SNP Detail For rs2293370
1.Mapping Information
Human SNP ID rs2293370
Human chromosome chr3
Human SNP position 119501087
Pig chromosome chr13
Pig SNP position 150048923
2.Annotation Information
PubMed ID21399635
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/21399635
StudyGenome-wide association study identifies 12 new susceptibility loci for primary biliary cirrhosis.
Disease/TraitPrimary biliary cirrhosis
Initial sample1,840 European ancestry cases, 5,163 European ancestry controls and (Liu et al)
Replication sample620 European ancestry cases, 2,514 European ancestry controls
Region3q13.33
Chromosome idchr3
Chromosome position119501087
Reported geneCD80
Mapped geneTIMMDC1
Upstream gene id
Downstream gene id
SNP gene ids51300
Upstream gene distance
Downstream gene distance
SNP risk allelers2293370-G
SNPsrs2293370
Merged0
SNP id current2293370
Contextintron_variant
Intergenic0
Allele frequency0.8
P value0.00000000003
Pvalue mlog10.5228787452803
P value text
Or beta1.35
%95 Ci[1.23-1.47]
PlatformIllumina [507467]
CNVN
Mapped traitbiliary liver cirrhosis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004267
Study accessionGCST001010
PubMed ID21833088
JournalNature
Linkwww.ncbi.nlm.nih.gov/pubmed/21833088
StudyGenetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.
Disease/TraitMultiple sclerosis
Initial sample9,772 European ancestry cases, 16,849 European ancestry controls
Replication sample4,218 European ancestry cases, 7,296 European ancestry controls
Region3q13.33
Chromosome idchr3
Chromosome position119501087
Reported geneC3orf1, TMEM39A
Mapped geneTIMMDC1
Upstream gene id
Downstream gene id
SNP gene ids51300
Upstream gene distance
Downstream gene distance
SNP risk allelers2293370-G
SNPsrs2293370
Merged0
SNP id current2293370
Contextintron_variant
Intergenic0
Allele frequencyNR
P value0.000000003
Pvalue mlog8.52287874528033
P value text
Or beta1.13
%95 Ci[1.11-1.15]
PlatformIllumina [465434]
CNVN
Mapped traitmultiple sclerosis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0003885
Study accessionGCST001198
PubMed ID23000144
JournalAm J Hum Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/23000144
StudyGenome-wide association study identifies TNFSF15 and POU2AF1 as susceptibility loci for primary biliary cirrhosis in the Japanese population.
Disease/TraitPrimary biliary cirrhosis
Initial sample487 Japanese ancestry cases, 476 Japanese ancestry controls
Replication sample787 Japanese ancestry cases, 615 Japanese ancestry controls
Region3q13.33
Chromosome idchr3
Chromosome position119501087
Reported geneCD80
Mapped geneTIMMDC1
Upstream gene id
Downstream gene id
SNP gene ids51300
Upstream gene distance
Downstream gene distance
SNP risk allelers2293370-C
SNPsrs2293370
Merged0
SNP id current2293370
Contextintron_variant
Intergenic0
Allele frequencyNR
P value0.000000003
Pvalue mlog8.52287874528033
P value text
Or beta1.48
%95 Ci[1.29-1.68]
PlatformAffymetrix [421245]
CNVN
Mapped traitbiliary liver cirrhosis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004267
Study accessionGCST001685
PubMed ID26394269
JournalNat Commun
Linkwww.ncbi.nlm.nih.gov/pubmed/26394269
StudyInternational genome-wide meta-analysis identifies new primary biliary cirrhosis risk loci and targetable pathogenic pathways.
Disease/TraitPrimary biliary cirrhosis
Initial sample2,764 European ancestry cases, 10,475 European ancestry controls
Replication sample3,716 European ancestry cases, 4,261 European ancestry controls
Region3q13.33
Chromosome idchr3
Chromosome position119501087
Reported geneTMEM39A, CD80
Mapped geneTIMMDC1
Upstream gene id
Downstream gene id
SNP gene ids51300
Upstream gene distance
Downstream gene distance
SNP risk allelers2293370-G
SNPsrs2293370
Merged0
SNP id current2293370
Contextintron_variant
Intergenic0
Allele frequency0.86
P value0.000000000000004
Pvalue mlog14.397940008672
P value text
Or beta1.42
%95 CiNR
PlatformIllumina [1143634] (imputed)
CNVN
Mapped traitprimary biliary cirrhosis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_1001486
Study accessionGCST003129