SNP Detail For rs1690789
1.Mapping Information
Human SNP ID rs1690789
Human chromosome chr1
Human SNP position 218524685
Pig chromosome chr10
Pig SNP position 10490972
2.Annotation Information
PubMed ID25006744
JournalAm J Respir Crit Care Med
Linkwww.ncbi.nlm.nih.gov/pubmed/25006744
StudyGenome-Wide Association Identifies Regulatory Loci Associated with Distinct Local Histogram Emphysema Patterns.
Disease/TraitLocal histogram emphysema pattern
Initial sample3,732 European ancestry smoker individuals, 2,724 European ancestry chronic obstructive pulmonary disease smoker cases, 2,372 African American smoker individuals, 786 African American chronic obstructive pulmonary disease smoker cases
Replication sampleNA
Region1q41
Chromosome idchr1
Chromosome position218524685
Reported geneTGFB2
Mapped geneTGFB2 - LOC105372924
Upstream gene id7042
Downstream gene id105372924
SNP gene ids
Upstream gene distance80066
Downstream gene distance173879
SNP risk allelers1690789-C
SNPsrs1690789
Merged0
SNP id current1690789
Contextintron_variant
Intergenic1
Allele frequency0.51
P value0.00000003
Pvalue mlog7.52287874528033
P value text(normal)
Or beta0.03
%95 Ci[0.022-0.038] unit increase
PlatformIllumina [6942916] (imputed)
CNVN
Mapped traitemphysema pattern measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0005850
Study accessionGCST002525
PubMed ID25006744
JournalAm J Respir Crit Care Med
Linkwww.ncbi.nlm.nih.gov/pubmed/25006744
StudyGenome-Wide Association Identifies Regulatory Loci Associated with Distinct Local Histogram Emphysema Patterns.
Disease/TraitLocal histogram emphysema pattern
Initial sample3,732 European ancestry smoker individuals, 2,724 European ancestry chronic obstructive pulmonary disease smoker cases, 2,372 African American smoker individuals, 786 African American chronic obstructive pulmonary disease smoker cases
Replication sampleNA
Region1q41
Chromosome idchr1
Chromosome position218524685
Reported geneTGFB2
Mapped geneTGFB2 - LOC105372924
Upstream gene id7042
Downstream gene id105372924
SNP gene ids
Upstream gene distance80066
Downstream gene distance173879
SNP risk allelers1690789-C
SNPsrs1690789
Merged0
SNP id current1690789
Contextintron_variant
Intergenic1
Allele frequency0.51
P value0.000000008
Pvalue mlog8.09691001300805
P value text(Moderate Centrilobular)
Or beta0.02
%95 Ci[0.016-0.024] unit decrease
PlatformIllumina [6942916] (imputed)
CNVN
Mapped traitemphysema pattern measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0005850
Study accessionGCST002525
PubMed ID25006744
JournalAm J Respir Crit Care Med
Linkwww.ncbi.nlm.nih.gov/pubmed/25006744
StudyGenome-Wide Association Identifies Regulatory Loci Associated with Distinct Local Histogram Emphysema Patterns.
Disease/TraitLocal histogram emphysema pattern
Initial sample3,732 European ancestry smoker individuals, 2,724 European ancestry chronic obstructive pulmonary disease smoker cases, 2,372 African American smoker individuals, 786 African American chronic obstructive pulmonary disease smoker cases
Replication sampleNA
Region1q41
Chromosome idchr1
Chromosome position218524685
Reported geneTGFB2
Mapped geneTGFB2 - LOC105372924
Upstream gene id7042
Downstream gene id105372924
SNP gene ids
Upstream gene distance80066
Downstream gene distance173879
SNP risk allelers1690789-C
SNPsrs1690789
Merged0
SNP id current1690789
Contextintron_variant
Intergenic1
Allele frequency0.51
P value0.000000007
Pvalue mlog8.15490195998574
P value text(normal, EA)
Or beta0.03
%95 Ci[0.022-0.038] unit increase
PlatformIllumina [6942916] (imputed)
CNVN
Mapped traitemphysema pattern measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0005850
Study accessionGCST002525
PubMed ID25006744
JournalAm J Respir Crit Care Med
Linkwww.ncbi.nlm.nih.gov/pubmed/25006744
StudyGenome-Wide Association Identifies Regulatory Loci Associated with Distinct Local Histogram Emphysema Patterns.
Disease/TraitLocal histogram emphysema pattern
Initial sample3,732 European ancestry smoker individuals, 2,724 European ancestry chronic obstructive pulmonary disease smoker cases, 2,372 African American smoker individuals, 786 African American chronic obstructive pulmonary disease smoker cases
Replication sampleNA
Region1q41
Chromosome idchr1
Chromosome position218524685
Reported geneTGFB2
Mapped geneTGFB2 - LOC105372924
Upstream gene id7042
Downstream gene id105372924
SNP gene ids
Upstream gene distance80066
Downstream gene distance173879
SNP risk allelers1690789-C
SNPsrs1690789
Merged0
SNP id current1690789
Contextintron_variant
Intergenic1
Allele frequency0.51
P value0.000000003
Pvalue mlog8.52287874528033
P value text(Moderate Centrilobular, EA)
Or beta0.02
%95 Ci[0.016-0.024] unit decrease
PlatformIllumina [6942916] (imputed)
CNVN
Mapped traitemphysema pattern measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0005850
Study accessionGCST002525
PubMed ID26634245
JournalBMC Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/26634245
StudyA genome-wide association study identifies risk loci for spirometric measures among smokers of European and African ancestry.
Disease/TraitPost bronchodilator FEV1/FVC ratio
Initial sample10,094 European ancestry current and former smoker individuals, 3,260 African American current and former smoker individuals, 178 current and former smoker individuals
Replication sampleNA
Region1q41
Chromosome idchr1
Chromosome position218524685
Reported geneIntergenic
Mapped geneTGFB2 - LOC105372924
Upstream gene id7042
Downstream gene id105372924
SNP gene ids
Upstream gene distance80066
Downstream gene distance173879
SNP risk allelers1690789-T
SNPsrs1690789
Merged0
SNP id current1690789
Contextintron_variant
Intergenic1
Allele frequency0.455
P value0.00000008
Pvalue mlog7.09691001300805
P value text
Or beta0.01
%95 Ciunit decrease
PlatformIllumina [NR] (imputed)
CNVN
Mapped traitresponse to bronchodilator, FEV/FEC ratio
Mapped trait URIhttp://purl.obolibrary.org/obo/GO_0097366, http://www.ebi.ac.uk/efo/EFO_0004713
Study accessionGCST003264