Variant report

Variant	rs10887843
Chromosome Location	chr10:90384000-90384001
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10749594	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10788608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10788610	0.83[ASN][1000 genomes]
rs10887837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10887839	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs10887840	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs10887841	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11202781	0.83[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs1409137	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs1555841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1769686	0.81[ASN][1000 genomes]
rs1934447	0.85[ASN][1000 genomes]
rs1980811	0.85[ASN][1000 genomes]
rs2274312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap]
rs2296545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs2576168	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs2576178	0.82[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs2765446	0.95[JPT][hapmap]
rs2765452	0.91[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs7476392	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs750507	0.85[ASN][1000 genomes]
rs7912280	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs845133	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv430254	chr10:90265420-90500520	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv1044680	chr10:90316066-90466092	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv540740	chr10:90316066-90466092	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv551839	chr10:90334835-90422136	Active TSS Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10887843	RNLS	cis	cerebellum	SCAN
rs10887843	WNT2	trans	cerebellum	SCAN
rs10887843	SNCG	cis	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90383000-90384000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr10:90383600-90384000	Enhancers	NHDF-Ad	bronchial
3	chr10:90383800-90384200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr10:90384000-90385600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links