Variant report

Variant	rs10009935
Chromosome Location	chr4:3077037-3077038
allele	C/T
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	PML	chr4:3076965-3077338	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:3076754-3077330	K562	blood:	n/a	n/a
3	EP300	chr4:3076951-3077151	HepG2	liver:	n/a	n/a
4	RCOR1	chr4:3077016-3077569	K562	blood:	n/a	n/a
5	CTCF	chr4:3076980-3077130	RPTEC	kidney:	n/a	n/a
6	POLR2A	chr4:3076901-3077344	PFSK-1	brain:	n/a	n/a
7	EGR1	chr4:3076591-3077089	K562	blood:	n/a	chr4:3076966-3076976 chr4:3076965-3076978 chr4:3076965-3076978
8	POLR2A	chr4:3076758-3078137	GM12891	blood:	n/a	n/a
9	YY1	chr4:3076147-3077339	GM12892	blood:	n/a	chr4:3076399-3076413 chr4:3076297-3076311 chr4:3076417-3076437 chr4:3076261-3076272 chr4:3076405-3076416
10	POLR2A	chr4:3075066-3078105	GM15510	blood:	n/a	n/a
11	YY1	chr4:3076738-3077357	GM12878	blood:	n/a	n/a
12	FOXM1	chr4:3076791-3077400	GM12878	blood:	n/a	n/a
13	TBP	chr4:3076869-3077523	HepG2	liver:	n/a	n/a
14	CHD2	chr4:3076812-3077389	HepG2	liver:	n/a	chr4:3076978-3076988 chr4:3077035-3077044
15	POLR2A	chr4:3076094-3078808	GM12878	blood:	n/a	n/a
16	BCLAF1	chr4:3076808-3077331	GM12878	blood:	n/a	chr4:3077266-3077279
17	YY1	chr4:3076812-3077229	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr4:3076873-3077717	MCF10A-Er-Src	breast:	n/a	n/a
19	PML	chr4:3076003-3078213	GM12878	blood:	n/a	n/a
20	EGR1	chr4:3076633-3077112	K562	blood:	n/a	chr4:3076966-3076976 chr4:3076965-3076978 chr4:3076965-3076978
21	POLR2A	chr4:3075327-3080089	GM18505	blood:	n/a	n/a
22	POU2F2	chr4:3076813-3077918	GM12878	blood:	n/a	chr4:3077377-3077389 chr4:3077373-3077385 chr4:3077370-3077382
23	BRCA1	chr4:3076899-3077271	H1-hESC	embryonic stem cell:	n/a	chr4:3077035-3077044
24	YY1	chr4:3076786-3077350	GM12891	blood:	n/a	n/a
25	RUNX3	chr4:3076776-3078119	GM12878	blood:	n/a	n/a
26	POLR2A	chr4:3076054-3080438	GM12891	blood:	n/a	n/a
27	POLR2A	chr4:3077003-3077349	HCT-116	colon:	n/a	n/a
28	HCFC1	chr4:3076909-3077251	K562	blood:	n/a	n/a
29	RELA	chr4:3077008-3078516	GM18505	blood:	n/a	n/a
30	FOXM1	chr4:3076919-3078036	GM12878	blood:	n/a	n/a
31	POU2F2	chr4:3076726-3077345	GM12891	blood:	n/a	n/a
32	STAT5A	chr4:3076785-3078582	GM12878	blood:	n/a	chr4:3077371-3077383 chr4:3077377-3077389 chr4:3077370-3077382 chr4:3077381-3077393
33	ZMIZ1	chr4:3076898-3077112	K562	blood:	n/a	n/a
34	NFIC	chr4:3076912-3077918	GM12878	blood:	n/a	n/a
35	SIN3A	chr4:3076044-3077367	H1-hESC	embryonic stem cell:	n/a	chr4:3076486-3076497 chr4:3076479-3076493
36	HMGN3	chr4:3076832-3077144	K562	blood:	n/a	n/a
37	CTCF	chr4:3077000-3077150	NHLF	lung:	n/a	n/a
38	TBP	chr4:3076135-3077374	H1-hESC	embryonic stem cell:	n/a	n/a
39	POLR2A	chr4:3076039-3077704	GM10847	blood:	n/a	n/a
40	TAF7	chr4:3076767-3077131	H1-hESC	embryonic stem cell:	n/a	n/a
41	SPI1	chr4:3076963-3077318	GM12891	blood:	n/a	chr4:3077229-3077242 chr4:3077235-3077248
42	HEY1	chr4:3076889-3077328	K562	blood:	n/a	n/a
43	BRCA1	chr4:3077033-3077221	GM12878	blood:	n/a	chr4:3077035-3077044
44	MAZ	chr4:3076867-3077775	GM12878	blood:	n/a	chr4:3077170-3077180 chr4:3077374-3077384 chr4:3077004-3077014 chr4:3076965-3076975
45	POLR2A	chr4:3076894-3077552	U87	brain:	n/a	n/a
46	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
47	RELA	chr4:3076849-3078101	GM12891	blood:	n/a	n/a
48	CHD2	chr4:3076851-3077329	K562	blood:	n/a	chr4:3076978-3076988 chr4:3077035-3077044
49	TAF1	chr4:3076774-3077363	ECC-1	luminal epithelium:	n/a	n/a
50	POLR2A	chr4:3077030-3077331	SK-N-MC	brain:	n/a	n/a

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	chr4:3076969..3077469-chr6:36853503..36854013,2	K562	blood:
5	chr17:16556241..16557924-chr4:3075466..3077603,2	MCF-7	breast:
6	chr4:3076858..3078560-chr4:3090552..3093969,4	MCF-7	breast:
7	chr4:3076735..3079040-chr4:3100560..3102807,2	K562	blood:
8	chr4:3074885..3077461-chr4:3292207..3294882,2	MCF-7	breast:
9	chr4:3076522..3079094-chr4:3136211..3138250,2	MCF-7	breast:
10	chr4:2935808..2938115-chr4:3076304..3078834,3	K562	blood:
11	chr4:3075973..3077923-chr4:3128614..3130547,2	MCF-7	breast:
12	chr4:3076560..3079556-chr4:3107118..3109310,3	MCF-7	breast:
13	chr4:2935808..2937729-chr4:3076912..3078834,2	K562	blood:
14	chr4:2964356..2966158-chr4:3074837..3077632,2	K562	blood:
15	chr4:2262471..2264332-chr4:3074788..3077577,2	MCF-7	breast:
16	chr4:2468745..2470693-chr4:3075535..3077781,3	K562	blood:

Variant related genes	Relation type
HTT-AS	TF binding region
ENSG00000249673	Chromatin interaction
ENSG00000197386	Chromatin interaction
ENSG00000188981	Chromatin interaction
ENSG00000264765	Chromatin interaction
ENSG00000087269	Chromatin interaction
ENSG00000197566	Chromatin interaction
ENSG00000063978	Chromatin interaction
ENSG00000123933	Chromatin interaction
ENSG00000125388	Chromatin interaction
ENSG00000198663	Chromatin interaction
ENSG00000159788	Chromatin interaction
ENSG00000109736	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10000252	1.00[CEU][hapmap]
rs10002065	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10006129	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10006977	0.97[EUR][1000 genomes]
rs10009229	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10010375	1.00[CEU][hapmap]
rs10011127	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10011412	1.00[CEU][hapmap]
rs10014333	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs10016755	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10034313	0.90[EUR][1000 genomes]
rs10222986	0.97[EUR][1000 genomes]
rs1419036	1.00[CEU][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16843857	0.84[EUR][1000 genomes]
rs16843866	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs16843869	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2471343	1.00[CEU][hapmap]
rs2515931	1.00[CEU][hapmap]
rs2515934	1.00[CEU][hapmap]
rs28377140	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28387056	0.90[EUR][1000 genomes]
rs28393280	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28394705	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28398130	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28468636	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28485764	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28564368	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28580164	0.84[EUR][1000 genomes]
rs28583447	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28583552	0.81[EUR][1000 genomes]
rs28584232	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28616835	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28629394	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28634516	0.84[EUR][1000 genomes]
rs28660254	0.84[EUR][1000 genomes]
rs28670335	0.90[EUR][1000 genomes]
rs28682489	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28696693	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28714390	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28718346	0.97[EUR][1000 genomes]
rs28755900	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3025837	1.00[ASN][1000 genomes]
rs363138	1.00[CEU][hapmap]
rs363140	1.00[ASN][1000 genomes]
rs4346595	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60215756	1.00[ASN][1000 genomes]
rs6813198	1.00[ASN][1000 genomes]
rs6813223	1.00[ASN][1000 genomes]
rs6813958	1.00[ASN][1000 genomes]
rs6830019	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6835897	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6856403	1.00[ASN][1000 genomes]
rs73792352	1.00[ASN][1000 genomes]
rs7436457	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7664480	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7678336	1.00[ASN][1000 genomes]
rs7693317	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs9291159	1.00[CEU][hapmap]
rs9991144	1.00[CEU][hapmap]
rs9995782	0.90[EUR][1000 genomes]
rs9996075	0.90[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	chr4:3075000-3077400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr4:3075000-3077400	Active TSS	HSMM	muscle
5	chr4:3075000-3077600	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr4:3075000-3077600	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr4:3075000-3077600	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr4:3075000-3077600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr4:3075000-3077600	Active TSS	Brain Germinal Matrix	brain
10	chr4:3075000-3077800	Active TSS	H9 Cell Line	embryonic stem cell
11	chr4:3075000-3078400	Active TSS	A549	lung
12	chr4:3075200-3077200	Active TSS	Sigmoid Colon	Sigmoid Colon
13	chr4:3075200-3077400	Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr4:3075200-3077400	Active TSS	Colonic Mucosa	Colon
15	chr4:3075200-3077400	Active TSS	Colon Smooth Muscle	Colon
16	chr4:3075200-3077400	Active TSS	Rectal Smooth Muscle	rectum
17	chr4:3075200-3077600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:3075200-3077600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr4:3075200-3077600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr4:3075200-3077600	Active TSS	Muscle Satellite Cultured Cells	--
21	chr4:3075200-3077600	Active TSS	Brain Cingulate Gyrus	brain
22	chr4:3075200-3077600	Active TSS	Duodenum Mucosa	Duodenum
23	chr4:3075200-3077600	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr4:3075200-3077600	Active TSS	Fetal Kidney	kidney
25	chr4:3075200-3077600	Active TSS	Hela-S3	cervix
26	chr4:3075200-3077600	Active TSS	HUVEC	blood vessel
27	chr4:3075200-3077600	Active TSS	NHEK	skin
28	chr4:3075200-3077800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:3075200-3077800	Active TSS	Aorta	Aorta
30	chr4:3075200-3077800	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr4:3075200-3078000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr4:3075200-3078600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr4:3075400-3077200	Active TSS	Stomach Mucosa	stomach
34	chr4:3075400-3077400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:3075400-3077400	Active TSS	Brain Inferior Temporal Lobe	brain
36	chr4:3075400-3077400	Active TSS	Fetal Lung	lung
37	chr4:3075400-3077400	Active TSS	Fetal Stomach	stomach
38	chr4:3075400-3077400	Active TSS	Gastric	stomach
39	chr4:3075400-3077400	Active TSS	Pancreas	Pancrea
40	chr4:3075400-3077400	Active TSS	Small Intestine	intestine
41	chr4:3075400-3077400	Active TSS	K562	blood
42	chr4:3075400-3077600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr4:3075400-3077600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr4:3075400-3077600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr4:3075400-3077600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr4:3075400-3077600	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr4:3075400-3077600	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr4:3075400-3077600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr4:3075400-3077600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr4:3075400-3077600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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