I responded to this question in Quora, too.
Soul does not live in any part of your body; it is rather connected to it. It does not live in any of the, so-called, chakras or brain or any other part of the body. Remove all chakras one by one from a body and you will still exist.
Soul has a separate existence. Before talking about the exact location of the soul in a body, you have to consider that soul, though attached with your body, exists in a separate dimension and is made up of a different energy; the energy that makes your soul differs from the one that made your body.
Here is my body and there is my soul; but where am I?
Where is the person whom I call ‘I’ or ‘you’?
To me, firstly, I am separate from both my soul and my body. Presently, I am aligned and connected to my soul and my body. The genetic code of almost all human beings is the same up to 99.9%. The remaining 0.1% difference is what is related to me. This is the very code or type-of-energy in which ‘I’ and ‘YOU’ exist.
Secondly, I have a unique code and this code of mine attaches my body to my soul. So, there is TRINITY or TRIO in the form of SOUL-BODY-I relationship. There may be a person who would travel to distant places in varying dimensions, during sleep or awaking, by combining himself with his soul. Similarly, there may also be a person who would stay with the current body but shift his soul into some other body. The rapid progression in science, psychology, computing, research in quantum fields and other discoveries are rapidly bringing the past impossibilities fade away and making every imaginable thing possible in the real world.
Thirdly, after death, my body will parish and decay; my soul will go somewhere in an other dimension but where will ‘I’ stay. Of course, I will stay even without my body and soul and I will join my soul and a new body, generated on the previous programming code, on the doomsday.
‘I’ would, of course, be taken into the direct custody of God and will remain there until required and released for the next adventure that God (the Supreme Power) wants me to perform.