1.Subtle energies ( nadis, a la Kirlian or Russian bioplasmatic
body/etheric of the theosophists
2. Their "gross" physiological connexions ( some try with glands or plexuses, as you know, but,..)
3. Psychological function ( if there is any, with emotions, intellect,.. Hindu/Buddhists don't think so.)
4. Spiritual dimension ( some say spiritual pole is dormant, and physiological active ( more or less ) Also, "lower" centers don't have even dormant spiritual function ).
5. Micro-macrocosmic relation: in theory, opening of one chakra ( non-physiological pole ) may lead to apperception of a concommitant universe ( psychic, causal,..)
6. Many tantrics insist that the way you die ( or get out through a chakra ( "you" are vijnana/principle of consciousness, star located either in head or breast according to Leadbeater, jiva etc.), that's the world you'll experience. Who knows ?
7. No unanimity regarding the number of centers, their "look", latency or potency, majors and minors,..