Variant report

Variant	rs1400946
Chromosome Location	chr2:189601032-189601033
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	chr2:189595413..189597122-chr2:189598566..189601054,2	MCF-7	breast:

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10166484	0.83[EUR][1000 genomes]
rs10209411	0.94[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10211163	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10804023	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10804024	0.81[EUR][1000 genomes]
rs10931381	0.90[EUR][1000 genomes]
rs10931382	0.87[EUR][1000 genomes]
rs1157434	0.82[EUR][1000 genomes]
rs11679794	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11686942	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11891828	0.98[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11902285	0.98[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12185550	0.84[CEU][hapmap]
rs12617610	0.90[EUR][1000 genomes]
rs12619491	0.86[EUR][1000 genomes]
rs12620233	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12624180	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs12624203	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12693513	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12998848	0.87[EUR][1000 genomes]
rs13001931	0.83[EUR][1000 genomes]
rs13017203	0.98[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13020633	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13024524	0.81[EUR][1000 genomes]
rs13026165	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1354906	0.85[CHB][hapmap]
rs1354907	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1395864	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1395865	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1507554	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1507555	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1516449	0.84[CEU][hapmap]
rs1518006	0.80[EUR][1000 genomes]
rs1518010	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs1518011	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1518012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1518013	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1518014	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1518016	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1524375	0.81[EUR][1000 genomes]
rs1568235	0.87[EUR][1000 genomes]
rs1589133	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1605462	0.85[CHB][hapmap]
rs1607315	0.92[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs17760712	1.00[JPT][hapmap]
rs1829305	0.91[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1848280	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1850553	0.87[EUR][1000 genomes]
rs1851878	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1878650	0.98[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs1995700	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1995701	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1995702	0.91[EUR][1000 genomes]
rs1996457	0.87[EUR][1000 genomes]
rs1996987	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2138959	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2138960	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2176501	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2177544	0.83[EUR][1000 genomes]
rs2351099	0.84[CEU][hapmap]
rs3856335	0.86[EUR][1000 genomes]
rs4306657	0.93[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4666764	0.87[EUR][1000 genomes]
rs4667243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4667244	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4667245	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4667249	0.80[EUR][1000 genomes]
rs6434294	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6710589	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6711038	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6744781	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6748400	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6757283	0.80[EUR][1000 genomes]
rs7583964	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7587646	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7587851	0.87[EUR][1000 genomes]
rs7590689	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7594142	0.87[EUR][1000 genomes]
rs7598731	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs981265	0.87[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:1 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189600400-189601200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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