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

Author

Listed:
  • Masato Akiyama

    (RIKEN Center for Integrative Medical Sciences
    Kyushu University
    RIKEN Center for Integrative Medical Sciences)

  • Kazuyoshi Ishigaki

    (RIKEN Center for Integrative Medical Sciences)

  • Saori Sakaue

    (RIKEN Center for Integrative Medical Sciences
    The University of Tokyo)

  • Yukihide Momozawa

    (RIKEN Center for Integrative Medical Sciences)

  • Momoko Horikoshi

    (RIKEN Center for Integrative Medical Sciences)

  • Makoto Hirata

    (The University of Tokyo)

  • Koichi Matsuda

    (The University of Tokyo)

  • Shiro Ikegawa

    (RIKEN Center for Integrative Medical Sciences)

  • Atsushi Takahashi

    (RIKEN Center for Integrative Medical Sciences
    National Cerebral and Cardiovascular Center)

  • Masahiro Kanai

    (RIKEN Center for Integrative Medical Sciences
    Harvard Medical School)

  • Sadao Suzuki

    (Nagoya City University Graduate School of Medical Sciences)

  • Daisuke Matsui

    (Graduate School of Medical Science)

  • Mariko Naito

    (Nagoya University Graduate School of Medicine
    Hiroshima University)

  • Taiki Yamaji

    (National Cancer Center)

  • Motoki Iwasaki

    (National Cancer Center)

  • Norie Sawada

    (National Cancer Center)

  • Kozo Tanno

    (Iwate Medical University
    Iwate Medical University)

  • Makoto Sasaki

    (Iwate Medical University)

  • Atsushi Hozawa

    (Tohoku University
    Tohoku University)

  • Naoko Minegishi

    (Tohoku University
    Tohoku University)

  • Kenji Wakai

    (Nagoya University Graduate School of Medicine)

  • Shoichiro Tsugane

    (National Cancer Center)

  • Atsushi Shimizu

    (Iwate Medical University)

  • Masayuki Yamamoto

    (Tohoku University
    Tohoku University)

  • Yukinori Okada

    (RIKEN Center for Integrative Medical Sciences
    Osaka University Graduate School of Medicine
    Osaka University)

  • Yoshinori Murakami

    (The University of Tokyo)

  • Michiaki Kubo

    (RIKEN Center for Integrative Medical Sciences)

  • Yoichiro Kamatani

    (RIKEN Center for Integrative Medical Sciences
    RIKEN Center for Integrative Medical Sciences
    The University of Tokyo)

Abstract

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

Suggested Citation

  • Masato Akiyama & Kazuyoshi Ishigaki & Saori Sakaue & Yukihide Momozawa & Momoko Horikoshi & Makoto Hirata & Koichi Matsuda & Shiro Ikegawa & Atsushi Takahashi & Masahiro Kanai & Sadao Suzuki & Daisuke, 2019. "Characterizing rare and low-frequency height-associated variants in the Japanese population," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-12276-5
    DOI: 10.1038/s41467-019-12276-5
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    Cited by:

    1. Gengjie Jia & Xue Zhong & Hae Kyung Im & Nathan Schoettler & Milton Pividori & D. Kyle Hogarth & Anne I. Sperling & Steven R. White & Edward T. Naureckas & Christopher S. Lyttle & Chikashi Terao & Yoi, 2022. "Discerning asthma endotypes through comorbidity mapping," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    2. Kenichi Yamamoto & Kyuto Sonehara & Shinichi Namba & Takahiro Konuma & Hironori Masuko & Satoru Miyawaki & Yoichiro Kamatani & Nobuyuki Hizawa & Keiichi Ozono & Loic Yengo & Yukinori Okada, 2023. "Genetic footprints of assortative mating in the Japanese population," Nature Human Behaviour, Nature, vol. 7(1), pages 65-73, January.
    3. Go Sato & Yuya Shirai & Shinichi Namba & Ryuya Edahiro & Kyuto Sonehara & Tsuyoshi Hata & Mamoru Uemura & Koichi Matsuda & Yuichiro Doki & Hidetoshi Eguchi & Yukinori Okada, 2023. "Pan-cancer and cross-population genome-wide association studies dissect shared genetic backgrounds underlying carcinogenesis," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    4. Kenichi Yamamoto & Shinichi Namba & Kyuto Sonehara & Ken Suzuki & Saori Sakaue & Niall P. Cooke & Shinichi Higashiue & Shuzo Kobayashi & Hisaaki Afuso & Kosho Matsuura & Yojiro Mitsumoto & Yasuhiko Fu, 2024. "Genetic legacy of ancient hunter-gatherer Jomon in Japanese populations," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    5. Kyuto Sonehara & Yui Kimura & Yoshiko Nakano & Tatsuya Ozawa & Meiko Takahashi & Ken Suzuki & Takashi Fujii & Yuko Matsushita & Arata Tomiyama & Toshihiro Kishikawa & Kenichi Yamamoto & Tatsuhiko Nait, 2022. "A common deletion at BAK1 reduces enhancer activity and confers risk of intracranial germ cell tumors," Nature Communications, Nature, vol. 13(1), pages 1-9, December.

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