Gene-based analyses identified five significant gene associations with COVID-19 positivity on chromosome 3 (p < 0.05/19,148 genes = 2.6 × 10−06): NXPE3 (p = 1.6 × 10−11), ZBTB11 (p = 5.8 × 10−11), CEP97 (p = 1.0 × 10−10), RPL24I (p = 9.4 × 10−09), and PCNP (p = 6.8 × 10−07). Here, NXPE3 is linked to COVID-19.