Variant report

Variant	rs10936043
Chromosome Location	chr3:156696506-156696507
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156677596..156679177-chr3:156696205..156698758,2	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10212230	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10936040	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs11707041	0.88[ASN][1000 genomes]
rs11709901	0.84[ASN][1000 genomes]
rs11712111	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12629380	0.87[ASN][1000 genomes]
rs12634915	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.99[ASN][1000 genomes]
rs12638253	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13070271	1.00[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs13088978	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1320011	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs13322318	0.83[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.83[TSI][hapmap];0.83[ASN][1000 genomes]
rs1384538	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1574980	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs17382070	0.86[ASN][1000 genomes]
rs1995425	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2060015	0.82[ASN][1000 genomes]
rs2321290	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.83[ASN][1000 genomes]
rs2321292	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2321455	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2874488	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs2874494	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2874495	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs344073	0.83[JPT][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]
rs344084	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs344087	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs34667021	0.83[ASN][1000 genomes]
rs3910072	0.82[ASN][1000 genomes]
rs4098	0.83[MEX][hapmap]
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	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680311	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs4680312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4680317	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.83[TSI][hapmap]
rs62275765	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6762708	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs6765353	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs6780427	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6784421	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6803064	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7615304	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7637701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7638330	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs7638625	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.83[TSI][hapmap];0.82[ASN][1000 genomes]
rs9812895	0.86[ASN][1000 genomes]
rs9814813	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap]
rs9818684	0.85[CEU][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs9820830	0.82[CEU][hapmap]
rs9837038	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9844054	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.99[ASN][1000 genomes]
rs9847187	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9858158	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9865905	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9866373	0.89[ASN][1000 genomes]
rs9867621	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9870137	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs9871817	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.86[ASN][1000 genomes]
rs9875585	0.99[ASN][1000 genomes]
rs9875688	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9876010	1.00[CHB][hapmap];1.00[JPT][hapmap];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[JPT][hapmap]
rs9878585	1.00[CHB][hapmap];1.00[JPT][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	esv3349885	chr3:156685409-156878910	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10936043	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx
rs10936043	LINC00886	cis	Adipose Subcutaneous	GTEx
rs10936043	LINC00886	cis	Artery Tibial	GTEx
rs10936043	VEPH1	cis	parietal	SCAN
rs10936043	TIPARP	cis	cerebellum	SCAN
rs10936043	VEPH1	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156692600-156698600	Enhancers	Primary B cells from peripheral blood	blood
2	chr3:156694800-156697000	Enhancers	Brain Hippocampus Middle	brain
3	chr3:156695200-156697000	Enhancers	Brain Anterior Caudate	brain
4	chr3:156695400-156697200	Enhancers	Brain Cingulate Gyrus	brain
5	chr3:156695600-156696600	Weak transcription	Brain Substantia Nigra	brain
6	chr3:156696200-156696600	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr3:156696200-156696600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr3:156696200-156696800	Enhancers	Primary T cells fromperipheralblood	blood
9	chr3:156696200-156696800	Enhancers	Primary T helper cells fromperipheralblood	blood
10	chr3:156696200-156696800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:156696200-156696800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:156696200-156696800	Enhancers	Fetal Thymus	thymus
13	chr3:156696200-156697000	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr3:156696200-156697000	Flanking Active TSS	GM12878-XiMat	blood
15	chr3:156696200-156697200	Enhancers	Primary T cells from cord blood	blood
16	chr3:156696400-156696600	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr3:156696400-156697000	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr3:156696400-156697000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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