Atlas of epistasis

We performed a genome-wide epistasis search across 502 phenotypes in case control matched cohorts from the UK Biobank. We identified 152,519 genome wide significant interactions in 68 distinct phenotypes, and 3,398 interactions in 19 phenotypes were successfully replicated in independent cohorts from the Finngen consortium. Most interactions (79%) involved variants that did not present significant marginal association and might explain part of the missing heritability for these diseases. In 10 phenotypes we show the presence of epistasis between common variants with intermediate to large effect size (OR > 2) supporting the hypothesis that common diseases are modulated by common variants. Most of the variants in interactions (82%) were more than 1Mb apart and cis-epistasis was hardly found outside the HLA region. Functional annotation of the variants suggests that most mechanisms behind epistasis occurs at the supra pathway level and that intra-gene or intra-pathway epistasis is rare. Surprisingly we find a significant biais toward antagonistic epistasis, representing 60% to 95% of interactions. In type 1 diabetes, hypothyroidism, disorders of mineral absorption, rheumatoid arthritis, asthma, and multiple sclerosis more than 50% of interactions were completely compensating the effect of the marginally associated variant. In psoriasis we identified an interaction between a stop gain variant in CCHCR1 with two missense variants in MUC22 and HSPA1L leading to a 3 fold increase of the effect of CCHCR1 variant on disease risk. Our study shows that there is still much to discover in epistasis and we provide the full summary statistics results to researchers interested in studying epistasis.