Variant report

Variant	rs39811
Chromosome Location	chr5:51988228-51988229
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12332623	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1303763	0.88[MEX][hapmap]
rs1626287	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1645393	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1645394	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs164611	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs164612	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1668506	0.91[ASN][1000 genomes]
rs244481	0.86[ASN][1000 genomes]
rs244491	0.81[ASN][1000 genomes]
rs244493	0.82[ASN][1000 genomes]
rs244495	0.82[ASN][1000 genomes]
rs29976	0.85[ASN][1000 genomes]
rs29977	0.86[ASN][1000 genomes]
rs29980	0.84[ASN][1000 genomes]
rs29982	0.86[ASN][1000 genomes]
rs350444	0.82[EUR][1000 genomes]
rs351933	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs351937	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs351940	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs599698	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs651393	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs657796	0.93[ASN][1000 genomes]
rs658771	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs664248	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2754787	chr5:51688543-52193243	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv462187	chr5:51758804-52333420	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv598163	chr5:51758804-52333420	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
4	nsv471013	chr5:51779197-52339114	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs39811	PPAP2A	cis	cerebellum	SCAN
rs39811	LY86AS	trans	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:51985400-51989200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr5:51985600-51988400	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr5:51985600-51988400	Enhancers	Hela-S3	cervix
4	chr5:51985600-51990600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr5:51985600-51993000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr5:51985800-51989000	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr5:51985800-51989600	Enhancers	Fetal Lung	lung
8	chr5:51986000-51988600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr5:51986200-51988400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr5:51986200-51988600	Enhancers	NHDF-Ad	bronchial
11	chr5:51986200-51988800	Enhancers	NH-A	brain
12	chr5:51986200-51989000	Enhancers	Fetal Stomach	stomach
13	chr5:51986200-51989000	Enhancers	HSMM	muscle
14	chr5:51986200-51989200	Enhancers	HSMMtube	muscle
15	chr5:51986200-51989600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr5:51986400-51988800	Weak transcription	Spleen	Spleen
17	chr5:51986600-51990000	Weak transcription	Adipose Nuclei	Adipose
18	chr5:51986800-51988400	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr5:51986800-51988400	Enhancers	Muscle Satellite Cultured Cells	--
20	chr5:51986800-51989200	Enhancers	NHLF	lung
21	chr5:51987400-51988400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr5:51987600-51989800	Weak transcription	Small Intestine	intestine
23	chr5:51987600-51990200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr5:51987600-51990200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr5:51987800-51990000	Weak transcription	Fetal Muscle Leg	muscle
26	chr5:51988000-51988400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:51988000-51988800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr5:51988000-51989400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr5:51988200-51988600	Weak transcription	Fetal Kidney	kidney
30	chr5:51988200-51989600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr5:51988200-51989600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr5:51988200-51990200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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