FUMA is a platform that can be used to annotate, prioritize, visualize and interpret GWAS results. The SNP2GENE module takes GWAS summary statistics as an input, and provides extensive functional annotation for all SNPs in genomic areas identified by lead SNPs.

Nov 28, 2017 · Here, the authors develop FUMA, a web-based bioinformatics tool that uses a combination of positional, eQTL and chromatin interaction mapping to prioritize likely causal variants and genes.

The main purpose of FUMA is to use functional and biological information to prioritize genes based on GWAS outcomes. FUMA consists of three modules: SNP2GENE, GENE2FUNC, and Cell Type.

FUMA. Upload GWAS summary statistics. Use default settings or adjust as desired. Output: • Defined risk loci • Manhattan & QQ plots • Gene-based and gene-set analyses, incl tissue and cell type • Extensive annotations of all SNPs in risk loci in LD with top SNPs • Variant to gene mapping using position, eQTL, chromatin interaction

Ensembl Variant Effect Predictor (VEP) VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.

In this practice, we will use publicly available results to explore what you can do with FUMA. If you are interested, you can create your own account and try submitting a job at the end of this section (optional).

FUMA is an online web application to annotate and prioritize genetic associations. The application is available at https://fuma.ctglab.nl.

Developed by: Kyoko Watanabe Update/maintenance: FUMA team ([email protected]) Dept. Complex Trait Genetics at VU University Amsterdam

Mar 2, 2025 · It provides essential data for variant annotation tools such as VEP, ANNOVAR, SnpEff, and FUMA, enabling them to annotate known polymorphisms and assess their potential impact based on population frequency and functional predictions.

be causal than non -functional ones (tools FUMA, VEP, ANNOVAR) Functional categories of SNPs For a SNP to be potentially causal, it needs to affect the gene, either via structure or