Boyang Fu; Prateek Anand; Aakarsh Anand; Joel Mefford; Sriram Sankararaman

Table 1.

Significant epistatic trait-gene pairs

Trait	Chr	Gene	Start (Mb)	End (Mb)	−log₁₀P-value	−log₁₀P-value (40 PC)	−log₁₀P-value (Imputed)
Alanine aminotransferase	22	PNPLA3	44.320	44.342	≥13	≥13	≥13
Alanine aminotransferase	22	SAMM50	44.351	44.392	8.02	7.97	6.61
Apolipoprotein B	19	BCAM	45.312	45.324	9.03	9.02	2.84
Apolipoprotein B	19	APOE	45.410	45.413	≥13	≥13	≥13
Aspartate aminotransferase	22	PNPLA3	44.320	44.342	11.92	11.91	≥13
Creatinine	1	DNAJC16	15.856	15.895	7.05	7.07	6.42
Direct bilirubin	2	SAG	234.218	234.256	7.56	7.55	3.43
	2	DGKD	234.263	234.378	≥13	≥13	7.02
	2	USP40	234.386	234.474	≥13	≥13	4.51
	2	UGT1A8	234.526	234.681	≥13	≥13	≥13
Eosinophil count	11	PRG3	57.144	57.148	≥13	≥13	5.17
HDL cholesterol	16	CETP	56.996	57.018	9.81	9.87	5.13
Hemoglobin A1c	10	HK1	71.048	71.161	7.71	7.68	1.55
LDL direct	19	APOE	45.410	45.413	8.91	8.88	9.37
Lipoprotein(a)	6	IGF2R	160.390	160.526	≥13	≥13	8.31
	6	SLC22A2	160.638	160.680	8.54	8.53	7.77
	6	SLC22A3	160.769	160.872	≥13	≥13	4.13
	6	LPA	160.953	161.085	≥13	≥13	≥13
	6	PLG	161.123	161.174	8.54	8.54	12.11
	6	AGPAT4	161.558	161.653	≥13	≥13	3.81
Mean corpuscular hemoglobin	22	TMPRSS6	37.462	37.500	8.72	8.75	2.69
Mean sphered cell volume	1	OR10Z1	158.576	158.577	7.39	7.4	7.71
Mean sphered cell volume	1	SPTA1	158.581	158.656	9.31	9.32	7.21
Monocyte count	22	ADA2	17.662	17.691	8.8	8.8	2.97
Platelet distribution width	20	TUBB1	57.595	57.600	≥13	≥13	≥13
Platelet distribution width	20	EDN3	57.876	57.900	9.45	9.5	0.01
SHBG	17	TNK1	7.286	7.292	7.37	7.35	2.42
Urate	1	DNAJC16	15.856	15.895	8.26	8.27	11.42
	4	SLC2A9	9.828	10.028	≥13	≥13	≥13
	4	WDR1	10.077	10.118	≥13	≥13	≥13
	4	MEPE	88.756	88.768	7.36	7.28	0.57
Urea	1	MUC1	155.159	155.163	8.33	8.34	7.14

We report trait-gene pairs with statistically significant epistatic effects ( $\text{[math]}$ accounting for the number of genes and traits tested). The −log₁₀ P-values were reported in entry −log₁₀ P-value, with a precision level bounded by 13. We report the P-values at these trait-gene pairs when the top 40 PCs were regressed out (−log₁₀ P-value [40 PC]) and when analyzing imputed genotypes (−log₁₀ P-value [Imputed]).

A scalable adaptive quadratic kernel method for interpretable epistasis analysis in complex traits

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