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We have grown site- and size-controlled InAs quantum dots (QDs) in shallow nanoholes prepared using atomic force microscope-assisted anodic nano-oxidation and subsequent etching, and investigated their transport properties by depositing metal nanogap electrodes on a single QD. We have observed clear diamond-like patterns in Coulomb stability diagrams, indicating that the fabricated single QD transistors operate as single electron transistors and that the site-controlled QDs have a good crystalline quality. Furthermore, we show that the charging energies and the orbital quantization energies can be controlled over a wide range by controlling the size of the QDs.