Table 4 Mediation analyses on candidate CpGs between cocaine use and VACS index (n = 467)
From: DNA methylation mediates the effect of cocaine use on HIV severity
CpG | Chr | Position | Nearest gene | Reference gene group | Relations to CpG islands | Average causal mediation effect | Proportion mediated | Average direct effect | Total effect | Sensitivity analysis: rho at which ACME = 0 | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Effect estimate | 95% CI | p value | Proportion mediated | 95% CI | p value | |||||||||
cg26312951 | 21 | 42797847 | MX1 | TSS200;5UTR | N_Shore | 0.097 | (0.051, 0.153) | 1.00E−06 | 29.5% | (15.9%, 53.0%) | 1.00E−06 | 0.231 | 0.329 | − 0.30 |
cg08122652 | 3 | 122281939 | PARP9 | 5UTR;TSS1500 | N_Shore | 0.092 | (0.049, 0.142) | 1.00E−06 | 28.2% | (15.7%, 49.2%) | 1.00E−06 | 0.236 | 0.329 | − 0.30 |
cg06188083 | 10 | 91093005 | IFIT3 | Body |  | 0.095 | (0.052, 0.145) | 2.00E−06 | 28.8% | (16.2%, 50.7%) | 2.00E−06 | 0.234 | 0.329 | − 0.30 |
cg03038262 | 11 | 315262 | IFITM1 | 3UTR | N_Shore | 0.078 | (0.040, 0.123) | 4.00E−06 | 23.7% | (12.4%, 42.8%) | 4.00E−06 | 0.251 | 0.329 | − 0.30 |
cg22930808 | 3 | 122281881 | PARP9 | 5UTR;TSS1500 | N_Shore | 0.091 | (0.047, 0.141) | 8.00E−06 | 27.7% | (15.1%, 48.9%) | 8.00E−06 | 0.237 | 0.329 | − 0.30 |
cg07839457 | 16 | 57023022 | NLRC5 | TSS1500 | N_Shore | 0.079 | (0.038, 0.127) | 8.00E−06 | 24.0% | (11.0%, 47.5%) | 8.00E−06 | 0.250 | 0.329 | − 0.25 |
cg03753191 | 13 | 43566902 | EPSTI1 | TSS1500 | S_Shore | 0.078 | (0.036, 0.128) | 3.90E−05 | 23.7% | (10.6%, 46.8%) | 3.90E−05 | 0.251 | 0.329 | − 0.25 |
cg06981309 | 3 | 146260954 | PLSCR1 | 5UTR | N_Shore | 0.074 | (0.033, 0.123) | 4.70E−05 | 22.6% | (10.7%, 41.8%) | 4.70E−05 | 0.254 | 0.329 | − 0.25 |
cg22940798 | 6 | 32805554 | TAP2 | Body | N_Shore | 0.058 | (0.025, 0.100) | 5.70E−05 | 17.6% | (7.6%, 35.6%) | 5.70E−05 | 0.271 | 0.329 | − 0.20 |
cg08818207 | 6 | 32820355 | TAP1 | Body | N_Shore | 0.081 | (0.037, 0.130) | 5.80E−05 | 24.5% | (11.9%, 44.7%) | 5.90E−05 | 0.248 | 0.329 | − 0.30 |
cg22917487 | 3 | 39322103 | CX3CR1 | Body;TSS200;5UTR;TSS1500 |  | 0.054 | (0.015, 0.104) | 1.81E−03 | 16.3% | (4.6%, 34.4%) | 1.81E−03 | 0.276 | 0.329 | 0.15 |
cg26396492 | 20 | 19915762 | RIN2 | Body |  | 0.037 | (0.009, 0.073) | 3.07E−03 | 11.3% | (2.7%, 24.9%) | 3.07E−03 | 0.291 | 0.329 | − 0.15 |
cg08623256 | 5 | 3858275 |  |  | S_Shelf | 0.009 | (− 0.012, 0.032) | 2.00E−01 | 0.026 | (− 0.038, 0.108) | 2.00E−01 | 0.321 | 0.329 | − 0.05 |
cg22385827 | 2 | 211036478 | C2orf67 | TSS1500 | Island | − 0.008 | (− 0.027, 0.007) | 8.28E−01 | − 0.023 | (− 0.089, 0.023) | 8.28E−01 | 0.336 | 0.329 | − 0.05 |
cg00096307 | 2 | 106761754 | UXS1 | Body |  | − 0.027 | (− 0.064, 0.000) | 9.75E−01 | − 0.084 | (− 0.221, 0.000) | 9.75E−01 | 0.356 | 0.329 | 0.10 |