Provided is a method of selecting an optimized SNP marker set from a plurality of SNP markers. The method includes selecting an SNP marker set having a high association from a plurality of SNP markers using set-association, selecting SNP markers having a high association by performing discrimination analysis on arbitrary combinations of the markers included in the SNP marker set, and selecting an optimized SNP marker combination satisfying predetermined selection criteria by using receiver operating characteristics (ROC) curve analysis of arbitrary combinations of the selected SNP markers.