Variant report

Variant	rs11145038
Chromosome Location	chr9:79361021-79361022
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10781375	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10781376	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10869808	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10869810	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10869811	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10869812	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11145017	0.81[CHB][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap]
rs11145018	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs11145019	0.91[JPT][hapmap]
rs11145021	0.81[CHB][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap]
rs11145032	0.99[ASN][1000 genomes]
rs11145033	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11145035	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11145036	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12238013	0.81[CHB][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap]
rs12345014	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12349206	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12683741	0.82[EUR][1000 genomes]
rs1571446	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2077181	0.86[JPT][hapmap];0.88[MEX][hapmap]
rs2277155	0.81[CHB][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap]
rs3739521	0.81[MEX][hapmap]
rs3739524	0.86[JPT][hapmap];0.88[MEX][hapmap]
rs56878970	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58570686	0.84[ASN][1000 genomes]
rs60820134	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs626837	0.81[CHB][hapmap]
rs641088	0.81[JPT][hapmap]
rs7848492	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9314853	0.81[EUR][1000 genomes]
rs9314856	0.88[MEX][hapmap]
rs9785303	0.81[CHB][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11145038	PRUNE2	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:79333200-79370000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr9:79348200-79370200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr9:79348400-79370200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr9:79348400-79370200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr9:79358400-79370800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr9:79359600-79365400	Weak transcription	HSMMtube	muscle
7	chr9:79360200-79361200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr9:79360600-79362400	Strong transcription	HSMM	muscle
9	chr9:79360800-79361200	Enhancers	Stomach Smooth Muscle	stomach
10	chr9:79361000-79361200	Strong transcription	Aorta	Aorta
11	chr9:79361000-79361200	Enhancers	Colon Smooth Muscle	Colon
12	chr9:79361000-79363800	Weak transcription	Brain Hippocampus Middle	brain
13	chr9:79361000-79365400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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