Variant report

Variant	rs239815
Chromosome Location	chr6:54816219-54816220
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	chr6:54711449..54713665-chr6:54815278..54817659,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168143	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11969918	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12192659	0.85[CEU][hapmap];1.00[YRI][hapmap]
rs148109	0.85[CEU][hapmap]
rs171224	0.89[CEU][hapmap];0.80[CHB][hapmap];0.83[EUR][1000 genomes]
rs181155	0.89[CEU][hapmap];0.80[CHB][hapmap];0.81[EUR][1000 genomes]
rs1963697	1.00[JPT][hapmap]
rs2134536	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2207025	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs2207026	0.88[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes]
rs239779	0.81[EUR][1000 genomes]
rs239781	0.89[CEU][hapmap];0.81[JPT][hapmap];0.82[EUR][1000 genomes]
rs239783	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs239790	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs239792	0.83[EUR][1000 genomes]
rs239794	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239796	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs239801	0.93[CEU][hapmap];0.80[CHB][hapmap];0.84[EUR][1000 genomes]
rs239813	0.83[EUR][1000 genomes]
rs239837	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs2746443	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2816810	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2816811	0.85[CEU][hapmap]
rs2816812	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs3996950	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs421957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4712082	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6459034	0.89[CEU][hapmap];0.86[CHB][hapmap];0.80[EUR][1000 genomes]
rs9382403	0.81[JPT][hapmap]

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	nsv885900	chr6:54517968-54852462	Active TSS Bivalent Enhancer Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	esv2763553	chr6:54687979-54820487	Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 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	chr6:54807400-54818000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:54809400-54817600	Weak transcription	HMEC	breast

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