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. 2022 Jul 22;13:862255. doi: 10.3389/fimmu.2022.862255

Table 2.

Results for the 55 independenta SKAT loci.

Chr Lead gene in the locus Other genes in the locus Lowest P-valueb GWAS overlap Significant gene(s) after GWAS adjustmentc GWAS-adjusted P-valued
1 TNFRSF8 TNFRSF14, MIIP 2.37E−08 No TNFRSF14 3.77E−07
1 CNR2 CEP85, FUCA1, E2F2 1.12E−13 Yes E2F2, CEP85 4.13E−06, 1.36E−06
1 ADGRL4 None 1.29E−12 No ADGRL4 9.00E−08
1 CCDC18 TMED5 2.73E−13 No None in locus 0.13
1 ARNT HORMAD1, CTSS, ARNT9 8.06E−10 No None in locus 0.07
1 NDUFS2 None 3.66E−08 No NDUFS2 6.31E−06
2 IL1RL1 ANKRD36C, GPAT2, ADRA2B, ASTL, FER1L5, IL1RL2, IL18RAP 2.96E−177 Yes None 0.02
2 PRKRA ITGA6 4.78E−22 No None 0.76
2 IKZF2 None 4.55E−08 Yes None 2.92E−04
2 D2HGDH GAL3ST2, FARP2, SCLY, INPP5D 1.77E−32 Yes None 0.02
3 IL5RA None 4.36E−08 Yes None in locus 2.38E−03
3 ACKR2 AC006059.2, CCDC13, GLB1, EOMES, FYCO1, CCR3, DALRD3, C3orf18 7.79E−21 Yes None in locus 2.35E−04
3 CD200 CD200R1, SLC9C1, SENP7 1.01E−17 Yes None in locus 0.016
3 GATA2 None 1.30E−55 No GATA2 9.99E−27
3 HTR3D None 2.33E−07 No None in locus 8.05E−05
4 REST None 3.06E−08 Yes None 0.08
5 OTULINL None 3.06E−07 No OTULINL 2.15E−06
5 IL7R None 2.60E−18 No None in locus 0.04
5 SLC22A4 IL9, TCF7, IL13, PDLIM4, CSF2, IL3M, FNIP1 1.11E−131 No None in locus 0.04
5 ADRB2 None 8.85E−28 No None in locus 0.26
6 HLA-A See belowe 1.55E−65 No None in locus 0.02
7 ABCB5 None 7.61E−08 No None in locus 0.09
7 CCL24 None 8.61E−28 No None in locus 0.06
7 GATAD1 None 4.15E−11 No None in locus 0.07
7 ZC3HC1 None 2.17E−08 No ZC3HC1 3.54E−06
8 TNFRSF10B None 4.68E−15 No None 2.05E−05
8 SHARPIN None 2.79E−21 No None 0.05
9 IL33 JAK2 2.40E−40 No IL33, JAK2 2.14E−21, 6.21E−08
9 RMI1 KIF27 1.53E−13 No RMI1 1.65E−07
9 SEC16A STKLD1 5.51E−09 No None in locus 1.37E−03
11 IFITM2 None 6.03E−26 Yes None in locus 0.06
11 PRG3 LTBP3, EHBP1L1, AP5B1, MUS81, TSGA10IP, SART1 3.30E−27 No PRG3 1.09E−06
11 NPAT None 2.16E−14 No NPAT 1.62E−07
12 SH2B3 PHETA1, CUX2, TMEM116 3.57E−247 No SH2B3 5.15E−12
12 NAA25 None 3.83E−25 No None in locus 0.17
12 FBRSL1 SBNO1 1.29E−12 No None in locus 0.04
13 MRPS31 None 3.53E−22 No None 5.46E−03
14 CEBPE None 7.81E−09 No None 1.02E−05
14 LGALS3 DLGAP5 2.50E−31 No None 0.08
14 FBXO34 None 7.44E−29 No None 0.06
14 ASB2 RIN3 4.46E−16 Yes None 0.07
15 NDUFAF1 MAP1A 2.45E−08 No None in locus 4.55E−05
15 ST20 BCL2A1, AKAP13 2.33E−19 Yes BLC2A1 1.94E−03
16 SOCS1 TNP2 1.68E−09 No SOCS1 1.41E−07
16 DOC2A IL4R, FBXL19 6.44E−21 No None in locus 0.58
16 ZNF668 None 7.95E−09 No ZNF668 6.20E−06
16 NFATC3 EXOC3L1 3.66E−07 No EXOC3L1 3.16E−07
17 ALOX15 PELP1, ZNF594, CTDNEP1 1.87E−71 Yes ALOX15, CTDNEP1 9.73E−07, 1.16E−06
17 IKZF3 GSDMA, ARHGAP27, SPPL2C, MAPT, STH, KANSL1, LRRC37A, LRRC37A2 1.57E−15 Yes GSDMA 1.97E−06
17 C17orf58 BPTF 8.79E−09 No None in locus 9.24E−06
18 SERPINB11 SERPINB13, CD226 4.22E−08 No SERPINB11 7.60E−07
19 S1PR4 ARHGAP45 2.52E−32 Yes S1PR4, ARHGAP45 8.76E−12, 7.50E−07
19 MAST3 None 5.43E−09 No None in locus 0.11
19 LGALS14 ZNF568, CLC, APOE, APOC4-APOC2, SIX5, CD33 4.57E−84 No None in locus 0.24
22 IL17RA GGT5, SFI1, CSF2RB, GTSE1 1.07E−26 No IL17RA, CSF2RB 3.18E−10, 1.47E−06
a

Significant genes from any of the SKAT models were clustered into independent loci based on the genomic distance. This was done by an iterative procedure, where the gene with the lowest P-value for each chromosome was considered to be the lead gene for the first locus of each chromosome, and all significant genes within 10 Mb were considered to belong to the same locus. Then, a second lead gene for each chromosome was identified as the most significant of the genes not belonging to any locus, and this procedure was repeated until no additional genes remained.

b

The lowest P-value from the five different gene-based models for the lead gene at each locus.

c

None: if no genes at that chromosome passed the significance threshold after adjusting for GWAS hits. None in locus: if no other gene in that particular locus passed the significance threshold.

d

P-value for the most significant gene at the locus after adjustment. If no gene in the locus was significant after GWAS adjustment, the adjusted P-value for the lead gene is presented.

e

The HLA locus contains the following genes: TRIM31, TRIM40, TRIM15, HLA-E, ABCF1, PPP1R18, VARS2, SFTA2, MUCL3, MUC21, MUC22, C6orf15, PSORS1C1, PSORS1C2, CCHCR1, TCF19, HLA-C, MICA, MCCD1, LTA, PRRC2A, BAG6, C6orf47, GPANK1, LY6G5C, CLIC1, VWA7, VARS1, HSPA1L, SLC44A4, EHMT2, SKIV2L, TNXB, PPT2, PPT2-EGFL8, EGFL8, AGER, NOTCH4, TSBP1, BTNL2, HLA-DRA, HLA-DRB5, HLA-DRB1, HLA-DQA1, HLA-DQB1, HLA-DQA2, HLA-DQB2, PSMB8, HLA-DPA1, HLA-DPB1, TAPBP, ZBTB22, ITPR3, IP6K3, TCP11, H1-1, BTN3A2, BTN3A1, BTN2A1, BTN1A1, ZNF322, PRSS16, POM121L2, H2BC13, OR2B2, ZKSCAN4, NKAPL, ZSCAN26, PGBD1, ZSCAN31, ZKSCAN3, ZSCAN12, OR2J3, OR14J1, OR12D3, OR12D2, MOG, and HLA-G.