Variant report

Variant	rs10053522
Chromosome Location	chr5:41961622-41961623
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	chr5:41954911..41956597-chr5:41960556..41962231,2	MCF-7	breast:

Extended variants
information (count: 117 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10035434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10040757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10043326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10043371	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10044526	0.88[AMR][1000 genomes]
rs10045473	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10051322	1.00[EUR][1000 genomes]
rs10052226	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10054130	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10057546	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10057587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10057645	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10059424	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs10060170	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10062703	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10064298	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10064380	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs10065016	1.00[CEU][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10065335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10069638	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10070201	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs10075429	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10076689	1.00[CEU][hapmap];0.94[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10077481	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs10078011	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10079651	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1027348	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs10472357	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs10472359	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10473252	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10473255	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11738449	0.82[AMR][1000 genomes]
rs11738956	0.95[EUR][1000 genomes]
rs11741731	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs11742939	0.82[AMR][1000 genomes]
rs11745460	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11745530	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11746530	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11747648	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11748575	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11748578	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs11748933	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13353950	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs13355194	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13357951	1.00[EUR][1000 genomes]
rs13357980	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs13358459	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13360765	0.88[AMR][1000 genomes]
rs13436920	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1567323	1.00[EUR][1000 genomes]
rs16872052	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16872094	0.85[AMR][1000 genomes]
rs16872097	0.88[AMR][1000 genomes]
rs16872100	0.82[AMR][1000 genomes]
rs17339188	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1813615	0.82[AMR][1000 genomes]
rs1813616	0.82[AMR][1000 genomes]
rs2011105	0.82[AMR][1000 genomes]
rs2113053	0.83[EUR][1000 genomes]
rs2231910	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs28647448	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34493032	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35890705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4957178	1.00[EUR][1000 genomes]
rs4957180	1.00[EUR][1000 genomes]
rs4957434	1.00[CEU][hapmap]
rs4957436	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4957437	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4957438	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs57944767	0.90[EUR][1000 genomes]
rs582920	0.92[EUR][1000 genomes]
rs61058110	0.95[EUR][1000 genomes]
rs67152480	0.95[EUR][1000 genomes]
rs72746926	0.95[EUR][1000 genomes]
rs72746928	0.95[EUR][1000 genomes]
rs72746930	0.95[EUR][1000 genomes]
rs72746932	0.95[EUR][1000 genomes]
rs72746933	0.93[EUR][1000 genomes]
rs72746952	0.95[EUR][1000 genomes]
rs72746962	0.90[EUR][1000 genomes]
rs72746966	0.95[EUR][1000 genomes]
rs72746968	0.95[EUR][1000 genomes]
rs72746975	0.95[EUR][1000 genomes]
rs72746983	0.95[EUR][1000 genomes]
rs72746985	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72746995	1.00[EUR][1000 genomes]
rs72746996	0.80[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs72746997	0.95[EUR][1000 genomes]
rs72746999	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72747000	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72747001	1.00[EUR][1000 genomes]
rs72747002	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72748607	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72748608	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72748609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72748611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72748613	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72748614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72748616	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72748619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72748620	1.00[EUR][1000 genomes]
rs72748623	0.83[EUR][1000 genomes]
rs72748635	0.85[AMR][1000 genomes]
rs72748641	0.82[AMR][1000 genomes]
rs7341062	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7712106	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7723992	1.00[EUR][1000 genomes]
rs9292826	0.95[EUR][1000 genomes]
rs9292828	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs9292832	1.00[CEU][hapmap];0.86[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9885033	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9885117	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs989747	0.82[AMR][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	nsv830272	chr5:41833365-41986167	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	111 gene(s)	inside rSNPs	diseases
2	nsv830273	chr5:41867296-42066070	Flanking Active TSS Active TSS Genic enhancers Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	111 gene(s)	inside rSNPs	diseases
3	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
4	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:41961200-41961800	ZNF genes & repeats	Pancreas	Pancrea
2	chr5:41961200-41962000	ZNF genes & repeats	Aorta	Aorta

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