SNP Detail For rs12199775
1.Mapping Information
Human SNP ID rs12199775
Human chromosome chr6
Human SNP position 143577757
Pig chromosome chr1
Pig SNP position 24070831
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
Region6q24.2
Chromosome idchr6
Chromosome position143577757
Reported genePHACTR2
Mapped geneLOC285740 - PHACTR2
Upstream gene id285740
Downstream gene id9749
SNP gene ids
Upstream gene distance8418
Downstream gene distance30423
SNP risk allelers12199775-A
SNPsrs12199775
Merged0
SNP id current12199775
Contextintron_variant
Intergenic1
Allele frequency0.929
P value0.00000002
Pvalue mlog7.69897000433601
P value text
Or beta1.129
%95 Ci[1.066-1.195]
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/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
Region6q24.2
Chromosome idchr6
Chromosome position143577757
Reported geneNR
Mapped geneLOC285740 - PHACTR2
Upstream gene id285740
Downstream gene id9749
SNP gene ids
Upstream gene distance8418
Downstream gene distance30423
SNP risk allelers12199775-G
SNPsrs12199775
Merged0
SNP id current12199775
Contextintron_variant
Intergenic1
Allele frequency0.93
P value0.000005
Pvalue mlog5.30102999566398
P value text(EA)
Or beta1.1207099
%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
Region6q24.2
Chromosome idchr6
Chromosome position143577757
Reported geneNR
Mapped geneLOC285740 - PHACTR2
Upstream gene id285740
Downstream gene id9749
SNP gene ids
Upstream gene distance8418
Downstream gene distance30423
SNP risk allelers12199775-A
SNPsrs12199775
Merged0
SNP id current12199775
Contextintron_variant
Intergenic1
Allele frequency0.93
P value0.0000004
Pvalue mlog6.39794000867203
P value text(EA)
Or beta1.1094881
%95 Ci
PlatformAffymetrix, Illumina [~ 9000000] (imputed)
CNVN
Mapped traitinflammatory bowel disease
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0003767
Study accessionGCST003043