Variant report

Variant	rs10509549
Chromosome Location	chr10:90214993-90214994
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10509547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10509548	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10509550	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10736359	0.81[ASW][hapmap];0.95[CEU][hapmap]
rs10736360	0.82[CEU][hapmap]
rs10788590	1.00[CHB][hapmap]
rs1169042	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11816967	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1237989	1.00[ASN][1000 genomes]
rs1325899	0.90[CEU][hapmap]
rs1325901	0.95[CEU][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1325904	0.95[CEU][hapmap];0.80[MEX][hapmap]
rs1342457	1.00[ASW][hapmap];0.95[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1359581	0.94[CEU][hapmap]
rs1359582	0.90[CEU][hapmap];0.80[MEX][hapmap]
rs1409136	0.82[CEU][hapmap]
rs1555839	0.85[CEU][hapmap];0.80[MEX][hapmap]
rs1573074	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17334741	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17336288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17426488	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1774977	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1974053	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1980813	0.82[CEU][hapmap];0.80[MEX][hapmap]
rs2437876	0.90[CEU][hapmap];1.00[YRI][hapmap]
rs2477953	0.95[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2576155	0.81[CEU][hapmap]
rs2576158	0.95[CEU][hapmap]
rs2576162	0.90[CEU][hapmap];0.80[MEX][hapmap]
rs2576163	0.89[CEU][hapmap]
rs2576167	0.82[CEU][hapmap];0.80[MEX][hapmap]
rs2576173	0.95[CEU][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2576175	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2576177	0.95[CEU][hapmap];1.00[YRI][hapmap]
rs2765451	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765453	0.90[CEU][hapmap]
rs2765457	1.00[ASW][hapmap];0.95[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs303516	1.00[ASN][1000 genomes]
rs303517	1.00[ASN][1000 genomes]
rs55713122	1.00[ASN][1000 genomes]
rs57260181	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61852496	1.00[ASN][1000 genomes]
rs61852497	1.00[ASN][1000 genomes]
rs792201	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs792202	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs792203	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs792216	1.00[ASN][1000 genomes]
rs792231	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814617	1.00[ASN][1000 genomes]
rs814619	1.00[ASN][1000 genomes]
rs875050	0.82[CEU][hapmap]

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

No data

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	chr10:90210200-90215400	Weak transcription	Adipose Nuclei	Adipose
3	chr10:90210400-90217600	Weak transcription	Right Atrium	heart
4	chr10:90211000-90215600	Weak transcription	Aorta	Aorta
5	chr10:90211400-90215800	Weak transcription	Ovary	ovary
6	chr10:90214200-90217000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr10:90214600-90215200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr10:90214800-90216200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr10:90214800-90217800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links