I read this manga about 3 to 4 years ago. The main character finds himself in a post-apocalyptic setting where an organisation rules over Japan, and humans with superpowers appear, and are forced to work for this organization.
He has a superpower where he has a hand made of stone(?), and can create earthquakes with it.
The one ruling the organization is a woman, who was the one to invent (or discover) those powers. He rejects the offer and is hunted by the organization, and his elder brother working for the organization is sent to deal with him.
He also meets a mute girl, who has the power to keep the other superpowers in check by sacrificing her own heart, and she can regenerate it.