Table 2. Details of Cis and trans effects.
| Protein (units) | Gene | SNP | MAF | Distance (bp) | Mean trait values | GC P | Perm P | ||
| 11 | 12 | 22 | |||||||
| TNFa (pg/ml) | ABO | rs505922 | 0.34 | intron | 2.68 (2.53–2.85) | 1.66 (1.61–1.72) | 1.71 (1.59–1.84) | 6.76×10−40 | <0.0001 |
| IL-6sR (ng/ml) | IL6R | rs4129267 | 0.37 | intron | 69.92 (66.95–72.99) | 100.65 (96.97–104.44) | 138.13 (129.94–146.77) | 1.82×10−57 | <0.00001 |
| MIPb (pg/ml) | CCL4L2 | rs4796217 | 0.34 | 227353 | 74.74 (68.85–81.03) | 53.32 (48.64–58.34) | 27.21 (21.48–33.83) | 3.87×10−21 | <0.00001 |
| IL18 (ug/ml) | IL18 | rs2250417 | 0.44 | 50476 | 406.79 (392.66–421.43) | 366.58 (355.39–378.12) | 330.73 (315.83–346.33) | 6.79×10−13 | <0.00001 |
| LPA (mg/dl) | LPA | rs7770628 | 0.49 | intron | 0.34/0.18 | 0.46/0.52 | 0.20/0.30 | 4.36×10−10 | <0.00001 |
| GGT1 (u/l) | GGT1 | rs5751901 | 0.39 | 6917 | 17.86 (17.11–18.67) | 19.6 (18.85–20.41) | 21.38 (19.88–23.07) | 1.52×10−7 | 0.00076 |
| SHBG (nmol/l) | SHBG | rs6761* | 0.31 | 115829 | 111.67 (106.77–116.77) | 100.9 (96.55–105.43) | 85.16 (77.65–93.31) | 3.08×10−7 | <0.00001 |
| CRP (ug/ml) | CRP | rs12093699 | 0.29 | 34092 | 2.26 (2.07–2.47) | 2.74 (2.48–3.03) | 3.64 (2.77–4.78) | 6.36×10−6 | 0.0038 |
| IL1RA (pg/ml) | IL1RN | rs6761276 | 0.37 | 43158 | 118.6 (112.49–125.05) | 142.16 (135.73–148.89) | 141.23 (126.74–157.37) | 7.27×10−6 | 0.00097 |
MAF = minor allele frequency, SNP = single nucleotide polymorphism and represents the best p value. Distance represents the distance from the gene or location within gene.
GC P represents the p value corrected for inflation factors but not multiple testing. Mean trait values are back transformed values from transformed means, except for LPA where frequencies of genotypes in the low (first value) and high (second value) level groups are given. 11 = common hom, 12 = het, 22 = minor allele homozygote. Perm = Permutation.
P values based on 100,000 region wide (gene +-300 kb) permutations for cis effects and 10,000 genome-wide permutations for trans effects (“<” indicates the observed p value did not occur in these numbers of permutations). *Further analysis shows that this signal is driven by a SNP, rs1799941, in partial LD with rs6761 – see text.