Fig. 1

Capturing cis-regulatory effects with phased allelic expression data. a The presence of a heterozygous cis-regulatory variant or eQTL produces an expression-level imbalance between the two haplotypes, which can be detected using allelic expression analysis. b RNA-seq reads overlapping heterozygous SNPs in expressed regions of the gene can be used to quantify the expression of alleles relative to one another. These SNPs can be phased with each other and their counts aggregated to produce haplotype-level expression estimates, or haplotypic counts. The effects of regulatory variants can be captured by phasing them with haplotypic counts. c Spearman correlation across the 49 GTEx v8 tissues where eQTLs were called between eQTL effect size (allelic fold change, aFC) and effect size measured using AE data from the single SNP with the highest coverage (SNP AE) or haplotype-level AE generated with phASER (phASER). Results are shown with and without allelic mapping bias correction from WASP. In each tissue, only a single top significant (FDR < 5%) eQTL per gene was analyzed. p values were calculated using a Wilcoxon paired signed rank test. For boxplots, bottom whisker: Q1 − 1.5*interquartile range (IQR), top whisker: Q3 + 1.5*IQR, box: IQR, and center: median