Variant report

Variant	rs10962119
Chromosome Location	chr9:15698391-15698392
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10119975	0.81[AMR][1000 genomes]
rs10121393	0.81[AMR][1000 genomes]
rs10756691	0.81[AMR][1000 genomes]
rs10810429	0.82[AMR][1000 genomes]
rs10810430	0.82[AMR][1000 genomes]
rs10962118	0.83[AMR][1000 genomes]
rs10962121	0.82[AMR][1000 genomes]
rs10962123	0.82[AMR][1000 genomes]
rs11793900	0.81[AMR][1000 genomes]
rs12004358	0.82[AMR][1000 genomes]
rs12352779	0.82[AMR][1000 genomes]
rs28403566	0.83[AMR][1000 genomes]
rs35057009	0.82[AMR][1000 genomes]
rs62573118	0.82[AMR][1000 genomes]
rs6474951	0.81[AMR][1000 genomes]
rs7037662	0.81[AMR][1000 genomes]
rs7037908	0.81[AMR][1000 genomes]
rs954663	0.82[AMR][1000 genomes]
rs954664	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv2752286	chr9:15578017-15794897	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv892632	chr9:15590116-15869845	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv892633	chr9:15604746-15889411	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv466262	chr9:15615321-15727518	ZNF genes & repeats Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv613657	chr9:15615321-15727518	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv613658	chr9:15636260-15727518	Strong transcription Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv466263	chr9:15641279-15726057	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv613659	chr9:15641279-15726057	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv892634	chr9:15696501-15746168	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10962119	CCDC171	cis	Nerve Tibial	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15669000-15720800	Weak transcription	Gastric	stomach
2	chr9:15675000-15699000	Weak transcription	Left Ventricle	heart
3	chr9:15676600-15725000	Weak transcription	Pancreas	Pancrea
4	chr9:15679800-15746800	Weak transcription	Ovary	ovary
5	chr9:15687600-15746600	Weak transcription	Aorta	Aorta
6	chr9:15690400-15721800	Weak transcription	Fetal Lung	lung
7	chr9:15691400-15699200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr9:15691800-15717000	Weak transcription	Thymus	Thymus
9	chr9:15693800-15703600	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr9:15694000-15700800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr9:15694200-15705600	Weak transcription	Adipose Nuclei	Adipose
12	chr9:15694600-15700200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr9:15694800-15700200	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr9:15695600-15700000	Weak transcription	Lung	lung
15	chr9:15695800-15699000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr9:15696800-15698400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr9:15697000-15698400	Enhancers	HSMM	muscle
18	chr9:15697400-15698600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr9:15697400-15700800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr9:15697800-15706400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr9:15698000-15698400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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