Variant report

Variant	rs7656390
Chromosome Location	chr4:82284314-82284315
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10006067	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11722445	0.90[EUR][1000 genomes]
rs11723613	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11723619	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11725731	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11732408	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1377057	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1443541	0.81[EUR][1000 genomes]
rs1452365	0.90[EUR][1000 genomes]
rs1452374	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1473160	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs17005118	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17427459	0.84[EUR][1000 genomes]
rs17427571	0.82[CEU][hapmap];0.93[CHB][hapmap];0.91[CHD][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap];0.85[ASN][1000 genomes]
rs17499327	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17499732	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs17499829	0.85[ASN][1000 genomes]
rs17499843	0.85[ASN][1000 genomes]
rs17500149	0.82[EUR][1000 genomes]
rs2011962	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2034629	0.82[ASN][1000 genomes]
rs2034632	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2058368	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2109662	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2839753	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3098972	0.81[EUR][1000 genomes]
rs3098973	0.81[EUR][1000 genomes]
rs34347934	0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs41501452	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs41515854	0.88[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4463061	0.90[EUR][1000 genomes]
rs56075827	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58877260	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59498284	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60825648	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62302314	0.89[EUR][1000 genomes]
rs62302352	0.85[ASN][1000 genomes]
rs62303570	0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6812825	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6824784	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs725826	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7658313	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7669368	0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7685840	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7696324	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7698086	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7699396	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7699600	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[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	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
rs7656390	PAQR3	cis	cerebellum	SCAN
rs7656390	PRKG2	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:82280600-82287200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr4:82281000-82287200	Weak transcription	NHLF	lung
3	chr4:82282800-82287000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:82283200-82284400	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr4:82283200-82284800	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr4:82283600-82287000	Weak transcription	NHDF-Ad	bronchial
7	chr4:82284200-82284600	Enhancers	HUES48 Cell Line	embryonic stem cell

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