In addition, our study successfully replicated three previously reported loci at the nominal significance level (P ≤ 0.05), namely EIF3A, FNDC3B and COL5A1. Specifically, we identified an upstream variant of EIF3A, rs3824830, associated with KC at significance level of P = 4.14 × 10−6. The gene discussed is FNDC3B; the disease is keratoconus.