Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.

GWAS does not require the identification of the target gene involved in the disease phenotype. It identifies the SNP associated with the disease and helps identify the individuals at risk. This method simplifies target gene identification, which is time-consuming and not accurate in many cases. GWAS was used to identify SNPs associated with an increased risk of myocardial infarction. GWAS has also identified SNPs associated with type 2 diabetes, Parkinson's disease, other heart disorders, obesity, Crohn's disease, and prostate cancer.