I just had the same thing. My understanding from the dentist office is that it could be a number of things. It might be a gum infection, such as gingivitis, or an abscess from a nearby broken tooth. In my case, my blister/cyst must have opened by itself; within 2-3 days it drained and the swelling in my cheek went away. The drainage was mostly watery with a little blood, so the dentists office advised using mouthwash at night, and saltwater rinses during the day. This combination was to keep my mouth as clean as possible, during that drainage time. I have to get in to the dentist office this week to have my gums checked, to rule out further problems.
It sounds like a kanker sore to me (I used to get them all the time) it's a very minor sore caused by a certain vitamin deficiency that is very common. Just rinse with salt water or hydrogen peroxide for a few days and it should go away, and use orajel to numb the pain. Hope this helped!
I agree with CLP up there. I too have this problem only mine was like a blackish blister above a tooth that was sore to the touch.I cried for 2 days with horrible pain and I started penicillin and taking mild pain killers. I am usually a go go go go girl but this knocked me out! I can't seem to wake up or do my normal activities but feel like it is getting better! Chin up and hope ur pain free...Melissa