Variant report

Variant	rs2960680
Chromosome Location	chr10:117542668-117542669
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 83 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10787598	0.82[CEU][hapmap]
rs10787603	0.91[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10787607	0.92[JPT][hapmap]
rs10885798	0.86[ASN][1000 genomes]
rs10885800	0.86[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs10885802	0.86[ASN][1000 genomes]
rs10885809	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10885811	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10885812	0.95[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10885816	0.90[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10885818	0.87[EUR][1000 genomes]
rs10885821	0.92[JPT][hapmap]
rs11197423	0.82[JPT][hapmap]
rs11197430	0.86[CEU][hapmap];0.83[GIH][hapmap]
rs11197439	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11197453	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11197460	0.86[CEU][hapmap];0.92[JPT][hapmap]
rs11197464	0.84[JPT][hapmap]
rs11593928	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12258630	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs12267719	0.84[ASN][1000 genomes]
rs12360291	0.87[ASN][1000 genomes]
rs12411613	0.95[CEU][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12413701	0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1552066	0.92[JPT][hapmap]
rs17093513	0.83[JPT][hapmap]
rs2255909	0.83[JPT][hapmap]
rs2420115	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2420121	0.91[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2420122	0.95[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2420125	0.86[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap]
rs2420126	0.86[CEU][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap]
rs2907531	0.86[CEU][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes]
rs2907551	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs2907552	0.86[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2907553	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2907554	0.86[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2907555	0.86[CEU][hapmap];0.92[JPT][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2907556	0.86[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2907558	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2907559	0.86[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2907561	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2907566	0.81[EUR][1000 genomes]
rs2907567	0.92[JPT][hapmap]
rs2907569	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2907570	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2907572	0.92[JPT][hapmap]
rs2907573	0.92[JPT][hapmap]
rs2907576	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2907577	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2907578	0.91[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2907580	0.91[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2907582	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2907584	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2907585	0.86[CEU][hapmap];0.92[JPT][hapmap]
rs2927373	0.85[JPT][hapmap]
rs2960660	0.91[CEU][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2960661	0.90[CEU][hapmap];0.83[JPT][hapmap];0.91[EUR][1000 genomes]
rs2960662	0.86[CEU][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs2960664	0.91[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2960665	0.89[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2960666	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2960668	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2960670	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2960671	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2960672	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2960675	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2960676	0.86[CEU][hapmap];1.00[JPT][hapmap]
rs2960678	0.86[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2960679	0.86[CEU][hapmap];0.87[CHD][hapmap];0.92[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs2960681	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2960687	0.91[CEU][hapmap];0.89[EUR][1000 genomes]
rs2960729	0.91[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4430419	0.92[JPT][hapmap]
rs4447088	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6585362	0.90[YRI][hapmap]
rs6585366	0.91[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7088912	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs723471	0.91[CEU][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs725556	0.86[CEU][hapmap];0.83[CHD][hapmap];0.92[JPT][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7478359	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs758579	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs875377	0.86[CEU][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2960680	HABP2	cis	cerebellum	SCAN
rs2960680	PCNXL2	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:117540000-117548200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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