There’s several clues throughout the show that hint 001 is 456’s father.

-When 456 refuses to drink regular milk, 001 says his son hated milk too.

-On October 24, 001 says his son’s birthday is coming soon. 456 birthday is Oct 31.

-During the marble game 001 says he lived in a similar neighborhood, 456 says so did he.

-The door of the house where 001 gets “killed” at is the same as 456’s mother’s house.