Human populations may have experienced both cultural and environmental adaptations, and such independent adaptations may be the cause of local genetic differentiation. It is beneficial to investigate genes which have played important roles in human population differentiation for comprehensive understanding of the relationships between human cultural/environmental adaptation and genetic diversity of human genomes. The aim of this research is identification of genes which are associated with human population differentiation through genome-wide analysis. To approach this aim, we performed pairwise comparisons of SNP allele frequencies and pairwise Wright’s Fst of chromosome 22 among 6 populations based on category of 1000 genome project database; African, European, American, South Asian, Han Chinese in Beijing, Japanese and the other East Asian populations. We focused on the Japanese population compared to the other populations and searched for SNPs with remarkably high or low frequency in Japanese. For results, we found 1) Fst values showed that Japanese is most closely related to East Asian populations (Han Chinese in Beijing and the other East Asian populations), and followed by South Asian and American populations. Relatively distant relationships with African and European populations were observed. 2) When comparing two populations, the more geographically differentiated they are, the more allele frequency differences were observed. 3) No remarkable changes of allele frequencies in Japanese relative to the other populations were detected, thus the other chromosomes will be further examined.