atom/docs/user-stylesheet.md

User Stylesheet

If you want to apply quick-and-dirty personal styling changes without creating an entire theme that you intend to distribute, you can add styles to user.css in your ~/.atom directory.

For example to change the color of the highlighted line number for the line that contains the cursor, you could add the following style to user.css:

.editor .line-number.cursor-line {
  color: pink;
}