Products and product displays (nodes) are connected via the Product reference field on the displays content type. The table for that field is called 'field_data_field_products' and contains the node id (called entity_id in the table) and product_id.

If you don't have access to the product_id then do a query first to get that:
$product_id = SELECT product_id
FROM commerce_product
WHERE sku=$your_sku;

Then query for the node id:
SELECT entity_id
FROM field_data_field_products
WHERE field_products_product_id = $product_id

Depending on your situation if you need to do a join you can do an inner join:
SELECT field_data_field_products.entity_id
FROM field_data_field_products
INNER JOIN commerce_product
ON field_data_field_products.field_products_product_id = commerce_product.product_id
WHERE sku=$your_sku;