Variant report

Variant	rs1384538
Chromosome Location	chr3:156695609-156695610
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TIPARP-4	chr3:156695347-156695614	NONHSAT092875

Extended variants
information (count: 70 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10212230	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs10936040	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]
rs10936043	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]
rs11707041	0.89[ASN][1000 genomes]
rs11707914	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11709901	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11712111	0.86[ASN][1000 genomes]
rs12629380	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12634915	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[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	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs1320011	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap]
rs13322318	0.92[ASW][hapmap];0.96[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.84[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1430410	0.82[TSI][hapmap]
rs1574980	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs17382070	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1995425	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2060015	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2321290	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2321292	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2321455	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2874488	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs2874494	0.96[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]
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	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3910072	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[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	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[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	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs62275765	0.82[ASN][1000 genomes]
rs6762708	0.94[CHB][hapmap];0.85[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs6765353	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs6780427	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][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];0.99[ASN][1000 genomes]
rs6784421	1.00[CHB][hapmap];1.00[JPT][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]
rs7637701	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7638330	0.94[CHB][hapmap];0.83[JPT][hapmap]
rs7638625	0.86[ASW][hapmap];0.92[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];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9812895	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[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	0.85[CEU][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap]
rs9820830	0.81[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];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9847187	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9858861	0.82[TSI][hapmap]
rs9865905	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9866373	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9867621	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[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];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9875585	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875688	0.87[ASN][1000 genomes]
rs9876010	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[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	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[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	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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs1384538	VEPH1	cis	parietal	SCAN
rs1384538	LINC00886	cis	Nerve Tibial	GTEx
rs1384538	LINC00886	cis	lung	GTEx
rs1384538	SNORA5C	trans	cerebellum	SCAN
rs1384538	VEPH1	cis	cerebellum	SCAN
rs1384538	LINC00886	cis	Artery Aorta	GTEx
rs1384538	LINC00886	cis	Adipose Subcutaneous	GTEx
rs1384538	LINC00886	cis	Artery Tibial	GTEx
rs1384538	LINC00886	cis	Skin Sun Exposed Lower leg	GTEx
rs1384538	LINC00886	cis	Stomach	GTEx
rs1384538	LINC00886	cis	Esophagus Muscularis	GTEx

Chromatin state (count:9 , 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	chr3:156694600-156696200	Enhancers	Primary B cells from cord blood	blood
3	chr3:156694800-156697000	Enhancers	Brain Hippocampus Middle	brain
4	chr3:156695200-156697000	Enhancers	Brain Anterior Caudate	brain
5	chr3:156695400-156695800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:156695400-156697200	Enhancers	Brain Cingulate Gyrus	brain
7	chr3:156695600-156695800	Flanking Active TSS	GM12878-XiMat	blood
8	chr3:156695600-156696400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:156695600-156696600	Weak transcription	Brain Substantia Nigra	brain

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