We used GARFIELD (unpublished; http://www.ebi.ac.uk/birney-srv/GARFIELD/) to test for enrichment of IGAP Alzheimer’s disease GWAS SNPs among sQTLs and other publicly available QTL datasets. GARFIELD performs greedy pruning of GWAS SNPs (LD r2 >0.1) and then annotates them based on functional information overlap. It quantifies fold enrichment at GWAS P <10−5 significant cutoff and assesses them by permutation testing, while matching for minor allele frequency, distance to nearest transcription start site and a number of LD proxies (r2 > 0.8).
