. Author manuscript; available in PMC: 2020 Jul 1.

Published in final edited form as: Cancer Epidemiol Biomarkers Prev. 2019 Apr 23;28(7):1238–1245. doi: 10.1158/1055-9965.EPI-18-1235

Table 2.

Estimates of Variance Explained by Imputed Variants in Four Functional Groups

		Above mean LD		Below mean LD		Row sum	s.e.	No. Variants (%)	Sub-category sum	s.e.
		Est	s.e.	Est	s.e.	Row sum	s.e.	No. Variants (%)	Sub-category sum	s.e.
Coding	MAF < 0.01	0.002	0.022	0.004	0.029	0.005	0.036	103,133 (0.6%)	0.010	0.039
Coding	MAF ≥ 0.01	0.005	0.009	0	0.014	0.005	0.017	50,753 (0.3%)	0.010	0.039

Intergenic	MAF < 0.01	0.033	0.036	0	0.059	0.033	0.063	4,305,707 (26.6%)	0.060	0.068
Intergenic	MAF ≥ 0.01	0	0.015	0.027	0.026	0.027	0.030	4,220,706 (26.1%)	0.060	0.068

Intronic	MAF < 0.01	0.042	0.037	0	0.055	0.042	0.061	3,173,417 (19.6%)	0.124	0.066
Intronic	MAF ≥ 0.01	0.009	0.014	0.074	0.025	0.082	0.028	2,856,226 (17.6%)	0.124	0.066

Regulatory	MAF < 0.01	0	0.024	0	0.036	0	0.043	746,866 (4.6%)	0.018	0.045
Regulatory	MAF ≥ 0.01	0.0002	0.009	0.018	0.014	0.018	0.016	676,634 (4.2%)	0.018	0.045

Abbreviations: LD, linkage disequilibrium; Est, estimate; s.e., standard error.