Variant report

Variant	rs10006977
Chromosome Location	chr4:3076955-3076956
allele	A/C
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	chr4:3076754-3077330	K562	blood:	n/a	n/a
2	EP300	chr4:3076951-3077151	HepG2	liver:	n/a	n/a
3	POLR2A	chr4:3076901-3077344	PFSK-1	brain:	n/a	n/a
4	EGR1	chr4:3076591-3077089	K562	blood:	n/a	chr4:3076966-3076976 chr4:3076965-3076978 chr4:3076965-3076978
5	POLR2A	chr4:3076758-3078137	GM12891	blood:	n/a	n/a
6	YY1	chr4:3076147-3077339	GM12892	blood:	n/a	chr4:3076399-3076413 chr4:3076297-3076311 chr4:3076417-3076437 chr4:3076261-3076272 chr4:3076405-3076416
7	POLR2A	chr4:3075066-3078105	GM15510	blood:	n/a	n/a
8	YY1	chr4:3076738-3077357	GM12878	blood:	n/a	n/a
9	FOXM1	chr4:3076791-3077400	GM12878	blood:	n/a	n/a
10	TBP	chr4:3076869-3077523	HepG2	liver:	n/a	n/a
11	CHD2	chr4:3076812-3077389	HepG2	liver:	n/a	chr4:3076978-3076988 chr4:3077035-3077044
12	POLR2A	chr4:3076094-3078808	GM12878	blood:	n/a	n/a
13	BCLAF1	chr4:3076808-3077331	GM12878	blood:	n/a	chr4:3077266-3077279
14	YY1	chr4:3076812-3077229	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr4:3076873-3077717	MCF10A-Er-Src	breast:	n/a	n/a
16	PML	chr4:3076003-3078213	GM12878	blood:	n/a	n/a
17	EGR1	chr4:3076633-3077112	K562	blood:	n/a	chr4:3076966-3076976 chr4:3076965-3076978 chr4:3076965-3076978
18	POLR2A	chr4:3075327-3080089	GM18505	blood:	n/a	n/a
19	POU2F2	chr4:3076813-3077918	GM12878	blood:	n/a	chr4:3077377-3077389 chr4:3077373-3077385 chr4:3077370-3077382
20	BRCA1	chr4:3076899-3077271	H1-hESC	embryonic stem cell:	n/a	chr4:3077035-3077044
21	YY1	chr4:3076786-3077350	GM12891	blood:	n/a	n/a
22	RUNX3	chr4:3076776-3078119	GM12878	blood:	n/a	n/a
23	POLR2A	chr4:3076054-3080438	GM12891	blood:	n/a	n/a
24	HCFC1	chr4:3076909-3077251	K562	blood:	n/a	n/a
25	FOXM1	chr4:3076919-3078036	GM12878	blood:	n/a	n/a
26	POU2F2	chr4:3076726-3077345	GM12891	blood:	n/a	n/a
27	STAT5A	chr4:3076785-3078582	GM12878	blood:	n/a	chr4:3077371-3077383 chr4:3077377-3077389 chr4:3077370-3077382 chr4:3077381-3077393
28	ZMIZ1	chr4:3076898-3077112	K562	blood:	n/a	n/a
29	NFIC	chr4:3076912-3077918	GM12878	blood:	n/a	n/a
30	SIN3A	chr4:3076044-3077367	H1-hESC	embryonic stem cell:	n/a	chr4:3076486-3076497 chr4:3076479-3076493
31	HMGN3	chr4:3076832-3077144	K562	blood:	n/a	n/a
32	TBP	chr4:3076135-3077374	H1-hESC	embryonic stem cell:	n/a	n/a
33	POLR2A	chr4:3076039-3077704	GM10847	blood:	n/a	n/a
34	TAF7	chr4:3076767-3077131	H1-hESC	embryonic stem cell:	n/a	n/a
35	HEY1	chr4:3076889-3077328	K562	blood:	n/a	n/a
36	MAZ	chr4:3076867-3077775	GM12878	blood:	n/a	chr4:3077170-3077180 chr4:3077374-3077384 chr4:3077004-3077014 chr4:3076965-3076975
37	POLR2A	chr4:3076894-3077552	U87	brain:	n/a	n/a
38	YY1	chr4:3076013-3077302	SK-N-SH	brain:	n/a	chr4:3076399-3076413 chr4:3076297-3076311 chr4:3076417-3076437 chr4:3076261-3076272 chr4:3076405-3076416
39	RELA	chr4:3076849-3078101	GM12891	blood:	n/a	n/a
40	CHD2	chr4:3076851-3077329	K562	blood:	n/a	chr4:3076978-3076988 chr4:3077035-3077044
41	TAF1	chr4:3076774-3077363	ECC-1	luminal epithelium:	n/a	n/a
42	POLR2A	chr4:3075462-3078579	GM19099	blood:	n/a	n/a
43	POLR2A	chr4:3075141-3077429	Raji	blood:	n/a	n/a
44	UBTF	chr4:3076790-3077007	K562	blood:	n/a	n/a
45	POLR2A	chr4:3076082-3078168	GM12878	blood:	n/a	n/a
46	POLR2A	chr4:3075958-3077371	GM12878	blood:	n/a	n/a
47	RUNX3	chr4:3076864-3077844	GM12878	blood:	n/a	n/a
48	POLR2A	chr4:3076770-3077332	GM12891	blood:	n/a	n/a
49	ATF2	chr4:3076817-3077785	GM12878	blood:	n/a	n/a
50	POLR2A	chr4:3076764-3077331	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr4:3076907-3076957	AG09319	gingival:	n/a
2	chr4:3076907-3076957	GM12878	blood:	n/a
3	chr4:3076907-3076957	SK-N-SH	brain:	n/a
4	chr4:3076907-3076957	RPTEC	kidney:	n/a
5	chr4:3076907-3076957	IMR90	lung:	fetal
6	chr4:3076907-3076957	Hela-S3	cervix:	n/a
7	chr4:3076907-3076957	MCF10A-Er-Src	breast:	n/a
8	chr4:3076907-3076957	T-47D	breast:	n/a
9	chr4:3076907-3076957	HEEpiC	esophagus:	n/a
10	chr4:3076907-3076957	AoSMC	blood vessel:	n/a
11	chr4:3076907-3076957	HAEpiC	amniotic membrane:	n/a
12	chr4:3076907-3076957	ECC-1	luminal epithelium:	n/a
13	chr4:3076907-3076957	NH-A	brain:	n/a
14	chr4:3076907-3076957	AG04449	skin:	fetal
15	chr4:3076907-3076957	HCM	heart:	n/a
16	chr4:3076907-3076957	HCF	heart:	n/a
17	chr4:3076907-3076957	A549	lung:	n/a
18	chr4:3076907-3076957	Hepatocyte	liver:	n/a
19	chr4:3076907-3076957	SAEC	small airway:	n/a
20	chr4:3076907-3076957	ProgFib	skin:	n/a
21	chr4:3076907-3076957	AG10803	skin:	n/a
22	chr4:3076907-3076957	NB4	blood:	n/a
23	chr4:3076907-3076957	NT2-D1	testis:	n/a
24	chr4:3076907-3076957	SK-N-SH_RA	brain:	n/a
25	chr4:3076907-3076957	NHBE	bronchial:	n/a
26	chr4:3076907-3076957	SKMC	muscle:	n/a
27	chr4:3076907-3076957	SK-N-MC	brain:	n/a
28	chr4:3076907-3076957	BJ	skin:	n/a
29	chr4:3076907-3076957	BE2_C	brain:	n/a
30	chr4:3076907-3076957	U87	brain:	n/a
31	chr4:3076907-3076957	HPAEpiC	pulmonary alveolar:	n/a
32	chr4:3076907-3076957	HRE	kidney:	n/a
33	chr4:3076907-3076957	GM19239	blood:	n/a
34	chr4:3076907-3076957	GM12892	blood:	n/a
35	chr4:3076907-3076957	HCT-116	colon:	n/a
36	chr4:3076907-3076957	MCF-7	breast:	n/a
37	chr4:3076907-3076957	HRPEpiC	eye:	n/a
38	chr4:3076907-3076957	Caco-2	colon:	n/a
39	chr4:3076907-3076957	HNPCEpiC	eye:	n/a
40	chr4:3076907-3076957	HepG2	liver:	n/a
41	chr4:3076907-3076957	HMEC	breast:	n/a
42	chr4:3076907-3076957	GM12891	blood:	n/a
43	chr4:3076907-3076957	H1-hESC	embryonic stem cell:	embryo
44	chr4:3076907-3076957	CMK	blood:	n/a
45	chr4:3076907-3076957	HIPEpiC	eye:	n/a
46	chr4:3076907-3076957	LNCaP	prostate:	n/a
47	chr4:3076907-3076957	HRCEpiC	kidney:	n/a
48	chr4:3076907-3076957	AG09309	skin:	n/a
49	chr4:3076907-3076957	GM06990	blood:	n/a
50	chr4:3076907-3076957	AG04450	lung:	fetal

No.	Distal block	Cell Line	Cell type
1	chr4:3074016..3078502-chr4:3111809..3117809,7	MCF-7	breast:
2	chr4:3075638..3077191-chr4:3246487..3249347,2	MCF-7	breast:
3	chr4:3076425..3077993-chr4:3087345..3089440,2	MCF-7	breast:
4	chr17:16556241..16557924-chr4:3075466..3077603,2	MCF-7	breast:
5	chr4:3076858..3078560-chr4:3090552..3093969,4	MCF-7	breast:
6	chr4:3076735..3079040-chr4:3100560..3102807,2	K562	blood:
7	chr4:3074885..3077461-chr4:3292207..3294882,2	MCF-7	breast:
8	chr4:3076522..3079094-chr4:3136211..3138250,2	MCF-7	breast:
9	chr4:2935808..2938115-chr4:3076304..3078834,3	K562	blood:
10	chr4:3075973..3077923-chr4:3128614..3130547,2	MCF-7	breast:
11	chr4:3076560..3079556-chr4:3107118..3109310,3	MCF-7	breast:
12	chr4:2935808..2937729-chr4:3076912..3078834,2	K562	blood:
13	chr4:2964356..2966158-chr4:3074837..3077632,2	K562	blood:
14	chr4:2262471..2264332-chr4:3074788..3077577,2	MCF-7	breast:
15	chr4:2468745..2470693-chr4:3075535..3077781,3	K562	blood:

Variant related genes	Relation type
HTT-AS	TF binding region
HTT-AS	CpG island
ENSG00000109736	Chromatin interaction
ENSG00000159788	Chromatin interaction
ENSG00000063978	Chromatin interaction
ENSG00000125388	Chromatin interaction
ENSG00000188981	Chromatin interaction
ENSG00000197386	Chromatin interaction
ENSG00000249673	Chromatin interaction
ENSG00000087269	Chromatin interaction
ENSG00000264765	Chromatin interaction
ENSG00000197566	Chromatin interaction
ENSG00000123933	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10002065	0.87[EUR][1000 genomes]
rs10006129	0.90[EUR][1000 genomes]
rs10009229	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10009935	0.97[EUR][1000 genomes]
rs10011127	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10014333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10016755	0.87[EUR][1000 genomes]
rs10034313	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10222986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1419036	0.87[EUR][1000 genomes]
rs16843857	0.87[EUR][1000 genomes]
rs16843866	0.87[EUR][1000 genomes]
rs16843869	0.87[EUR][1000 genomes]
rs28387056	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28393280	0.93[EUR][1000 genomes]
rs28394705	0.97[EUR][1000 genomes]
rs28398130	0.83[EUR][1000 genomes]
rs28468636	0.93[EUR][1000 genomes]
rs28485764	0.97[EUR][1000 genomes]
rs28564368	0.87[EUR][1000 genomes]
rs28580164	0.87[EUR][1000 genomes]
rs28583447	0.93[EUR][1000 genomes]
rs28583552	0.84[EUR][1000 genomes]
rs28584232	0.97[EUR][1000 genomes]
rs28616835	0.85[EUR][1000 genomes]
rs28629394	0.97[EUR][1000 genomes]
rs28634516	0.87[EUR][1000 genomes]
rs28660254	0.87[EUR][1000 genomes]
rs28670335	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28682489	0.91[EUR][1000 genomes]
rs28696693	0.93[EUR][1000 genomes]
rs28714390	0.97[EUR][1000 genomes]
rs28718346	1.00[EUR][1000 genomes]
rs28755900	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3025836	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs363138	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4346595	0.93[EUR][1000 genomes]
rs6830019	0.93[EUR][1000 genomes]
rs6835897	0.93[EUR][1000 genomes]
rs7436457	0.93[EUR][1000 genomes]
rs7664480	0.93[EUR][1000 genomes]
rs7693317	0.87[EUR][1000 genomes]
rs9994689	0.80[EUR][1000 genomes]
rs9995782	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9996075	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
5	esv3326369	chr4:3074679-3077527	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	esv3406168	chr4:3075379-3078127	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	esv3435763	chr4:3075704-3077902	Active TSS Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3074800-3077600	Active TSS	Fetal Brain Female	brain
2	chr4:3074800-3078600	Active TSS	HUES6 Cell Line	embryonic stem cell
3	chr4:3075000-3077000	Active TSS	Osteobl	bone
4	chr4:3075000-3077400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:3075000-3077400	Active TSS	HSMM	muscle
6	chr4:3075000-3077600	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr4:3075000-3077600	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr4:3075000-3077600	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr4:3075000-3077600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr4:3075000-3077600	Active TSS	Brain Germinal Matrix	brain
11	chr4:3075000-3077800	Active TSS	H9 Cell Line	embryonic stem cell
12	chr4:3075000-3078400	Active TSS	A549	lung
13	chr4:3075200-3077000	Active TSS	Primary T cells from cord blood	blood
14	chr4:3075200-3077000	Active TSS	Brain Substantia Nigra	brain
15	chr4:3075200-3077200	Active TSS	Sigmoid Colon	Sigmoid Colon
16	chr4:3075200-3077400	Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr4:3075200-3077400	Active TSS	Colonic Mucosa	Colon
18	chr4:3075200-3077400	Active TSS	Colon Smooth Muscle	Colon
19	chr4:3075200-3077400	Active TSS	Rectal Smooth Muscle	rectum
20	chr4:3075200-3077600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr4:3075200-3077600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr4:3075200-3077600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr4:3075200-3077600	Active TSS	Muscle Satellite Cultured Cells	--
24	chr4:3075200-3077600	Active TSS	Brain Cingulate Gyrus	brain
25	chr4:3075200-3077600	Active TSS	Duodenum Mucosa	Duodenum
26	chr4:3075200-3077600	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr4:3075200-3077600	Active TSS	Fetal Kidney	kidney
28	chr4:3075200-3077600	Active TSS	Hela-S3	cervix
29	chr4:3075200-3077600	Active TSS	HUVEC	blood vessel
30	chr4:3075200-3077600	Active TSS	NHEK	skin
31	chr4:3075200-3077800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
32	chr4:3075200-3077800	Active TSS	Aorta	Aorta
33	chr4:3075200-3077800	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr4:3075200-3078000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr4:3075200-3078600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr4:3075400-3077000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
37	chr4:3075400-3077000	Active TSS	Brain Hippocampus Middle	brain
38	chr4:3075400-3077000	Weak transcription	Fetal Heart	heart
39	chr4:3075400-3077000	Active TSS	Skeletal Muscle Male	skeletal muscle
40	chr4:3075400-3077200	Active TSS	Stomach Mucosa	stomach
41	chr4:3075400-3077400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr4:3075400-3077400	Active TSS	Brain Inferior Temporal Lobe	brain
43	chr4:3075400-3077400	Active TSS	Fetal Lung	lung
44	chr4:3075400-3077400	Active TSS	Fetal Stomach	stomach
45	chr4:3075400-3077400	Active TSS	Gastric	stomach
46	chr4:3075400-3077400	Active TSS	Pancreas	Pancrea
47	chr4:3075400-3077400	Active TSS	Small Intestine	intestine
48	chr4:3075400-3077400	Active TSS	K562	blood
49	chr4:3075400-3077600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr4:3075400-3077600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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