Variant report

Variant	rs10963072
Chromosome Location	chr9:17378776-17378777
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 84 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10810755	0.87[EUR][1000 genomes]
rs10810759	0.87[EUR][1000 genomes]
rs10810762	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10810772	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10810776	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10810780	0.85[EUR][1000 genomes]
rs10962996	1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs10963015	0.87[ASW][hapmap];0.84[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.94[YRI][hapmap]
rs10963017	0.84[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap]
rs10963030	0.87[EUR][1000 genomes]
rs10963031	0.87[EUR][1000 genomes]
rs10963036	0.86[EUR][1000 genomes]
rs10963039	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10963040	1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs10963041	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10963046	0.92[YRI][hapmap]
rs10963060	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10963064	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10963065	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10963069	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10963073	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10963077	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10963078	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1160340	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs11789741	0.86[CHD][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs11789786	0.87[EUR][1000 genomes]
rs11791000	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12156444	1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12376973	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12377334	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12378677	1.00[CHB][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12379538	1.00[CHB][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12551355	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12553516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12555830	0.90[ASN][1000 genomes]
rs13283291	0.82[CEU][hapmap];0.84[EUR][1000 genomes]
rs13283891	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13285577	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13285704	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13286365	1.00[CHB][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13289670	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13289968	1.00[CHB][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13292550	0.84[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap]
rs13294241	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs13298547	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs13301284	1.00[CHB][hapmap];0.95[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1372703	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1442516	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[ASN][1000 genomes]
rs1442517	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17829280	1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs1953106	0.84[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap]
rs1967356	0.82[CHD][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs2151342	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2584538	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34256131	0.84[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap]
rs35375281	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35601090	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36051199	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs36063154	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs36088847	0.90[ASN][1000 genomes]
rs3808791	0.82[CEU][hapmap];0.92[YRI][hapmap]
rs3808795	0.89[MEX][hapmap];0.81[TSI][hapmap]
rs4317676	1.00[CHB][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs4405013	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[LWK][hapmap];0.94[MKK][hapmap];0.95[YRI][hapmap];0.86[EUR][1000 genomes]
rs4961559	0.84[MEX][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs58474114	0.82[EUR][1000 genomes]
rs61565870	0.81[EUR][1000 genomes]
rs62558966	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7028577	1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7031442	0.90[ASN][1000 genomes]
rs894379	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv892658	chr9:17041557-17532840	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv892661	chr9:17134245-17532840	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv613693	chr9:17147191-17710407	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv471287	chr9:17165698-17708814	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv466269	chr9:17165698-17710407	Weak transcription ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv466271	chr9:17329964-17438391	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv613696	chr9:17329964-17438391	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv1015524	chr9:17350843-17419424	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv892668	chr9:17371690-17532840	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
11	nsv892669	chr9:17378776-17438391	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv892670	chr9:17378776-17507277	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
13	nsv892671	chr9:17378776-17610211	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10963072	C9orf39	cis	multi-tissue	Pritchard
rs10963072	CNTLN	cis	Liver	GTEx
rs10963072	CNTLN	cis	parietal	SCAN
rs10963072	KIAA1797	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17362000-17394600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr9:17368400-17394600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr9:17368400-17457800	Weak transcription	Pancreas	Pancrea
4	chr9:17368600-17394800	Weak transcription	Adipose Nuclei	Adipose
5	chr9:17368600-17411200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:17368600-17411400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr9:17368600-17411400	Weak transcription	Aorta	Aorta
8	chr9:17368800-17380400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr9:17368800-17411400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr9:17369000-17380600	Weak transcription	Fetal Lung	lung
11	chr9:17369000-17395000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr9:17369200-17380000	Weak transcription	Left Ventricle	heart
13	chr9:17369200-17380200	Weak transcription	Fetal Muscle Leg	muscle
14	chr9:17369400-17411200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr9:17370000-17380200	Weak transcription	Ovary	ovary
16	chr9:17370600-17386600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:17371400-17394800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr9:17371600-17380200	Weak transcription	Liver	Liver
19	chr9:17377600-17403000	Weak transcription	Fetal Stomach	stomach
20	chr9:17377800-17383800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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