At the time of writing, there are very few publicly accessible web-based tools that perform the same function as SPOT, namely taking GWAS results as input and as output providing a table with rankings that take into account user-defined measures of biological relevance. A number of web tools dealing with SNP biological properties are shown in Table 1. GenePipe (43) is the closet to SPOT in purpose and functionality. It takes association results as input, as well as user-defined weights for various forms of genomic annotation, and provides an annotated table as output. Currently, GenePipe incorporates more databases while SPOT offers greater transparency in conveying the prioritization method by providing side by side GIN versus P-value rankings, graphical representations of the GIN calculations and tables showing the details of the prioritization process step by step, all presented interactively in the web browser. Table 1.Some web tools dealing with SNP biological properties and their characteristics related to the prioritization of GWAS resultsWeb toolExclusively for non-synonymous SNPsAccepts multiple SNPsAccepts P-valuesPerforms customizable GWAS prioritizationIncorporates LD proxiesSome external data sources used (Table 2)F-SNP (44)NoNoNoNoNo1,4,5,6,9–20FastSNP
