Variant report

Variant	rs11145023
Chromosome Location	chr9:79332718-79332719
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10781370	0.92[ASN][1000 genomes]
rs10781371	0.92[ASN][1000 genomes]
rs10869798	0.82[ASN][1000 genomes]
rs10869800	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10869801	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10869802	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10869804	0.90[AMR][1000 genomes]
rs10869805	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10869806	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11145011	0.88[ASN][1000 genomes]
rs11145012	0.88[ASN][1000 genomes]
rs11145017	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.91[ASN][1000 genomes]
rs11145018	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11145019	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs11145021	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.90[ASN][1000 genomes]
rs12238013	0.92[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.91[ASN][1000 genomes]
rs12552182	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12553799	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12683741	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1329014	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1329015	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1329016	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1329017	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1329018	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1536820	0.81[MEX][hapmap]
rs2077181	0.92[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.89[ASN][1000 genomes]
rs2277155	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35141311	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3739521	0.92[CEU][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.81[ASN][1000 genomes]
rs3739524	1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57347426	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57608282	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs577993	0.86[JPT][hapmap]
rs58286902	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs626837	0.86[JPT][hapmap]
rs641088	0.86[JPT][hapmap]
rs658548	0.86[JPT][hapmap]
rs683866	0.86[JPT][hapmap]
rs7042953	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs724017	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7864794	0.81[AMR][1000 genomes]
rs9314853	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9785303	0.92[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.91[ASN][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11145023	PRUNE2	cis	cerebellum	SCAN
rs11145023	VPS13A	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79327800-79341800	Weak transcription	Fetal Stomach	stomach
2	chr9:79328000-79341200	Weak transcription	Aorta	Aorta
3	chr9:79329200-79333200	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr9:79330400-79333600	Enhancers	Rectal Smooth Muscle	rectum
5	chr9:79330400-79334000	Enhancers	Brain Hippocampus Middle	brain
6	chr9:79330800-79333400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr9:79330800-79333400	Enhancers	HUVEC	blood vessel
8	chr9:79331000-79333600	Enhancers	HSMMtube	muscle
9	chr9:79331000-79333800	Enhancers	Brain Cingulate Gyrus	brain
10	chr9:79331000-79334000	Enhancers	Brain Substantia Nigra	brain
11	chr9:79331200-79333000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr9:79331200-79333200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr9:79331200-79333200	Enhancers	Brain Anterior Caudate	brain
14	chr9:79331200-79333200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
15	chr9:79331200-79333200	Enhancers	NHDF-Ad	bronchial
16	chr9:79331200-79333600	Enhancers	Osteobl	bone
17	chr9:79331400-79333200	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr9:79331600-79333200	Enhancers	HSMM	muscle
19	chr9:79331600-79333800	Enhancers	Colon Smooth Muscle	Colon
20	chr9:79331800-79333200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr9:79331800-79333400	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr9:79332000-79332800	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr9:79332000-79332800	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr9:79332000-79333000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr9:79332000-79333000	Enhancers	Stomach Smooth Muscle	stomach
26	chr9:79332000-79333200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr9:79332000-79333200	Enhancers	Muscle Satellite Cultured Cells	--
28	chr9:79332000-79333200	Enhancers	Brain Angular Gyrus	brain
29	chr9:79332000-79333800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr9:79332200-79332800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr9:79332200-79332800	Enhancers	Right Atrium	heart
32	chr9:79332200-79333000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr9:79332200-79333000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr9:79332400-79332800	Enhancers	Monocytes-CD14+_RO01746	blood
35	chr9:79332600-79332800	Enhancers	Fetal Muscle Leg	muscle
36	chr9:79332600-79333600	Enhancers	ES-I3 Cell Line	embryonic stem cell

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