Fig. 2: Regulatory activity of enhancer variants (enVars).
From: Global discovery of lupus genetic risk variant allelic enhancer activity
a Distribution of MPRA regulatory activity. The normalized fold change of MPRA activity relative to plasmid control (X-axis) was calculated using DESeq2 (n = 3 biological replicates). Enhancer alleles (enAlleles) (blue) were identified as those alleles with significant activity relative to control (padj < 0.05) and at least a 50% increase in activity (see “Methods”). The p-values were generated by two-sided Wald tests with Benjamini–Hochberg multiple testing correction. Full results are provided in Supplementary Data 6. b Enrichment of histone marks in GM12878 cells at enVars compared to non-enVars. p-values were estimated by one-sided z-test with Bonferroni multiple testing correction using RELI (see “Methods”). Full results are provided in Supplementary Data 9. c Enrichment of regulatory protein and transcription factor (TF) binding at enVars compared to non-enVars. p-values were estimated by one-sided z-test with Bonferroni multiple testing correction using RELI (see “Methods”). The top 15 TFs (based on RELI p-values) that overlap at least 10% of enVars are shown. Full results are provided in Supplementary Data 9. d TF binding site motif enrichment for enVars compared to non-enVars. p-values were estimated by one-sided hypergeometric test with Benjamini–Hochberg multiple testing correction by HOMER using the full oligo sequences of enVars and non-enVars (see “Methods”). The top 15 enriched TF motif families are shown. Full results are provided in Supplementary Data 10.
