It could be from a bad chain, bent chainring/sprocket, worn out cassette or freewheel, incorrect installation of chainring/bolts, bent tooth, missing spacer in the bottom bracket/cranks, bent crank arm, etc etc.
Have you inspected every single tooth on your sprocket to see if any of them are bent? A bent tooth might cause a clicking sound.
Does your chain have even slack or does it fluctuate from more to less slack as you pedal?
If this is the case, you can fix the slack issue by tightening the chainring bolts in the correct way.
Is your chain clean and lubed?
A chain line issue could be causing the problem. If any of the parts on your bike have ever been changed/upgraded, there's a good chance the size of the part was slightly off causing the chain to not be in perfect alignment.
Flip your bike upside down and look where the sprocket teeth are coming up through the chain. Are the teeth perfectly centered in the chain or does it favor one side of the gap?
If it's uneven, you can try using a bottom bracket spacer/washer to center the chain line.
Your bottom bracket/bearings might need to be checked out. I once had a sealed bearing cartridge that was too old and used to make a popping/cracking sound every few pedal rotations. Replacing it fixed the problem.
If it's none of these, try swapping out different parts and you'll locate the problem pretty fast. Start with a part you were planning to upgrade or replace soon anyway or whatever's easiest/cheapest.