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In the cyclone II handbook,page 5-4,pin pull-up resistance values will be lower if an external source drivers the pin higher than Vccio.
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If you drive the pin at a higher voltage than Vccio, the clamping diode will start drawing current, thus lowering the impedance seen from outside.
The pull-up resistors are implemented by PMOS transistors, exposing a non-linear I/V characteristic.
