Additional file 9: Table S7a. of Chromosome contacts in activated T cells identify autoimmune disease candidate genes

Autoimmune disease COGS gene prioritisation. Overall COGS gene scores (COGS_Overall_Gene_Score) for each gene and autoimmune disease are shown together with the prioritised category and score associated with that category (COGS_Category_Gene_Score) (Fig. 3). The ‘analysis’ column describes whether the input data was GWAS or ImmunoChip (ICHIP) and whether summary statistic (SS) or GUESSFM (GF) fine-mapping was used. ‘diff.expr’ indicates whether the gene was not expressed (NA) or, if expressed, whether there was differential expression at the FDR < 0.01 level (up, down or nsig). Similarly, ‘diff.erna’ indicates whether the HindIII fragment containing the strongest SNP signal is differentially expressed with the same categories. Using data from ImmunoBase ( https://www.immunobase.org - accessed 06/06/2016), we annotate genes near (within 5 Mb) previously reported disease susceptibility regions, with contextual annotation ‘Closest_Disease_Susceptibility_Region’, ‘Closest_Min_P_Value_Susceptibility_SNP’, ‘Closest_Min_P_Value_Susceptibility_SNP_P_Value’, ‘PIR_Overlaps_Disease_DSR’ indicates that the PIR driving the prioritisation for a gene/disease overlaps an ImmunoBase known disease susceptibility region for that trait. Restricted to the subset of genes with scores > 0.5 that are analysed in this paper. (GZ 37 kb