SNP Detail For rs12621278
1.Mapping Information
Human SNP ID rs12621278
Human chromosome chr2
Human SNP position 172446825
Pig chromosome chr15
Pig SNP position 87851480
2.Annotation Information
PubMed ID19767753
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/19767753
StudyIdentification of seven new prostate cancer susceptibility loci through a genome-wide association study.
Disease/TraitProstate cancer
Initial sample1,854 European ancestry cases, 1,894 European ancestry controls
Replication sample19,879 cases and 18,761 controls of European, East Asian, African American, Latino, and Hawaiian ancestry
Region2q31.1
Chromosome idchr2
Chromosome position172446825
Reported geneITGA6
Mapped geneITGA6
Upstream gene id
Downstream gene id
SNP gene ids3655
Upstream gene distance
Downstream gene distance
SNP risk allelers12621278-?
SNPsrs12621278
Merged0
SNP id current12621278
Contextintron_variant
Intergenic0
Allele frequency0.94
P value9E-23
Pvalue mlog22.0457574905606
P value text
Or beta1.33
%95 Ci[1.25-1.43]
PlatformIllumina [541129]
CNVN
Mapped traitprostate carcinoma
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001663
Study accessionGCST000488
PubMed ID22219177
JournalCarcinogenesis
Linkwww.ncbi.nlm.nih.gov/pubmed/22219177
StudyA genome-wide search for loci interacting with known prostate cancer risk-associated genetic variants.
Disease/TraitProstate cancer (gene x gene interaction)
Initial sample4,723 European ancestry cases, 4,792 European ancestry controls
Replication sampleNA
Region3q13.2 x 2q31.1
Chromosome idchr3 x 2
Chromosome position112779033 x 172446825
Reported geneCD200R1L x ITAGA6
Mapped geneLOC101929694 - CD200R1L x ITGA6
Upstream gene id
Downstream gene id
SNP gene ids
Upstream gene distance
Downstream gene distance
SNP risk allelers1002979-? x rs12621278-?
SNPsrs1002979 x rs12621278
Merged0
SNP id current
Contextregulatory_region_variant x intron_variant
Intergenic
Allele frequencyNR
P value0.000003
Pvalue mlog5.52287874528033
P value text
Or beta1.5873
%95 Ci[1.32-1.92]
PlatformAffymetrix, Illumina [1117531] (imputed)
CNVN
Mapped traitprostate carcinoma
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001663
Study accessionGCST001370