These pins may not be able to supply enough current for a fan.
The graphics card may also not power these unless a connected monitor is detected.
If you want to power a fan out side the case, use a fan cable extension and feed it out of an expansion card slot or other hole in the case.
Bitfenix makes long sheathed cables suitable for this:http://www.bitfenix.com/global/en/products/premium-modding/alchemy-cables/
They also have molex to fan adapter cables if you don't have an available 3 pin fan connector in the case.
These are available in 12V, 7V or 5V which each use different available pins on the molex connector.