We study supersymmetric (SUSY) models derived from the ten-dimensional SUSY Yang-Mills theory compactified on magnetized orbifolds, with nonvanishing Fayet-Iliopoulos (FI) terms induced by magnetic fluxes in extra dimensions. Allowing the presence of FI-terms relaxes a constraint on flux configurations in SUSY model building based on magnetized backgrounds. In this case, charged fields develop their vacuum expectation values to cancel the FI-terms in the D-flat directions of fluxed gauge symmetries, which break the gauge symmetries and lead to a SUSY vacuum. Based on this idea, we propose a new class of SUSY magnetized orbifold models with three generations of quarks and leptons. Especially, we construct a model where the right-handed sneutrinos develop their vacuum expectation values which restore the supersymmetry but yield lepton number violating terms below the compactification scale, and show their phenomenological consequences.
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