Table 2.

Top associations between phenotypes and common variants

Phenotypes	Genome position (GRCh38)	Effect allele (Other allele)	Effect allele frequency	Effect size [95% CI]	P-value	Mapped gene	Additional independent SNVs (P-value in conditional analysis)
Disease
Atrial Fibrillation	chr4:110743002	A (G)	0.15	1.26 [1.18, 1.34]	2.40×10−13	PITX2	No
Type 2 Diabetes	chr6:26276061	G (T)	0.04	0.79 [0.73, 0.86]	4.22×10−8	HFE	No
	chr9:22136441	C (G)	0.25	1.11 [1.07, 1.16]	3.39×10−8	CDKN2B	No
	chr10:113039134	A (T)	0.25	1.19 [1.15, 1.24]	4.87×10−20	TCF7L2	No
	chr12:4275678	G (T)	0.01	0.66 [0.57, 0.77]	4.23×10−8	CCND2	No
	chr16:53773852	G (A)	0.46	1.12 [1.08, 1.16]	1.33×10−11	FTO	No
Quantitative traits
Low-density lipoprotein	chr1:55055522	T (C)	0.10	−0.09 [−0.11, −0.06]	1.71×10−12	PCSK9	No
	chr1:109274968	T (G)	0.22	−0.12 [−0.13, −0.10]	3.49×10−38	CELSR2	No
	chr2:21040767	G (T)	0.83	0.10 [0.08, 0.12]	1.59×10−21	APOB	No
	chr2:21072960	A (G)	0.31	0.07 [0.06, 0.09]	7.75×10−20	TDRD15	Yes (6.23×10−13)
	chr5:75360714	C (T)	0.38	0.06 [0.04, 0.07]	1.18×10−12	HMGCR	No
	chr6:160589086	G (A)	0.05	0.12 [0.09, 0.16]	2.94×10−12	LPA	No
	chr19:11085680	A (AC)	0.11	−0.13 [−0.15, −0.10]	3.73×10−27	LDLR	No
	chr19:44908684	C (T)	0.14	0.18 [0.16, 0.20]	9.51×10−62	APOE	Yes (6.62×10−39)
	chr19:44908822	T (C)	0.08	−0.40 [−0.42, −0.37]	2.03×10−181	APOE	No
	chr19:44935906	G (C)	0.23	−0.03 [−0.05, −0.02]	1.46×10−4	APOC1P1, APOC4	Yes (1.02×10−9)

Common variants: variants with a minor allele frequency (MAF) > 1%. Effect size: Odds Ratios (OR) for binary traits, beta for quantitative traits. CI: confidence interval. Mapped gene: variants were mapped to either the closest or trait-associated genes located within 500kb around the variant. Additional independent SNVs: SNVs that were independently significantly associated with the trait, identified in conditional analyses.