SNP Detail For rs9292777
1.Mapping Information
Human SNP ID rs9292777
Human chromosome chr5
Human SNP position 40437846
Pig chromosome chr16
Pig SNP position 26741937
2.Annotation Information
PubMed ID17554261
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/17554261
StudySequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn__s disease susceptibility.
Disease/TraitCrohn__s disease
Initial sample1,748 cases, 2,938 controls
Replication sample1,182 European ancestry cases, 2,024 European ancestry controls
Region5p13.1
Chromosome idchr5
Chromosome position40437846
Reported geneintergenic
Mapped geneLOC105374736 - LOC105374737
Upstream gene id105374736
Downstream gene id105374737
SNP gene ids
Upstream gene distance91291
Downstream gene distance162034
SNP risk allelers9292777-?
SNPsrs9292777
Merged0
SNP id current9292777
Contextregulatory_region_variant
Intergenic1
Allele frequency0.4
P value0.000000000000000003
Pvalue mlog17.5228787452803
P value text
Or beta1.34
%95 Ci[1.20-1.50]
PlatformAffymetrix [see WTCCC]
CNVN
Mapped traitCrohn__s disease
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000384
Study accessionGCST000039
PubMed ID22570697
JournalPLoS One
Linkwww.ncbi.nlm.nih.gov/pubmed/22570697
StudyGenome-wide association study of multiple sclerosis confirms a novel locus at 5p13.1.
Disease/TraitMultiple sclerosis
Initial sample2,127 European ancestry cases, 4,558 European ancestry controls
Replication sample2,785 European ancestry cases, 2,940 European ancestry controls
Region5p13.1
Chromosome idchr5
Chromosome position40437846
Reported genePTGER4
Mapped geneLOC105374736 - LOC105374737
Upstream gene id105374736
Downstream gene id105374737
SNP gene ids
Upstream gene distance91291
Downstream gene distance162034
SNP risk allelers9292777-T
SNPsrs9292777
Merged0
SNP id current9292777
Contextregulatory_region_variant
Intergenic1
Allele frequencyNR
P value0.000000001
Pvalue mlog9
P value text
Or beta1.19
%95 Ci[1.12-1.25]
PlatformAffymetrix, Illumina [130903]
CNVN
Mapped traitmultiple sclerosis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0003885
Study accessionGCST001505
PubMed ID22412388
JournalPLoS Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/22412388
StudyA genome-wide scan of Ashkenazi Jewish Crohn__s disease suggests novel susceptibility loci.
Disease/TraitCrohn__s disease
Initial sample737 Ashkenazi Jewish cases, 2,257 Ashkenazi Jewish controls
Replication sample971 Ashkenazi Jewish cases, 2,124 Ashkenazi Jewish controls
Region5p13.1
Chromosome idchr5
Chromosome position40437846
Reported genePTGER4
Mapped geneLOC105374736 - LOC105374737
Upstream gene id105374736
Downstream gene id105374737
SNP gene ids
Upstream gene distance91291
Downstream gene distance162034
SNP risk allelers9292777-T
SNPsrs9292777
Merged0
SNP id current9292777
Contextregulatory_region_variant
Intergenic1
Allele frequency0.597
P value0.00000000002
Pvalue mlog10.698970004336
P value text
Or beta1.37
%95 Ci[1.28-1.48]
PlatformAffymetrix, Illumina [1060934] (imputed)
CNVN
Mapped traitCrohn__s disease
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000384
Study accessionGCST001438