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We introduce poly-adenine CRISPR gRNA-based single-cell RNA-sequencing (pAC-Seq), a method that enables the direct observation of guide RNAs (gRNAs) in scRNA-seq. We use pAC-Seq to assess the phenotypic consequences of CRISPR/Cas9 based alterations of gene cis-regulatory regions. We show that pAC-Seq is able to detect cis-regulatory-induced alteration of target gene expression even when biallelic loss of target gene expression occurs in only ~5% of cells. This low rate of biallelic loss significantly increases the number of cells required to detect the consequences of changes to the regulatory genome, but can be ameliorated by transcript-targeted sequencing. Based on our experimental results we model the power to detect regulatory genome induced transcriptomic effects based on the rate of mono/biallelic loss, baseline gene expression, and the number of cells per target gRNA., Author summary Predicting how mutations in non-coding regions impact gene expression is an important step towards understanding how non-coding variants contribute to human variation and disease. CRISPR/Cas9 enables programmable and scalable alteration of genomic regions of interest. More recently, CRISPR/Cas9 based screens have been combined with single-cell RNA-sequencing (scRNA-seq) technology to provide cellular transcriptomes as screen readouts. However, existing studies coupling CRISPR screens with scRNA-seq have focused on perturbations to open reading frames (ORFs). We develop an assay for directly observing CRISPR/Cas9 guide RNAs (gRNAs) in scRNA-seq, and apply it to monitoring gene expression changes induced by perturbations to the regulatory genome. We find that in contrast to ORF targeting, altering regulatory regions rarely results in total knock-out of the targeted gene. We analyze how the power to detect the consequences of changes to the regulatory genome depends on factors such as number of cells receiving a gRNA, the extent of a knock-out, and the baseline gene expression in the control.