I've got an upstairs bath that I'm ready to floor with ceramic; the bath has not been used since I've owned the house ( 12 years ). If you sit on the potty and stretch your leg out, you'll put your foot on a ~4" round screwed-on floor plate which is a cover for a vertical flush-mounted pipe. This bath is the highest in the house, so I'm wondering if it's a vent. The house was built in 1950. I"d like to start putting down the wonderboard, but I'm 'wondering' if I should cap it off or cutout the wonderboard and tile and keep it intact. It sure looks crummy and I'd like to be rid of it; I’m afraid my small kids will discover it and drop ‘fun things’ down the pipe, but the last time I removed something that I didn't comprehend, it was the deadend hot and cold 'shock absorbers' ( ~12" of closed-end pipe at the highest point ) to prevent water hammer and I'm still thumping myself in the head for that one.
If it was a vent, I doubt that it would be capped off. It could be a stubbed drain pipe, however, tied into your drain system.
It may be a drain connection for a sink, tub/shower, or floor drain. Remove the cap and see if the pipe is 1.5"-2" or has a trap in it (flashlight look). If it is, that's probably its original purpose.
You can always put your ear to it, and have someone run water downstairs to see if you can hear it rushing through the pipe, to see if it's tied in to the rest of the drain/waste/vent system.