SNP Detail For rs9905704
1.Mapping Information
Human SNP ID rs9905704
Human chromosome chr17
Human SNP position 58555182
Pig chromosome chr12
Pig SNP position 36001181
2.Annotation Information
PubMed ID23666240
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/23666240
StudyIdentification of nine new susceptibility loci for testicular cancer, including variants near DAZL and PRDM14.
Disease/TraitTesticular germ cell tumor
Initial sample986 European ancestry cases, 4,946 European ancestry controls
Replication sample1,064 European ancestry cases, 10,082 European ancestry controls
Region17q22
Chromosome idchr17
Chromosome position58555182
Reported geneRAD51C, TEX14
Mapped geneSEPT4-AS1
Upstream gene id
Downstream gene id
SNP gene ids101927688
Upstream gene distance
Downstream gene distance
SNP risk allelers9905704-T
SNPsrs9905704
Merged0
SNP id current9905704
Contextintron_variant
Intergenic0
Allele frequency0.67
P value0.000000003
Pvalue mlog8.52287874528033
P value text
Or beta1.21
%95 Ci[1.10-1.34]
PlatformIllumina [307291]
CNVN
Mapped traittesticular carcinoma
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0005088
Study accessionGCST002022
PubMed ID23666239
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/23666239
StudyMeta-analysis identifies four new loci associated with testicular germ cell tumor.
Disease/TraitTesticular germ cell tumor
Initial sample582 European ancestry male cases, 1,056 European ancestry male controls
Replication sample3,560 European ancestry male cases, 8,510 European ancestry male controls
Region17q22
Chromosome idchr17
Chromosome position58555182
Reported geneC17orf47, RAD51C, PPM1E, SEPT4, TRIM37, SKA2, TEX14
Mapped geneSEPT4-AS1
Upstream gene id
Downstream gene id
SNP gene ids101927688
Upstream gene distance
Downstream gene distance
SNP risk allelers9905704-T
SNPsrs9905704
Merged0
SNP id current9905704
Contextintron_variant
Intergenic0
Allele frequency0.68
P value0.0000000000004
Pvalue mlog12.397940008672
P value text
Or beta1.27
%95 Ci[1.18-1.33]
PlatformIllumina [NR]
CNVN
Mapped traittesticular carcinoma
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0005088
Study accessionGCST002023
PubMed ID25877299
JournalHum Mol Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/25877299
StudyTwo new loci and gene sets related to sex determination and cancer progression are associated with susceptibility to testicular germ cell tumor.
Disease/TraitTesticular germ cell tumor
Initial sample1,326 European ancestry cases, 6,687 European ancestry controls
Replication sample710 European ancestry case-parent triads, 289 European ancestry cases, 290 European ancestry controls
Region17q22
Chromosome idchr17
Chromosome position58555182
Reported geneTEX14
Mapped geneSEPT4-AS1
Upstream gene id
Downstream gene id
SNP gene ids101927688
Upstream gene distance
Downstream gene distance
SNP risk allelers9905704-T
SNPsrs9905704
Merged0
SNP id current9905704
Contextintron_variant
Intergenic0
Allele frequency0.708
P value0.000004
Pvalue mlog5.39794000867203
P value text
Or beta1.23
%95 Ci[NR]
PlatformIllumina [610240]
CNVN
Mapped traitTesticular Germ Cell Tumor
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_1000566
Study accessionGCST002855