Fig. 1: Discovery and characterization of eQTLs in iPSC-PPC.

a Study overview created using PowerPoint. b Density plots showing the distribution of PDX1⁺ cells (%; regardless of NKX6-1 status; light green) and PDX1⁺/NKX6-1⁺ cells (%; dark green) in the 107 iPSC-PPC samples. c Bar plot showing the number of eGenes with primary and conditional e_gQTLs. d Bar plot showing the number of eIsoforms with primary and conditional e_iQTLs. e Enrichment (odds ratio, X-axis) of eQTLs in genomic regions (Y-axis) using two-sided Fisher’s Exact Tests comparing the proportion of variants with causal posterior probability (PP) \(\ge\)5% in the genomic regions between e_gQTLs (blue; n = 8763) and e_iQTLs (yellow; n = 8919). f Line plot showing Pearson correlations of TF binding score and eQTL effect size at different thresholds of causal PP for e_gQTLs (blue) and e_iQTLs (yellow) (Supplementary Data 8). Closed points indicate significant correlations (nominal p < 0.05) while open points indicate non-significant correlations (nominal (p > 0.05). g Bar plot showing the number of genes with only e_gQTLs (blue; n = 3057), only e_iQTLs (green; n = 1554), or both. Orange represents genes whose e_gQTLs colocalized with all their corresponding e_iQTLs (PP.H4 \(\ge\) 80%; n = 333). Red represents genes whose e_gQTLs did not colocalize with any of their corresponding e_iQTLs (PP.H3 \(\ge\) 80%; n = 38), and pink represents genes with both shared and distinct e_gQTLs and e_iQTLs (i.e., an eGene with two eIsoforms may colocalize with one eIsoform but not the other) (n = 39). Gray represents genes whose eQTL signals were not sufficiently powered to test for colocalization (PP.H4 < 80% and PP.H3 < 80%; n = 598).