SNP Detail For rs9788721
1.Mapping Information
Human SNP ID rs9788721
Human chromosome chr15
Human SNP position 78510527
Pig chromosome chr7
Pig SNP position 52962920
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
Region15q25.1
Chromosome idchr15
Chromosome position78510527
Reported geneAGPHD1
Mapped geneHYKK
Upstream gene id
Downstream gene id
SNP gene ids123688
Upstream gene distance
Downstream gene distance
SNP risk allelers9788721-T
SNPsrs9788721
Merged0
SNP id current9788721
Contextintron_variant
Intergenic0
Allele frequency0.62
P value0.0000000000002
Pvalue mlog12.698970004336
P value text(Severe Centrilobular)
Or beta0.007
%95 Ci[0.0050-0.0090] 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
Region15q25.1
Chromosome idchr15
Chromosome position78510527
Reported geneAGPHD1
Mapped geneHYKK
Upstream gene id
Downstream gene id
SNP gene ids123688
Upstream gene distance
Downstream gene distance
SNP risk allelers9788721-T
SNPsrs9788721
Merged0
SNP id current9788721
Contextintron_variant
Intergenic0
Allele frequency0.62
P value0.000000000001
Pvalue mlog12
P value text(Severe Centrilobular, EA)
Or beta0.007
%95 Ci[0.0050-0.0090] unit decrease
PlatformIllumina [6942916] (imputed)
CNVN
Mapped traitemphysema pattern measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0005850
Study accessionGCST002525
PubMed ID26030696
JournalAm J Respir Crit Care Med
Linkwww.ncbi.nlm.nih.gov/pubmed/26030696
StudyA Genome-wide Association Study of Emphysema and Airway Quantitative Imaging Phenotypes.
Disease/TraitEmphysema imaging phenotypes
Initial sample5,385 European ancestry chronic obstructive pulmonary disease cases, 901 African American chronic obstructive pulmonary disease cases, 3,613 European ancestry controls, 2,132 African American controls
Replication sampleNA
Region15q25.1
Chromosome idchr15
Chromosome position78510527
Reported geneAGPHD1
Mapped geneHYKK
Upstream gene id
Downstream gene id
SNP gene ids123688
Upstream gene distance
Downstream gene distance
SNP risk allelers9788721-T
SNPsrs9788721
Merged0
SNP id current9788721
Contextintron_variant
Intergenic0
Allele frequencyNR
P value0.0000006
Pvalue mlog6.22184874961635
P value text(%LAA-950, Cases)
Or beta0.1
%95 Ciunit decrease
PlatformIllumina [7600000] (imputed)
CNVN
Mapped traitemphysema imaging measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0007626
Study accessionGCST002945
PubMed ID26030696
JournalAm J Respir Crit Care Med
Linkwww.ncbi.nlm.nih.gov/pubmed/26030696
StudyA Genome-wide Association Study of Emphysema and Airway Quantitative Imaging Phenotypes.
Disease/TraitEmphysema imaging phenotypes
Initial sample5,385 European ancestry chronic obstructive pulmonary disease cases, 901 African American chronic obstructive pulmonary disease cases, 3,613 European ancestry controls, 2,132 African American controls
Replication sampleNA
Region15q25.1
Chromosome idchr15
Chromosome position78510527
Reported geneAGPHD1
Mapped geneHYKK
Upstream gene id
Downstream gene id
SNP gene ids123688
Upstream gene distance
Downstream gene distance
SNP risk allelers9788721-T
SNPsrs9788721
Merged0
SNP id current9788721
Contextintron_variant
Intergenic0
Allele frequencyNR
P value0.000001
Pvalue mlog6
P value text(Perc15, All)
Or beta1.7
%95 Ci[1.01-2.39] unit increase
PlatformIllumina [7600000] (imputed)
CNVN
Mapped traitemphysema imaging measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0007626
Study accessionGCST002945
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
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
Region15q25.1
Chromosome idchr15
Chromosome position78510527
Reported geneAGPHD1
Mapped geneHYKK
Upstream gene id
Downstream gene id
SNP gene ids123688
Upstream gene distance
Downstream gene distance
SNP risk allelers9788721-T
SNPsrs9788721
Merged0
SNP id current9788721
Contextintron_variant
Intergenic0
Allele frequency0.62
P value0.00000000000002
Pvalue mlog13.698970004336
P value text
Or beta0.068
%95 CiNR unit increase
PlatformIllumina [NR] (imputed)
CNVN
Mapped traitforced expiratory volume, response to bronchodilator
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004314, http://purl.obolibrary.org/obo/GO_0097366
Study accessionGCST003262
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 in COPD
Initial sample5,439 European ancestry current and former smoker cases, 821 African American current and former smoker cases
Replication sampleNA
Region15q25.1
Chromosome idchr15
Chromosome position78510527
Reported geneAGPHD1
Mapped geneHYKK
Upstream gene id
Downstream gene id
SNP gene ids123688
Upstream gene distance
Downstream gene distance
SNP risk allelers9788721-T
SNPsrs9788721
Merged0
SNP id current9788721
Contextintron_variant
Intergenic0
Allele frequency0.595
P value0.0000007
Pvalue mlog6.15490195998574
P value text
Or beta0.012
%95 CiNR unit increase
PlatformIllumina [NR] (imputed)
CNVN
Mapped traitresponse to bronchodilator, chronic obstructive pulmonary disease, FEV/FEC ratio
Mapped trait URIhttp://purl.obolibrary.org/obo/GO_0097366, http://www.ebi.ac.uk/efo/EFO_0000341, http://www.ebi.ac.uk/efo/EFO_0004713
Study accessionGCST003265
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
Region15q25.1
Chromosome idchr15
Chromosome position78510527
Reported geneAGPHD1
Mapped geneHYKK
Upstream gene id
Downstream gene id
SNP gene ids123688
Upstream gene distance
Downstream gene distance
SNP risk allelers9788721-T
SNPsrs9788721
Merged0
SNP id current9788721
Contextintron_variant
Intergenic0
Allele frequency0.621
P value0.00000000000002
Pvalue mlog13.698970004336
P value text
Or beta0.014
%95 Ciunit increase
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