This study estimates the relative position between body segments using segment orientation and segment-to-joint center (S2J) vectors. In many wearable motion tracking technologies, the S2J vector is treated as a constant based on the assumption that rigid body segments are connected by a mechanical ball joint. However, human body segments are deformable non-rigid bodies, and they are connected via ligaments and tendons; therefore, the S2J vector should be determined as a time-varying vector, instead of a constant. In this regard, our previous study (2021) proposed a method for determining the time-varying S2J vector from the learning dataset using a regression method. Because that method uses a deformation-related variable to consider the deformation of S2J vectors, the optimal variable must be determined in terms of estimation accuracy by motion and segment. In this study, we investigated the effects of deformation-related variables on the estimation accuracy of the relative position. The experimental results showed that the estimation accuracy was the highest when the flexion and adduction angles of the shoulder and the flexion angles of the shoulder and elbow were selected as deformationrelated variables for the sternum-to-upper arm and upper arm-to-forearm, respectively. Furthermore, the case with multiple deformationrelated variables was superior by an average of 2.19 mm compared to the case with a single variable.