Hi... I'm not an engineer... but if you are under the California code (CBC) which is basiically the 2006 IBC, solid sawn joists can be bored (a hole cut) to one third their depth (in your case a 3" hole in a 9.25" joist) in the outer 1/3 of the joist with a 2" minimum clearance from the edges (top and bottom).

Therfore, your situation (at 3.5") would not be compliant with the above code.

However, your question was, is that a structural issue... not is it within code. I don't have enough detail to know... and if it seems like it might be... you might have to consult an engineer with the full set of detail.

(In general circumstances, I would bet that it will not be a material structural issue... but I can not be certain.)

Good luck... Peter

Thanks for the input. I laminated 3/4 inch plywood on either side of the joist and drilled the hole. Second floor is still standing :)