Functionally annotated SNPs are subsequently mapped to genes based on functional consequences on genes by (i) physical position on the genome (positional mapping), (ii) eQTL associations (eQTL mapping), and (iii) 3D chromatin interactions (chromatin interaction mapping). Gene mapping can be controlled by setting several parameters (Supplementary Table 2) that allow to in- or exclude specific functional categories of SNPs (Supplementary Fig. 1). Positional mapping is used to map SNPs based on being physically located inside a gene using a default of 10 kb windows, yet custom windows around a gene can be set by the user. Users can select to only use SNPs that have specified functional consequences, such as coding or splicing SNPs, to limit the positional mapping to functionally relevant SNPs. Thus, by selecting to exclude intronic SNPs from the positional mapping function, genes that contain only intronic SNPs in LD of independent significant SNPs will not be prioritized by FUMA. eQTL mapping is used to map SNPs to genes which they show a significant eQTL association with (i.e., the expression of that gene is associated with allelic
