Variant report

Variant	rs1426619
Chromosome Location	chr10:90091540-90091541
allele	C/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];0.89[ASN][1000 genomes]
rs10887801	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]
rs10887802	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10887803	0.83[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs10887804	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10887805	0.88[ASN][1000 genomes]
rs10887806	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10887818	0.83[JPT][hapmap]
rs11202702	0.92[CEU][hapmap];0.86[CHB][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11202712	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11202713	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11202715	0.89[ASN][1000 genomes]
rs11202716	0.83[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11202723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1342451	0.83[JPT][hapmap]
rs1346226	0.83[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1426618	0.83[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs1582784	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1617881	0.86[JPT][hapmap]
rs2433340	0.87[JPT][hapmap]
rs4933476	0.98[ASN][1000 genomes]
rs4934403	0.83[JPT][hapmap]
rs61853517	0.83[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6586125	0.88[ASN][1000 genomes]
rs6586129	0.86[JPT][hapmap]
rs6586132	0.90[JPT][hapmap]
rs7069120	0.82[CHB][hapmap];0.86[ASN][1000 genomes]
rs7089911	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7091137	0.83[CHB][hapmap];0.84[ASN][1000 genomes]
rs7096330	0.92[ASN][1000 genomes]
rs7895582	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs7895674	0.91[CHB][hapmap];0.89[ASN][1000 genomes]
rs7899861	0.91[CHB][hapmap];0.87[ASN][1000 genomes]
rs7905573	0.84[ASN][1000 genomes]
rs7905600	0.91[ASN][1000 genomes]
rs7917640	0.82[CHB][hapmap];0.91[JPT][hapmap];0.87[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	0.89[CHD][hapmap];0.82[JPT][hapmap]
rs919115	0.82[CHB][hapmap];0.87[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
rs1426619	IFIT2	cis	parietal	SCAN
rs1426619	FLJ37201	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90084600-90103600	Weak transcription	Ovary	ovary
2	chr10:90085000-90091800	Weak transcription	Primary hematopoietic stem cells	blood
3	chr10:90086600-90091600	Weak transcription	Aorta	Aorta
4	chr10:90089000-90093800	Enhancers	Dnd41	blood
5	chr10:90089200-90091600	Weak transcription	Primary T cells from cord blood	blood
6	chr10:90089600-90094200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr10:90090000-90096600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr10:90090200-90091800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr10:90090400-90091600	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr10:90090400-90091600	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr10:90090800-90093400	Enhancers	Adipose Nuclei	Adipose
12	chr10:90090800-90093800	Enhancers	Primary B cells from cord blood	blood
13	chr10:90090800-90093800	Enhancers	Primary B cells from peripheral blood	blood
14	chr10:90091000-90094400	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr10:90091000-90095000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr10:90091400-90091800	Enhancers	Psoas Muscle	Psoas
17	chr10:90091400-90091800	Enhancers	Right Atrium	heart
18	chr10:90091400-90092000	Enhancers	Fetal Thymus	thymus

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