We identified 8 SNPs in 6 genes/loci that were associated with keratoconus, i.e., FOXO1 rs2721051, FNDC3B rs4894535 and BANP-ZNF469 rs9938149 for the overall combined cohorts, and RXRA-COL5A1 rs1536482, IMMP2L rs757219 and rs214884, and COL4A4 rs2229813 and rs2228557 for Whites. Here, FNDC3B is linked to keratoconus.