S1 Table. Summary of simulation settings. - PLOS

S1 Table. Summary of simulation settings.

Phenotypic covariance matrix

Genetic covariance matrix

Population stratification

Causal SNPs

Sample overlap

1. Blood lipids

1a

0.87 −0.04 0.30 0.85

" #$% = ℎ()*

1b



0.30 −0.62 0.93 0.30

0.5#$% + 0.5ABCD(#$% ) 0.87 −0.02 0.15 −0.02 1.00 −0.31 0.15 −0.31 0.93 0.43 0.09 0.15

" = ℎ()*

1c

−0.04 1.00 −0.62 0.18

Same set of ~12K across all traits with effect sizes generated from distribution

0.85 0.18 0.30 0.95

8(0,

;

).

Same set of ~12K across all traits with effect sizes generated from distribution

0.85 0.18 0.30 0.95

No

from 8(0, ); %"> c) ~6K only causal for trait 2 and 3 with effect size generated from 8(0,

−0.04 1.00 −0.62 0.18

Yes

a) ~6K causal for all traits with effect size generated from

Same heritability as 1a, 1b and 1d, half of the genetic covariance.

0.87 −0.04 0.30 0.85

No

8(0,

;

).

"JJ KLM

KLM

8 overlap.

No Yes

a) ~6K shared by all traits with effect size generated from ; d) ~6K only causal for trait 3 and with effect size generated from 8(0,

2d

All traits are measured on the same set of subjects.

F J.NMOPQR

F OPQR

%">

).

Same set of ~12K across all traits with effect sizes generated from distribution



8(0,

;

All traits are measured on the same set of subjects.

No

).