Variant report

Variant	rs2138960
Chromosome Location	chr2:189631167-189631168
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	chr2:189470137..189473271-chr2:189629493..189632032,3	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10084412	0.81[EUR][1000 genomes]
rs10166484	0.86[EUR][1000 genomes]
rs10209411	0.91[EUR][1000 genomes]
rs10211163	0.83[EUR][1000 genomes]
rs10804023	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10804024	0.84[EUR][1000 genomes]
rs10931381	0.93[EUR][1000 genomes]
rs10931382	0.90[EUR][1000 genomes]
rs1157434	0.85[EUR][1000 genomes]
rs11679794	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11686942	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11891828	0.91[EUR][1000 genomes]
rs11902285	0.91[EUR][1000 genomes]
rs12185550	0.84[CEU][hapmap]
rs12470289	0.82[EUR][1000 genomes]
rs12617610	0.93[EUR][1000 genomes]
rs12619491	0.89[EUR][1000 genomes]
rs12620233	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12624180	0.93[EUR][1000 genomes]
rs12624203	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12693513	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12998848	0.90[EUR][1000 genomes]
rs13001931	0.86[EUR][1000 genomes]
rs13017203	0.91[EUR][1000 genomes]
rs13020633	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13024524	0.84[EUR][1000 genomes]
rs13026165	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1354906	0.85[CHB][hapmap]
rs1354907	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1395864	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1395865	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1400946	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1507554	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1507555	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1516449	0.84[CEU][hapmap]
rs1518006	0.83[EUR][1000 genomes]
rs1518010	0.85[EUR][1000 genomes]
rs1518011	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1518012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1518013	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1518014	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1518016	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1524375	0.84[EUR][1000 genomes]
rs1568235	0.90[EUR][1000 genomes]
rs1589133	0.90[EUR][1000 genomes]
rs1605462	0.85[CHB][hapmap]
rs1607315	0.91[EUR][1000 genomes]
rs17760712	1.00[JPT][hapmap]
rs1829305	0.90[EUR][1000 genomes]
rs1848280	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1850553	0.96[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1851878	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1878650	0.91[EUR][1000 genomes]
rs1995700	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1995701	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1995702	0.87[EUR][1000 genomes]
rs1996457	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1996987	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2138959	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176501	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2177544	0.85[EUR][1000 genomes]
rs2351099	0.84[CEU][hapmap]
rs34017611	0.81[EUR][1000 genomes]
rs3845632	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3856335	0.89[EUR][1000 genomes]
rs4261667	0.84[EUR][1000 genomes]
rs4306657	0.90[EUR][1000 genomes]
rs4666764	0.91[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4667243	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4667244	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4667245	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4667249	0.83[EUR][1000 genomes]
rs6434294	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6710589	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6711038	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6744781	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6748400	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6757283	0.83[EUR][1000 genomes]
rs7583964	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7587646	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7587851	0.96[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7590689	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7594142	0.96[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7598731	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs981265	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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
7	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
8	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
9	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:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189630200-189631600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr2:189630200-189631600	Enhancers	Osteobl	bone
3	chr2:189630200-189632200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr2:189630200-189632200	Enhancers	NHDF-Ad	bronchial
5	chr2:189630400-189631600	Enhancers	Muscle Satellite Cultured Cells	--
6	chr2:189630400-189631600	Enhancers	NH-A	brain
7	chr2:189630600-189631400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr2:189630600-189631800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:189630800-189632000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr2:189630800-189641200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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