Here is the original fragment regarding the "birth" of the Emperor first described in the "Realms of Chaos: the Lost and the Damned in 1990
Since then a new story has been described in the "Master of Mankind" by Aaron Dembski-Bowden, that describes Emperor as a human child that has awakened his powers when his uncle murdered his father, which was apparently the first murder committed by a human with cold blood. Emperor shows this vision to Ra, one of his Custodes, but then the same story can be a metaphor since Emperor doesn't respond to the outright question "Did this truly happen?"
This doesn't negate the shamans' origin story - the "Master of Mankind" version simply says that Emperor was a child at some stage and his father (real or adopted) has been murdered and "the boy who will be king" was able to stop the heart of the murderer.
Both of those origins date his birth to around 8000 BCE and place it in Anatolia (modern day Turkey).
In the afterword to the "Emperor of Mankind" the author says:
I didn’t want to reveal anything about the Emperor as
any kind of definitive, objective truth. I don’t think anyone should, either - partly because understanding
the Emperor’s nature and origins hasn’t been important for three decades of enjoyment in the supremely
popular setting (and it’s never going to be necessary for that), and partly because, well, no answer will
ever be satisfying enough or believable enough for everybody.[...]
Could the Emperor have
been born from the souls of primitive shamans? Is he a Dark Age construct aping human form, left out to
enact his will over the now-ignorant species? Was he a manipulative overlord and tyrant who knew
everything of Chaos? Was he just a good man whose intellect strained to work alongside the levels of
those beneath him, and was he ultimately failed by lesser beings?
All of them might be true. None of them might be true.