TABLE 2.
Top 10 CpG sites in tests of association between methylation level and bladder cancer risk in pre-diagnostic blood from the Women’s Health Initative.
| Illumina ID | Chra | Position | Gene | Gene Groupa | Relation to CpG Islandb | Average β-value in Controls | Odds Ratio | 95% CIc | P-value | Q-valued |
|---|---|---|---|---|---|---|---|---|---|---|
| cg22748573 | chr1 | 41327924 | CITED4 | 5′UTR;1stExon | Island | 0.058 | 0.18 | (0.09, 0.34) | 1.5×10−7 | 0.05 |
| cg20010635 | chr1 | 7811409 | CAMTA1 | Body | OpenSea | 0.952 | 8.42 | (3.48, 20.33) | 2.2×10−6 | 0.40 |
| cg25955565 | chr14 | 71863756 | SNORD56B | TSS1500 | OpenSea | 0.945 | 9.29 | (3.59, 24.08) | 4.5×10−6 | 0.41 |
| cg26492847 | chr11 | 96063104 | MAML2 | Body | OpenSea | 0.929 | 7.24 | (3.01, 17.38) | 9.5×10−6 | 0.41 |
| cg06414161 | chr16 | 53534040 | AKTIP | Body | Shelf | 0.931 | 8.93 | (3.36, 23.72) | 1.1×10−5 | 0.41 |
| cg27627854 | chr11 | 108158382 | ATM | Body;1stExon | OpenSea | 0.905 | 4.19 | (2.21, 7.98) | 1.2×10−5 | 0.41 |
| cg02393449 | chr10 | 70743010 | DDX21 | 3′UTR | OpenSea | 0.929 | 6.91 | (2.89, 16.53) | 1.4×10−5 | 0.41 |
| cg26695157 | chr12 | 109985283 | OpenSea | 0.917 | 3.71 | (2.05, 6.72) | 1.5×10−5 | 0.41 | ||
| cg17803089 | chr6 | 35419793 | FANCE | TSS1500 | Shore | 0.036 | 0.18 | (0.08, 0.39) | 1.8×10−5 | 0.41 |
| cg26729242 | chr10 | 96980135 | C10orf129 | Body | OpenSea | 0.906 | 3.00 | (1.81, 4.96) | 1.9×10−5 | 0.41 |
Chr = Chromosome
Functional region of gene as indicated in v1.2 Illumina annotation: TSS1500 = 200–1500 bases upstream of the transcription start site; TSS200 = 0–200 bases upstream of the transcription start site; 5′UTR = Within the 5 prime untranslated region; 1stExon = First segment of gene coding for peptide sequence; Body = Between the ATG and stop codon; 3′UTR = Between the stop codon and poly A signal; Multiple listings indicate a locus in a region with multiple splice variants.
Position relative to CpG island as indicated in v1.2 Illumina annotation: Island = Within CpG island (CG content > 50%, Obs/Exp CpG ratio > 0.60, and length > 200 bps); OpeanSea = Non-island region; Shore = 0–2 kb flanking CpG Island; Shelf = 2–4 kb flanking CpG Island.
95% confidence interval for odds ratio estimate.
Q-values represent p-values adjusted for multiple testing using the FDR method.