Variant report

Variant	rs2586403
Chromosome Location	chr1:172262494-172262495
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:172256870..172259800-chr1:172260361..172262827,2	MCF-7	breast:
2	chr1:172261558..172263643-chr1:172263765..172267506,3	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10911387	0.92[ASN][1000 genomes]
rs11808940	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs12034440	0.85[EUR][1000 genomes]
rs12039027	0.81[EUR][1000 genomes]
rs12049422	1.00[CEU][hapmap];0.97[GIH][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs12069167	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16844255	0.82[CHD][hapmap]
rs2421994	0.81[CHD][hapmap]
rs2586389	0.94[ASN][1000 genomes]
rs2586392	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2586394	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2586401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2586404	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2586407	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2586408	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2586410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2586411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2586412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2586413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2757493	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2757495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2757496	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs477289	0.93[CEU][hapmap]
rs479336	0.93[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap]
rs6684830	0.80[EUR][1000 genomes]
rs6701929	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7550558	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.94[ASN][1000 genomes]
rs9425543	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9425545	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006542	chr1:172253765-172304690	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172256200-172267400	Weak transcription	Left Ventricle	heart
2	chr1:172256200-172267400	Weak transcription	Psoas Muscle	Psoas
3	chr1:172256200-172290000	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:172256400-172290200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:172256600-172265200	Weak transcription	NH-A	brain
6	chr1:172256600-172289800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr1:172257600-172267400	Weak transcription	Pancreas	Pancrea
8	chr1:172260600-172271000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:172261800-172263400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:172261800-172264000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:172262000-172263000	Enhancers	Fetal Lung	lung
12	chr1:172262000-172263200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:172262000-172263200	Enhancers	Ovary	ovary
14	chr1:172262000-172263400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:172262000-172263800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:172262200-172262600	Weak transcription	Fetal Muscle Leg	muscle
17	chr1:172262200-172262600	Weak transcription	NHLF	lung
18	chr1:172262200-172263000	Enhancers	Osteobl	bone
19	chr1:172262200-172263200	Enhancers	Adipose Nuclei	Adipose

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