2. Xu, J. et al. Nat. Genet. 49, 377–386 (2017). 3. Huang, F.W. et al. Science 339, 957–959 (2013). 4. Stern, J.L., Theodorescu, D., Vogelstein, B., Papadopoulos, N. & Cech, T.R. Genes Dev. 29, 2219–2224 (2015). specific and universal normalization controls (Supplementary Fig. 3). A targeted allelic ATAC assay is highly desirable because only a small fraction of DNA elements (~1%) both possess informative sequence variants and demonstrate allelic regulation2. Inclusion of an informative SNP between primer-binding sites allows for targeted analysis of allele-specific accessibility by ATAC-PCR, for example, to assess the effect of disease-associated variants on allele-specific accessibility. For well-characterized TERT promoter mutations3,4, ATAC-PCR and Sanger sequencing demonstrated that only the mutant allele conferred TERT promoter chromatin accessibility (Fig. 1c, Supplementary Table 4). We further validated allelic ATAC-PCR on a panel of DNA elements with random monoallelic accessibility in hybrid mouse NPC cells2 (Supplementary Table 5). Allele-specific quantification by ATAC-PCR correlated strongly with the allelic accessibility determined by ATAC-seq (R = 0.962) (Supplementary Fig. 4), thus demonstrating accurate quantification of targeted and allelespecific accessibility by ATAC-PCR enabled by APT. Further information on experimental design is available in the Supplementary Methods and the Life Sciences Reporting Summary.