A comparison of the effects of single nucleotide polymorphism (SNP) marker, overlapping fixed-size haplotype and block constructed on the basis of non-random association of markers by genome-wide association was done. Three datasets each contains five simulated quantitative trait loci (QTL) on SNP map of Bos taurus 29 and 80 replicates were analyzed. The SNP real genotype, real pedigree and simulated phenotypes of 2,531 bulls from Danish Holstein dairy cattle were used. When marker alleles were treated as random effect, the models using individual SNP gave better results than using overlapping fixed-size haplotype or block in terms of power and false discovery rate. The power decreased while the false discovery rate increased as the size of used haplotype or block increased. The results suggest use of individual SNP rather than SNP based haplotype or block in mapping genes causing genetic variation in quantitative traits.