SNP Detail For rs9653442
1.Mapping Information
Human SNP ID rs9653442
Human chromosome chr2
Human SNP position 100208905
Pig chromosome chr3
Pig SNP position 56666356
2.Annotation Information
PubMed ID17554260
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/17554260
StudyRobust associations of four new chromosome regions from genome-wide analyses of type 1 diabetes.
Disease/TraitType 1 diabetes
Initial sample2,000 European ancestry cases, 3,000 European ancestry controls
Replication sample2,997 European ancestry trios, 4,000 European ancestry cases, 5,000 European ancestry controls
Region2q11.2
Chromosome idchr2
Chromosome position100208905
Reported geneAFF3, LOC150577
Mapped geneLINC01104
Upstream gene id
Downstream gene id
SNP gene ids150577
Upstream gene distance
Downstream gene distance
SNP risk allelers9653442-G
SNPsrs9653442
Merged0
SNP id current9653442
Contextintron_variant
Intergenic0
Allele frequency0.46
P value0.000005
Pvalue mlog5.30102999566398
P value text
Or beta1.11
%95 Ci[1.05-1.17]
PlatformAffymetrix [NR]
CNVN
Mapped traittype I diabetes mellitus
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0001359
Study accessionGCST000038
PubMed ID24390342
JournalNature
Linkwww.ncbi.nlm.nih.gov/pubmed/24390342
StudyGenetics of rheumatoid arthritis contributes to biology and drug discovery.
Disease/TraitRheumatoid arthritis
Initial sampleup to 14,361 European ancestry cases, up to 42,923 European ancestry controls, up to 4,873 East Asian ancestry cases, up to 17,642 East Asian ancestry controls
Replication sampleup to 3,775 European ancestry cases, up to 5,801 European ancestry controls, up to 6,871 East Asian ancestry cases, up to 6,392 East Asian ancestry controls
Region2q11.2
Chromosome idchr2
Chromosome position100208905
Reported geneAFF3
Mapped geneLINC01104
Upstream gene id
Downstream gene id
SNP gene ids150577
Upstream gene distance
Downstream gene distance
SNP risk allelers9653442-C
SNPsrs9653442
Merged0
SNP id current9653442
Contextintron_variant
Intergenic0
Allele frequency0.46
P value0.000000000000000002
Pvalue mlog17.698970004336
P value text
Or beta1.11
%95 Ci[1.09-1.14]
PlatformAffymetrix, Illumina [up to 9739303] (imputed)
CNVN
Mapped traitrheumatoid arthritis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000685
Study accessionGCST002318
PubMed ID24390342
JournalNature
Linkwww.ncbi.nlm.nih.gov/pubmed/24390342
StudyGenetics of rheumatoid arthritis contributes to biology and drug discovery.
Disease/TraitRheumatoid arthritis
Initial sampleup to 14,361 European ancestry cases, up to 42,923 European ancestry controls, up to 4,873 East Asian ancestry cases, up to 17,642 East Asian ancestry controls
Replication sampleup to 3,775 European ancestry cases, up to 5,801 European ancestry controls, up to 6,871 East Asian ancestry cases, up to 6,392 East Asian ancestry controls
Region2q11.2
Chromosome idchr2
Chromosome position100208905
Reported geneAFF3
Mapped geneLINC01104
Upstream gene id
Downstream gene id
SNP gene ids150577
Upstream gene distance
Downstream gene distance
SNP risk allelers9653442-C
SNPsrs9653442
Merged0
SNP id current9653442
Contextintron_variant
Intergenic0
Allele frequency0.46
P value0.00000000000001
Pvalue mlog14
P value text(EA)
Or beta1.12
%95 Ci[1.09-1.15]
PlatformAffymetrix, Illumina [up to 9739303] (imputed)
CNVN
Mapped traitrheumatoid arthritis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000685
Study accessionGCST002318