Despite extensive advances in disease genetics, the target population of the genetic studies has largely focused on individuals of European descendants, limiting further discovery of novel functional genetic variants in other ethnic groups. To support human genetics studies on East Asian populations, we established Korean Variant Archive II (KOVA II), composed of 1,896 whole genome sequencing and 3,409 whole exome sequencing data from healthy individuals of Korean ethnicity. This is so far the largest genome database from ethnic Korean population to date, surpassing 2,604 East Asian individuals deposited in gnomAD. Variants in KOVA II followed all known genetic parameters, and we report Korean- specific runs of homozygosity and positively selected intervals. Finally, our analysis of allele age revealed a correlation of functionality and evolutionary age in the variants. The data can be browsed and downloaded in the open website (KOBIC). Therefore, KOVA II will serve as a valuable resource in genetic studies on East Asian populations.