rs10783298 (WNT1): Height-Associated Genetic Variant
Key takeaways
- rs10783298 is one of 12,111 common SNPs linked to height variation in a genome-wide study of 5.4 million people
- These height-associated variants together explain about 40% of height variation in European ancestry populations
- Height prediction accuracy drops to roughly 10-20% in non-European ancestry populations
- The ALT allele reduces BCDIN3D gene expression in colon and esophageal tissue and increases ARF3 expression in whole blood
Key takeaways
- rs10783298 is one of 12,111 common SNPs linked to height variation in a genome-wide study of 5.4 million people
- These height-associated variants together explain about 40% of height variation in European ancestry populations
- Height prediction accuracy drops to roughly 10-20% in non-European ancestry populations
- The ALT allele reduces BCDIN3D gene expression in colon and esophageal tissue and increases ARF3 expression in whole blood
What the research says rs10783298, near the WNT1 (Wingless Integration Site 1) and DDN (Dendrin) genes, is one of 12,111 independent genome-wide significant SNPs (single-nucleotide polymorphisms, meaning single-letter DNA changes) associated with adult height in a genome-wide association study of up to 5,380,080 individuals drawn from 281 studies in the GIANT consortium and 23andMe. Together, these height-associated variants, clustered across 7,209 non-overlapping genomic segments covering roughly 21% of the genome, account for approximately 40% of height phenotypic variance in European ancestry populations and roughly 10-20% in other ancestry groups. Tissue gene-expression data from GTEx v11 shows the ALT allele at this locus is associated with reduced expression of BCDIN3D in colon sigmoid and esophagus muscularis tissue, and with increased expression of ARF3 (ADP Ribosylation Factor 3) in whole blood GTEx Portal.
Reported associations
- Adult height: rs10783298 is among 12,111 genome-wide significant SNPs linked to adult height in a study of up to 5.38 million people spanning five ancestry groups; the full set of variants accounts for approximately 40% of height variance in European ancestry populations and roughly 10-20% in other ancestries
- BCDIN3D expression - colon sigmoid: The ALT allele is associated with reduced BCDIN3D gene expression in colon sigmoid tissue (log2-expression slope: -0.26, p=9.9e-5) GTEx Portal
- BCDIN3D expression - esophagus muscularis: The ALT allele is associated with reduced BCDIN3D expression in esophagus muscularis tissue (log2-expression slope: -0.21, p=1.1e-4) GTEx Portal
- ARF3 expression - whole blood: The ALT allele is associated with increased ARF3 expression in whole blood (log2-expression slope: +0.11, p=1.8e-6) GTEx Portal
Evidence quality The height association comes from a large-scale meta-analysis of up to 5,380,080 individuals from 281 studies, predominantly of European ancestry (75.8%), with East Asian (8.8%), Hispanic/admixed (8.5%), African (5.5%), and South Asian (1.4%) participants also represented. The study identifies 12,111 height-associated SNPs at genome-wide significance that together account for nearly all common SNP-based heritability of adult height; the specific per-variant effect size for rs10783298 on height is not isolated in the provided text. Effect sizes and associated regions were broadly consistent across ancestries, but prediction accuracy in non-European populations is substantially reduced, which the study attributes to differences in linkage disequilibrium (the tendency of nearby DNA variants to be inherited together) and allele frequencies. The tissue-expression associations from GTEx v11 are based on 953 donors and pass an FDR threshold below 0.05, providing robust expression-level evidence; however, eQTL associations (relationships between a DNA variant and nearby gene expression levels) reflect changes in gene activity rather than direct clinical outcomes.
Tissue-specific expression effects
- BCDIN3D: The ALT allele is associated with reduced expression in colon sigmoid and esophagus muscularis tissue GTEx Portal
- ARF3: The ALT allele is associated with increased expression in whole blood GTEx Portal
Lifestyle considerations No lifestyle considerations on file for this variant.
Frequently asked questions
What is rs10783298?
rs10783298 is a common genetic variant near the WNT1 and DDN genes. It was identified as one of 12,111 variants significantly linked to differences in adult human height in one of the largest genetic studies ever conducted, involving 5.4 million people.
Is rs10783298 associated with height?
Yes. It is among 12,111 common SNPs found to be genome-wide significantly associated with adult height in a study of up to 5.4 million people across five ancestry groups.
What genes does the rs10783298 variant affect?
Tissue expression data shows the ALT allele is associated with reduced expression of BCDIN3D in colon and esophageal tissue, and increased expression of ARF3 in whole blood. The variant sits near the WNT1 and DDN genes.
How reliable are the rs10783298 findings?
The height association is based on one of the largest genetic studies ever conducted, involving 5.4 million people across diverse ancestries. The gene expression effects from GTEx v11 are drawn from 953 donors at FDR below 0.05. The individual effect size for this specific variant on height is not separately reported.
Do rs10783298 findings apply equally across ancestry groups?
Height prediction accuracy from these variants is substantially lower in non-European ancestry populations, explaining roughly 10-20% of variation compared to about 40% in European ancestry groups. The study attributes this gap to differences in linkage disequilibrium and allele frequencies across populations.