Variant report

Variant	rs1318162
Chromosome Location	chr9:17453919-17453920
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10046851	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs10114730	0.81[CHB][hapmap];0.80[JPT][hapmap]
rs10116428	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs10119233	0.83[JPT][hapmap]
rs10119370	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs10120006	0.82[JPT][hapmap]
rs10120733	0.81[JPT][hapmap]
rs10120761	0.83[JPT][hapmap]
rs10123715	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs10738474	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs10756867	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs10756874	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs10756875	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs10756878	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs10756879	0.83[JPT][hapmap]
rs10810764	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs10810765	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs10810773	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs10963081	0.83[JPT][hapmap]
rs10963105	0.83[JPT][hapmap]
rs12379104	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs1372702	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs1372704	0.83[JPT][hapmap]
rs1442521	0.83[JPT][hapmap]
rs1442522	0.85[JPT][hapmap]
rs1442525	0.83[JPT][hapmap]
rs1442526	0.87[JPT][hapmap]
rs1442530	0.81[EUR][1000 genomes]
rs1442531	0.81[EUR][1000 genomes]
rs1583987	0.85[CHB][hapmap];0.80[JPT][hapmap]
rs1808894	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2044119	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs2083694	0.83[JPT][hapmap]
rs2099858	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2225598	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2274916	0.87[JPT][hapmap]
rs2441991	0.83[JPT][hapmap]
rs2584539	0.83[JPT][hapmap]
rs2584546	0.83[JPT][hapmap]
rs2584548	0.87[JPT][hapmap]
rs2593382	0.83[EUR][1000 genomes]
rs2593388	0.87[JPT][hapmap]
rs2593389	0.83[JPT][hapmap]
rs2593397	0.83[JPT][hapmap]
rs2593418	0.81[JPT][hapmap]
rs2780203	0.87[JPT][hapmap]
rs2780213	0.87[JPT][hapmap]
rs2990670	0.89[JPT][hapmap]
rs3739488	0.87[JPT][hapmap]
rs3739489	0.87[JPT][hapmap]
rs3780258	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs3808781	0.83[JPT][hapmap]
rs3824392	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs4246136	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs4961437	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs4961539	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs4961544	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs4961545	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs4961547	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs4961552	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs4961556	0.83[JPT][hapmap]
rs6475139	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs6475141	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs6475142	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs6475143	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs6475144	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs654521	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs7023540	0.81[JPT][hapmap]
rs7027292	0.87[JPT][hapmap]
rs7028779	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs7031133	0.88[JPT][hapmap]
rs7035276	0.87[JPT][hapmap]
rs7035357	0.86[JPT][hapmap]
rs7046933	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs7848397	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs7849084	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs7851890	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs7854724	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs7862069	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs7864919	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs7870101	0.83[CHB][hapmap];0.88[JPT][hapmap]
rs7870427	0.82[JPT][hapmap]
rs7873708	0.84[CHB][hapmap];0.89[JPT][hapmap]
rs7874945	0.83[JPT][hapmap]
rs9298774	0.85[CHB][hapmap];0.89[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	nsv523411	chr9:17394536-17454799	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv2422265	chr9:17396711-17598187	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer 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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1318162	C9orf39	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17368400-17457800	Weak transcription	Pancreas	Pancrea
2	chr9:17411800-17481000	Weak transcription	Aorta	Aorta
3	chr9:17426400-17466800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr9:17439400-17466800	Weak transcription	NHDF-Ad	bronchial
5	chr9:17440400-17494600	Weak transcription	Left Ventricle	heart
6	chr9:17441200-17458000	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr9:17441200-17467000	Weak transcription	Adipose Nuclei	Adipose
8	chr9:17441400-17466800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr9:17442000-17491800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:17442200-17467200	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr9:17446000-17467400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr9:17448000-17457600	Weak transcription	Liver	Liver
13	chr9:17448000-17466800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr9:17448000-17503400	Weak transcription	Ovary	ovary
15	chr9:17448400-17496400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr9:17448600-17495800	Weak transcription	Dnd41	blood
17	chr9:17452800-17495600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr9:17453000-17472200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr9:17453000-17497000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr9:17453600-17454000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr9:17453800-17466800	Weak transcription	Fetal Lung	lung
22	chr9:17453800-17504200	Weak transcription	Fetal Muscle Trunk	muscle

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