This will be very specific to your hardware platform. It depends on what the fan control signals are connected to. They can be connected to chipsets, Super I / O or a separate SMbus control manager . You will need to find out how it is connected, and then read the data tables for the chip to figure out how to interact with it.
Once you know how to talk to the device, you can use a set of tools, such as WinIO , to talk to registers.
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