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       x       x
FUMA
  Web x x x x x x x x x x x x