Table 2.
S-PrediXcan Significant Genes in PAGE with Colocalization Probability (P4) > 0.5 that Replicated in Independent Studies in PhenomeXcan
| Gene Name | Z Score | Effect Size | P | CHR | P3 | P4 | Model | Phenotype | Best PhenomeXcan P | RCP |
|---|---|---|---|---|---|---|---|---|---|---|
| CETP | −18 | −12 | 4.2 × 10−73 | 16 | 2.3 × 10−3 | 1 | AFHI | HDL cholesterol | 6.1 × 10−97 | NA |
| TMEM258 | −4.8 | −17 | 1.7 × 10−6 | 11 | 7.1 × 10−3 | 0.95 | AFHI | HDL cholesterol | 1.6 × 10−6 | NA |
| SETD9 | 4.7 | −9.7 | 2.3 × 10−6 | 5 | 0.19 | 0.80 | AFHI | Height | 9.6 × 10−17 | 0.57 |
| RASA2 | 4.5 | −7.7 | 5.7 × 10−6 | 3 | 6.5 × 10−2 | 0.92 | AFHI | Height | 2.1 × 10−105 | NA |
| UBE2Z | 5.4 | 9.4 | 2.7 × 10−8 | 17 | 0.23 | 0.77 | AFHI | Height | 4.5 × 10−48 | NA |
| ISCA2 | 4.8 | 0.09 | 1.3 × 10−6 | 14 | 0.03 | 0.97 | AFHI | Height | 5.8 × 10−25 | NA |
| SLC22A4 | −5.0 | −0.05 | 5.3 × 10−7 | 5 | 0.17 | 0.81 | AFHI | Height | 6.2 × 10−47 | NA |
| SMIM19 | −6.6 | 0.16 | 3.1 × 10−11 | 8 | 0.10 | 0.90 | AFHI | MCHC | 2.8 × 10−23 | 0.58 |
| BAK1 | −11 | 0.02 | 2.6E-30 | 6 | 4.4 × 10−3 | 1 | AFHI | Platelet count | 2.6 × 10−149 | 0.97 |
| CBL | −4.5 | −0.06 | 6.0 × 10−6 | 11 | 1.8 × 10−2 | 0.98 | AFHI | Platelet count | 6.9 × 10−60 | 0.81 |
| VPS45 | 9.7 | −0.05 | 3.9 × 10−22 | 1 | 2.2 × 10−2 | 0.95 | AFHI | WBC count | 5.8 × 10−6 | NA |
| ZBTB38 | 4.9 | −0.11 | 1.2 × 10−6 | 3 | 1.7 × 10−2 | 0.98 | EUR | Height | 9.5 × 10−150 | 0.58 |
| PGP | −4.9 | −2.6 | 8.0 × 10−7 | 16 | 6.7 × 10−3 | 0.99 | EUR | Height | 1.9 × 10−32 | NA |
| SLC22A4 | −4.4 | 0.08 | 9.8 × 10−6 | 5 | 4.8 × 10−2 | 0.95 | EUR | Height | 6.2 × 10−47 | NA |
| BAK1 | −12 | 0.08 | 2.8 × 10−32 | 6 | 2.5 × 10−3 | 1 | EUR | Platelet count | 2.6 × 10−149 | 0.97 |
| GPR84 | −5.7 | 0.11 | 1.4 × 10−6 | 12 | 3.3 × 10−3 | 1 | EUR | Platelet count | 3.9 × 10−47 | NA |
| BAK1 | −12 | −13 | 7.0 × 10−34 | 6 | 3.9 × 10−3 | 1 | ALL | Platelet count | 2.6 × 10−149 | 0.97 |
| c6orf1 | 7.5 | 0.74 | 6.7 × 10−14 | 6 | 0.21 | 0.54 | ALL | Height | 9.0 × 10−132 | NA |
| CETP | −20 | −7.7 | 4.2 × 10−73 | 16 | 2.3 × 10−3 | 1 | ALL | HDL cholesterol | 6.1 × 10−97 | NA |
| NLRC5 | −7.1 | −3.7 | 1.4 × 10−12 | 16 | 0.31 | 0.66 | ALL | HDL cholesterol | 2.0 × 10−65 | NA |
| PGP | −4.5 | −0.04 | 5.6 × 10−6 | 16 | 1.3 × 10−2 | 0.95 | ALL | Height | 1.9 × 10−32 | NA |
| SETD9 | 4.6 | 0.02 | 4.3 × 10−6 | 5 | 0.19 | 0.80 | ALL | Height | 9.6 × 10−17 | 0.57 |
| SLC20A2 | −4.5 | −0.25 | 7.9 × 10−6 | 8 | 0.32 | 0.68 | ALL | MCHC | 7.3 × 10−21 | 0.51 |
| SLC22A4 | −4.7 | −0.05 | 2.4 × 10−6 | 5 | 0.10 | 0.89 | ALL | Height | 6.2 × 10−47 | NA |
| VPS45 | 8.8 | 0.08 | 1.2 × 10−18 | 1 | 0.27 | 0.69 | ALL | WBC count | 5.8 × 10−6 | NA |
| ZBTB38 | 6.7 | 0.18 | 2.6 × 10−11 | 3 | 8.3 × 10−3 | 0.99 | ALL | Height | 9.5 × 10−150 | 0.58 |
Details of the studies used in PhenomeXcan are in Table S2.
P3 = COLOC probability eQTL and GWAS signals are independent; P4 = COLOC probability eQTL and GWAS signals are colocalized; AFHI = African American and Hispanic/Latino transcriptome prediction model; EUR = European transcriptome model; ALL = African American, Hispanic/Latino, and European transcriptome model; MESA = Multi-Ethnic Study of Atherosclerosis; PAGE = Population Architecture using Genomics and Epidemiology study; RCP = PhenomeXcan regional colocalization probability.