SNP Detail For rs9466056
1.Mapping Information
Human SNP ID rs9466056
Human chromosome chr6
Human SNP position 21384382
Pig chromosome chr7
Pig SNP position 17611110
2.Annotation Information
PubMed ID21533022
JournalPLoS Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/21533022
StudyGenome-wide association study using extreme truncate selection identifies novel genes affecting bone mineral density and fracture risk.
Disease/TraitBone mineral density
Initial sample900 European ancestry female individuals with low hip bone mineral density, 1,055 European ancestry female individuals with high hip bone mineral density
Replication sample20,898 European ancestry female individuals
Region6p22.3
Chromosome idchr6
Chromosome position21384382
Reported geneSOX4
Mapped geneCDKAL1 - LINC00581
Upstream gene id54901
Downstream gene id100874531
SNP gene ids
Upstream gene distance151978
Downstream gene distance101679
SNP risk allelers9466056-G
SNPsrs9466056
Merged0
SNP id current9466056
Contextintergenic_variant
Intergenic1
Allele frequencyNR
P value0.000004
Pvalue mlog5.39794000867203
P value text(femoral neck)
Or beta0.05
%95 Ci[NR] unit increase
PlatformIllumina [2543887] (imputed)
CNVN
Mapped traitbone density
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0003923
Study accessionGCST001050
PubMed ID22504420
JournalNat Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/22504420
StudyGenome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
Disease/TraitBone mineral density
Initial sampleUp to 32,961 European and East Asian ancestry individuals
Replication sampleUp to 50,933 European and East Asian ancestry individuals
Region6p22.3
Chromosome idchr6
Chromosome position21384382
Reported geneCDKAL1
Mapped geneCDKAL1 - LINC00581
Upstream gene id54901
Downstream gene id100874531
SNP gene ids
Upstream gene distance151978
Downstream gene distance101679
SNP risk allelers9466056-A
SNPsrs9466056
Merged0
SNP id current9466056
Contextintergenic_variant
Intergenic1
Allele frequency0.38
P value0.0000000000003
Pvalue mlog12.5228787452803
P value text(FNBMD)
Or beta0.04
%95 Ci[NR] unit decrease
PlatformAffymetrix, Illumina [~ 2500000] (imputed)
CNVN
Mapped traitbone density
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0003923
Study accessionGCST001482