Daniel Whitehall the Hydra Nazi officer will play a huge role on Magneto's origin story

In agents of shield, Daniel Whitehall was a hydra Nazi SS officer who wanted to find a serum that would grant him immortality and was able to obtain it by harvesting the organs of an inhuman person.

I'd imagine young magneto during WW2 was captured by Daniel whitehall back in his days as an SS officer and was granted immortality hence why in the present day was ageing slowly.

Alternatively if people want to go magneto is a descendant of Holocaust survivors they can do the following: Daniel whitehall captured magneto around the 1990s and whitehall subjected him to horrific experiments causing magneto to believe the Holocaust never ended and people like Whitehall wanted to continue what Hitler started which cemented his hatred for humanity.

In both scenarios he saw Whitehall also experimenting on mutants which led him to believe there can never be peaceful coexistence with humans and mutants.