SNP effects and allele frequency differences (AFD) between the elite cows and the average cows for four chromosome regions with confirmation between GWAS and effect size distribution from USDA genomic evaluation. A) The DGAT1-NIBP region for production traits, showing that the consensus effect in DGAT1 had a low AFD of 0.05 while a SNP in NIBP had the largest AFD (0.36) in this region and also was also highly significant for protein percentage (#2 by EMMAX-IBS and EMMAX-BN, #3 by GLS, #7 by PCA, and #19 by LS). B) The BTA18 region for production, somatic cell score, daughter pregnancy rate and calving traits, showing that the two SNP markers detected by the LS method for many traits had the largest AFD (0.48 at 53.95 Mb and 0.46 at 58.7 Mb) in this region while the consensus effect in SIGLEC12 had a low AFD of 0.03. In this figure, the vertical red line indicates the significant marker, and the vertical blue line indicates an adjacent marker. C) The BTA6 region for protein percentage, showing that the consensus effect between HERC3 and PIGY had nearly identical frequencies in the elite and the average cows. D) The BTA6 region for somatic cell score, showing that the consensus effect had a low AFD of 0.09, while the upstream marker identified by LS and GLS as highly significant for somatic cell had a high AFD of 0.37.