Table 1:
Eleven loci identified by BN-cGAS and uGAS on metabolites for which at least one one-reaction-step neighbor was available
| uGAS | cGAS | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Locus | SNP | Metabolite | chr:pos | Gene | effA/refA | EAF | Beta (se) | P- value GC | Beta (se) | P- value GC | Ncov | Noise | Pleiotropic |
| uGAS and cGAS | |||||||||||||
| 1 | rs211718 | C8 | 1:75879263 | ACADM | T/C | 0.3 | −0.45 (0.034) | 6.35E-39 | −0.10 (0.012) | 4.45E-17 | 1 | 0.92 | −1.29 |
| 1 | rs211718 | C12 | 1:75879263 | ACADM | T/C | 0.3 | −0.04 (0.036) | 2.21E-01 | 0.20 (0.014) | 4.07E-42 | 3 | 0.80 | 1.29 |
| 2 | rs7705189 | PC ae C42:5 | 5:131651257 | SLC22A4 | G/A | 0.47 | 0.15 (0.034) | 8.83E-06 | 0.06 (0.009) | 9.63E-11 | 3 | 1.16 | −0.83 |
| 2 | rs419291 | C5 | 5:131661254 | SLC22A4 | T/C | 0.38 | 0.26 (0.035) | 6.62E-14 | 0.17 (0.029) | 1.40E-08 | 1 | 0.16 | −0.40 |
| 3 | rs9368564 | PC aa C42:5 | 6:11168269 | ELOVL2 | G/A | 0.25 | −0.29 (0.039) | 4.64E-14 | −0.15 (0.024) | 1.06E-10 | 3 | 0.45 | −0.58 |
| 4 | rs12356193 | C0 | 10:61083359 | SLC16A9 | G/A | 0.17 | −0.51 (0.046) | 4.93E-28 | −0.42 (0.042) | 8.83E-23 | 1 | 0.07 | −0.17 |
| 5 | rs174547 | lyso-PC a C20:4 | 11:61327359 | FADS1 | C/T | 0.7 | 0.61 (0.033) | 2.12E-75 | 0.66 (0.024) | 2.65E-169 | 1 | 0.29 | 0.07 |
| 6 | rs2066938 | C4 | 12:119644998 | ACADS | G/A | 0.27 | 0.73 (0.033) | 1.07E-104 | 0.72 (0.031) | 4.26E-116 | 1 | 0.05 | 0.00 |
| 7 | rs10873201 | PC ae C36:5 | 14:67036352 | PLEKHH1 | T/C | 0.45 | −0.26 (0.034) | 6.34E-14 | −0.21 (0.018) | 5.72E-31 | 2 | 0.55 | −0.18 |
| 7 | rs1077989 | PC ae C32:2 | 14:67045575 | PLEKHH1 | C/A | 0.46 | −0.30 (0.034) | 9.22E-19 | −0.06 (0.016) | 5.39E-05 | 3 | 0.66 | −1.34 |
| 8 | rs4814176 | PC ae C40:2 | 20:12907398 | SPTLC3 | T/C | 0.36 | 0.24 (0.035) | 5.60E-12 | 0.25 (0.023) | 1.28E-25 | 4 | 0.35 | 0.02 |
| Only uGAS | |||||||||||||
| 9 | rs8396 | C10 | 4:159850267 | ETFDH | C/T | 0.71 | 0.26 (0.037) | 1.32E-12 | 0.05 (0.010) | 5.08E-07 | 2 | 1.09 | −1.39 |
| Only cGAS | |||||||||||||
| 10 | rs4862429 | PC ae C42:5 | 4:186006834 | ACSL1 | T/C | 0.31 | 0.02 (0.037) | 6.63E-01 | −0.06 (0.010) | 7.01E-11 | 3 | 1.15 | 1.20 |
| 11 | rs603424 | Lyso-PC a C16:1 | 10:102065469 | PKD2L1 | A/G | 0.8 | 0.23 (0.042) | 4.83E-08 | 0.21 (0.031) | 1.76E-11 | 1 | 0.26 | −0.07 |
Notes: The best SNP-metabolite pair is shown for each locus. chr: pos, the physical position of the SNP; EAF, effect allele frequency; beta (se), the estimated effect and standard error of the SNP; effA/refA, effect allele/reference allele; P-value, the P-value of the additive model; Gene, the most likely (according to Data-driven Expression-Prioritized Integration for Complex Traits [DEPICT] software) associated gene in the region; Ncov, the number of covariates used in cGAS; Noise/Pleiotropic, the values of noise and pleiotropic components of the log-ratio of cGAS and uGAS T2 statistics.