Extended Data Fig. 2: Variant locations relative to cis-regulatory features.
a) Location relative to TSSs of all MPRA tested variants, active elements (pCRE), and emVars. b) Enrichment of variants within pCREs (light blue) and emVars (dark blue) within chromHMM-defined genomic regions in human T cells. * for P < 0.05; *** P < 1.4 ×10−3 (Bonferroni-corrected for 36 independent tests). c) Functional enrichment of variants within pCREs and emVars. *** for P < 6.3 ×10−3 (nominal p-value threshold of 0.05 Bonferroni-corrected for 8 independent tests). d) Proportion of inactive element and pCRE variants and emVars that have allelic bias in ATAC-seq. e) Scatter plot comparing MPRA log2 allelic bias (y axis) with allelic bias in ATAC-seq from hematopoietic cells (x axis)5. Red dots are emVars (n = 5) and gray dots are pCRE variants (n = 45). f) Proportion of MPRA inactive and pCRE variants, and emVars that are chromatin accessibility QTLs (caQTLs) from T cells65. g) Scatter plot comparing caQTL effect size (beta; x axis) and MPRA log2 allelic bias (y axis). Red dots are emVars (n = 6) and gray dots are pCREs (n = 22). h) Scatter plot comparing deltaSVM score (x axis) with MPRA log2 allelic bias (y axis) (n = 278). i) Proportion of MPRA inactive and pCRE variants and emVars that overlap TF motifs. j) Scatter plot comparing allele-specific TF binding scores (y axis) and MPRA allelic bias (x axis) for emVars predicted to perturb TF binding (n = 11). Enrichment of emVars for TF ChIP-seq (-log10P on y axis). Calculations for (b and c) are risk ratios (see Methods) with Fisher’s exact test P values and Bonferroni correction (see Supplementary Tables 5 and 6 for exact P values). (d, f, and i) P values calculated using two-sided two proportions z test with no multiple comparisons adjustment. (e, g, h and j) P values are from linear regression F statistic. (k) P values are from a two-sided binomial test.
