South Korea, one of the most rapidly aging populations in the world, has a high incidence and prevalence of Alzheimer’s disease (AD) among individuals aged 65 years or older. Like other East Asian countries, the number of AD cases in Korea is expected to increase enormously in a few decades. Unfortunately, only a few genome-wide association studies (GWAS) using variants genotyped by microarrays, imputed with population reference panels, or called by next-generation sequencing have included Koreans, so a large portion of the genetic basis of AD still needs to be unveiled. We included 3,540 Koreans aged 60 years or older (1,583 AD cases, 1,957 controls) having whole-genome sequencing (WGS) data to identify genetic associations with AD. We also included 2,978 Japanese aged 65 years or older (1,336 AD cases, 1,642 controls) having single nucleotide polymorphism (SNP) array data, imputed using the TOPMed reference panel aligned to GRCh38, to enhance the findings in an enlarged East Asian dataset. GWAS were conducted using the WGS data (minor allele count ≥ 10, call rate > 0.95) and the SNP array data (minor allele frequency > 0.01, call rate > 0.95) separately and were combined using the inverse variance weighted approach implemented in METAL.