Variant report

Variant	rs10817802
Chromosome Location	chr9:118362166-118362167
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs1006008	0.92[EUR][1000 genomes]
rs10116519	0.92[EUR][1000 genomes]
rs10123924	0.89[EUR][1000 genomes]
rs10124673	0.84[EUR][1000 genomes]
rs10817790	0.90[EUR][1000 genomes]
rs10817791	0.90[EUR][1000 genomes]
rs10817792	0.90[EUR][1000 genomes]
rs10982789	0.90[EUR][1000 genomes]
rs10982791	0.90[EUR][1000 genomes]
rs10982846	0.92[EUR][1000 genomes]
rs11999332	0.92[EUR][1000 genomes]
rs12342529	0.89[EUR][1000 genomes]
rs2027929	0.81[EUR][1000 genomes]
rs2188052	0.89[EUR][1000 genomes]
rs2188053	0.89[EUR][1000 genomes]
rs2188067	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2418367	0.92[EUR][1000 genomes]
rs2418393	0.92[EUR][1000 genomes]
rs3899074	0.92[EUR][1000 genomes]
rs4246911	0.92[EUR][1000 genomes]
rs4979550	0.89[EUR][1000 genomes]
rs4979551	0.92[EUR][1000 genomes]
rs4979569	0.92[EUR][1000 genomes]
rs4997383	0.92[EUR][1000 genomes]
rs6478180	0.88[EUR][1000 genomes]
rs6478181	0.82[EUR][1000 genomes]
rs6478183	0.90[EUR][1000 genomes]
rs6478184	0.90[EUR][1000 genomes]
rs6478185	0.90[EUR][1000 genomes]
rs6478196	0.92[EUR][1000 genomes]
rs7024456	0.93[EUR][1000 genomes]
rs7026805	0.90[EUR][1000 genomes]
rs7027022	0.90[EUR][1000 genomes]
rs7029913	0.91[EUR][1000 genomes]
rs7030481	0.92[EUR][1000 genomes]
rs7033287	0.84[EUR][1000 genomes]
rs7046356	0.92[EUR][1000 genomes]
rs718019	0.92[EUR][1000 genomes]
rs7466595	0.90[EUR][1000 genomes]
rs7466771	0.88[EUR][1000 genomes]
rs7467026	0.86[EUR][1000 genomes]
rs7467728	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7468290	0.90[EUR][1000 genomes]
rs7469165	0.85[EUR][1000 genomes]
rs7469418	0.89[EUR][1000 genomes]
rs7469817	0.85[EUR][1000 genomes]
rs7470070	0.92[EUR][1000 genomes]
rs7855143	0.91[EUR][1000 genomes]
rs7858000	0.89[EUR][1000 genomes]
rs916554	0.84[EUR][1000 genomes]
rs916555	0.83[EUR][1000 genomes]
rs963115	0.94[EUR][1000 genomes]
rs969832	0.92[EUR][1000 genomes]
rs976499	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv615251	chr9:117975864-118514444	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv948346	chr9:118107565-118718197	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1046948	chr9:118185587-118926891	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv916622	chr9:118206309-118952390	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	nsv540207	chr9:118206311-118920304	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv491661	chr9:118206312-118802177	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv831698	chr9:118284259-118446456	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv1047164	chr9:118286742-118456851	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10817802	DEC1	cis	parietal	SCAN
rs10817802	C9orf27	cis	parietal	SCAN
rs10817802	HDHD3	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:118357200-118367000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:118358200-118362200	Enhancers	Fetal Stomach	stomach
3	chr9:118358400-118377800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:118358800-118366400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr9:118360000-118362200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:118360000-118362600	Enhancers	NHDF-Ad	bronchial
7	chr9:118360400-118367000	Weak transcription	NH-A	brain
8	chr9:118360600-118362400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr9:118360600-118362600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr9:118360600-118367200	Weak transcription	HSMM	muscle
11	chr9:118360600-118367400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:118360800-118362400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr9:118361200-118362200	Weak transcription	Osteobl	bone
14	chr9:118361400-118364000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr9:118361600-118362800	Enhancers	Rectal Smooth Muscle	rectum
16	chr9:118361600-118366600	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr9:118361800-118367200	Weak transcription	NHLF	lung
18	chr9:118362000-118362200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:118362000-118365200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:118362000-118371600	Weak transcription	HSMMtube	muscle

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