mysql is not picking up the my.cnf in linux

I have got an environment with in Linux with mysql 5.5 + wordpress + php 5.6 + phpmyadmin
I have found out that no matter what value of system variable / option changed in the phpmyadmin will be reset after service / server restart
Also, none of the options in the /etc/my.cnf is being picked up
How would I be possible to resolve this problem?

location of my.cnf = /etc/my.cnf

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mysql datadir = /var/lib/mysql

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