We investigated the Altrans-specific asQTLs further. First we find that the majority of the Altrans-specific asQTLs originate from links between exons that are not annotated in the GENCODE v.12 annotation and therefore were never tested by Cufflinks (89% and 83% not annotated for Europeans and Africans, respectively; Figure S3). Next, we assessed whether Altrans-specific discoveries replicate, and to do so we tested the Altrans-specific discoveries originating from the 91 CEU individuals in the remaining Europeans, and these associations achieve a π1 statistic of 93%, indicating a high true positive rate in Altrans-specific asQTLs (Figure S4A). We also estimate that 63% of the Altrans-specific asQTLs in Europeans are replicated in Africans and 95% of the African Altrans-specific asQTLs are replicated in Europeans.