Figure 2.

Genetic effects on the whole-skin methylome

(A) Distance between lead cis-meQTL and CpG vs. strength of association of the meQTL effect.

(B) Most associated cis-meQTL association between variant rs1253098 (chr14:59945536) and cg01543583 (chr14:59947673).

(C) Most associated trans-meQTL association between the variant rs10744202 (chr12:125800244) and cg03923277 (chr12:104359732).

(D) Enrichment and depletion of meQTL effects in different genomic contexts. Green indicates significant (FDR $<$ 0.05) enrichment, purple indicates significant depletion. CpG islands based on UCSC refGene annotations (CpG shore, $<$2 kbp from CpG island; CpG shelf, 2–4 kbp from CpG island; open sea, $>$4 kbp from CpG island), and gene context is based on refGene annotations (TSS200, $<$200 bp from transcription start site (TSS); TSS1500, 200–1,500 bp from TSS).

(E) Enrichment and depletion of meQTL effects in transcription factor binding sites (TFBSs) in suprapubic skin and genomic states in leg skin generated using an 18-state ChromHMM model from the Roadmap Epigenomics Consortium.⁵⁹ White asterisks indicate significant depletion, black asterisks indicate significant enrichment. Suprapubic skin TFBS and leg skin chromatin state annotations were obtained from the EpiMap Repository⁶⁰ (TssA, active TSS; TssBiv, bivalent/poised TSS; TssFlnk, flanking active TSS; TssFlnkU, flanking TSS upstream; TssFlnkD, flanking TSS downstream; Tx, strong transcription; TxWk, weak transcription; EnhA1, active enhancers 1; EnhA2, active enhancers 2; EnhG1, genic enhancers 1; EnhG2, genic enhancers 2; EnhBiv, bivalent enhancer; EnhWk, weak enhancer; ReprPC, repressed polycomb; ReprPCWk, weak repressed polycomb; ZNF_Rpts, ZNF genes and repeats; Quies, quiscent chromatin; Het, heterochromatin; see Kundaje et al.⁵⁹).