Two types of variant annotations are supported, gene‐based annotation and region‐based annotation. For gene‐based annotation, sequence variants are annotated by their induced changes on the amino acid. A variety of gene/transcript definitions are supported, including UCSC KnownGenes, RefSeq, and GENCODE. In region‐based annotation, genomic regions of interest (e.g., transcription factor binding sites, known GWAS signals, etc.) are listed by chromosomal position in the BED files. Sequence variants are annotated by whether they overlap with these genomic regions. Using the functionality of region‐based annotation, SEQMINER can integrate numerous bioinformatics databases, e.g., PolyPhen2, SIFT, GERP scores, etc.
