Variant report

Variant	rs10123080
Chromosome Location	chr9:94962103-94962104
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10081693	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10119535	1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[ASN][1000 genomes]
rs10156530	0.82[ASN][1000 genomes]
rs10283718	0.91[ASN][1000 genomes]
rs10820954	0.91[ASN][1000 genomes]
rs10820956	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10820962	0.91[ASN][1000 genomes]
rs10820963	1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10820970	0.91[ASN][1000 genomes]
rs10820973	0.91[ASN][1000 genomes]
rs10992265	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10992266	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10992267	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10992270	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10992308	0.83[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.91[ASN][1000 genomes]
rs10992312	0.83[CEU][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.91[ASN][1000 genomes]
rs10992314	0.91[ASN][1000 genomes]
rs10992334	0.91[ASN][1000 genomes]
rs12345822	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12349712	0.91[ASN][1000 genomes]
rs12352447	0.91[ASN][1000 genomes]
rs1447114	1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.91[ASN][1000 genomes]
rs1951849	0.91[ASN][1000 genomes]
rs3858097	0.88[ASW][hapmap];0.89[CEU][hapmap];0.83[MKK][hapmap];0.85[YRI][hapmap]
rs3889951	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58391046	0.91[ASN][1000 genomes]
rs60993552	0.91[ASN][1000 genomes]
rs6479412	0.91[ASN][1000 genomes]
rs6479413	0.91[ASN][1000 genomes]
rs7036078	0.82[CEU][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7860297	0.91[ASN][1000 genomes]
rs7863859	0.94[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7873882	1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9695754	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv969760	chr9:94877924-94966209	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs10123080	OMD	cis	cerebellum	SCAN
rs10123080	CENPP	cis	parietal	SCAN
rs10123080	ZNF484	cis	parietal	SCAN
rs10123080	CENPP	cis	Adipose Subcutaneous	GTEx
rs10123080	CENPP	cis	Artery Tibial	GTEx
rs10123080	CENPP	cis	Esophagus Muscularis	GTEx
rs10123080	CENPP	cis	Thyroid	GTEx
rs10123080	CENPP	cis	cerebellum	SCAN
rs10123080	AUH	cis	parietal	SCAN
rs10123080	CENPP	cis	Muscle Skeletal	GTEx
rs10123080	IPPK	cis	cerebellum	SCAN
rs10123080	CENPP	cis	Nerve Tibial	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94954400-94971000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr9:94959400-94969000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr9:94959400-94971200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:94959400-94973200	Weak transcription	Pancreas	Pancrea
5	chr9:94959600-94969800	Weak transcription	Osteobl	bone
6	chr9:94959600-94970800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr9:94960600-94970400	Weak transcription	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links