Variant report

Variant	rs10887801
Chromosome Location	chr10:90079714-90079715
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10788592	0.87[JPT][hapmap]
rs10887800	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs10887802	0.96[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10887803	0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs10887804	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10887805	0.82[ASN][1000 genomes]
rs10887806	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10887818	0.83[JPT][hapmap]
rs11202702	0.88[CEU][hapmap];0.86[CHB][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11202712	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11202713	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11202715	0.84[ASN][1000 genomes]
rs11202716	0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs11202723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1342451	0.83[JPT][hapmap]
rs1346226	0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.87[ASN][1000 genomes]
rs1426618	0.83[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[JPT][hapmap];0.85[LWK][hapmap];0.81[YRI][hapmap];0.90[ASN][1000 genomes]
rs1426619	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1582784	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1617881	0.86[JPT][hapmap]
rs2433340	0.87[JPT][hapmap]
rs4933476	0.93[ASN][1000 genomes]
rs4934403	0.83[JPT][hapmap]
rs61853517	0.92[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6586125	0.84[ASN][1000 genomes]
rs6586129	0.86[JPT][hapmap]
rs6586132	0.90[JPT][hapmap]
rs7069120	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs7089911	0.96[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7091137	0.83[CHB][hapmap]
rs7096330	0.86[ASN][1000 genomes]
rs7895582	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs7895674	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs7899861	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs7905573	0.80[ASN][1000 genomes]
rs7905600	0.87[ASN][1000 genomes]
rs7917640	0.82[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs7918921	0.82[JPT][hapmap]
rs7920126	0.87[JPT][hapmap]
rs792205	0.83[JPT][hapmap]
rs792209	0.83[JPT][hapmap]
rs792230	0.83[JPT][hapmap]
rs792234	0.86[JPT][hapmap]
rs796945	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs919115	0.82[CHB][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
2	nsv551838	chr10:90058637-90137045	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv482385	chr10:90066140-90259751	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv948664	chr10:90076715-90517150	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10887801	IFIT2	cis	parietal	SCAN
rs10887801	FLJ37201	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90078000-90082200	ZNF genes & repeats	Primary B cells from peripheral blood	blood
2	chr10:90078600-90080400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
3	chr10:90079000-90080400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr10:90079000-90081400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr10:90079000-90082200	Weak transcription	Pancreas	Pancrea

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