Variant report

Variant	rs560618
Chromosome Location	chr11:62475253-62475254
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:54)
CpG islands
(count:0)
Chromatin interactive
region (count:34)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:54 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ATF2	chr11:62474520-62475276	H1-hESC	embryonic stem cell:	n/a	n/a
2	YY1	chr11:62474513-62475401	H1-hESC	embryonic stem cell:	n/a	n/a
3	SIX5	chr11:62474822-62475280	H1-hESC	embryonic stem cell:	n/a	n/a
4	RCOR1	chr11:62474939-62475312	K562	blood:	n/a	n/a
5	BHLHE40	chr11:62474705-62475267	K562	blood:	n/a	n/a
6	REST	chr11:62474426-62475519	H1-neurons	neurons:	n/a	chr11:62475142-62475150
7	POLR2A	chr11:62475066-62475337	GM12878	blood:	n/a	n/a
8	POLR2A	chr11:62472750-62475476	H1-hESC	embryonic stem cell:	n/a	n/a
9	CHD1	chr11:62474640-62475303	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr11:62474459-62475648	PANC-1	pancreas:	n/a	n/a
11	RCOR1	chr11:62475026-62475280	K562	blood:	n/a	n/a
12	POLR2A	chr11:62474665-62475563	K562	blood:	n/a	n/a
13	TAF1	chr11:62473242-62475572	H1-neurons	neurons:	n/a	n/a
14	POLR2A	chr11:62474778-62475334	ECC-1	luminal epithelium:	n/a	n/a
15	JUND	chr11:62474659-62475273	K562	blood:	n/a	n/a
16	POLR2A	chr11:62473201-62475950	H1-neurons	neurons:	n/a	n/a
17	REST	chr11:62472987-62476045	H1-neurons	neurons:	n/a	chr11:62475142-62475150 chr11:62473445-62473463 chr11:62476001-62476010
18	TAF1	chr11:62474596-62475435	H1-neurons	neurons:	n/a	n/a
19	CREB1	chr11:62474661-62475311	H1-hESC	embryonic stem cell:	n/a	n/a
20	TAF7	chr11:62474548-62475298	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr11:62472775-62476654	K562	blood:	n/a	n/a
22	SIX5	chr11:62474835-62475260	H1-hESC	embryonic stem cell:	n/a	n/a
23	CREB1	chr11:62474632-62475275	H1-hESC	embryonic stem cell:	n/a	n/a
24	MAX	chr11:62474637-62475350	H1-hESC	embryonic stem cell:	n/a	chr11:62474855-62474865
25	MAX	chr11:62474498-62475330	H1-hESC	embryonic stem cell:	n/a	chr11:62474855-62474865
26	POLR2A	chr11:62474622-62475624	HepG2	liver:	n/a	n/a
27	ZNF263	chr11:62474642-62476365	HEK293-T-REx	kidney:	n/a	chr11:62474852-62474861 chr11:62475636-62475645 chr11:62475639-62475648 chr11:62475975-62475984 chr11:62475633-62475642
28	POLR2A	chr11:62474593-62475434	K562	blood:	n/a	n/a
29	ATF2	chr11:62474534-62475447	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr11:62474621-62477898	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr11:62473118-62478469	HepG2	liver:	n/a	n/a
32	POLR2A	chr11:62474902-62475559	MCF-7	breast:	n/a	n/a
33	EP300	chr11:62474730-62475279	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr11:62474532-62475550	PFSK-1	brain:	n/a	n/a
35	EP300	chr11:62474728-62475261	H1-hESC	embryonic stem cell:	n/a	n/a
36	TAF1	chr11:62474556-62475295	H1-hESC	embryonic stem cell:	n/a	n/a
37	EGR1	chr11:62474893-62475254	K562	blood:	n/a	n/a
38	POLR2A	chr11:62473169-62475614	H1-neurons	neurons:	n/a	n/a
39	POLR2A	chr11:62474793-62476670	Hela-S3	cervix:	n/a	n/a
40	EGR1	chr11:62474808-62475287	H1-hESC	embryonic stem cell:	n/a	n/a
41	TEAD4	chr11:62474803-62475302	H1-hESC	embryonic stem cell:	n/a	n/a
42	POLR2A	chr11:62474751-62475277	H1-hESC	embryonic stem cell:	n/a	n/a
43	YY1	chr11:62474590-62475266	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr11:62473247-62475412	PANC-1	pancreas:	n/a	n/a
45	JUND	chr11:62474639-62475285	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr11:62473857-62475370	H1-hESC	embryonic stem cell:	n/a	n/a
47	CTBP2	chr11:62474637-62475428	H1-hESC	embryonic stem cell:	n/a	n/a
48	TEAD4	chr11:62474750-62475332	H1-hESC	embryonic stem cell:	n/a	n/a
49	SIN3A	chr11:62472966-62475279	H1-hESC	embryonic stem cell:	n/a	chr11:62473592-62473603 chr11:62473600-62473611 chr11:62473591-62473604
50	SP1	chr11:62474642-62475351	H1-hESC	embryonic stem cell:	n/a	chr11:62475037-62475046 chr11:62475038-62475047 chr11:62475033-62475047 chr11:62475036-62475048 chr11:62475037-62475047 chr11:62475036-62475048 chr11:62474850-62474864 chr11:62475036-62475047

No data

(count:34 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:62472165..62476250-chr11:62556778..62559261,3	MCF-7	breast:
2	chr11:62472932..62477098-chr11:62554264..62558225,4	K562	blood:
3	chr11:62454251..62459827-chr11:62470958..62475427,7	MCF-7	breast:
4	chr11:62473263..62476310-chr11:62622744..62625720,5	K562	blood:
5	chr11:62455845..62461275-chr11:62472394..62475433,5	K562	blood:
6	chr11:62474385..62478486-chr11:62621122..62625313,5	MCF-7	breast:
7	chr11:62430865..62437145-chr11:62471927..62479051,19	K562	blood:
8	chr11:62472359..62475828-chr11:62647268..62649751,3	K562	blood:
9	chr11:62474564..62476753-chr11:62571468..62573235,2	MCF-7	breast:
10	chr11:62473752..62475685-chr11:62552595..62555245,2	MCF-7	breast:
11	chr11:62438216..62442259-chr11:62472089..62478443,13	MCF-7	breast:
12	chr11:62473515..62476746-chr11:62603608..62610455,10	K562	blood:
13	chr11:62389028..62390565-chr11:62473010..62475503,2	MCF-7	breast:
14	chr11:62472417..62476831-chr11:62520357..62523886,4	MCF-7	breast:
15	chr11:62472166..62476448-chr11:62602967..62610801,11	MCF-7	breast:
16	chr11:62472026..62478669-chr11:62605440..62610848,12	MCF-7	breast:
17	chr11:62472130..62477497-chr11:62520063..62523778,7	MCF-7	breast:
18	chr11:62474806..62478433-chr11:62571000..62575830,4	MCF-7	breast:
19	chr11:62473762..62475422-chr11:62555428..62558096,2	MCF-7	breast:
20	chr11:62473852..62475558-chr17:57914270..57916733,2	MCF-7	breast:
21	chr11:62444508..62449947-chr11:62472248..62477977,7	K562	blood:
22	chr11:62436317..62438708-chr11:62474733..62477422,2	MCF-7	breast:
23	chr11:62473515..62476425-chr11:62607404..62610455,6	K562	blood:
24	chr11:62432560..62437098-chr11:62470787..62476744,13	MCF-7	breast:
25	chr11:62473688..62475805-chr11:62622758..62625720,5	K562	blood:
26	chr11:62432133..62436222-chr11:62470338..62477424,11	MCF-7	breast:
27	chr11:62472932..62475905-chr11:62571487..62574388,4	K562	blood:
28	chr11:62416571..62422086-chr11:62473445..62479277,7	MCF-7	breast:
29	chr11:62445054..62448802-chr11:62471640..62476934,8	MCF-7	breast:
30	chr11:62412420..62415681-chr11:62473795..62477393,4	MCF-7	breast:
31	chr11:62357192..62359984-chr11:62474188..62476260,2	K562	blood:
32	chr11:62473858..62475905-chr11:62571487..62573051,2	K562	blood:
33	chr11:62388071..62390566-chr11:62472774..62475427,2	K562	blood:
34	chr11:62444596..62448445-chr11:62472565..62478023,8	MCF-7	breast:

No data

Variant related genes	Relation type
BSCL2	TF binding region
ENSG00000206597	Chromatin interaction
ENSG00000204922	Chromatin interaction
ENSG00000168000	Chromatin interaction
ENSG00000162191	Chromatin interaction
ENSG00000214756	Chromatin interaction
ENSG00000255432	Chromatin interaction
ENSG00000255508	Chromatin interaction
ENSG00000269176	Chromatin interaction
ENSG00000149541	Chromatin interaction
ENSG00000168569	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000269463	Chromatin interaction
ENSG00000162231	Chromatin interaction
ENSG00000185085	Chromatin interaction
ENSG00000162194	Chromatin interaction
ENSG00000168003	Chromatin interaction
ENSG00000185670	Chromatin interaction
ENSG00000255717	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000089597	Chromatin interaction
ENSG00000185475	Chromatin interaction
ENSG00000177363	Chromatin interaction
ENSG00000062716	Chromatin interaction

Extended variants
information (count: 52 )
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	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2510538	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2584915	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2584917	0.91[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	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs489275	1.00[EUR][1000 genomes]
rs4963309	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs506132	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs507101	1.00[EUR][1000 genomes]
rs514401	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs518780	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs519473	1.00[EUR][1000 genomes]
rs523328	1.00[EUR][1000 genomes]
rs544573	0.94[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	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs573146	0.94[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	0.94[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	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs646194	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs692773	0.96[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:7 , 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	nsv555174	chr11:62334096-62496519	Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	243 gene(s)	inside rSNPs	diseases
6	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
7	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:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62473200-62477400	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr11:62474000-62475600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr11:62474000-62475600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
4	chr11:62474000-62476800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
5	chr11:62474200-62476000	Weak transcription	Aorta	Aorta
6	chr11:62474200-62476200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr11:62474200-62476200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr11:62474200-62476200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr11:62474200-62476200	Enhancers	Spleen	Spleen
10	chr11:62474200-62478600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr11:62474400-62475400	Enhancers	Primary B cells from cord blood	blood
12	chr11:62474400-62475400	Enhancers	Esophagus	oesophagus
13	chr11:62474400-62475400	Enhancers	Gastric	stomach
14	chr11:62474400-62475600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
15	chr11:62474400-62475800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr11:62474400-62475800	Enhancers	Primary T cells from cord blood	blood
17	chr11:62474400-62475800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr11:62474400-62475800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr11:62474400-62475800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr11:62474400-62475800	Active TSS	Brain Anterior Caudate	brain
21	chr11:62474400-62476000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr11:62474400-62476000	Enhancers	Primary hematopoietic stem cells	blood
23	chr11:62474400-62476000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr11:62474400-62476000	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr11:62474400-62476000	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr11:62474400-62476000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
27	chr11:62474400-62476000	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr11:62474400-62476000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr11:62474400-62476000	Active TSS	Brain Inferior Temporal Lobe	brain
30	chr11:62474400-62476000	Enhancers	Colonic Mucosa	Colon
31	chr11:62474400-62476000	Enhancers	Fetal Lung	lung
32	chr11:62474400-62476000	Enhancers	Fetal Thymus	thymus
33	chr11:62474400-62476000	Weak transcription	Right Atrium	heart
34	chr11:62474400-62476000	Enhancers	Thymus	Thymus
35	chr11:62474400-62476000	Strong transcription	NHLF	lung
36	chr11:62474400-62476200	Enhancers	Primary B cells from peripheral blood	blood
37	chr11:62474400-62476200	Enhancers	Primary T cells fromperipheralblood	blood
38	chr11:62474400-62476200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr11:62474400-62476200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
40	chr11:62474400-62476200	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr11:62474400-62476200	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr11:62474400-62476200	Enhancers	Fetal Muscle Trunk	muscle
43	chr11:62474400-62476200	Genic enhancers	Fetal Muscle Leg	muscle
44	chr11:62474400-62476200	Enhancers	Left Ventricle	heart
45	chr11:62474400-62476200	Enhancers	Placenta Amnion	Placenta Amnion
46	chr11:62474400-62476200	Weak transcription	Small Intestine	intestine
47	chr11:62474400-62476200	Enhancers	GM12878-XiMat	blood
48	chr11:62474400-62476200	Weak transcription	HepG2	liver
49	chr11:62474400-62476200	Weak transcription	HSMM	muscle
50	chr11:62474400-62476200	Weak transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links