Fig. 3: Conditional cis-eQTLs.
a, Number of conditional cis-eQTLs per eQTL dataset. b, Comparison of characteristics between primary and non-primary eQTLs. For the mean expression and pLI score values, each row compares the eQTL genes for that rank with eQTL genes from the previous rank (for example, for tertiary eQTLs, the non-significant (grey) distribution is from genes that have secondary but lack tertiary eQTLs). P values were calculated using a Wilcoxon test between significant and non-significant genes. Differences in mean gene expression levels (left), the distance between the most significant SNP–gene combination and the TSS (middle), and pLI scores (right) are shown. For primary, secondary and quaternary eQTLs, non-significant eQTLs have higher pLI scores. Vertical dotted lines indicate median of the distribution for the current rank (coloured) versus the previous rank (black). c,d, Number of overlapping eQTLs along with the Rb and standard error (s.e.) values of primary cis-eQTLs between the cortex eQTLs of different ancestries (c) and the different brain regions for the EUR datasets (d). n, sample size of the dataset. e, Correlation of effect sizes and standard error of primary cis-eQTLs of Cortex-EUR (discovery, excluding GTEx) in all of the GTEx tissues (replication). Each dot is a different GTEx tissue; the x axis indicates the number of eQTLs that are significant in both discovery and replication.
