Variant report

Variant	rs778653
Chromosome Location	chr3:160716041-160716042
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 103 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1026572	0.81[CEU][hapmap]
rs1037888	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs10513559	1.00[CEU][hapmap];0.87[GIH][hapmap];0.98[TSI][hapmap];0.89[EUR][1000 genomes]
rs10513561	0.90[JPT][hapmap]
rs10513562	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11708076	0.89[EUR][1000 genomes]
rs11708813	1.00[CEU][hapmap]
rs11716265	1.00[CEU][hapmap]
rs11922752	1.00[CEU][hapmap]
rs12486103	0.90[JPT][hapmap]
rs12487156	0.90[JPT][hapmap]
rs12488403	0.90[JPT][hapmap]
rs12496235	0.80[JPT][hapmap]
rs12639128	1.00[CEU][hapmap]
rs13064176	1.00[CEU][hapmap];0.87[GIH][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs13073571	0.89[EUR][1000 genomes]
rs13086250	1.00[CEU][hapmap]
rs13089559	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs13092102	1.00[CEU][hapmap]
rs13097130	0.89[EUR][1000 genomes]
rs13098884	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1374793	1.00[CEU][hapmap]
rs1447618	1.00[CEU][hapmap]
rs1447619	1.00[CEU][hapmap]
rs1447620	1.00[CEU][hapmap]
rs1599374	0.85[CEU][hapmap];0.80[TSI][hapmap]
rs1610158	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs16831581	0.90[JPT][hapmap]
rs16831611	0.90[JPT][hapmap]
rs16831799	0.90[JPT][hapmap]
rs16831850	0.80[JPT][hapmap]
rs16831864	0.80[JPT][hapmap]
rs17236725	1.00[CEU][hapmap]
rs17236746	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs17826438	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2121718	1.00[CEU][hapmap]
rs2306061	0.85[CEU][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs2593812	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs34168351	0.88[EUR][1000 genomes]
rs3925722	0.80[JPT][hapmap]
rs4342141	0.81[CEU][hapmap]
rs4557202	0.85[CEU][hapmap]
rs4679662	1.00[CEU][hapmap]
rs4679666	1.00[CEU][hapmap]
rs4679671	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4679922	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs4679924	0.96[CEU][hapmap];0.87[GIH][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs4679926	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs5004752	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs55672403	0.96[EUR][1000 genomes]
rs55888276	0.86[EUR][1000 genomes]
rs61105146	0.85[EUR][1000 genomes]
rs62280303	0.85[EUR][1000 genomes]
rs62280331	0.96[EUR][1000 genomes]
rs62280333	0.98[EUR][1000 genomes]
rs6441339	1.00[CEU][hapmap]
rs6441348	0.86[EUR][1000 genomes]
rs6441350	0.80[JPT][hapmap]
rs6441354	0.85[CEU][hapmap]
rs6764019	1.00[CEU][hapmap]
rs6769642	0.89[EUR][1000 genomes]
rs6772578	0.87[EUR][1000 genomes]
rs6786871	0.93[EUR][1000 genomes]
rs6787599	0.90[JPT][hapmap]
rs6790705	0.90[JPT][hapmap]
rs6796168	0.80[JPT][hapmap]
rs6799160	0.92[CEU][hapmap]
rs6804650	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs6806054	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6806729	0.90[JPT][hapmap]
rs6807796	0.90[JPT][hapmap]
rs6809177	1.00[CEU][hapmap]
rs723757	0.84[EUR][1000 genomes]
rs7622047	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs7627500	0.90[JPT][hapmap]
rs7628880	0.95[EUR][1000 genomes]
rs7632423	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs778642	1.00[CEU][hapmap];0.87[GIH][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes]
rs778643	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs778645	0.99[EUR][1000 genomes]
rs778646	0.99[EUR][1000 genomes]
rs778648	0.93[EUR][1000 genomes]
rs778649	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs778654	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs778657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs778663	0.97[EUR][1000 genomes]
rs796609	1.00[CEU][hapmap];0.87[GIH][hapmap];0.98[TSI][hapmap];0.99[EUR][1000 genomes]
rs898680	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs898681	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs9290065	0.96[CEU][hapmap];0.84[GIH][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs935499	0.90[JPT][hapmap]
rs9790132	0.96[CEU][hapmap]
rs980975	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs980976	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs9811594	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9818992	0.80[JPT][hapmap]
rs9820825	0.87[CEU][hapmap]
rs9826857	0.80[JPT][hapmap]
rs9847866	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs9860360	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs9875200	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1007004	chr3:160695108-160718154	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs778653	NMD3	cis	parietal	SCAN
rs778653	PPM1L	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160705000-160720000	Weak transcription	Gastric	stomach
2	chr3:160716000-160718400	Enhancers	Primary T cells from cord blood	blood

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