Variant report

Variant	rs10810739
Chromosome Location	chr9:17246782-17246783
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10046851	0.80[EUR][1000 genomes]
rs10123715	0.80[EUR][1000 genomes]
rs10124487	0.83[EUR][1000 genomes]
rs10125333	0.81[EUR][1000 genomes]
rs10481559	0.80[EUR][1000 genomes]
rs10738474	0.81[EUR][1000 genomes]
rs10756855	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10756856	0.85[EUR][1000 genomes]
rs10756857	0.82[AMR][1000 genomes]
rs10756858	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10756860	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10756869	0.83[EUR][1000 genomes]
rs10810740	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10810748	0.84[EUR][1000 genomes]
rs10810749	0.84[EUR][1000 genomes]
rs10810750	0.84[EUR][1000 genomes]
rs10810751	0.84[EUR][1000 genomes]
rs10810752	0.84[EUR][1000 genomes]
rs10810761	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10810763	0.81[EUR][1000 genomes]
rs10810764	0.81[EUR][1000 genomes]
rs10962947	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10962950	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10962982	0.88[EUR][1000 genomes]
rs10962988	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10963026	0.84[EUR][1000 genomes]
rs10963042	0.80[EUR][1000 genomes]
rs10963063	0.83[EUR][1000 genomes]
rs11560448	0.83[AMR][1000 genomes]
rs12236820	0.86[EUR][1000 genomes]
rs12337171	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12342180	0.81[EUR][1000 genomes]
rs13290922	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1576962	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1582030	0.82[EUR][1000 genomes]
rs1582031	0.82[EUR][1000 genomes]
rs1591138	0.80[EUR][1000 genomes]
rs1596193	0.81[EUR][1000 genomes]
rs1759454	0.86[EUR][1000 genomes]
rs1759613	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2151290	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2779773	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2779775	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2779776	0.84[EUR][1000 genomes]
rs2780206	0.81[EUR][1000 genomes]
rs2990670	0.87[EUR][1000 genomes]
rs36057268	0.81[EUR][1000 genomes]
rs3765040	0.81[EUR][1000 genomes]
rs3808784	0.81[EUR][1000 genomes]
rs3824391	0.80[EUR][1000 genomes]
rs3824392	0.80[EUR][1000 genomes]
rs4246135	0.81[EUR][1000 genomes]
rs4246136	0.80[EUR][1000 genomes]
rs4272484	0.83[EUR][1000 genomes]
rs4409489	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4424358	0.82[EUR][1000 genomes]
rs4563978	0.84[EUR][1000 genomes]
rs4961539	0.81[EUR][1000 genomes]
rs593614	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs595894	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs605916	0.88[EUR][1000 genomes]
rs619380	0.86[EUR][1000 genomes]
rs632265	0.86[EUR][1000 genomes]
rs645117	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6475139	0.80[EUR][1000 genomes]
rs654521	0.90[EUR][1000 genomes]
rs670058	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs670511	0.88[EUR][1000 genomes]
rs7018705	0.83[EUR][1000 genomes]
rs7022024	0.81[EUR][1000 genomes]
rs7022060	0.82[EUR][1000 genomes]
rs7028593	0.81[EUR][1000 genomes]
rs7028930	0.81[EUR][1000 genomes]
rs7031133	0.81[EUR][1000 genomes]
rs7033974	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7037111	0.82[EUR][1000 genomes]
rs7038064	0.81[EUR][1000 genomes]
rs7038197	0.81[EUR][1000 genomes]
rs7044823	0.81[EUR][1000 genomes]
rs7046933	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7849084	0.84[EUR][1000 genomes]
rs7849085	0.84[EUR][1000 genomes]
rs7854802	0.80[EUR][1000 genomes]
rs7864650	0.84[EUR][1000 genomes]
rs7864919	0.80[EUR][1000 genomes]
rs7865766	0.82[EUR][1000 genomes]
rs7870101	0.80[EUR][1000 genomes]
rs870271	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9298772	0.80[EUR][1000 genomes]
rs9298773	0.80[EUR][1000 genomes]
rs9298774	0.81[EUR][1000 genomes]
rs9406666	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv892660	chr9:17134245-17269437	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	nsv1030291	chr9:17216945-17262803	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	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
14	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
15	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10810739	C9orf39	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17217600-17247000	Weak transcription	Left Ventricle	heart
2	chr9:17223600-17279400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr9:17229800-17251600	Weak transcription	HSMM	muscle
4	chr9:17234600-17249400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr9:17235000-17249600	Weak transcription	Dnd41	blood
6	chr9:17235800-17249400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr9:17236400-17262000	Weak transcription	Ovary	ovary
8	chr9:17240600-17248400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr9:17240800-17248600	Weak transcription	NHDF-Ad	bronchial
10	chr9:17241000-17247000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr9:17241000-17249800	Weak transcription	Fetal Heart	heart
12	chr9:17241200-17249000	Weak transcription	Gastric	stomach
13	chr9:17241400-17249400	Weak transcription	Right Ventricle	heart
14	chr9:17242600-17247000	Weak transcription	Pancreas	Pancrea
15	chr9:17244600-17247000	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr9:17244600-17249600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr9:17244800-17248600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr9:17245600-17248000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
19	chr9:17246000-17247600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr9:17246000-17248400	ZNF genes & repeats	Fetal Lung	lung
21	chr9:17246200-17246800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
22	chr9:17246200-17247000	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr9:17246400-17247200	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr9:17246400-17247200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr9:17246400-17247200	Strong transcription	Fetal Kidney	kidney
26	chr9:17246400-17247200	ZNF genes & repeats	Fetal Stomach	stomach
27	chr9:17246400-17247400	ZNF genes & repeats	Adipose Nuclei	Adipose
28	chr9:17246400-17247600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr9:17246400-17247600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr9:17246400-17248200	ZNF genes & repeats	Fetal Muscle Leg	muscle
31	chr9:17246400-17249400	Weak transcription	Small Intestine	intestine
32	chr9:17246600-17247400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr9:17246600-17247400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr9:17246600-17247400	Strong transcription	Fetal Muscle Trunk	muscle
35	chr9:17246600-17247800	Strong transcription	Aorta	Aorta
36	chr9:17246600-17247800	Strong transcription	Liver	Liver

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