Table 2.
Significant (P < 5e−08) SNPs and genetic loci associated with bacterial and viral infections in the GWAS.
| Phenotype | SNP | CH | Position (b37) | Effect allele | Other allele | EAF cases | EAF controls | Odds ratio (95% CI) | Beta | SE | P | MACH-Rsq | Nearby genes (+ / − 100 kb) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Abdominal infections | rs6717024 | 2 | 144,308,780 | C | G | 0.2 | 0.18 | 1.133 (1.111–1.156) | 0.125 | 0.010 | 1.22e−34 | 1.00 | ARHGAP15 |
| rs4333882 | 1 | 234,352,899 | G | A | 0.2 | 0.19 | 1.081 (1.060–1.103) | 0.078 | 0.010 | 2.14e−14 | 0.97 | MIR4671, SLC35F3 | |
| rs7609897 | 3 | 15,502,681 | T | G | 0.2 | 0.21 | 0.925 (0.907–0.943) | − 0.078 | 0.010 | 9.76e−14 | 0.91 | COLQ, EAF1, HACL1, METTL6, MIR4270 | |
| rs760364725 | 19 | 38,757,315 | CA | C | 0.49 | 0.48 | 1.062 (1.045–1.079) | 0.060 | 0.008 | 5.59e−13 | 0.94 | C19orf33, CATSPERG, DPF1, KCNK6, PPP1R14A, SIPA1L3, SPINT2, YIF1B | |
| rs61823192 | 1 | 219,294,570 | T | C | 0.026 | 0.03 | 0.828 (0.785–0.873) | − 0.189 | 0.027 | 1.26e−12 | 0.90 | LYPLAL1, LYPLAL1-DT | |
| rs1802575 | 2 | 56,093,204 | C | G | 0.14 | 0.13 | 1.081 (1.056–1.107) | 0.078 | 0.012 | 1.56e−11 | 1.00 | EFEMP1, MIR217HG | |
| rs11428277 | 10 | 101,425,013 | G | GA | 0.19 | 0.18 | 1.075 (1.052–1.098) | 0.072 | 0.011 | 1.69e−11 | 0.91 | COX15, CUTC, ENTPD7, SLC25A28 | |
| rs570640158 | 6 | 32,517,793 | C | T | 0.27 | 0.26 | 1.070 (1.050–1.092) | 0.068 | 0.010 | 2.13e−11 | 0.81 | HLA-DQA1, HLA-DRB1, HLA-DRB5, HLA-DRB6 | |
| rs4782673 | 16 | 84,884,072 | T | G | 0.28 | 0.3 | 0.945 (0.928–0.961) | − 0.057 | 0.009 | 1.37e−10 | 1.00 | CRISPLD2, USP10 | |
| rs7464710 | 8 | 120,624,386 | G | C | 0.25 | 0.26 | 0.943 (0.926–0.959) | − 0.059 | 0.009 | 4.13e−10 | 0.98 | ENPP2 | |
| rs2049865 | 8 | 116,588,546 | C | A | 0.41 | 0.42 | 0.950 (0.935–0.965) | − 0.051 | 0.008 | 4.67e−10 | 0.98 | TRPS1 | |
| rs61817723 | 1 | 151,920,865 | A | G | 0.27 | 0.28 | 0.945 (0.928–0.961) | − 0.057 | 0.009 | 4.71e−10 | 0.99 | C2CD4D-AS1, NBPF18P, S100A10, S100A11, THEM4, THEM5 | |
| rs2276068 | 11 | 70,007,484 | C | G | 0.49 | 0.48 | 1.050 (1.034–1.067) | 0.049 | 0.008 | 1.04e−09 | 1.00 | ANO1, FADD, LINC02584, LOC101928443 | |
| rs9372625 | 6 | 98,344,031 | A | G | 0.37 | 0.38 | 0.951 (0.936–0.966) | − 0.050 | 0.008 | 2.02e−09 | 0.99 | ||
| rs2280028 | 16 | 86,233,413 | A | G | 0.13 | 0.14 | 0.932 (0.911–0.955) | − 0.070 | 0.012 | 3.23e−09 | 0.99 | LINC01081, LINC01082, LINC02135 | |
| rs71472433 | 15 | 40,649,609 | C | A | 0.17 | 0.17 | 1.064 (1.041–1.087) | 0.062 | 0.011 | 5.24e−09 | 0.99 | ANKRD63, BAHD1, BUB1B-PAK6, CCDC9B, DISP2, INAFM2, IVD, KNSTRN, PAK6, PHGR1, PLCB2 | |
| rs2973068 | 5 | 37,778,273 | G | C | 0.24 | 0.25 | 0.947 (0.931–0.964) | − 0.054 | 0.009 | 8.15e−09 | 0.99 | GDNF, GDNF-AS1, WDR70 | |
| rs761264338 | 7 | 102,444,156 | GGAAG | G | 0.34 | 0.33 | 1.050 (1.032–1.069) | 0.049 | 0.009 | 1.03e−08 | 0.98 | FAM185A, FBXL13, RASA4DP | |
| rs1888693 | 10 | 18,440,444 | A | G | 0.33 | 0.34 | 0.952 (0.936–0.969) | − 0.049 | 0.009 | 1.14e−08 | 1.00 | CACNB2 | |
| rs3732760 | 3 | 151,074,941 | C | A | 0.38 | 0.37 | 1.048 (1.032–1.065) | 0.047 | 0.008 | 1.17e−08 | 1.00 | GPR87, IGSF10, MED12L, P2RY12, P2RY13, P2RY14 | |
| rs575909118 | 11 | 15,065,235 | CT | C | 0.27 | 0.27 | 1.053 (1.035–1.072) | 0.052 | 0.009 | 1.40e−08 | 0.98 | CALCA, CALCB, INSC | |
| rs11030119 | 11 | 27,728,102 | A | G | 0.3 | 0.31 | 0.951 (0.935–0.968) | − 0.050 | 0.009 | 1.44e−08 | 1.00 | BDNF, BDNF-AS, LINC00678 | |
| rs60731259 | 7 | 73,439,465 | CA | C | 0.066 | 0.061 | 1.096 (1.063–1.131) | 0.092 | 0.016 | 1.96e−08 | 0.99 | ELN, LIMK1 | |
| rs9411377 | 9 | 136,145,404 | A | C | 0.28 | 0.29 | 0.950 (0.934–0.967) | − 0.051 | 0.009 | 2.01e−08 | 0.96 | MED22, OBP2B, RPL7A, SNORD24, SNORD36A, SNORD36B, SNORD36C, STKLD1, SURF1, SURF2, SURF4, SURF6 | |
| rs377411728 | 18 | 6,305,754 | T | C | 0.00071 | 0.00031 | 2.641 (1.878–3.714) | 0.971 | 0.174 | 2.42e−08 | 0.83 | L3MBTL4, L3MBTL4-AS1, MIR4317 | |
| Not available | 1 | 214,458,533 | C | CT | 0.46 | 0.45 | 1.046 (1.030–1.063) | 0.045 | 0.008 | 3.67e−08 | 0.99 | PTPN14, SMYD2 | |
| Gastroenteritis | rs115809651 | 4 | 162,414,623 | A | G | 0.0014 | 0.00046 | 3.525 (2.359–5.269) | 1.260 | 0.205 | 8.07e−10 | 0.86 | FSTL5 |
| rs138491114 | 22 | 47,432,980 | A | G | 0.0035 | 0.0018 | 1.986 (1.557–2.532) | 0.686 | 0.124 | 3.14e−08 | 0.97 | TBC1D22A | |
| rs772878892 | 16 | 49,404,415 | G | A | 0.0011 | 0.00032 | 3.597 (2.274–5.690) | 1.280 | 0.234 | 4.77e−08 | 0.90 | C16orf78, CBLN1 | |
| a. Bacterial gastroenteritis | rs143977447 | 5 | 164,646,152 | A | C | 0.011 | 0.0053 | 2.375 (1.787–3.156) | 0.865 | 0.145 | 2.20e−09 | 0.85 | |
| rs547484470 | 7 | 68,931,296 | A | C | 0.0045 | 0.0014 | 3.710 (2.396–5.744) | 1.311 | 0.223 | 4.13e−09 | 0.88 | ||
| b. Viral gastroenteritis | rs116879283 | 7 | 52,434,143 | C | T | 0.017 | 0.0063 | 2.956 (2.033–4.299) | 1.084 | 0.191 | 1.49e−08 | 0.90 | |
| Heart infections | rs564399474 | 13 | 54,865,197 | G | A | 0.016 | 0.0039 | 4.527 (2.930–6.994) | 1.510 | 0.222 | 1.02e−11 | 0.93 | MIR1297 |
| rs182592259 | 14 | 96,788,318 | A | T | 0.016 | 0.005 | 3.589 (2.323–5.546) | 1.278 | 0.222 | 8.73e−09 | 0.88 | AK7, ATG2B, BDKRB1, BDKRB2, GSKIP | |
| rs139809494 | 17 | 79,796,214 | T | C | 0.019 | 0.0064 | 3.139 (2.117–4.655) | 1.144 | 0.201 | 1.30e−08 | 0.96 | ALYREF, ANAPC11, ARHGDIA, GCGR, MAFG, MAFG-DT, MCRIP1, NPB, P4HB, PCYT2, PPP1R27, PYCR1, SIRT7 | |
| rs2181386 | 14 | 94,039,907 | G | A | 0.16 | 0.12 | 1.490 (1.294–1.716) | 0.399 | 0.072 | 3.51e−08 | 1.00 | UNC79 | |
| Respiratory tract infections | rs28752520 | 6 | 32,584,739 | C | T | 0.24 | 0.25 | 0.931 (0.911–0.951) | − 0.072 | 0.011 | 1.77e−10 | 0.99 | HLA-DQA1, HLA-DQB1, HLA-DQB1-AS1, HLA-DRB1, HLA-DRB5, HLA-DRB6 |
| Not available | 9 | 128,648,077 | ATG | A | 0.34 | 0.35 | 0.937 (0.919–0.956) | − 0.065 | 0.010 | 1.94e−10 | 0.98 | PBX3 | |
| a. Bacterial pneumonia | rs374402947 | 16 | 89,154,513 | T | C | 0.0014 | 0.00048 | 3.391 (2.300–4.998) | 1.221 | 0.198 | 6.86e−10 | 0.88 | ACSF3, CDH15, LINC00304, LINC02138 |
| rs77438700 | 15 | 78,906,637 | G | A | 0.064 | 0.074 | 0.839 (0.795–0.887) | − 0.175 | 0.028 | 7.72e−10 | 0.97 | CHRNA3, CHRNA5, CHRNB4, HYKK, PSMA4 | |
| rs532298826 | 4 | 138,378,079 | A | T | 0.0016 | 0.00064 | 3.056 (2.093–4.461) | 1.117 | 0.193 | 6.62e−09 | 0.80 | LINC02172, PCDH18 | |
| rs763947133 | 5 | 127,719,333 | T | C | 0.00098 | 0.00029 | 3.971 (2.466–6.393) | 1.379 | 0.243 | 1.33e−08 | 0.81 | FBN2 | |
| b. Influenza and viral pneumonia | rs376768393 | 3 | 154,969,551 | C | T | 0.021 | 0.0064 | 3.850 (2.434–6.090) | 1.348 | 0.234 | 8.57e−09 | 0.87 | DWORF, LINC01487, MME |
| Sepsis | rs532825748 | 1 | 169,752,583 | G | A | 0.0078 | 0.0041 | 2.018 (1.586–2.568) | 0.702 | 0.123 | 1.13e−08 | 0.89 | C1orf112, METTL18, SCYL3, SELE, SELL |
| rs147389769 | 2 | 231,527,107 | T | C | 0.007 | 0.0036 | 2.130 (1.638–2.769) | 0.756 | 0.134 | 1.60e−08 | 0.83 | CAB39, LINC01907 | |
| rs564716204 | 4 | 151,664,401 | T | C | 0.0027 | 0.00092 | 3.353 (2.200–5.111) | 1.210 | 0.215 | 1.90e−08 | 0.82 | LRBA | |
| rs539059490 | 6 | 122,025,326 | G | T | 0.0073 | 0.0039 | 2.006 (1.567–2.568) | 0.696 | 0.126 | 3.65e−08 | 0.89 | ||
| Sexually transmitted diseases | rs62441491 | 7 | 41,892,859 | A | G | 0.056 | 0.018 | 3.438 (2.274–5.199) | 1.235 | 0.211 | 4.73e−09 | 0.94 | INHBA-AS1 |
| Skin infections | rs6595799 | 5 | 127,408,683 | C | T | 0.28 | 0.27 | 1.092 (1.058–1.127) | 0.088 | 0.016 | 2.39e−08 | 0.98 | LINC01184, SLC12A2 |
| Specified viral infections | rs568156598 | 7 | 94,453,230 | G | A | 0.0029 | 0.00091 | 3.747 (2.397–5.858) | 1.321 | 0.228 | 6.68e−09 | 0.85 | PPP1R9A |
| Urinary tract infections (UTI) | rs771331833 | 8 | 118,513,358 | A | C | 0.0013 | 0.00049 | 2.989 (2.096–4.262) | 1.095 | 0.181 | 1.62e−09 | 0.93 | MED30 |
| Not available | 3 | 47,875,364 | A | AT | 0.009 | 0.0064 | 1.471 (1.285–1.684) | 0.386 | 0.069 | 2.81e−08 | 0.90 | DHX30, MAP4, MIR1226, SMARCC1 | |
| rs189319388 | 3 | 7,867,797 | T | C | 0.0077 | 0.0055 | 1.527 (1.313–1.775) | 0.423 | 0.077 | 4.63e−08 | 0.81 | GRM7 | |
| a. Cystitis | rs192629083 | 7 | 14,037,179 | T | C | 0.0077 | 0.0025 | 3.702 (2.396–5.721) | 1.309 | 0.222 | 3.50e−09 | 0.86 | ETV1 |
| rs77261774 | 4 | 60,641,124 | A | G | 0.034 | 0.02 | 1.788 (1.461–2.188) | 0.581 | 0.103 | 1.49e−08 | 1.00 | LINC02429 | |
| Urogenital (non-UTI) infections | rs188692128 | 8 | 126,584,263 | T | C | 0.005 | 0.0017 | 3.589 (2.282–5.645) | 1.278 | 0.231 | 3.13e−08 | 0.85 | |
| Not available | 1 | 240,891,604 | T | TA | 0.0052 | 0.0018 | 3.456 (2.219–5.381) | 1.240 | 0.226 | 4.30e−08 | 0.83 | RGS7 |
Phenotypes are listed in alphabetical order.