SNP Detail For rs9525638
1.Mapping Information
Human SNP ID rs9525638
Human chromosome chr13
Human SNP position 42554441
Pig chromosome chr11
Pig SNP position 25168466
2.Annotation Information
PubMed ID22792071
JournalPLoS Genet
Linkwww.ncbi.nlm.nih.gov/pubmed/22792071
StudyWNT16 influences bone mineral density, cortical bone thickness, bone strength, and osteoporotic fracture risk.
Disease/TraitCortical thickness
Initial sample5,878 European ancestry individuals
Replication sample1,032 European ancestry individuals
Region13q14.11
Chromosome idchr13
Chromosome position42554441
Reported geneTNFSF11, RANKL
Mapped geneLOC105370177 - TNFSF11
Upstream gene id105370177
Downstream gene id8600
SNP gene ids
Upstream gene distance68485
Downstream gene distance8295
SNP risk allelers9525638-T
SNPsrs9525638
Merged0
SNP id current9525638
Contextintergenic_variant
Intergenic1
Allele frequencyNR
P value0.000000004
Pvalue mlog8.39794000867203
P value text
Or beta0.09
%95 Ci[0.051-0.129] mm decrease
PlatformAffymetrix, Illumina [~ 2500000] (imputed)
CNVN
Mapped traitcortical thickness
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0004840
Study accessionGCST001593
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, upper limb)
Initial sample8,007 European ancestry children, 289 Surinamese ancestry children, 300 Turkish ancestry children, 232 Moroccan ancestry children, 588 children
Replication sampleNA
Region13q14.11
Chromosome idchr13
Chromosome position42554441
Reported geneTNFSF11
Mapped geneLOC105370177 - TNFSF11
Upstream gene id105370177
Downstream gene id8600
SNP gene ids
Upstream gene distance68485
Downstream gene distance8295
SNP risk allelers9525638-C
SNPsrs9525638
Merged0
SNP id current9525638
Contextintergenic_variant
Intergenic1
Allele frequency0.42
P value0.000000003
Pvalue mlog8.52287874528033
P value text
Or beta0.089
%95 Ci[0.060-0.118] unit increase
PlatformIllumina [~ 2500000] (imputed)
CNVN
Mapped traitbone density
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0003923
Study accessionGCST002496
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, upper limb)
Initial sample8,007 European ancestry children, 289 Surinamese ancestry children, 300 Turkish ancestry children, 232 Moroccan ancestry children, 588 children
Replication sampleNA
Region13q14.11
Chromosome idchr13
Chromosome position42554441
Reported geneTNFSF11
Mapped geneLOC105370177 - TNFSF11
Upstream gene id105370177
Downstream gene id8600
SNP gene ids
Upstream gene distance68485
Downstream gene distance8295
SNP risk allelers9525638-C
SNPsrs9525638
Merged0
SNP id current9525638
Contextintergenic_variant
Intergenic1
Allele frequencyNR
P value0.00000002
Pvalue mlog7.69897000433601
P value text(EA)
Or beta0.0949
%95 Ci[0.062-0.128] unit increase
PlatformIllumina [~ 2500000] (imputed)
CNVN
Mapped traitbone density
Mapped trait URIhttp://www.ebi.ac.uk/efo/EFO_0003923
Study accessionGCST002496