Extended Data Fig. 6: Features of ASCA.

a, Density plot for caPeak length from shared caQTLs and ASCA, and from peaks only significant in ASCA in neurons (top) and progenitors (bottom). P values are estimated by two-sided Student’s t-tests. b, The neuron ASCA (caSNP: rs62332390; caPeak: chr4:148,441,611-148,46,300; P values are estimated by the negative binomial generalized linear models from DESeq2 using a two-sided test⁶²) is not a significant caQTL (N = 61; P values are estimated by the mixed linear model using a two sided test) in neurons because the caPeak was very wide (4,689 bp) and only the region near the ASCA SNP shows an association with genotype. c, The neuron ASCA (caSNP:rs77191441; caPeak:chr5:116,571,961-116,576,710; P values are estimated by the negative binomial generalized linear models from DESeq2 using a two-sided test⁶²) is not a significant caQTL (N = 61; P values are estimated by the mixed linear effects model with a two-sided test) in neurons due to low minor allele frequency leading to less power to detect a caQTL. d, ASCA between rs185220 (see Fig. 3) and chromatin accessibility in progenitors (left) and neurons (right). P-values are estimated by the negative binomial generalized linear models from DESeq2 using a two-sided test⁶². (For box plots in (b) and (c), 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.).