Fig. 6: Example of colocalisation between an IBD risk locus at 18p11.21 and an sQTL for PTPN2.
a GWAS regional association plots of the IBD association signal (top), and sQTL association signal for the splice junction chr18:12,817,365-chr18:12,818,944 in unstimulated macrophages (Ctrl_6; middle) and macrophages stimulated with sLPS after 6 h (sLPS_6; bottom). Lead IBD SNP rs80262450 is indicated with an arrow. Colours represent linkage disequillibrium with the index SNP. b Normalised intron usage ratios of different genotypes of the lead IBD SNP rs80262450 in Ctrl_6 and sLPS_6, (c) heatmap showing evidence of colocalisation (PP4) between the IBD association signal at 18p11.21 and all macrophage eQTLs/sQTLs in the locus (in all conditions), (d) RNA-seq coverage of the intron cluster where the PTPN2 sQTL effect is detected in sLPS_6 stratified by the number of copies of the alternative allele of rs80262450. Bars represent the number of reads and arcs represent the usage of different introns (only five splice junction ratios are shown for clarity and the colocalised sQTL splice junction is indicated in a red box). Canonical transcript PTPN2-201 and non-canonical transcript PTPN2-205 (the only annotated transcript with the implicated splice junction) are shown underneath, with blue boxes representing exons and the position of rs80262450 on PTPN2-205 is shown by the green line. A similar RNA-seq coverage plot in unstimulated macrophages (Ctrl_6) is shown in Supplementary Fig. 21.
