Table 1. Properties of datasets and estimates of $h_{\text{SNP}}^2$.

n = sample size (cases + controls), m = number of SNPs, ${\Sigma }_{j=1}^m{w}_j$ = sum of SNP weights which can be interpreted as an effective number of independent SNPs. All values are post quality control; values for m and Σw_j are rounded to the nearest K (thousand). For UCLEB, m and Σw_j refer to our main analysis, which considers only high-quality, common SNPs. The final column provides our best estimates of $h_{\text{SNP}}^2$ from common SNPs, computed using LDAK with α = –0.25 (see main text for explanation of α). For comparison, we include previously published estimates of $h_{\text{SNP}}^2$ (note that the previous analyses for rheumatoid arthritis, type 1 diabetes and multiple sclerosis excluded major histocompatibility SNPs, which we estimate contribute 0.07, 0.20 and 0.05, respectively), as well as $h_{\text{GWAS}}^2$, the proportion of phenotypic variance explained by SNPs reported as GWAS significant (P < 5 × 10^–8). For disease traits, estimates of $h_{\text{SNP}}^2$ and $h_{\text{GWAS}}^2$ have been converted to the liability scale assuming the stated prevalence.

Collection	Trait (Disease Prevalence, %)	n	m	${\Sigma }_{j=1}^m{w}_j$	$h_{\text{GWAS}}^2$	Estimates of $h_{\text{SNP}}^2$ (SD)
						Previous	LDAK
Welcome Trust Case Control Consortium 1 (WTCCC 1)	Bipolar Disorder (0.5)	1 840 + 2 913	3 729 K	79 K	0.02	0.24 (0.04)7	0.35 (0.03)
	Coronary Artery Disease (6)	1 907 + 2 918	3 738 K	80 K	0.03	0.25 (0.06)7	0.40 (0.06)
	Crohn’s Disease (0.5)	1 691 + 2 905	3 723 K	79 K	0.21	0.26 (0.01)16	0.32 (0.03)
	Hypertension (5)	1 918 + 2 916	3 739 K	80 K	<0.01	0.33 (0.06)7	0.46 (0.06)
	Rheumatoid Arthritis (0.5)	1 846 + 2 918	3 735 K	80 K	0.19	0.09 (0.03)7	0.21 (0.03)
	Type 1 Diabetes (0.5)	1 941 + 2 907	3 731 K	80 K	0.27	0.13 (0.03)7	0.31 (0.02)
	Type 2 Diabetes (8)	1 896 + 2 917	3 735 K	80 K	0.08	0.42 (0.07)7	0.54 (0.07)
Welcome Trust Case Control Consortium 2 (WTCCC 2)	Barrett’s Oesophagus (1.6)	1 861 + 5 138	4 830 K	116 K	<0.01	0.25 (0.05)17	0.32 (0.04)
	Ischaemic Stroke (2)	3 769 + 5 139	4 797 K	115 K	<0.01	0.25 (0.03)18	0.34 (0.03)
	Parkinson’s Disease (0.2)	1 687 + 5 136	4 819 K	116 K	0.03	0.27 (0.05)19	0.20 (0.03)
	Psoriasis (0.5)	2 267 + 5 143	4 814 K	116 K	0.21	0.35 (0.06)20	0.34 (0.02)
	Schizophrenia (1)	2 068 + 2 615	3 481 K	111 K	0.07	0.23 (0.01)21	0.30 (0.04)
	Ulcerative Colitis (0.2)	2 614 + 5 327	4 061 K	115 K	0.12	0.19 (0.01)16	0.28 (0.02)
WTCCC 2 +	Celiac Disease (1)	2 492 + 7 376	3 681 K	88 K	0.29	0.33 (0.04)22	0.35 (0.02)
	Multiple Sclerosis (0.1)	8 553 + 5 667	4 702 K	113 K	0.17	0.17 (0.01)7	0.24 (0.01)
	Partial Epilepsy (0.3)	1 217 + 5 152	3 399 K	108 K	<0.01	0.33 (0.05)3	0.27 (0.04)
RPTB	Pulmonary Tuberculosis (4)	5 142 + 5 283	3 987 K	102 K	<0.01	None Found	0.26 (0.03)
Blue Mountain	Intraocular Pressure	2 235	4 149 K	125 K	0.02	None Found	0.38 (0.17)
CHOP	Wide-Range Achievement Test	3 747	3 593 K	88 K	<0.01	0.43 (0.10)23	0.21 (0.09)
UCLEB	23 Quantitative Traits	6 458 to 11 005	353 K	39 K	---	Supplementary Table 1