We identified significant associations between six immune phenotypes and benign thymic tumors (P < 0.001 for IVW), of which four were harmful to benign neoplasm of thymus: C-C motif chemokine receptor 2 (CCR2) on CD14+ CD16+ Monocyte (Monocyte panel), Transitional AC (B cell panel), CD19 on IgD− CD38− (B cell panel), and CD3 on HLA DR + CD4+ (T cell panel); and two were protective to benign neoplasm of thymus: naive-mature B cell AC (B cell panel) and NK AC (NK cell panel). This evidence concerns the gene CD4 and benign neoplasm of thymus.