Table 2: Genetic and phenotypic correlations between GWAS, GWAX and LT-FH phenotypes.

We report the genetic correlation (estimated using BOLT-REML) and phenotypic correlation between each pair of GWAS, GWAX and LT-FH phenotypes. BOLT-REML estimates are constrained to be ≤ 1.00. Standard errors of genetic correlation estimates are reported in parentheses. Standard errors of phenotypic correlation estimates are ≤ 0.003 in each case.

Trait	Genetic Correlation (rg)						Phenotypic Correlation
	GWAS/GWAX		GWAS/LT-FH		GWAX/LT-FH		GWAS/GWAX	GWAS/LT-FH	GWAX/LT-FH
	rg	s.e.	rg	s.e.	rg	s.e.
AD	1.00	0.38	1.00	0.34	1.00	0.002	0.09	0.30	0.96
PD	1.00	0.16	1.00	0.10	1.00	0.009	0.26	0.57	0.93
Lung cancer	1.00	0.14	1.00	0.12	1.00	0.004	0.20	0.49	0.91
Bowel cancer	0.95	0.06	0.97	0.03	0.99	0.006	0.30	0.64	0.91
Stroke	0.83	0.07	0.88	0.04	0.99	0.008	0.24	0.62	0.86
COPD	0.90	0.02	0.95	0.01	0.99	0.003	0.40	0.77	0.87
Prostate cancer	1.00	0.03	1.00	0.006	1.00	0.005	0.56	0.88	0.89
T2D	0.97	0.01	0.99	0.004	0.99	0.002	0.38	0.77	0.86
Breast cancer	1.00	0.02	1.00	0.006	1.00	0.004	0.58	0.87	0.89
Depression	0.88	0.02	0.93	0.007	0.98	0.003	0.58	0.84	0.89
CAD	0.89	0.02	0.96	0.005	0.98	0.005	0.31	0.76	0.78
HTN	0.95	0.006	0.98	0.001	0.98	0.003	0.52	0.86	0.75
Average	0.95		0.97		0.99		0.37	0.70	0.88