Single nucleotide polymorphisms (SNPs) may act as biological markers, as they can relate to the genes that are associated with various complex diseases such as heart diseases, diabetes, cancer, schizophrenia, blood pressure, migraine, and Alzheimer. These SNPs mostly locate within a gene or in a regulatory region near a gene and can affect the gene's function to play a more direct role in disease. Hence, SNPs allow scientists to develop candidate drug therapy by evaluating an individual's genetic makeup to develop a particular disease. Gene-gene interactions generally complicate migraine and its genetics and further gene-environmental interactions that often misguide the true defying causes of this disease. Due to its complex nature, it is difficult for scientists to reveal a complete list of SNPs or even all the genes that are related with the pathogenesis of this disease. Nowadays, much work has been done in this direction and new variants of migraine are being constantly identified. In this review article, the role of various SNPs reported to be disease-associated in published migraine GWAS has been discussed. To understand the molecular mechanisms of migraine attack by identifying new genetic variants of migraine can be a key to develop new therapeutic strategies in the future.