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 2.0 archives genomic data of 126,590 Han Chinese individuals (a.k.a. Han100K), including high coverage WGS data (n = 7,124), low coverage WGS data (n = 11878), high coverage WES data (n = 5,002) and genotyping or partially imputed data (n = 102,586)(more). Totally 104,805,763 variants are deposited, which are more than 13-folds of that in the old version. PGG.Han 2.0 includes much high coverage sequencing data to meaningfully facilitate: 1) variant query; 2) imputation; 3) GWAS. Computational tools are improved in PGG.Han 2.0, and an online user interface is provided for variant query , data analysis and results visualization (more).