Chakra is a Sanskrit word, and it means "wheel" or "vortex" because that's what it looks like when we look at it. Each chakra is like a solid ball of energy interpenetrating the physical body, in the same way that a magnetic field can interpenetrate the physical body. The chakras are not physical. They are aspects of consciousness in the same way that the auras are aspects of consciousness.
The chakras are more dense than the auras, but not as dense as the physical body, but they interact with the physical body through two major vehicles, the endocrine system and the nervous system.
Each of the seven chakras is associated with one of the seven endocrine glands, and also with a particular group of nerves called a plexus. Thus, each chakra can be associated with particular parts of the body and particular functions within the body controlled by that plexus or that endocrine gland associated with that chakra.