(A) Schematic representation of cis-regulatory eQTL model in Equations 1 and 2. (B) Example of allelic expression associated with each of the alleles of a cis-eQTL (eVariant Chr 5: 96252589 T/C; eGene ERAP2) in GTEx adipose subcutaneous. Each dot corresponds to allelic imbalance in one individual heterozygous for the eVariant, measured using reads that overlap heterozygous SNPs (aeSNP) in the eGene. Phasing between the aeSNP and the eQTL SNP is utilized to associate the measured allelic expression with each of the eQTL alleles. (C,D) eGene expression for the same example eQTL. The green dashed line connects the median expression of the two homozygous classes. Expression is linear with number of alternative alleles (C), but the linearity is lost after log transformation (D).
