Variant report

Variant	rs514401
Chromosome Location	chr11:62500504-62500505
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:132)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:132 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr11:62500380-62500530	SK-N-SH_RA	brain:	n/a	n/a
2	CTCF	chr11:62500380-62500530	NHDF-neo	bronchial:	n/a	n/a
3	CTCF	chr11:62500400-62500550	AG09319	gingival:	n/a	n/a
4	MYC	chr11:62500395-62500619	MCF10A-Er-Src	breast:	n/a	n/a
5	CTCF	chr11:62500360-62500510	BJ	skin:	n/a	n/a
6	CTCF	chr11:62500420-62500570	HMF	breast:	n/a	n/a
7	CTCF	chr11:62500277-62500560	A549	lung:	n/a	n/a
8	STAT3	chr11:62500418-62500653	MCF10A-Er-Src	breast:	n/a	n/a
9	CTCF	chr11:62500380-62500530	HBMEC	blood vessel:	n/a	n/a
10	CTCF	chr11:62500360-62500510	GM12865	blood:	n/a	n/a
11	CTCF	chr11:62500308-62500678	GM12878	blood:	n/a	n/a
12	CTCF	chr11:62500380-62500530	NHLF	lung:	n/a	n/a
13	CTCF	chr11:62500360-62500510	HPAF	blood vessel:	n/a	n/a
14	CTCF	chr11:62500380-62500530	GM12878	blood:	n/a	n/a
15	CTCF	chr11:62500360-62500510	HepG2	liver:	n/a	n/a
16	CTCF	chr11:62500360-62500510	HRPEpiC	eye:	n/a	n/a
17	RAD21	chr11:62500308-62500688	MCF-7	breast:	n/a	n/a
18	CTCF	chr11:62500400-62500550	GM12872	blood:	n/a	n/a
19	RAD21	chr11:62500338-62500595	GM12878	blood:	n/a	n/a
20	CTCF	chr11:62500367-62500552	MCF-7	breast:	n/a	n/a
21	CTCF	chr11:62500460-62500610	HEEpiC	esophagus:	n/a	n/a
22	BATF	chr11:62500394-62500651	GM12878	blood:	n/a	n/a
23	CTCF	chr11:62500460-62500610	BE2_C	brain:	n/a	n/a
24	CTCF	chr11:62500400-62500630	GM12871	blood:	n/a	n/a
25	CTCF	chr11:62500380-62500530	WERI-Rb-1	eye:	n/a	n/a
26	CTCF	chr11:62500460-62500610	NB4	blood:	n/a	n/a
27	CTCF	chr11:62500307-62500716	HCT-116	colon:	n/a	n/a
28	FOS	chr11:62500492-62500716	MCF10A-Er-Src	breast:	n/a	chr11:62500688-62500699
29	RAD21	chr11:62500314-62500702	MCF-7	breast:	n/a	n/a
30	CTCF	chr11:62500380-62500530	GM12864	blood:	n/a	n/a
31	MYC	chr11:62500373-62500566	MCF10A-Er-Src	breast:	n/a	n/a
32	CTCF	chr11:62500380-62500530	HUVEC	blood vessel:	n/a	n/a
33	CTCF	chr11:62500500-62500650	HCT-116	colon:	n/a	n/a
34	CTCF	chr11:62500360-62500510	HEK293	kidney:	n/a	n/a
35	CTCF	chr11:62500400-62500550	HVMF	connective:	n/a	n/a
36	RAD21	chr11:62500327-62500639	K562	blood:	n/a	n/a
37	CTCF	chr11:62500319-62500751	SK-N-SH	brain:	n/a	n/a
38	FOS	chr11:62500375-62500798	MCF10A-Er-Src	breast:	n/a	chr11:62500414-62500423 chr11:62500688-62500699
39	CTCF	chr11:62500400-62500550	AG04450	lung:	n/a	n/a
40	CTCF	chr11:62500376-62500587	SK-N-SH_RA	brain:	n/a	n/a
41	CTCF	chr11:62500360-62500510	GM12871	blood:	n/a	n/a
42	RAD21	chr11:62500330-62500622	A549	lung:	n/a	n/a
43	CTCF	chr11:62500402-62500555	Hela-S3	cervix:	n/a	n/a
44	RAD21	chr11:62500309-62500653	HepG2	liver:	n/a	n/a
45	RAD21	chr11:62500254-62500579	H1-hESC	embryonic stem cell:	n/a	n/a
46	RAD21	chr11:62500320-62500636	SK-N-SH_RA	brain:	n/a	n/a
47	CTCF	chr11:62500400-62500550	K562	blood:	n/a	n/a
48	CTCF	chr11:62500360-62500510	AG09309	skin:	n/a	n/a
49	CTCF	chr11:62500429-62500519	LNCaP	prostate:	n/a	n/a
50	FOS	chr11:62500408-62500717	MCF10A-Er-Src	breast:	n/a	chr11:62500414-62500423 chr11:62500688-62500699

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:62500420..62503058-chr11:62607981..62610367,3	K562	blood:
2	chr11:62493487..62501439-chr11:62552997..62556820,17	MCF-7	breast:
3	chr11:62487017..62500577-chr11:62602457..62611761,54	MCF-7	breast:
4	chr11:62446326..62448445-chr11:62498481..62500616,2	MCF-7	breast:
5	chr11:62500420..62503058-chr11:62607981..62610367,2	K562	blood:
6	chr11:62500244..62500923-chr11:62553685..62554225,2	MCF-7	breast:
7	chr11:62499024..62507318-chr11:62604678..62610455,13	MCF-7	breast:
8	chr11:62500067..62500672-chr11:62536957..62537853,3	MCF-7	breast:
9	chr11:62499396..62502018-chr11:62503269..62504907,2	MCF-7	breast:
10	chr11:62498670..62500573-chr11:62507466..62509054,2	MCF-7	breast:
11	chr11:62499174..62500991-chr11:62510148..62512896,2	K562	blood:
12	chr11:62498734..62500589-chr11:62571465..62573205,2	MCF-7	breast:

No data

Variant related genes	Relation type
TTC9C	TF binding region
ENSG00000162191	Chromatin interaction
ENSG00000162231	Chromatin interaction
ENSG00000269176	Chromatin interaction
ENSG00000185475	Chromatin interaction
ENSG00000133316	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11822922	1.00[EUR][1000 genomes]
rs12273912	1.00[EUR][1000 genomes]
rs1787724	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2510538	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2584915	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2584917	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2730030	1.00[EUR][1000 genomes]
rs2956139	1.00[EUR][1000 genomes]
rs2958240	1.00[EUR][1000 genomes]
rs481272	1.00[EUR][1000 genomes]
rs482331	1.00[EUR][1000 genomes]
rs486451	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs489275	1.00[EUR][1000 genomes]
rs4963309	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs506132	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs507101	1.00[EUR][1000 genomes]
rs518780	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs519473	1.00[EUR][1000 genomes]
rs523328	1.00[EUR][1000 genomes]
rs544573	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs560618	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs561385	1.00[EUR][1000 genomes]
rs56226867	1.00[EUR][1000 genomes]
rs56262657	1.00[EUR][1000 genomes]
rs564587	1.00[EUR][1000 genomes]
rs572513	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs573146	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57338459	1.00[EUR][1000 genomes]
rs575134	1.00[EUR][1000 genomes]
rs577071	1.00[EUR][1000 genomes]
rs57858466	1.00[EUR][1000 genomes]
rs592337	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs595108	1.00[EUR][1000 genomes]
rs60568977	1.00[EUR][1000 genomes]
rs60668695	1.00[EUR][1000 genomes]
rs619109	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs646194	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs692773	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs694678	1.00[EUR][1000 genomes]
rs73487834	1.00[EUR][1000 genomes]
rs73487878	1.00[EUR][1000 genomes]
rs73487879	1.00[EUR][1000 genomes]
rs73487880	1.00[EUR][1000 genomes]
rs73490026	1.00[EUR][1000 genomes]
rs73502133	1.00[EUR][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	nsv915636	chr11:62016992-62713565	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1441 gene(s)	inside rSNPs	diseases
2	nsv532283	chr11:62201358-62863475	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1433 gene(s)	inside rSNPs	diseases
3	nsv532284	chr11:62220043-62630253	Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1401 gene(s)	inside rSNPs	diseases
4	nsv497903	chr11:62330308-62608042	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	489 gene(s)	inside rSNPs	diseases
5	nsv897623	chr11:62438819-62603916	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	215 gene(s)	inside rSNPs	diseases
6	nsv348	chr11:62474450-62519712	Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62496800-62500600	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr11:62496800-62500800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr11:62496800-62502000	Weak transcription	Brain Substantia Nigra	brain
4	chr11:62496800-62516400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr11:62496800-62521000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr11:62497000-62508200	Weak transcription	Aorta	Aorta
7	chr11:62497400-62502600	Weak transcription	Esophagus	oesophagus
8	chr11:62497400-62520400	Weak transcription	Psoas Muscle	Psoas
9	chr11:62497600-62502600	Weak transcription	HSMMtube	muscle
10	chr11:62497600-62503200	Weak transcription	Right Atrium	heart
11	chr11:62497600-62504800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr11:62497600-62519400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr11:62497800-62500800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr11:62497800-62502200	Weak transcription	Rectal Smooth Muscle	rectum
15	chr11:62497800-62502400	Weak transcription	Ovary	ovary
16	chr11:62497800-62502400	Weak transcription	Pancreas	Pancrea
17	chr11:62497800-62509600	Strong transcription	Fetal Intestine Small	intestine
18	chr11:62497800-62519600	Weak transcription	Gastric	stomach
19	chr11:62498000-62500600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr11:62498000-62500600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr11:62498000-62500600	Weak transcription	Primary B cells from cord blood	blood
22	chr11:62498000-62500600	Weak transcription	Fetal Kidney	kidney
23	chr11:62498000-62500600	Weak transcription	NHDF-Ad	bronchial
24	chr11:62498000-62500800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr11:62498000-62500800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr11:62498000-62502200	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr11:62498000-62502600	Weak transcription	NH-A	brain
28	chr11:62498000-62505600	Weak transcription	Small Intestine	intestine
29	chr11:62498000-62505800	Weak transcription	Right Ventricle	heart
30	chr11:62498000-62509600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr11:62498000-62509600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr11:62498000-62509600	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr11:62498200-62500600	Weak transcription	HMEC	breast
34	chr11:62498200-62500600	Weak transcription	Osteobl	bone
35	chr11:62498200-62502000	Weak transcription	Left Ventricle	heart
36	chr11:62498200-62502400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr11:62498200-62502600	Weak transcription	Primary hematopoietic stem cells	blood
38	chr11:62498400-62500600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr11:62498600-62501000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
40	chr11:62498600-62503800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr11:62498600-62503800	Strong transcription	Placenta	Placenta
42	chr11:62498600-62509600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr11:62498800-62500600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr11:62498800-62500600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr11:62498800-62502600	Weak transcription	NHEK	skin
46	chr11:62498800-62505800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr11:62498800-62509200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr11:62498800-62509600	Strong transcription	Fetal Stomach	stomach
49	chr11:62499000-62500600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr11:62499000-62500600	Weak transcription	Primary B cells from peripheral blood	blood

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