For a non-coding SNP, if its location is in the downstream region, it is unlikely that it has any functional effect. We classify this type of SNP as ‘downstream with no known function’ and assign no risk to it. However, if the transcription factor-binding site of the gene is changed by this polymorphism in the promoter region, then this SNP may affect the level, location, or timing of gene expression. In this case, it will be classified as ‘promoter/regulatory region’ with a low or moderate risk ranking; otherwise, it will be classified as ‘upstream with no known function.’ If it is in the intronic region, it may alter a binding site of the transcription factor and will be classified as ‘intronic enhancer’ with a low-risk ranking. A SNP at the ‘splicing site’ may break the consensus splicing site sequence and will thus be assigned a high-risk ranking.
