In genome-wide association studies (GWAS), variants showing consistent effect directions across populations are considered as true discoveries. We model this information in an Effect Direction MEta-analysis (EDME) to quantify pleiotropy using GWAS of 34 Cholesky-decorrelated traits in 44,000+ cattle with sequence variants. The effect-direction agreement between independent bull and cow datasets was used to quantify the false discovery rate by effect direction (FDRed) and the number of affected traits for prioritised variants. Variants with multi-trait p < 1e-6 affected 1∼22 traits with an average of 10 traits. EDME assigns pleiotropic variants to each trait which informs the biology behind complex traits. New pleiotropic loci are identified, including signals from the cattle FTO locus mirroring its bystander effects on human obesity. When validated in the 1000-Bull Genome database, the prioritized pleiotropic variants consistently predicted expected phenotypic differences between dairy and beef cattle. EDME provides robust approaches to control GWAS FDR and quantify pleiotropy.