Variant report

Variant	rs2488271
Chromosome Location	chr10:90228162-90228163
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	chr10:90212145..90213848-chr10:90226282..90228506,2	MCF-7	breast:

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

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

rs_ID	r²[population]
rs10749586	0.85[CEU][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10749587	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10749588	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10788604	0.96[ASN][1000 genomes]
rs10788605	0.96[ASN][1000 genomes]
rs10887827	0.96[ASN][1000 genomes]
rs10887829	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs11202750	0.86[CEU][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1177587	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1183901	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12778446	0.81[CHB][hapmap]
rs1325900	0.85[YRI][hapmap]
rs1325903	0.86[CHB][hapmap]
rs1325906	0.85[YRI][hapmap]
rs1325907	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1359580	0.87[CHB][hapmap]
rs1409134	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs17112571	0.86[YRI][hapmap]
rs17112575	0.86[YRI][hapmap]
rs1925937	0.90[AMR][1000 genomes]
rs1935578	0.85[CEU][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1952122	0.86[CHB][hapmap]
rs1980812	0.88[AMR][1000 genomes]
rs2077890	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2153856	0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs2437871	0.86[CHB][hapmap];0.90[AMR][1000 genomes]
rs2437872	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2437874	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2437877	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2437878	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2477952	0.81[CHB][hapmap];0.89[AMR][1000 genomes]
rs2477955	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2477957	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2576166	0.86[CHB][hapmap];0.88[AMR][1000 genomes]
rs2576174	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2576179	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap]
rs2576180	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2765441	0.86[AFR][1000 genomes]
rs2765442	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2765444	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2986118	0.81[CEU][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4403718	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4934414	0.86[YRI][hapmap]
rs7076491	0.81[YRI][hapmap]
rs725683	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs725684	1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs745354	0.87[CHB][hapmap]
rs7902230	0.96[ASN][1000 genomes]
rs7904229	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7916937	0.89[CEU][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7917100	0.95[CHB][hapmap];0.95[JPT][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	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:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90225800-90228600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr10:90226200-90228800	Enhancers	HSMM	muscle
3	chr10:90226400-90228200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr10:90226800-90228600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr10:90226800-90228600	Enhancers	HMEC	breast
6	chr10:90226800-90228800	Enhancers	Psoas Muscle	Psoas
7	chr10:90227200-90228400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr10:90227200-90228800	Enhancers	Hela-S3	cervix
9	chr10:90227400-90228200	Enhancers	Ovary	ovary
10	chr10:90227400-90228400	Enhancers	Muscle Satellite Cultured Cells	--
11	chr10:90227400-90228400	Enhancers	NHDF-Ad	bronchial
12	chr10:90227400-90228400	Enhancers	Osteobl	bone
13	chr10:90227400-90228600	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr10:90227400-90228600	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr10:90227600-90228200	Enhancers	NH-A	brain
16	chr10:90227600-90228400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr10:90227600-90237000	Weak transcription	Left Ventricle	heart
18	chr10:90227800-90228600	Flanking Active TSS	HSMMtube	muscle
19	chr10:90228000-90228200	Enhancers	Aorta	Aorta
20	chr10:90228000-90228600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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