Table 1.
Association of gene variants in central MHC with HIV-related Kaposi’s sarcoma in HIV-positive men enrolled in the Multicenter AIDS Cohort Study
| obs | polymorphism | position | gene/ closest gene | function | MAF*, count (%) | OR¶ (95% CI) | p | |
|---|---|---|---|---|---|---|---|---|
| cases | controls | |||||||
| 66 | rs356971 (A>C) | 30087776 | ZNRD1-AS1 | ncRNA | 88 (0.14) | 118 (0.19) | 0.73 (0.53–0.99) | 0.0422 |
| 72 | rs1116221 (G>A) | 30179309 | TRIM31 | Glu421Lys | 141 (0.23) | 177 (0.28) | 0.74 (0.56–0.96) | 0.0328 |
| 88 | rs9357097 (G>A) | 30393100 | HCG18 | intron | 185 (0.30) | 157 (0.25) | 1.32 (1.02–1.72) | 0.0394 |
| 100 | rs2429657 (A>G) | 30579499 | HLA-E | intergenic | 119 (0.19) | 152 (0.24) | 0.68 (0.51–0.90) | 0.0081 |
| 105 | rs1076829 (A>G) | 30735195 | DHX16 | intron | 194 (0.31) | 230 (0.37) | 0.76 (0.60–0.96) | 0.0229 |
| 169 | rs2071594 (G>C) | 31620699 | NFKBIL1 | 3'UTR | 188 (0.30) | 220 (0.35) | 0.74 (0.58–0.96) | 0.0220 |
| 170 | rs2071592 (T>A) | 31623319 | NFKBIL1 | intron | 174 (0.28) | 212 (0.34) | 0.70 (0.54–0.90) | 0.0063 |
| 172 | rs6929796 (G>A) | 31630648 | NFKBIL1 | intron | 89 (0.14) | 119 (0.19) | 0.74 (0.55–0.99) | 0.0444 |
| 174 | rs2239707 (A>G) | 31633298 | NFKBIL1 | intron | 217 (0.35) | 189 (0.30) | 1.26 (0.98–1.60) | 0.0683 |
| 185 | rs1800683 (G>A) | 31648050 | LTA | 5'UTR | 188 (0.30) | 220 (0.35) | 0.75 (0.58–0.96) | 0.0223 |
| 187 | rs909253 (A>G) | 31648292 | LTA | 5' region | 188 (0.30) | 220 (0.35) | 0.75 (0.58–0.96) | 0.0223 |
| 189 | rs1041981 (C>A) | 31648763 | LTA | Thr60Asn | 188 (0.30) | 220 (0.35) | 0.75 (0.58–0.96) | 0.0223 |
| 200 | rs3093665 (A>C) | 31653370 | TNF | 3'UTR | 19 (0.03) | 7 (0.01) | 2.00 (0.89–4.53) | 0.0965 |
| 214 | rs2844477 (A>G) | 31686751 | AIF-1, NCR3 | intergenic | 220 (0.35) | 263 (0.42) | 0.75 (0.59–0.96) | 0.0207 |
| 221 | rs7029 (A>G) | 31737932 | GPANK1 | 3'UTR | 167 (0.27) | 137 (0.22) | 1.55 (1.17–2.05) | 0.0022 |
| 224 | rs1065356 (G>A) | 31794987 | LY6G6C | cds-syn | 137 (0.22) | 109 (0.17) | 1.60 (1.18–2.16) | 0.0024 |
| 225 | rs3749953 (A>G) | 31821103 | MSH5-SAPCD1 | intronic | 92 (0.13) | 76 (0.11) | 1.45 (1.01–2.10) | 0.0459 |
| 227 | rs707926 (G>A) | 31856799 | VARS | cds-syn | 107 (0.17) | 84 (0.13) | 1.42 (1.03–1.97) | 0.0323 |
| 264 | rs3749962 (G>A) | 32144335 | TNXB | cds-syn | 41 (0.07) | 60 (0.10) | 0.57 (0.38–0.87) | 0.0084 |
| 349 | rs2071541 (A>G) | 32920836 | TAP1, TAPSAR1 | nearGene-3 | 100 (0.16) | 75 (0.12) | 1.60 (1.11–2.32) | 0.0124 |
| 350 | rs1800453 (A>G) | 32922953 | TAP1 | Asp697Gly | 116 (0.19) | 91 (0.14) | 1.54 (1.09–2.18) | 0.0136 |
| 352 | rs4148880 (A>G) | 32926752 | TAP1 | Ile393Val | 143 (0,21) | 117 (0.17) | 1.45 (1.05–1.99) | 0.0236 |
| 353 | rs4713600 (C>A) | 32930836 | TAP1 | nearGene-5 | 331 (0.48) | 293 (0.42) | 1.31 (1.04–1.66) | 0.0236 |
| 355 | rs9276820 (G>A) | 32937254 | PSMB9 | downstream | 305 (0.49) | 279 (0.44) | 1.33 (1.06–1.67) | 0.0140 |
| 356 | rs1383266 (G>A) | 32942710 | PSMB9, HLA-DMB | intergenic | 135 (0.22) | 169 (0.27) | 0.75 (0.58–0.97) | 0.0309 |
| 359 | rs2187688 (G>A) | 32979979 | PSMB9, HLA-DMB | intergenic | 274 (0.44) | 307 (0.49) | 0.75 (0.59–0.96) | 0.0199 |
| 367 | rs151719 (A>G) | 33011878 | HLA-DMB | intron | 161 (0.26) | 121 (0.19) | 1.39 (1.03–1.86) | 0.0291 |
| 370 | rs194675 (T>A) | 33013724 | HLA-DMB | intron | 272 (0.44) | 309 (0.49) | 0.77 (0.61–0.99) | 0.0383 |
| 372 | rs6902982 (A>G) | 33015859 | HLA-DMB | intron | 32 (0.05) | 10 (0.02) | 4.09 (1.90–8.80) | 0.0003 |
| 377 | rs209475 (G>A) | 33033563 | HLA-DMA | upstream | 215 (0.35) | 254 (0.41) | 0.78 (0.60–1.04) | 0.0533 |
| 379 | rs683208 (A>G) | 33045879 | BRD2 | nearGene-5 | 219 (0.35) | 257 (0.41) | 0.78 (0.60–1.00) | 0.0539 |
| 388 | rs12174395(A>G) | 33122296 | HLA-DPA1 | upstream | 191 (0.31) | 230 (0.37) | 0.75 (0.59–0.97) | 0.0270 |
| 389 | rs375912 (A>G) | 33124706 | HLA-DPA1 | upstream | 198 (0.32) | 236 (0.38) | 0.76 (0.60–0.98) | 0.0319 |
| 408 | rs461338 (A>G) | 33326158 | VPS52 | 3'UTR | 88 (0.14) | 115 (0.18) | 0.66 (0.47–0.92) | 0.0152 |
| 411 | rs466384 (A>G) | 33362643 | WDR46 | Val287Ala | 84 (0.13) | 110 (0.17) | 0.64 (0.45–0.91) | 0.0132 |
| 415 | rs1061801 (G>A) | 33390316 | ZBTB22 | UTR-3 | 123 (0.18) | 150 (0.22) | 0.72 (0.53–0.97) | 0.0288 |
(¶)
Odds ratios (OR) and lower and upper 95% Wald confidence interval (CI) from conditional logistic models (assuming additive variance) with adjustment for baseline age, degree of immunosuppression (area under CD4+ count of 300) and rate of CD4+ count change (slope of CD4 counts).
(*)
Minor allele frequency (MAF).