Variant report

Variant	rs2339967
Chromosome Location	chr3:179892820-179892821
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	chr3:179888173..179890774-chr3:179892672..179895400,2	MCF-7	breast:

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10222466	0.92[EUR][1000 genomes]
rs10513771	0.86[ASN][1000 genomes]
rs10937020	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10937021	0.90[EUR][1000 genomes]
rs11709960	0.97[EUR][1000 genomes]
rs11718127	0.81[ASN][1000 genomes]
rs12487650	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492526	0.95[ASN][1000 genomes]
rs12636328	0.93[EUR][1000 genomes]
rs13322790	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1357904	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1404743	0.84[ASN][1000 genomes]
rs1404744	0.91[EUR][1000 genomes]
rs1464844	0.87[EUR][1000 genomes]
rs1464845	0.85[ASN][1000 genomes]
rs1525269	0.88[EUR][1000 genomes]
rs1525272	0.86[EUR][1000 genomes]
rs1525276	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1525277	0.95[EUR][1000 genomes]
rs1568859	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1568860	0.96[ASN][1000 genomes]
rs1581549	0.87[EUR][1000 genomes]
rs1589858	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs16831126	0.81[ASN][1000 genomes]
rs16831219	0.90[ASN][1000 genomes]
rs16831288	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1852121	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1852122	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1852123	0.85[EUR][1000 genomes]
rs1921676	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1950124	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2049472	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2091273	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2177723	0.91[ASN][1000 genomes]
rs2339968	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2879654	0.96[ASN][1000 genomes]
rs28865282	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3849420	0.93[EUR][1000 genomes]
rs3906013	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3906014	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4109306	0.86[EUR][1000 genomes]
rs4854901	0.81[ASN][1000 genomes]
rs4854902	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4854903	0.86[ASN][1000 genomes]
rs4854961	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4854962	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4854964	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4854966	0.85[ASN][1000 genomes]
rs56234136	0.85[ASN][1000 genomes]
rs59555202	0.86[EUR][1000 genomes]
rs60057308	0.81[ASN][1000 genomes]
rs62290558	0.81[ASN][1000 genomes]
rs62292283	0.87[ASN][1000 genomes]
rs62292284	0.87[ASN][1000 genomes]
rs62292290	0.85[ASN][1000 genomes]
rs62292291	0.85[ASN][1000 genomes]
rs62292292	0.83[ASN][1000 genomes]
rs6790229	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6790465	0.92[EUR][1000 genomes]
rs67979781	0.81[ASN][1000 genomes]
rs68014168	0.88[ASN][1000 genomes]
rs6803764	0.82[EUR][1000 genomes]
rs7619775	0.88[EUR][1000 genomes]
rs7621628	0.93[EUR][1000 genomes]
rs7622125	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7635210	0.85[EUR][1000 genomes]
rs7652322	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7652473	0.81[ASN][1000 genomes]
rs9290696	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9290697	0.91[EUR][1000 genomes]
rs9812621	0.89[EUR][1000 genomes]
rs9819178	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9821124	0.96[EUR][1000 genomes]
rs9837718	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9840477	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9840775	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9845934	0.90[EUR][1000 genomes]
rs9851723	0.85[EUR][1000 genomes]
rs9857420	0.88[EUR][1000 genomes]
rs9860526	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9862989	0.91[EUR][1000 genomes]
rs9863693	0.85[EUR][1000 genomes]
rs9868908	0.86[EUR][1000 genomes]
rs9869517	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9871928	0.81[ASN][1000 genomes]
rs9871936	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9877454	0.87[EUR][1000 genomes]
rs9880357	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534210	chr3:179666123-179899347	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1012271	chr3:179806875-180234871	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv878040	chr3:179823887-180128288	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179885400-179898200	Weak transcription	HMEC	breast
2	chr3:179889600-179896800	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr3:179891600-179893200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:179891800-179893000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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