(Edit) The correct perfect of "run" is run not ran. However, it is not uncommon when talking about the sport of running to instead use ran.
Have you ran the Boston Marathon? It's difficult to even qualify.
Because this is a specialized use and not universally accepted, in this answer I will use have run instead.
There is a difference between "have you run?" and "did you run?" The use of the present perfect tense implies a relationship between the time the action took place and now. So using it in a question implies an unspoken "yet", or "before this moment".
Have you eaten dinner? (= Have you eaten dinner yet)
Also there is a reasonable expectation that the activity could have or should have been done before now.
Have you called her back (yet)? It's been three days!
Have you prepared lunch (yet)? It's after 1pm and I'm starving!
Have you brushed your teeth (yet)? It's almost bedtime!
So asking "have you run" is a little strange unless you expected the person would have been running before now.
The response is usually "Yes, I have" or "No, I have not". On the other hand, if someone asks a question using the simple past such as:
Did you call her back?
Did you make lunch?
Did you brush your teeth?
You would normally match the verb tense: "Yes, I did", or "No, I did not".
Note that this isn't the only use of the present perfect tense. It can also indicate an existing or ongoing condition, including some kind of life experience:
Have you been running? You look sweaty.
Have you been to Japan? I heard that you lived there when you were in your twenties.
Have you been sick? You don't look so good.
Again, the answer would be "Yes, I have" or "No, I haven't" to match the verb tense of the question.