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Chunk #39 — Materials and Methods — Utilizing Expression Information in GWAS

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Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS.
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We repeated the Crohn's disease enrichment studies in the other WTCCC phenotypes. As with Crohn's disease, we first conducted analyses checking for an excess of small association p-values in the SNPs that have high expression annotation scores (Figure 4). Finally, we ranked the SNPs according to their association p-values and looked for an enrichment of high expression scores (Figure 5).