It doesn't do it all the time. I have a fan control and the sound makes no difference when I turn it off or on full. Doesn't seem like it's the CPU, so maybe the GPU?
I'll have to listen for it without the side cover in place.
Is the rattling noise consistent or only occurring at boot?. Sometimes a busted ball-bearing can cause that rattle noise in the larger case fans. As Mantadog said ripping the side off the comptuer is the best bet. removing the fans one by one from the motherboard (they are held in by a small pin connector.) until you can identify which is causing the rattle.