rs9594759

This is a intergenic variant variant in the LINC02341 gene.

GWAS Catalog Trait Associations (1)

Genome-wide significant associations (p < 5×10⁻⁸) from the NHGRI-EBI GWAS Catalog.

bone tissue density

Styrkarsdottir U et al. Multiple genetic loci for bone mineral density and fractures. The New England Journal of Medicine 358(22):2355-65 (2008)
Allele T
OR 0.17
p 2.0e-21
N 5,861
Large GWAS
European
Styrkarsdottir U et al. New sequence variants associated with bone mineral density. Nature Genetics 41(1):15-7 (2009)
Allele T
OR 0.12
p 2.0e-17
N 6,865
Large GWAS
European

Research that mentions this SNP (4)

Polymorphisms in genes in the RANKL/RANK/OPG pathway are associated with bone mineral density at different skeletal sites in post-menopausal women
AssociationN=874Tu P. et al.(2015)· Osteoporosis International

A cross-sectional study of 881 postmenopausal Chinese women examined associations between 22 SNPs in the RANKL/RANK/OPG pathway genes (TNFSF11, TNFRSF11A, TNFRSF11B) and bone mineral density (BMD). Two TNFSF11 SNPs (rs2277439 and rs2324851; p=0.014, 0.013) and one TNFRSF11A SNP (rs7239261; p=0.047) were significantly associated with femoral neck BMD. A haplotype in TNFSF11 was a genetic risk factor for lower femoral neck BMD (beta=-0.1473; p=0.011), while another was protective for lumbar spine BMD (beta=0.3923; p=0.049).

Traits studied:Bone mineral density (BMD)Femoral neck bone mineral densityLumbar spine bone mineral density
Influence of Polymorphisms in the RANKL/RANK/OPG Signaling Pathway on Volumetric Bone Mineral Density and Bone Geometry at the Forearm in Men
AssociationN=589Delnaz Roshandel et al.(2011)· Calcified Tissue International

This association study examined 589 European men to determine whether SNPs in RANKL, RANK, and OPG genes influence volumetric bone mineral density (vBMD) and bone geometry at the radius. The authors identified 12 OPG SNPs associated with vBMD and geometric parameters (e.g., rs10505348 associated with total vBMD β=9.35, P=0.011; rs2073618 associated with cortical vBMD β=-4.30, P=0.015), three RANK SNPs associated with vBMD including rs12956925 associated with trabecular vBMD β=-7.58, P=0.021, and five RANK SNPs associated with geometric parameters including rs8083511 associated with cross-sectional area β=8.90, P=0.029. No significant associations were found with RANKL SNPs, suggesting genetic variation in OPG and RANK influences radius bone density and geometry in men.

Traits studied:Bone geometryCortical thicknessCortical vBMDCross-sectional areaMedullary areaStress strain indexTotal vBMDTrabecular vBMDVolumetric bone mineral density
Genetic variation in the RANKL/RANK/OPG signaling pathway is associated with bone turnover and bone mineral density in men
AssociationN=159Delnaz Roshandel et al.(2010)· Journal of Bone and Mineral Research

This case-control study of 159 Ukrainian individuals (144 born macrosomic, 27 normosomic) investigates genetic associations with deciduous tooth eruption timing. The study identified associations between RANKL rs9594759 (multiplicative model, increased risk of delayed eruption) and IL10 rs1800896 (overdominant model, increased risk of delayed eruption). CYP19A1 rs2414096 G allele and ESR1 rs9340799 -351 A allele were found as risk factors for fetal macrosomia formation. RANKL and IL10 variants showed multidirectional modifying effects on tooth eruption timing in macrosomic individuals.

Traits studied:Bone metabolismDeciduous tooth eruption timing (premature and delayed eruption)Fetal macrosomia
Replication study of candidate genes/loci associated with osteoporosis based on genome-wide screening
AssociationN=1,000Zhang YP et al.(2010)· Osteoporosis International

A replication study of 139 SNPs from three prior genome-wide association studies of bone mineral density in an independent sample of 1,000 unrelated US whites confirmed 38 SNPs (27% replication rate). Two SNPs achieved the most significant replication: rs3762397 in NR5A2 and rs3736228 in LRP5. Ten SNPs achieved combined p-values less than 3.6×10⁻⁴ across datasets, including rs3736228 (LRP5) with combined p=5.3×10⁻¹² for spinal BMD.

Traits studied:Bone mineral densityFemoral neck bone mineral density (FNBMD)Hip bone mineral density (HIPBMD)OsteoporosisSpinal bone mineral density (SPNBMD)

This variant is in our database but has no known associations or PRS memberships yet.

Gene information from NCBI Gene. Variant classifications from ClinVar.

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