Supplementary Figure 3: Selection of genes based on SMR and coloc results. | Nature Genetics

Supplementary Figure 3: Selection of genes based on SMR and coloc results.

From: Transcriptional risk scores link GWAS to eQTLs and predict complications in Crohn's disease

Supplementary Figure 3

(a) Each point represents the –log10 (P value) (NLP) for the blood eQTL association and Crohn’s disease GWAS association for 157 candidate genes. Colors represent the significance of the SMR statistic, clearly showing that the most highly significant genes are strongly associated with both traits. Similar plots are observed for ulcerative colitis and IBD. All 39 genes with SMR P < 2.3 × 10−4 (red and brown dots) for all three disease classifications were included in the final SMR-based TRS. (b) The coloc H4 score estimates the posterior probability that the same causal variant drives both the GWAS and eQTL associations. This plot shows that poor SMR values (small NLPs) tend also to have low coloc H4 scores; however, only approximately half of the strong SMR values (large NLPs) have strong coloc H4 posterior probabilities. The 29 genes with coloc H4 greater than 0.8 for the three disease phenotypes were included in the final coloc-based TRS. This includes 14 genes not in the SMR set.

Back to article page