In conclusion, we found that haplotypes formed from three SNPs located in APOA5 and ZNF259, viz., rs662799, rs651821, and rs6589566, were significantly associated with susceptibility to MS and elevation of the log[TG]:HDL-C ratio, sex-dependently, in Koreans; in particular, the ht3 haplotype was associated with these traits in women. Here, ZPR1 is linked to myeloid sarcoma.