Variant report

Variant	rs10085239
Chromosome Location	chr6:54166333-54166334
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:54164489..54166885-chr6:54172521..54174692,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137251	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12204972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12212836	0.93[GIH][hapmap]
rs12213363	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12215705	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs16885209	0.84[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs2136134	0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2202801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2211241	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297980	0.86[GIH][hapmap]
rs2297982	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2297985	0.84[CHB][hapmap];0.89[CHD][hapmap]
rs3777650	0.84[CHB][hapmap]
rs3777658	0.84[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap]
rs3777659	0.83[CHB][hapmap]
rs3777660	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs3822896	0.84[CHB][hapmap]
rs3822897	0.83[CHB][hapmap]
rs57447968	0.97[ASN][1000 genomes]
rs58128009	0.93[ASN][1000 genomes]
rs59348077	0.93[ASN][1000 genomes]
rs61106945	0.97[ASN][1000 genomes]
rs73442548	0.82[AMR][1000 genomes]
rs9464051	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9464052	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs9474797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv885888	chr6:54132353-54266032	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv2762594	chr6:54159146-54168766	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54164800-54166800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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