Table 2.
Top findings for the summary data-based Mendelian randomization (SMR) of expression in blood on circulating APOB concentrations
| Gene | Top SNP | Top SNP Chr | Top SNP bp | Effect allele | Other allele | SMR effect estimate | SMR P | Coloc region (500kb +/− lead SNP from SMR) | No. Coloc SNPs | PP4 | Causal SNP |
|---|---|---|---|---|---|---|---|---|---|---|---|
| PELO | rs1499279 | 5 | 52106278 | G | T | 0.004 | 4.52E-27 | 5:51606278-52606278 | 2860 | 9.88E-01 | rs1499279 |
| RASIP1 | rs1231281 | 19 | 49239200 | A | G | 0.043 | 2.33E-12 | 19:48739200-49739200 | 2726 | 1.61E-44 | NA |
| ILRUN | rs3800461 | 6 | 34616322 | C | G | 0.007 | 2.52E-12 | 6:34116322-35116322 | 1958 | 2.93E-13 | NA |
| SARM1 | rs4795434 | 17 | 26716917 | G | T | 0.010 | 3.05E-11 | 17:26216917-27216917 | 1097 | 5.19E-09 | NA |
| GRINA | rs57957974 | 8 | 145076529 | A | C | 0.004 | 6.77E-11 | 8:144576529-145576529 | 1544 | 1.93E-13 | NA |
| SKAP1 | rs34791545 | 17 | 46488447 | C | T | 0.007 | 3.14E-10 | 17:45988447-46988447 | 1939 | 5.09E-10 | NA |
| ZNF664 | rs7958691 | 12 | 124440743 | T | G | 0.013 | 4.68E-10 | 12:123940743-124940743 | 2192 | 7.89E-12 | NA |
| PARP10 | rs11784833 | 8 | 145063412 | C | T | 0.010 | 5.05E-10 | 8:144563412-145563412 | 1561 | 1.93E-13 | NA |
| PYGB | rs11699953 | 20 | 25241345 | G | C | 0.003 | 9.40E-09 | 20:24741345-25741345 | 2696 | 9.14E-01 | rs11699953 |
| EVI2B | rs9902893 | 17 | 29625638 | A | G | 0.023 | 1.01E-08 | 17:29125638-30125638 | 1829 | 1.27E-04 | NA |
SNP single-nucleotide polymorphism, Chr chromosome, Bp top SNP base pair. Displayed SMR findings had heterogeneity in dependent instruments (HEIDI) P > 0.05 and F-statistics > 10 (Supplementary Data 14). SMR P Bonferroni-corrected P-value for the SMR test. Coloc Fully Bayesian Genetic Colocalization using Bayes Factors. PP4 = posterior probability that a single genetic variant affects both traits (PP4 > 0.80 suggests evidence that a single variant is responsible for the eQTL and apolipoprotein B (APOB) signal32).