We sought to test the hypothesis that the top associations from the WTCCC Bipolar Disorder study are enriched for variants that affect methylation levels. This follows our earlier study on the use of eQTL enrichment analysis and eQTL-based annotation to enhance discovery of reproducible signals from GWA studies 6. That initial study was performed on (transformed) lymphocytes. We thus wanted to test a secondary hypothesis, whether SNPs that exert an influence on methylation levels in brain, the presumed tissue of relevance for Bipolar Disorder, are enriched in SNPs showing strong associations with Bipolar Disorder.
