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If it's still there when you stop the fan, then it's not that particular fan. I assume you are talking about the processor fan, so try stopping the power supply fan at the same time.
I'd guess it's the power supply fan and it's vibrating the power unit, and that in turn is causing vibration somewhere on the case (doesn't even have to be near the power supply). The cases are made so thin these days that audible vibration is a common problem.
Pinpoint where it's coming from and pack some foam or cloth in if you can. I put some between the metal top and the plastic outer shell and it took care of a very high pitched vibrating on mine.
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