Variant report

Variant	rs542925
Chromosome Location	chr6:128980678-128980679
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	chr6:128840533..128842502-chr6:128979632..128981294,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152894	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs12191852	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12194587	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12201837	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12212602	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1508436	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2096099	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2153707	0.92[EUR][1000 genomes]
rs2202776	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2326737	0.99[ASN][1000 genomes]
rs471145	0.99[ASN][1000 genomes]
rs472588	0.85[ASN][1000 genomes]
rs478551	0.80[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs478649	0.84[ASN][1000 genomes]
rs479187	0.85[ASN][1000 genomes]
rs479357	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs479641	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs480169	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs482607	0.99[ASN][1000 genomes]
rs4895836	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4897267	0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs508972	0.99[ASN][1000 genomes]
rs521638	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs525293	0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs532291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs542404	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs545102	0.97[ASN][1000 genomes]
rs545332	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs546085	0.84[ASN][1000 genomes]
rs551729	0.84[ASN][1000 genomes]
rs562490	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs565485	0.99[ASN][1000 genomes]
rs565685	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs572745	0.86[ASN][1000 genomes]
rs575131	0.99[ASN][1000 genomes]
rs62425863	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62427801	0.99[ASN][1000 genomes]
rs6911133	0.99[ASN][1000 genomes]
rs6926043	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6927678	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs699424	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs699425	0.85[ASN][1000 genomes]
rs699426	0.85[ASN][1000 genomes]
rs7753787	0.99[ASN][1000 genomes]
rs7771173	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs9321126	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9372899	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9375584	0.92[EUR][1000 genomes]
rs9388658	1.00[CEU][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9402063	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs969970	0.81[ASN][1000 genomes]
rs972997	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][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	nsv1020071	chr6:128579774-129048919	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv538441	chr6:128579774-129048919	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv830801	chr6:128878436-129064667	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:128975600-128981000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:128977400-128980800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr6:128977400-128982000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:128977600-128980800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:128978000-128981000	Weak transcription	Hela-S3	cervix
6	chr6:128978400-128980800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr6:128978600-128981000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:128978800-128981000	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr6:128979000-128981000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:128979800-128981200	Enhancers	Fetal Thymus	thymus
11	chr6:128980400-128981000	Enhancers	NHEK	skin
12	chr6:128980400-128981200	Enhancers	Stomach Mucosa	stomach
13	chr6:128980400-128981600	Enhancers	Fetal Heart	heart
14	chr6:128980600-128982000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr6:128980600-128982000	Enhancers	HMEC	breast

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