Because I worked in Saudi Arabia and Kazakhstan, I have had an interest in the those areas for some years now. I have tried to read about it but books are hard to get. I have found some video lectures on the subject. So, here is what I understand. The purpose of this article is that it serve as a conversation starter rather than an authoritative statement.
To my understanding, that entire area was controlled by Iranian tribes for centuries. The Iranians controlled everything from the Ukraine, to Iran, to Kazakhstan, to India. The Iranians invented the “nomad” lifestyle in the Steppes of Asia Thus, early on, the Uyghurs were Iranians.
For centuries, China was primarily a little country in southeast Asia. What blocked them from moving West were the Himalayas and a huge desert, namely the Gobi desert. I have flown over the Steppes of Asia. It is brutal – no trees, no water, just desert and a few bushes. Part of the desert is an area called the Hexi Corridor, a section of land that can be traveled. To my knowledge, that desert range was never really claimed. The area was disputed by the Iranians, Turks, Mongolians, and Chinese. In fact, the Hexi Corridor is an important part of the Silk Road.
Things changed when the Arabs moved up to spread Islam around 900 AD. The Persian Empire was overtaken in that area, and it became Islamic – by the way, Persians are an Iranian tribe. The Arabs ruled there for many years, then came the jolt, the rise of the Altaic people,. The Altaic people includes Mongolians and Turks. So, first the Mongolian empire came, then the Turkic empires.
So what do we have now? A mixed group of people of mostly Iranian and Turkish backgrounds and I would estimate to some extent Chinese too. Like most normal human beings, I would suspect that the Uyghurs there just consider themselves to be Uyghurs – they are Muslim and speak a variation of the Turkic languages. I figure that although the Uyghurs have linguistic and religious differences, they are bound by culture. The same is true of me and my Catholic, Hispanic background, I am still bound to Texas because of culture.
It appears that the Communist in China basically took control of that area after WWII. I doubt that the Uyghurs have any heart felt affinity for the Chinese. I think the Gobi desert was a huge natural impediment to those cultures really ever mixing. It is possible. Look at the difference between the North and the South in the USA. Football really gets serious around Pennsylvania and Ohio, then becomes a religion in the deep South. Large geographical distances can make a huge cultural difference.