Variant report

Variant	rs10936040
Chromosome Location	chr3:156677025-156677026
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10212230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10936043	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.99[ASN][1000 genomes]
rs11707041	0.89[ASN][1000 genomes]
rs11707914	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs11709901	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11712111	0.86[ASN][1000 genomes]
rs11927500	0.85[YRI][hapmap]
rs12629380	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12634915	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12638253	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.89[ASN][1000 genomes]
rs13070271	1.00[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs13088978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1320011	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs13321802	0.84[YRI][hapmap]
rs13322318	0.91[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1384538	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1430410	0.82[TSI][hapmap]
rs1574980	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs168248	0.81[YRI][hapmap]
rs16826858	0.85[YRI][hapmap]
rs16826899	0.85[YRI][hapmap]
rs17382070	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1995425	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2060015	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2321290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2321292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2321455	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2633815	0.85[YRI][hapmap]
rs2874488	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs2874494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2874495	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs344073	0.83[JPT][hapmap]
rs344076	0.85[YRI][hapmap]
rs344078	0.84[YRI][hapmap]
rs344079	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs344080	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs344082	0.88[CHB][hapmap];0.83[JPT][hapmap]
rs344083	0.85[YRI][hapmap]
rs344084	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs344087	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs344092	0.85[YRI][hapmap]
rs34667021	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3910072	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4315647	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs453219	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs4589888	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4680311	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs4680312	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4680317	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs491423	0.85[YRI][hapmap]
rs62275765	0.82[ASN][1000 genomes]
rs6441099	0.85[YRI][hapmap]
rs6441100	0.83[YRI][hapmap]
rs6441103	0.85[YRI][hapmap]
rs6762708	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs6763644	0.85[YRI][hapmap]
rs6765353	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs6780427	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6784421	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6786167	0.85[YRI][hapmap]
rs6787535	0.85[YRI][hapmap]
rs6792917	0.85[YRI][hapmap]
rs6803064	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7615304	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.99[ASN][1000 genomes]
rs7630909	0.85[YRI][hapmap]
rs7635521	0.85[YRI][hapmap]
rs7637701	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7638330	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs7638625	0.85[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9812895	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9814813	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap]
rs9818684	0.89[CEU][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs9820830	0.85[CEU][hapmap]
rs9837038	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[ASN][1000 genomes]
rs9844054	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9858861	0.82[TSI][hapmap]
rs9861359	0.85[YRI][hapmap]
rs9865905	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9866373	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9867621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9870137	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs9871817	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9875585	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875688	0.87[ASN][1000 genomes]
rs9876010	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9876148	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs987724	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs9878585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9878709	0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829765	chr3:156568263-156718496	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv592120	chr3:156626091-156691604	Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10936040	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx
rs10936040	LINC00886	cis	Stomach	GTEx
rs10936040	LINC00886	cis	Esophagus Muscularis	GTEx
rs10936040	LINC00886	cis	Nerve Tibial	GTEx
rs10936040	SCHIP1	cis	cerebellum	SCAN
rs10936040	LINC00886	cis	Artery Tibial	GTEx
rs10936040	VEPH1	cis	cerebellum	SCAN
rs10936040	LINC00886	cis	Adipose Subcutaneous	GTEx
rs10936040	LINC00886	cis	Artery Aorta	GTEx
rs10936040	LINC00886	cis	lung	GTEx

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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