Extended Data Fig. 5: Examples of fine-mapping and regulatory mechanisms underlying eQTLs.

a, Colocalization of a progenitor-specific caQTL and fetal cortical eQTL for ETFDH. b, caQTL for rs11544037 and the labeled peak in progenitor (N = 76). P-values are estimated by a mixed linear effects model using a two-sided test (Methods). c, eQTL of ETFDH in bulk fetal cortex (N = 235). P-values are estimated by a mixed linear effects model using a two-sided test (Methods). d, The expression of TFs whose motifs are disrupted by rs11544037²² (LFC = -0.32, FDR = 7.55e-18)²⁶. e, The motif Logo of RAD21, where the red box shows the position disrupted by rs11544037. Schematic cartoon of mechanisms for rs11544037 regulating chromatin accessibility and gene expression. f, Luciferase signals for alleles of rs11544037 in progenitors (N = 8). P value is from two-sided paired t-tests. g, Co-localization of a progenitor-specific caQTL and eQTL for FGF1. h, CaQTL for rs11960262 and the labeled peak in progenitor (N = 76). P-values are estimated by a mixed linear effects model using a two-sided test (Methods). i, eQTL of ETFDH in progenitors (N = 85). P-values are estimated by a mixed linear effects model using a two-sided test (Methods). j, The expression of TFs in which motifs are disrupted by rs11960262. k, The motif Logo of EGR1, where the red box shows the position disrupted by rs11960262. Schematic cartoon of mechanisms for rs11960262 regulating chromatin accessibility and gene expression. (For box plots in (b-c), (f) and (h-i), the center of the box is the median, the bounds of the box are 25th percentile and 75th percentile of the data, and the whisker boundary is 1.5 times the IQR. Maximum and minimum are the maximum and minimum of the data.).