Variant report

Variant	rs4711071
Chromosome Location	chr6:25043014-25043015
allele	A/C/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	JUND	chr6:25042953-25043025	H1-hESC	embryonic stem cell:	n/a	n/a
2	PML	chr6:25042170-25043982	GM12878	blood:	n/a	n/a
3	CTCF	chr6:25042900-25043050	HepG2	liver:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
4	CTCF	chr6:25042900-25043050	GM12867	blood:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
5	CTCF	chr6:25042900-25043050	SAEC	small airway:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
6	CTCF	chr6:25042880-25043030	GM12865	blood:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
7	CEBPB	chr6:25042495-25043183	GM12878	blood:	n/a	n/a
8	CTCF	chr6:25042900-25043050	GM12872	blood:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
9	CTCF	chr6:25042866-25043073	MCF-7	breast:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
10	CTCF	chr6:25042915-25043022	LNCaP	prostate:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
11	FOXM1	chr6:25042320-25043220	GM12878	blood:	n/a	n/a
12	CTCF	chr6:25042900-25043050	WERI-Rb-1	eye:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
13	CTCF	chr6:25042860-25043057	GM19238	blood:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
14	CTCF	chr6:25042919-25043109	Spleen_OC	spleen:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
15	CTCF	chr6:25042920-25043028	Hela-S3	cervix:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
16	CTCF	chr6:25042920-25043070	GM12871	blood:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
17	RELA	chr6:25042155-25043993	GM18951	blood:	n/a	n/a
18	NFIC	chr6:25041052-25044467	GM12878	blood:	n/a	n/a
19	CTCF	chr6:25042882-25043056	GM12891	blood:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
20	FOXM1	chr6:25042741-25043826	GM12878	blood:	n/a	n/a
21	CTCF	chr6:25042900-25043050	Hela-S3	cervix:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
22	MAX	chr6:25042825-25043190	MCF-7	breast:	n/a	n/a
23	CTCF	chr6:25042888-25043043	GM12878	blood:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
24	ZEB1	chr6:25042793-25043163	GM12878	blood:	n/a	chr6:25042968-25042975 chr6:25042966-25042975
25	CTCF	chr6:25042900-25043050	HCT-116	colon:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
26	CTCF	chr6:25042900-25043050	GM12864	blood:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
27	CTCF	chr6:25042880-25043030	HEK293	kidney:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
28	CTCF	chr6:25042900-25043050	GM12875	blood:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
29	CTCF	chr6:25042880-25043030	HRE	kidney:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
30	CTCF	chr6:25042880-25043030	NHEK	skin:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
31	CTCF	chr6:25042851-25043103	MCF-7	breast:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
32	CTCF	chr6:25042882-25043073	MCF-7	breast:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
33	CHD1	chr6:25041115-25043023	GM12878	blood:	n/a	n/a
34	ZNF143	chr6:25042881-25043148	GM12878	blood:	n/a	n/a
35	POLR2A	chr6:25041928-25043097	Raji	blood:	n/a	n/a
36	RAD21	chr6:25042840-25043103	H1-hESC	embryonic stem cell:	n/a	n/a
37	CTCF	chr6:25042920-25043070	GM12864	blood:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
38	CTCF	chr6:25042909-25043040	LNCaP	prostate:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
39	RUNX3	chr6:25042723-25044045	GM12878	blood:	n/a	n/a
40	POLR2A	chr6:25042191-25043634	GM12878	blood:	n/a	n/a
41	CTCF	chr6:25042920-25043070	RPTEC	kidney:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
42	CTCF	chr6:25042892-25043057	H1-hESC	embryonic stem cell:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
43	CTCF	chr6:25042770-25043150	GM12878	blood:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
44	CTCF	chr6:25042933-25043024	GM10248	blood:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
45	CTCF	chr6:25042874-25043075	GM19239	blood:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
46	ZNF384	chr6:25042977-25043673	GM12878	blood:	n/a	n/a
47	CTCF	chr6:25042900-25043050	GM12868	blood:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
48	CTCF	chr6:25042900-25043050	MCF-7	breast:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
49	CTCF	chr6:25042940-25043049	Lung_OC	lung:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979
50	CTCF	chr6:25042919-25043014	GM13977	blood:	n/a	chr6:25042972-25042980 chr6:25042972-25042985 chr6:25042971-25042979

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:25029897..25032330-chr6:25040931..25043429,2	K562	blood:

Variant related genes	Relation type
ENSG00000272053	TF binding region
FAM65B	TF binding region
ENSG00000244618	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs12524842	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12525328	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12525405	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12528227	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12661796	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12663160	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12665174	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13195161	0.94[ASN][1000 genomes]
rs13196712	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13203073	0.86[ASN][1000 genomes]
rs13218879	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1562422	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1562423	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1597010	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1597011	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1597012	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs160034	0.86[ASN][1000 genomes]
rs1900551	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1923192	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1923193	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs192773	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs2273671	1.00[YRI][hapmap]
rs302992	0.86[ASN][1000 genomes]
rs303879	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs303880	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs303884	0.86[ASN][1000 genomes]
rs34475409	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34693126	0.89[ASN][1000 genomes]
rs35028017	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35553146	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36030790	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3792974	1.00[YRI][hapmap]
rs3792983	1.00[YRI][hapmap]
rs4711072	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4712882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56108659	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67240854	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67795839	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7738141	1.00[YRI][hapmap]
rs895676	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9358827	0.94[JPT][hapmap]
rs9461093	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022966	chr6:24763776-25154212	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv538160	chr6:24763776-25154212	Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1023989	chr6:24930362-25285679	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
4	nsv830610	chr6:24951741-25124239	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv830611	chr6:25039374-25199112	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25035200-25044600	Weak transcription	Right Atrium	heart
2	chr6:25039000-25043800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr6:25040600-25043200	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr6:25041400-25043200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
5	chr6:25041800-25043200	Enhancers	Spleen	Spleen
6	chr6:25041800-25043400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr6:25041800-25044000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:25042200-25050200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr6:25042400-25043200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
10	chr6:25042400-25043400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr6:25042400-25043400	Flanking Active TSS	Dnd41	blood
12	chr6:25042400-25044200	Flanking Active TSS	GM12878-XiMat	blood
13	chr6:25042800-25043200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
14	chr6:25042800-25043200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
15	chr6:25042800-25043400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr6:25042800-25043600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr6:25042800-25043800	Enhancers	Primary B cells from cord blood	blood
18	chr6:25042800-25043800	Enhancers	Fetal Thymus	thymus
19	chr6:25042800-25044200	Enhancers	Primary B cells from peripheral blood	blood
20	chr6:25042800-25044400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr6:25042800-25044400	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr6:25043000-25043600	Enhancers	Thymus	Thymus
23	chr6:25043000-25043800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr6:25043000-25043800	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr6:25043000-25044200	Enhancers	Primary T cells from cord blood	blood
26	chr6:25043000-25044200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr6:25043000-25044400	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr6:25043000-25044400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr6:25043000-25044400	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr6:25043000-25044600	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr6:25043000-25044600	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr6:25043000-25044800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr6:25043000-25044800	Enhancers	Placenta	Placenta

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