SNP Detail For rs9275572
1.Mapping Information
Human SNP ID rs9275572
Human chromosome chr6
Human SNP position 32711222
Pig chromosome chr7
Pig SNP position 29228737
2.Annotation Information
PubMed ID20596022
JournalNature
Linkwww.ncbi.nlm.nih.gov/pubmed/20596022
StudyGenome-wide association study in alopecia areata implicates both innate and adaptive immunity.
Disease/TraitAlopecia areata
Initial sampleUp to 1,054 European ancestry cases, 3,278 European ancestry controls
Replication sampleNA
Region6p21.32
Chromosome idchr6
Chromosome position32711222
Reported geneHLA-DQA2
Mapped geneHLA-DQB1 - LOC102725019
Upstream gene id3119
Downstream gene id102725019
SNP gene ids
Upstream gene distance44533
Downstream gene distance6794
SNP risk allelers9275572-G
SNPsrs9275572
Merged0
SNP id current9275572
Contextupstream_gene_variant
Intergenic1
Allele frequency0.59
P value1E-35
Pvalue mlog35
P value text
Or beta2.21
%95 Ci[1.98-2.47]
PlatformIllumina [463301]
CNVN
Mapped traitalopecia areata
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004192
Study accessionGCST000719
PubMed ID21499248
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/21499248
StudyGenome-wide association study identifies a susceptibility locus for HCV-induced hepatocellular carcinoma.
Disease/TraitHepatocellular carcinoma
Initial sample721 Japanese ancestry cases, 2,890 Japanese ancestry controls
Replication sample673 Japanese ancestry cases, 2,596 Japanese ancestry controls
Region6p21.32
Chromosome idchr6
Chromosome position32711222
Reported geneHLA-DQ, HLA-DR
Mapped geneHLA-DQB1 - LOC102725019
Upstream gene id3119
Downstream gene id102725019
SNP gene ids
Upstream gene distance44533
Downstream gene distance6794
SNP risk allelers9275572-A
SNPsrs9275572
Merged0
SNP id current9275572
Contextupstream_gene_variant
Intergenic1
Allele frequency0.36
P value0.000000006
Pvalue mlog8.22184874961635
P value text
Or beta1.3
%95 Ci[1.19-1.42]
PlatformIllumina [432703]
CNVN
Mapped traithepatocellular carcinoma
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000182
Study accessionGCST001041
PubMed ID24871463
JournalGenes Immun
Linkwww.ncbi.nlm.nih.gov/pubmed/24871463
StudyGWAS identifies novel SLE susceptibility genes and explains the association of the HLA region.
Disease/TraitSystemic lupus erythematosus
Initial sample725 European ancestry cases, 2,438 European ancestry controls
Replication sampleNA
Region6p21.32
Chromosome idchr6
Chromosome position32711222
Reported geneHLA-DQA2
Mapped geneHLA-DQB1 - LOC102725019
Upstream gene id3119
Downstream gene id102725019
SNP gene ids
Upstream gene distance44533
Downstream gene distance6794
SNP risk allelers9275572-A
SNPsrs9275572
Merged0
SNP id current9275572
Contextupstream_gene_variant
Intergenic1
Allele frequency0.4
P value0.0000000000000005
Pvalue mlog15.3010299956639
P value text
Or beta1.74
%95 Ci[1.64-1.85]
PlatformIllumina [NR]
CNVN
Mapped traitrheumatoid arthritis
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000685
Study accessionGCST002463
PubMed ID24376798
JournalPLoS One
Linkwww.ncbi.nlm.nih.gov/pubmed/24376798
StudyHLA-DQB1*03 confers susceptibility to chronic hepatitis C in Japanese: a genome-wide association study.
Disease/TraitChronic hepatitis C infection
Initial sample481 Japanese ancestry cases, 2,963 Japanese ancestry controls
Replication sample5,737 Japanese ancestry cases, 26,931 Japanese ancestry controls
Region6p21.32
Chromosome idchr6
Chromosome position32711222
Reported geneHLA-DQB1, HLA-DQA1
Mapped geneHLA-DQB1 - LOC102725019
Upstream gene id3119
Downstream gene id102725019
SNP gene ids
Upstream gene distance44533
Downstream gene distance6794
SNP risk allelers9275572-T
SNPsrs9275572
Merged0
SNP id current9275572
Contextupstream_gene_variant
Intergenic1
Allele frequency0.359
P value0.0000000000000004
Pvalue mlog15.397940008672
P value text
Or beta1.27
%95 Ci[1.19-1.33]
PlatformIllumina [458207]
CNVN
Mapped traitChronic Hepatitis C infection
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004220
Study accessionGCST002316