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. 2018 Jun 21;9:2427. doi: 10.1038/s41467-018-04365-8

Table 1.

IBD risk loci for which at least one cis-eQTL association pattern (EAP) was found to match the disease association pattern (DAP)

Loc Chr Beg End cRM Nr Genes with correlated DAP–EAP Implicated cell types Best θ Best p Ref
CD UC CD UC
HD1 1 2.4 2.8 271 2 TNFRSF14 CD4 CD8 IL TR −0.74 −0.79 0.02 0.03 4,48
HD2 1 7.7 8.3 2900 1 PARK7 CD15 TR RE −0.8 −0.82 0.01 0.06 48
N_1_62 1 62.5 63.5 109 3 DOCK7 USP1 ATG4C CD4 CD8 CD19 CD14 CD15 −0.9 0 0.01 1.00 3
N_1_100 1 101.0 102.0 6008 1 SLC30A7 TR 0 −0.71 1.00 0.06
J_1_119 1 120.2 120.7 9459 1 NOTCH2 CD19 0.68 0 0.13 1.00
HD14 1 155.0 156.1 5 8 GBA CD4 −0.65 0 0.01 1.00
238 3 THBS3 GBA MUC1 CD14 CD15 TR 0 0.81 1.00 0.02
4513 1 THBS3 CD4 0 0.66 1.00 0.02
HD21 1 197.3 198.0 6071 1 DENND1B CD4 0.7 0.78 0.03 0.02
HD30 2 62.4 62.7 3716 1 B3GNT2 CD8 −0.63 0 0.01 1.00
HD35 2 102.8 103.3 1132 1 IL18R1 CD4 CD8 −0.93 −0.87 0.01 0.03 4
8912 1 (IL18RAP) CD8 −0.42 0 0.11 0.38 4
J_2_197 2 198.2 199.1 325 2 MARS2 PLCL1 CD4 CD14 −0.72 0 0.06 1.00 2,48
J_2_218 2 218.9 219.4 216 3 PNKD GPBAR1 CD14 TR RE 0.72 0.72 0.01 0.06 2,48
HD43 2 234.1 234.6 1177 1 ATG16L1 CD4 CD8 IL TR RE 0.94 0 0.05 1.00 2,49
N_3_45 3 46.0 47.0 2930 1 CCR2 CD19 0.77 0 0.02 1.00
1203 1 CCR2 CD4 −0.62 0 0.07 1.00
7768 1 CCR9 CD19 0 −0.67 1.00 0.06
6798 1 KLHL18 CD14 0 −0.68 1.00 0.03
HD50 3 48.4 51.4 8 7 USP4 CD19 0.64 0.63 0.06 0.07 2
217 3 GPX1 APEH IP6K1 CD19 CD14 TR RE 0.91 0.97 0.01 0.01 2,49
122 3 FAM212A CD19 0 0.61 1.00 0.05
J_3_52 3 52.8 53.3 3190 1 SFMBT1 TR RE 0 −0.88 1.00 0.01 50
J_4_73 4 74.6 75.1 1271 1 CXCL5 CD4 CD8 CD19 CD14 PLA 0 −0.84 1.00 0.01 2
HD60 5 40.0 40.7 (PTGER4) CD15 0 0 0.28 0.15 51
HD61 5 55.4 55.5 360 2 ANKRD55 IL6ST CD4 CD8 0.9 0 0.02 1.00 4
HD62 5 72.4 72.6 6625 1 FOXD1 IL −0.74 0 0.03 1.00 4
HD63 5 95.9 96.5 365 2 ERAP2 LNPEP CD4 CD8 CD19 CD14 CD15 PLA IL TR RE 0.94 0.71 0.01 0.02 2,4,50
HD65 5 130.4 132.0 55 4 (SLC22A4) (SLC22A5) CD4 CD15 −0.55 0 0.06 0.07 4,52
HD66 5 141.4 141.7 2389 1 NDFIP1 CD8 PLA 0.87 0.88 0.04 0.01 2
HD67 5 149.0 151.0 – – (IRGM) – – – – – 53
HD71 5 173.2 173.6 1349 1 CPEB4 CD4 CD8 CD19 CD14 CD15 PLA TR −0.92 0 0.01 1.00 2,4
J_66_32 6 32.3 32.9 7853 1 HLA-DQA2 IL 0 −0.62 1.00 0.02
HD76 6 90.8 91.1 1404 1 BACH2 CD4 0.67 0 0.14 1.00
HD78 6 111.3 112.0 9603 1 SLC16A10 IL 0 −0.71 1.00 0.11
HD80 6 127.9 128.4 707 2 THEMIS PTPRK CD8 −0.92 0 0.01 1.00
HD83 6 167.3 167.6 1425 1 RNASET2 CD4 CD8 CD15 PLA −0.87 0 0.02 1.00 4
J_7_1 7 2.5 3.0 2729 1 GNA12 CD19 CD14 TR 0 −0.94 1.00 0.02 2
HD84 7 26.6 27.3 1441 1 SKAP2 CD4 CD8 CD19 0.97 0 0.01 1.00 4
HD85 7 28.1 28.3 6438 1 JAZF1 CD4 0.78 0 0.01 1.00 2
HD92 7 128.5 128.8 401 2 IRF5 TNPO3 CD15 IL 0 −0.64 1.00 0.02 2,48
7046 1 TSPAN33 CD19 −0.64 0 0.01 1.00
N_8_26 8 26.7 27.7 5869 1 PTK2B CD14 −0.69 0 0.01 1.00
5841 1 TRIM35 CD4 0 0.66 1.00 0.01
HD106 9 139.1 139.5 64 4 CARD9 INPP5E SEC16A SDCCAG3 CD4 CD8 CD19 CD14 CD15 IL TR RE 0.95 0.86 0.01 0.02 2,4,50
HD109 10 30.6 30.9 1603 1 MTPAP TR −0.62 0 0.11 1.00
HD112 10 59.8 60.2 1609 1 CISD1 CD4 CD8 CD19 CD14 CD15 TR RE 0.94 0.83 0.04 0?01 2,4,48
J_10_74 10 75.4 75.9 436 2 VCL CD4 CD8 CD19 CD14 RE 0 −0.79 1.00 0.04
4279 1 CAM2KG CD4 −0.67 0 0.04 1.00
HD114 10 81.0 81.2 5476 1 ZMIZ1 CD8 −0.91 −0.86 0.03 0.01
J_10_80 10 82.0 82.5 712 2 TSPAN14 TR −0.71 0 0.01 1.00
2216 1 TSPAN14 CD4 CD14 0.76 0 0.01 1.00 2
HD116 10 101.2 101.4 5439 1 SLC25A28 CD14 −0.61 0 0.22 1.00
J_11_57 11 58.1 58.6 7164 1 ZFP91 PLA −0.64 −0.75 0.02 0.07
J_11_59 11 61.3 61.8 1670 1 TMEM258 CD4 CD8 CD19 0.83 0 0.04 1.00
J_11_65 11 65.4 65.9 451 2 CTSW FIBP CD4 CD8 −0.73 0 0.01 1.00 2
HD122 11 114.2 114.6 268 3 REXO2 NXPE1 NXPE4 TR RE 0 −0.89 1.00 0.02 4,50
HD123 11 118.3 118.8 8200 1 TREH IL 0 0.7 1.00 0.05
HD142 14 88.2 88.7 8940 1 GPR65 CD14 0.8 0.79 0.01 0.01
6353 1 (GALC) CD14 −0.52 −0.23 0.06 0.06 4
J_15_40 15 41.3 41.8 9109 1 CHP1 IL 0.62 0 0.01 1.00
J_16_22 16 23.6 24.1 2672 1 PRKCB CD14 0 0.64 1.00 0.05 2
HD150 16 28.2 29.1 6 8 TUFM SBK1 APOBR SGF29 CLN3 SPNS1 CD4 CD8 CD19 CD14 CD15 IL TR RE 0.81 0.86 0.05 0.03 4
HD151 16 30.4 31.4 2673 1 RNF40 CD15 −0.63 0 0.02 1.00
1886 1 ITGAL CD4 CD8 CD19 0 0.74 1.00 0.01 54
HD153 16 68.4 68.9 1894 1 ZFP90 CD4 CD8 CD19 CD14 TR 0 0.83 1.00 0.07 2,48
HD156 16 85.9 86.1 3328 1 IRF8 TR RE 0 0.72 1.00 0.01
HD159 17 37.3 38.3 37 5 GSDMB ORMDL3 PGAP3 (GSDMA) CD4 CD8 CD19 CD14 IL TR RE −0.98 −0.92 0.02 0.01 2,4
HD161 17 40.3 41.0 836 2 STAT3 PLA 0.67 0 0.10 1.00
HD164 18 67.4 67.6 1988 1 CD226 CD4 CD8 PLA 0 −0.86 1.00 0.01 2
N_18_76 18 76.7 77.7 7292 1 PQLC1 PLA −0.68 0 0.01 1.00
HD166 19 10.3 10.7 9232 1 (TYK2) CD14 −0.44 −0.09 0.10 0.10
HD168 19 47.1 47.4 581 2 GNG8 CD4 0 −0.63 1.00 0.06
HD169 19 49.0 49.3 3128 1 FUT2 IL TR RE −0.95 0 0.01 1.00 4
J_20_31 20 31.1 31.6 593 2 COMMD7 CD14 0 0.61 1.00 0.01
J_20_32 20 33.6 34.1 7 8 UQCC1 CD19 −0.69 0 0.02 1.00 2
3369 1 MMP24-AS1 RE −0.63 −0.71 0.03 0.03
HD175 20 62.2 62.5 2322 1 LIME1 CD4 CD19 −0.86 0 0.01 1.00 2
HD176 21 16.6 16.9 9578 1 NRIP1 CD4 0 −0.69 1.00 0.02
HD180 22 21.7 22.1 2130 1 UBE2L3 CD4 CD8 CD19 CD14 CD15 IL TR RE 0.97 0.92 0.01 0.07 2,4
N_22_41 22 41.4 42.4 2149 1 EP300 CD8 CD19 CD15 0 0.71 1.00 0.02

Given are (i) the name and chromosomal coordinates of the corresponding loci (Locus, Chr, Beg, End) (GRCh37/hg19 in Mb), (ii) the identifier and total number of genes in the matching cis-acting regulatory module (cRM, Nr), (iii) the genes and tissues involved in matching DAP–EAP (|ϑ| > 0.6) (bold when |ϑ| ≥ 0.9), (iv) the best ϑ-values and corresponding empirical p values obtained for CD and UC, respectively, and (vi) references reporting a link between one or more of the same genes and IBD on the basis of eQTL information. Genes that were resequenced are shown in italics. Genes that were resequenced despite |ϑ| ≤ 0.6 are bracketed, and the supporting references provided in “Ref”. The higher number of matching DAP–EAP in this study when compared to Huang et al.4 are primarily due to the fact that (i) we herein study 200 IBD risk loci (vs 97), and (ii) we increase the number of detected cis-eQTL approximately two-fold by correcting for hidden confounders using PCs