Non-coding variability at the APOE locus contributes to the Alzheimer’s risk

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Alzheimer’s disease (AD) is a leading cause of mortality in the elderly. While the coding change of APOE-ε4 is a key risk factor for late-onset AD and has been believed to be the only risk factor in the APOE locus, it does not fully explain the risk effect conferred by the locus. Here, we report the identification of AD causal variants in PVRL2 and APOC1 regions in proximity to APOE and define common risk haplotypes independent of APOE-ε4 coding change. These risk haplotypes are associated with changes of AD-related endophenotypes including cognitive performance, and altered expression of APOE and its nearby genes in the human brain and blood. High-throughput genome-wide chromosome conformation capture analysis further supports the roles of these risk haplotypes in modulating chromatin states and gene expression in the brain. Our findings provide compelling evidence for additional risk factors in the APOE locus that contribute to AD pathogenesis.

Original languageEnglish
Article number3310
JournalNature Communications
Issue number1
StatePublished - Dec 1 2019

Bibliographical note

Funding Information:
We thank Dr. Yu Pong Ng, Dr. Kwok Wang Hung, Ka Chun Lok, Cara Kwong, Yuling Zhang, Saijuan Liu, Shuangshuang Ma, Yan Ma, and Chi Wai Ng for their excellent technical assistance, as well as other members of the Ip laboratory for many helpful discussions. This study was supported in part by the National Basic Research Program of China (973 Program; 2013CB530900), the Hong Kong Research Grants Council Theme-based Research Scheme (T13-607/12R), the General Research Fund (grant number GRF CUHK 471911), the Area of Excellence Scheme of the University Grants Committee (AoE/M-604/16), Innovation Technology Commission (ITS/393/15FP and ITCPD/17-9), the National Natural Science Foundation of China (31671047 and 31400923), the National Key R&D Program of China (SQ2018YFE020417, 2017YFE0190000), the Guangdong Provincial Key S&T Program (2018B030336001), and the Shenzhen Knowledge Innovation Program (JCYJ20151030140325152, JCYJ20170413173717055, JCYJ20151030154629774, JCYJ20170413165053031, and JCYJ20160428145818099). X.Z. was a recipient of the Hing Kee Java Edible Bird’s Nest (HKJEBN) Company Limited Scholarship for Health and Quality Living. Please refer to the Supplementary Notes 1 and 2 for corresponding acknowledgments for the ADNI dataset, Alzheimer’s Disease Genetics Consortium (ADGC) Genome Wide Association Study–NIA Alzheimer’s Disease Centers Cohort (ADC dataset, the National Institute on Aging–Late Onset Alzheimer’s Disease Family Study (LOAD dataset), funding support for the “Genetic Consortium for Late Onset Alzheimer’s Disease”, the Genotype-Tissue Expression (GTEx) Project and the CommonMind dataset. Part of the data used in the preparation of this article were obtained from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) database ( As such, the investigators within ADNI contributed to the design and implementation of ADNI and/or provided data but did not participate in the analysis or writing of this report. A complete listing of ADNI investigators can be found in the Supplementary Note and at the following URL: [ wp-content/uploads/how_to_apply/ADNI_Acknowledgement_List.pdf].

Publisher Copyright:
© 2019, The Author(s).

ASJC Scopus subject areas

  • Chemistry (all)
  • Biochemistry, Genetics and Molecular Biology (all)
  • General
  • Physics and Astronomy (all)


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