Variant report

Variant	rs13102260
Chromosome Location	chr4:3076405-3076406
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	chr4:3076322-3076593	SK-N-MC	brain:	n/a	n/a
2	MAX	chr4:3076141-3076504	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr4:3076359-3076547	HepG2	liver:	n/a	n/a
4	TAF1	chr4:3076212-3076593	HepG2	liver:	n/a	n/a
5	STAT1	chr4:3075636-3076538	GM12878	blood:	n/a	n/a
6	MXI1	chr4:3075132-3076606	HepG2	liver:	n/a	n/a
7	POLR2A	chr4:3076031-3076656	PFSK-1	brain:	n/a	n/a
8	RELA	chr4:3076056-3076617	GM15510	blood:	n/a	n/a
9	TAF1	chr4:3076036-3076641	K562	blood:	n/a	n/a
10	POLR2A	chr4:3076009-3076689	ECC-1	luminal epithelium:	n/a	n/a
11	TBP	chr4:3076282-3076488	Hela-S3	cervix:	n/a	n/a
12	YY1	chr4:3076147-3077339	GM12892	blood:	n/a	chr4:3076399-3076413 chr4:3076297-3076311 chr4:3076417-3076437 chr4:3076261-3076272 chr4:3076405-3076416
13	POLR2A	chr4:3075066-3078105	GM15510	blood:	n/a	n/a
14	HCFC1	chr4:3076063-3076624	K562	blood:	n/a	n/a
15	POLR2A	chr4:3076272-3076587	HepG2	liver:	n/a	n/a
16	POLR2A	chr4:3076335-3076565	A549	lung:	n/a	n/a
17	POLR2A	chr4:3075339-3076734	MCF-7	breast:	n/a	n/a
18	POLR2A	chr4:3076012-3076728	GM12891	blood:	n/a	n/a
19	POLR2A	chr4:3076094-3078808	GM12878	blood:	n/a	n/a
20	PML	chr4:3076003-3078213	GM12878	blood:	n/a	n/a
21	YY1	chr4:3076164-3076654	SK-N-SH_RA	brain:	n/a	chr4:3076399-3076413 chr4:3076297-3076311 chr4:3076417-3076437 chr4:3076261-3076272 chr4:3076405-3076416
22	YY1	chr4:3076233-3076618	NT2-D1	testis:	n/a	chr4:3076399-3076413 chr4:3076297-3076311 chr4:3076417-3076437 chr4:3076261-3076272 chr4:3076405-3076416
23	POLR2A	chr4:3076257-3076640	K562	blood:	n/a	n/a
24	MXI1	chr4:3074910-3076677	SK-N-SH	brain:	n/a	n/a
25	POU2F2	chr4:3076029-3076599	GM12891	blood:	n/a	n/a
26	POLR2A	chr4:3076241-3076671	A549	lung:	n/a	n/a
27	EP300	chr4:3076118-3076516	GM12878	blood:	n/a	n/a
28	GTF2F1	chr4:3076384-3076487	H1-hESC	embryonic stem cell:	n/a	n/a
29	CREB1	chr4:3075473-3076678	K562	blood:	n/a	n/a
30	POLR2A	chr4:3076164-3076595	K562	blood:	n/a	n/a
31	JUND	chr4:3076232-3076503	HepG2	liver:	n/a	n/a
32	POLR2A	chr4:3076328-3076594	HepG2	liver:	n/a	n/a
33	MAZ	chr4:3075228-3076619	K562	blood:	n/a	n/a
34	POLR2A	chr4:3076171-3076674	HCT-116	colon:	n/a	n/a
35	POLR2A	chr4:3075327-3080089	GM18505	blood:	n/a	n/a
36	ZEB1	chr4:3076107-3076571	GM12878	blood:	n/a	n/a
37	YY1	chr4:3076209-3076737	SK-N-SH	brain:	n/a	chr4:3076399-3076413 chr4:3076297-3076311 chr4:3076417-3076437 chr4:3076261-3076272 chr4:3076405-3076416
38	BCLAF1	chr4:3076054-3076689	GM12878	blood:	n/a	chr4:3076489-3076502
39	REST	chr4:3076288-3076775	HL-60	blood:	n/a	chr4:3076480-3076494 chr4:3076482-3076492
40	RCOR1	chr4:3076049-3076509	Hela-S3	cervix:	n/a	n/a
41	SP1	chr4:3075387-3076643	HCT-116	colon:	n/a	chr4:3075447-3075457 chr4:3076267-3076276 chr4:3076265-3076276 chr4:3075447-3075456
42	MAZ	chr4:3075379-3076478	HepG2	liver:	n/a	n/a
43	YY1	chr4:3076288-3076624	K562	blood:	n/a	chr4:3076399-3076413 chr4:3076297-3076311 chr4:3076417-3076437 chr4:3076405-3076416
44	TAF1	chr4:3075990-3076722	MCF-7	breast:	n/a	n/a
45	POLR2A	chr4:3076054-3080438	GM12891	blood:	n/a	n/a
46	POLR2A	chr4:3076219-3076633	HCT-116	colon:	n/a	n/a
47	CCNT2	chr4:3076021-3076570	K562	blood:	n/a	n/a
48	POLR2A	chr4:3076029-3076598	GM12892	blood:	n/a	n/a
49	POLR2A	chr4:3076225-3076744	HL-60	blood:	n/a	n/a
50	TBL1XR1	chr4:3076092-3076522	GM12878	blood:	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	chr17:16556241..16557924-chr4:3075466..3077603,2	MCF-7	breast:
4	chr4:3074885..3077461-chr4:3292207..3294882,2	MCF-7	breast:
5	chr4:2935808..2938115-chr4:3076304..3078834,3	K562	blood:
6	chr4:3075973..3077923-chr4:3128614..3130547,2	MCF-7	breast:
7	chr4:2964356..2966158-chr4:3074837..3077632,2	K562	blood:
8	chr4:2262471..2264332-chr4:3074788..3077577,2	MCF-7	breast:
9	chr4:2468745..2470693-chr4:3075535..3077781,3	K562	blood:

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

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs13122415	0.93[ASN][1000 genomes]
rs28656215	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35631490	0.91[ASN][1000 genomes]
rs9996199	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][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	chr4:3075000-3076600	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:3075000-3077000	Active TSS	Osteobl	bone
5	chr4:3075000-3077400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr4:3075000-3077400	Active TSS	HSMM	muscle
7	chr4:3075000-3077600	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr4:3075000-3077600	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr4:3075000-3077600	Active TSS	iPS-15b Cell Line	embryonic stem cell
10	chr4:3075000-3077600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:3075000-3077600	Active TSS	Brain Germinal Matrix	brain
12	chr4:3075000-3077800	Active TSS	H9 Cell Line	embryonic stem cell
13	chr4:3075000-3078400	Active TSS	A549	lung
14	chr4:3075200-3077000	Active TSS	Primary T cells from cord blood	blood
15	chr4:3075200-3077000	Active TSS	Brain Substantia Nigra	brain
16	chr4:3075200-3077200	Active TSS	Sigmoid Colon	Sigmoid Colon
17	chr4:3075200-3077400	Active TSS	Primary T killer memory cells from peripheral blood	blood
18	chr4:3075200-3077400	Active TSS	Colonic Mucosa	Colon
19	chr4:3075200-3077400	Active TSS	Colon Smooth Muscle	Colon
20	chr4:3075200-3077400	Active TSS	Rectal Smooth Muscle	rectum
21	chr4:3075200-3077600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:3075200-3077600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr4:3075200-3077600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:3075200-3077600	Active TSS	Muscle Satellite Cultured Cells	--
25	chr4:3075200-3077600	Active TSS	Brain Cingulate Gyrus	brain
26	chr4:3075200-3077600	Active TSS	Duodenum Mucosa	Duodenum
27	chr4:3075200-3077600	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr4:3075200-3077600	Active TSS	Fetal Kidney	kidney
29	chr4:3075200-3077600	Active TSS	Hela-S3	cervix
30	chr4:3075200-3077600	Active TSS	HUVEC	blood vessel
31	chr4:3075200-3077600	Active TSS	NHEK	skin
32	chr4:3075200-3077800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr4:3075200-3077800	Active TSS	Aorta	Aorta
34	chr4:3075200-3077800	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr4:3075200-3078000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:3075200-3078600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr4:3075400-3077000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
38	chr4:3075400-3077000	Active TSS	Brain Hippocampus Middle	brain
39	chr4:3075400-3077000	Weak transcription	Fetal Heart	heart
40	chr4:3075400-3077000	Active TSS	Skeletal Muscle Male	skeletal muscle
41	chr4:3075400-3077200	Active TSS	Stomach Mucosa	stomach
42	chr4:3075400-3077400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr4:3075400-3077400	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr4:3075400-3077400	Active TSS	Fetal Lung	lung
45	chr4:3075400-3077400	Active TSS	Fetal Stomach	stomach
46	chr4:3075400-3077400	Active TSS	Gastric	stomach
47	chr4:3075400-3077400	Active TSS	Pancreas	Pancrea
48	chr4:3075400-3077400	Active TSS	Small Intestine	intestine
49	chr4:3075400-3077400	Active TSS	K562	blood
50	chr4:3075400-3077600	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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