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Reign as Khan of Moghulistan
Tarikh-i-Rashidi by Mirza Muhammad Haidar Dughlat says that Tughluk Timur Khán's youngest son was Khizir Khwája Khán, and that while he was yet at his mother's breast, he was saved from the cruelty and enmity of Kamaruddin by Mir Ághá, the mother of Amir Khudáidád. When the child attained twelve years, his friends, still fearing Amir Kamaruddin, took him from Káshghar.
Amir Khudáidád wished to send a few trustworthy men with him, but Mir Ághá opposed this plan, saying: "Do not send any of your own servants, for when the boy becomes Khán, base born people [such as they] will become influential, and then they will prove enemies to yourself and your children. They will imagine that the people do not pay them sufficient respect, but say among themselves, ‘These are only servants.’ For this reason rather send others than your own retainers—send strangers." So twelve men were sent, and each eventually became an Amir. Many of their descendants are alive now. Among their number was Arjirák, from whom are descended the Amirs of Itárji; Tájri of Khwárizm, from whom are sprung the Amirs of Kunji; while another was of the tribe of Chálish Siádi [or Sayyádi]; and his sons also became Amirs, with the style [lakab] of Kushji, but they are also called Kukildásh.
They took Khizir Khwája Khán up to the hills which lie between Badakhshán and Káshghar. But the spies of Kamaruddin got news of his hiding-place, so he abandoned it and fled to the hills of Khotan. Fearing discovery, he went on to Sárigh Uighur, Jurján, and Lob Katak, where he remained for twelve years. On the death of Kamaruddin, search was made for Khizir Khwája Khán, and Amir Khudáidád sent for him from where he was in hiding. As soon as he was brought in, Khudáidád called the people together and raised him to the Khánship. Thus did the splendour of the Khán come to illumine the sovereignty of the Moghuls, so that the affairs of Moghulistán prospered. The Khán then concluded a peace with Amir Timur, who formed an alliance with him by marrying Tavakkul Khánim, a maiden from the royal haram.
Oh! God, make all the world my ill-wishers,
And keep me apart from them all.
Keep my heart from worldly matters,
And cause me to have but one purpose and aim in life.
Genealogy of Chughatai Khanates
In Babr Nama written by Babur, Page 19, Chapter 1; described genealogy of his maternal grandfather Yunas Khan as:
"Yunas Khan descended from Chaghatai Khan, the second son of Chingiz Khan (as follows,) Yunas Khan, son of Wais Khan, son of Sher-'ali Aughlon, son of Muhammad Khan, son of Khizr Khwaja Khan, son of Tughluq-timur Khan, son of Aisan-bugha Khan, son of Dawa Khan, son of Baraq Khan, son of Yesuntawa Khan, son of Muatukan, son of Chaghatai Khan, son of Chingiz Khan"
- Mirza Muhammad Haidar. The Tarikh-i-Rashidi: A History of the Moghuls of Central Asia.Trans. Edward Denison Ross. ISBN 81-86787-02-X
- Tarikh-i-Rashidi. Wikisource.
- The Babur Nama in English, Zahiru'd-din Mubammad Babur Padshah Ghdzt, ANNETTE SUSANNAH BEVERIDGE
- The Tarikh-i-Rashidi: a history of the Moghuls of central Asia by Mirza Muhammad Haidar Dughlat; Editor: N. Elias,Translated by Sir Edward Denison Ross,Publisher:S. Low, Marston and co., 1895