SELECT 
  DISTINCT variant_id 
FROM 
  cscart_vd_vendors_relationships 
WHERE 
  feature_id = 654

Query time 0.00104

JSON explain

{
  "query_block": {
    "select_id": 1,
    "temporary_table": {
      "nested_loop": [
        {
          "table": {
            "table_name": "cscart_vd_vendors_relationships",
            "access_type": "ALL",
            "rows": 5489,
            "filtered": 100,
            "attached_condition": "cscart_vd_vendors_relationships.feature_id = 654"
          }
        }
      ]
    }
  }
}