We describe tests for detecting and locating quantitative traits loci (QTL) for traits in Hanwoo. Lod scores and a permutation test have been described. From results of a permutation test to detect QTL, we select major DNA markers of ILSTS098 microsatellite locus in Hanwoo chromosome 2 for further analysis. K-means clustering analysis applied to four traits and eight DNA markers in ILSTS098 resulted in three cluster groups. We conclude that the major DNA markers of BMS1167 microsatellite locus in Hanwoo chromosome 2 are markers 105bp, 113bp and 115bp. Finally, bootstrap testing method has been adapted to calculate confidence intervals and for finding major DNA Markers.