ECLIPSER (Enrichment of Causal Loci and Identification of Pathogenic cells in Single Cell Expression and Regulation data) is a tool that tests whether the expression of genes mapped to GWAS loci of complex diseases or traits, based on eQTLs and sQTLs or other functional data, are enriched in specific cell types in single cell/nucleus RNA-seq data of one or more tissues:

QTLEnrich v2 tests whether trait associations (genome-wide significant and nominal) are enriched among expression or splicing QTLs in a given tissue in GTEx v8 compared to confounder-matched null variants. It also evaluates the number of trait associations beyond genome-wide significance that may exert their causal effects via e/sQTLs. Available on Github:

The confounder and null variant tables needed to run QTLEnrich v2 on GTEx v8 eQTLs and sQTLs can be downloaded here.

QTLEnrich v2 was applied to 87 GWAS of complex diseases and traits and eQTLs and sQTLs in 49 tissues in the GTEx v8 Science 2020. A methods paper is in preparation.

eQTLEnrich, tests for enrichment of(modest to genome-wide significant common variant associations amongst a set of eQTLs in a given tissue applied to GTEx v6. Software package can be downloaded here (version on github coming soon):

Gamazon ER*,†, Segrè AV*,†, van de Bunt M*, et al., Using an atlas of gene regulation across 44 human tissues to illuminate complex disease- and trait-associated variation, Nature Genetics 2018.

eGeneEnrich tests whether target genes of eQTLs or sQTLs with top ranked GWAS p-values (e.g., p<0.05) are enriched in specific biological pathways or other types of gene sets. Software package can be downloaded here:

Described in: Gamazon ER*,†, Segrè AV*,†, van de Bunt M*, et al., Nature Genetics 2018.

Meta-Analysis Gene-set Enrichment of variaNT Associations (MAGENTA)

A computational tool that applies gene set enrichment analysis to genome-wide association variant summary statistics for a given complex disease or trait, testing whether genetic associations in or around genes are enriched specific biological pathways or functional modules, correcting for variant to gene confounding factors (Segrè et al., PLoS Genetics 2010).