Fig. 4

Identification of chromatin QTLs (cQTLs). a QQ plot of cQTLs using window size of 5 kb (green) or 50 kb (black). Both show marked deviations from the expected. b Distance of cQTLs relative to the center of ATAC-seq peaks as a function of minor allele frequency. c Most significant cQTL, rs1549428 (chr12:9,436,157−9,436,457); individuals homozygous for the reference allele (0) display more chromatin accessibility than individuals that are heterozygous (1) and homozygous for the alternate allele (2). d Most significant cQTL that is also a schizophrenia GWA loci, rs11615998 (chr12:2,364,960−2,365,260). Due to a low minor allele frequency (MAF = 0.059), only one individual was homozygous for the alternate allele. The results were comparable with or without this homozygous individual. The boxplots represent the following statistics: median (bolded line), the 1st and 3rd quartiles (bounds of box) and 1.5× the inter-quartile range (whiskers)