Variant report

Variant	rs11709960
Chromosome Location	chr3:179889013-179889014
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:9824972..9827874-chr3:179888956..179891080,2	MCF-7	breast:
2	chr3:179888173..179890774-chr3:179892672..179895400,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264462	Chromatin interaction
ENSG00000264063	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10222466	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10937020	0.95[EUR][1000 genomes]
rs10937021	0.90[EUR][1000 genomes]
rs10937022	0.81[ASN][1000 genomes]
rs12487650	0.97[EUR][1000 genomes]
rs12631680	0.84[ASN][1000 genomes]
rs12631948	0.94[ASN][1000 genomes]
rs12633042	0.81[ASN][1000 genomes]
rs12636328	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12637429	0.94[ASN][1000 genomes]
rs13322790	0.89[EUR][1000 genomes]
rs1357904	0.86[EUR][1000 genomes]
rs1404744	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1464844	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1525269	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1525272	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1525276	0.86[EUR][1000 genomes]
rs1525277	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1568859	0.97[EUR][1000 genomes]
rs1581549	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1589858	0.87[EUR][1000 genomes]
rs1608796	0.81[ASN][1000 genomes]
rs16831259	0.81[ASN][1000 genomes]
rs16831288	0.85[EUR][1000 genomes]
rs1830044	0.83[ASN][1000 genomes]
rs1852121	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1852122	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1852123	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1921676	0.87[EUR][1000 genomes]
rs1950124	0.85[EUR][1000 genomes]
rs2049472	0.85[EUR][1000 genomes]
rs2091273	0.85[EUR][1000 genomes]
rs2178582	0.85[ASN][1000 genomes]
rs2339967	0.97[EUR][1000 genomes]
rs2339968	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28703130	0.84[ASN][1000 genomes]
rs28865282	0.93[EUR][1000 genomes]
rs3849420	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3906013	0.85[EUR][1000 genomes]
rs3906014	0.85[EUR][1000 genomes]
rs4109306	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4343625	0.81[ASN][1000 genomes]
rs4854902	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4854961	0.93[EUR][1000 genomes]
rs4854962	0.93[EUR][1000 genomes]
rs4854964	0.89[EUR][1000 genomes]
rs59555202	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60202080	0.84[ASN][1000 genomes]
rs62292260	0.83[ASN][1000 genomes]
rs62292286	0.81[ASN][1000 genomes]
rs62292288	0.81[ASN][1000 genomes]
rs6790229	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6790465	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6803764	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7619775	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7621628	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7622125	0.85[EUR][1000 genomes]
rs7635210	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7652322	0.86[EUR][1000 genomes]
rs9290696	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9290697	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9812621	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9819178	0.85[EUR][1000 genomes]
rs9821124	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9837718	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9840477	0.88[EUR][1000 genomes]
rs9840775	0.89[EUR][1000 genomes]
rs9845934	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9851723	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9857420	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9860526	0.88[EUR][1000 genomes]
rs9862989	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9863693	0.85[EUR][1000 genomes]
rs9868908	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9869517	0.88[EUR][1000 genomes]
rs9871936	0.83[EUR][1000 genomes]
rs9877454	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9880357	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][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:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:179885400-179898200	Weak transcription	HMEC	breast
2	chr3:179887400-179889400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:179887400-179890400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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