Variant report

Variant	rs2765456
Chromosome Location	chr10:90282582-90282583
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10736351	1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs10736352	0.81[AMR][1000 genomes]
rs10749589	0.81[AMR][1000 genomes]
rs10749590	1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs10749591	0.84[AMR][1000 genomes]
rs10788598	1.00[MEX][hapmap]
rs10788599	1.00[MEX][hapmap]
rs10788602	0.81[AMR][1000 genomes]
rs10887823	0.84[AMR][1000 genomes]
rs10887824	0.84[AMR][1000 genomes]
rs1169043	0.84[AMR][1000 genomes]
rs1342450	0.84[AMR][1000 genomes]
rs1342456	0.84[AMR][1000 genomes]
rs1750274	0.87[JPT][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs1935579	1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs2096194	0.83[AMR][1000 genomes]
rs2185786	0.86[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.84[AMR][1000 genomes]
rs2209553	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2312610	0.84[AMR][1000 genomes]
rs2437875	0.81[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2477954	0.88[AMR][1000 genomes]
rs2477956	0.86[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes]
rs2576159	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2576169	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2576170	0.81[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2576171	0.81[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes]
rs2576172	0.81[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.81[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs2576176	0.86[JPT][hapmap]
rs2576181	0.86[CHB][hapmap];0.86[CHD][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.84[AMR][1000 genomes]
rs2765440	0.95[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap]
rs2765454	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2872092	0.81[AMR][1000 genomes]
rs3740279	1.00[YRI][hapmap]
rs4509673	0.81[AMR][1000 genomes]
rs4596981	0.81[AMR][1000 genomes]
rs4606392	0.84[AMR][1000 genomes]
rs4619060	0.81[AMR][1000 genomes]
rs4934404	1.00[MEX][hapmap]
rs4934409	0.84[AMR][1000 genomes]
rs4934411	0.81[AMR][1000 genomes]
rs6586139	0.84[AMR][1000 genomes]
rs7899828	0.84[AMR][1000 genomes]
rs7909697	0.81[AMR][1000 genomes]
rs7921352	0.93[MEX][hapmap]
rs7922551	0.81[AMR][1000 genomes]
rs796945	0.85[MEX][hapmap]
rs813782	0.93[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv825500	chr10:90221443-90302503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv533167	chr10:90236197-90341481	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2765456	RNLS	cis	cerebellum	SCAN
rs2765456	LIPM	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90279800-90284000	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr10:90280400-90285200	Weak transcription	HMEC	breast
3	chr10:90281200-90283800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr10:90281200-90283800	Enhancers	Fetal Lung	lung
5	chr10:90281400-90282600	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr10:90281800-90283600	Weak transcription	Ovary	ovary
7	chr10:90281800-90283600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr10:90281800-90286800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr10:90282000-90283200	Weak transcription	Liver	Liver
10	chr10:90282000-90285000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr10:90282000-90285200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr10:90282000-90286800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr10:90282200-90286400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr10:90282400-90282800	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr10:90282400-90282800	Enhancers	HSMMtube	muscle
16	chr10:90282400-90284000	Enhancers	Fetal Kidney	kidney

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