Variant report

Variant	rs592642
Chromosome Location	chr1:216386864-216386865
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:216386376..216389105-chr1:216390818..216392919,2	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11120739	0.82[CEU][hapmap];0.88[CHB][hapmap]
rs11120740	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs1115436	0.82[CHB][hapmap]
rs1324330	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17026208	0.87[CEU][hapmap];0.88[CHB][hapmap]
rs17026219	0.82[CEU][hapmap];0.88[CHB][hapmap]
rs1805049	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs2034960	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs2274117	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs2669057	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs301736	0.83[CHB][hapmap]
rs301737	0.82[CHB][hapmap]
rs301742	0.83[CHB][hapmap]
rs301744	0.83[CHB][hapmap]
rs301745	0.82[CHB][hapmap]
rs301750	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs301752	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs301759	0.81[CHB][hapmap]
rs301760	0.82[CHB][hapmap]
rs301761	1.00[CEU][hapmap]
rs3754064	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3767692	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs378340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs385463	1.00[CEU][hapmap]
rs386654	1.00[CEU][hapmap]
rs401269	0.87[CEU][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs404925	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs407590	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs415508	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs430652	0.83[CHB][hapmap]
rs439940	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs588516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs600535	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs62906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs636457	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs643416	0.80[CHB][hapmap]
rs646094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs659875	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs669616	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs677648	0.82[CHB][hapmap]
rs680410	1.00[CEU][hapmap];0.89[CHB][hapmap]
rs696719	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs700015	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs773498	0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9660965	0.83[CEU][hapmap];0.88[CHB][hapmap]
rs9661602	0.83[CEU][hapmap];0.88[CHB][hapmap]

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	nsv1006504	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv535288	chr1:215890460-216642124	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1006028	chr1:216268796-216432545	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv549199	chr1:216384908-216814702	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:216382800-216388800	Weak transcription	Fetal Heart	heart
2	chr1:216384000-216389400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:216385800-216388600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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