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N⁶-methyladenosine (m⁶A) plays important roles in regulating messenger RNA processing. Despite rapid progress in this field, little is known about the genetic determinants of m⁶A modification and their role in common diseases. In this study, we mapped the quantitative trait loci (QTLs) of m⁶A peaks in 60 Yoruba (YRI) lymphoblastoid cell lines. We found that m⁶A QTLs are largely independent of expression and splicing QTLs and are enriched with binding sites of RNA-binding proteins, RNA structure-changing variants and transcriptional features. Joint analysis of the QTLs of m⁶A and related molecular traits suggests that the downstream effects of m⁶A are heterogeneous and context dependent. We identified proteins that mediate m⁶A effects on translation. Through integration with data from genome-wide association studies, we show that m⁶A QTLs contribute to the heritability of various immune and blood …