Table 1.
Genomic biomarker panel of 26 SNPs and their allelic states.
| SNP | Gene | Chromosome | Position GRCh37 |
Minor Allele Frequency (dbSNP) |
|---|---|---|---|---|
| Macrophage | ||||
| rs17215556 | SLC11A1/NRAMP | 2 | 219,258,856 | 0.0060 (T > C) |
| rs17235409 | SLC11A1/NRAMP | 2 | 219,259,732 | 0.0702 (G > A) |
| rs17235416 | SLC11A1/NRAMP | 2 | 219,259,814 | 0.1024 (del TGTG) |
| rs34448891 | SLC11A1/NRAMP | 2 | 219,246,649 | MAF not reported (ins GT) |
| rs3731865 | SLC11A1/NRAMP | 2 | 219,250,003 | 0.1680 (G > C) |
| rs2569190 | CD14 | 5 | 140,012,916 | 0.4734 (A > G) |
| rs2569193 | CD14 | 5 | 140,015,495 | 0.2172 (G > A) |
| rs684 | CD18 | 21 | 46,306,161 | 0.1639 (G > A) |
| rs117989670 | CD18 | 21 | 46,305,913 | 0.0069 (A > C) |
| Dendritic cells | ||||
| rs4804803 | CD209 | 19 | 7,812,733 | 0.2117 (A > G) |
| Toll-like receptor | ||||
| rs4696480 | TLR2 | 4 | 154,607,126 | 0.4601 (T > A) |
| rs5743708 | TLR2 | 4 | 154,626,317 | 0.0119 (G > A) |
| Inflammatory cytokines | ||||
| rs1800629 | TNF | 6 | 31,543,031 | 0.0955 (G > A) |
| rs361525 | TNF | 6 | 31,543,101 | 0.0505 (G > A) |
| rs1143627 | IL1B | 2 | 113,594,387 | 0.4803 (C > T) |
| rs1143634 | IL1B | 2 | 113,590,390 | 0.1455 (C > T) |
| rs16944 | IL1B | 2 | 113,594,867 | 0.4651 (A > G) |
| rs4073 | IL8 | 4 | 74,606,024 | 0.4972 (A > T) |
| rs1800896 | IL10 | 1 | 206,946,897 | 0.3026 (A > G) |
| rs17860508 | IL12B-near 5′ | 5 | 158,760,200 | not reported |
| rs1343151 | IL23R | 1 | 67,719,129 | 0.3237 (G > A) |
| Chemokines/Chemokine receptor | ||||
| rs1799987 | CCR5 | 3 | 46,411,935 | 0.4871 (A > G) |
| rs1801157 | CXCL12 | 10 | 44,868,257 | 0.2080 (G > A) |
| Others | ||||
| rs3948464 | SP110 | 2 | 231,050,715 | 0.1028 (C > T) |
| rs1135791 | SP110 | 2 | 231,042,276 | 0.3375 (T > C) |
| rs2076530 | BTNL2 | 6 | 32,363,816 | 0.3779 (A > G) |