SNP Detail For rs754388
1.Mapping Information
Human SNP ID rs754388
Human chromosome chr14
Human SNP position 92649065
Pig chromosome chr7
Pig SNP position 120740666
2.Annotation Information
PubMed ID24945404
JournalPLoS Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/24945404
StudyPhenotypic dissection of bone mineral density reveals skeletal site specificity and facilitates the identification of novel loci in the genetic regulation of bone mass attainment.
Disease/TraitBone mineral density (paediatric, total body less head)
Initial sample8,007 European ancestry children, 289 Surinamese ancestry children, 300 Turkish ancestry children, 232 Moroccan ancestry children, 588 children
Replication sampleNA
Region14q32.12
Chromosome idchr14
Chromosome position92649065
Reported geneRIN3
Mapped geneRIN3
Upstream gene id
Downstream gene id
SNP gene ids79890
Upstream gene distance
Downstream gene distance
SNP risk allelers754388-C
SNPsrs754388
Merged0
SNP id current754388
Contextintron_variant
Intergenic0
Allele frequency0.82
P value0.000000003
Pvalue mlog8.52287874528033
P value text
Or beta0.12
%95 Ci[0.081-0.159] unit increase
PlatformIllumina [~ 2500000] (imputed)
CNVN
Mapped traitbone density
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0003923
Study accessionGCST002494
PubMed ID24945404
JournalPLoS Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/24945404
StudyPhenotypic dissection of bone mineral density reveals skeletal site specificity and facilitates the identification of novel loci in the genetic regulation of bone mass attainment.
Disease/TraitBone mineral density (paediatric, total body less head)
Initial sample8,007 European ancestry children, 289 Surinamese ancestry children, 300 Turkish ancestry children, 232 Moroccan ancestry children, 588 children
Replication sampleNA
Region14q32.12
Chromosome idchr14
Chromosome position92649065
Reported geneRIN3
Mapped geneRIN3
Upstream gene id
Downstream gene id
SNP gene ids79890
Upstream gene distance
Downstream gene distance
SNP risk allelers754388-C
SNPsrs754388
Merged0
SNP id current754388
Contextintron_variant
Intergenic0
Allele frequencyNR
P value0.00000005
Pvalue mlog7.30102999566398
P value text(EA)
Or beta0.1219
%95 Ci[0.078-0.166] unit increase
PlatformIllumina [~ 2500000] (imputed)
CNVN
Mapped traitbone density
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0003923
Study accessionGCST002494
PubMed ID24945404
JournalPLoS Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/24945404
StudyPhenotypic dissection of bone mineral density reveals skeletal site specificity and facilitates the identification of novel loci in the genetic regulation of bone mass attainment.
Disease/TraitBone mineral density (paediatric, lower limb)
Initial sample8,007 European ancestry children, 289 Surinamese ancestry children, 300 Turkish ancestry children, 232 Moroccan ancestry children, 588 children
Replication sampleNA
Region14q32.12
Chromosome idchr14
Chromosome position92649065
Reported geneRIN3
Mapped geneRIN3
Upstream gene id
Downstream gene id
SNP gene ids79890
Upstream gene distance
Downstream gene distance
SNP risk allelers754388-C
SNPsrs754388
Merged0
SNP id current754388
Contextintron_variant
Intergenic0
Allele frequency0.82
P value0.0000000001
Pvalue mlog10
P value text
Or beta0.13
%95 Ci[0.091-0.169] unit increase
PlatformIllumina [~ 2500000] (imputed)
CNVN
Mapped traitbone density
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0003923
Study accessionGCST002492
PubMed ID24945404
JournalPLoS Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/24945404
StudyPhenotypic dissection of bone mineral density reveals skeletal site specificity and facilitates the identification of novel loci in the genetic regulation of bone mass attainment.
Disease/TraitBone mineral density (paediatric, lower limb)
Initial sample8,007 European ancestry children, 289 Surinamese ancestry children, 300 Turkish ancestry children, 232 Moroccan ancestry children, 588 children
Replication sampleNA
Region14q32.12
Chromosome idchr14
Chromosome position92649065
Reported geneRIN3
Mapped geneRIN3
Upstream gene id
Downstream gene id
SNP gene ids79890
Upstream gene distance
Downstream gene distance
SNP risk allelers754388-C
SNPsrs754388
Merged0
SNP id current754388
Contextintron_variant
Intergenic0
Allele frequencyNR
P value0.000000002
Pvalue mlog8.69897000433601
P value text(EA)
Or beta0.1351
%95 Ci[0.091-0.179] unit increase
PlatformIllumina [~ 2500000] (imputed)
CNVN
Mapped traitbone density
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0003923
Study accessionGCST002492
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
Region14q32.12
Chromosome idchr14
Chromosome position92649065
Reported geneRIN3
Mapped geneRIN3
Upstream gene id
Downstream gene id
SNP gene ids79890
Upstream gene distance
Downstream gene distance
SNP risk allelers754388-C
SNPsrs754388
Merged0
SNP id current754388
Contextintron_variant
Intergenic0
Allele frequency
P value0.0000002
Pvalue mlog6.69897000433601
P value text(Moderate Centrilobular)
Or beta
%95 Ci
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
Region14q32.12
Chromosome idchr14
Chromosome position92649065
Reported geneRIN3
Mapped geneRIN3
Upstream gene id
Downstream gene id
SNP gene ids79890
Upstream gene distance
Downstream gene distance
SNP risk allelers754388-C
SNPsrs754388
Merged0
SNP id current754388
Contextintron_variant
Intergenic0
Allele frequency
P value0.0000003
Pvalue mlog6.52287874528033
P value text(Severe Centrilobular)
Or beta
%95 Ci
PlatformIllumina [6942916] (imputed)
CNVN
Mapped traitemphysema pattern measurement
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0005850
Study accessionGCST002525
PubMed ID24621683
JournalLancet Respir Med
Linkwww.ncbi.nlm.nih.gov/pubmed/24621683
StudyRisk loci for chronic obstructive pulmonary disease: a genome-wide association study and meta-analysis.
Disease/TraitChronic obstructive pulmonary disease (severe)
Initial sample3,145 European ancestry cases, 3,955 European ancestry controls, 352 African American cases, 1,749 African American controls
Replication sample2,651 cases and their relatives
Region14q32.12
Chromosome idchr14
Chromosome position92649065
Reported geneRIN3
Mapped geneRIN3
Upstream gene id
Downstream gene id
SNP gene ids79890
Upstream gene distance
Downstream gene distance
SNP risk allelers754388-C
SNPsrs754388
Merged0
SNP id current754388
Contextintron_variant
Intergenic0
Allele frequency0.83
P value0.00000007
Pvalue mlog7.15490195998574
P value text
Or beta
%95 Ci
PlatformIllumina [up to 701491] (imputed)
CNVN
Mapped traitchronic obstructive pulmonary disease
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000341
Study accessionGCST002350
PubMed ID24621683
JournalLancet Respir Med
Linkwww.ncbi.nlm.nih.gov/pubmed/24621683
StudyRisk loci for chronic obstructive pulmonary disease: a genome-wide association study and meta-analysis.
Disease/TraitChronic obstructive pulmonary disease (moderate to severe)
Initial sample5,812 European ancestry cases, 3,955 European ancestry controls, 821 African American cases, 1,749 African American controls
Replication sample2,651 cases and their relatives
Region14q32.12
Chromosome idchr14
Chromosome position92649065
Reported geneRIN3
Mapped geneRIN3
Upstream gene id
Downstream gene id
SNP gene ids79890
Upstream gene distance
Downstream gene distance
SNP risk allelers754388-C
SNPsrs754388
Merged0
SNP id current754388
Contextintron_variant
Intergenic0
Allele frequency0.83
P value0.000000005
Pvalue mlog8.30102999566398
P value text
Or beta
%95 Ci
PlatformIllumina [up to 701491] (imputed)
CNVN
Mapped traitchronic obstructive pulmonary disease
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000341
Study accessionGCST002351
PubMed ID25101718
JournalAm J Respir Cell Mol Biol
Linkwww.ncbi.nlm.nih.gov/pubmed/25101718
StudyIREB2 and GALC are Associated with Pulmonary Artery Enlargement in Chronic Obstructive Pulmonary Disease.
Disease/TraitChronic obstructive pulmonary disease
Initial sample3,281 European ancestry cases, 494 African American cases, 2,712 European ancestry smoker controls, 1,749 African American smoker controls
Replication sampleNA
Region14q32.12
Chromosome idchr14
Chromosome position92649065
Reported geneRIN3
Mapped geneRIN3
Upstream gene id
Downstream gene id
SNP gene ids79890
Upstream gene distance
Downstream gene distance
SNP risk allelers754388-C
SNPsrs754388
Merged0
SNP id current754388
Contextintron_variant
Intergenic0
Allele frequencyNR
P value0.000001
Pvalue mlog6
P value text
Or beta1.29
%95 Ci[NR]
PlatformIllumina [NR] (imputed)
CNVN
Mapped traitchronic obstructive pulmonary disease
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0000341
Study accessionGCST002795
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
Region14q32.12
Chromosome idchr14
Chromosome position92649065
Reported geneRIN3
Mapped geneRIN3
Upstream gene id
Downstream gene id
SNP gene ids79890
Upstream gene distance
Downstream gene distance
SNP risk allelers754388-C
SNPsrs754388
Merged0
SNP id current754388
Contextintron_variant
Intergenic0
Allele frequency0.829
P value0.000000006
Pvalue mlog8.22184874961635
P value text
Or beta0.014
%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