Fig. 2: SNP and gene mapping in the tQTL profiles.

Manhattan plots of independent monocyte tQTL-associations for the naïve state (a), or after treatment with LPS (b), or IFN-γ (c). Top condition-specific independent SNPs can be found in highlighted SNPs on Manhattan plots. The y-axis displays the -log₁₀(FDR) of each association, while the x-axis displays the chromosomal position of SNPs. d Functional annotation of independent g/tSNPs using genomic features. The plot displays the z-score calculated using the proportion of SNPs (independent g/tSNP and their LD proxies) which have corresponding functional annotations assigned by biomaRt (Ensembl) and UCSC databases in comparison with background SNP. The foreground SNP sets for each gene/transcript were made up of g/tSNP with FDR <0.001, and other gSNPs within the 1 Mb and tSNPs within the 100 Kb window around the TSS were used as background. e The enrichment of independent g/tSNP with chromatin state (E029 chromatin states dataset provided by the Roadmap Epigenomics Consortium) across primary monocytes from peripheral blood tissue. f Highlighted isoforms (red colour) of MUC1, including ENST00000612778 and ENST00000620103 show significant tQTL in IFN-γ stimulated condition. g For MUC1, we found an independent SNP (rs4072037) which is associated with two transcripts in a context-specific manner. The display of splice junctions is limited to those that are not present in all transcripts. Abbreviations: TssAFlnk Active TSS Flank, TxFlnk Transcription, Tx Transcription Flank, TxWk Weak Transcription, EnhG Gene Enhancer, Enh Enhancer, ZNF/Rpts Zinc Finger/Repeats, Het Heterochromatin, TssBiv Bivalent TSS, BivFlnk Bivalent Flank, EnhBiv Bivalent Enhancer, ReprPC Repressed Polycomb-repressed Complex, ReprPCWk Weak Repressed Polycomb-repressed Complex, Quies Quiescent chromatin. fiveUTRs 5’ Untranslated Regions. threeUTRs 3’ Untranslated Regions. “N” represents and lists the specific number of donors. The x-axis of the boxplot represents the different alleles of the SNP that are related to the expression. Each box indicates a particular SNP allele, and the y-axis displays the expression levels of individuals with that allele. The normalised read count and Fragments Per Kilobase Million (FPKM) metrics display the expression levels of genes and transcripts, respectively.