Variant report

Variant	rs7677239
Chromosome Location	chr4:82271823-82271824
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10013788	0.88[AMR][1000 genomes]
rs10017744	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10021462	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10028610	0.88[AMR][1000 genomes]
rs11099465	0.91[EUR][1000 genomes]
rs11727754	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11731567	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11732090	0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs11732106	0.88[AMR][1000 genomes]
rs11736471	0.88[AMR][1000 genomes]
rs11736583	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11939135	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12332030	0.88[AMR][1000 genomes]
rs13435660	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1349641	0.92[EUR][1000 genomes]
rs1377059	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1443543	0.85[EUR][1000 genomes]
rs1452366	0.80[CEU][hapmap]
rs1452367	0.97[EUR][1000 genomes]
rs1551236	0.88[AMR][1000 genomes]
rs1662845	0.84[AFR][1000 genomes]
rs17428097	0.88[AMR][1000 genomes]
rs17428153	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17500037	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17500100	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1993160	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2034628	0.92[EUR][1000 genomes]
rs2041461	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2058367	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2159656	0.98[EUR][1000 genomes]
rs2903765	0.85[EUR][1000 genomes]
rs4693996	0.87[EUR][1000 genomes]
rs4694006	0.91[EUR][1000 genomes]
rs6535242	0.91[EUR][1000 genomes]
rs6535243	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6814785	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6819909	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6821450	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6839968	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs6851443	0.85[EUR][1000 genomes]
rs6853731	0.91[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7654102	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7660089	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7664953	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7669131	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7673578	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7681976	0.94[EUR][1000 genomes]
rs7694769	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9307782	0.92[AMR][1000 genomes];0.94[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
rs7677239	PAQR3	cis	cerebellum	SCAN
rs7677239	PRKG2	cis	Nerve Tibial	GTEx

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:82267600-82273400	Enhancers	Fetal Intestine Large	intestine
2	chr4:82270000-82272400	Weak transcription	NHDF-Ad	bronchial
3	chr4:82270200-82273000	Weak transcription	Fetal Lung	lung
4	chr4:82271000-82273000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr4:82271000-82273000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr4:82271000-82273800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr4:82271400-82272400	Enhancers	Pancreas	Pancrea
8	chr4:82271400-82273400	Enhancers	Fetal Intestine Small	intestine
9	chr4:82271600-82272800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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