Variant report

Variant	rs10749586
Chromosome Location	chr10:90202441-90202442
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10736353	0.90[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10736355	0.95[ASN][1000 genomes]
rs10749587	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10749588	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10788601	0.94[ASN][1000 genomes]
rs11202750	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1177587	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1183901	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12778446	0.90[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1325907	0.93[ASW][hapmap];0.81[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.93[AMR][1000 genomes]
rs1925937	0.85[AMR][1000 genomes]
rs1935578	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1980812	0.85[AMR][1000 genomes]
rs2077890	0.91[AMR][1000 genomes]
rs2437871	1.00[MEX][hapmap];0.85[AMR][1000 genomes]
rs2437872	0.81[CEU][hapmap];0.91[AMR][1000 genomes]
rs2437874	0.92[AMR][1000 genomes]
rs2437877	0.89[AMR][1000 genomes]
rs2437878	0.93[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2477952	0.84[AMR][1000 genomes]
rs2477955	0.87[AMR][1000 genomes]
rs2477957	1.00[CEU][hapmap];0.83[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2488271	0.85[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2576166	0.85[AMR][1000 genomes]
rs2576174	0.80[ASW][hapmap];0.81[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.80[TSI][hapmap];0.93[AMR][1000 genomes]
rs2576179	0.81[CEU][hapmap]
rs2576180	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2765442	0.92[AMR][1000 genomes]
rs2765444	0.81[CEU][hapmap];0.92[AMR][1000 genomes]
rs2986118	0.92[AMR][1000 genomes]
rs4403718	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6586134	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7077182	0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7096710	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs725683	0.81[CEU][hapmap];0.92[AMR][1000 genomes]
rs725684	0.81[CEU][hapmap];0.80[GIH][hapmap];0.96[MEX][hapmap];0.91[AMR][1000 genomes]
rs7904229	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7907866	0.97[ASN][1000 genomes]
rs7913372	0.80[JPT][hapmap]
rs7916937	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7919420	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv482385	chr10:90066140-90259751	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	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
4	nsv1054984	chr10:90122512-90278038	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv1050587	chr10:90146582-90272627	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv540739	chr10:90146582-90272627	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10749586	LIPA	cis	cerebellum	SCAN
rs10749586	CCNJ	trans	cerebellum	SCAN
rs10749586	IFIT3	cis	parietal	SCAN
rs10749586	IFIT2	cis	cerebellum	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90193800-90227600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr10:90201600-90202800	Enhancers	Right Atrium	heart
3	chr10:90202200-90202800	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr10:90202200-90203200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr10:90202400-90202600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr10:90202400-90202800	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr10:90202400-90202800	Enhancers	Fetal Heart	heart
8	chr10:90202400-90202800	Enhancers	Right Ventricle	heart
9	chr10:90202400-90203000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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