Chief Judicial Magistrate K P Singh sent Rana to 14-day judicial custody. His bail application would be heard on Wednesday.
Earlier, the court had issued non-bailable warrants against 16 politicians including Rana.
He was among the politicians facing arrest for inciting communal clashes in Muzaffarnagar and adjoining areas in September this year that claimed more than 60 lives and displaced over 40,000 people.
Rana was booked for his alleged hate speech in Khalapar area of the city on August 30, when public gatherings were banned by the authorities after three young men were killed due to a communal dispute in Kawal village in the district on August 27.
The Lok Sabha MP from Muzaffarnagar had been missing ever since the riots broke out on September 7.
Rana left the Samajwadi Party in 2007 to join RashtriyaLok Dal and then switched to BSP in 2009. There are a total of four criminal cases against him, including murder, attempt to murder and robbery.


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