Variant report

Variant	rs12492055
Chromosome Location	chr3:56239203-56239204
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	chr3:56164542..56167534-chr3:56237841..56240212,2	MCF-7	breast:

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10433621	0.98[ASN][1000 genomes]
rs1078309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1078310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11926826	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12485705	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12486948	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12487839	0.97[EUR][1000 genomes]
rs12488237	1.00[AFR][1000 genomes]
rs12490280	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12491217	1.00[EUR][1000 genomes]
rs12492253	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12494857	0.80[EUR][1000 genomes]
rs12496048	1.00[ASW][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs1352008	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1352012	0.97[EUR][1000 genomes]
rs1376984	0.82[CHD][hapmap];0.81[MEX][hapmap]
rs1452218	0.91[ASN][1000 genomes]
rs17056646	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17288728	0.88[EUR][1000 genomes]
rs17732598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1901554	0.91[ASN][1000 genomes]
rs2167617	0.91[EUR][1000 genomes]
rs2316481	0.97[EUR][1000 genomes]
rs2316482	0.97[EUR][1000 genomes]
rs35431468	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35995295	0.85[EUR][1000 genomes]
rs4425224	0.89[ASN][1000 genomes]
rs4974120	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4974121	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4974123	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4974130	0.91[EUR][1000 genomes]
rs4974170	0.97[EUR][1000 genomes]
rs4974171	0.97[EUR][1000 genomes]
rs4974173	0.88[CEU][hapmap];0.97[EUR][1000 genomes]
rs4974176	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4974179	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4974180	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4974196	0.85[EUR][1000 genomes]
rs55849756	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56004380	0.91[EUR][1000 genomes]
rs58413645	0.91[EUR][1000 genomes]
rs59079055	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60383545	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60384923	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61689518	0.97[EUR][1000 genomes]
rs6763791	0.97[EUR][1000 genomes]
rs6764295	0.88[CEU][hapmap];0.82[CHD][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs6780051	0.97[EUR][1000 genomes]
rs6782034	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6783356	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6786058	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6788949	0.97[EUR][1000 genomes]
rs6789409	0.91[EUR][1000 genomes]
rs6801342	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6803165	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6804221	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6810099	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71309946	0.88[EUR][1000 genomes]
rs724929	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.86[ASN][1000 genomes]
rs72870171	0.97[EUR][1000 genomes]
rs72870196	0.97[EUR][1000 genomes]
rs73834604	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs755321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7613726	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7650293	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs977313	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009709	chr3:56000827-56294945	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	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	chr3:56230400-56239400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:56239000-56240000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr3:56239200-56239800	Enhancers	Brain Germinal Matrix	brain

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