Variant report

Variant	rs10756856
Chromosome Location	chr9:17242708-17242709
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10756860	0.81[EUR][1000 genomes]
rs10810739	0.85[EUR][1000 genomes]
rs10810740	0.83[EUR][1000 genomes]
rs10962947	0.81[EUR][1000 genomes]
rs10962950	0.83[EUR][1000 genomes]
rs13290922	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1576962	0.80[EUR][1000 genomes]
rs1759613	0.81[EUR][1000 genomes]
rs2151290	0.87[EUR][1000 genomes]
rs2779773	0.82[EUR][1000 genomes]
rs2779775	0.83[EUR][1000 genomes]
rs593614	0.82[EUR][1000 genomes]
rs595894	0.80[EUR][1000 genomes]
rs605916	0.80[EUR][1000 genomes]
rs645117	0.81[EUR][1000 genomes]
rs654521	0.83[EUR][1000 genomes]
rs670058	0.82[EUR][1000 genomes]
rs670511	0.80[EUR][1000 genomes]
rs7033974	0.83[EUR][1000 genomes]
rs7046933	0.83[EUR][1000 genomes]
rs870271	0.82[EUR][1000 genomes]
rs9406667	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10756856	C9orf39	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:17207800-17246400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr9:17217600-17247000	Weak transcription	Left Ventricle	heart
3	chr9:17223600-17279400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr9:17224400-17242800	Weak transcription	Colon Smooth Muscle	Colon
5	chr9:17225400-17246600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr9:17229800-17251600	Weak transcription	HSMM	muscle
7	chr9:17234600-17249400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr9:17235000-17249600	Weak transcription	Dnd41	blood
9	chr9:17235800-17249400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr9:17236400-17262000	Weak transcription	Ovary	ovary
11	chr9:17237600-17243000	Weak transcription	NH-A	brain
12	chr9:17240600-17248400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr9:17240800-17248600	Weak transcription	NHDF-Ad	bronchial
14	chr9:17241000-17246600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr9:17241000-17247000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr9:17241000-17249800	Weak transcription	Fetal Heart	heart
17	chr9:17241200-17249000	Weak transcription	Gastric	stomach
18	chr9:17241400-17249400	Weak transcription	Right Ventricle	heart
19	chr9:17241800-17242800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr9:17242000-17243000	Strong transcription	Liver	Liver
21	chr9:17242000-17243200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
22	chr9:17242000-17243200	Strong transcription	Fetal Lung	lung
23	chr9:17242200-17243000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
24	chr9:17242400-17245000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr9:17242600-17242800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr9:17242600-17244200	Weak transcription	Fetal Stomach	stomach
27	chr9:17242600-17244600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
28	chr9:17242600-17246600	Weak transcription	Aorta	Aorta
29	chr9:17242600-17247000	Weak transcription	Pancreas	Pancrea

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