rs12432901 (LINC02306): Height-Associated Variant

Key takeaways

• rs12432901 is one of 12,111 genetic variants linked to adult height in a study of 5.4 million people
• These height variants together explain about 40-45% of height differences in people of European ancestry
• The same variants explain only 10-24% of height variation in non-European populations
• The genetic height map is now considered nearly complete for European-ancestry populations
• The locus sits within a region containing LINC02306, a long intergenic non-coding RNA gene

What the research says A genome-wide association study (GWAS - a method that scans hundreds of thousands of genetic positions across many people to find variants linked to a trait) of 5.4 million individuals of diverse ancestries identified 12,111 independent SNPs (single-nucleotide polymorphisms, single-letter differences in DNA) significantly associated with adult height, with rs12432901 at the LINC02306 locus among the variants documented in this map. These variants cluster within 7,209 non-overlapping genomic regions averaging roughly 90 kilobases (approximately 90,000 DNA letters) each, covering about 21% of the human genome. The 12,111 SNPs account for approximately 40% of height phenotypic variance in European-ancestry populations (rising to 45% when all variants in the HapMap 3 reference panel are included), but only about 10-20% in populations of other ancestries - a gap the authors attribute to differences in linkage disequilibrium (the tendency for nearby genetic variants to be inherited together) and allele frequencies across populations, rather than to different underlying biology.

Reported associations

• Adult height: rs12432901 at the LINC02306 locus is among 12,111 genome-wide significant SNPs associated with adult height in a discovery sample of approximately 5.4 million individuals; together these variants account for about 40-45% of height variance in European-ancestry populations and roughly 10-24% in other ancestries

Evidence quality Evidence for this locus derives from a large-scale GWAS conducted on approximately 5.4 million individuals pooled across 281 studies, spanning five broad ancestry groups: predominantly European (about 4.1 million, 75.8%), East Asian (about 473,000, 8.8%), Hispanic and admixed (about 455,000, 8.5%), predominantly African (about 294,000, 5.5%), and South Asian (about 78,000, 1.4%). The study identified 12,111 genome-wide significant height variants in total; no individual p-value or per-SNP effect size for rs12432901 specifically is available in the provided study summary. The authors characterize the common-variant map for height as near-saturated for European-ancestry populations, meaning essentially all common height-associated signals detectable by GWAS have likely been identified in that group. The authors also note that higher prediction accuracy in non-European populations will require further research, and that identification of specific causal genes and variants within associated regions remains ongoing. No conflicting findings regarding rs12432901 specifically are reported in the provided study material.

Lifestyle considerations No lifestyle considerations on file for this variant.