Variant report

Variant	rs1878650
Chromosome Location	chr2:189637643-189637644
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10084412	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10166484	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10209411	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10804023	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10804024	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10931381	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10931382	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1157434	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11679794	0.98[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs11686942	0.87[EUR][1000 genomes]
rs11891828	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11901929	0.82[EUR][1000 genomes]
rs11902285	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12185550	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs12470289	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12617610	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12619491	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12620233	0.87[EUR][1000 genomes]
rs12624180	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12624203	0.90[EUR][1000 genomes]
rs12693513	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12998848	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13001931	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13017203	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13020633	0.90[EUR][1000 genomes]
rs13024524	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13026165	0.98[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1354906	1.00[CHB][hapmap]
rs1354907	0.84[EUR][1000 genomes]
rs1395864	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1395865	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1400946	0.98[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1507554	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1507555	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1516449	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs1518006	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1518010	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1518011	0.87[EUR][1000 genomes]
rs1518012	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1518013	0.98[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1518014	0.91[EUR][1000 genomes]
rs1518016	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1524375	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1568235	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1589133	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1605462	0.86[CHB][hapmap]
rs1607315	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17355585	1.00[JPT][hapmap]
rs1829305	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1848280	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1850553	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1851878	0.90[AFR][1000 genomes]
rs1995700	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1995701	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1995702	0.89[EUR][1000 genomes]
rs1996457	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1996987	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2138959	0.91[EUR][1000 genomes]
rs2138960	0.91[EUR][1000 genomes]
rs2176501	0.98[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2177544	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2351099	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs2708209	1.00[JPT][hapmap]
rs34017611	0.89[EUR][1000 genomes]
rs3856335	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4261667	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4306657	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4666764	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4667243	0.98[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4667244	0.87[EUR][1000 genomes]
rs4667245	0.87[EUR][1000 genomes]
rs4667249	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6434294	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6710589	0.98[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6711038	0.91[EUR][1000 genomes]
rs6744781	0.87[EUR][1000 genomes]
rs6748400	0.89[EUR][1000 genomes]
rs6757283	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7583964	0.96[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7587646	0.92[EUR][1000 genomes]
rs7587851	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7590689	0.93[EUR][1000 genomes]
rs7594142	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598731	0.91[EUR][1000 genomes]
rs7600697	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs981265	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
5	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
6	nsv1008847	chr2:189603961-189769705	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
7	nsv997454	chr2:189615728-189770133	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1002175	chr2:189615728-189776301	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189630800-189641200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:189631600-189650000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr2:189631800-189640800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr2:189632200-189637800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:189637600-189638400	Enhancers	Muscle Satellite Cultured Cells	--
6	chr2:189637600-189638800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links