noahconnally.bsky.social @noahconnally.bsky.social · 05/02/2026Our take-aways are that GWAS can be broadly linked to eQTLs—just not in humans (yet). This is probably due to selection and population history. We expect that as we find human eQTLs under stronger selection, colocalizations will increase. 011
noahconnally.bsky.social @noahconnally.bsky.social · 05/02/2026These high-frequency selected variants lead to higher colocalization success. There are other differences we look at in the paper, including the spatial distribution of ascertained eQTLs across species, and the different strengths of selection for eQTLs across species. 110
noahconnally.bsky.social @noahconnally.bsky.social · 05/02/2026These population histories lead to very different allele frequency distributions. When we simulate genomes based on the human population histories, most deleterious variants are uncommon. When we use the cattle population history, we observe many high-frequency deleterious variants. 120
noahconnally.bsky.social @noahconnally.bsky.social · 05/02/2026Why is this? Humans, cattle, and pigs have similar genomes. The main difference is that cattle and pigs have experienced strong recent selection due to agricultural breeding. The breeding has decreased the effective population size, while the human effective population size has increased. 100
noahconnally.bsky.social @noahconnally.bsky.social · 05/02/2026Recently, large eQTL-mapping datasets were released in cattle and pigs. To our surprise, colocalization explained a much higher percentage of GWAS loci. Here we compare the three species (using fastEnloc, a colocalization method). 100
noahconnally.bsky.social @noahconnally.bsky.social · 05/02/2026Most GWAS variants are non-coding, and evidence suggests that they may act as eQTLs: variants that alter the expression of a gene. Colocalization is a way of testing whether a GWAS and an eQTL share a causative variant. But previous work has found that most GWAS loci don’t colocalize with eQTLs. 110
noahconnally.bsky.social @noahconnally.bsky.social · 05/02/2026A new preprint out with Shamil Sunyaev. We talk about GWAS, gene expression, evolution, and why searching for trait-associated eQTLs is easier in cattle and pigs. www.biorxiv.org/content/10.6...biorxiv.org 161
