1. Population-specific putative causal variants shape quantitative traits
- Author
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Koyama, Satoshi, Liu, Xiaoxi, Koike, Yoshinao, Hikino, Keiko, Koido, Masaru, Li, Wei, Akaki, Kotaro, Tomizuka, Kohei, Ito, Shuji, Otomo, Nao, Suetsugu, Hiroyuki, Yoshino, Soichiro, Akiyama, Masato, Saito, Kohei, Ishikawa, Yuki, Benner, Christian, Natarajan, Pradeep, Ellinor, Patrick T., Mushiroda, Taisei, Horikoshi, Momoko, Ikeda, Masashi, Iwata, Nakao, Matsuda, Koichi, Niida, Shumpei, Ozaki, Kouichi, Momozawa, Yukihide, Ikegawa, Shiro, Takeuchi, Osamu, Ito, Kaoru, and Terao, Chikashi
- Abstract
Human genetic variants are associated with many traits through largely unknown mechanisms. Here, combining approximately 260,000 Japanese study participants, a Japanese-specific genotype reference panel and statistical fine-mapping, we identified 4,423 significant loci across 63 quantitative traits, among which 601 were new, and 9,406 putatively causal variants. New associations included Japanese-specific coding, splicing and noncoding variants, exemplified by a damaging missense variant rs730881101 in TNNT2associated with lower heart function and increased risk for heart failure (P= 1.4 × 10−15and odds ratio = 4.5, 95% confidence interval = 3.1–6.5). Putative causal noncoding variants were supported by state-of-art in silico functional assays and had comparable effect sizes to coding variants. A plausible example of new mechanisms of causal variants is an enrichment of causal variants in 3′ untranslated regions (UTRs), including the Japanese-specific rs13306436 in IL6associated with pro-inflammatory traits and protection against tuberculosis. We experimentally showed that transcripts with rs13306436 are resistant to mRNA degradation by regnase-1, an RNA-binding protein. Our study provides a list of fine-mapped causal variants to be tested for functionality and underscores the importance of sequencing, genotyping and association efforts in diverse populations.
- Published
- 2024
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