Variant report

Variant	rs17564980
Chromosome Location	chr1:171085677-171085678
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10489229	0.87[ASN][1000 genomes]
rs1080197	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10910879	0.85[AMR][1000 genomes]
rs11809504	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11812044	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11812061	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12402295	0.92[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes]
rs12403297	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12404455	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12405599	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12406572	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16864042	0.81[ASN][1000 genomes]
rs17565336	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17565579	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17565766	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17565793	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17565983	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17565990	0.93[AMR][1000 genomes]
rs17566256	0.87[ASN][1000 genomes]
rs17623477	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17623598	0.89[ASN][1000 genomes]
rs17623833	0.87[ASN][1000 genomes]
rs17640463	0.92[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs2066529	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2142630	0.82[ASN][1000 genomes]
rs2266780	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2266782	0.81[ASN][1000 genomes]
rs2272797	0.92[CHB][hapmap];0.92[CHD][hapmap];0.80[JPT][hapmap];0.87[ASN][1000 genomes]
rs2272799	0.87[ASN][1000 genomes]
rs2272800	0.92[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.87[ASN][1000 genomes]
rs2281006	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2281007	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2281008	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28363530	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28363536	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28363537	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28363541	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28363571	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28745585	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs28745586	0.86[AMR][1000 genomes]
rs28745588	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs35156637	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3817765	0.87[ASN][1000 genomes]
rs55639094	0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs57147275	0.87[ASN][1000 genomes]
rs57519348	0.87[ASN][1000 genomes]
rs57678907	0.87[ASN][1000 genomes]
rs58044560	0.87[ASN][1000 genomes]
rs58374074	0.87[ASN][1000 genomes]
rs58509777	0.87[ASN][1000 genomes]
rs59184216	0.87[ASN][1000 genomes]
rs6608452	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6608453	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6608454	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7051747	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7054839	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7061710	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7063044	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7066454	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72712649	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72712658	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72712685	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7879557	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7885569	0.87[ASN][1000 genomes]
rs7886938	0.92[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.87[ASN][1000 genomes]
rs7887142	0.92[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.87[ASN][1000 genomes]
rs7889807	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7889839	0.92[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.87[ASN][1000 genomes]
rs909531	0.98[EUR][1000 genomes];1.00[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	nsv1001228	chr1:170885787-171452579	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
2	esv14617	chr1:171016086-171726961	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1005902	chr1:171036690-171254916	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv535203	chr1:171036690-171254916	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171080800-171086200	Weak transcription	Fetal Stomach	stomach
2	chr1:171081400-171085800	Weak transcription	Fetal Lung	lung
3	chr1:171082200-171087800	Genic enhancers	Liver	Liver
4	chr1:171083400-171085800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr1:171083400-171086200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:171084200-171092200	Weak transcription	Small Intestine	intestine
7	chr1:171084600-171086200	Weak transcription	Aorta	Aorta
8	chr1:171085000-171086400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr1:171085600-171091400	Weak transcription	Adipose Nuclei	Adipose

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