Table 1.

Estimates of Total SNP Heritability and the Amount of ${\mathit{h}}_{\mathit{g}}^{\mathbf{2}}$ Attributable to Loci Containing GWAS Index SNPs, ${\mathit{h}}_{\mathit{g},\text{local,GWAS}}^{\mathbf{2}}$, and Index SNPs Only, ${\mathit{h}}_{\text{GWAS}}^{\mathbf{2}}$

Trait	${\mathit{h}}_{\mathit{g}}^{\mathbf{2}}$(% SE)	${\mathit{h}}_{\mathbf{pub}}^{\mathbf{2}}$(%)	${\mathit{h}}_{\mathit{g}}^{\mathbf{2}}\mathbf{/}{\mathit{h}}_{\mathbf{pub}}^{\mathbf{2}}$	${\mathit{h}}_{\mathbf{GWAS}}^{\mathbf{2}}$(% SE)	${\mathit{h}}_{\mathit{g}\mathbf{,}\mathbf{local,GWAS}}^{\mathbf{2}}$(% SE)	${\mathit{h}}_{\mathit{g}\mathbf{,}\mathbf{local,GWAS}}^{\mathbf{2}\mathbf{\ast }}$(% SE)	Enrichmenta(SE)
BMI1	16.5 (0.5)	4223	0.39	1.6 (0.001)	3.1 (0.1)	3.1 (0.1)	3.7 (0.4)
Height2	59.4 (0.3)	6923	0.86	13.9 (0.002)	32.0 (0.2)	24.0 (0.2)	1.5 (0.1)
Hemoglobin24	17.9 (2.1)	3725	0.48	2.2 (0.003)	1.9 (0.3)	1.8 (0.3)	7.6 (1.4)
Mean cell hemoglobin24	29.3 (2.2)	5226	0.56	7.2 (0.003)	6.2 (0.4)	6.1 (0.4)	9.9 (1.9)
Concentration of mean cell hemoglobin24	10.9 (2.5)	4827	0.23	0.4 (0.003)	0.5 (0.2)	0.5 (0.2)	6.7 (1.8)
Mean cell volume24	26.3 (2.0)	5226	0.51	6.5 (0.004)	5.7 (0.4)	5.6 (0.4)	8.1 (1.3)
Packed cell volume24	16.7 (2.5)	3025	0.56	1.4 (0.003)	0.9 (0.2)	0.8 (0.2)	6.0 (1.4)
Red blood cell count24	22.0 (2.3)	5626	0.39	3.6 (0.004)	2.6 (0.3)	2.6 (0.3)	6.4 (1.6)
Number of platelets28	27.5 (1.5)	5725	0.48	3.5 (0.003)	3.9 (0.3)	3.9 (0.3)	5.7 (0.9)
Fasting glucose29	22.3 (2.3)	6630	0.34	2.6 (0.002)	1.7 (0.2)	1.6 (0.2)	8.0 (2.5)
Fasting insulin29	19.9 (2.4)	3631	0.55	–	–	–	–
HBA1C32	20.8 (2.3)	7530	0.28	1.8 (0.003)	0.9 (0.2)	0.9 (0.2)	6.6 (1.9)
HOMA-B29	20.3 (2.4)	7233	0.28	0.6 (0.001)	0.4 (0.1)	0.4 (0.1)	7.5 (1.9)
HOMA-IR29	19.9 (2.4)	3831	0.52	–	–	–	–
HDL3	39.4 (0.9)	4234	0.94	5.8 (0.002)	10.7 (0.2)	10.5 (0.2)	4.6 (1.3)
LDL3	33.0 (1.0)	4034	0.82	7.8 (0.002)	8.4 (0.2)	8.3 (0.2)	5.1 (0.9)
TC3	35.5 (0.9)	5035	0.71	8.0 (0.002)	9.3 (0.2)	9.3 (0.2)	4.3 (0.6)
TG3	34.8 (0.9)	4036	0.87	5.2 (0.002)	8.0 (0.2)	8.0 (0.2)	5.8 (1.4)
Education years37	19.9 (0.8)	4037	0.50	0.1 (0.002)	0.2 (0.0)	0.2 (0.0)	3.2 (1.4)
Forearm BMD38	17.4 (2.2)	8439	0.21	0.3 (0.001)	0.5 (0.1)	0.5 (0.1)	22.4 (7.7)
Femoral-neck BMD38	24.1 (2.1)	8439	0.29	2.0 (0.003)	2.0 (0.2)	2.0 (0.2)	7.1 (1.0)
Lumbar spine38	25.1 (2.0)	8439	0.30	2.2 (0.003)	2.2 (0.3)	2.2 (0.3)	6.1 (0.8)
Age at menarche40	27.8 (0.7)	4941	0.57	2.6 (0.002)	3.8 (0.2)	3.7 (0.2)	2.9 (0.2)
College37	19.4 (0.8)	4037	0.48	0.1 (0.001)	0.1 (0.0)	0.1 (0.0)	3.5 (0.9)
RA42	66.3 (0.9)	5543	1.21	11.2 (0.003)	22.0 (0.3)	22.1 (0.3)	9.8 (4.3)
SCZ44	64.5 (0.7)	8145	0.80	6.2 (0.004)	9.2 (0.2)	9.2 (0.2)	2.3 (0.1)
Crohn disease46	35.9 (1.8)	5347	0.68	3.8 (0.002)	5.9 (0.4)	5.9 (0.4)	4.8 (0.7)
Inflammatory bowel disease46,b	35.3 (1.4)	–	–	4.9 (0.002)	6.7 (0.3)	6.6 (0.3)	4.6 (0.5)
Ulcerative colitis46	31.9 (2.1)	5847	0.55	2.7 (0.002)	4.1 (0.3)	4.1 (0.3)	5.4 (1.0)
Type 2 diabetes48	25.4 (1.6)	2649	0.98	1.3 (0.002)	1.1 (0.2)	1.1 (0.2)	3.9 (0.7)

$h_{g,\text{local,GWAS}}^{2\ast }$ is the same as $h_{g,\text{local,GWAS}}^2$ except that GWAS index SNPs were excluded from the computation. In Table S2, we report $h_{g,\text{local,GWAS}}^{2†}$, which we obtained by excluding all GWAS hits. We also report estimates of familial heritability $\left(h_{\text{pub}}^2\right)$ obtained from twin or family studies. At the bottom of the table, we list case-control traits where our estimate of $h_g^2$ is biased as a result of ascertainment.

^aSimilar to Finucane et al.,⁷ we define enrichment as the ratio between the fraction of $h_g^2$ attributable to $h_{g,\text{local,GWAS}}^{2\ast }$ and the genomic fraction covered by these loci. We obtained SEs by a jackknife over the loci.

^bInflammatory bowel disease refers to the union of Crohn disease and ulcerative colitis.