SNP Detail For rs11465804
1.Mapping Information
Human SNP ID rs11465804
Human chromosome chr1
Human SNP position 67236843
Pig chromosome chr6
Pig SNP position 134231276
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
Region1p31.3
Chromosome idchr1
Chromosome position67236843
Reported geneIL23R
Mapped geneIL23R
Upstream gene id
Downstream gene id
SNP gene ids149233
Upstream gene distance
Downstream gene distance
SNP risk allelers11465804-T
SNPsrs11465804
Merged0
SNP id current11465804
Contextintron_variant
Intergenic0
Allele frequency0.93
P value7E-63
Pvalue mlog62.1549019599857
P value text
Or beta2.5
%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 ID20570966
JournalHum Mol Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/20570966
StudyFucosyltransferase 2 (FUT2) non-secretor status is associated with Crohn__s disease.
Disease/TraitCrohn__s disease
Initial sample896 European ancestry cases, 3,204 European ancestry controls
Replication sample1,174 European ancestry cases, 357 European ancestry controls
Region1p31.3
Chromosome idchr1
Chromosome position67236843
Reported geneIL23R
Mapped geneIL23R
Upstream gene id
Downstream gene id
SNP gene ids149233
Upstream gene distance
Downstream gene distance
SNP risk allelers11465804-?
SNPsrs11465804
Merged0
SNP id current11465804
Contextintron_variant
Intergenic0
Allele frequencyNR
P value0.000001
Pvalue mlog6
P value text
Or beta1.89
%95 Ci[1.47-2.44]
PlatformIllumina [304825]
CNVN
Mapped traitCrohn__s disease
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000384
Study accessionGCST000705
PubMed ID17804789
JournalProc Natl Acad Sci U S A
Linkwww.ncbi.nlm.nih.gov/pubmed/17804789
StudyGenome-wide association study for Crohn__s disease in the Quebec Founder Population identifies multiple validated disease loci.
Disease/TraitCrohn__s disease
Initial sample382 French Canadian founder trios
Replication sample750 European ancestry cases, 828 European ancestry controls, 521 European ancestry trios
Region1p31.3
Chromosome idchr1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1
Chromosome position67264945;67240275;67253446;67264372;67256884;67135449;67262335;67124778;67236843;67259437;67228519;67204530;67260421;67205233;67187327;67219915
Reported geneIL23R
Mapped geneIL23R - LOC100130497; IL23R; IL23R; IL23R - LOC100130497; IL23R; C1orf141; IL23R - LOC100130497; C1orf141; IL23R; IL23R; IL23R; IL23R; IL23R - RNU4ATAC4P; IL23R; IL23R; IL23R
Upstream gene id
Downstream gene id
SNP gene ids
Upstream gene distance
Downstream gene distance
SNP risk allelers10789230-?; rs11209026-?; rs1343151-?; rs6669582-?; rs10889676-?; rs11209003-?; rs12567232-?; rs11209002-?; rs11465804-?; rs10889677-?; rs2201841-?; rs1004819-?; rs9988642-?; rs2902440-?; rs2064689-?; rs11465802-?
SNPsrs10789230; rs11209026; rs1343151; rs6669582; rs10889676; rs11209003; rs12567232; rs11209002; rs11465804; rs10889677; rs2201841; rs1004819; rs9988642; rs2902440; rs2064689; rs11465802
Merged0
SNP id current
Contextdownstream_gene_variant; missense_variant; intron_variant; downstream_gene_variant; intron_variant; intron_variant; downstream_gene_variant; intron_variant; intron_variant; 3_prime_UTR_variant; intron_variant; intron_variant; downstream_gene_variant; intr
Intergenic
Allele frequency0.23
P value0.00000001
Pvalue mlog8
P value text
Or beta1.38
%95 Ci[1.23-1.53]
PlatformPerlegen [164279]
CNVN
Mapped traitCrohn__s disease
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000384
Study accessionGCST000071
PubMed ID17804789
JournalProc Natl Acad Sci U S A
Linkwww.ncbi.nlm.nih.gov/pubmed/17804789
StudyGenome-wide association study for Crohn__s disease in the Quebec Founder Population identifies multiple validated disease loci.
Disease/TraitCrohn__s disease
Initial sample382 French Canadian founder trios
Replication sample750 European ancestry cases, 828 European ancestry controls, 521 European ancestry trios
Region1p31.3
Chromosome idchr1;1;1;1;1;1;1;1;1;1;1;1;1;1;1;1
Chromosome position67264945;67240275;67253446;67264372;67256884;67135449;67262335;67124778;67236843;67259437;67228519;67204530;67260421;67205233;67187327;67219915
Reported geneIL23R
Mapped geneIL23R - LOC100130497; IL23R; IL23R; IL23R - LOC100130497; IL23R; C1orf141; IL23R - LOC100130497; C1orf141; IL23R; IL23R; IL23R; IL23R; IL23R - RNU4ATAC4P; IL23R; IL23R; IL23R
Upstream gene id
Downstream gene id
SNP gene ids
Upstream gene distance
Downstream gene distance
SNP risk allelers10789230-?; rs11209026-?; rs1343151-?; rs6669582-?; rs10889676-?; rs11209003-?; rs12567232-?; rs11209002-?; rs11465804-?; rs10889677-?; rs2201841-?; rs1004819-?; rs9988642-?; rs2902440-?; rs2064689-?; rs11465802-?
SNPsrs10789230; rs11209026; rs1343151; rs6669582; rs10889676; rs11209003; rs12567232; rs11209002; rs11465804; rs10889677; rs2201841; rs1004819; rs9988642; rs2902440; rs2064689; rs11465802
Merged0
SNP id current
Contextdownstream_gene_variant; missense_variant; intron_variant; downstream_gene_variant; intron_variant; intron_variant; downstream_gene_variant; intron_variant; intron_variant; 3_prime_UTR_variant; intron_variant; intron_variant; downstream_gene_variant; intr
Intergenic
Allele frequency0.97
P value0.0000002
Pvalue mlog6.69897000433601
P value text
Or beta2.56
%95 Ci[1.75-3.70]
PlatformPerlegen [164279]
CNVN
Mapped traitCrohn__s disease
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000384
Study accessionGCST000071