Variant report

Variant	rs4109306
Chromosome Location	chr3:179973959-179973960
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	chr3:179966877..179968813-chr3:179972881..179975215,2	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10222466	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10937020	0.83[EUR][1000 genomes]
rs10937021	0.91[EUR][1000 genomes]
rs10937022	0.90[ASN][1000 genomes]
rs11709960	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12108145	0.87[ASN][1000 genomes]
rs12487650	0.86[EUR][1000 genomes]
rs12633042	0.90[ASN][1000 genomes]
rs12636328	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12638766	0.96[ASN][1000 genomes]
rs13322790	0.95[EUR][1000 genomes]
rs1357904	0.97[EUR][1000 genomes]
rs1404744	0.83[EUR][1000 genomes]
rs1464844	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1525269	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1525272	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1525276	0.97[EUR][1000 genomes]
rs1525277	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1568859	0.86[EUR][1000 genomes]
rs1581549	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1589858	0.98[EUR][1000 genomes]
rs1608796	0.92[ASN][1000 genomes]
rs16831259	0.90[ASN][1000 genomes]
rs16831288	0.99[EUR][1000 genomes]
rs1852121	0.83[EUR][1000 genomes]
rs1852122	0.82[EUR][1000 genomes]
rs1852123	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2030763	0.92[ASN][1000 genomes]
rs2091273	0.99[EUR][1000 genomes]
rs2178582	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2222858	0.91[ASN][1000 genomes]
rs2339967	0.86[EUR][1000 genomes]
rs2339968	0.85[EUR][1000 genomes]
rs28865282	0.85[EUR][1000 genomes]
rs3849420	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3906012	0.94[ASN][1000 genomes]
rs3906013	0.99[EUR][1000 genomes]
rs3906014	0.99[EUR][1000 genomes]
rs4343625	0.90[ASN][1000 genomes]
rs4854902	0.85[EUR][1000 genomes]
rs4854907	0.95[ASN][1000 genomes]
rs4854961	0.85[EUR][1000 genomes]
rs4854962	0.85[EUR][1000 genomes]
rs4854964	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4854968	0.93[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs57131411	0.91[ASN][1000 genomes]
rs62292286	0.89[ASN][1000 genomes]
rs62292288	0.90[ASN][1000 genomes]
rs62292294	0.92[ASN][1000 genomes]
rs6780998	0.92[ASN][1000 genomes]
rs6790229	0.88[EUR][1000 genomes]
rs6790465	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7619775	0.86[AFR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7621628	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7622125	0.99[EUR][1000 genomes]
rs7622865	0.85[AFR][1000 genomes]
rs7643438	0.81[EUR][1000 genomes]
rs7652322	0.95[EUR][1000 genomes]
rs7652473	0.82[EUR][1000 genomes]
rs9290696	0.85[EUR][1000 genomes]
rs9290697	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs939441	0.81[CEU][hapmap]
rs9812621	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9815922	0.94[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9815923	0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9819178	0.98[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs9821124	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9837718	0.88[EUR][1000 genomes]
rs9840477	0.86[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs9840775	0.93[EUR][1000 genomes]
rs9845934	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9857420	0.81[EUR][1000 genomes]
rs9860526	0.84[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs9862989	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9864555	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9868908	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9869517	0.94[EUR][1000 genomes]
rs9871936	0.97[EUR][1000 genomes]
rs9877454	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9880357	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv997388	chr3:179899279-180172349	Enhancers Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv536817	chr3:179899279-180172349	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179973200-179974400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:179973400-179974400	Enhancers	HMEC	breast

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