PHP_INI_USER Entry can be set in user scripts (like with ini_set()) or in the Windows registry. Since PHP 5.3, entry can be set in .user.ini

PHP_INI_PERDIR Entry can be set in php.ini, .htaccess, httpd.conf or .user.ini (since PHP 5.3)

PHP_INI_SYSTEM Entry can be set in php.ini or httpd.conf

Entry can be set anywhere