Variant Annotation is required to obtain information on biological consequences of SNPs in the risk loci. There are several tools such as ANNOVAR12 and VEP28 which annotate functional consequences on genes, and variant scores such as deleteriousness and phylogenetic conservations (extensive review is available in Hou and Zhang29). Particularly for non-coding SNPs, SCAN30, RegulomeDB14 and HaploReg31 annotate regulatory information, such as eQTLs, enhancer/promoter regions, and transcription factor binding sites (see Tak and Farnham32 for extensive overview). Although SCAN and HaploReg correct for LD, the input of the tools mentioned above is a list of SNPs of interest which does not take genetic associations into account and thus requires pre-processing of GWAS results by the user. FUMA performs annotation of SNPs that are in LD of independent significant SNPs in a single flow, and does not require additional data preformatting.
