We observed that PD-1 rs2227981 significantly decreased the risk of gastrointestinal (GI) cancer (OR = 0.68, 95% CI = 0.56–0.84, p = 0.000, TT vs. CC; OR = 0.60, 95% CI = 0.40–0.89, p = 0.011, TT vs. CT+CC; OR = 0.83, 95% CI = 0.75–0.91, p = 0.000, T vs. C), lung cancer (OR = 0.65, 95% CI = 0.44–0.97, p = 0.030, TT vs. CC; OR = 0.84, 95% CI = 0.71–0.99, p = 0.043, CT+TT vs. CC; OR = 0.83, 95% CI = 0.72–0.95, p = 0.009, T vs. C), and breast cancer (OR = 0.82, 95% CI = 0.70–0.06, p = 0.012, T vs. C). Here, PDCD1 is linked to lung cancer.