Variant report

Variant	rs56083876
Chromosome Location	chr6:45598025-45598026
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:45527779..45529420-chr6:45596792..45598594,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10080253	0.85[ASN][1000 genomes]
rs12528502	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12661055	0.80[ASN][1000 genomes]
rs12661124	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12663210	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12665637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1491142	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16873543	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16873550	0.86[AFR][1000 genomes]
rs16873554	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2020084	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58129892	0.80[ASN][1000 genomes]
rs59074904	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs60540355	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60884282	0.85[ASN][1000 genomes]
rs6458449	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6458450	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6458453	0.82[ASN][1000 genomes]
rs6458454	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6458455	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6899443	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6902401	0.80[ASN][1000 genomes]
rs6916895	0.80[ASN][1000 genomes]
rs6917651	0.80[ASN][1000 genomes]
rs6930188	0.80[ASN][1000 genomes]
rs6934210	0.85[ASN][1000 genomes]
rs6936365	0.82[ASN][1000 genomes]
rs6938247	0.87[AFR][1000 genomes]
rs6938489	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6940187	0.80[ASN][1000 genomes]
rs713270	0.83[ASN][1000 genomes]
rs73457129	0.84[AFR][1000 genomes]
rs73738526	0.82[ASN][1000 genomes]
rs73738528	0.80[ASN][1000 genomes]
rs7742335	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7752200	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7758915	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7759415	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7760394	0.82[AFR][1000 genomes]
rs7763886	0.85[ASN][1000 genomes]
rs7764338	0.81[AFR][1000 genomes]
rs9296462	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9296463	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9463108	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9472518	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9472524	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9472525	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9472530	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9472531	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9472532	0.85[ASN][1000 genomes]
rs9472534	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv427755	chr6:45474631-45627025	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45588600-45601000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr6:45594000-45598200	Weak transcription	Ovary	ovary
3	chr6:45594200-45604400	Weak transcription	Colon Smooth Muscle	Colon
4	chr6:45594600-45598400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:45594800-45599200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr6:45595000-45607600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:45595200-45598400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr6:45595200-45598800	Weak transcription	HMEC	breast
9	chr6:45595200-45598800	Weak transcription	NHEK	skin
10	chr6:45595400-45598200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:45595400-45598200	Weak transcription	Osteobl	bone
12	chr6:45595400-45598600	Weak transcription	Hela-S3	cervix
13	chr6:45596600-45601200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr6:45596800-45598200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:45596800-45601200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:45597200-45599000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:45597600-45599400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr6:45597800-45598600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:45597800-45598600	Enhancers	Pancreas	Pancrea
20	chr6:45597800-45599400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr6:45597800-45599600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:45597800-45599800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr6:45598000-45598800	Enhancers	NHLF	lung
24	chr6:45598000-45599200	Enhancers	NHDF-Ad	bronchial

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