Characterizing rare and low-frequency height-associated variants in the Japanese population

Nat Commun. 2019 Sep 27;10(1):4393. doi: 10.1038/s41467-019-12276-5.


Human height is a representative phenotype to elucidate genetic architecture. However, the majority of large studies have been performed in European population. To investigate the rare and low-frequency variants associated with height, we construct a reference panel (N = 3,541) for genotype imputation by integrating the whole-genome sequence data from 1,037 Japanese with that of the 1000 Genomes Project, and perform a genome-wide association study in 191,787 Japanese. We report 573 height-associated variants, including 22 rare and 42 low-frequency variants. These 64 variants explain 1.7% of the phenotypic variance. Furthermore, a gene-based analysis identifies two genes with multiple height-increasing rare and low-frequency nonsynonymous variants (SLC27A3 and CYP26B1; PSKAT-O < 2.5 × 10-6). Our analysis shows a general tendency of the effect sizes of rare variants towards increasing height, which is contrary to findings among Europeans, suggesting that height-associated rare variants are under different selection pressure in Japanese and European populations.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Asian People / genetics
  • Body Height / genetics*
  • Fatty Acid Transport Proteins / genetics
  • Female
  • Gene Frequency
  • Genetic Variation*
  • Genome-Wide Association Study / methods*
  • Genotype
  • Humans
  • Japan
  • Male
  • Phenotype
  • Polymorphism, Single Nucleotide
  • Quantitative Trait Loci / genetics*
  • Retinoic Acid 4-Hydroxylase / genetics


  • Fatty Acid Transport Proteins
  • SLC27A4 protein, human
  • Retinoic Acid 4-Hydroxylase