Mapping of promoter usage QTL using RNA-seq data reveals their contributions to complex traits
Fig 3
puQTL-associated gene classification.
(A) The procedure used for puQTL gene classification. (B) Count of each group of puQTL genes. (C) The TMEM200A gene locus. The structures of the TMEM200A gene in the Ensembl 104 annotation and assembled in this study are presented in black and red, respectively, with ENCODE GM12878 H3K4me3 and H3K27ac ChIP-seq signals. The vertical blue bars indicate the location of active promoters. The black bar indicates the location of the rs11154537 variant. (D, E) Comparison of the promoter activities (D) and total expression levels (E) of the TMEM200A gene among the rs11154537 genotypes. The numbers in parentheses indicate sample size. (F) The associations of puQTL, fine-mapped puQTL for prmtr.94867, and eQTL for TMEM200A are shown in the top, middle, and bottom panels. rs11154537 is plotted in a red diamond, and the colors indicate the r-squared values between rs11154537 and other variants. (G) The SYNJ2BP-COX16 gene locus. (H, I) The promoter activities (H) and total expression levels (I) of the SYNJ2BP-COX16 gene were compared among the rs145415365 genotypes. (J) Associations of puQTL, fine-mapped puQTL for prmtr.136781, and eQTL for SYNJ2BP-COX16 are shown in the top, middle, and bottom panels.