Variant report

Variant	rs2465589
Chromosome Location	chr12:47269854-47269855
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	chr12:47266835..47268379-chr12:47268939..47270586,2	MCF-7	breast:

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10748455	0.91[CEU][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes]
rs10785645	0.89[CEU][hapmap];0.97[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11183626	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2465212	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2465592	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2465603	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2465631	0.99[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2715784	0.80[ASN][1000 genomes]
rs2715785	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4323984	0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4340151	0.90[CEU][hapmap];0.80[CHB][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4497488	0.95[AMR][1000 genomes]
rs4516050	0.99[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4533116	0.99[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4569081	0.91[CEU][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes]
rs4627160	0.90[CEU][hapmap];0.83[AMR][1000 genomes]
rs7489259	0.90[CEU][hapmap];0.80[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7955552	0.86[ASW][hapmap];0.91[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.89[JPT][hapmap];0.86[LWK][hapmap];0.94[MKK][hapmap];0.99[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7959916	0.81[AMR][1000 genomes]
rs7974393	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1845143	chr12:47051076-47431496	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv899054	chr12:47224325-47280079	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 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	chr12:47260200-47270600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr12:47268200-47270800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr12:47268800-47270800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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