Current genome-wide association studies (GWAS) for kidney function lack ancestral diversity, limiting the applicability to broader populations. The East-Asian population is especially under-represented, despite having the highest global burden of end-stage kidney disease. We conducted a meta-analysis of multiple GWASs (
n
= 244,952) on estimated glomerular filtration rate and a replication dataset (
n
= 27,058) from Taiwan and Japan. This study identified 111 lead SNPs in 97 genomic risk loci. Functional enrichment analyses revealed that variants associated with
F12
gene and a missense mutation in
ABCG2
may contribute to chronic kidney disease (CKD) through influencing inflammation, coagulation, and urate metabolism pathways. In independent cohorts from Taiwan (
n
= 25,345) and the United Kingdom (
n
= 260,245), polygenic risk scores (PRSs) for CKD significantly stratified the risk of CKD (
p
< 0.0001). Further research is required to evaluate the clinical effectiveness of PRS
CKD
in the early prevention of kidney disease.