Variant report

Variant	rs1583989
Chromosome Location	chr9:17367617-17367618
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 101 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10114083	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10114688	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10114730	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10116428	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10119297	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10119370	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10120757	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10122987	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10123745	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10124513	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10125333	0.80[EUR][1000 genomes]
rs10738476	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10756874	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10756875	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10756876	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10756877	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10756878	0.80[ASN][1000 genomes]
rs10810754	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10810763	0.80[EUR][1000 genomes]
rs10810764	0.80[EUR][1000 genomes]
rs10810765	0.81[EUR][1000 genomes]
rs10810770	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10810773	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10810774	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10810775	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10810777	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10963057	0.80[EUR][1000 genomes]
rs10963071	0.81[AMR][1000 genomes]
rs12379102	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12379104	0.83[ASN][1000 genomes]
rs1372702	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1583987	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2044119	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2044120	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2099858	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2225598	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3765040	0.80[EUR][1000 genomes]
rs3808784	0.80[EUR][1000 genomes]
rs3824391	0.80[EUR][1000 genomes]
rs3824392	0.80[EUR][1000 genomes]
rs3861711	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4246135	0.80[EUR][1000 genomes]
rs4961437	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4961539	0.80[EUR][1000 genomes]
rs4961540	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4961541	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4961542	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4961543	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4961544	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4961545	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4961547	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4961548	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4961552	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4961553	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6475139	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6475141	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6475142	0.80[EUR][1000 genomes]
rs6475143	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6475144	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6475145	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6475147	0.83[ASN][1000 genomes]
rs7022024	0.80[EUR][1000 genomes]
rs7028593	0.80[EUR][1000 genomes]
rs7028779	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7028930	0.80[EUR][1000 genomes]
rs7030452	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7031133	0.80[EUR][1000 genomes]
rs7038197	0.80[EUR][1000 genomes]
rs7044462	0.80[EUR][1000 genomes]
rs7044823	0.80[EUR][1000 genomes]
rs7848397	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7848980	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7851890	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7854802	0.80[EUR][1000 genomes]
rs7854818	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7858760	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7858762	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7862069	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7864270	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7864271	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7864919	0.81[EUR][1000 genomes]
rs7868700	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7869727	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7870101	0.80[EUR][1000 genomes]
rs7872831	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7873708	0.80[ASN][1000 genomes]
rs7874453	0.80[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9298774	0.80[EUR][1000 genomes]
rs9695844	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv466270	chr9:17236376-17377629	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv613694	chr9:17236376-17377629	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv892665	chr9:17250170-17371690	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	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
11	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
12	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1583989	C9orf39	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17338800-17371800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr9:17341400-17369600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr9:17344400-17368800	Weak transcription	A549	lung
4	chr9:17354800-17368000	Weak transcription	Fetal Intestine Large	intestine
5	chr9:17355600-17372200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr9:17362000-17369400	Weak transcription	Fetal Kidney	kidney
7	chr9:17362000-17372600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr9:17362000-17394600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr9:17364000-17368600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr9:17364200-17368800	Weak transcription	Brain Substantia Nigra	brain
11	chr9:17364600-17369000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr9:17364600-17376800	Weak transcription	Hela-S3	cervix
13	chr9:17365000-17369400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr9:17365000-17370000	Strong transcription	Fetal Stomach	stomach
15	chr9:17365000-17373600	Weak transcription	HSMM	muscle
16	chr9:17365400-17368600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr9:17365600-17369200	Strong transcription	Left Ventricle	heart
18	chr9:17365600-17370000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr9:17365600-17370200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr9:17365800-17367800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr9:17366000-17368400	Weak transcription	Brain Hippocampus Middle	brain
22	chr9:17366000-17369000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr9:17366200-17369000	Weak transcription	NHLF	lung
24	chr9:17366400-17368000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr9:17366800-17367800	Strong transcription	Pancreas	Pancrea
26	chr9:17366800-17368400	Strong transcription	HUES64 Cell Line	embryonic stem cell
27	chr9:17366800-17368600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
28	chr9:17366800-17370000	Strong transcription	Ovary	ovary
29	chr9:17367000-17368000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr9:17367000-17368200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr9:17367000-17368400	Strong transcription	H1 Cell Line	embryonic stem cell
32	chr9:17367000-17368400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr9:17367000-17368400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr9:17367000-17368600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr9:17367000-17368600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr9:17367000-17368600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr9:17367000-17368600	Strong transcription	Adipose Nuclei	Adipose
38	chr9:17367000-17368600	ZNF genes & repeats	Aorta	Aorta
39	chr9:17367000-17368600	Strong transcription	Right Ventricle	heart
40	chr9:17367000-17368600	Strong transcription	Dnd41	blood
41	chr9:17367000-17368800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr9:17367000-17368800	Strong transcription	Duodenum Smooth Muscle	Duodenum
43	chr9:17367000-17368800	ZNF genes & repeats	Lung	lung
44	chr9:17367000-17369000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
45	chr9:17367000-17369000	Strong transcription	Fetal Lung	lung
46	chr9:17367000-17369000	Strong transcription	Stomach Smooth Muscle	stomach
47	chr9:17367000-17369000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
48	chr9:17367000-17369400	Strong transcription	Fetal Muscle Trunk	muscle
49	chr9:17367000-17369800	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr9:17367000-17370600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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