Table 4.
Replication of SNP-level lincRNA associations in PROMIS GWAS datasets
| Trait | Original GWAS | Replication in PROMIS | |||||||
|---|---|---|---|---|---|---|---|---|---|
| Bonferroni significance threshold | Number of SNPs meeting Bonferroni significance threshold | Number of lincRNAs with ≥1 SNP meeting the Bonferroni significance threshold | Number of original significant SNPs also present in PROMIS data | Replication significance threshold | Number of PROMIS SNPs meeting replication significance threshold | Number of PROMIS lincRNAs with ≥1 SNP meeting the replication- significant SNP | Percent of original Bonferroni- significant SNPs also significant in PROMIS | Percent of original significant lincRNAs also significant in PROMIS | |
| MI | 2.34 × 10−7 | 31 | 10 | 31 | 1.61 × 10−3 | 25 | 8 | 81% | 80% |
| HDL-C | 2.12 × 10−7 | 163 | 42 | 162 | 3.09 × 10−4 | 37 | 8 | 23% | 19% |
| LDL-C | 2.12 × 10−7 | 156 | 39 | 155 | 3.23 × 10−4 | 21 | 7 | 14% | 18% |
| Total cholesterol | 2.12 × 10−7 | 199 | 44 | 197 | 2.54 × 10−4 | 52 | 9 | 26% | 21% |
| Triglycerides | 2.12 × 10−7 | 122 | 22 | 121 | 4.13 × 10−4 | 69 | 12 | 57% | 55% |
The replication results are shown here for five cardiometabolic traits. The number of SNPs and lincRNAs meeting the specified significance threshold are shown for the original GWAS and the corresponding PROMIS replication dataset. The percentage of originally significant SNPs and lincRNAs significant in PROMIS are also reported.