Recent advancements in foundation models have been successfully extended to the time series (TS) domain, facilitated by the emergence of large-scale TS datasets. However, previous efforts have primarily Capturing channel dependency (CD) is essential for modeling multivariate time series (TS), and attention-based methods have been widely employed for this purpose. Nonetheless, these methods primarily focus on modifying the architecture, often neglecting the importance of dataset-specific characteristics. In this work, we introduce the concept of partial channel dependence (PCD) to enhance CD modeling in Transformer-based models by leveraging dataset-specific information to refine the CD captured by the model. To achieve PCD, we propose channel masks (CMs), which are integrated into the attention matrices of Transformers via element-wise multiplication. CMs consist of two components: 1) a similarity matrix that captures relationships between the channels, and 2) dataset-specific and learnable domain parameters that refine the similarity matrix. We validate the effectiveness of PCD across diverse tasks and datasets with various backbones. Code is available at this repository: https://github.com/YonseiML/pcd.