> [ ... ] my filesystem is "ext4", which directories are part of
> it.
'ext4' is a file system *type*. You can have many filesystems of
that type, each with its own tree of directories and files etc.
Each filesystem of type 'ext4' will be stored on a particular
storage device or a subsection of one, and will have some kind
of indentifying label.
Usually each filesystem tree will be stored in a partition on
some disk, and will be "mounted" on (that is, its directories
and files will appear under) some directory.
You can see a list of those by reading the file '/proc/mounts';
in a terminal shell the command 'grep ext4 /proc/mounts' will
print a list of all the currently active ("mounted") devices
containing an 'ext4' filesystem.
For a list of the more important ones in a more readable format
run in a terminal shell the command 'df -T -BG -a'.
> I mean from the root I can see some directories such as /proc,
> /tmp, /dev etc.
Those 3 directories are usually the mount points for special
file system types, and almost never 'ext4' type.
> Are they store on the disk which have formatted with ext4, of
> certain files resides somewhere else.
Some filesystems are stored only in memory as they are not
persistent, as they represent temporary entities.
> I am only sure only about /home directory because I keep my
> disk mobile and data goes with me all the time.
Most likely both the devices mounted on the "/" and "/home"
directories contain filesystems of type 'ext4'.
There are several tutorials online and in print that explain
what is a file system type, a filesystem instance of a type,
and the storage ("block device") holding that instance.