Variant report

Variant	rs2159656
Chromosome Location	chr4:82256697-82256698
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10017744	0.98[EUR][1000 genomes]
rs11099465	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11727754	0.98[EUR][1000 genomes]
rs11731567	0.98[EUR][1000 genomes]
rs11736583	0.91[EUR][1000 genomes]
rs11939135	0.98[EUR][1000 genomes]
rs13435660	0.98[EUR][1000 genomes]
rs1349641	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1443542	0.94[AMR][1000 genomes]
rs1443543	0.99[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1452366	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1452367	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1662845	0.85[AMR][1000 genomes]
rs17427571	0.80[CEU][hapmap]
rs17428153	0.92[EUR][1000 genomes]
rs17500037	0.92[EUR][1000 genomes]
rs17500100	0.91[EUR][1000 genomes]
rs1993160	0.98[EUR][1000 genomes]
rs2034628	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2034630	0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2041461	0.97[EUR][1000 genomes]
rs2058367	0.98[EUR][1000 genomes]
rs2903765	0.83[EUR][1000 genomes]
rs3114135	0.90[JPT][hapmap]
rs4693234	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4693996	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4694006	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6535242	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6535243	0.96[EUR][1000 genomes]
rs6814785	0.98[EUR][1000 genomes]
rs6819909	0.98[EUR][1000 genomes]
rs6831114	0.83[AMR][1000 genomes]
rs6839968	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6851443	0.83[EUR][1000 genomes]
rs7654102	0.98[EUR][1000 genomes]
rs7660089	0.92[EUR][1000 genomes]
rs7664953	0.98[EUR][1000 genomes]
rs7669131	0.98[EUR][1000 genomes]
rs7673578	0.98[EUR][1000 genomes]
rs7677239	0.98[EUR][1000 genomes]
rs7680637	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7681976	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7685645	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9307782	0.92[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	nsv999729	chr4:81802554-82627820	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv537156	chr4:81802554-82627820	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv829985	chr4:82199328-82353656	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2159656	PAQR3	cis	cerebellum	SCAN
rs2159656	PRKG2	cis	Nerve Tibial	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:82254000-82258400	Enhancers	NHDF-Ad	bronchial
2	chr4:82255800-82257000	Enhancers	NHLF	lung
3	chr4:82256000-82257400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr4:82256000-82257600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr4:82256200-82256800	Enhancers	Adipose Nuclei	Adipose
6	chr4:82256200-82257000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr4:82256400-82257000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr4:82256600-82257000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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