Variant report

Variant	rs12693513
Chromosome Location	chr2:189591624-189591625
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	chr2:189583743..189586666-chr2:189589000..189591672,2	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10166484	0.80[EUR][1000 genomes]
rs10209411	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10211163	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10804023	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931381	0.87[EUR][1000 genomes]
rs10931382	0.84[EUR][1000 genomes]
rs11679794	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11685321	0.85[CHB][hapmap]
rs11686942	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11891828	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11902285	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12185550	0.81[CEU][hapmap]
rs12617610	0.87[EUR][1000 genomes]
rs12619491	0.83[EUR][1000 genomes]
rs12620233	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12624180	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12624203	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12998848	0.84[EUR][1000 genomes]
rs13001931	0.80[EUR][1000 genomes]
rs13017203	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs13020633	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13026165	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1354906	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs1354907	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1400946	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1507554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1507555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1516449	0.81[CEU][hapmap]
rs1518010	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1518011	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1518012	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1518013	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1518014	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1518016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1568235	0.84[EUR][1000 genomes]
rs1589133	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1605462	0.85[CHB][hapmap]
rs1607315	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs17760712	1.00[JPT][hapmap]
rs1829305	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1848280	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1850553	0.85[EUR][1000 genomes]
rs1851878	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1878650	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1995700	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1995701	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1995702	0.93[EUR][1000 genomes]
rs1996457	0.85[EUR][1000 genomes]
rs1996987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2138959	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2138960	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2176501	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2351099	0.81[CEU][hapmap]
rs3856335	0.83[EUR][1000 genomes]
rs4306657	0.85[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4666764	0.85[EUR][1000 genomes]
rs4667241	0.82[AFR][1000 genomes]
rs4667243	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4667244	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4667245	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6434294	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6710589	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6711038	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6744781	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6748400	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7583964	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7587646	0.91[EUR][1000 genomes]
rs7587851	0.85[EUR][1000 genomes]
rs7590689	0.91[EUR][1000 genomes]
rs7594142	0.85[EUR][1000 genomes]
rs7598731	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs981265	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003974	chr2:189331760-189827814	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1000932	chr2:189542210-189677277	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv536088	chr2:189542210-189677277	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv1842768	chr2:189555506-189635696	Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv875606	chr2:189579045-189688463	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv875607	chr2:189579045-189711790	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189588000-189592800	Weak transcription	Fetal Lung	lung
2	chr2:189590200-189592800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:189590400-189593000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:189590600-189592400	Enhancers	NH-A	brain
5	chr2:189590800-189592200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:189590800-189592400	Enhancers	NHEK	skin
7	chr2:189591200-189591800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:189591200-189591800	Enhancers	NHDF-Ad	bronchial
9	chr2:189591200-189592200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr2:189591200-189592400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr2:189591200-189592400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:189591400-189592000	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr2:189591400-189592800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:189591600-189592400	Enhancers	HSMMtube	muscle

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