rs3801387

This variant is located in the WNT16 gene.

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GWAS Catalog Trait Associations (2)

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

heart shape trait

Burns R et al. “Genetic basis of right and left ventricular heart shape.” Nature Communications 15(1):9437 (2024)
Allele A
OR 0.05
p 5.0e-13
N 35,055
Large GWAS
European

bone tissue density

Estrada K et al. “Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.” Nature Genetics 44(5):491-501 (2012)
Allele A
OR —
β 0.090
p 3.0e-51
N 32,961
Meta-analysisLarge GWAS
multi-ancestry
Medina-Gomez C et al. “Life-Course Genome-wide Association Study Meta-analysis of Total Body BMD and Assessment of Age-Specific Effects.” American Journal of Human Genetics 102(1):88-102 (2018)
Allele A
OR 0.14
p 3.0e-30
N 18,805
Meta-analysisLarge GWAS
European
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Research that mentions this SNP (1)

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Meta-analysis of genome-wide studies identifies WNT16 and ESR1 SNPs associated with bone mineral density in premenopausal women
Meta-analysisN=9,658Koller DL et al.(2013)· Journal of Bone and Mineral Research

Meta-analysis of GWAS in 4,061 premenopausal women (ages 20-45) identified two genes associated with bone mineral density at the lumbar spine and femoral neck. WNT16 SNP rs3801387 showed the strongest association (joint p=1.3×10^-11, beta=-0.115) and ESR1/C6orf97 SNPs including rs4870044 (joint p=1.4×10^-10) and rs6930633 (joint p=1.16×10^-8) achieved genome-wide significance. Results were replicated in 5,597 additional premenopausal women from diverse ancestries, confirming that genetic variants in bone formation genes similarly affect peak bone mass during the premenopausal period.

Traits studied:Bone mineral densityFemoral neck BMDLumbar spine BMDOsteoporosisPeak bone mass
PubMedDOIMetascience Observatory

About WNT16

The WNT gene family consists of structurally related genes which encode secreted signaling proteins. These proteins have been implicated in oncogenesis and in several developmental processes, including regulation of cell fate and patterning during embryogenesis. This gene is a member of the WNT gene family. It contains two transcript variants diverging at the 5' termini. These two variants are proposed to be the products of separate promoters and not to be splice variants from a single promoter. They are differentially expressed in normal tissues, one of which (variant 2) is expressed at significant levels only in the pancreas, whereas another one (variant 1) is expressed more ubiquitously with highest levels in adult kidney, placenta, brain, heart, and spleen. [provided by RefSeq, Jul 2008]

View all WNT16 variants →

Gene information from NCBI Gene. Variant classifications from ClinVar.

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