SNP Detail For rs1678542
1.Mapping Information
Human SNP ID rs1678542
Human chromosome chr12
Human SNP position 57574932
Pig chromosome JH118928-1
Pig SNP position 75356
2.Annotation Information
PubMed ID18794853
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/18794853
StudyCommon variants at CD40 and other loci confer risk of rheumatoid arthritis.
Disease/TraitRheumatoid arthritis
Initial sample3,393 European ancestry cases, 12,460 European ancestry controls
Replication sample3,929 European ancestry cases, 5,807 European ancestry controls
Region12q13.3
Chromosome idchr12
Chromosome position57574932
Reported geneKIF5A, PIP4K2C
Mapped geneKIF5A
Upstream gene id
Downstream gene id
SNP gene ids3798
Upstream gene distance
Downstream gene distance
SNP risk allelers1678542-C
SNPsrs1678542
Merged0
SNP id current1678542
Contextintron_variant
Intergenic0
Allele frequency0.37
P value0.00000009
Pvalue mlog7.04575749056067
P value text
Or beta1.12
%95 Ci[NR]
PlatformAffymetrix, Illumina [at least 315971] (imputed)
CNVN
Mapped traitrheumatoid arthritis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000685
Study accessionGCST000232
PubMed ID24449572
JournalArthritis Rheumatol
Linkwww.ncbi.nlm.nih.gov/pubmed/24449572
StudyNovel rheumatoid arthritis susceptibility locus at 22q12 identified in an extended UK genome-wide association study.
Disease/TraitRheumatoid arthritis
Initial sample3,034 European ancestry cases, 5,271 European ancestry controls
Replication sample4,726 European ancestry cases, 2,625 European ancestry controls
Region12q13.3
Chromosome idchr12
Chromosome position57574932
Reported geneKIF5A
Mapped geneKIF5A
Upstream gene id
Downstream gene id
SNP gene ids3798
Upstream gene distance
Downstream gene distance
SNP risk allelers1678542-?
SNPsrs1678542
Merged0
SNP id current1678542
Contextintron_variant
Intergenic0
Allele frequency
P value0.0000001
Pvalue mlog7
P value text
Or beta1.2
%95 Ci[1.12-1.28]
PlatformAffymetrix, Illumina [1831729] (imputed)
CNVN
Mapped traitrheumatoid arthritis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000685
Study accessionGCST002323