Variant report

Variant	rs6023079
Chromosome Location	chr20:52874109-52874110
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:103363122..103363960-chr20:52873238..52874146,2	MCF-7	breast:
2	chr20:52700468..52702286-chr20:52872421..52874639,2	MCF-7	breast:
3	chr20:52853706..52856539-chr20:52873064..52874754,2	MCF-7	breast:
4	chr20:52823743..52826229-chr20:52873790..52875755,3	MCF-7	breast:
5	chr20:52195149..52196759-chr20:52873374..52876133,2	MCF-7	breast:
6	chr13:85330865..85331631-chr20:52873521..52874297,2	MCF-7	breast:
7	chr20:52691602..52694513-chr20:52873450..52876265,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1157418	1.00[CEU][hapmap]
rs11698157	0.83[EUR][1000 genomes]
rs16999320	1.00[CEU][hapmap]
rs16999351	1.00[CEU][hapmap]
rs16999393	0.82[CEU][hapmap]
rs28460139	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs292116	0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs292117	1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs292122	1.00[ASN][1000 genomes]
rs292128	1.00[ASN][1000 genomes]
rs292142	0.84[AMR][1000 genomes]
rs3787559	0.92[JPT][hapmap]
rs4811496	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56726174	0.93[ASN][1000 genomes]
rs6013926	0.92[JPT][hapmap]
rs6023096	1.00[CEU][hapmap]
rs6127146	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73137452	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs986709	0.83[EUR][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	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv834010	chr20:52759824-52932939	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
3	nsv834011	chr20:52858341-53086042	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52870600-52874400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr20:52870800-52874200	Enhancers	Muscle Satellite Cultured Cells	--
3	chr20:52870800-52874400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr20:52871000-52875000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr20:52871000-52875000	Enhancers	HMEC	breast
6	chr20:52871000-52875400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr20:52871200-52874200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr20:52871200-52875000	Enhancers	NHEK	skin
9	chr20:52871400-52874200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr20:52871400-52874400	Enhancers	Hela-S3	cervix
11	chr20:52871400-52874400	Enhancers	Osteobl	bone
12	chr20:52871400-52875000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr20:52871800-52874200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr20:52872000-52874200	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr20:52872200-52874400	Enhancers	NH-A	brain
16	chr20:52872400-52875000	Enhancers	Placenta Amnion	Placenta Amnion
17	chr20:52872800-52883800	Weak transcription	Pancreas	Pancrea
18	chr20:52873000-52874200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr20:52873000-52874200	Enhancers	NHLF	lung
20	chr20:52873400-52874200	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr20:52874000-52879200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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