SNP Detail For rs10934853
1.Mapping Information
Human SNP ID rs10934853
Human chromosome chr3
Human SNP position 128319530
Pig chromosome JH118478-1
Pig SNP position 163631
2.Annotation Information
PubMed ID19767754
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/19767754
StudyGenome-wide association and replication studies identify four variants associated with prostate cancer susceptibility.
Disease/TraitProstate cancer
Initial sampleUp to 1,968 European ancestry cases, 35,382 European ancestry controls
Replication sampleUp to 11,806 European ancestry cases, 12,387 European ancestry controls
Region3q21.3
Chromosome idchr3
Chromosome position128319530
Reported geneintergenic
Mapped geneEEFSEC
Upstream gene id
Downstream gene id
SNP gene ids60678
Upstream gene distance
Downstream gene distance
SNP risk allelers10934853-A
SNPsrs10934853
Merged0
SNP id current10934853
Contextintron_variant
Intergenic0
Allele frequency0.28
P value0.0000000003
Pvalue mlog9.52287874528033
P value text
Or beta1.12
%95 Ci[1.08-1.16]
PlatformIllumina [310520]
CNVN
Mapped traitprostate carcinoma
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001663
Study accessionGCST000489
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
Region14q32.31 x 3q21.3
Chromosome idchr14 x 3
Chromosome position101260770 x 128319530
Reported geneMIR656 x EEFSEC
Mapped geneLOC101929422 - LOC105370671 x EEFSEC
Upstream gene id
Downstream gene id
SNP gene ids
Upstream gene distance
Downstream gene distance
SNP risk allelers2400997-? x rs10934853-?
SNPsrs2400997 x rs10934853
Merged0
SNP id current
Contextintron_variant x intron_variant
Intergenic
Allele frequencyNR
P value0.000003
Pvalue mlog5.52287874528033
P value text
Or beta1.25
%95 Ci[1.14-1.38]
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
Region18q12.3 x 3q21.3
Chromosome idchr18 x 3
Chromosome position45145697 x 128319530
Reported geneMIR4319 x EEFSEC
Mapped geneLOC105372091 x EEFSEC
Upstream gene id
Downstream gene id
SNP gene ids
Upstream gene distance
Downstream gene distance
SNP risk allelers998124-? x rs10934853-?
SNPsrs998124 x rs10934853
Merged0
SNP id current
Contextintron_variant x intron_variant
Intergenic
Allele frequencyNR
P value0.000005
Pvalue mlog5.30102999566398
P value text
Or beta1.33
%95 Ci[1.18-1.51]
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
Region9q33.1 x 3q21.3
Chromosome idchr9 x 3
Chromosome position115068533 x 128319530
Reported geneTNC x EEFSEC
Mapped geneTNC x EEFSEC
Upstream gene id
Downstream gene id
SNP gene ids
Upstream gene distance
Downstream gene distance
SNP risk allelers7847271-? x rs10934853-?
SNPsrs7847271 x rs10934853
Merged0
SNP id current
Contextintron_variant x intron_variant
Intergenic
Allele frequencyNR
P value0.000004
Pvalue mlog5.39794000867203
P value text
Or beta1.4925
%95 Ci[1.27-1.79]
PlatformAffymetrix, Illumina [1117531] (imputed)
CNVN
Mapped traitprostate carcinoma
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001663
Study accessionGCST001370