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[Preprint]. 2023 Dec 15:2023.12.15.571696. [Version 1] doi: 10.1101/2023.12.15.571696

Figure 2: Thousands of e/ca QTLs identified in clusters.

Figure 2:

(A) UpSet plot showing the number of shared and specific eGenes, and (B) caPeaks across five clusters (C) An example caQTL is depicted in a heatmap of normalized snATAC-seq reads across samples in the type 1 cluster, separated by caSNP rs12336284 genotype classes. Aggregate profiles by genotype are shown on top. Examples of shared and cluster-specific caQTL are shown in (D) , (E) , and (F) . Top two rows show snATAC-seq profiles by the caSNP genotype classes in type 1 and FAPs, followed by aggregate snATAC profiles across all 13 clusters. (G) Reconstruction of the BACH_1 TF motif using caQTL data. From top, row 1: original motif PWM. Row 2: genetically reconstructed motif PWM. For all BACH_1 motifs occurring in type 1 snATAC-seq peaks (peak-motifs) that also overlapped type 1 caSNPs, alleles associated with higher chromatin accessibility (“favored alleles”) were quantified using the caQTL allelic fold change, followed by generating a PWM. Row 3: favored allele counts for caSNPs in BACH_1 peak-motifs. Row 4: PWM reconstructed using the nucleotide counts for all heterozygous SNPs overlapping the BACH_1 peak-motifs. Row 5: nucleotide counts for all heterozygous SNPs in the BACH_1 peak-motifs. (H) Comparison of caSNP effect size and MAF with the replication of snATAC-seq peaks in a reference scATAC dataset (K. Zhang et al., 2021). (I) Allelic fold change for type 1 e/caSNPs that overlap skeletal muscle active TSS or stretch enhancer chromatin states.