The following is a general summary of my understanding of the physical locations and elements associated with each chakra. The base chakra extends down and the crown chakra extends up...the chakras in between have vortexes both to the front of the body and to the back.

When all the chakras are open, bright and clean, then our chakra system is balanced. When a chakra becomes blocked or damaged with residual energy, then our physical and emotional health can be affected. The effects of our habits, feelings, beliefs, thoughts, fears and desires can be found in our chakras.

If you eat poorly, or eat  alot of processed food,  and don't exercise, chances are your root chakra is going to become darkened and dull. If you "close off" your emotions because they're painful or overwhelming, your heart chakra is likely to become tight and closed and block emotional energy. If you are extremely centered in your intellect, you may have a bulging and bright third eye chakra but a disproportionately small heart chakra or root chakra. Or perhaps you're cerebrally focused on finding answers to deep questions about "reality."