If a set has $n$ elements, how many transitive relations are there on it?
For example if set $A$ has $2$ elements then how many transitive relations. I know the total number of relations is $16$ but how to find only the transitive relations? Is there a formula for finding this or is it a counting problem?
Also how to find this for any number of elements $n$?

There is no simple formula for this number (but see http://oeis.org/A006905 for the values for small $n$). The case $n=2$ is small enough that you can list out all 16 different relations and count the ones that are transitive. (You should get 13 of them.)