Prompted by a comment below I decided to “quick & dirty” double-check whether the Uygurs’ East Asian ancestry was more Han or Japanese in affinity. My recollection was that it was more shifted toward sub-Siberian populations, such as Mongolians, who also are suggested to have affinities with Koreans and Japanese. My method was simple, I ran ADMIXTURE in supervised mode with a sample of 10 Han and 10 Japanese I randomly yanked out of the HGDP along with Uygurs, and assorted other groups. I left Uygurs, Chuvash, Turks, and Mongolians “free” to be linear combinations of the ancestry of other populations. The marker set was 290,000 (I pruned somewhat from 500,000+), and K = 11 (there were 11 populations which were part of the supervised run). It looks like the Uygurs have more of an affinity to the Japanese, or at least their East Asian ancestors did.