Variant report

Variant	rs636295
Chromosome Location	chr6:92404169-92404170
allele	G/T
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	TCF7L2	chr6:92403708-92404415	Hela-S3	cervix:	n/a	chr6:92403832-92403841
2	STAT3	chr6:92403748-92404250	MCF10A-Er-Src	breast:	n/a	chr6:92403832-92403841 chr6:92403831-92403840
3	POLR2A	chr6:92403809-92404178	MCF10A-Er-Src	breast:	n/a	n/a
4	STAT3	chr6:92403692-92404355	MCF10A-Er-Src	breast:	n/a	chr6:92403832-92403841 chr6:92403831-92403840 chr6:92404347-92404355
5	FOS	chr6:92403615-92404347	MCF10A-Er-Src	breast:	n/a	chr6:92403832-92403840 chr6:92403833-92403840 chr6:92403832-92403841 chr6:92403828-92403839
6	TCF7L2	chr6:92403644-92404285	HCT-116	colon:	n/a	chr6:92403832-92403841
7	STAT3	chr6:92403795-92404300	MCF10A-Er-Src	breast:	n/a	chr6:92403832-92403841 chr6:92403831-92403840
8	FOS	chr6:92403643-92404312	MCF10A-Er-Src	breast:	n/a	chr6:92403832-92403840 chr6:92403833-92403840 chr6:92403832-92403841 chr6:92403828-92403839
9	EP300	chr6:92403729-92404471	ECC-1	luminal epithelium:	n/a	chr6:92403831-92403840 chr6:92403832-92403841 chr6:92403902-92403916
10	MYC	chr6:92403664-92404196	MCF10A-Er-Src	breast:	n/a	chr6:92403832-92403841 chr6:92403831-92403840

Variant related genes	Relation type
CASC6	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1761783	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs478120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs478536	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs481555	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs482426	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs484288	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs484406	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs488091	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504879	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs506122	0.80[ASN][1000 genomes]
rs508629	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs511077	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs512950	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs520631	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs524271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs525943	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs533135	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs538723	0.89[YRI][hapmap]
rs539526	0.81[AFR][1000 genomes]
rs540315	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs542101	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs548810	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs548887	0.82[AFR][1000 genomes]
rs567888	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs570258	0.85[EUR][1000 genomes]
rs570400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs571387	0.86[EUR][1000 genomes]
rs574724	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs574892	0.83[AFR][1000 genomes]
rs578427	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs583239	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs599553	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs601701	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs605570	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs605594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs609383	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs614298	0.85[EUR][1000 genomes]
rs615105	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs633637	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs635450	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs648475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs650256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs650804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs652135	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs655846	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs658041	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs661782	0.89[CEU][hapmap];1.00[CHB][hapmap]
rs666390	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs673677	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs676663	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs678605	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71556396	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][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	nsv1017467	chr6:91802015-92417554	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv538360	chr6:91802015-92417554	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1034981	chr6:92280070-92530848	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv1018145	chr6:92328392-92951562	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv428491	chr6:92329694-92474678	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv1028736	chr6:92362109-92423792	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
7	nsv1067623	chr6:92383159-92939893	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv531366	chr6:92383159-92939893	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:92403800-92404600	Enhancers	Hela-S3	cervix
2	chr6:92404000-92404400	Enhancers	HMEC	breast
3	chr6:92404000-92404600	Enhancers	Muscle Satellite Cultured Cells	--
4	chr6:92404000-92404600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:92404000-92404800	Enhancers	NHEK	skin

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