SNP Detail For rs11742570
1.Mapping Information
Human SNP ID rs11742570
Human chromosome chr5
Human SNP position 40410482
Pig chromosome chr16
Pig SNP position 26717282
2.Annotation Information
PubMed ID21102463
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/21102463
StudyGenome-wide meta-analysis increases to 71 the number of confirmed Crohn__s disease susceptibility loci.
Disease/TraitCrohn__s disease
Initial sample6,333 European ancestry cases, 15,056 European ancestry controls
Replication sample15,694 European ancestry cases, 14,026 European ancestry controls, 414 European ancestry trios
Region5p13.1
Chromosome idchr5
Chromosome position40410482
Reported genePTGER4
Mapped geneLOC105374736 - LOC105374737
Upstream gene id105374736
Downstream gene id105374737
SNP gene ids
Upstream gene distance63927
Downstream gene distance189398
SNP risk allelers11742570-C
SNPsrs11742570
Merged0
SNP id current11742570
Contextupstream_gene_variant
Intergenic1
Allele frequency0.606
P value7E-36
Pvalue mlog35.1549019599857
P value text
Or beta1.33
%95 Ci[1.27-1.39]
PlatformAffymetrix, Illumina [953241] (imputed)
CNVN
Mapped traitCrohn__s disease
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000384
Study accessionGCST000879
PubMed ID22936669
JournalGut
Linkwww.ncbi.nlm.nih.gov/pubmed/22936669
StudyA genome-wide association study on a southern European population identifies a new Crohn__s disease susceptibility locus at RBX1-EP300.
Disease/TraitCrohn__s disease
Initial sample1,277 European ancestry cases, 1,488 European ancestry controls
Replication sample1,365 European ancestry cases, 1,396 European ancestry controls
Region5p13.1
Chromosome idchr5
Chromosome position40410482
Reported genePTGER4
Mapped geneLOC105374736 - LOC105374737
Upstream gene id105374736
Downstream gene id105374737
SNP gene ids
Upstream gene distance63927
Downstream gene distance189398
SNP risk allelers11742570-C
SNPsrs11742570
Merged0
SNP id current11742570
Contextupstream_gene_variant
Intergenic1
Allele frequencyNR
P value0.000001
Pvalue mlog6
P value text
Or beta1.32
%95 Ci[NR]
PlatformIllumina [508934]
CNVN
Mapped traitCrohn__s disease
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000384
Study accessionGCST001652
PubMed ID23128233
JournalNature
Linkwww.ncbi.nlm.nih.gov/pubmed/23128233
StudyHost-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
Disease/TraitInflammatory bowel disease
Initial sample12,924 European ancestry cases, 21,442 European ancestry controls
Replication sample25,683 European ancestry cases, 17,015 European ancestry controls
Region5p13.1
Chromosome idchr5
Chromosome position40410482
Reported genePTGER4
Mapped geneLOC105374736 - LOC105374737
Upstream gene id105374736
Downstream gene id105374737
SNP gene ids
Upstream gene distance63927
Downstream gene distance189398
SNP risk allelers11742570-C
SNPsrs11742570
Merged0
SNP id current11742570
Contextupstream_gene_variant
Intergenic1
Allele frequency0.605
P value2E-82
Pvalue mlog81.698970004336
P value text
Or beta1.198
%95 Ci[1.164-1.234]
PlatformAffymetrix, Illumina [1230000] (imputed)
CNVN
Mapped traitinflammatory bowel disease
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0003767
Study accessionGCST001725
PubMed ID26192919
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/26192919
StudyAssociation analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations.
Disease/TraitUlcerative colitis
Initial sample6,968 European ancestry cases, 20,464 European ancestry controls
Replication sample10,679 European ancestry cases, 26,715 European ancestry controls, 397 Iranian ancestry cases, 342 Iranian ancestry controls, 1,239 Indian ancestry cases, 990 Indian ancestry controls, 1,134 East Asian ancestry cases, 3,719 East Asian ancestry controls
Region5p13.1
Chromosome idchr5
Chromosome position40410482
Reported geneNR
Mapped geneLOC105374736 - LOC105374737
Upstream gene id105374736
Downstream gene id105374737
SNP gene ids
Upstream gene distance63927
Downstream gene distance189398
SNP risk allelers11742570-G
SNPsrs11742570
Merged0
SNP id current11742570
Contextupstream_gene_variant
Intergenic1
Allele frequency0.61
P value0.00000000006
Pvalue mlog10.2218487496163
P value text(EA)
Or beta1.0874969
%95 Ci
PlatformAffymetrix, Illumina [~ 9000000] (imputed)
CNVN
Mapped traitulcerative colitis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000729
Study accessionGCST003045
PubMed ID26192919
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/26192919
StudyAssociation analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations.
Disease/TraitCrohn__s disease
Initial sample5,956 European ancestry cases, 14,927 European ancestry controls
Replication sample14,594 European ancestry cases, 26,715 European ancestry controls, 151 Iranian ancestry cases, 342 Iranian ancestry controls, 184 Indian ancestry cases, 990 Indian ancestry controls, 1,690 East Asian ancestry cases, 3,719 East Asian ancestry controls
Region5p13.1
Chromosome idchr5
Chromosome position40410482
Reported geneNR
Mapped geneLOC105374736 - LOC105374737
Upstream gene id105374736
Downstream gene id105374737
SNP gene ids
Upstream gene distance63927
Downstream gene distance189398
SNP risk allelers11742570-A
SNPsrs11742570
Merged0
SNP id current11742570
Contextupstream_gene_variant
Intergenic1
Allele frequency0.61
P value4E-87
Pvalue mlog86.397940008672
P value text(EA)
Or beta1.2804482
%95 Ci
PlatformAffymetrix, Illumina [~ 9000000] (imputed)
CNVN
Mapped traitCrohn__s disease
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000384
Study accessionGCST003044