SELECT 
  product_id 
FROM 
  cscart_simple_variations 
WHERE 
  product_id != 591116 
  AND variation_product = 0

Query time 0.00155

JSON explain

{
  "query_block": {
    "select_id": 1,
    "cost_info": {
      "query_cost": "157.19"
    },
    "table": {
      "table_name": "cscart_simple_variations",
      "access_type": "index",
      "possible_keys": [
        "PRIMARY"
      ],
      "key": "PRIMARY",
      "used_key_parts": [
        "product_id",
        "variation_product"
      ],
      "key_length": "8",
      "rows_examined_per_scan": 1548,
      "rows_produced_per_join": 154,
      "filtered": "10.00",
      "using_index": true,
      "cost_info": {
        "read_cost": "141.71",
        "eval_cost": "15.48",
        "prefix_cost": "157.19",
        "data_read_per_join": "24K"
      },
      "used_columns": [
        "product_id",
        "variation_product"
      ],
      "attached_condition": "((`maniamall_cscart`.`cscart_simple_variations`.`variation_product` = 0) and (`maniamall_cscart`.`cscart_simple_variations`.`product_id` <> 591116))"
    }
  }
}