In this Rapid Communication, we determine the fluctuations of the initial eccentricity in heavy-ion collisions caused by fluctuations of the nucleon configurations. This is done via a Monte Carlo implementation of a color glass condensate k(t)-factorization approach. The eccentricity fluctuations are found to nearly saturate elliptic flow fluctuations measured recently at RHIC. Extrapolations to LHC energies are shown.
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