Table 1.
Features of the probes (X, Z) and SNPs (G) analyzed at 10 genes selected due to the associations between methylation levels and ΔHDL in Zhao et al. [3]
| Gene | CpGs: # in gene a/# nearby b (# genes nearby) | SNPs: # in Set F/# in Set R | # probes associated with ΔHDL c | Gene | CpGs: # in gene a/# nearby b (# genes nearby) | SNPs: # in Set F/# in Set R | #CpGs associated with ΔHDL c |
|---|---|---|---|---|---|---|---|
| RNMT;C18orf19 | 15/31(4) | 128/21 | 1 | GTF2IRD2 | 6/20 (4) | 0/0 | 1 |
| MIR130B | 3/77(9) | 90/10 | 2 | VPS25 d | 11/41(19) | 59/3 | 4 |
| C6orf141 | 14/34(5) | 53/8 | 2 | SBSN d | 8/45 (3) | 102/4 | 1 |
| TUBB3 | 20/214 (8) | 0/0 | 1 | TPM4 | 29/74 (7) | 161/14 | 1 |
| TBX15 | 109/57(1) | 91/63 | 2 | PARP15 | 17/60(5) | 146/1 | 4 |
a Probes located within 20 kb of the gene of interest
b Probes within 20 kb of neighboring genes, and up to (±100 kb) from the gene of interest; ie, CpGs used as potential pleiotropic phenotypes in the CIV method
c Probes that showed significant associations in univariate analysis at significance level 0.01 with Bonferroni correction
d Only probes within 20 kb (instead of 100 kb) of neighboring genes around genesVPS25and SBSN were used as Z