SNP Detail For rs11889341
1.Mapping Information
Human SNP ID rs11889341
Human chromosome chr2
Human SNP position 191079016
Pig chromosome JH118841-1
Pig SNP position 51482
2.Annotation Information
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
Region2q32.2
Chromosome idchr2
Chromosome position191079016
Reported geneSTAT4
Mapped geneSTAT4
Upstream gene id
Downstream gene id
SNP gene ids6775
Upstream gene distance
Downstream gene distance
SNP risk allelers11889341-T
SNPsrs11889341
Merged0
SNP id current11889341
Contextintron_variant
Intergenic0
Allele frequency0.25
P value4E-19
Pvalue mlog18.397940008672
P value text
Or beta1.13
%95 Ci[1.10-1.17]
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
Region2q32.2
Chromosome idchr2
Chromosome position191079016
Reported geneSTAT4
Mapped geneSTAT4
Upstream gene id
Downstream gene id
SNP gene ids6775
Upstream gene distance
Downstream gene distance
SNP risk allelers11889341-T
SNPsrs11889341
Merged0
SNP id current11889341
Contextintron_variant
Intergenic0
Allele frequency0.23
P value0.000000000001
Pvalue mlog12
P value text(EA)
Or beta1.12
%95 Ci[1.09-1.16]
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
Region2q32.2
Chromosome idchr2
Chromosome position191079016
Reported geneSTAT4
Mapped geneSTAT4
Upstream gene id
Downstream gene id
SNP gene ids6775
Upstream gene distance
Downstream gene distance
SNP risk allelers11889341-T
SNPsrs11889341
Merged0
SNP id current11889341
Contextintron_variant
Intergenic0
Allele frequency0.3
P value0.00000002
Pvalue mlog7.69897000433601
P value text(East Asian)
Or beta1.16
%95 Ci[1.10-1.22]
PlatformAffymetrix, Illumina [up to 9739303] (imputed)
CNVN
Mapped traitrheumatoid arthritis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000685
Study accessionGCST002318
PubMed ID26502338
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/26502338
StudyGenetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus.
Disease/TraitSystemic lupus erythematosus
Initial sample5,201 European ancestry cases, 9,066 European ancestry controls
Replication sample2,018 European ancestry cases, 6,925 European ancestry controls
Region2q32.2
Chromosome idchr2
Chromosome position191079016
Reported geneSTAT4
Mapped geneSTAT4
Upstream gene id
Downstream gene id
SNP gene ids6775
Upstream gene distance
Downstream gene distance
SNP risk allelers11889341-T
SNPsrs11889341
Merged0
SNP id current11889341
Contextintron_variant
Intergenic0
Allele frequency
P value6E-122
Pvalue mlog121.221848749616
P value text
Or beta1.73
%95 Ci(1.65鈥?.81]
PlatformIllumina [644674]
CNVN
Mapped traitsystemic lupus erythematosus
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0002690
Study accessionGCST003155
PubMed ID26502338
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/26502338
StudyGenetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus.
Disease/TraitSystemic lupus erythematosus
Initial sample5,201 European ancestry cases, 9,066 European ancestry controls
Replication sampleNA
Region2q32.2
Chromosome idchr2
Chromosome position191079016
Reported geneSTAT4
Mapped geneSTAT4
Upstream gene id
Downstream gene id
SNP gene ids6775
Upstream gene distance
Downstream gene distance
SNP risk allelers11889341-T
SNPsrs11889341
Merged0
SNP id current11889341
Contextintron_variant
Intergenic0
Allele frequency
P value2E-76
Pvalue mlog75.698970004336
P value text
Or beta1.68
%95 Ci[NR]
PlatformIllumina [> 644674] (imputed)
CNVN
Mapped traitsystemic lupus erythematosus
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0002690
Study accessionGCST003156
PubMed ID26606652
JournalArthritis Rheumatol
Linkwww.ncbi.nlm.nih.gov/pubmed/26606652
StudyGWAS in an Amerindian ancestry population reveals novel systemic lupus erythematosus risk loci and the role of European admixture.
Disease/TraitSystemic lupus erythematosus
Initial sample862 Native American ancestry-enriched North American cases, 531 Native American ancestry-enriched South American cases, 1,973 Native American ancestry-enriched North American controls, 344 Native American ancestry-enriched South American controls
Replication sampleNA
Region2q32.2
Chromosome idchr2
Chromosome position191079016
Reported geneSTAT4
Mapped geneSTAT4
Upstream gene id
Downstream gene id
SNP gene ids6775
Upstream gene distance
Downstream gene distance
SNP risk allelers11889341-T
SNPsrs11889341
Merged0
SNP id current11889341
Contextintron_variant
Intergenic0
Allele frequency0.407
P value0.0000000000007
Pvalue mlog12.1549019599857
P value text
Or beta1.5
%95 Ci[1.36-1.66]
PlatformIllumina [580483] (imputed)
CNVN
Mapped traitsystemic lupus erythematosus
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0002690
Study accessionGCST003252