For expression quantitative trait locus (eQTL) analyses, we retrieved lymphoblastoid cell line SLC1A1 expression values for the 60 HapMap Centre d'Etude du Polymorphisme Humain founders with northern and western European ancestry from 2 independent platforms: the Gene Expression Omnibus data set GSE5859 (Affymetrix platform, probe No. 213664_at; replicates were averaged and transformed as above)24 and from the Gene Expression Variation Web site hosted by the Wellcome Trust Sanger Institute (http://www.sanger.ac.uk/humgen/genevar; Illumina platform, probe No. GI_31543625-S).25 Genotypes for all 90 individuals from the Centre d'Etude du Polymorphisme Humain HapMap data were downloaded from the HapMap Web site (http://www.hapmap.org, release 22) for the entire SLC1A1 region plus 1 megabase (Mb) flanking both sides (corresponding to position 3 480 444 to 5 577 469 on chromosome 9 in the University of California–Santa Cruz Genome Browser Human, March 2006 assembly). Markers inconsistent with mendelian inheritance patterns, with minor allele frequencies of less than 1%, or with more than 10% missing genotypes were removed, resulting in a total of 2467 polymorphisms that were analyzed. These SNPs were then tested for quantitative association with SLC1A1 expression using PLINK,26 Microsoft Excel (Microsoft, Redmond, Washington), and Prism 4 (GraphPad Software, San Diego, California).
