Single nucleotide polymorphisms (SNPs) represent to the genetics variant most common founded in the human genome. These polymorphisms have a wide distribution and can found in any region of gene or mRNA, the SNPs that have functional implications on the levels of gene expression are called regulatory SNPs (rSNPs), while those that affect translation, splicing, efficiency to enhance or inhibit the alternative, mRNA stability and protein function (without altering its structure), they are called structural RNA SNPs (srSNPs). Several studies have identified to these polymorphisms associated with different common diseases e.g. hypertension, obesity, rheumatoid arthritis and coronary artery disease. The aim of this review is to discuss the functional implication of rSNPs and srSNPs in the common diseases.