Variant report

Variant	rs670058
Chromosome Location	chr9:17292890-17292891
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 196 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:179)

rs_ID	r²[population]
rs10046851	0.89[EUR][1000 genomes]
rs10114083	0.87[EUR][1000 genomes]
rs10114662	0.88[EUR][1000 genomes]
rs10114688	0.89[EUR][1000 genomes]
rs10114730	0.89[EUR][1000 genomes]
rs10116093	0.88[EUR][1000 genomes]
rs10116140	0.88[EUR][1000 genomes]
rs10116428	0.89[EUR][1000 genomes]
rs10119297	0.89[EUR][1000 genomes]
rs10119370	0.89[EUR][1000 genomes]
rs10120757	0.89[EUR][1000 genomes]
rs10121841	0.89[EUR][1000 genomes]
rs10122987	0.88[EUR][1000 genomes]
rs10123109	0.88[EUR][1000 genomes]
rs10123715	0.89[EUR][1000 genomes]
rs10123745	0.88[EUR][1000 genomes]
rs10124487	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10124513	0.89[EUR][1000 genomes]
rs10125333	0.90[EUR][1000 genomes]
rs10283690	0.87[EUR][1000 genomes]
rs10481559	0.89[EUR][1000 genomes]
rs10738474	0.90[EUR][1000 genomes]
rs10738476	0.88[EUR][1000 genomes]
rs10756855	0.81[EUR][1000 genomes]
rs10756856	0.82[EUR][1000 genomes]
rs10756858	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10756860	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10756866	0.89[EUR][1000 genomes]
rs10756867	0.89[EUR][1000 genomes]
rs10756869	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10756874	0.88[EUR][1000 genomes]
rs10756875	0.88[EUR][1000 genomes]
rs10756876	0.89[EUR][1000 genomes]
rs10756877	0.88[EUR][1000 genomes]
rs10756878	0.87[EUR][1000 genomes]
rs10810739	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10810740	0.91[EUR][1000 genomes]
rs10810748	0.93[EUR][1000 genomes]
rs10810749	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10810750	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10810751	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10810752	0.94[EUR][1000 genomes]
rs10810756	0.89[EUR][1000 genomes]
rs10810761	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10810763	0.90[EUR][1000 genomes]
rs10810764	0.90[EUR][1000 genomes]
rs10810765	0.89[EUR][1000 genomes]
rs10810773	0.88[EUR][1000 genomes]
rs10810774	0.88[EUR][1000 genomes]
rs10810775	0.88[EUR][1000 genomes]
rs10810777	0.88[EUR][1000 genomes]
rs10810781	0.89[EUR][1000 genomes]
rs10962947	0.89[EUR][1000 genomes]
rs10962950	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10962982	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10962988	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10963026	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10963027	0.83[EUR][1000 genomes]
rs10963042	0.89[EUR][1000 genomes]
rs10963057	0.88[EUR][1000 genomes]
rs10963063	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12236820	0.86[EUR][1000 genomes]
rs12337154	0.88[EUR][1000 genomes]
rs12337171	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12342180	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12379102	0.87[EUR][1000 genomes]
rs12379104	0.82[EUR][1000 genomes]
rs13290922	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1372702	0.88[EUR][1000 genomes]
rs1442523	0.88[EUR][1000 genomes]
rs1442524	0.87[EUR][1000 genomes]
rs1442533	0.82[EUR][1000 genomes]
rs1576962	0.88[EUR][1000 genomes]
rs1582030	0.83[EUR][1000 genomes]
rs1582031	0.83[EUR][1000 genomes]
rs1583987	0.87[EUR][1000 genomes]
rs1591138	0.81[EUR][1000 genomes]
rs1596193	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1759454	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1759613	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2044119	0.88[EUR][1000 genomes]
rs2044120	0.88[EUR][1000 genomes]
rs2099858	0.88[EUR][1000 genomes]
rs2151290	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2225598	0.88[EUR][1000 genomes]
rs2593387	0.87[EUR][1000 genomes]
rs2779773	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2779775	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2779776	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2780206	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2990670	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34105027	0.87[EUR][1000 genomes]
rs36057268	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3765040	0.90[EUR][1000 genomes]
rs3780258	0.85[EUR][1000 genomes]
rs3808784	0.90[EUR][1000 genomes]
rs3824391	0.89[EUR][1000 genomes]
rs3824392	0.89[EUR][1000 genomes]
rs3861711	0.88[EUR][1000 genomes]
rs4246135	0.90[EUR][1000 genomes]
rs4246136	0.89[EUR][1000 genomes]
rs4272484	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4409489	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4424358	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4563978	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4961437	0.89[EUR][1000 genomes]
rs4961439	0.87[EUR][1000 genomes]
rs4961539	0.90[EUR][1000 genomes]
rs4961540	0.89[EUR][1000 genomes]
rs4961541	0.88[EUR][1000 genomes]
rs4961542	0.88[EUR][1000 genomes]
rs4961543	0.88[EUR][1000 genomes]
rs4961544	0.88[EUR][1000 genomes]
rs4961545	0.88[EUR][1000 genomes]
rs4961547	0.88[EUR][1000 genomes]
rs4961548	0.89[EUR][1000 genomes]
rs4961552	0.88[EUR][1000 genomes]
rs4961553	0.88[EUR][1000 genomes]
rs4961555	0.89[EUR][1000 genomes]
rs4961557	0.87[EUR][1000 genomes]
rs593614	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs595894	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs605916	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs619380	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs632265	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs645117	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6475137	0.81[AMR][1000 genomes]
rs6475139	0.89[EUR][1000 genomes]
rs6475141	0.89[EUR][1000 genomes]
rs6475142	0.88[EUR][1000 genomes]
rs6475143	0.89[EUR][1000 genomes]
rs6475144	0.89[EUR][1000 genomes]
rs6475145	0.88[EUR][1000 genomes]
rs6475147	0.81[EUR][1000 genomes]
rs654521	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs670511	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7018705	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7022024	0.90[EUR][1000 genomes]
rs7022060	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7028593	0.90[EUR][1000 genomes]
rs7028779	0.89[EUR][1000 genomes]
rs7028930	0.90[EUR][1000 genomes]
rs7031133	0.90[EUR][1000 genomes]
rs7033974	0.92[EUR][1000 genomes]
rs7037111	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7038064	0.90[EUR][1000 genomes]
rs7038197	0.90[EUR][1000 genomes]
rs7041840	0.87[EUR][1000 genomes]
rs7044462	0.85[EUR][1000 genomes]
rs7044823	0.90[EUR][1000 genomes]
rs7046933	0.93[EUR][1000 genomes]
rs7848397	0.87[EUR][1000 genomes]
rs7848980	0.88[EUR][1000 genomes]
rs7849084	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7849085	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7851890	0.88[EUR][1000 genomes]
rs7854724	0.88[EUR][1000 genomes]
rs7854802	0.89[EUR][1000 genomes]
rs7854818	0.88[EUR][1000 genomes]
rs7862069	0.88[EUR][1000 genomes]
rs7864270	0.87[EUR][1000 genomes]
rs7864271	0.87[EUR][1000 genomes]
rs7864650	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7864919	0.89[EUR][1000 genomes]
rs7865766	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7868684	0.81[EUR][1000 genomes]
rs7868700	0.88[EUR][1000 genomes]
rs7869727	0.88[EUR][1000 genomes]
rs7870101	0.89[EUR][1000 genomes]
rs7871926	0.87[EUR][1000 genomes]
rs7872831	0.88[EUR][1000 genomes]
rs7873708	0.88[EUR][1000 genomes]
rs7874453	0.86[EUR][1000 genomes]
rs870271	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9298772	0.89[EUR][1000 genomes]
rs9298773	0.89[EUR][1000 genomes]
rs9298774	0.90[EUR][1000 genomes]
rs9406666	0.91[EUR][1000 genomes]
rs9695844	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	esv2764141	chr9:16903446-17351711	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv428537	chr9:17146369-17308494	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	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
7	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
8	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
9	nsv892662	chr9:17168867-17329964	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv1031269	chr9:17204320-17316969	Flanking Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	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
12	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
13	nsv892663	chr9:17243746-17329964	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	nsv892664	chr9:17250170-17296630	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
15	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
16	nsv892667	chr9:17269437-17296630	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
17	nsv613695	chr9:17273731-17348412	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs670058	C9orf39	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17262800-17339800	Weak transcription	Left Ventricle	heart
2	chr9:17272800-17293000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr9:17273200-17301800	Weak transcription	Dnd41	blood
4	chr9:17274800-17323200	Weak transcription	Aorta	Aorta
5	chr9:17277000-17293000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr9:17278400-17293600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr9:17281000-17293000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr9:17281000-17300400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr9:17281800-17293000	Weak transcription	Liver	Liver
10	chr9:17281800-17293000	Weak transcription	Fetal Muscle Trunk	muscle
11	chr9:17282200-17293200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr9:17284400-17309600	Weak transcription	Ovary	ovary
13	chr9:17284400-17344800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr9:17284600-17299600	Weak transcription	Adipose Nuclei	Adipose
15	chr9:17284800-17308000	Weak transcription	Fetal Lung	lung
16	chr9:17285000-17311600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr9:17290400-17293000	Weak transcription	Fetal Stomach	stomach
18	chr9:17290800-17293000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr9:17291200-17293000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr9:17291400-17293000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:17291800-17294200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr9:17292000-17297800	Weak transcription	HSMMtube	muscle
23	chr9:17292200-17294000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr9:17292200-17294000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
25	chr9:17292200-17294600	Weak transcription	HSMM	muscle
26	chr9:17292200-17367200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr9:17292400-17293600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr9:17292400-17294400	Weak transcription	Gastric	stomach
29	chr9:17292400-17303800	Weak transcription	Right Ventricle	heart
30	chr9:17292600-17294000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr9:17292600-17295200	Weak transcription	Osteobl	bone
32	chr9:17292800-17293000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr9:17292800-17293400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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