Variant report

Variant	rs6082809
Chromosome Location	chr20:22742766-22742767
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:22737582..22739507-chr20:22742394..22744607,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1997880	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2424462	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424467	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2424471	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2424472	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2424474	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2424477	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2424478	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4815142	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048344	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6082843	0.82[AMR][1000 genomes]
rs6113805	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6132546	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6137748	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs932466	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[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	nsv1061382	chr20:22706041-22763200	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv544213	chr20:22722740-22791150	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv528221	chr20:22732749-22767280	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:22734800-22745200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr20:22737800-22749000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr20:22738600-22743000	Weak transcription	A549	lung
4	chr20:22739000-22742800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr20:22739400-22743200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr20:22739400-22743200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr20:22739600-22743200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr20:22739600-22743200	Weak transcription	Fetal Muscle Leg	muscle
9	chr20:22739600-22743400	Weak transcription	Aorta	Aorta
10	chr20:22739600-22743600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr20:22740000-22744600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr20:22740800-22746000	Enhancers	Placenta	Placenta
13	chr20:22741200-22743400	Weak transcription	Right Atrium	heart
14	chr20:22741400-22742800	Weak transcription	Spleen	Spleen
15	chr20:22741400-22743000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr20:22741400-22743400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr20:22741400-22743600	Enhancers	HSMMtube	muscle
18	chr20:22741600-22743200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr20:22741600-22743400	Weak transcription	Esophagus	oesophagus
20	chr20:22741600-22745200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr20:22742200-22743000	Enhancers	NHEK	skin
22	chr20:22742200-22743400	Enhancers	HMEC	breast
23	chr20:22742200-22745800	Enhancers	Placenta Amnion	Placenta Amnion
24	chr20:22742400-22743600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr20:22742400-22746000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr20:22742400-22746000	Enhancers	Lung	lung
27	chr20:22742600-22742800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr20:22742600-22744000	Enhancers	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links