SNP Detail For rs3764147
1.Mapping Information
Human SNP ID rs3764147
Human chromosome chr13
Human SNP position 43883789
Pig chromosome chr11
Pig SNP position 23607533
2.Annotation Information
PubMed ID18587394
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/18587394
StudyGenome-wide association defines more than 30 distinct susceptibility loci for Crohn__s disease.
Disease/TraitCrohn__s disease
Initial sample3,230 European ancestry cases, 4,829 European ancestry controls
Replication sample1,339 European ancestry trios, 2,325 European ancestry cases, 1,809 European ancestry controls
Region13q14.11
Chromosome idchr13
Chromosome position43883789
Reported geneUnknown
Mapped geneLACC1
Upstream gene id
Downstream gene id
SNP gene ids144811
Upstream gene distance
Downstream gene distance
SNP risk allelers3764147-G
SNPsrs3764147
Merged0
SNP id current3764147
Contextmissense_variant
Intergenic0
Allele frequency0.22
P value0.0000000000002
Pvalue mlog12.698970004336
P value text
Or beta1.25
%95 Ci[NR]
PlatformAffymetrix, Illumina [635547] (imputed)
CNVN
Mapped traitCrohn__s disease
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000384
Study accessionGCST000207
PubMed ID20018961
JournalN Engl J Med
Linkwww.ncbi.nlm.nih.gov/pubmed/20018961
StudyGenomewide association study of leprosy.
Disease/TraitLeprosy
Initial sample706 Han Chinese ancestry cases, 1,225 Han Chinese ancestry controls
Replication sample3,254 Chinese ancestry cases, 5,955 Chinese ancestry controls
Region13q14.11
Chromosome idchr13
Chromosome position43883789
Reported geneC13orf31
Mapped geneLACC1
Upstream gene id
Downstream gene id
SNP gene ids144811
Upstream gene distance
Downstream gene distance
SNP risk allelers3764147-G
SNPsrs3764147
Merged0
SNP id current3764147
Contextmissense_variant
Intergenic0
Allele frequency0.31
P value4E-54
Pvalue mlog53.397940008672
P value text
Or beta1.68
%95 Ci[1.57-1.80]
PlatformIllumina [491883]
CNVN
Mapped traitleprosy
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001054
Study accessionGCST000546
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
Region13q14.11
Chromosome idchr13
Chromosome position43883789
Reported geneC13orf31
Mapped geneLACC1
Upstream gene id
Downstream gene id
SNP gene ids144811
Upstream gene distance
Downstream gene distance
SNP risk allelers3764147-G
SNPsrs3764147
Merged0
SNP id current3764147
Contextmissense_variant
Intergenic0
Allele frequency0.245
P value0.0000000001
Pvalue mlog10
P value text
Or beta1.17
%95 Ci[1.12-1.23]
PlatformAffymetrix, Illumina [953241] (imputed)
CNVN
Mapped traitCrohn__s disease
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000384
Study accessionGCST000879
PubMed ID23128233
JournalNature
Linkwww.ncbi.nlm.nih.gov/pubmed/23128233
StudyHost-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
Disease/TraitCrohn__s disease
Initial sampleUp to 12,924 European ancestry cases, up to 21,442 European ancestry controls
Replication sampleUp to 25,683 European ancestry cases, up to 17,015 European ancestry controls
Region13q14.11
Chromosome idchr13
Chromosome position43883789
Reported geneLACC1
Mapped geneLACC1
Upstream gene id
Downstream gene id
SNP gene ids144811
Upstream gene distance
Downstream gene distance
SNP risk allelers3764147-G
SNPsrs3764147
Merged0
SNP id current3764147
Contextmissense_variant
Intergenic0
Allele frequency0.248
P value2E-21
Pvalue mlog20.698970004336
P value text
Or beta1.155
%95 Ci[1.112-1.199]
PlatformAffymetrix, Illumina [1230000] (imputed)
CNVN
Mapped traitCrohn__s disease
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000384
Study accessionGCST001729
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
Region13q14.11
Chromosome idchr13
Chromosome position43883789
Reported geneNR
Mapped geneLACC1
Upstream gene id
Downstream gene id
SNP gene ids144811
Upstream gene distance
Downstream gene distance
SNP risk allelers3764147-G
SNPsrs3764147
Merged0
SNP id current3764147
Contextmissense_variant
Intergenic0
Allele frequency0.2297
P value0.0000000000000009
Pvalue mlog15.0457574905606
P value text(EA)
Or beta1.099218
%95 Ci[1.08-1.12]
PlatformAffymetrix, Illumina [~ 9000000] (imputed)
CNVN
Mapped traitinflammatory bowel disease
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0003767
Study accessionGCST003043