Table 1.
Summary of the proportion (%) of heritability (SNP-based) and trait-associated variants (trait QTLs) affecting gene expression (eVariants), RNA splicing (sVariants), or variants affecting both expression and splicing (esVariants)
| Tissue | Class | N class | % class | Small (SE) | Medium (SE) | Large (SE) | O[% h2] (SE), % | E[% h2] (SE), % | O[% QTLs] (SE), % | E[% QTLs] (SE), % |
|---|---|---|---|---|---|---|---|---|---|---|
| Single tissue | cis.eVariants | 7,921 | 0.42 | 166.5 (3.9) | 16.7 (0.5) | 0.6 (0.0) | 3.78 (0.09)∗∗∗∗ | 0.32 (0.01) | 9.12 (0.30)∗∗∗∗ | 0.002 (0.000) |
| cis.sVariants | 26,222 | 1.39 | 324.9 (11.7) | 25.0 (0.8) | 0.7 (0.0) | 6.23 (0.18)∗∗∗∗ | 1.05 (0.05) | 4.60 (0.20)∗∗∗∗ | 0.005 (0.000) | |
| cis.esVariants | 4,598 | 0.24 | 106.4 (3.3) | 11.2 (0.3) | 0.6 (0.0) | 2.66 (0.08)∗∗∗∗ | 0.18 (0.01) | 20.86 (1.06)∗∗∗∗ | 0.001 (0.000) | |
| trans.eVariants | 3,003 | 0.16 | 128.4 (3.0) | 13.9 (0.4) | 0.5 (0.0) | 3.04 (0.07)∗∗∗∗ | 0.13 (0.00) | 19.03 (0.77)∗∗∗∗ | 0.001 (0.000) | |
| trans.sVariants | 32,083 | 1.70 | 296.9 (4.6) | 28.9 (0.8) | 0.7 (0.0) | 6.27 (0.11)∗∗∗∗ | 1.34 (0.02) | 2.61 (0.08)∗∗∗∗ | 0.007 (0.000) | |
| trans.esVariants | 2,740 | 0.15 | 109.9 (2.5) | 12.0 (0.4) | 0.5 (0.0) | 2.65 (0.06)∗∗∗∗ | 0.11 (0.00) | 17.25 (0.96)∗∗∗∗ | 0.001 (0.000) | |
| remaining | 1,805,933 | 95.93 | 6,726.8 (53.7) | 98.1 (2.1) | 1.7 (0.1) | 75.38 (0.41) | 75.38 (0.41) | 0.38 (0.00) | 0.38 (0.003) | |
| Multi-tissue | cis.eVariants | 1,919 | 0.10 | 84.9 (9.3) | 9.5 (1.0) | 0.4 (0.0) | 2.09 (0.18)∗∗∗∗ | 0.06 (0.00) | 14.53 (1.47)∗∗∗∗ | 0.000 (0.000) |
| cis.sVariants | 252,518 | 13.41 | 1,611.2 (74.4) | 55.7 (5.5) | 1.0 (0.1) | 21.46 (0.77)∗∗∗∗ | 7.57 (0.39) | 1.29 (0.05)∗∗∗∗ | 0.066 (0.003) | |
| cis.esVariants | 275,390 | 14.63 | 1,593.8 (60.3) | 53.6 (4.8) | 1.5 (0.3) | 21.77 (1.01)∗∗∗∗ | 8.26 (0.43) | 1.18 (0.04)∗∗∗∗ | 0.072 (0.004) | |
| trans.eVariants | 227,126 | 12.07 | 987.8 (39.6) | 32.3 (3.2) | 0.8 (0.0) | 13.13 (0.36)∗∗∗∗ | 6.81 (0.35) | 0.93 (0.04)∗∗∗∗ | 0.059 (0.003) | |
| trans.sVariants | 47,694 | 2.53 | 365.4 (25.7) | 23.0 (2.0) | 0.6 (0.0) | 6.21 (0.36)∗∗∗∗ | 1.43 (0.07) | 2.31 (0.16)∗∗∗∗ | 0.012 (0.001) | |
| trans.esVariants | 49,692 | 2.64 | 244.6 (18.8) | 17.8 (1.7) | 0.6 (0.0) | 4.51 (0.30)∗∗∗∗ | 1.49 (0.08) | 1.89 (0.16)∗∗∗∗ | 0.013 (0.001) | |
| remaining | 1,028,161 | 54.62 | 2,708.2 (138.5) | 44.1 (9.5) | 0.9 (0.2) | 30.83 (1.59) | 30.83 (1.59) | 0.27 (0.01) | 0.27 (0.014) |
Within each non-overlapping class, the total number of variants (N class) and their genome proportion (% class, number of variants in the class/total number of variants analyzed), the number of variants with small effects (“small”), medium effects (“medium”), and large effects (“large”) averaged across 16 tissues and 37 traits are given. These numbers are used to estimate the observed heritability explained (O[% h2]) and the proportion of trait QTLs in each class (O[% QTLs]). The number of variants within the remaining class (no regulatory evidence) is used to estimate the expected proportion of heritability explained (E[% h2]) and the proportion of trait QTLs in each class (E[% QTLs]). The standard errors as shown in parentheses are derived based on the estimates across 37 traits. ∗∗∗∗p of heritability enrichment < 0.0001 (difference between observed and expected across 37 traits and 16 single tissues or 1 multi-tissue, two-sided test).