SNPs are the most recurrent polymorphisms at the genome and they appear about one per each kilobase between both chromosomes of an individual. A principal approach of research investigation is the use of SNPs to identify genomic variation of diverse phenotypic traits. A method for identifying nsSNPs for any given organism, based on genotypes obtained from commercial SNPchips, is presented. Using the Illumina BovineHD SNPchip, which covers about 777,000 polymorphisms (an average of 26,105.43 per chromosome), nsSNPs were discovered by processing the SNP values and their corresponding flanking sequences. Translation was obtained analyzing the sequences in all forward and reverse strands, leading to the detection of nsSNPs. The non synonym sequences detected were located within the UMD 3.1 annotation; all sequences which fell into the “gene / every other” category were selected for further analysis. The second phase of the research was to detect all the previously selected sequences which lead to a change at the secondary structure of the protein product. Once the sequences that originated a secondary structure change were detected they were linked to their phenotype via GO and KEGG. An average of 39.79% of nsSNPs fell into the boundaries of the UMD3.1 annotation; out of this percentage, a 3.65% occurred within the “gene / every other” simultaneous selection of the annotation categories. 62.28% of these “gene / every other” - nsSNPs originate a change in their secondary structure.