In the present study, we carried out deep RNA sequencing and genome-wide genotyping on a large collection of human brains from the second trimester of gestation (n = 120), providing the first eQTL dataset derived exclusively from the prenatal human brain. We identify high confidence cis-acting eQTL at the individual transcript as well as whole gene level, including many mapping to a common inversion polymorphism on chromosome 17q21. We further show that fetal brain eQTL are enriched among risk variants for neuropsychiatric disorders and identify genetically influenced changes in gene expression within the developing brain that potentially mediate risk for these conditions.
