rs11249209 (RUNX3): Height-Associated Variant

Key takeaways

• rs11249209 sits near the RUNX3-AS1 and RUNX3 genes and has been identified as one of thousands of common variants associated with adult height
• The association derives from a genome-wide study of more than 5.4 million people spanning five ancestry groups - one of the largest genetic studies ever conducted for any human trait
• All 12,111 height-associated variants identified in this study together explain about 40% of height variation among people of European ancestry
• Effect sizes for this class of height variant are broadly similar across ancestries, but prediction accuracy is notably lower outside European populations

What the research says A genome-wide association study (a large-scale scan linking genetic variants to a measured trait) of 5,380,080 individuals from 281 studies identified 12,111 independent SNPs (single-nucleotide polymorphisms, or single-letter changes in the DNA code) significantly associated with adult height, with rs11249209 in the RUNX3-AS1 and RUNX3 region among them. These variants are distributed across 7,209 genomic segments covering about 21% of the human genome, and together account for approximately 40% of phenotypic variance in height in populations of European ancestry (roughly 45% when including all variants in the HapMap 3 reference panel). Prediction accuracy falls to about 10-20% in non-European ancestry populations, a gap attributed to differences in linkage disequilibrium (the tendency of nearby genetic variants to be inherited together) and allele frequency rather than differences in the underlying biology of height.

Reported associations

• Adult height: rs11249209 is one of 12,111 independent variants significantly associated with adult height in a genome-wide study of 5,380,080 individuals of diverse ancestries; a specific per-variant effect size for rs11249209 is not reported in the available study excerpt

Evidence quality The height association is based on a very large meta-analysis of 5,380,080 individuals across 281 studies, including participants of European (75.8%), East Asian (8.8%), Hispanic admixed (8.5%), African American admixed (5.5%), and South Asian (1.4%) ancestries. The study describes its findings as a saturated map, meaning that common variant associations with height are considered comprehensively catalogued for European-ancestry populations. Effect sizes and the identity of associated genomic regions are reported to be broadly consistent across ancestry groups. No conflicting findings for this variant are described in the available text. Specific p-values and per-variant effect sizes for rs11249209 are not available in the provided study excerpt, which limits granularity at the individual variant level.

Lifestyle considerations No lifestyle considerations on file for this variant.