Figure 6. Colocalization of cell-type-specific edQTLs and apaQTLs with brain-relevant trait GWAS loci.
(A) Genomics tracks illustrating that an edQTL within CCDC88A gene locus in neurons was colocalized with an index variant for education attainment GWAS; whereas there was not any significant eQTL for CCDC88A. Data points were colored based on the pairwise LD r2 with rs563320407; p-values for each association are shown on the y-axis and genomic positions of genetic variants are shown on the x-axis.
(B) Boxplot illustrating distribution of editing rate across rs56320407.
(C) The predicted secondary structure of the IRAlu hairpin for T and C alleles of rs56320407. Edit sites and genetic variants are indicated by red and blue colors, respectively.
(D) Genomics tracks illustrating that an apaQTL within EP300 gene locus in progenitor was colocalized with an index variant for schizophrenia GWAS; whereas there was not any significant eQTL for EP300 gene. Data points were colored based on the pairwise LD r2 with rs35508493; p-values for each association are shown on the y-axis and genomic positions of genetic variants are shown on the x-axis.
(E) Boxplot illustrating distribution of editing rate across rs56320407.
(F) microRNA binding sites are shown for the genomic region which differs between two potential 3’UTR isoforms of EP300 gene (genomic coordinates for APA site 1: chr22:41,178,956-41,180,079 and APA site 2: chr22:41,178,956-41,179,495).