Correlation with endometrial, GTEx and eQTLGen eQTLs

To evaluate whether the genetic effects on gene expression in endometrial tissue also occurred in other tissues, we correlated eQTL effects with 48 tissues from the GTEx v7 project (Supplementary Table SI) (Consortium, 2015; Consortium et al., 2017) and the blood eQTL dataset from eQTLGen Consortium (eQTLGen) consisting of 31 684 individuals (Võsa et al., 2018). We used the r_b method developed by Qi et al. (2018) to estimate the correlation between genetic effects at top cis-eQTLs whilst accounting for eQTL effect estimation errors (Qi et al., 2018). Briefly, we used the top significant brain eQTLs (P_eQTL < 5 × 10⁻⁸) from the religious orders study and memory and ageing project (ROSMAP) (Ng et al., 2017) as a reference to avoid ascertainment bias. Subsequently top ROSMAP cis-eQTLs present in both the endometrium eQTL dataset and the GTEx tissue eQTL dataset being tested were used in the effect size (ES) correlation analysis. Genome positions of endometrial eQTLs from this study were converted from the GRCh38 assembly back to the GRCh37 assembly for direct comparison with ROSMAP, GTEx and eQTLGen datasets.