A literature search led us to previous work identifying DNase I hypersensitivity sites and CTCF binding sites important in regulating the expression of genes in the PCDH gene cluster.47–49 The positions of NicW-associated SNPs relative to these regulatory regions were examined using the following UCSC Genome Browser tracks: “DNaseI HS Density Signal from ENCODE/Duke” track for ventromedial prefrontal cortex and fibroblast tissue, and “Transcription Factor ChIP-seq (161 factors) from ENCODE” track for CCCTC-binding factor (CTCF).50–52 HS5-1 sites were mapped to the genome using primers that had been previously used to generate electrophoretic mobility shift assay probes for HS5-1a and HS5-1b.47 UCSC Genome Browser51 screenshots containing the indicated track data were used to illustrate the relative position of the SNPs and regulatory elements. The P-values for the association of rs31746 with PCDH-α, -β and -γ gene cluster mRNA expression were extracted from BrainCloud (http://braincloud.jhmi.edu/; dbGaP Study Accession: phs000417.v2.p1).53 BrainCloud includes data from human prefrontal cortex (PFC) tissue and an association with gene expression in other brain regions was not tested. Fifty-five different PCDH-α, -β and -γ gene mRNAs were targeted by 63 probes. All gene names and corresponding expression P-values are shown in Table S3.
