Variant report

Variant	rs6079482
Chromosome Location	chr20:14517220-14517221
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs16990099	1.00[JPT][hapmap]
rs17227118	1.00[JPT][hapmap]
rs1884700	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1998234	1.00[JPT][hapmap]
rs2327860	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2423820	1.00[JPT][hapmap]
rs4814314	1.00[JPT][hapmap]
rs4814315	1.00[JPT][hapmap]
rs6033988	1.00[JPT][hapmap]
rs6042781	0.94[EUR][1000 genomes]
rs6042808	1.00[JPT][hapmap]
rs6042809	1.00[JPT][hapmap]
rs6042814	1.00[JPT][hapmap]
rs6042830	1.00[JPT][hapmap]
rs6042831	1.00[JPT][hapmap]
rs6074753	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs6074754	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6079397	1.00[JPT][hapmap]
rs6079480	0.97[EUR][1000 genomes]
rs6079481	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes]
rs6079484	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6079485	1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6079516	1.00[JPT][hapmap]
rs6110333	1.00[JPT][hapmap]
rs6110372	1.00[JPT][hapmap]
rs73901271	0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055499	chr20:14224873-14848061	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv1064721	chr20:14384931-14648223	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv833926	chr20:14410153-14572336	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1059770	chr20:14432394-14549781	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv544187	chr20:14432394-14549781	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv529577	chr20:14434373-14799157	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1064008	chr20:14477895-14540691	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1060786	chr20:14486713-14648467	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv544188	chr20:14486713-14648467	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv912690	chr20:14488761-14553745	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1060985	chr20:14488785-14759939	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv912691	chr20:14495489-14536808	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
13	nsv1060291	chr20:14498526-14578899	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv458874	chr20:14509449-14553745	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv585446	chr20:14509449-14553745	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	nsv1057540	chr20:14510033-14598427	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6079482	PCSK2	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:14517000-14517400	Enhancers	HMEC	breast
2	chr20:14517200-14518000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr20:14517200-14518200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr20:14517200-14518600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr20:14517200-14518600	Enhancers	NHEK	skin
6	chr20:14517200-14519200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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