SNP Detail For rs1517352
1.Mapping Information
Human SNP ID rs1517352
Human chromosome chr2
Human SNP position 191066738
Pig chromosome chr15
Pig SNP position 106952865
2.Annotation Information
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
Region2q32.2
Chromosome idchr2
Chromosome position191066738
Reported geneSTAT1, STAT4
Mapped geneSTAT4
Upstream gene id
Downstream gene id
SNP gene ids6775
Upstream gene distance
Downstream gene distance
SNP risk allelers1517352-C
SNPsrs1517352
Merged0
SNP id current1517352
Contextintron_variant
Intergenic0
Allele frequency0.6
P value0.00000000003
Pvalue mlog10.5228787452803
P value text
Or beta1.077
%95 Ci[1.046-1.109]
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
Region2q32.2
Chromosome idchr2
Chromosome position191066738
Reported geneNR
Mapped geneSTAT4
Upstream gene id
Downstream gene id
SNP gene ids6775
Upstream gene distance
Downstream gene distance
SNP risk allelers1517352-C
SNPsrs1517352
Merged0
SNP id current1517352
Contextintron_variant
Intergenic0
Allele frequency0.6
P value0.000000002
Pvalue mlog8.69897000433601
P value text(EA)
Or beta1.0808891
%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
Region2q32.2
Chromosome idchr2
Chromosome position191066738
Reported geneNR
Mapped geneSTAT4
Upstream gene id
Downstream gene id
SNP gene ids6775
Upstream gene distance
Downstream gene distance
SNP risk allelers1517352-A
SNPsrs1517352
Merged0
SNP id current1517352
Contextintron_variant
Intergenic0
Allele frequency0.6
P value0.0000000001
Pvalue mlog10
P value text(EA)
Or beta1.0832976
%95 Ci
PlatformAffymetrix, Illumina [~ 9000000] (imputed)
CNVN
Mapped traitCrohn__s disease
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000384
Study accessionGCST003044
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/TraitInflammatory bowel disease
Initial sample12,882 European ancestry cases, 21,770 European ancestry controls
Replication sample25,273 European ancestry cases, 26,715 European ancestry controls, 548 Iranian ancestry cases, 342 Iranian ancestry control, 1,423 Indian ancestry cases, 990 Indian ancestry controls, 2,824 East Asian ancestry cases, 3,719 East Asian ancestry controls
Region2q32.2
Chromosome idchr2
Chromosome position191066738
Reported geneNR
Mapped geneSTAT4
Upstream gene id
Downstream gene id
SNP gene ids6775
Upstream gene distance
Downstream gene distance
SNP risk allelers1517352-C
SNPsrs1517352
Merged0
SNP id current1517352
Contextintron_variant
Intergenic0
Allele frequency0.6
P value0.00000000000004
Pvalue mlog13.397940008672
P value text(EA)
Or beta1.0809946
%95 Ci
PlatformAffymetrix, Illumina [~ 9000000] (imputed)
CNVN
Mapped traitinflammatory bowel disease
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0003767
Study accessionGCST003043