Single nucleotide polymorphisms (SNPs) represent the most common type of variation in the human genome. The SNPs located in protein-coding and non-coding RNA genes are classified as neutral and functional. The neutral have no effect, while the functional affect different biological processes and continually confer risk for multifactorial diseases. Functional SNPs found in the promoters of protein-coding and non-coding RNA genes (microRNAs: miRNAs) termed regulatory SNP (rSNPs) and miRNAs rSNPs (miR-rSNPs), respectively, affect the gene expression. Functional SNPs located on the structure of the precursor mRNAs (exons and introns), mature mRNA (5´ untranslated region [UTR], coding sequence, and 3´ UTR), and primary, precursor, and mature miRNAs are termed structural RNA SNPs (srSNPs) and miR-srSNPs, respectively. The srSNPs affect the splicing (and alternative splicing), srSNPs affect the splicing (and alternative splicing), the translation, stability, amino acid sequence, structure, and function of proteins and interaction between mRNA/miRNAs. Finally, the miR-srSNPs affect the structure, processing and interaction between miRNAs/mRNAs. Functional characterization of potentially harmful risk alleles of the SNPs located in protein-coding and non-coding RNA genes have contributed to an understanding of their functions in the complex diseases. The objective of this review is update the reader on the functional role of the SNPs located in protein-coding and non-coding RNA genes and their relationship with multifactorial diseases.
