SNP Detail For rs10781499
1.Mapping Information
Human SNP ID rs10781499
Human chromosome chr9
Human SNP position 136371953
Pig chromosome chr5
Pig SNP position 7899105
2.Annotation Information
PubMed ID21297633
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/21297633
StudyMeta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
Disease/TraitUlcerative colitis
Initial sample6,687 European ancestry cases, 19,718 European ancestry controls
Replication sample9,628 European ancestry cases, 12,917 European ancestry controls
Region9q34.3
Chromosome idchr9
Chromosome position136371953
Reported geneINPP5E, SDCCAG3, SEC16A, CARD9, SNAPC4
Mapped geneCARD9
Upstream gene id
Downstream gene id
SNP gene ids64170
Upstream gene distance
Downstream gene distance
SNP risk allelers10781499-A
SNPsrs10781499
Merged0
SNP id current10781499
Contextsynonymous_variant
Intergenic0
Allele frequency0.41
P value3E-19
Pvalue mlog18.5228787452803
P value text
Or beta1.12
%95 Ci[1.08-1.17]
PlatformAffymetrix, Illumina [~ 1100000] (imputed)
CNVN
Mapped traitulcerative colitis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000729
Study accessionGCST000964
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
Region9q34.3
Chromosome idchr9
Chromosome position136371953
Reported geneINPP5E, SDCCAG3, CARD9, PMPCA
Mapped geneCARD9
Upstream gene id
Downstream gene id
SNP gene ids64170
Upstream gene distance
Downstream gene distance
SNP risk allelers10781499-A
SNPsrs10781499
Merged0
SNP id current10781499
Contextsynonymous_variant
Intergenic0
Allele frequency0.412
P value4E-56
Pvalue mlog55.397940008672
P value text
Or beta1.188
%95 Ci[1.154-1.222]
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
Region9q34.3
Chromosome idchr9
Chromosome position136371953
Reported geneNR
Mapped geneCARD9
Upstream gene id
Downstream gene id
SNP gene ids64170
Upstream gene distance
Downstream gene distance
SNP risk allelers10781499-A
SNPsrs10781499
Merged0
SNP id current10781499
Contextsynonymous_variant
Intergenic0
Allele frequency0.4263
P value4E-26
Pvalue mlog25.397940008672
P value text(EA)
Or beta1.142511
%95 Ci[1.12-1.17]
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
Region9q34.3
Chromosome idchr9
Chromosome position136371953
Reported geneNR
Mapped geneCARD9
Upstream gene id
Downstream gene id
SNP gene ids64170
Upstream gene distance
Downstream gene distance
SNP risk allelers10781499-A
SNPsrs10781499
Merged0
SNP id current10781499
Contextsynonymous_variant
Intergenic0
Allele frequency0.4263
P value8E-43
Pvalue mlog42.096910013008
P value text(EA)
Or beta1.181867
%95 Ci[1.16-1.21]
PlatformAffymetrix, Illumina [~ 9000000] (imputed)
CNVN
Mapped traitCrohn__s disease
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000384
Study accessionGCST003044