Variant report

Variant	rs520365
Chromosome Location	chr9:79304043-79304044
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:79300396..79301994-chr9:79302706..79305324,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10512061	0.80[JPT][hapmap]
rs11145009	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1536820	0.80[JPT][hapmap]
rs2553212	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2553213	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs488165	0.83[CEU][hapmap];0.80[JPT][hapmap];0.80[EUR][1000 genomes]
rs489069	0.80[EUR][1000 genomes]
rs498266	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs506965	0.92[CEU][hapmap];0.84[CHB][hapmap];0.80[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs511545	0.92[CEU][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.82[MKK][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs519983	0.83[CEU][hapmap];0.80[JPT][hapmap]
rs530978	0.83[CEU][hapmap];0.84[GIH][hapmap];0.80[JPT][hapmap];0.81[TSI][hapmap]
rs551262	0.83[CEU][hapmap];0.80[JPT][hapmap]
rs557352	0.83[CEU][hapmap];0.80[GIH][hapmap];0.81[TSI][hapmap]
rs571960	0.84[GIH][hapmap];0.80[JPT][hapmap];0.81[TSI][hapmap]
rs579025	1.00[CEU][hapmap];0.84[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs620985	0.84[GIH][hapmap];0.80[JPT][hapmap];0.81[TSI][hapmap]
rs625426	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs630423	0.83[CEU][hapmap];0.80[JPT][hapmap]
rs677061	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs684639	0.83[CEU][hapmap];0.88[JPT][hapmap];0.80[EUR][1000 genomes]
rs685011	0.83[CEU][hapmap];0.80[JPT][hapmap];0.80[EUR][1000 genomes]
rs700757	0.90[JPT][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs786597	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs520365	PRUNE2	cis	Whole Blood	GTEx
rs520365	TMC1	cis	parietal	SCAN
rs520365	TLE4	cis	parietal	SCAN
rs520365	VPS13A	cis	parietal	SCAN
rs520365	PRUNE2	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79266400-79306800	Weak transcription	Fetal Stomach	stomach
2	chr9:79290400-79306000	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr9:79296800-79304800	Weak transcription	Fetal Thymus	thymus
4	chr9:79300400-79332200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr9:79300800-79304200	Enhancers	NHDF-Ad	bronchial
6	chr9:79301600-79305000	Enhancers	Stomach Mucosa	stomach
7	chr9:79302000-79304200	Enhancers	HMEC	breast
8	chr9:79302000-79304200	Enhancers	HSMM	muscle
9	chr9:79302200-79304200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr9:79302200-79304200	Enhancers	HUVEC	blood vessel
11	chr9:79302400-79304200	Enhancers	HSMMtube	muscle
12	chr9:79302600-79304200	Enhancers	Pancreatic Islets	Pancreatic Islet
13	chr9:79302600-79304400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr9:79302600-79305600	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr9:79302600-79306600	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr9:79302600-79306800	Enhancers	Fetal Intestine Large	intestine
17	chr9:79302600-79306800	Enhancers	Fetal Intestine Small	intestine
18	chr9:79302800-79306600	Weak transcription	Adipose Nuclei	Adipose
19	chr9:79303000-79304200	Enhancers	Brain Angular Gyrus	brain
20	chr9:79303000-79304200	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr9:79303000-79305800	Weak transcription	Brain Germinal Matrix	brain
22	chr9:79303000-79306600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr9:79303200-79306000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr9:79303200-79306000	Weak transcription	Rectal Smooth Muscle	rectum
25	chr9:79303200-79306200	Enhancers	HepG2	liver
26	chr9:79303400-79304200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr9:79303400-79304200	Enhancers	Brain Substantia Nigra	brain
28	chr9:79303400-79304200	Enhancers	Stomach Smooth Muscle	stomach
29	chr9:79303400-79305200	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr9:79303400-79306800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr9:79303600-79304600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr9:79303600-79304600	Weak transcription	Aorta	Aorta
33	chr9:79303600-79305600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr9:79303600-79306000	Weak transcription	Brain Hippocampus Middle	brain
35	chr9:79303600-79306000	Weak transcription	Gastric	stomach
36	chr9:79303800-79304200	Enhancers	Osteobl	bone
37	chr9:79303800-79304400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr9:79303800-79304400	Enhancers	Muscle Satellite Cultured Cells	--
39	chr9:79303800-79304800	Weak transcription	Duodenum Mucosa	Duodenum
40	chr9:79303800-79305000	Weak transcription	Brain Anterior Caudate	brain
41	chr9:79303800-79305200	Weak transcription	Colon Smooth Muscle	Colon
42	chr9:79303800-79305200	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr9:79303800-79305400	Weak transcription	Small Intestine	intestine
44	chr9:79303800-79305800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr9:79303800-79306800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr9:79304000-79304400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr9:79304000-79306400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr9:79304000-79306800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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