What really are the genetic basis to say Japan is a country that's markedly different from other asian populations?
The people living in Japan have not lived there for long enough for their genetic to become too different from those of other asian countries. Culture on the other hand changes much more rapidly. Culture is the "genetics" of society, it is passed down from generation to generation and it mutates and these mutations are also hereditary... it's just much faster than biological processes.
But ultimately, it seems very unlikely (and as far as I know, there's very little evidence that suggests this is the case) that race and genetics will have a huge effect on culture. Specially given that countries with similar genetic populations will have vastly different cultures.