Panels Regions

This module allows you to selectively disable regions on a variant-by-variant basis within Panels. It's somewhat of a replacement for the 'Disable Drupal blocks/regions" checkbox.

You can find the settings within your panel variant, under the 'General' menu item.

The only drawback with this module is if your parent theme (be it core or a base theme) adds body classes for regions, they are not updated. To circumvent this, copy the body class code from the parent theme's preprocess_page function and paste it within your theme's template.php in the same location.