Variant report

Variant	rs10869805
Chromosome Location	chr9:79340206-79340207
allele	A/G
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:44)

rs_ID	r²[population]
rs10781370	0.87[ASN][1000 genomes]
rs10781371	0.87[ASN][1000 genomes]
rs10781375	0.80[ASN][1000 genomes]
rs10869800	0.87[ASN][1000 genomes]
rs10869801	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10869802	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10869804	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs10869806	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10869808	0.80[ASN][1000 genomes]
rs11145011	0.83[ASN][1000 genomes]
rs11145012	0.83[ASN][1000 genomes]
rs11145017	0.90[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.86[ASN][1000 genomes]
rs11145018	0.90[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs11145019	0.85[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs11145021	0.90[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.85[ASN][1000 genomes]
rs11145023	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12238013	0.90[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.86[ASN][1000 genomes]
rs12552182	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12553799	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12683741	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1329014	0.87[ASN][1000 genomes]
rs1329015	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1329016	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1329017	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1329018	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1536820	0.82[MEX][hapmap]
rs2077181	0.86[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.84[ASN][1000 genomes]
rs2277155	0.90[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35141311	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3739521	0.81[JPT][hapmap];0.81[MEX][hapmap]
rs3739524	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57347426	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57608282	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs577993	0.81[JPT][hapmap]
rs58286902	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs626837	0.82[JPT][hapmap]
rs641088	0.81[JPT][hapmap]
rs658548	0.82[JPT][hapmap]
rs683866	0.82[JPT][hapmap]
rs7042953	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs724017	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7864794	0.83[AMR][1000 genomes]
rs9314853	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9785303	0.90[CHB][hapmap];0.86[CHD][hapmap];0.90[GIH][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap];0.86[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10869805	VPS13A	cis	parietal	SCAN
rs10869805	PRUNE2	cis	cerebellum	SCAN

Chromatin state (count:20 , 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	chr9:79333200-79346800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr9:79333200-79359000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr9:79333200-79370000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr9:79333600-79342200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr9:79333600-79344000	Weak transcription	HSMMtube	muscle
8	chr9:79333800-79341000	Weak transcription	Colon Smooth Muscle	Colon
9	chr9:79333800-79342200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr9:79333800-79347800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr9:79338200-79343000	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr9:79339200-79340600	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr9:79339400-79340800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr9:79339400-79341000	Enhancers	Primary hematopoietic stem cells	blood
15	chr9:79339400-79341400	Enhancers	Fetal Lung	lung
16	chr9:79339600-79340400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr9:79339800-79340400	Strong transcription	HSMM	muscle
18	chr9:79339800-79341800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr9:79340000-79340800	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr9:79340000-79341000	Strong transcription	Stomach Smooth Muscle	stomach

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