Variant report

Variant	rs6123369
Chromosome Location	chr20:52871244-52871245
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:52852456..52856671-chr20:52869199..52873917,7	MCF-7	breast:
2	chr20:52870852..52872943-chr3:64020016..64022874,4	MCF-7	breast:
3	chr20:52841956..52843835-chr20:52870841..52872482,2	MCF-7	breast:
4	chr20:52823499..52826425-chr20:52871011..52873800,2	MCF-7	breast:
5	chr20:52870717..52873614-chr20:52960428..52962256,2	MCF-7	breast:
6	chr20:52867514..52871887-chr3:64023901..64028023,6	MCF-7	breast:
7	chr1:155055878..155058411-chr20:52870566..52873238,2	MCF-7	breast:
8	chr20:52722574..52724626-chr20:52869342..52872286,2	MCF-7	breast:
9	chr20:52838493..52841252-chr20:52870452..52872363,2	MCF-7	breast:
10	chr20:52868969..52871919-chr3:64020009..64024128,5	MCF-7	breast:
11	chr20:46413266..46415386-chr20:52869733..52871786,2	MCF-7	breast:

No data

No data

No data

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10485793	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1477722	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1477723	0.82[ASN][1000 genomes]
rs1477731	0.81[EUR][1000 genomes]
rs28555372	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4811499	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4811500	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62216588	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62216601	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[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	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:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52868200-52871400	Weak transcription	Hela-S3	cervix
2	chr20:52868200-52871800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr20:52870600-52874400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr20:52870800-52874200	Enhancers	Muscle Satellite Cultured Cells	--
5	chr20:52870800-52874400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr20:52871000-52875000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr20:52871000-52875000	Enhancers	HMEC	breast
8	chr20:52871000-52875400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr20:52871200-52872000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr20:52871200-52874200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr20:52871200-52875000	Enhancers	NHEK	skin

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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