Figure 2. Direction of allele-specific expression bias measured at SNPs in the same exon disagrees more frequently than expected by chance.

(A) Expression bias at 1,388 pairs of SNPs under ASE (chi-square p<1e-4 for both SNPs) disagrees in direction for 20.0% of pairs in E17.5 BxC data. (B) Discordance improves with increasing p-value thresholds but is higher than simulated data where allelic counts for one SNP in each pair are randomly sampled from the χ ² distribution (broken lines; see Materials and Methods).