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Magnetic microstructures in the reference layer in magnetic tunneling junctions (MTJs) are tuned by a reversal field under ambient conditions to investigate their effects on the magnetoresistance (MR) and the exchange coupling field (HE) between the reference layer and the free layer. Magnetization changes in the reference layer can be probed by measuring minor MR loops. The results show the HE of the minor MR loops versus the applied reversal field changes from negative to positive and crosses zero. These results can be explained by the magnetic inhomogeneities at the interface between anti-ferromagnetic/pinned-ferromagnetic layers, which causes the partial magnetization reversal in the reference layer.