Notably, we identified 22 tCNVs (r2 = 1) that predict the transcript level of 10 or more genes. These CNVs are regulating the expression of distal transcripts. By performing simulations on frequency-matched SNPs as the tCNVs, we observed an enrichment (expected count = 14.7, SD = 3.8) for CNVs controlling the expression of 10 or more, often distal, transcripts (See Figure S1). We identified 2 CNVs CNVR4596.1 (chrom10:4698559–4700493) and CNVR1045.1 (chrom2:165722938–165725072) that predict the expression of at least 100 transcripts. CNVR4596.1 does not contain any genes; on the other hand, CNVR1045.1 overlaps with SCN3A. Additional CNVs CNVR3307.1 (chrom7:17780194–17781249), CNVR3500.1 (chrom7:97233946–97240537), and CNVR7062.1 (chrom17:27130696–27131638) predict the expression of at least 50 transcripts. The CNV region CNVR3307.1 contains several SNPs (e.g., rs2723520, rs1404418, and rs1404419) in strong LD, which individually predict the expression of more than 80 transcripts.
