The Han Chinese Genomes Database (PGG.Han) serves as the central repository of the genomic data of the Han Chinese Genomes Project (Phase I). As is its current version, PGG.Han archives genomic data of 114,783 Han Chinese individuals (a.k.a. Han100K), including high coverage WGS data (n = 319), low coverage WGS data (n = 11878), and high-density SNV data with 8,056,973 variants genotyped or partially imputed (n = 102,586)(more). PGG.Han aims to facilitate: 1) population structure analysis; 2) ancestry inference; 3) imputation; 4) GWAS. Computational tools are implemented into the PGG.Han, and an online user interface is provided for data analysis and results visualization (more).