To test the associations between the most significant variants and gene expressions, human autopsy brain samples were obtained from the New South Wales Brain Tissue Resource Centre (NSWBTRC) at the University of Sydney (http://sydney.edu.au/medicine/pathology/btrc/). Fresh frozen samples of the superior frontal cortex (Brodmann area 8) were used. This region was selected because a prior enrichment analysis suggests aggregation of AD-associated GWAS signals in this brain region (Kapoor et al., 2018). In addition, there was an adequate sample size available for this region. The samples were sequenced on Illumina Hi-Seq (Illumina, CA, USA) at the New York Sequencing center (N=83) and at the Waggoner Center for Alcohol and Addiction Research (N=60). Total RNA was extracted from frozen tissue and samples with contamination or degraded quality RNA (RNA integrity numbers (RIN) <5.0) were excluded. 138 samples passed quality review and were used in analysis (65 AD, 73 age and sex matched controls). The KAPA Stranded RNA-Seq Kit with RiboErase was used for library preparation. The library QC included a measurement of the average size of library fragments using the Fragment Analyzer (Advanced
