods.	Immunohistochemical staining	We conclude that our proposed method is potentially useful and is complementary to TWAS and other standard gene- and pathway-based methods.		ChIA-PET,RNA-seq,GWAS,TWAS,			CUL9,MRPL33		We conclude that our proposed method is potentially useful and is complementary to TWAS and other standard gene- and pathway-based methods.;We conclude that our proposed method is potentially useful and is complementary to TWAS and other standard gene- and pathway-based methods.	
29726894	chr1	56491946	56493946	PLPP3	DNA methylation of a MIR-based enhancer downregulates the expression of PLPP3 and promotes the mineralization of the AV.	human		High+Lowthroughput	DNA methylation of a PLPP3 MIR transposon-based enhancer promotes an osteogenic programme in calcific aortic valve disease	否		Calcific aortic valve disease (cavd)	HEK293T	E_01_0519	Real-time PCR,Western blot,Whole-genome gene expression,DNA methylation,Pyrosequencing,ChIP,Cell Transfection,Luciferase reporter assay,Determination of alkaline phosphatase activity,	DNA methylation of a MIR-based enhancer downregulates the expression of PLPP3 and promotes the mineralization of the AV.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		DNA methylation of a MIR-based enhancer downregulates the expression of PLPP3 and promotes the mineralization of the AV.	Immunohistochemical staining	DNA methylation of a MIR-based enhancer downregulates the expression of PLPP3 and promotes the mineralization of the AV.		Real-time PCR,Western blot,Whole-genome gene expression,DNA methylation,Pyrosequencing,ChIP,Cell Transfection,Luciferase reporter assay,Determination of alkaline phosphatase activity,				PLPP3		DNA methylation of a MIR-based enhancer downregulates the expression of PLPP3 and promotes the mineralization of the AV.
29725441	chr17	28503593	28505593	FOXN1	In conclusion, the present study demonstrated that FOXN1 served major roles in NSCLC proliferation and invasion by directly repressing EZH2 and β-catenin, which suggested that FOXN1 may function as a tumor suppressor in NSCLC.	human	Epithelial	High+Lowthroughput	Forkhead box N1 inhibits the progression of non-small cell lung cancer and serves as a tumor suppressor	否		Non small cell lung cancer (NSCLC)	Normal human bronchial epithelial cell	E_01_0520	Transfection,Western blot,RNA extraction,RT‑qPCR,Invasion assay,MTT,Quantitative chromatin immunoprecipitation (qChIP),Dual‑luciferase reporter assay,	In conclusion, the present study demonstrated that FOXN1 served major roles in NSCLC proliferation and invasion by directly repressing EZH2 and β-catenin, which suggested that FOXN1 may function as a tumor suppressor in NSCLC.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In conclusion, the present study demonstrated that FOXN1 served major roles in NSCLC proliferation and invasion by directly repressing EZH2 and β-catenin, which suggested that FOXN1 may function as a tumor suppressor in NSCLC.	Immunohistochemical staining	In conclusion, the present study demonstrated that FOXN1 served major roles in NSCLC proliferation and invasion by directly repressing EZH2 and β-catenin, which suggested that FOXN1 may function as a tumor suppressor in NSCLC.		Transfection,Western blot,RNA extraction,RT‑qPCR,Invasion assay,MTT,Quantitative chromatin immunoprecipitation (qChIP),Dual‑luciferase reporter assay,			FOXN1	EZH2	In conclusion, the present study demonstrated that FOXN1 served major roles in NSCLC proliferation and invasion by directly repressing EZH2 and β-catenin, which suggested that FOXN1 may function as a tumor suppressor in NSCLC.	In conclusion, the present study demonstrated that FOXN1 served major roles in NSCLC proliferation and invasion by directly repressing EZH2 and β-catenin, which suggested that FOXN1 may function as a tumor suppressor in NSCLC.
29725411	chr7	148804870	148806870	EZH2	The results of the present study suggested that COE prevents migration and invasion by suppressing the EZH2/ROCK1 signaling pathway in NPC cells. On the basis of the results of the present study, COE may be a novel anticancer agent for the treatment of metastasis in NPC.	human	NPC	High+Lowthroughput	Efficacy of extracts of Celastrus orbiculatus in suppressing migration and invasion by inhibiting the EZH2/ROCK1 signaling pathway in human nasopharyngeal carcinoma	否		Nasopharyngeal carcinoma (NPC)	human NPC cell line 5-8F	E_01_0521	Western blot,flow cytometry,MTS cytotoxicity assay,RT‑qPCR,	The results of the present study suggested that COE prevents migration and invasion by suppressing the EZH2/ROCK1 signaling pathway in NPC cells. On the basis of the results of the present study, COE may be a novel anticancer agent for the treatment of metastasis in NPC.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The results of the present study suggested that COE prevents migration and invasion by suppressing the EZH2/ROCK1 signaling pathway in NPC cells. On the basis of the results of the present study, COE may be a novel anticancer agent for the treatment of metastasis in NPC.	Immunohistochemical staining	The results of the present study suggested that COE prevents migration and invasion by suppressing the EZH2/ROCK1 signaling pathway in NPC cells. On the basis of the results of the present study, COE may be a novel anticancer agent for the treatment of metastasis in NPC.		Western blot,flow cytometry,MTS cytotoxicity assay,RT‑qPCR,			ROCK1	EZH2	The results of the present study suggested that COE prevents migration and invasion by suppressing the EZH2/ROCK1 signaling pathway in NPC cells. On the basis of the results of the present study, COE may be a novel anticancer agent for the treatment of metastasis in NPC.	The results of the present study suggested that COE prevents migration and invasion by suppressing the EZH2/ROCK1 signaling pathway in NPC cells. On the basis of the results of the present study, COE may be a novel anticancer agent for the treatment of metastasis in NPC.
29725368	chr7	45108303	45110303	Bax	In the present study, diabetes complicated by MI promoted ST-segment elevation and myocardial apoptosis, increased infarct size, induced pathological changes and elevated LVEDP, CK-MB, cTnT, GRP78, CHOP, Bax, Ero1α, Ero1β and PDI; however, it decreased heart rate, LVSP and Bcl-2. Additionally, high glucose combined with hypoxic treatment reduced cell viability, induced cell cycle arrest at G1 phase, promoted cell apoptosis, and activated the GRP78/CHOP and Ero1/PDI signaling pathways, which were reversed by CHOP knockdown. Thus, CHOP may be an effective therapeutic target for the treatment of diabetes complicated by MI.	mouse	Myocardial	High+Lowthroughput	CCAAT/enhancer binding protein homologous protein knockdown alleviates hypoxia-induced myocardial injury in rat cardiomyocytes exposed to high glucose	否		Diabetes complicating myocardial infarction	H9c2 cell	E_01_0522	H&E staining,TUNEL assay,Western blot,ELISA,Triphenyltetrazolium chloride (TTC) staining,Hoechst 33258 staining,Cell Counting Kit‑8 (CCK‑8) assay,	In the present study, diabetes complicated by MI promoted ST-segment elevation and myocardial apoptosis, increased infarct size, induced pathological changes and elevated LVEDP, CK-MB, cTnT, GRP78, CHOP, Bax, Ero1α, Ero1β and PDI; however, it decreased heart rate, LVSP and Bcl-2. Additionally, high glucose combined with hypoxic treatment reduced cell viability, induced cell cycle arrest at G1 phase, promoted cell apoptosis, and activated the GRP78/CHOP and Ero1/PDI signaling pathways, which were reversed by CHOP knockdown. Thus, CHOP may be an effective therapeutic target for the treatment of diabetes complicated by MI.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		In the present study, diabetes complicated by MI promoted ST-segment elevation and myocardial apoptosis, increased infarct size, induced pathological changes and elevated LVEDP, CK-MB, cTnT, GRP78, CHOP, Bax, Ero1α, Ero1β and PDI; however, it decreased heart rate, LVSP and Bcl-2. Additionally, high glucose combined with hypoxic treatment reduced cell viability, induced cell cycle arrest at G1 phase, promoted cell apoptosis, and activated the GRP78/CHOP and Ero1/PDI signaling pathways, which were reversed by CHOP knockdown. Thus, CHOP may be an effective therapeutic target for the treatment of diabetes complicated by MI.	Immunohistochemical staining	In the present study, diabetes complicated by MI promoted ST-segment elevation and myocardial apoptosis, increased infarct size, induced pathological changes and elevated LVEDP, CK-MB, cTnT, GRP78, CHOP, Bax, Ero1α, Ero1β and PDI; however, it decreased heart rate, LVSP and Bcl-2. Additionally, high glucose combined with hypoxic treatment reduced cell viability, induced cell cycle arrest at G1 phase, promoted cell apoptosis, and activated the GRP78/CHOP and Ero1/PDI signaling pathways, which were reversed by CHOP knockdown. Thus, CHOP may be an effective therapeutic target for the treatment of diabetes complicated by MI.		H&E staining,TUNEL assay,Western blot,ELISA,Triphenyltetrazolium chloride (TTC) staining,Hoechst 33258 staining,Cell Counting Kit‑8 (CCK‑8) assay,			Bax		In the present study, diabetes complicated by MI promoted ST-segment elevation and myocardial apoptosis, increased infarct size, induced pathological changes and elevated LVEDP, CK-MB, cTnT, GRP78, CHOP, Bax, Ero1α, Ero1β and PDI; however, it decreased heart rate, LVSP and Bcl-2. Additionally, high glucose combined with hypoxic treatment reduced cell viability, induced cell cycle arrest at G1 phase, promoted cell apoptosis, and activated the GRP78/CHOP and Ero1/PDI signaling pathways, which were reversed by CHOP knockdown. Thus, CHOP may be an effective therapeutic target for the treatment of diabetes complicated by MI.	
29725115	chr8	17024798	17026798	MICU3	We here investigate the role of MICU3, an EF-hand containing protein expressed at high levels, especially in brain. We show that MICU3 forms a disulfide bond-mediated dimer with MICU1, but not with MICU2, and it acts as enhancer of MCU-dependent mitochondrial Ca2+ uptake. Silencing of MICU3 in primary cortical neurons impairs Ca2+ signals elicited by synaptic activity, thus suggesting a specific role in regulating neuronal function.	human	connective	High+Lowthroughput	MICU3 is a tissue-specific enhancer of mitochondrial calcium uptake	否		Other		E_01_0523	transfection,Co-immunoprecipitation,Aequorin measurements,SDS-PAGE,western blot,RNA extraction,reverse transcription PCR,quantitative real-time PCR,RNA-seq,bioinformatics,	We here investigate the role of MICU3, an EF-hand containing protein expressed at high levels, especially in brain. We show that MICU3 forms a disulfide bond-mediated dimer with MICU1, but not with MICU2, and it acts as enhancer of MCU-dependent mitochondrial Ca2+ uptake. Silencing of MICU3 in primary cortical neurons impairs Ca2+ signals elicited by synaptic activity, thus suggesting a specific role in regulating neuronal function.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We here investigate the role of MICU3, an EF-hand containing protein expressed at high levels, especially in brain. We show that MICU3 forms a disulfide bond-mediated dimer with MICU1, but not with MICU2, and it acts as enhancer of MCU-dependent mitochondrial Ca2+ uptake. Silencing of MICU3 in primary cortical neurons impairs Ca2+ signals elicited by synaptic activity, thus suggesting a specific role in regulating neuronal function.	Immunohistochemical staining	We here investigate the role of MICU3, an EF-hand containing protein expressed at high levels, especially in brain. We show that MICU3 forms a disulfide bond-mediated dimer with MICU1, but not with MICU2, and it acts as enhancer of MCU-dependent mitochondrial Ca2+ uptake. Silencing of MICU3 in primary cortical neurons impairs Ca2+ signals elicited by synaptic activity, thus suggesting a specific role in regulating neuronal function.		transfection,Co-immunoprecipitation,Aequorin measurements,SDS-PAGE,western blot,RNA extraction,reverse transcription PCR,quantitative real-time PCR,RNA-seq,bioinformatics,			MICU3,MICU1,MICU2		We here investigate the role of MICU3, an EF-hand containing protein expressed at high levels, especially in brain. We show that MICU3 forms a disulfide bond-mediated dimer with MICU1, but not with MICU2, and it acts as enhancer of MCU-dependent mitochondrial Ca2+ uptake. Silencing of MICU3 in primary cortical neurons impairs Ca2+ signals elicited by synaptic activity, thus suggesting a specific role in regulating neuronal function.;We here investigate the role of MICU3, an EF-hand containing protein expressed at high levels, especially in brain. We show that MICU3 forms a disulfide bond-mediated dimer with MICU1, but not with MICU2, and it acts as enhancer of MCU-dependent mitochondrial Ca2+ uptake. Silencing of MICU3 in primary cortical neurons impairs Ca2+ signals elicited by synaptic activity, thus suggesting a specific role in regulating neuronal function.;We here investigate the role of MICU3, an EF-hand containing protein expressed at high levels, especially in brain. We show that MICU3 forms a disulfide bond-mediated dimer with MICU1, but not with MICU2, and it acts as enhancer of MCU-dependent mitochondrial Ca2+ uptake. Silencing of MICU3 in primary cortical neurons impairs Ca2+ signals elicited by synaptic activity, thus suggesting a specific role in regulating neuronal function.	
29721194	chr10	32265166	32267166	EPC1	Involvement of the PHF1 gene in chromosomal rearrangements targeting band 6p21 has been found in LG-ESS with different partners from JAZF1 mapping in 7p15, to EPC1 from 10p11, MEAF6 from 1p34, and BRD8 from 5q31.In the present study, RNA sequencing of a LG-ESS showed a novel recombination of PHF1 with the Enhancer of Polycomb homolog 2 (EPC2). RT-PCR followed by Sanger sequencing and FISH analysis confirmed the EPC2-PHF1 fusion transcript.	human		High+Lowthroughput	Identification of an EPC2-PHF1 fusion transcript in low-grade endometrial stromal sarcoma	否		Endometrial stromal sarcoma (lg-ess)		E_01_0524	Fluorescence in situ hybridization (FISH),Molecular genetic analyses,PCR,RT-PCR,RNA-seq,	Involvement of the PHF1 gene in chromosomal rearrangements targeting band 6p21 has been found in LG-ESS with different partners from JAZF1 mapping in 7p15, to EPC1 from 10p11, MEAF6 from 1p34, and BRD8 from 5q31.In the present study, RNA sequencing of a LG-ESS showed a novel recombination of PHF1 with the Enhancer of Polycomb homolog 2 (EPC2). RT-PCR followed by Sanger sequencing and FISH analysis confirmed the EPC2-PHF1 fusion transcript.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Involvement of the PHF1 gene in chromosomal rearrangements targeting band 6p21 has been found in LG-ESS with different partners from JAZF1 mapping in 7p15, to EPC1 from 10p11, MEAF6 from 1p34, and BRD8 from 5q31.In the present study, RNA sequencing of a LG-ESS showed a novel recombination of PHF1 with the Enhancer of Polycomb homolog 2 (EPC2). RT-PCR followed by Sanger sequencing and FISH analysis confirmed the EPC2-PHF1 fusion transcript.	Immunohistochemical staining	Involvement of the PHF1 gene in chromosomal rearrangements targeting band 6p21 has been found in LG-ESS with different partners from JAZF1 mapping in 7p15, to EPC1 from 10p11, MEAF6 from 1p34, and BRD8 from 5q31.In the present study, RNA sequencing of a LG-ESS showed a novel recombination of PHF1 with the Enhancer of Polycomb homolog 2 (EPC2). RT-PCR followed by Sanger sequencing and FISH analysis confirmed the EPC2-PHF1 fusion transcript.		Fluorescence in situ hybridization (FISH),Molecular genetic analyses,PCR,RT-PCR,RNA-seq,			EPC1,EPC2,PHF1,JAZF1,MEAF6,BRD8		Involvement of the PHF1 gene in chromosomal rearrangements targeting band 6p21 has been found in LG-ESS with different partners from JAZF1 mapping in 7p15, to EPC1 from 10p11, MEAF6 from 1p34, and BRD8 from 5q31.In the present study, RNA sequencing of a LG-ESS showed a novel recombination of PHF1 with the Enhancer of Polycomb homolog 2 (EPC2). RT-PCR followed by Sanger sequencing and FISH analysis confirmed the EPC2-PHF1 fusion transcript.;Involvement of the PHF1 gene in chromosomal rearrangements targeting band 6p21 has been found in LG-ESS with different partners from JAZF1 mapping in 7p15, to EPC1 from 10p11, MEAF6 from 1p34, and BRD8 from 5q31.In the present study, RNA sequencing of a LG-ESS showed a novel recombination of PHF1 with the Enhancer of Polycomb homolog 2 (EPC2). RT-PCR followed by Sanger sequencing and FISH analysis confirmed the EPC2-PHF1 fusion transcript.;Involvement of the PHF1 gene in chromosomal rearrangements targeting band 6p21 has been found in LG-ESS with different partners from JAZF1 mapping in 7p15, to EPC1 from 10p11, MEAF6 from 1p34, and BRD8 from 5q31.In the present study, RNA sequencing of a LG-ESS showed a novel recombination of PHF1 with the Enhancer of Polycomb homolog 2 (EPC2). RT-PCR followed by Sanger sequencing and FISH analysis confirmed the EPC2-PHF1 fusion transcript.;Involvement of the PHF1 gene in chromosomal rearrangements targeting band 6p21 has been found in LG-ESS with different partners from JAZF1 mapping in 7p15, to EPC1 from 10p11, MEAF6 from 1p34, and BRD8 from 5q31.In the present study, RNA sequencing of a LG-ESS showed a novel recombination of PHF1 with the Enhancer of Polycomb homolog 2 (EPC2). RT-PCR followed by Sanger sequencing and FISH analysis confirmed the EPC2-PHF1 fusion transcript.;Involvement of the PHF1 gene in chromosomal rearrangements targeting band 6p21 has been found in LG-ESS with different partners from JAZF1 mapping in 7p15, to EPC1 from 10p11, MEAF6 from 1p34, and BRD8 from 5q31.In the present study, RNA sequencing of a LG-ESS showed a novel recombination of PHF1 with the Enhancer of Polycomb homolog 2 (EPC2). RT-PCR followed by Sanger sequencing and FISH analysis confirmed the EPC2-PHF1 fusion transcript.;Involvement of the PHF1 gene in chromosomal rearrangements targeting band 6p21 has been found in LG-ESS with different partners from JAZF1 mapping in 7p15, to EPC1 from 10p11, MEAF6 from 1p34, and BRD8 from 5q31.In the present study, RNA sequencing of a LG-ESS showed a novel recombination of PHF1 with the Enhancer of Polycomb homolog 2 (EPC2). RT-PCR followed by Sanger sequencing and FISH analysis confirmed the EPC2-PHF1 fusion transcript.	
29720835	chr10	88951288	88953288	FAS	PE and GE efficiently inhibited adipocyte differentiation by suppressing the expression of adipogenic transcription factor CEBP-α and PPAR-γ.PE and GE significantly decreased the expression of adipogenic enzyme FAS.PE and GE increased the expression of lipid degrading enzyme HSL.Mixture of PE and GE exhibited additive or moderately synergistic effect on adipocyte differentiation and lipid accumulation. 	human	adipose	High+Lowthroughput	Combination of Garcinia cambogia Extract and Pear Pomace Extract Additively Suppresses Adipogenesis and Enhances Lipolysis in 3T3-L1 Cells	否		Obesity, diabetes, hypertension, atherosclerosis, cancer	3T3-L1 cell	E_01_0525	MTS‑PMS assay,Oil Red O staining,Immunocytochemistry,	PE and GE efficiently inhibited adipocyte differentiation by suppressing the expression of adipogenic transcription factor CEBP-α and PPAR-γ.PE and GE significantly decreased the expression of adipogenic enzyme FAS.PE and GE increased the expression of lipid degrading enzyme HSL.Mixture of PE and GE exhibited additive or moderately synergistic effect on adipocyte differentiation and lipid accumulation. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		PE and GE efficiently inhibited adipocyte differentiation by suppressing the expression of adipogenic transcription factor CEBP-α and PPAR-γ.PE and GE significantly decreased the expression of adipogenic enzyme FAS.PE and GE increased the expression of lipid degrading enzyme HSL.Mixture of PE and GE exhibited additive or moderately synergistic effect on adipocyte differentiation and lipid accumulation. 	Immunohistochemical staining	PE and GE efficiently inhibited adipocyte differentiation by suppressing the expression of adipogenic transcription factor CEBP-α and PPAR-γ.PE and GE significantly decreased the expression of adipogenic enzyme FAS.PE and GE increased the expression of lipid degrading enzyme HSL.Mixture of PE and GE exhibited additive or moderately synergistic effect on adipocyte differentiation and lipid accumulation. 		MTS‑PMS assay,Oil Red O staining,Immunocytochemistry,				FAS		PE and GE efficiently inhibited adipocyte differentiation by suppressing the expression of adipogenic transcription factor CEBP-α and PPAR-γ.PE and GE significantly decreased the expression of adipogenic enzyme FAS.PE and GE increased the expression of lipid degrading enzyme HSL.Mixture of PE and GE exhibited additive or moderately synergistic effect on adipocyte differentiation and lipid accumulation. 
29719267	chr17	43751286	43753286	SOST	We demonstrate significant enrichment of common variants associated with orofacial clefting in enhancers active early in embryonic development, while those associated with normal facial variation are enriched near the end of the embryonic period. 	human	Embryonic craniofacial	High+Lowthroughput	High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development	否		Cleft lip, cleft palate	cranial neural crest cell	E_01_0526	ChIP-Seq,ChIP	We demonstrate significant enrichment of common variants associated with orofacial clefting in enhancers active early in embryonic development, while those associated with normal facial variation are enriched near the end of the embryonic period. 	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We demonstrate significant enrichment of common variants associated with orofacial clefting in enhancers active early in embryonic development, while those associated with normal facial variation are enriched near the end of the embryonic period. 	Immunohistochemical staining	We demonstrate significant enrichment of common variants associated with orofacial clefting in enhancers active early in embryonic development, while those associated with normal facial variation are enriched near the end of the embryonic period. 		ChIP-Seq,ChIP			SOST,PRDM16	SOX9,MYC	We demonstrate significant enrichment of common variants associated with orofacial clefting in enhancers active early in embryonic development, while those associated with normal facial variation are enriched near the end of the embryonic period. ;We demonstrate significant enrichment of common variants associated with orofacial clefting in enhancers active early in embryonic development, while those associated with normal facial variation are enriched near the end of the embryonic period. 	We demonstrate significant enrichment of common variants associated with orofacial clefting in enhancers active early in embryonic development, while those associated with normal facial variation are enriched near the end of the embryonic period. ;We demonstrate significant enrichment of common variants associated with orofacial clefting in enhancers active early in embryonic development, while those associated with normal facial variation are enriched near the end of the embryonic period. 
29714661	chr5	88714300	88716300	MEF2C	Our study provides novel insight into the regulation mechanism of MIG6 and suggests potential implications for the therapeutic strategies of gefitinib resistance through inhibiting MEF2C in hepatic cancer cells.	human	Liver cancer	High+Lowthroughput	MEF2C promotes gefitinib resistance in hepatic cancer cells through regulating MIG6 transcription	否		liver cancer	Hepatic cancer cell lines PHCC 	E_01_0527	 MEF2C knockdown,Chromatin immunoprecipitation assay,Dual luciferase assay,Western blot,Real-time quantitative PCR,CCK-8 method,	Our study provides novel insight into the regulation mechanism of MIG6 and suggests potential implications for the therapeutic strategies of gefitinib resistance through inhibiting MEF2C in hepatic cancer cells.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Our study provides novel insight into the regulation mechanism of MIG6 and suggests potential implications for the therapeutic strategies of gefitinib resistance through inhibiting MEF2C in hepatic cancer cells.	Immunohistochemical staining	Our study provides novel insight into the regulation mechanism of MIG6 and suggests potential implications for the therapeutic strategies of gefitinib resistance through inhibiting MEF2C in hepatic cancer cells.		 MEF2C knockdown,Chromatin immunoprecipitation assay,Dual luciferase assay,Western blot,Real-time quantitative PCR,CCK-8 method,				MEF2C,EGFR		Our study provides novel insight into the regulation mechanism of MIG6 and suggests potential implications for the therapeutic strategies of gefitinib resistance through inhibiting MEF2C in hepatic cancer cells.;Our study provides novel insight into the regulation mechanism of MIG6 and suggests potential implications for the therapeutic strategies of gefitinib resistance through inhibiting MEF2C in hepatic cancer cells.
29714127	chr14	104767057	104769057	AKT1	The present study is a novel finding of the possible role of AKT1 mutations which might help to identify gastric cancer patients.	human		High+Lowthroughput	Novel AKT1 mutations associated with cell-cycle abnormalities in gastric carcinoma	否		gastric cancer	gastric cancer cell	E_01_0528	PCR,cell-cycle analysis	The present study is a novel finding of the possible role of AKT1 mutations which might help to identify gastric cancer patients.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The present study is a novel finding of the possible role of AKT1 mutations which might help to identify gastric cancer patients.	Immunohistochemical staining	The present study is a novel finding of the possible role of AKT1 mutations which might help to identify gastric cancer patients.		PCR,cell-cycle analysis				AKT1		The present study is a novel finding of the possible role of AKT1 mutations which might help to identify gastric cancer patients.
29710537	chr7	148804458	148806458	EZH2	These results demonstrated that the hsa_circ_0071589/miR-600/EZH2 axis may play critical regulatory roles in the pathogenesis of CRC and may serve as a novel therapy target in CRC.	human	Colon	High+Lowthroughput	Hsa_circ_0071589 promotes carcinogenesis via the miR-600/EZH2 axis in colorectal cancer	否		Colorectal cancer (CRC)	colon cancer cell line HCT116	E_01_0529	Cell transfection, reverse transcription PCR,quantitative real-time PCR(qRT-PCR),wound-healing assay,Colony formation assay,Cell viability assay (MTT assay),Western blot,Plasmid construction,Dual luciferase activity assay,RNA immunoprecipitation (RIP) assay,	These results demonstrated that the hsa_circ_0071589/miR-600/EZH2 axis may play critical regulatory roles in the pathogenesis of CRC and may serve as a novel therapy target in CRC.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		These results demonstrated that the hsa_circ_0071589/miR-600/EZH2 axis may play critical regulatory roles in the pathogenesis of CRC and may serve as a novel therapy target in CRC.	Immunohistochemical staining	These results demonstrated that the hsa_circ_0071589/miR-600/EZH2 axis may play critical regulatory roles in the pathogenesis of CRC and may serve as a novel therapy target in CRC.		Cell transfection, reverse transcription PCR,quantitative real-time PCR(qRT-PCR),wound-healing assay,Colony formation assay,Cell viability assay (MTT assay),Western blot,Plasmid construction,Dual luciferase activity assay,RNA immunoprecipitation (RIP) assay,				EZH2		These results demonstrated that the hsa_circ_0071589/miR-600/EZH2 axis may play critical regulatory roles in the pathogenesis of CRC and may serve as a novel therapy target in CRC.
29710475	chr1	60862803	60864803	NFIA	miR-200c repressed HBV replication by directly targeting NFIA, which might provide a novel therapeutic target for HBV infection.	human		High+Lowthroughput	miR-200c targets nuclear factor IA to suppress HBV replication and gene expression via repressing HBV Enhancer I activity	否		Hepatitis B virus (HBV) chronic infection, cirrhosis, hepatocellular carcinoma	293T cell	E_01_0530	qRT-PCR,Western blot,Dual-Luciferase Reporter assay,ELISA,qRCR,	miR-200c repressed HBV replication by directly targeting NFIA, which might provide a novel therapeutic target for HBV infection.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		miR-200c repressed HBV replication by directly targeting NFIA, which might provide a novel therapeutic target for HBV infection.	Immunohistochemical staining	miR-200c repressed HBV replication by directly targeting NFIA, which might provide a novel therapeutic target for HBV infection.		qRT-PCR,Western blot,Dual-Luciferase Reporter assay,ELISA,qRCR,				NFIA		miR-200c repressed HBV replication by directly targeting NFIA, which might provide a novel therapeutic target for HBV infection.
29709906	chr8	81476346	81478346	FABP4	DBM significantly increased the translocation of nuclear factor (erythroid-derived 2)-like 2(Nrf2) into the nucleus, promoting the protein expression of its target gene, heme oxygenase-1 (HO-1). DBM significantly suppressed the insulin-mediated activation of phosphoinositide 3-kinase (PI3K) and protein kinase B (Akt), which are components of insulin signaling. In addition, intracellular ROS production was effectively reduced by DBM treatment, which upregulated antioxidant genes such as glutathione peroxidase (Gpx), catalase (CAT), and superoxide dismutase 1 (SOD1). Furthermore, DBM significantly regulated the expression of the adipokines, resistin and adiponectin. This DBM-mediated regulation of lipid accumulation, ROS production, and adipokine production was shown to be involved in the regulation of the Nrf2 and insulin signaling.	human	adipose	High+Lowthroughput	Dibenzoylmethane Suppresses Lipid Accumulation and Reactive Oxygen Species Production through Regulation of Nuclear Factor (Erythroid-Derived 2)-Like 2 and Insulin Signaling in Adipocytes	否		Other	3T3-L1 preadipocytes	E_01_0531	ORO Staining,Western Blot,MTT Assay,Real Time PCR,immunoblotting,	DBM significantly increased the translocation of nuclear factor (erythroid-derived 2)-like 2(Nrf2) into the nucleus, promoting the protein expression of its target gene, heme oxygenase-1 (HO-1). DBM significantly suppressed the insulin-mediated activation of phosphoinositide 3-kinase (PI3K) and protein kinase B (Akt), which are components of insulin signaling. In addition, intracellular ROS production was effectively reduced by DBM treatment, which upregulated antioxidant genes such as glutathione peroxidase (Gpx), catalase (CAT), and superoxide dismutase 1 (SOD1). Furthermore, DBM significantly regulated the expression of the adipokines, resistin and adiponectin. This DBM-mediated regulation of lipid accumulation, ROS production, and adipokine production was shown to be involved in the regulation of the Nrf2 and insulin signaling.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		DBM significantly increased the translocation of nuclear factor (erythroid-derived 2)-like 2(Nrf2) into the nucleus, promoting the protein expression of its target gene, heme oxygenase-1 (HO-1). DBM significantly suppressed the insulin-mediated activation of phosphoinositide 3-kinase (PI3K) and protein kinase B (Akt), which are components of insulin signaling. In addition, intracellular ROS production was effectively reduced by DBM treatment, which upregulated antioxidant genes such as glutathione peroxidase (Gpx), catalase (CAT), and superoxide dismutase 1 (SOD1). Furthermore, DBM significantly regulated the expression of the adipokines, resistin and adiponectin. This DBM-mediated regulation of lipid accumulation, ROS production, and adipokine production was shown to be involved in the regulation of the Nrf2 and insulin signaling.	Immunohistochemical staining	DBM significantly increased the translocation of nuclear factor (erythroid-derived 2)-like 2(Nrf2) into the nucleus, promoting the protein expression of its target gene, heme oxygenase-1 (HO-1). DBM significantly suppressed the insulin-mediated activation of phosphoinositide 3-kinase (PI3K) and protein kinase B (Akt), which are components of insulin signaling. In addition, intracellular ROS production was effectively reduced by DBM treatment, which upregulated antioxidant genes such as glutathione peroxidase (Gpx), catalase (CAT), and superoxide dismutase 1 (SOD1). Furthermore, DBM significantly regulated the expression of the adipokines, resistin and adiponectin. This DBM-mediated regulation of lipid accumulation, ROS production, and adipokine production was shown to be involved in the regulation of the Nrf2 and insulin signaling.		ORO Staining,Western Blot,MTT Assay,Real Time PCR,immunoblotting,			CAT,SOD1	FABP4,KLF2	DBM significantly increased the translocation of nuclear factor (erythroid-derived 2)-like 2(Nrf2) into the nucleus, promoting the protein expression of its target gene, heme oxygenase-1 (HO-1). DBM significantly suppressed the insulin-mediated activation of phosphoinositide 3-kinase (PI3K) and protein kinase B (Akt), which are components of insulin signaling. In addition, intracellular ROS production was effectively reduced by DBM treatment, which upregulated antioxidant genes such as glutathione peroxidase (Gpx), catalase (CAT), and superoxide dismutase 1 (SOD1). Furthermore, DBM significantly regulated the expression of the adipokines, resistin and adiponectin. This DBM-mediated regulation of lipid accumulation, ROS production, and adipokine production was shown to be involved in the regulation of the Nrf2 and insulin signaling.;DBM significantly increased the translocation of nuclear factor (erythroid-derived 2)-like 2(Nrf2) into the nucleus, promoting the protein expression of its target gene, heme oxygenase-1 (HO-1). DBM significantly suppressed the insulin-mediated activation of phosphoinositide 3-kinase (PI3K) and protein kinase B (Akt), which are components of insulin signaling. In addition, intracellular ROS production was effectively reduced by DBM treatment, which upregulated antioxidant genes such as glutathione peroxidase (Gpx), catalase (CAT), and superoxide dismutase 1 (SOD1). Furthermore, DBM significantly regulated the expression of the adipokines, resistin and adiponectin. This DBM-mediated regulation of lipid accumulation, ROS production, and adipokine production was shown to be involved in the regulation of the Nrf2 and insulin signaling.	DBM significantly increased the translocation of nuclear factor (erythroid-derived 2)-like 2(Nrf2) into the nucleus, promoting the protein expression of its target gene, heme oxygenase-1 (HO-1). DBM significantly suppressed the insulin-mediated activation of phosphoinositide 3-kinase (PI3K) and protein kinase B (Akt), which are components of insulin signaling. In addition, intracellular ROS production was effectively reduced by DBM treatment, which upregulated antioxidant genes such as glutathione peroxidase (Gpx), catalase (CAT), and superoxide dismutase 1 (SOD1). Furthermore, DBM significantly regulated the expression of the adipokines, resistin and adiponectin. This DBM-mediated regulation of lipid accumulation, ROS production, and adipokine production was shown to be involved in the regulation of the Nrf2 and insulin signaling.;DBM significantly increased the translocation of nuclear factor (erythroid-derived 2)-like 2(Nrf2) into the nucleus, promoting the protein expression of its target gene, heme oxygenase-1 (HO-1). DBM significantly suppressed the insulin-mediated activation of phosphoinositide 3-kinase (PI3K) and protein kinase B (Akt), which are components of insulin signaling. In addition, intracellular ROS production was effectively reduced by DBM treatment, which upregulated antioxidant genes such as glutathione peroxidase (Gpx), catalase (CAT), and superoxide dismutase 1 (SOD1). Furthermore, DBM significantly regulated the expression of the adipokines, resistin and adiponectin. This DBM-mediated regulation of lipid accumulation, ROS production, and adipokine production was shown to be involved in the regulation of the Nrf2 and insulin signaling.
29707136	chr3	108040485	108042485	CD47	Thus, normoxic vs. hypoxic and live vs. dying cell contexts influence the ultimate immunomodulatory roles of melanoma cell-associated BNIP3.	human		High+Lowthroughput	BNIP3 modulates the interface between B16-F10 melanoma cells and immune cells	否		Cancer, melanoma	B16-F10 cell 	E_01_0532	Flow Cytometry,Immunoblotting,ATP assay,In vitro phagocytosis assay,In vivo phagocytosis assay,western blot,	Thus, normoxic vs. hypoxic and live vs. dying cell contexts influence the ultimate immunomodulatory roles of melanoma cell-associated BNIP3.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Thus, normoxic vs. hypoxic and live vs. dying cell contexts influence the ultimate immunomodulatory roles of melanoma cell-associated BNIP3.	Immunohistochemical staining	Thus, normoxic vs. hypoxic and live vs. dying cell contexts influence the ultimate immunomodulatory roles of melanoma cell-associated BNIP3.		Flow Cytometry,Immunoblotting,ATP assay,In vitro phagocytosis assay,In vivo phagocytosis assay,western blot,			CALR,BNIP3	CD47	Thus, normoxic vs. hypoxic and live vs. dying cell contexts influence the ultimate immunomodulatory roles of melanoma cell-associated BNIP3.;Thus, normoxic vs. hypoxic and live vs. dying cell contexts influence the ultimate immunomodulatory roles of melanoma cell-associated BNIP3.	Thus, normoxic vs. hypoxic and live vs. dying cell contexts influence the ultimate immunomodulatory roles of melanoma cell-associated BNIP3.
29706346	chr1	22021633	22023633	LINC00339	Through an integrative functional genomic and epigenomic analyses, we prioritized rs6426749 as a potential causal SNP for osteoporosis at 1p36.12. Dual-luciferase assay and CRISPR/Cas9 experiments demonstrate that rs6426749 acts as a distal allele-specific enhancer regulating expression of a lncRNA (LINC00339)(_x0001_360 kb) via long-range chromatin loop formation and that this loop is mediated by CTCF occupied near rs6426749 and LINC00339 promoter region. Specifically, rs6426749-G allele can bind transcription factor TFAP2A, which efficiently elevates the enhancer activity and increases LINC00339 expression. Downregulation of LINC00339 significantly increases the expression of CDC42 in osteoblast cells, which is a pivotal regulator involved in bone metabolism. Our study provides mechanistic insight into how a noncoding SNP affects osteoporosis by long-range interaction, a finding that could indicate promising therapeutic targets for osteoporosis.	human		High+Lowthroughput	An Osteoporosis Risk SNP at 1p36.12 Acts as an Allele-Specific Enhancer to Modulate LINC00339 Expression via Long-Range Loop Formation	是	rs6426749,rs34963268,rs6684375	Osteoporosis	The hFOB 1.19 cells 	E_01_0533	Motif Analysis,SMR analysis,Quantitative Real-Time PCR,siRNA knocdown,shRNA Knockdown,Chromatin Immunoprecipitation (ChIP) Assay,Dual-Luciferase Reporter Assays,Site-Directed Mutagenesis,Analysis of Shared Causal Genetic Variants,AseQTL Analysis,Genotyping,Association Analysis,cis-eQTL Analysis,Hi-C,TAD Analysis,Haplotype Analysis,GWAS,CRISPR/Cas9,	Through an integrative functional genomic and epigenomic analyses, we prioritized rs6426749 as a potential causal SNP for osteoporosis at 1p36.12. Dual-luciferase assay and CRISPR/Cas9 experiments demonstrate that rs6426749 acts as a distal allele-specific enhancer regulating expression of a lncRNA (LINC00339)(_x0001_360 kb) via long-range chromatin loop formation and that this loop is mediated by CTCF occupied near rs6426749 and LINC00339 promoter region. Specifically, rs6426749-G allele can bind transcription factor TFAP2A, which efficiently elevates the enhancer activity and increases LINC00339 expression. Downregulation of LINC00339 significantly increases the expression of CDC42 in osteoblast cells, which is a pivotal regulator involved in bone metabolism. Our study provides mechanistic insight into how a noncoding SNP affects osteoporosis by long-range interaction, a finding that could indicate promising therapeutic targets for osteoporosis.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Through an integrative functional genomic and epigenomic analyses, we prioritized rs6426749 as a potential causal SNP for osteoporosis at 1p36.12. Dual-luciferase assay and CRISPR/Cas9 experiments demonstrate that rs6426749 acts as a distal allele-specific enhancer regulating expression of a lncRNA (LINC00339)(_x0001_360 kb) via long-range chromatin loop formation and that this loop is mediated by CTCF occupied near rs6426749 and LINC00339 promoter region. Specifically, rs6426749-G allele can bind transcription factor TFAP2A, which efficiently elevates the enhancer activity and increases LINC00339 expression. Downregulation of LINC00339 significantly increases the expression of CDC42 in osteoblast cells, which is a pivotal regulator involved in bone metabolism. Our study provides mechanistic insight into how a noncoding SNP affects osteoporosis by long-range interaction, a finding that could indicate promising therapeutic targets for osteoporosis.	Immunohistochemical staining	Through an integrative functional genomic and epigenomic analyses, we prioritized rs6426749 as a potential causal SNP for osteoporosis at 1p36.12. Dual-luciferase assay and CRISPR/Cas9 experiments demonstrate that rs6426749 acts as a distal allele-specific enhancer regulating expression of a lncRNA (LINC00339)(_x0001_360 kb) via long-range chromatin loop formation and that this loop is mediated by CTCF occupied near rs6426749 and LINC00339 promoter region. Specifically, rs6426749-G allele can bind transcription factor TFAP2A, which efficiently elevates the enhancer activity and increases LINC00339 expression. Downregulation of LINC00339 significantly increases the expression of CDC42 in osteoblast cells, which is a pivotal regulator involved in bone metabolism. Our study provides mechanistic insight into how a noncoding SNP affects osteoporosis by long-range interaction, a finding that could indicate promising therapeutic targets for osteoporosis.		Motif Analysis,SMR analysis,Quantitative Real-Time PCR,siRNA knocdown,shRNA Knockdown,Chromatin Immunoprecipitation (ChIP) Assay,Dual-Luciferase Reporter Assays,Site-Directed Mutagenesis,Analysis of Shared Causal Genetic Variants,AseQTL Analysis,Genotyping,Association Analysis,cis-eQTL Analysis,Hi-C,TAD Analysis,Haplotype Analysis,GWAS,CRISPR/Cas9,			LINC00339,CDC42	CTCF,TFAP2A	Through an integrative functional genomic and epigenomic analyses, we prioritized rs6426749 as a potential causal SNP for osteoporosis at 1p36.12. Dual-luciferase assay and CRISPR/Cas9 experiments demonstrate that rs6426749 acts as a distal allele-specific enhancer regulating expression of a lncRNA (LINC00339)(_x0001_360 kb) via long-range chromatin loop formation and that this loop is mediated by CTCF occupied near rs6426749 and LINC00339 promoter region. Specifically, rs6426749-G allele can bind transcription factor TFAP2A, which efficiently elevates the enhancer activity and increases LINC00339 expression. Downregulation of LINC00339 significantly increases the expression of CDC42 in osteoblast cells, which is a pivotal regulator involved in bone metabolism. Our study provides mechanistic insight into how a noncoding SNP affects osteoporosis by long-range interaction, a finding that could indicate promising therapeutic targets for osteoporosis.;Through an integrative functional genomic and epigenomic analyses, we prioritized rs6426749 as a potential causal SNP for osteoporosis at 1p36.12. Dual-luciferase assay and CRISPR/Cas9 experiments demonstrate that rs6426749 acts as a distal allele-specific enhancer regulating expression of a lncRNA (LINC00339)(_x0001_360 kb) via long-range chromatin loop formation and that this loop is mediated by CTCF occupied near rs6426749 and LINC00339 promoter region. Specifically, rs6426749-G allele can bind transcription factor TFAP2A, which efficiently elevates the enhancer activity and increases LINC00339 expression. Downregulation of LINC00339 significantly increases the expression of CDC42 in osteoblast cells, which is a pivotal regulator involved in bone metabolism. Our study provides mechanistic insight into how a noncoding SNP affects osteoporosis by long-range interaction, a finding that could indicate promising therapeutic targets for osteoporosis.	Through an integrative functional genomic and epigenomic analyses, we prioritized rs6426749 as a potential causal SNP for osteoporosis at 1p36.12. Dual-luciferase assay and CRISPR/Cas9 experiments demonstrate that rs6426749 acts as a distal allele-specific enhancer regulating expression of a lncRNA (LINC00339)(_x0001_360 kb) via long-range chromatin loop formation and that this loop is mediated by CTCF occupied near rs6426749 and LINC00339 promoter region. Specifically, rs6426749-G allele can bind transcription factor TFAP2A, which efficiently elevates the enhancer activity and increases LINC00339 expression. Downregulation of LINC00339 significantly increases the expression of CDC42 in osteoblast cells, which is a pivotal regulator involved in bone metabolism. Our study provides mechanistic insight into how a noncoding SNP affects osteoporosis by long-range interaction, a finding that could indicate promising therapeutic targets for osteoporosis.;Through an integrative functional genomic and epigenomic analyses, we prioritized rs6426749 as a potential causal SNP for osteoporosis at 1p36.12. Dual-luciferase assay and CRISPR/Cas9 experiments demonstrate that rs6426749 acts as a distal allele-specific enhancer regulating expression of a lncRNA (LINC00339)(_x0001_360 kb) via long-range chromatin loop formation and that this loop is mediated by CTCF occupied near rs6426749 and LINC00339 promoter region. Specifically, rs6426749-G allele can bind transcription factor TFAP2A, which efficiently elevates the enhancer activity and increases LINC00339 expression. Downregulation of LINC00339 significantly increases the expression of CDC42 in osteoblast cells, which is a pivotal regulator involved in bone metabolism. Our study provides mechanistic insight into how a noncoding SNP affects osteoporosis by long-range interaction, a finding that could indicate promising therapeutic targets for osteoporosis.
29704115	chr11	27652286	27654286	BDNF	Taken together, our results suggest that BDNF/TrkB pathway plays an important mediatory role in the antidepressant-like action of H2S in CUMS-exposed rats, which is by suppression of hippocampal ER stress. These data provide a novel mechanism underlying the protection of H2S against CUMS-induced depressive-like behaviors.	human	/	High+Lowthroughput	BDNF/TrkB Pathway Mediates the Antidepressant-Like Role of H(2)S in CUMS-Exposed Rats by Inhibition of Hippocampal ER Stress	否		depression		E_01_0534	Western Blot,BCA assay,	Taken together, our results suggest that BDNF/TrkB pathway plays an important mediatory role in the antidepressant-like action of H2S in CUMS-exposed rats, which is by suppression of hippocampal ER stress. These data provide a novel mechanism underlying the protection of H2S against CUMS-induced depressive-like behaviors.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		Taken together, our results suggest that BDNF/TrkB pathway plays an important mediatory role in the antidepressant-like action of H2S in CUMS-exposed rats, which is by suppression of hippocampal ER stress. These data provide a novel mechanism underlying the protection of H2S against CUMS-induced depressive-like behaviors.	Immunohistochemical staining	Taken together, our results suggest that BDNF/TrkB pathway plays an important mediatory role in the antidepressant-like action of H2S in CUMS-exposed rats, which is by suppression of hippocampal ER stress. These data provide a novel mechanism underlying the protection of H2S against CUMS-induced depressive-like behaviors.		Western Blot,BCA assay,				BDNF		Taken together, our results suggest that BDNF/TrkB pathway plays an important mediatory role in the antidepressant-like action of H2S in CUMS-exposed rats, which is by suppression of hippocampal ER stress. These data provide a novel mechanism underlying the protection of H2S against CUMS-induced depressive-like behaviors.
29702085	chr17	42310982	42312982	STAT3	STAT3 contributed to TNF-α induced nuclear translocation of phospho-NFκB in pericytes. TNF-α-induced IL-6 release in astrocytes was mediated by NFκB but not by STAT3. The presence of pericytes amplified TNF-α-induced iNOS mRNA expression in BV-2 microglia. This effect was blocked by a neutralizing antibody for IL-6. These findings indicated that crosstalk between the IκB-NFκB and JAK-STAT3 pathways is a pericyte specific mechanism, not occurring in astrocytes, for TNF-α-induced IL-6 release. IL-6 derived from pericytes enhanced microglial activation. Our findings increase understanding of the role of pericyte-microglia crosstalk in the brain under neuroinflammatory conditions and suggest a potentially attractive therapeutic target for brain inflammation.	human	Nervous	High+Lowthroughput	TNF-α-sensitive brain pericytes activate microglia by releasing IL-6 through cooperation between IκB-NFκB and JAK-STAT3 pathways	否		Neuroinflammation	brain pericyte	E_01_0535	Western blot,RT-PCR,	STAT3 contributed to TNF-α induced nuclear translocation of phospho-NFκB in pericytes. TNF-α-induced IL-6 release in astrocytes was mediated by NFκB but not by STAT3. The presence of pericytes amplified TNF-α-induced iNOS mRNA expression in BV-2 microglia. This effect was blocked by a neutralizing antibody for IL-6. These findings indicated that crosstalk between the IκB-NFκB and JAK-STAT3 pathways is a pericyte specific mechanism, not occurring in astrocytes, for TNF-α-induced IL-6 release. IL-6 derived from pericytes enhanced microglial activation. Our findings increase understanding of the role of pericyte-microglia crosstalk in the brain under neuroinflammatory conditions and suggest a potentially attractive therapeutic target for brain inflammation.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		STAT3 contributed to TNF-α induced nuclear translocation of phospho-NFκB in pericytes. TNF-α-induced IL-6 release in astrocytes was mediated by NFκB but not by STAT3. The presence of pericytes amplified TNF-α-induced iNOS mRNA expression in BV-2 microglia. This effect was blocked by a neutralizing antibody for IL-6. These findings indicated that crosstalk between the IκB-NFκB and JAK-STAT3 pathways is a pericyte specific mechanism, not occurring in astrocytes, for TNF-α-induced IL-6 release. IL-6 derived from pericytes enhanced microglial activation. Our findings increase understanding of the role of pericyte-microglia crosstalk in the brain under neuroinflammatory conditions and suggest a potentially attractive therapeutic target for brain inflammation.	Immunohistochemical staining	STAT3 contributed to TNF-α induced nuclear translocation of phospho-NFκB in pericytes. TNF-α-induced IL-6 release in astrocytes was mediated by NFκB but not by STAT3. The presence of pericytes amplified TNF-α-induced iNOS mRNA expression in BV-2 microglia. This effect was blocked by a neutralizing antibody for IL-6. These findings indicated that crosstalk between the IκB-NFκB and JAK-STAT3 pathways is a pericyte specific mechanism, not occurring in astrocytes, for TNF-α-induced IL-6 release. IL-6 derived from pericytes enhanced microglial activation. Our findings increase understanding of the role of pericyte-microglia crosstalk in the brain under neuroinflammatory conditions and suggest a potentially attractive therapeutic target for brain inflammation.		Western blot,RT-PCR,				STAT3		STAT3 contributed to TNF-α induced nuclear translocation of phospho-NFκB in pericytes. TNF-α-induced IL-6 release in astrocytes was mediated by NFκB but not by STAT3. The presence of pericytes amplified TNF-α-induced iNOS mRNA expression in BV-2 microglia. This effect was blocked by a neutralizing antibody for IL-6. These findings indicated that crosstalk between the IκB-NFκB and JAK-STAT3 pathways is a pericyte specific mechanism, not occurring in astrocytes, for TNF-α-induced IL-6 release. IL-6 derived from pericytes enhanced microglial activation. Our findings increase understanding of the role of pericyte-microglia crosstalk in the brain under neuroinflammatory conditions and suggest a potentially attractive therapeutic target for brain inflammation.
29696026	chr16	23780812	23782812	Bcl6	The inhibitory functions of Bcl6 in MPT and MPTH2 cells attenuated allergic responses. Bcl6 is a critical regulator of IL-4 production by MPT and MPTH2 cells in TH2 immune responses related to the pathogenesis of allergies.	mouse	lymphoid	High+Lowthroughput	Allergic T(H)2 Response Governed by B-Cell Lymphoma 6 Function in Naturally Occurring Memory Phenotype CD4(+) T Cells	否		asthma	cD4+ T cell	E_01_0536	Fluorescence-activated cell sorting(Facs) analysis,chromatin immunoprecipitation(ChIP),ELISA,retroviral Vectors With a d2EGFP reporter gene,Western Blot,OVA Challenge,Bronchoalveolar lavage (BAL),Histologic Examination,transgenic mice,	The inhibitory functions of Bcl6 in MPT and MPTH2 cells attenuated allergic responses. Bcl6 is a critical regulator of IL-4 production by MPT and MPTH2 cells in TH2 immune responses related to the pathogenesis of allergies.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		The inhibitory functions of Bcl6 in MPT and MPTH2 cells attenuated allergic responses. Bcl6 is a critical regulator of IL-4 production by MPT and MPTH2 cells in TH2 immune responses related to the pathogenesis of allergies.	Immunohistochemical staining	The inhibitory functions of Bcl6 in MPT and MPTH2 cells attenuated allergic responses. Bcl6 is a critical regulator of IL-4 production by MPT and MPTH2 cells in TH2 immune responses related to the pathogenesis of allergies.		Fluorescence-activated cell sorting(Facs) analysis,chromatin immunoprecipitation(ChIP),ELISA,retroviral Vectors With a d2EGFP reporter gene,Western Blot,OVA Challenge,Bronchoalveolar lavage (BAL),Histologic Examination,transgenic mice,			Bcl6		The inhibitory functions of Bcl6 in MPT and MPTH2 cells attenuated allergic responses. Bcl6 is a critical regulator of IL-4 production by MPT and MPTH2 cells in TH2 immune responses related to the pathogenesis of allergies.	
29695774	chr8	7052292	7054292	DEFA5	We find that as few as 35 TSSs can distinguish active CD, UC, and controls with 85% accuracy in an independent cohort. Our data constitute a foundation for understanding the molecular pathology, gene regulation, and genetics of IBD.	human	Colon	High+Lowthroughput	Characterization of the enhancer and promoter landscape of inflammatory bowel disease from human colon biopsies	是	rs11676348	Inflammatory bowel disease (IBD)	monocyte cells	E_01_0537	CAGE assay,real-time quantitative reverse transcription polymerase chain reaction (qPCR),TSS-enhancer linkage,ChIP,RNA-seq,ChIPseq,FAIRE-seq,motif-seq,	We find that as few as 35 TSSs can distinguish active CD, UC, and controls with 85% accuracy in an independent cohort. Our data constitute a foundation for understanding the molecular pathology, gene regulation, and genetics of IBD.	Enhancer	qRT-PCR,qPCR,ChIP,3C	RNA-Seq		We find that as few as 35 TSSs can distinguish active CD, UC, and controls with 85% accuracy in an independent cohort. Our data constitute a foundation for understanding the molecular pathology, gene regulation, and genetics of IBD.	Immunohistochemical staining	We find that as few as 35 TSSs can distinguish active CD, UC, and controls with 85% accuracy in an independent cohort. Our data constitute a foundation for understanding the molecular pathology, gene regulation, and genetics of IBD.		CAGE assay,real-time quantitative reverse transcription polymerase chain reaction (qPCR),TSS-enhancer linkage,ChIP,RNA-seq,ChIPseq,FAIRE-seq,motif-seq,			DEFA5,DEFA6,REG1A,REG1B,REG3A,CLDN2,CLDN10,CLDN14,CLDN18,ST6GAL1,PF4V1,CXCL1,PF4,PPBP,CXCL5,PPBPP2,CXCL2	CLDN1,CXCL8,CXCL6,CXCL3	We find that as few as 35 TSSs can distinguish active CD, UC, and controls with 85% accuracy in an independent cohort. Our data constitute a foundation for understanding the molecular pathology, gene regulation, and genetics of IBD.;We find that as few as 35 TSSs can distinguish active CD, UC, and controls with 85% accuracy in an independent cohort. Our data constitute a foundation for understanding the molecular pathology, gene regulation, and genetics of IBD.;We find that as few as 35 TSSs can distinguish active CD, UC, and controls with 85% accuracy in an independent cohort. Our data constitute a foundation for understanding the mol