You could define a getter that acts as a reference to the live variable:

var myArray = Object.defineProperty([0,1], 2, {
    get() { return x },
    enumerable: true,
    configurable: true
});
var x = 2;
console.log(myArray);
x = 3;
console.log(myArray);

Of course, this is a horrible thing to do to an array, and will probably incur heavy performance penalties in every place where the array is used. So: don't do this. Just assign to myArray[2] instead of x in every place, or use a getter/setter function pair instead of the x variable that does this.

function setX(v) { myArray[2] = v; }
var myArray = [0,1,2];
setX(2);
console.log(myArray);
setX(3);
console.log(myArray);

I tried to use Array.filter() function, but it returns a new array instead of a reference to the original array. which I can not use to mutate the original array.

It returns a new array, but the array's entries are still references to the same objects. So filter is just fine for this.

var filteredUsers = users.filter(function(entry) { return entry.id === 2; });
var item = filteredUsers[0];
item.name = "user2 name updated";
console.log(users[1].name) // "user2 name updated"

The array contains references to the objects, not copies of them. When we do item = users[1], or use filter to get a new array containing a subset of the objects, we get a copy of the object reference, and so the variable now refers to the same object, like this:

                +−−−−−−−−−−+
users−−−−−−−−−−>| (array)  |          
                +−−−−−−−−−−+           +−−−−−−−−−−−−−−−+
                |   0      |−−−−−−−−−−>|    (object)   |
                |          |           +−−−−−−−−−−−−−−−+
                |          |           | id:   1       |
                |          |           | name: "name1" |
                |          |           +−−−−−−−−−−−−−−−+
                |   1      |−−+
                |          |  |
                |          |  |        +−−−−−−−−−−−−−−−+
                |          |  +−−−+−+−>|    (object)   |
                +−−−−−−−−−−+     / /   +−−−−−−−−−−−−−−−+
                                 | |   | id:   2       |
                +−−−−−−−−−−+     | |   | name: "name2" |
filteredUsers−−>| (array)  |     | |   +−−−−−−−−−−−−−−−+
                +−−−−−−−−−−+     | |   
                |   0      |−−−−−+ |
                +−−−−−−−−−−+       |   
                                   |
item−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−−+

Changing the object changes the object, and those changes are visible regardless of which reference to the object you use to look at its properties.

Now if you had an array of primitives:

var a = [1, 2, 3, 4, 5];

...then of course, you can't use the approach above because they aren't objects. In that case, you'd use indexOf to find the index:

var index = a.indexOf(3); // Find the first entry === 3

...and then modify the entry

a[index] = 42;

This also applies to strings (provided they're nice normal string primitives, not things you created via new String(), which there's virtually never a reason to do).

Put an object into the array instead:

var name = {};
name.title = "foo";

var array = [];

array["reference"] = name;

name.title = "bar";

// now returns "bar"
array["reference"].title;