Table 1. Names and abbreviations of phenotypes and polymorphisms included in the analysis.
| Variable | Abr. used | Indicator variable selected | |||
|---|---|---|---|---|---|
| 1 | 2 | 3 | |||
| Smoking (yes/no) | smoking | yes | |||
| Age | age | X | X | ||
| Body Mass Index | bmi | X | X | X | |
| Systolic Blood pressure | sysbp | X | X | ||
| Diastolic Blood pressure | diabp | X | X | X | |
| Triglycerides | tg | X | |||
| Total Cholesterol | chol | X | X | ||
| Low Density Lipoprotein | ldl | X | X | ||
| High Density Lipoprotein | hdl | X | X | ||
| Apolipoprotein B | apob | X | X | ||
| Apolipoprotein A | apoa | X | X | ||
| Lipoprotein-associated phospholipase | lppla2 | ||||
| C-reactive protein | crp | X | X | ||
| Factor VII coagulant activity | viic | X | X | ||
| Fibrinogen | fib | ||||
| ALX homeobox 4 gene | rs729287 | ALX4 | X | ||
| Angiopoietin-like 4 gene | E40K | ANGPTL4 | X | ||
| Apolipoprotein B gene | rs585967 | APOB | |||
| Apolipoprotein E gene | APOE | X | X | ||
| Apolipoprotein-A5-A4-C3-A1 gene cluster | rs6589566 | ApoA5-A4-C3-A1 | X | ||
| Arachidonate 5-lipoxygenase-activating protein gene | rs3885907 | ALOX5AP | X | ||
| Calpain 10 gene | rs4676411 | CAPN10 | |||
| Cathepsin S gene | rs11576175 | CTSS | X | ||
| Cholesteryl ester transfer protein gene | rs708272 | CETP | X | ||
| Coagulation factor VII gene | rs6046 | F7 | X | ||
| Complement component 2 gene | rs7746553 | C2 | |||
| Complement component 3 gene | rs344550 | C3 | |||
| C-reactive protein gene | rs3093077 | CRP | X | X | X |
| Cyclin-dependent kinase inhibitor 2A/B (Chr9p21) | rs10811661 | CDKN | X | X | |
| Exostosin 2 gene | rs3740878 | EXT2 | X | X | |
| Fibrinogen alpha chain gene | rs4508864 | FGA | X | X | |
| Glucokinase (hexokinase 4) regulator gene | rs780094 | GCKR | X | X | |
| Glutathione S-transferase mu 3 gene | rs3814309 | GSTM3 | X | X | |
| Glutathione S-transferase mu 4 gene | rs1537236 | GSTM4 | X | X | |
| Hepatic lipase gene | rs1800588 | LIPC | X | X | X |
| Insulin gene | rs689 | INS | |||
| Insulin-like growth factor 2 gene | 1252T/C AluI | IGF2 | X | X | |
| Interleukin 1 receptor antagonist gene | rs397211 | ILRN1 | X | X | |
| Interleukin 18 receptor accessory protein gene | rs11465699 | IL18RAP | X | ||
| Interleukin 6 receptor gene | rs4075015 | IL6R | |||
| Lipoprotein lipase gene | rs301 | LPL | X | X | |
| Low density lipoprotein receptor gene | rs6511720 | LDLR | |||
| Low density lipoprotein receptor-related protein 5 gene | rs11602256 | LRP5 | X | ||
| Nitric oxide synthase 3 gene | rs3918232S3 | NOS3 | X | ||
| Phospholipase A2, group VII gene | rs1051931 | PLA2G7 | X | X | |
| Platelet/endothelial cell adhesion molecule gene | rs1131012 | PECAM1 | X | X | X |
| Proprotein convertase subtilisin/kexin type 9 gene | rs11591147 | PCSK9 | X | ||
| Protein C receptor gene | rs867186 | PROCR | X | ||
| Toll-like receptor 4 gene | rs11536857 | TLR4 | X | X | |
| Transforming growth factor, beta 1 gene | rs4803455 | TGFB1 | X | X | |
| Uncoupling protein 2 gene | rs11602906 | UCP2 | |||
| Uncoupling protein 3 gene | rs1685354 | UCP3 | X | X | |
The phenotypes were selected as established risk factors or markers of CHD and their associated polymorphisms. [7]. Only the single top SNP was included for each gene considered. Before analysis each SNP was recoded as three indicator variables. To maintain the three variables per genotype coding, the continuous phenotypes were transformed to tertiles (S1 Table). The full list of phenotypic tertiles and indicator variables used can be found in S2 Table. The three last columns show the generated indicator variables selected from the TWIST procedure as predictive of CHD. Out of the original 150 variables, 75 were retained. Continuous traits in tertiles and genotypes as three genotyping classes. In the abbreviations, index numbers after the gene names refer to common homozygote (1), heterozygote (2) and rare homozygote (3). The APOE gene polymorphism was coded so that 1 were the E2 carriers, 2 were those within the E3E3 category and 3 were the E4 carriers. Smoking is a dichotomous variables of yes or no smoking.