Rei Ayanami is not human, but a creation of the human instrumentality project and cloned after Gendo's dead wife, Yui.

(Author's Note:  This particular question originally stated that Rei had the soul of Gendo's wife, Yui.  In actuality, Yui's soul is in the Evangelion Unit 1, as noted in the Red Cross Book.  Thanks to J. Brown for pointing out the discretion.   :)

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