/etc/my.cnf

/var/run/mysqld/mysqld.pid

/var/lib/mysql

/var/run/mysqld/mysqld.sock

/home/username/.cpanel-datastore/_usr_sbin_mysqld_–version

/scripts/mysqlup –force

/etc/rc.d/init.d/mysql restart

There are other places MySQL looks for configuration files

/etc/my.cnf
/etc/mysql/my.cnf
~/my.cnf
<$MYSQLHOME>/my.cnf
~/.my.cnf