Press r r. Now you are asked what branch you want to rebase to. Instead of just pressing RET without reading the prompt (which would cause the default to be used, i.e. the upstream branch) instead select/type the branch you actually want to rebase to and then press RET.
Edit: Starting with v2.4 the r r r binding has been replaced with three new bindings. r p p rebases onto the configured push-remote, r u u onto the configured upstream, and r e e onto any other branch.