Variant report

Variant	rs2216999
Chromosome Location	chr15:62133731-62133732
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs1000598	0.85[CEU][hapmap];0.81[YRI][hapmap]
rs1046156	0.92[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap]
rs10851703	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10851704	0.96[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10851705	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11071634	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11071635	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11071636	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11071641	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11071647	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs11629528	0.88[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes]
rs11631013	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11631970	0.85[CEU][hapmap];0.83[TSI][hapmap]
rs11632774	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11632842	0.95[JPT][hapmap];0.82[MEX][hapmap]
rs11634516	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11634693	0.81[EUR][1000 genomes]
rs11636504	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11638344	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12438431	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12439330	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12439934	0.83[JPT][hapmap]
rs12443311	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12708468	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12708469	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12708470	0.85[CEU][hapmap];0.83[TSI][hapmap]
rs12901171	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12901481	0.85[CEU][hapmap];0.85[TSI][hapmap]
rs12902092	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12902409	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12909692	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12910541	0.81[JPT][hapmap];0.81[YRI][hapmap]
rs1346036	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1364810	0.96[CEU][hapmap];0.87[JPT][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1370177	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs1561197	0.82[CHB][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap]
rs17238252	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs17271151	0.85[CEU][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap]
rs17271235	0.96[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17303968	0.85[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17304010	0.85[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap]
rs1991205	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2042608	0.83[JPT][hapmap]
rs2042610	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2059470	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2059471	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2098850	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2113932	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2113933	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2162064	0.89[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap]
rs2241491	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2414754	0.85[CEU][hapmap]
rs28413840	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3210522	0.82[CHB][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes]
rs3743294	0.96[CEU][hapmap];0.86[JPT][hapmap]
rs3784445	0.81[CEU][hapmap]
rs3784632	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs3809517	1.00[CEU][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3886246	1.00[CEU][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4541010	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4581655	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4620905	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4774425	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4775442	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4775443	0.86[AMR][1000 genomes]
rs4775444	0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes]
rs4775445	0.82[CHB][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes]
rs4775447	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4775448	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4775451	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56215106	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6494299	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6494300	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7163441	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7164933	0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap]
rs7168164	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.81[TSI][hapmap]
rs7172838	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7402374	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8025282	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8028217	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8033816	0.85[YRI][hapmap]
rs8034185	0.85[CEU][hapmap]
rs8035049	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8037603	0.95[JPT][hapmap];0.86[AMR][1000 genomes]
rs8038328	0.85[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9788670	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9920945	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904284	chr15:62123600-62243197	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv521334	chr15:62129809-62340126	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv527451	chr15:62129809-62340126	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2216999	VPS13C	cis	cerebellum	SCAN
rs2216999	TEX9	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62132400-62159000	Weak transcription	HSMM	muscle
2	chr15:62132400-62171200	Weak transcription	HMEC	breast
3	chr15:62132800-62146600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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