SNP Detail For rs6908425
1.Mapping Information
Human SNP ID rs6908425
Human chromosome chr6
Human SNP position 20728500
Pig chromosome chr7
Pig SNP position 16984628
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
Region6p22.3
Chromosome idchr6
Chromosome position20728500
Reported geneCDKAL1
Mapped geneCDKAL1
Upstream gene id
Downstream gene id
SNP gene ids54901
Upstream gene distance
Downstream gene distance
SNP risk allelers6908425-C
SNPsrs6908425
Merged0
SNP id current6908425
Contextintron_variant
Intergenic0
Allele frequency0.78
P value0.0000000009
Pvalue mlog9.04575749056067
P value text
Or beta1.21
%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 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
Region6p22.3
Chromosome idchr6
Chromosome position20728500
Reported geneCDKAL1
Mapped geneCDKAL1
Upstream gene id
Downstream gene id
SNP gene ids54901
Upstream gene distance
Downstream gene distance
SNP risk allelers6908425-C
SNPsrs6908425
Merged0
SNP id current6908425
Contextintron_variant
Intergenic0
Allele frequency0.784
P value0.00000001
Pvalue mlog8
P value text
Or beta1.17
%95 Ci[1.11-1.23]
PlatformAffymetrix, Illumina [953241] (imputed)
CNVN
Mapped traitCrohn__s disease
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000384
Study accessionGCST000879
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
Region6p22.3
Chromosome idchr6
Chromosome position20728500
Reported geneNR
Mapped geneCDKAL1
Upstream gene id
Downstream gene id
SNP gene ids54901
Upstream gene distance
Downstream gene distance
SNP risk allelers6908425-G
SNPsrs6908425
Merged0
SNP id current6908425
Contextintron_variant
Intergenic0
Allele frequency0.78
P value0.000004
Pvalue mlog5.39794000867203
P value text(EA)
Or beta1.0734457
%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
Region6p22.3
Chromosome idchr6
Chromosome position20728500
Reported geneNR
Mapped geneCDKAL1
Upstream gene id
Downstream gene id
SNP gene ids54901
Upstream gene distance
Downstream gene distance
SNP risk allelers6908425-A
SNPsrs6908425
Merged0
SNP id current6908425
Contextintron_variant
Intergenic0
Allele frequency0.78
P value0.000000000005
Pvalue mlog11.3010299956639
P value text(EA)
Or beta1.1095867
%95 Ci
PlatformAffymetrix, Illumina [~ 9000000] (imputed)
CNVN
Mapped traitCrohn__s disease
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000384
Study accessionGCST003044