It really depends what you are trying to accomplish, you can set a JS global var and pass it the same way as any other URL. Basically you need to pass it as a $_GET variable, you can do it with $_POST too, but you need to use XMLHttpRequest and what not which I am not going to go into. Here is an easy example.
var myvar = "12345"; window.open('http://mydomain.com/mypage.php?id='+myvar,'_PARENT');
In your PHP code you access it like any other request.
<?php echo $_GET['id']; ?>
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