Query custom node by user Entity Reference
The column name for an entity reference field is target_id, so your code should be:

$query = new EntityFieldQuery();

$query
  -&gt;entityCondition('entity_type', 'node', '=')
  -&gt;propertyCondition('type', 'custom_node', '=')
  -&gt;fieldCondition('field_marketer', 'target_id', $user-&gt;uid, '=');

$entities = $query-&gt;execute();