Variant report

Variant	rs12439116
Chromosome Location	chr15:57039566-57039567
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:57038395..57040361-chr15:57049426..57051956,2	K562	blood:
2	chr15:57039206..57041236-chr15:57044908..57046817,2	MCF-7	breast:
3	chr15:57024390..57027645-chr15:57035934..57039963,3	K562	blood:

Variant related genes	Relation type
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10518872	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1087705	0.94[EUR][1000 genomes]
rs11071285	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11071286	0.82[AMR][1000 genomes]
rs12437635	1.00[CEU][hapmap]
rs12437714	0.80[AMR][1000 genomes]
rs12437735	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12438377	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12438728	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12439563	1.00[EUR][1000 genomes]
rs12439586	0.94[EUR][1000 genomes]
rs12439697	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12440006	1.00[EUR][1000 genomes]
rs12440725	1.00[CEU][hapmap]
rs12440891	1.00[CEU][hapmap]
rs12441746	0.95[EUR][1000 genomes]
rs12441769	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12441792	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12442069	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12442630	0.80[AMR][1000 genomes]
rs12442662	1.00[CEU][hapmap]
rs12443178	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12903143	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12907983	1.00[EUR][1000 genomes]
rs1364541	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1564557	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1586022	0.89[EUR][1000 genomes]
rs1600829	1.00[EUR][1000 genomes]
rs1600831	0.95[EUR][1000 genomes]
rs1631905	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1647386	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1647391	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs16977123	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17238859	0.89[EUR][1000 genomes]
rs17238880	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17238894	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17238901	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17238971	1.00[CEU][hapmap]
rs17819592	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17819616	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17819646	1.00[CEU][hapmap]
rs1834199	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2052641	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2161935	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2170461	0.89[EUR][1000 genomes]
rs2170462	0.94[EUR][1000 genomes]
rs2459565	0.94[EUR][1000 genomes]
rs2676178	0.94[EUR][1000 genomes]
rs2676181	0.94[EUR][1000 genomes]
rs2733231	0.89[EUR][1000 genomes]
rs2899599	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4287503	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4424865	0.80[AMR][1000 genomes]
rs4594195	0.89[EUR][1000 genomes]
rs4774869	0.89[EUR][1000 genomes]
rs4774885	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs480701	1.00[CEU][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6493888	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7176472	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs74015901	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs8029710	0.90[EUR][1000 genomes]
rs966807	0.87[AMR][1000 genomes];0.89[EUR][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	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv569576	chr15:57012816-57126917	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57038800-57040800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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