Due to religious ethics and morals some might find themselves 'frowned upon' or worse, hated because they are not part of a religious community. SO, religion effects prejudice by having strict ethics and morals that are not inclusive.
At the same time religion has been known to break down racial barriers (Christian missions to Africa), Bring fighting factions together (Christmas in the trenches, WWI) and often teaches that we are all the same and therefore deserve equal respect from each other. SO, religion effects prejudice by functioning as a bridge between different nations, cultures and races.
From another point of view:
The Main Theme of Religion is simply "Faith without Proof" Which is the Main Theme of Prejudice. Period