SNP Detail For rs6465657
1.Mapping Information
Human SNP ID rs6465657
Human chromosome chr7
Human SNP position 98187015
Pig chromosome chr3
Pig SNP position 5447326
2.Annotation Information
PubMed ID18264097
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/18264097
StudyMultiple newly identified loci associated with prostate cancer susceptibility.
Disease/TraitProstate cancer
Initial sample1,854 European ancestry cases, 1,894 European ancestry controls
Replication sample3,268 European ancestry cases, 3,366 European ancestry controls
Region7q21.3
Chromosome idchr7
Chromosome position98187015
Reported geneLMTK2
Mapped geneLMTK2
Upstream gene id
Downstream gene id
SNP gene ids22853
Upstream gene distance
Downstream gene distance
SNP risk allelers6465657-C
SNPsrs6465657
Merged0
SNP id current6465657
Contextintron_variant
Intergenic0
Allele frequency0.46
P value0.000000001
Pvalue mlog9
P value text
Or beta1.12
%95 Ci[1.05-1.20]
PlatformIllumina [541129]
CNVN
Mapped traitprostate carcinoma
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001663
Study accessionGCST000152
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
Region7q21.3
Chromosome idchr7
Chromosome position98187015
Reported geneNR
Mapped geneLMTK2
Upstream gene id
Downstream gene id
SNP gene ids22853
Upstream gene distance
Downstream gene distance
SNP risk allelers6465657-?
SNPsrs6465657
Merged0
SNP id current6465657
Contextintron_variant
Intergenic0
Allele frequencyNR
P value0.00000002
Pvalue mlog7.69897000433601
P value text
Or beta
%95 Ci
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
Region16q12.1 x 7q21.3
Chromosome idchr16 x 7
Chromosome position49360365 x 98187015
Reported geneC16orf78 x LMTK2
Mapped geneLOC105371243 - C16orf78 x LMTK2
Upstream gene id
Downstream gene id
SNP gene ids
Upstream gene distance
Downstream gene distance
SNP risk allelers8057939-? x rs6465657-?
SNPsrs8057939 x rs6465657
Merged0
SNP id current
Contextintergenic_variant x intron_variant
Intergenic
Allele frequencyNR
P value0.000005
Pvalue mlog5.30102999566398
P value text
Or beta1.37
%95 Ci[1.20-1.57]
PlatformAffymetrix, Illumina [1117531] (imputed)
CNVN
Mapped traitprostate carcinoma
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001663
Study accessionGCST001370
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
Region3p26.3 x 7q21.3
Chromosome idchr3 x 7
Chromosome position108303 x 98187015
Reported geneCHL1 x LMTK2
Mapped geneLOC105376920 - LOC101927174 x LMTK2
Upstream gene id
Downstream gene id
SNP gene ids
Upstream gene distance
Downstream gene distance
SNP risk allelers12485321-? x rs6465657-?
SNPsrs12485321 x rs6465657
Merged0
SNP id current
Contextintergenic_variant x intron_variant
Intergenic
Allele frequencyNR
P value0.000003
Pvalue mlog5.52287874528033
P value text
Or beta1.2346
%95 Ci[1.14-1.35]
PlatformAffymetrix, Illumina [1117531] (imputed)
CNVN
Mapped traitprostate carcinoma
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001663
Study accessionGCST001370