Allelic transcript ratio mapping for 300 SNPs across ∼1200 kb centered on IL13 revealed a region located 200–300 kb upstream of IL13 containing nine SNP markers with marked differences between MTR and NTR in both (A) non-activated cells and (B) activated cells. These nine SNPs fall within a genomic block of high linkage disequilibrium spanning APXL2 (SHROOM1), GDF1, QP-C (UQCRQ), LEAP2, and AFF4 and are all unique to (C) haplotype A4, which has an average haplotype-specific transcript ratio (HTR) of 1.28 (95% CI, 1.19–1.37). (D) Haplotype analysis of the proximal 100-kb region containing IL13, IL4, and RAD50 highlighted haplotype B4 with an HTR much more apparent in activated cells (HTR = 0.78, 95% CI, 0.65–0.91) than in non-activated cells (HTR = 0.93, 95% CI, 0.76–1.10).
