Variant report

Variant	rs509489
Chromosome Location	chr9:79326931-79326932
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10869799	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs500952	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs505034	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs506086	0.89[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs512110	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs517634	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs556725	0.89[CEU][hapmap]
rs560094	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs561970	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs566584	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs572737	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs591411	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs594498	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs594586	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs611461	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs615187	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs618145	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs620321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs620476	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs620552	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs620737	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs625981	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs626416	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs646698	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs650682	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs678943	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs680729	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs680775	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7018971	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7033978	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7870516	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869152	chr9:78742197-79583399	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv931033	chr9:78850330-79366454	Genic enhancers Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1040363	chr9:79246366-79711737	Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv893481	chr9:79304043-79348193	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv2754389	chr9:79318677-79333056	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs509489	PRUNE2	cis	Whole Blood	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79300400-79332200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr9:79315200-79327600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr9:79316200-79330800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr9:79316400-79332000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr9:79316800-79331000	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr9:79316800-79331200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr9:79317400-79327800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr9:79317400-79328600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr9:79317600-79330800	Strong transcription	HSMM	muscle
10	chr9:79317800-79328600	Strong transcription	HSMMtube	muscle
11	chr9:79318000-79330400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr9:79318400-79330000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr9:79320000-79328000	Strong transcription	Aorta	Aorta
14	chr9:79320000-79328800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr9:79320000-79331200	Weak transcription	Brain Anterior Caudate	brain
16	chr9:79320000-79332000	Weak transcription	Brain Angular Gyrus	brain
17	chr9:79320400-79328600	Strong transcription	Stomach Smooth Muscle	stomach
18	chr9:79322400-79327000	Strong transcription	Colon Smooth Muscle	Colon
19	chr9:79324000-79332200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:79324400-79328000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr9:79324800-79327800	Strong transcription	Fetal Stomach	stomach
22	chr9:79324800-79331000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr9:79326000-79330400	Weak transcription	Brain Hippocampus Middle	brain
24	chr9:79326200-79328000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr9:79326200-79332000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr9:79326200-79332000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr9:79326400-79327600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr9:79326400-79331000	Weak transcription	Brain Substantia Nigra	brain
29	chr9:79326800-79327000	Enhancers	H9 Cell Line	embryonic stem cell

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