SNP Detail For rs2494938
1.Mapping Information
Human SNP ID rs2494938
Human chromosome chr6
Human SNP position 40568389
Pig chromosome chr7
Pig SNP position 41121500
2.Annotation Information
PubMed ID23103227
JournalAm J Hum Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/23103227
StudyGenetic variants at 6p21.1 and 7p15.3 are associated with risk of multiple cancers in Han Chinese.
Disease/TraitMultiple cancers (lung cancer, gastric cancer, and squamous cell carcinoma)
Initial sample2,331 Han Chinese ancestry lung cancer cases, 1,006 Han Chinese ancestry non-cardia gastric cancer cases, 2,031 Han Chinese ancestry esophageal squamous-cell carcinoma cases, 4,006 Han Chinese ancestry controls
Replication sample2,665 Han Chinese ancestry lung cancer cases, 3,330 Han Chinese ancestry non-cardia gastric cancer cases, 3,006 Han Chinese ancestry esophageal squamous-cell carcinoma cases, 11,436 Han Chinese ancestry controls
Region6p21.1
Chromosome idchr6
Chromosome position40568389
Reported geneLRFN2
Mapped geneLRFN2
Upstream gene id
Downstream gene id
SNP gene ids57497
Upstream gene distance
Downstream gene distance
SNP risk allelers2494938-A
SNPsrs2494938
Merged0
SNP id current2494938
Contextintron_variant
Intergenic0
Allele frequency0.23
P value0.000002
Pvalue mlog5.69897000433601
P value text(Lung Cancer)
Or beta1.15
%95 Ci[1.08-1.22]
PlatformAffymetrix [NR]
CNVN
Mapped traitlung carcinoma
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001071
Study accessionGCST001718
PubMed ID23103227
JournalAm J Hum Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/23103227
StudyGenetic variants at 6p21.1 and 7p15.3 are associated with risk of multiple cancers in Han Chinese.
Disease/TraitMultiple cancers (lung cancer, gastric cancer, and squamous cell carcinoma)
Initial sample2,331 Han Chinese ancestry lung cancer cases, 1,006 Han Chinese ancestry non-cardia gastric cancer cases, 2,031 Han Chinese ancestry esophageal squamous-cell carcinoma cases, 4,006 Han Chinese ancestry controls
Replication sample2,665 Han Chinese ancestry lung cancer cases, 3,330 Han Chinese ancestry non-cardia gastric cancer cases, 3,006 Han Chinese ancestry esophageal squamous-cell carcinoma cases, 11,436 Han Chinese ancestry controls
Region6p21.1
Chromosome idchr6
Chromosome position40568389
Reported geneLRFN2
Mapped geneLRFN2
Upstream gene id
Downstream gene id
SNP gene ids57497
Upstream gene distance
Downstream gene distance
SNP risk allelers2494938-A
SNPsrs2494938
Merged0
SNP id current2494938
Contextintron_variant
Intergenic0
Allele frequency0.23
P value0.000000005
Pvalue mlog8.30102999566398
P value text(NCGC)
Or beta1.18
%95 Ci[1.12-1.25]
PlatformAffymetrix [NR]
CNVN
Mapped traitsquamous cell carcinoma
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000707
Study accessionGCST001718
PubMed ID23103227
JournalAm J Hum Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/23103227
StudyGenetic variants at 6p21.1 and 7p15.3 are associated with risk of multiple cancers in Han Chinese.
Disease/TraitMultiple cancers (lung cancer, gastric cancer, and squamous cell carcinoma)
Initial sample2,331 Han Chinese ancestry lung cancer cases, 1,006 Han Chinese ancestry non-cardia gastric cancer cases, 2,031 Han Chinese ancestry esophageal squamous-cell carcinoma cases, 4,006 Han Chinese ancestry controls
Replication sample2,665 Han Chinese ancestry lung cancer cases, 3,330 Han Chinese ancestry non-cardia gastric cancer cases, 3,006 Han Chinese ancestry esophageal squamous-cell carcinoma cases, 11,436 Han Chinese ancestry controls
Region6p21.1
Chromosome idchr6
Chromosome position40568389
Reported geneLRFN2
Mapped geneLRFN2
Upstream gene id
Downstream gene id
SNP gene ids57497
Upstream gene distance
Downstream gene distance
SNP risk allelers2494938-A
SNPsrs2494938
Merged0
SNP id current2494938
Contextintron_variant
Intergenic0
Allele frequency0.23
P value0.000000000001
Pvalue mlog12
P value text(All Cancers)
Or beta1.15
%95 Ci[1.10-1.19]
PlatformAffymetrix [NR]
CNVN
Mapped traitlung carcinoma, squamous cell carcinoma, gastric carcinoma
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001071, http://www.ebi.ac.uk/efo/EFO_0000707, http://www.ebi.ac.uk/efo/EFO_0000178
Study accessionGCST001718