The aim of this study was to quantify the variation in linkage disequilibrium patterns between populations of Slovak Pinzgau, Austrian Pinzgau, Simmental, Charolais and Holstein. These comparisons included differences between the genetically close populations as well as between dairy and beef breed types. Total number of genes in regions with top 0.01 and 0.1 percentile was 202. The most significant SNPs for production, reproduction and functional traits were positioned in the chromosome 7, 9, 11, 14, 20 and 24 (H2AFY, MAP3K, FAM110B, UBXN2B, CYP7A1, SDCBP, NSMAF, PRKAA1, PTGER4, MIR2361, CDH18 and C9). Genome scans confirmed the presence of selective sweeps in the genomic regions that harbour candidate genes that are known to affect productive traits in cattle such as CAST, COQ3, GJA1, ACYP2, SPTBN1, EML6, RTN4, MAP3K7, PLAG1, CHCHD7, PENK, PRLR, GHR, C6, C7, LIFR, MOCOS, GALNT1, COLEC12, CETN1, TYMS, YES1, NDC80, LPIN2, MYOM1, MYL12A, MYL12B and DLGAP1. Although phenotypic diversity is not sufficiently large to be detected, investigating the polymorphisms presented in the regions of the genome that are involved in breeding traits can be very useful in terms of genetic improvement.