Variant report

Variant	rs6977632
Chromosome Location	chr7:66057749-66057750
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:66056666-66057796	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr7:66056915-66057751	K562	blood:	n/a	n/a
3	MAX	chr7:66056046-66057789	K562	blood:	n/a	chr7:66056734-66056743
4	SIN3AK20	chr7:66056635-66057800	MCF-7	breast:	n/a	n/a
5	JUN	chr7:66056103-66057943	K562	blood:	n/a	chr7:66057182-66057191
6	CREB1	chr7:66056771-66057763	HepG2	liver:	n/a	n/a
7	ZNF143	chr7:66057098-66057750	K562	blood:	n/a	n/a
8	MXI1	chr7:66055210-66058700	SK-N-SH	brain:	n/a	n/a
9	MYBL2	chr7:66057019-66057769	HepG2	liver:	n/a	n/a
10	POLR2A	chr7:66056726-66057989	HepG2	liver:	n/a	n/a
11	MAX	chr7:66056736-66057764	SK-N-SH	brain:	n/a	n/a
12	POLR2A	chr7:66057019-66057791	PBDE	blood:	n/a	n/a
13	MAX	chr7:66056702-66057773	A549	lung:	n/a	chr7:66056734-66056743
14	HCFC1	chr7:66056563-66057820	Hela-S3	cervix:	n/a	n/a
15	MYC	chr7:66057102-66057792	A549	lung:	n/a	n/a
16	GABPA	chr7:66056753-66057781	SK-N-SH	brain:	n/a	chr7:66057057-66057066
17	TCF12	chr7:66056796-66057751	ECC-1	luminal epithelium:	n/a	n/a
18	MAX	chr7:66056942-66057761	HCT-116	colon:	n/a	n/a
19	NR2F2	chr7:66055450-66057883	K562	blood:	n/a	n/a
20	MAX	chr7:66056792-66057781	HepG2	liver:	n/a	n/a
21	MAX	chr7:66056741-66057779	HCT-116	colon:	n/a	n/a
22	POLR2A	chr7:66056596-66057796	PFSK-1	brain:	n/a	n/a
23	GATA2	chr7:66057133-66057827	SH-SY5Y	brain:	n/a	n/a
24	GATA3	chr7:66056889-66057798	A549	lung:	n/a	n/a
25	CREB1	chr7:66056840-66057755	K562	blood:	n/a	n/a
26	GATA3	chr7:66057391-66057798	SH-SY5Y	brain:	n/a	n/a
27	MAX	chr7:66056916-66057759	A549	lung:	n/a	n/a
28	TAF1	chr7:66057063-66057757	MCF-7	breast:	n/a	n/a
29	HEY1	chr7:66056849-66057780	HepG2	liver:	n/a	chr7:66057127-66057142 chr7:66057185-66057200
30	GATA2	chr7:66057240-66057763	K562	blood:	n/a	n/a
31	REST	chr7:66056529-66057836	H1-neurons	neurons:	n/a	chr7:66057086-66057099 chr7:66056681-66056695 chr7:66056917-66056930 chr7:66056989-66057009 chr7:66057352-66057365 chr7:66057185-66057203
32	GATA3	chr7:66057045-66057755	MCF-7	breast:	n/a	n/a
33	RELA	chr7:66057172-66057801	GM18951	blood:	n/a	n/a
34	GATA3	chr7:66056976-66057761	MCF-7	breast:	n/a	n/a
35	BHLHE40	chr7:66057096-66057756	K562	blood:	n/a	n/a
36	PML	chr7:66056738-66057826	GM12878	blood:	n/a	chr7:66057004-66057012
37	TEAD4	chr7:66056721-66057765	K562	blood:	n/a	chr7:66057076-66057085
38	MTA3	chr7:66056865-66057782	GM12878	blood:	n/a	n/a
39	GATA1	chr7:66057221-66058118	PBDE	blood:	n/a	n/a
40	CBX3	chr7:66056063-66058024	K562	blood:	n/a	n/a
41	RUNX3	chr7:66056627-66057785	GM12878	blood:	n/a	chr7:66056775-66056790
42	GATA2	chr7:66057298-66057763	HUVEC	blood vessel:	n/a	n/a
43	CHD1	chr7:66055223-66057756	IMR90	lung:	n/a	chr7:66057150-66057160

No.	Distal block	Cell Line	Cell type
1	chr7:66054686..66058308-chr7:66092199..66095155,8	MCF-7	breast:
2	chr7:66055738..66058439-chr7:66119494..66121209,2	MCF-7	breast:
3	chr7:66057103..66058075-chr7:66118859..66119855,2	MCF-7	breast:
4	chr7:66057440..66059000-chr7:66060580..66062147,2	K562	blood:
5	chr7:66055516..66058509-chr7:66093670..66096346,2	MCF-7	breast:
6	chr7:66055703..66058887-chr7:66117840..66121190,6	MCF-7	breast:
7	chr7:66051779..66054394-chr7:66057602..66059398,2	K562	blood:
8	chr12:120729624..120730457-chr7:66057252..66057789,2	Hela-S3	cervix:
9	chr16:4664369..4665081-chr7:66057213..66057926,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000232559	TF binding region
ENSG00000243335	Chromatin interaction
ENSG00000226824	Chromatin interaction
ENSG00000153443	Chromatin interaction
ENSG00000202538	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10215132	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10242423	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10249404	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10253883	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10255377	0.85[AMR][1000 genomes]
rs10258739	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10263935	0.80[AFR][1000 genomes]
rs10272357	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs10274773	0.80[AFR][1000 genomes]
rs10278371	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10278816	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10281080	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10281646	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10950044	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs10950045	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11765356	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11772179	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11773829	0.81[AFR][1000 genomes]
rs12532355	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12534943	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1860468	0.81[AFR][1000 genomes]
rs1860470	0.80[AFR][1000 genomes]
rs1968127	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2191268	0.80[AFR][1000 genomes]
rs2286683	0.80[AFR][1000 genomes]
rs2286684	0.80[AFR][1000 genomes]
rs28846700	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35117338	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3764903	0.80[AFR][1000 genomes]
rs3857686	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs3898855	0.82[AMR][1000 genomes]
rs4398788	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4718378	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62467809	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6460305	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs66525610	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6943696	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6947808	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6960778	0.85[AFR][1000 genomes]
rs6961186	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6965056	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6967809	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6968619	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71563125	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs732465	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7357230	0.85[AFR][1000 genomes]
rs7785213	0.80[AFR][1000 genomes]
rs801190	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs801191	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs801193	0.82[AMR][1000 genomes]
rs801207	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1035107	chr7:65814901-66114919	Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv538909	chr7:65814901-66114919	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv888326	chr7:65825257-66066999	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv482441	chr7:65885824-66061788	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs6977632	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs6977632	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs6977632	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs6977632	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs6977632	RP4-756H11.3	cis	Artery Aorta	GTEx
rs6977632	RP4-756H11.3	cis	Artery Tibial	GTEx
rs6977632	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs6977632	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs6977632	GTF2IRD1P1	cis	Thyroid	GTEx
rs6977632	RP4-756H11.3	cis	Thyroid	GTEx
rs6977632	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs6977632	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs6977632	LOC493754,TOMM20,LOC441245	cis	brain	BrainEAC
rs6977632	RP4-756H11.3	cis	lung	GTEx
rs6977632	VKORC1L1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66055000-66057800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr7:66055200-66057800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr7:66055200-66058000	Active TSS	HSMM	muscle
4	chr7:66055400-66057800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr7:66055400-66057800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr7:66055400-66058000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr7:66055400-66058000	Active TSS	Fetal Kidney	kidney
8	chr7:66055600-66057800	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr7:66055600-66057800	Active TSS	Psoas Muscle	Psoas
10	chr7:66055600-66057800	Active TSS	HSMMtube	muscle
11	chr7:66055800-66057800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr7:66055800-66057800	Active TSS	Fetal Stomach	stomach
13	chr7:66055800-66057800	Active TSS	Rectal Smooth Muscle	rectum
14	chr7:66055800-66058000	Active TSS	Breast Myoepithelial Primary Cells	Breast
15	chr7:66055800-66058000	Active TSS	NHDF-Ad	bronchial
16	chr7:66055800-66058200	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr7:66055800-66058200	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr7:66055800-66058200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr7:66056000-66057800	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr7:66056000-66057800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr7:66056000-66057800	Active TSS	Brain Cingulate Gyrus	brain
22	chr7:66056000-66057800	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr7:66056000-66058000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr7:66056000-66058200	Active TSS	HUES6 Cell Line	embryonic stem cell
25	chr7:66056200-66057800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr7:66056200-66057800	Active TSS	Brain Anterior Caudate	brain
27	chr7:66056200-66057800	Active TSS	Rectal Mucosa Donor 31	rectum
28	chr7:66056400-66058000	Active TSS	Fetal Brain Female	brain
29	chr7:66056600-66057800	Active TSS	Thymus	Thymus
30	chr7:66056800-66057800	Active TSS	Primary B cells from cord blood	blood
31	chr7:66056800-66057800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr7:66057000-66057800	Active TSS	HepG2	liver
33	chr7:66057200-66057800	Active TSS	Brain Germinal Matrix	brain
34	chr7:66057400-66057800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr7:66057400-66057800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr7:66057400-66057800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr7:66057400-66057800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
38	chr7:66057400-66057800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr7:66057400-66057800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
40	chr7:66057400-66057800	Flanking Active TSS	Primary B cells from peripheral blood	blood
41	chr7:66057400-66057800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
42	chr7:66057400-66057800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
43	chr7:66057400-66057800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
44	chr7:66057400-66057800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr7:66057400-66057800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
46	chr7:66057400-66057800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr7:66057400-66057800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr7:66057400-66057800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
49	chr7:66057400-66057800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr7:66057400-66057800	Flanking Active TSS	Adipose Nuclei	Adipose

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