Don't run it without the fan its there for a purpose. Without the fan it may overheat and you will have to buy a new motherboard.
It sounds like the Northbridge fan and if so failure is pretty common. You can either buy a replacement Northbridge fan or a Northbridge heatsink. I prefer the heatsink. The last board I had had 3 fan failures in two years so I replaced it with a heatsink. 5 years later its still going strong.
click here or have a look through these click here though most are out of stock at the moment.