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The main objective of dairy farmers is to maximize their profit. Increased incidence of mastitis in farms is one of the health problems, causing in serious economic losses as a consequence of treatment costs and reduction of production and longevity. The objective of this study was to evaluate the genetic architecture and associated genomic regions with milk production and somatic cell score (SCS) as an indirect measure of mastitis and the quality of raw milk. Thus, an SNP data set from 1938 Holstein bulls were used in a single-step genome-wide association study. The proportion of additive genetic variance (agv) for each of 1.5-Mb genomic window (adjacent SNPs) was used to identify informative genomic regions, accounting for more than 1% of the agv. A total of 11 significant windows over 9 bovine autosomes were found for the SCS. A peak on BTA14 explained the largest proportion of variance (3.85%). These regions together, explained 20% of agv and harbored 94 candidate genes. For milk yield, we identified 6 informative windows across 6 chromosomes, and a peak on BTA10 explained 2.08% of agv. These regions, explained 8.8% of the agv and sheltered 89 candidate genes. For the fat yield, 9 significant windows were identified on 7 chromosomes and explained 15.6% of agv, and 9 windows contained 87 candidate genes on 8 bovine autosomes were associated with milk protein yield (10.6% of agv). Four genomic regions had a pleiotropic effect. These findings can be an important source of information in genomic evaluation of dairy cattle. [ABSTRACT FROM AUTHOR]