Variant report

Variant	rs2477956
Chromosome Location	chr10:90235457-90235458
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:90144173..90146300-chr10:90233140..90235508,2	MCF-7	breast:

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10509552	0.82[JPT][hapmap]
rs1067839	0.96[CEU][hapmap];0.91[AMR][1000 genomes]
rs1067840	0.96[CEU][hapmap];0.91[AMR][1000 genomes]
rs10736351	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10736352	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10736354	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10749589	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10749590	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10749591	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10788598	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10788599	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10788600	0.96[CEU][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10788602	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10887817	0.86[CEU][hapmap]
rs10887818	0.85[CEU][hapmap]
rs10887821	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10887823	0.96[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10887824	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1169043	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1342450	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1342451	0.86[CEU][hapmap]
rs1342456	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1578696	0.82[CHB][hapmap]
rs1617881	0.86[CEU][hapmap]
rs1750274	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1935579	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1935581	0.82[CHB][hapmap]
rs1935582	0.82[CHB][hapmap]
rs1935584	0.90[AMR][1000 genomes]
rs2096194	0.96[CEU][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2185786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2209553	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs2312610	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2433340	0.96[CEU][hapmap]
rs2437875	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2477954	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576159	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs2576169	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576170	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576171	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576172	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2576176	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap]
rs2576181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2765440	0.81[CHB][hapmap]
rs2765454	0.81[AMR][1000 genomes]
rs2765456	0.86[CHB][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes]
rs2872092	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4509673	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4596981	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4606392	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4619060	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4934403	0.86[CEU][hapmap]
rs4934404	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4934409	0.96[CEU][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4934411	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6586132	0.96[CEU][hapmap]
rs6586134	0.86[CEU][hapmap]
rs6586139	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7899828	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7909697	0.96[CEU][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7910594	0.89[CEU][hapmap];0.83[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7911996	0.96[CEU][hapmap];0.80[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7918921	0.85[CEU][hapmap]
rs7921352	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs792205	0.86[CEU][hapmap]
rs792207	0.85[CEU][hapmap]
rs792208	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs792209	0.85[CEU][hapmap]
rs792211	0.90[AMR][1000 genomes]
rs792213	0.86[CEU][hapmap]
rs792214	0.93[CEU][hapmap];0.90[AMR][1000 genomes]
rs792215	0.95[CEU][hapmap];0.91[AMR][1000 genomes]
rs792230	0.86[CEU][hapmap]
rs792234	0.85[CEU][hapmap]
rs792235	0.96[CEU][hapmap];0.90[AMR][1000 genomes]
rs7922551	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs796945	0.81[CEU][hapmap]
rs806694	0.96[CEU][hapmap];0.90[AMR][1000 genomes]
rs813782	0.96[CEU][hapmap];0.90[AMR][1000 genomes]
rs814242	0.90[AMR][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	nsv482385	chr10:90066140-90259751	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv1050587	chr10:90146582-90272627	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv540739	chr10:90146582-90272627	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	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
7	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

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90227600-90237000	Weak transcription	Left Ventricle	heart
2	chr10:90233000-90236000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr10:90233800-90239200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr10:90234000-90235600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr10:90234000-90235600	Enhancers	Liver	Liver
6	chr10:90234000-90235600	Enhancers	Ovary	ovary
7	chr10:90234200-90235600	Enhancers	Skeletal Muscle Male	skeletal muscle
8	chr10:90234200-90236000	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr10:90234400-90235600	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr10:90234400-90235600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr10:90234400-90238200	Weak transcription	Right Ventricle	heart
12	chr10:90234600-90235600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr10:90234800-90235800	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr10:90235000-90235600	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr10:90235000-90235800	Weak transcription	Pancreas	Pancrea
16	chr10:90235000-90236000	Enhancers	HMEC	breast
17	chr10:90235000-90237000	Weak transcription	Psoas Muscle	Psoas
18	chr10:90235000-90240400	Weak transcription	Aorta	Aorta
19	chr10:90235200-90237000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr10:90235200-90237200	Weak transcription	NHEK	skin
21	chr10:90235400-90237400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr10:90235400-90237800	Weak transcription	Fetal Heart	heart
23	chr10:90235400-90238200	Weak transcription	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links