If you want to enable to disable PHP variable for all domains then you can do that using the below steps :
Here we have taken an example of safe_mode varibale
[email protected][#] cd /etc/httpd/conf.d
[email protected][#] vi safemode.conf
and just add the below lines in the safemode.conf file
<Location />php_admin_flag safe_mode off< /Location>
Finally restart the apache service on the server and it will work like a charm.