Many hadith proves the verse of rajm(stoning) is abrogated. But my question is the verse is abrogated with which verse? Please give the reference in your answer.
Stoning does not appear in the Qur'an (ref.). It's instead mentioned in multiple hadith, e.g.:
The Jews brought a man and a woman who had committed illegal sexual intercourse, to the Prophet and the Prophet ordered them to be stoned to death, and they were stoned to death near the mosque where the biers used to be placed.
Sahih al-Bukhari 7332
Further ahadith are cited in: How many cases of stoning are documented in the hadiths? The closest the Qur'an mentions is:
The [unmarried] woman or [unmarried] man found guilty of sexual intercourse - lash each one of them with a hundred lashes ...
I don't believe stoning is considered "abrogated" by scholars (Wikipedia surveys the major schools of thought), e.g.:
...stoning is due upon a married person (men and women) who commit Zina if there is a clear evidence...
There are some arguments against stoning, although they go against the majority of scholars. Opposition to Rajm (Stoning): Analysis and Refutation debates this issue.