SNP Detail For rs17728338
1.Mapping Information
Human SNP ID rs17728338
Human chromosome chr5
Human SNP position 151098757
Pig chromosome chr16
Pig SNP position 78149479
2.Annotation Information
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
Region5q33.1
Chromosome idchr5
Chromosome position151098757
Reported geneTNIP1
Mapped geneTNIP1 - ANXA6
Upstream gene id10318
Downstream gene id309
SNP gene ids
Upstream gene distance11097
Downstream gene distance1949
SNP risk allelers17728338-A
SNPsrs17728338
Merged0
SNP id current17728338
Contextdownstream_gene_variant
Intergenic1
Allele frequency0.054
P value1E-20
Pvalue mlog20
P value text
Or beta1.59
%95 Ci[NR]
PlatformPerlegen [~ 2500000] (imputed)
CNVN
Mapped traitpsoriasis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000676
Study accessionGCST000322
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/TraitInflammatory skin disease
Initial sample2,079 European ancestry atopic dermatitis cases, 4,212 European ancestry psoriasis cases, 11,899 European ancestry controls
Replication sampleNA
Region5q33.1
Chromosome idchr5
Chromosome position151098757
Reported geneANXA6, TNIP1
Mapped geneTNIP1 - ANXA6
Upstream gene id10318
Downstream gene id309
SNP gene ids
Upstream gene distance11097
Downstream gene distance1949
SNP risk allelers17728338-?
SNPsrs17728338
Merged0
SNP id current17728338
Contextdownstream_gene_variant
Intergenic1
Allele frequencyNR
P value4E-38
Pvalue mlog37.397940008672
P value text(Opposed)
Or beta
%95 Ci
PlatformAffymetrix, Illumina [~ 5200000]
CNVN
Mapped traitatopic eczema, psoriasis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000274, http://www.ebi.ac.uk/efo/EFO_0000676
Study accessionGCST002740
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
Region5q33.1
Chromosome idchr5
Chromosome position151098757
Reported geneTNIP1, ANXA6
Mapped geneTNIP1 - ANXA6
Upstream gene id10318
Downstream gene id309
SNP gene ids
Upstream gene distance11097
Downstream gene distance1949
SNP risk allelers17728338-A
SNPsrs17728338
Merged0
SNP id current17728338
Contextdownstream_gene_variant
Intergenic1
Allele frequency0.054
P value0.00000000000004
Pvalue mlog13.397940008672
P value text(EA)
Or beta1.64
%95 Ci[1.44-1.86]
PlatformIllumina [up to 4778154] (imputed)
CNVN
Mapped traitpsoriasis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000676
Study accessionGCST002874
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
Region5q33.1
Chromosome idchr5
Chromosome position151098757
Reported geneTNIP1, ANXA6
Mapped geneTNIP1 - ANXA6
Upstream gene id10318
Downstream gene id309
SNP gene ids
Upstream gene distance11097
Downstream gene distance1949
SNP risk allelers17728338-A
SNPsrs17728338
Merged0
SNP id current17728338
Contextdownstream_gene_variant
Intergenic1
Allele frequency0.10115
P value0.0000003
Pvalue mlog6.52287874528033
P value text(Chinese)
Or beta1.54
%95 Ci[1.31-1.82]
PlatformIllumina [up to 4778154] (imputed)
CNVN
Mapped traitpsoriasis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000676
Study accessionGCST002874
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
Region5q33.1
Chromosome idchr5
Chromosome position151098757
Reported geneTNIP, ANXA6
Mapped geneTNIP1 - ANXA6
Upstream gene id10318
Downstream gene id309
SNP gene ids
Upstream gene distance11097
Downstream gene distance1949
SNP risk allelers17728338-A
SNPsrs17728338
Merged0
SNP id current17728338
Contextdownstream_gene_variant
Intergenic1
Allele frequency0.054
P value6E-20
Pvalue mlog19.2218487496163
P value text
Or beta1.6
%95 Ci[1.45-1.77]
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
Region5q33.1
Chromosome idchr5
Chromosome position151098757
Reported geneTNIP1
Mapped geneTNIP1 - ANXA6
Upstream gene id10318
Downstream gene id309
SNP gene ids
Upstream gene distance11097
Downstream gene distance1949
SNP risk allelers17728338-A
SNPsrs17728338
Merged0
SNP id current17728338
Contextdownstream_gene_variant
Intergenic1
Allele frequencyNR
P value0.00000000000002
Pvalue mlog13.698970004336
P value text
Or beta1.557
%95 CiNR
PlatformIllumina [11532644] (imputed)
CNVN
Mapped traitpsoriasis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000676
Study accessionGCST003269