SNP Detail For rs20541
1.Mapping Information
Human SNP ID rs20541
Human chromosome chr5
Human SNP position 132660272
Pig chromosome chr2
Pig SNP position 140443258
2.Annotation Information
PubMed ID22075330
JournalJ Allergy Clin Immunol
Linkwww.ncbi.nlm.nih.gov/pubmed/22075330
StudyA genome-wide association study of plasma total IgE concentrations in the Framingham Heart Study.
Disease/TraitIgE levels
Initial sample6,819 European ancestry individuals
Replication sample7,809 European ancestry indivduals
Region5q31.1
Chromosome idchr5
Chromosome position132660272
Reported geneIL13
Mapped geneIL13
Upstream gene id
Downstream gene id
SNP gene ids3596
Upstream gene distance
Downstream gene distance
SNP risk allelers20541-A
SNPsrs20541
Merged0
SNP id current20541
Contextmissense_variant
Intergenic0
Allele frequencyNR
P value0.000000000000000003
Pvalue mlog17.5228787452803
P value text
Or beta0.08
%95 Ci[NR] unit increase
PlatformAffymetrix [2540223] (imputed)
CNVN
Mapped traitserum IgE measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004579
Study accessionGCST001316
PubMed ID19169254
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/19169254
StudyGenome-wide scan reveals association of psoriasis with IL-23 and NF-kappaB pathways.
Disease/TraitPsoriasis
Initial sample1,359 European ancestry cases, 1,400 European ancestry controls
Replication sample5,048 European ancestry cases, 5,041 European ancestry controls
Region5q31.1
Chromosome idchr5
Chromosome position132660272
Reported geneIL13
Mapped geneIL13
Upstream gene id
Downstream gene id
SNP gene ids3596
Upstream gene distance
Downstream gene distance
SNP risk allelers20541-G
SNPsrs20541
Merged0
SNP id current20541
Contextmissense_variant
Intergenic0
Allele frequency0.79
P value0.000000000000005
Pvalue mlog14.3010299956639
P value text
Or beta1.27
%95 Ci[NR]
PlatformPerlegen [~ 2500000] (imputed)
CNVN
Mapped traitpsoriasis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000676
Study accessionGCST000322
PubMed ID22286212
JournalJ Natl Cancer Inst
Linkwww.ncbi.nlm.nih.gov/pubmed/22286212
StudyGenome-wide association study of classical Hodgkin lymphoma and Epstein-Barr virus status-defined subgroups.
Disease/TraitHodgkin__s lymphoma
Initial sample1,200 European ancestry cases, 6,417 European ancestry controls
Replication sample563 European ancestry cases, 613 European ancestry controls
Region5q31.1
Chromosome idchr5
Chromosome position132660272
Reported geneIL13
Mapped geneIL13
Upstream gene id
Downstream gene id
SNP gene ids3596
Upstream gene distance
Downstream gene distance
SNP risk allelers20541-?
SNPsrs20541
Merged0
SNP id current20541
Contextmissense_variant
Intergenic0
Allele frequencyNR
P value0.00000001
Pvalue mlog8
P value text(EBV-negative cHL)
Or beta1.47
%95 Ci[1.29-1.68]
PlatformIllumina [502514]
CNVN
Mapped traitHodgkins lymphoma
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000183
Study accessionGCST001387
PubMed ID23817569
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/23817569
StudyA genome-wide association meta-analysis of self-reported allergy identifies shared and allergy-specific susceptibility loci.
Disease/TraitSelf-reported allergy
Initial sample53,862 European ancestry individuals
Replication sampleNA
Region5q31.1
Chromosome idchr5
Chromosome position132660272
Reported geneintergenic
Mapped geneIL13
Upstream gene id
Downstream gene id
SNP gene ids3596
Upstream gene distance
Downstream gene distance
SNP risk allelers20541-A
SNPsrs20541
Merged0
SNP id current20541
Contextmissense_variant
Intergenic0
Allele frequency0.2019
P value0.000001
Pvalue mlog6
P value text
Or beta0.0724
%95 Ci[0.043-0.101] unit increase
PlatformIllumina [2400000] (imputed)
CNVN
Mapped traitallergy
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0003785
Study accessionGCST002083
PubMed ID25574825
JournalAm J Hum Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/25574825
StudyGenome-wide Comparative Analysis of Atopic Dermatitis and Psoriasis Gives Insight into Opposing Genetic Mechanisms.
Disease/TraitPsoriasis
Initial sample4,212 European ancestry cases, 8,032 European ancestry controls
Replication sampleNA
Region5q31.1
Chromosome idchr5
Chromosome position132660272
Reported geneIL13, IL4
Mapped geneIL13
Upstream gene id
Downstream gene id
SNP gene ids3596
Upstream gene distance
Downstream gene distance
SNP risk allelers20541-A
SNPsrs20541
Merged0
SNP id current20541
Contextmissense_variant
Intergenic0
Allele frequencyNR
P value0.000005
Pvalue mlog5.30102999566398
P value text
Or beta1.1890606
%95 Ci[1.14-1.23]
PlatformAffymetrix, Illumina, Perlegen [up to 5493100] (imputed)
CNVN
Mapped traitpsoriasis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000676
Study accessionGCST002738
PubMed ID25903422
JournalNat Commun
Linkwww.ncbi.nlm.nih.gov/pubmed/25903422
StudyGenome-wide meta-analysis identifies multiple novel associations and ethnic heterogeneity of psoriasis susceptibility.
Disease/TraitPsoriasis
Initial sample3,496 European ancestry cases, 5,186 European ancestry controls, 1,588 Chinese ancestry cases, 3,546 Chinese ancestry controls
Replication sample5,134 European ancestry cases, 5,633 European ancestry controls, 5,151 Chinese ancestry cases, 5,152 Chinese ancestry controls
Region5q31.1
Chromosome idchr5
Chromosome position132660272
Reported geneIL13
Mapped geneIL13
Upstream gene id
Downstream gene id
SNP gene ids3596
Upstream gene distance
Downstream gene distance
SNP risk allelers20541-G
SNPsrs20541
Merged0
SNP id current20541
Contextmissense_variant
Intergenic0
Allele frequency0.79
P value0.000000005
Pvalue mlog8.30102999566398
P value text
Or beta1.14
%95 Ci[1.09-1.19]
PlatformIllumina [up to 4778154] (imputed)
CNVN
Mapped traitpsoriasis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000676
Study accessionGCST002874
PubMed ID26626624
JournalAm J Hum Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/26626624
StudyGenome-wide Association Analysis of Psoriatic Arthritis and Cutaneous Psoriasis Reveals Differences in Their Genetic Architecture.
Disease/TraitCutaneous psoriasis
Initial sample1,363 European ancestry cases, 4,934 European ancestry controls
Replication sampleup to 2,969 European ancestry cases, up to European ancestry 14,384 controls
Region5q31.1
Chromosome idchr5
Chromosome position132660272
Reported geneIL13
Mapped geneIL13
Upstream gene id
Downstream gene id
SNP gene ids3596
Upstream gene distance
Downstream gene distance
SNP risk allelers20541-G
SNPsrs20541
Merged0
SNP id current20541
Contextmissense_variant
Intergenic0
Allele frequencyNR
P value0.00000003
Pvalue mlog7.52287874528033
P value text
Or beta1.237
%95 CiNR
PlatformIllumina [11532644] (imputed)
CNVN
Mapped traitpsoriasis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000676
Study accessionGCST003269