Variant report

Variant	rs471083
Chromosome Location	chr9:79331723-79331724
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10512061	0.89[JPT][hapmap]
rs10735649	0.89[JPT][hapmap]
rs1536820	0.89[JPT][hapmap]
rs2487263	0.88[ASN][1000 genomes]
rs488165	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs489069	0.88[ASN][1000 genomes]
rs491798	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs498266	0.89[JPT][hapmap]
rs506965	0.89[JPT][hapmap]
rs511545	0.89[JPT][hapmap]
rs519983	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs530978	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs537903	0.85[AMR][1000 genomes]
rs551262	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs557352	0.83[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs571960	1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs577993	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs579025	0.89[JPT][hapmap]
rs620985	1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs626837	0.81[AMR][1000 genomes]
rs630423	1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs641088	0.85[AMR][1000 genomes]
rs658548	0.84[AMR][1000 genomes]
rs659003	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs684639	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs685011	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs700757	0.89[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
rs471083	PRUNE2	cis	Whole Blood	GTEx

Chromatin state (count:35 , 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	chr9:79316400-79332000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr9:79320000-79332000	Weak transcription	Brain Angular Gyrus	brain
4	chr9:79324000-79332200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr9:79326200-79332000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr9:79326200-79332000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr9:79327800-79332000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr9:79327800-79341800	Weak transcription	Fetal Stomach	stomach
9	chr9:79328000-79341200	Weak transcription	Aorta	Aorta
10	chr9:79328200-79332000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr9:79328600-79332000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr9:79328600-79332600	Weak transcription	Fetal Muscle Leg	muscle
13	chr9:79329200-79333200	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr9:79330400-79333600	Enhancers	Rectal Smooth Muscle	rectum
15	chr9:79330400-79334000	Enhancers	Brain Hippocampus Middle	brain
16	chr9:79330800-79333400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:79330800-79333400	Enhancers	HUVEC	blood vessel
18	chr9:79331000-79332400	Enhancers	Fetal Intestine Small	intestine
19	chr9:79331000-79332600	Enhancers	Fetal Intestine Large	intestine
20	chr9:79331000-79333600	Enhancers	HSMMtube	muscle
21	chr9:79331000-79333800	Enhancers	Brain Cingulate Gyrus	brain
22	chr9:79331000-79334000	Enhancers	Brain Substantia Nigra	brain
23	chr9:79331200-79331800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:79331200-79333000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr9:79331200-79333200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr9:79331200-79333200	Enhancers	Brain Anterior Caudate	brain
27	chr9:79331200-79333200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
28	chr9:79331200-79333200	Enhancers	NHDF-Ad	bronchial
29	chr9:79331200-79333600	Enhancers	Osteobl	bone
30	chr9:79331400-79331800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr9:79331400-79331800	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr9:79331400-79333200	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr9:79331600-79332000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr9:79331600-79333200	Enhancers	HSMM	muscle
35	chr9:79331600-79333800	Enhancers	Colon Smooth Muscle	Colon

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