Table 1 Feature comparison of bioinformatics tools and data sources
From: Functional mapping and annotation of genetic associations with FUMA
Tools | Format | GWAS summary statistics | LD | Functional consequences on genes | Regulatory elements | eQTLs | 3D chromatin interactions | Prioritize SNPs | Map SNPs to genes | Gene expression | Pathways and gene sets | Prioritize genes | Visualization |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
LD calculation | |||||||||||||
 PLINK | St | x | x |  |  |  |  |  |  |  |  |  |  |
Variant annotations | |||||||||||||
 ANNOVAR | St |  |  | x | x |  |  | x | x |  |  |  |  |
 VEP | St |  |  | x | x |  |  | x | x |  |  |  |  |
 SCAN | Web |  | x |  |  | x |  | x |  | x |  |  |  |
 ReglomeDB | Web |  |  |  | x | x |  | x |  |  |  |  | x |
 HaploReg | Web |  | x |  | x | x |  | x |  |  |  |  |  |
Gene-based test/Gene-set analyses | |||||||||||||
 VEGAS | St | x |  |  |  |  |  |  | x |  |  | x |  |
 MAGMA | St | x |  |  |  |  |  |  | x |  | x | x |  |
 Pascal | St | x |  |  |  |  |  |  | x |  | x | x |  |
 MAGENTA | St | x |  |  |  |  |  |  | x |  | x | x |  |
 INRICH | St | x |  |  |  |  |  |  | x |  | x |  |  |
 DEPICT | St | x |  |  |  |  |  |  | x |  | x | x |  |
Visualization tools | |||||||||||||
 LocusZoom | St/Web | x |  |  |  |  |  |  |  |  |  |  | x |
 LocusTrack | St/Web | x |  |  | x |  |  |  |  |  |  |  | x |
3D genome browser | Web | Â | Â | Â | Â | Â | x | Â | Â | Â | Â | Â | x |
FUMA | |||||||||||||
| Â | Web | x | x | x | x | x | x | x | x | x | x | x | x |
