Besides annotating functional effects of variants with respect to genes, ANNOVAR has several other functionalities, including the ability to perform genomic region-based annotations, as well as the ability to compare variants to existing variation databases. Region-based annotations refer to the annotations of variants based on specific genomic elements other than genes, for example, conserved genomic regions, predicted transcription factor binding sites, predicted microRNA target sites and predicted stable RNA secondary structures. These annotations are especially important for whole-genome sequencing data, as the vast majority of variants will be outside of protein coding regions and their functional effects cannot be assessed by gene-based annotations. ANNOVAR can utilize annotation databases from the UCSC Genome Browser as flat text files; however, essentially any annotation database can be handled as long as they conform to Generic Feature Format version 3 (GFF3) standards (http://www.sequenceontology.org/gff3.shtml) for sequence-level feature annotations. Additionally, ANNOVAR can evaluate and filter out subsets of variants that are not reported in public databases such as dbSNP and the 1000 Genomes Project. Typically, rare variants causing Mendelian diseases are less likely to be present
