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Table 1 Methods to characterize SNPs across coding and non-coding regions

From: Innovative strategies for annotating the “relationSNP” between variants and molecular phenotypes

Methodology Tool Website
Annotates and/or filters SNPs, insertions, and deletions for any study design. ANNOVAR [52]
Biofilter [165] [53]
aSnpEff [27]
SNPnexus [166]
VCFanno [167]
VEP [35]
Annotates GWAS SNPs based on functional information and visualizes results FUMA [137]
Associate SNP with phenotype information mediated by gene expression data. COLOC http://cran.r-
eCAVIAR [168]
enoloc [122]
FOCUS [134]
PrediXcan [128]
SMR [169]
TWAS [125]
UTMOST [132]
Methods that generated predictive scores that suggest a SNP may influence a molecular phenotype. CADD [40]
DANN [170]
FIRE [171]
  1. aSNPeff also has the ability to perform visualization