Kazakhstan, the ninth-largest country in the world, is located along the Great Silk Road and connects Europe with Asia. Historically, its territory has been inhabited by nomadic tribes, and modern-day Kazakhstan is a multiethnic country with a dominant Kazakh population. We sequenced and analyzed the hundreds of Kazakh individuals at high coverage using next-generation sequencing platform. This high quality big whole-genome dataset was analyzed and annotated for establishing a pilot national genomic database of Kazakh genetic variation of representatives from the Central Asian region. These whole-genome sequence data of healthy Kazakhs could contribute significantly to biomedical studies of common diseases as their findings could allow better insight into the genotype–phenotype relations at the population level.