One way to do it:
(Assuming you already know how to open a file and execute a query.)
First read rows from your CSV and assume the data is missing in SQL.
while (($row = fgetcsv($file)) !== FALSE) {
    $num = $row[0];  // or whatever CSV column the value you want is in
    $result[$num] = ['csv' => $num, 'sql' => '', 'status' => 'MISSING IN SQL'];
}
Then fetch rows from your query and fill the array you created from the CSV accordingly.
while ($row = $stmt->fetch(PDO::FETCH_ASSOC)) {
    $num = $row['EAN']; // or whatever your column is named
    if (isset($result[$num])) {
        // This has a value from the CSV, so update the array
        $result[$num]['sql'] = $num;
        $result[$num]['status'] = 'OK';
    } else {
        // This doesn't have a value from the CSV, so insert a new row
        $result[$num] = ['csv' => '', 'sql' => $num, 'status' => 'MISSING IN CSV'];
    }
}
You could change the order of this and process the query results first. Either order will work, just as long as you do the update/insert logic with the second data source.
You can ksort($result); if you want the merged values to be in order, then output $result however you need to.