Table 3. Top-ranked annotations for HDL trait.

Cell line	Type	CAVIARBF_ENET_CV		CAVIARBF_Individual_Annotation		CAVIARBF_top10t	PAINTOR_Individual_Annotation		PAINTOR_top10t
		γ	standardized γ	P-value	γ	γ	P-value	γ	γ
—	distance to TSS	−0.053	−0.053	0.290	−0.210	0.000	0.186	0.313	0.000
K562	repressed	−0.060	−0.030	0.041	−0.755	−0.369	0.096	0.650	0.000
hepg2	repressed	−0.045	−0.023	0.062	−0.715	0.000	0.121	0.641	0.000
LCL	repressed	−0.038	−0.019	0.138	−0.512	0.000	0.243	0.455	0.000
k562	transcribed	0.037	0.016	0.116	0.634	0.000	0.140	−0.672	0.000
hela	repressed	−0.029	−0.014	0.220	−0.477	0.000	0.316	0.444	0.000
H1hesc	repressed	−0.029	−0.014	0.185	−0.507	0.000	0.315	0.424	0.000
fIntestine (Lg)	DHS	0.051	0.013	0.005	1.721	0.000	0.012	−1.760	0.000
fMuscle (trunk)	DHS	0.038	0.010	0.014	1.641	0.000	0.032	−1.743	0.000
fMuscle (arm)	DHS	0.039	0.010	0.010	1.738	1.401	0.019	−1.877	−1.064
Conjunctival fibroblasts	DHS	0.043	0.008	0.005	1.945	0.000	0.019	−1.940	0.000
fThymus	DHS	0.034	0.007	0.016	1.822	0.000	0.042	−1.886	0.000
Villous mesenchymal fibroblast	DHS	0.031	0.007	0.031	1.468	0.000	0.035	−1.601	0.000
hepg2	TSS	0.033	0.005	0.004	2.145	1.041	0.005	−2.249	−1.341
—	coding exons	0.028	0.004	0.008	2.190	1.552	0.017	−2.238	0.000
—	3′ UTR exons	0.025	0.003	0.022	2.211	2.007	0.010	−2.482	−2.316
—	nonsynonymous	0.024	0.002	0.009	1.923	0.000	0.003	−3.038	−2.394

Rows in boldface font indicate the top 10 annotations by different methods. To be consistent with the annotation parameterization as in CAVIARBF, the sign of effect sizes from PAINTOR need to be flipped.