The combined haplotype test (CHT) determines whether the genotype of a “test SNP”, \(m\), is associated with read depth and allelic imbalance within a nearby “target region”, \(j\), on the same chromosome. A single target region may be discontiguous and span multiple genomic loci. For example, the exons of a gene can be used as a single target region, which is useful when searching for expression QTLs using RNA-seq reads. The test SNP is not required to be within the target region, but is assumed to be nearby and cis-acting. This allows us to combine information from across phased heterozygous SNPs and assign reads to one haplotype or the other.