Variant report

Variant	rs17427571
Chromosome Location	chr4:82254908-82254909
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10006067	0.84[ASN][1000 genomes]
rs10488936	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11722445	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11723613	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11723619	0.85[ASN][1000 genomes]
rs11725731	0.92[ASN][1000 genomes]
rs11732408	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11938641	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1377057	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1452365	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1452374	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1473160	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1517550	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1568201	0.81[ASN][1000 genomes]
rs1662837	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1662838	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1662839	0.81[ASN][1000 genomes]
rs1662840	0.82[ASN][1000 genomes]
rs1662842	0.82[ASN][1000 genomes]
rs1662843	0.82[ASN][1000 genomes]
rs1662844	0.81[ASN][1000 genomes]
rs17005118	0.83[AMR][1000 genomes]
rs1712374	0.81[ASN][1000 genomes]
rs1712379	0.81[ASN][1000 genomes]
rs17427459	0.94[ASN][1000 genomes]
rs17499327	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17499732	0.97[EUR][1000 genomes]
rs17499829	0.85[EUR][1000 genomes]
rs17499843	0.85[EUR][1000 genomes]
rs17556750	0.81[ASN][1000 genomes]
rs1878528	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1975474	0.82[EUR][1000 genomes]
rs2011962	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2034629	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2034632	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2058368	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2109662	0.90[ASN][1000 genomes]
rs2197271	0.82[ASN][1000 genomes]
rs2868182	0.81[ASN][1000 genomes]
rs3098970	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3114136	0.82[ASN][1000 genomes]
rs3114140	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34347934	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41501452	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs41515854	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4463061	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs56075827	0.92[ASN][1000 genomes]
rs57222629	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58877260	0.92[ASN][1000 genomes]
rs59498284	0.92[ASN][1000 genomes]
rs60825648	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs61371439	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62302285	0.81[ASN][1000 genomes]
rs62302286	0.82[ASN][1000 genomes]
rs62302305	0.81[ASN][1000 genomes]
rs62302314	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs62302352	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62303570	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6535240	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6812825	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6813437	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6824784	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6839968	0.80[CEU][hapmap]
rs710835	1.00[JPT][hapmap]
rs725826	0.89[ASN][1000 genomes]
rs7656390	0.85[ASN][1000 genomes]
rs7658313	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7661369	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7669368	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7685840	0.85[ASN][1000 genomes]
rs7696324	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7698086	0.92[ASN][1000 genomes]
rs7698361	0.83[EUR][1000 genomes]
rs7699396	0.92[ASN][1000 genomes]
rs7699600	0.92[ASN][1000 genomes]
rs788855	1.00[JPT][hapmap]
rs788861	1.00[JPT][hapmap]

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
rs17427571	PRKG2	cis	parietal	SCAN
rs17427571	COPS4	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:82254000-82256600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr4:82254000-82258400	Enhancers	NHDF-Ad	bronchial
3	chr4:82254800-82255800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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