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

Annotates and/or filters SNPs, insertions, and deletions for any study design.

ANNOVAR [52]

http://annovar.openbioinformatics.org/en/latest/

Biofilter [165]

https://ritchielab.org/software/biofilter-download-1

Myvariant.info [53]

http://myvariant.info

^aSnpEff [27]

http://snpeff.sourceforge.net

SNPnexus [166]

http://www.snp-nexus.org

VCFanno [167]

https://github.com/brentp/vcfanno

VEP [35]

https://useast.ensembl.org/info/docs/tools/vep/index.html

Annotates GWAS SNPs based on functional information and visualizes results

FUMA [137]

http://fuma.ctglab.nl

INFERNO [136]

http://inferno.lisanwanglab.org/index.php

Associate SNP with phenotype information mediated by gene expression data.

COLOC

http://cran.r- project.org/web/packages/coloc

eCAVIAR [168]

http://genetics.cs.ucla.edu/caviar/index.html

enoloc [122]

https://github.com/xqwen/integrative

FOCUS [134]

https://github.com/bogdanlab/focus

PrediXcan [128]

https://github.com/hakyimlab/PrediXcan

SMR [169]

https://cnsgenomics.com/software/smr/#Overview

TWAS [125]

http://gusevlab.org/projects/fusion/

UTMOST [132]

https://github.com/Joker-Jerome/UTMOST/

Methods that generated predictive scores that suggest a SNP may influence a molecular phenotype.

CADD [40]

https://cadd.gs.washington.edu

DANN [170]

https://cbcl.ics.uci.edu/public_data/DANN/

FIRE [171]

https://sites.google.com/site/fireregulatoryvariation/

LINSIGHT [142]

https://github.com/CshlSiepelLab/LINSIGHTCA