Variant report

Variant	rs12295052
Chromosome Location	chr11:62624121-62624122
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:128)
CpG islands
(count:0)
Chromatin interactive
region (count:36)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:128 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr11:62622543-62624236	K562	blood:	n/a	chr11:62623413-62623427 chr11:62623269-62623283 chr11:62623275-62623289
2	PML	chr11:62622167-62624299	K562	blood:	n/a	n/a
3	BCLAF1	chr11:62622164-62624199	GM12878	blood:	n/a	n/a
4	RELA	chr11:62622666-62624222	GM19099	blood:	n/a	n/a
5	POLR2A	chr11:62617628-62624283	PANC-1	pancreas:	n/a	n/a
6	MYC	chr11:62623044-62624187	MCF10A-Er-Src	breast:	n/a	n/a
7	MAX	chr11:62622547-62624336	A549	lung:	n/a	n/a
8	POLR2A	chr11:62621995-62624279	GM12891	blood:	n/a	n/a
9	POLR2A	chr11:62618490-62624274	GM12878	blood:	n/a	n/a
10	POLR2A	chr11:62620494-62624294	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr11:62614241-62624321	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr11:62620277-62624182	HCT-116	colon:	n/a	n/a
13	SIX5	chr11:62621991-62624362	A549	lung:	n/a	chr11:62622215-62622224
14	KAP1	chr11:62622837-62624130	U2OS	brain:	n/a	n/a
15	WRNIP1	chr11:62622128-62624236	GM12878	blood:	n/a	n/a
16	RPC155	chr11:62623970-62624628	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr11:62620269-62624353	H1-hESC	embryonic stem cell:	n/a	n/a
18	RUNX3	chr11:62622224-62624373	GM12878	blood:	n/a	n/a
19	CHD1	chr11:62620648-62624364	IMR90	lung:	n/a	chr11:62623537-62623544
20	MYC	chr11:62622973-62624250	MCF10A-Er-Src	breast:	n/a	n/a
21	E2F4	chr11:62624074-62624269	MCF10A-Er-Src	breast:	n/a	n/a
22	RUNX3	chr11:62622476-62624288	GM12878	blood:	n/a	n/a
23	POLR2A	chr11:62620391-62624313	HL-60	blood:	n/a	n/a
24	YY1	chr11:62624033-62624255	K562	blood:	n/a	n/a
25	MYC	chr11:62622088-62624122	K562	blood:	n/a	n/a
26	MXI1	chr11:62622623-62624239	Hela-S3	cervix:	n/a	n/a
27	MAX	chr11:62622826-62624160	H1-hESC	embryonic stem cell:	n/a	n/a
28	FOXM1	chr11:62622368-62624263	GM12878	blood:	n/a	n/a
29	HCFC1	chr11:62618424-62624359	Hela-S3	cervix:	n/a	n/a
30	GTF2F1	chr11:62622904-62624281	Hela-S3	cervix:	n/a	n/a
31	MAX	chr11:62622226-62624367	HCT-116	colon:	n/a	n/a
32	POLR2A	chr11:62617338-62625222	HepG2	liver:	n/a	n/a
33	POLR2A	chr11:62617697-62624345	HUVEC	blood vessel:	n/a	n/a
34	NFATC1	chr11:62622256-62624139	GM12878	blood:	n/a	n/a
35	SIN3AK20	chr11:62622141-62624257	A549	lung:	n/a	n/a
36	STAT5A	chr11:62620798-62624193	GM12878	blood:	n/a	chr11:62623472-62623495 chr11:62622243-62622266 chr11:62622026-62622037
37	POLR2A	chr11:62617721-62624372	GM12892	blood:	n/a	n/a
38	POLR2A	chr11:62620317-62624267	GM12891	blood:	n/a	n/a
39	RELA	chr11:62622492-62624223	GM15510	blood:	n/a	n/a
40	MXI1	chr11:62621440-62624280	IMR90	lung:	n/a	n/a
41	YY1	chr11:62623948-62624248	GM12878	blood:	n/a	n/a
42	MTA3	chr11:62620597-62624422	GM12878	blood:	n/a	n/a
43	POLR2A	chr11:62617309-62624309	MCF-7	breast:	n/a	n/a
44	TAF1	chr11:62622906-62624287	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr11:62618403-62625433	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr11:62622500-62624278	Raji	blood:	n/a	n/a
47	POLR2A	chr11:62618403-62624340	GM12892	blood:	n/a	n/a
48	MTA3	chr11:62622387-62624185	GM12878	blood:	n/a	n/a
49	MAX	chr11:62622993-62624148	SK-N-SH	brain:	n/a	n/a
50	POLR2A	chr11:62617682-62625430	PFSK-1	brain:	n/a	n/a

No data

(count:36 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:62623008..62624324-chr3:49395247..49395868,3	Hela-S3	cervix:
2	chr11:62597102..62625754-chr11:62640222..62672995,305	MCF-7	breast:
3	chr11:62474385..62478486-chr11:62621122..62625313,5	MCF-7	breast:
4	chr11:62621914..62624685-chr8:87526558..87528139,2	MCF-7	breast:
5	chr11:62493159..62495020-chr11:62623607..62625320,2	MCF-7	breast:
6	chr11:62565367..62576307-chr11:62617328..62626616,39	K562	blood:
7	chr11:62339984..62344096-chr11:62621681..62625316,4	K562	blood:
8	chr11:62473263..62476310-chr11:62622744..62625720,5	K562	blood:
9	chr11:62359506..62362353-chr11:62619695..62624770,4	K562	blood:
10	chr11:62432496..62434344-chr11:62623258..62625470,4	K562	blood:
11	chr11:62543432..62547564-chr11:62620532..62624657,4	K562	blood:
12	chr11:62357996..62360027-chr11:62622057..62624821,2	K562	blood:
13	chr11:62623504..62624125-chr4:6675184..6676050,2	NB4	blood:
14	chr11:62492410..62497430-chr11:62621392..62625675,11	K562	blood:
15	chr11:62536052..62541340-chr11:62621462..62624868,6	K562	blood:
16	chr11:62355177..62359057-chr11:62621096..62624754,3	K562	blood:
17	chr11:62552943..62561747-chr11:62616572..62625876,31	K562	blood:
18	chr11:62526894..62529687-chr11:62620957..62624297,6	K562	blood:
19	chr11:62614063..62631836-chr11:62641578..62658963,131	K562	blood:
20	chr11:62622571..62624950-chr17:56708103..56709921,2	MCF-7	breast:
21	chr11:62547933..62549912-chr11:62621671..62624268,3	K562	blood:
22	chr11:62339818..62342516-chr11:62622172..62625340,3	MCF-7	breast:
23	chr11:62492343..62497215-chr11:62619514..62625025,15	MCF-7	breast:
24	chr11:62488201..62492065-chr11:62621719..62624928,3	MCF-7	breast:
25	chr11:62622647..62624760-chr17:56735142..56736993,2	MCF-7	breast:
26	chr11:62621913..62624821-chr17:57922662..57925594,2	MCF-7	breast:
27	chr11:62388618..62392022-chr11:62621970..62625527,4	K562	blood:
28	chr11:62357691..62360390-chr11:62623455..62624975,2	MCF-7	breast:
29	chr11:62492410..62497148-chr11:62620379..62625675,11	K562	blood:
30	chr11:62473688..62475805-chr11:62622758..62625720,5	K562	blood:
31	chr11:62431862..62434344-chr11:62623258..62625462,3	K562	blood:
32	chr11:62431791..62434160-chr11:62621539..62624310,3	MCF-7	breast:
33	chr11:62365338..62373022-chr11:62621930..62625872,13	K562	blood:
34	chr11:62526685..62530530-chr11:62620957..62624924,5	K562	blood:
35	chr11:62365951..62369565-chr11:62622521..62625872,5	K562	blood:
36	chr11:62476521..62478365-chr11:62623672..62625247,2	MCF-7	breast:

No data

Variant related genes	Relation type
SNHG1	TF binding region
ENSG00000234857	Chromatin interaction
ENSG00000269176	Chromatin interaction
ENSG00000162227	Chromatin interaction
ENSG00000254772	Chromatin interaction
ENSG00000214756	Chromatin interaction
ENSG00000185475	Chromatin interaction
ENSG00000269463	Chromatin interaction
ENSG00000162194	Chromatin interaction
ENSG00000206597	Chromatin interaction
ENSG00000255432	Chromatin interaction
ENSG00000255508	Chromatin interaction
ENSG00000168569	Chromatin interaction
ENSG00000168000	Chromatin interaction
ENSG00000267811	Chromatin interaction
ENSG00000149480	Chromatin interaction
ENSG00000085719	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000168002	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000214753	Chromatin interaction
ENSG00000201524	Chromatin interaction
ENSG00000162231	Chromatin interaction
ENSG00000162222	Chromatin interaction
ENSG00000176623	Chromatin interaction
ENSG00000149499	Chromatin interaction
ENSG00000233276	Chromatin interaction
ENSG00000149541	Chromatin interaction
ENSG00000168003	Chromatin interaction
ENSG00000149016	Chromatin interaction
ENSG00000162188	Chromatin interaction
ENSG00000251580	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11231220	1.00[AMR][1000 genomes]
rs12270342	0.88[LWK][hapmap];0.92[MKK][hapmap];1.00[AMR][1000 genomes]
rs12274689	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs12288417	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12290152	0.88[LWK][hapmap];0.92[MKK][hapmap];1.00[AMR][1000 genomes]
rs12292281	1.00[ASW][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12295516	1.00[AMR][1000 genomes]
rs28400288	1.00[AMR][1000 genomes]
rs56994557	1.00[AMR][1000 genomes]
rs58003814	1.00[AMR][1000 genomes]
rs58505493	1.00[AMR][1000 genomes]
rs58792209	1.00[AMR][1000 genomes]
rs59143369	1.00[AMR][1000 genomes]
rs61088491	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73483955	1.00[AMR][1000 genomes]
rs73483965	1.00[AMR][1000 genomes]
rs73483978	1.00[AMR][1000 genomes]
rs73485621	1.00[AMR][1000 genomes]
rs73485634	1.00[AMR][1000 genomes]
rs73485689	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73487820	1.00[AMR][1000 genomes]
rs73487823	1.00[AMR][1000 genomes]
rs73487824	1.00[AMR][1000 genomes]
rs73487852	1.00[AMR][1000 genomes]
rs73487868	1.00[AMR][1000 genomes]
rs73502144	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv508636	chr11:62547114-62644458	Transcr. at gene 5' and 3' Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1195 gene(s)	inside rSNPs	diseases
5	nsv1051308	chr11:62564713-62673136	Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1199 gene(s)	inside rSNPs	diseases
6	nsv541058	chr11:62564713-62673136	Strong transcription Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1199 gene(s)	inside rSNPs	diseases
7	nsv1041770	chr11:62610353-62871767	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	263 gene(s)	inside rSNPs	diseases
8	nsv983154	chr11:62621265-62625410	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	133 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62620600-62626000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:62620800-62626000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:62621400-62624400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr11:62621800-62624200	Active TSS	Esophagus	oesophagus
5	chr11:62621800-62624200	Active TSS	Gastric	stomach
6	chr11:62621800-62624200	Active TSS	Ovary	ovary
7	chr11:62621800-62624600	Active TSS	Fetal Intestine Small	intestine
8	chr11:62621800-62624600	Active TSS	Small Intestine	intestine
9	chr11:62622000-62624200	Active TSS	Sigmoid Colon	Sigmoid Colon
10	chr11:62622200-62624200	Active TSS	Aorta	Aorta
11	chr11:62622200-62624600	Active TSS	Pancreas	Pancrea
12	chr11:62622200-62624800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:62622200-62624800	Active TSS	Fetal Brain Female	brain
14	chr11:62622200-62625000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr11:62622400-62624200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr11:62622400-62624200	ZNF genes & repeats	Fetal Brain Male	brain
17	chr11:62622400-62624200	Active TSS	Psoas Muscle	Psoas
18	chr11:62622400-62624400	Active TSS	Pancreatic Islets	Pancreatic Islet
19	chr11:62622400-62624400	Active TSS	Fetal Stomach	stomach
20	chr11:62622400-62624600	Active TSS	Fetal Intestine Large	intestine
21	chr11:62622400-62625600	Active TSS	GM12878-XiMat	blood
22	chr11:62622600-62624200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr11:62622600-62624200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
24	chr11:62622600-62624400	Active TSS	NHDF-Ad	bronchial
25	chr11:62622600-62624600	Active TSS	HUVEC	blood vessel
26	chr11:62622600-62625200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr11:62622800-62624200	Active TSS	Rectal Smooth Muscle	rectum
28	chr11:62622800-62624400	Active TSS	Brain Anterior Caudate	brain
29	chr11:62622800-62624400	Active TSS	Fetal Kidney	kidney
30	chr11:62622800-62624800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr11:62622800-62624800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr11:62622800-62625000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:62622800-62625600	Active TSS	H9 Cell Line	embryonic stem cell
34	chr11:62622800-62625600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr11:62623000-62624200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr11:62623000-62624400	Active TSS	Muscle Satellite Cultured Cells	--
37	chr11:62623000-62624400	Active TSS	HSMM	muscle
38	chr11:62623000-62625200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr11:62623000-62625200	Active TSS	Hela-S3	cervix
40	chr11:62623000-62625400	Active TSS	iPS-18 Cell Line	embryonic stem cell
41	chr11:62623000-62626000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr11:62623000-62626400	Active TSS	H1 Cell Line	embryonic stem cell
43	chr11:62623000-62626400	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr11:62623000-62626600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr11:62623000-62627000	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr11:62623200-62624600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr11:62623200-62624600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr11:62623200-62625000	Active TSS	K562	blood
49	chr11:62623200-62625200	Active TSS	A549	lung
50	chr11:62623200-62625600	Active TSS	HUES6 Cell Line	embryonic stem cell

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