rs12144971 (LINC01705): Height-Associated Variant

Key takeaways

• rs12144971, in the LINC01705 region, is one of 12,111 common variants significantly linked to adult height in a genome-wide study of 5.4 million people.
• The alternate allele increases LINC01705 expression in lung tissue and tibial nerve, based on GTEx data from 953 donors.
• The same allele also increases DUSP10 expression in sun-protected skin.
• The full set of 12,111 height SNPs explains roughly 40% of height variation in European-ancestry populations and 10-20% in other ancestry groups.

What the research says

A genome-wide association study (GWAS) of 5.4 million individuals from 281 cohorts identified 12,111 independent common SNPs significantly associated with adult height, covering roughly 21% of the genome across 7,209 non-overlapping segments with a mean size of about 90 kb. rs12144971, located in the LINC01705 locus (a long intergenic non-coding RNA - a genomic region that produces RNA but encodes no protein), falls within this mapped region. GTEx v11 expression data from 953 donors show that the alternate allele is linked to increased LINC01705 expression in lung tissue (slope +0.28, p = 2.9 x 10^-9) and tibial nerve (slope +0.17, p = 8.2 x 10^-5), and increased DUSP10 (dual-specificity phosphatase 10, a cellular signaling enzyme) expression in sun-protected skin (slope +0.11, p = 1.1 x 10^-4) GTEx Portal.

Reported associations

• Adult height: rs12144971 is in the LINC01705 region and was among the 12,111 independent SNPs significantly associated with adult height in a meta-analysis of 5.4 million individuals from diverse ancestries, spanning 7,209 genomic segments covering approximately 21% of the genome.
• LINC01705 expression (lung): The alternate allele is associated with increased LINC01705 expression in lung tissue (slope +0.28, p = 2.9 x 10^-9) GTEx Portal.
• LINC01705 expression (tibial nerve): The alternate allele is associated with increased LINC01705 expression in tibial nerve (slope +0.17, p = 8.2 x 10^-5) GTEx Portal.
• DUSP10 expression (skin): The alternate allele is associated with increased DUSP10 expression in sun-protected (suprapubic) skin (slope +0.11, p = 1.1 x 10^-4) GTEx Portal.

Evidence quality

The height association comes from one of the largest GWASs conducted to date, encompassing 5.4 million individuals across five ancestry groups from 281 studies. The combined 12,111-SNP set explains approximately 40% of height variance in European-ancestry populations but only around 10-20% in non-European populations, a gap attributed to differences in linkage disequilibrium (the tendency for nearby variants to be inherited together) and allele frequency across groups. The available study text does not report an individual effect size for rs12144971, so its specific contribution to height variance cannot be quantified here. The GTEx eQTL findings for LINC01705 and DUSP10 are based on 953 donors with FDR-controlled thresholds, indicating high-confidence expression associations; however, eQTL results are correlational and do not establish causal biological mechanisms. No conflicting studies are present in the provided literature.

Tissue-specific expression effects

• LINC01705: The alternate allele is associated with increased expression in lung tissue and tibial nerve; the lung signal is the stronger of the two detected effects GTEx Portal.
• DUSP10: The alternate allele is associated with increased expression in sun-protected (suprapubic) skin; DUSP10 encodes a dual-specificity phosphatase involved in cellular signaling pathways GTEx Portal.

Lifestyle considerations

No lifestyle considerations on file for this variant.