Table 2. Observed heritability (h2 obs) and its standard error (SE), expected heritability (h2 exp) and the adjusted P-value from LD-score regression for enrichment in CAD.
Also, the distances between p-value distributions (D-statistics) from Kolmogorov-Smirnov tests are shown, comparing different MAF groups: (a) [0.005–0.01) vs. [0.01–0.05); (b) [0.005–0.001) vs. (≥0.05); (c) [0.01–0.05) vs. (≥0.05).
| Annotation Category | h2 obs (SE) | h2 exp | P-value (adjusted)(1) | # of SNPs (2) | KS-test D measure (a,b,c) |
|---|---|---|---|---|---|
| Enhancer_Hoffman. extend.500(3) | 0.18 (0.03) | 0.03 | 1.1x10-04 | 401,897 | 0.030, 0.069, 0.042 |
| H3K9ac_Trynka | 0.15 (0.03) | 0.02 | 2.7x10-04 | 322,412 | 0.027, 0.074, 0.048 |
| H3K9ac_Trynka.extend.500 | 0.18 (0.03) | 0.04 | 3.7x10-04 | 601,848 | 0.028, 0.072, 0.045 |
| Enhancer_Hoffman | 0.14 (0.03) | 0.01 | 4.1x10-04 | 163,480 | 0.030, 0.072, 0.044 |
| H3K27ac_PGC2.extend.500 | 0.19 (0.03) | 0.07 | 3.8x10-03 | 962,593 | 0.024, 0.065, 0.041 |
| H3K4me3_Trynka.extend.500 | 0.20 (0.04) | 0.05 | 3.9x10-03 | 713,844 | 0.024, 0.065, 0.042 |
| H3K27ac_PGC2 | 0.18 (0.03) | 0.05 | 3.9x10-03 | 768,410 | 0.024, 0.065, 0.042 |
| H3K9ac_peaks_Trynka | 0.11 (0.03) | 0.01 | 4.0x10-03 | 95,531 | 0.032, 0.079, 0.049 |
| FetalDHS_Trynka | 0.18 (0.04) | 0.02 | 9.1x10-03 | 255,582 | 0.022, 0.059, 0.039 |
(1) Adjusted p-value for enrichment, using a Bonferroni correction
(2) The number of SNPs used for the adjusted p-value
(3) “extend.500” implies that a 500 base pair window around the category was included with the annotation to minimize inflation of heritability from flanking regions[22]