Table 2.
Summary of intraclass correlation coefficients (β-scale) of CpG locus methylation, by genomic location and probe type, X chromosome.1
| Δβ < 0.1
|
0.1 ≤ Δβ < 0.2
|
Δβ ≥ 0.2
|
|||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Location/probe type | ICC
|
Percent loci by ICC range
|
Percent loci by ICC range
|
Percent loci by ICC range
|
Percent loci by ICC range
|
||||||||||||||
| N | Median | IQR | 0 – 0.5 | 0.5 – 0.8 | 0.8 – 1 | N | 0 – 0.5 | 0.5 – 0.8 | 0.8 – 1 | N | 0 – 0.5 | 0.5 – 0.8 | 0.8 – 1 | N | 0 – 0.5 | 0.5 – 0.8 | 0.8 – 1 | ||
| All CpG loci | 11215 | 0.80 | 0.60 | 0.89 | 18.5 | 31.8 | 49.7 | 9014 | 23.0 | 38.4 | 38.6 | 2161 | 0.1 | 5.0 | 95.0 | 40 | 0.0 | 2.5 | 97.5 |
| Enhancer | 629 | 0.84 | 0.71 | 0.91 | 9.9 | 31.5 | 58.7 | 478 | 13.0 | 40.2 | 46.9 | 149 | 0.0 | 4.0 | 96.0 | 2 | 0.0 | 0.0 | 100.0 |
| Known DMR2 | 1231 | 0.85 | 0.72 | 0.91 | 10.6 | 27.8 | 61.6 | 936 | 14.0 | 34.9 | 51.1 | 290 | 0.0 | 5.2 | 94.8 | 5 | 0.0 | 0.0 | 100.0 |
| Location with respect to CpG island: | |||||||||||||||||||
| CpG Island | 4272 | 0.82 | 0.67 | 0.90 | 13.2 | 32.0 | 54.8 | 3391 | 16.6 | 38.9 | 44.4 | 867 | 0.0 | 5.2 | 94.8 | 14 | 0.0 | 0.0 | 100.0 |
| Shore3 | 2837 | 0.82 | 0.63 | 0.90 | 17.3 | 29.7 | 53.0 | 2176 | 22.5 | 37.2 | 40.3 | 649 | 0.3 | 5.1 | 94.6 | 12 | 0.0 | 0.0 | 100.0 |
| Shelf3 | 1138 | 0.71 | 0.46 | 0.85 | 28.0 | 36.3 | 35.7 | 1003 | 31.8 | 40.4 | 27.8 | 130 | 0.0 | 6.2 | 93.8 | 5 | 0.0 | 0.0 | 100.0 |
| Functional location: | |||||||||||||||||||
| TSS1500 | 2777 | 0.80 | 0.60 | 0.90 | 18.5 | 31.3 | 50.2 | 2211 | 23.2 | 38.4 | 38.4 | 555 | 0.0 | 3.4 | 96.6 | 11 | 0.0 | 0.0 | 100.0 |
| TSS200 | 2441 | 0.82 | 0.67 | 0.90 | 13.5 | 31.4 | 55.1 | 1866 | 17.5 | 39.3 | 43.2 | 564 | 0.4 | 5.9 | 93.8 | 11 | 0.0 | 9.1 | 90.9 |
| 5′UTR | 2401 | 0.82 | 0.67 | 0.90 | 13.2 | 32.1 | 54.7 | 1873 | 16.9 | 39.6 | 43.5 | 522 | 0.0 | 5.6 | 94.4 | 6 | 0.0 | 0.0 | 100.0 |
| 1st Exon | 1635 | 0.83 | 0.67 | 0.90 | 12.3 | 32.9 | 54.8 | 1293 | 15.5 | 40.7 | 43.8 | 340 | 0.0 | 3.5 | 96.5 | 2 | 0.0 | 0.0 | 100.0 |
| Body | 2893 | 0.76 | 0.52 | 0.88 | 23.3 | 32.5 | 44.2 | 2407 | 28.0 | 38.3 | 33.7 | 481 | 0.0 | 3.7 | 96.3 | 5 | 0.0 | 0.0 | 100.0 |
| 3′UTR | 513 | 0.71 | 0.44 | 0.84 | 28.7 | 37.4 | 33.9 | 466 | 31.5 | 40.1 | 28.3 | 46 | 0.0 | 10.9 | 89.1 | 1 | 0.0 | 0.0 | 100.0 |
| Location by probe type: | |||||||||||||||||||
| Infinium I | 3042 | 0.78 | 0.60 | 0.87 | 16.8 | 38.3 | 44.8 | 2444 | 20.9 | 45.7 | 33.4 | 583 | 0.2 | 8.4 | 91.4 | 15 | 0.0 | 6.7 | 93.3 |
| Infinium II | 8173 | 0.81 | 0.60 | 0.90 | 19.1 | 29.4 | 51.5 | 6570 | 23.7 | 35.7 | 40.6 | 1578 | 0.1 | 3.7 | 96.3 | 25 | 0.0 | 0.0 | 100.0 |
1
All estimates are adjusted for cell-type composition. Δβ is estimated as twice the between-person standard error (β-scale).
2
DMR: differentially methylated region; TSS: transcription start site; UTR: untranslated region.
3
Shores: up to 2 kb from CpG islands; shelves: from 2 to 4 kb from CpG islands.