Fig. 6: Mapping cis-eQTL across the HLA in diverse immune cells.
a, Effect of the index variant (rs34951355) associated with differential DT response in African infants on normalized HLA-DRB1 expression in immortalized LCLs from individuals from four African populations (99 individuals from ESN, 112 from GWD, 97 from LWK and 166 from MKK). Only those with more than a single observation in each genotype category are shown. A plot of the data from the pooled set of four populations is also shown. The x-axes numbers refer to the number of copies of the C allele compared to the A allele in each group of individuals per population. Differences between allele copies within the final pooled set were calculated using unadjusted linear regression, P = 4.7 × 10−5. b, The effect of the same variant on normalized HLA-DRB4 expression in the same individuals as detailed in a, P = 1.6 × 10−215. c, The effect of rs545690952 (a variant in LD with rs34951355) on HLA-DRB1 expression in circulating monocytes, naive B cells, naive CD4+ and CD8+ T cells and natural killer (NK) cells from 80 individuals with expression and HLA allele data available from the DICE study demonstrating a consistent direction of reduced HLA-DRB1 expression in monocytes with significance tested using linear regression. Monocytes, P = 8.6 × 10−3. d, The effect of alternate T alleles of rs72851029 on PT antibody response in the African infant GWAS, n = 2,499 with significance tested in a recessive model using linear regression, P = 6.9 × 10−29. e, The effect of rs72851029 on HLA-DRB1 expression in monocytes from 80 individuals from DICE with significance tested using a recessive model using linear regression, P = 0.001. f, The effect of rs72851029 on HLA-DQB1 expression in monocytes from the same 80 individuals with significance tested between groups using an additive model with linear regression and testing only the difference between individuals carrying one or two T alleles of the variant, P = 0.05. In the box plots, the center line represents the median, the box limits denote the upper and lower quartiles, and the whiskers are 1.5 times the interquartile range. *P ≤ 0.05, ***P ≤ 0.001.
