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I once have the first Skaven army book, back in about '94. Somehow I always got the impression that they were rats who were mutated by Warpstone and Chaos. Is that true i fluff? Does this make them as much children of chaos as Beastmen are?

Following this line a bit, does this make The Horned Rat a chaos god somehow??

They do respect chaos as it gave the world magic. But they do see themselfs as the master race

Horned rat I think is just the ideology of the hooded man who supposedly created the Skaven according to the history of them but I don't think the 'horned rat' while it might have been something chaos may have had a part in, isn't actually anything directly linked to chaos.

It would be uncharacteristic of the great 4 to hide behind the guise of a hooded / horned rat and see there forces separate from one another.

As for who the hooded man in there background is, could quite easily of been a servant of chaos placing a curse that merely went beyond his control. At the same time though it could of been any number of people, could even of been Sigmar after he vanished to the north (if the timeline cooperates) its really hard to tell.

In old times, Skaven were just another Chaos fraction.
Now the Horned One actually is one independent Chaos God with at least one serving Greater Daemon (Vermin Lord):
http://warhammeronline.wikia.com/wiki/Horned_Rat
He is also featured in an expansion of the Game "Chaos in the Old World" as the 5th fraction:
http://www.fantasyflightgames.com/edge_npm.asp?eidm=61