Variant report

Variant	rs1426617
Chromosome Location	chr10:90055527-90055528
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10887807	0.98[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11202703	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11202705	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11202706	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11202722	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11202726	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs11202731	0.83[ASN][1000 genomes]
rs11202734	0.95[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs11528433	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11598623	0.90[ASN][1000 genomes]
rs12217988	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs12219687	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12219831	0.81[JPT][hapmap]
rs12220632	0.95[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs12221213	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12569922	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs12572813	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1582224	0.82[CHD][hapmap];0.88[JPT][hapmap]
rs1613409	0.95[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs1648512	0.95[CHB][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap];0.84[MEX][hapmap];0.83[ASN][1000 genomes]
rs1648523	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs17111200	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1774970	0.81[JPT][hapmap]
rs1774971	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs2195013	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2241515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3740279	0.95[CHB][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.85[ASN][1000 genomes]
rs3781201	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs55749454	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59513062	0.82[AFR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7086211	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7097606	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs74149704	0.80[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs752709	0.86[ASN][1000 genomes]
rs7919335	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs792225	0.95[CHB][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs792227	0.84[ASN][1000 genomes]
rs792228	0.84[ASN][1000 genomes]
rs792232	0.82[CHD][hapmap];0.88[JPT][hapmap]
rs880793	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs880794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895879	chr10:90015725-90219298	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1426617	CH25H	cis	parietal	SCAN
rs1426617	TBC1D22A	cis	Cerebellum	GTEx
rs1426617	ATAD1	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90042800-90071600	Weak transcription	Psoas Muscle	Psoas
2	chr10:90049000-90056800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr10:90051800-90063200	Weak transcription	Pancreas	Pancrea
4	chr10:90052600-90059800	Weak transcription	Primary B cells from cord blood	blood
5	chr10:90053200-90056000	Weak transcription	Dnd41	blood
6	chr10:90053800-90061000	Weak transcription	NHDF-Ad	bronchial
7	chr10:90054000-90055800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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