Table 1.

Lead genome-wide significant variants (P < 5.0 × 10⁻⁸) for continuous antibody response phenotypes for antigens with at least 20% seroprevalence

Antigen		N	Chr	Position	Variant	Alleles		EAF	Beta2	(SE)	P	Function	Nearest gene
						Effect	Other
CMV	pp52	5000	6	32301427	rs115378818	C	T	0.978	0.633	(0.095)	2.9 × 10−11	intronic	TSBP1
EBV	EA-D	6806	6	32665840	rs34825357	T	TC	0.409	− 0.114	(0.017)	2.0 × 10−11	intergenic	MTCO3P1
EBV	EBNA	7003	3	151114852	rs67886110*	G	T	0.596	0.103	(0.017)	1.3 × 10−9	intronic	MED12L
			6	32451762	rs9269233	A	C	0.249	0.315	(0.019)	3.5 × 10−61	intergenic	HLA-DRB9
EBV	VCA p18	7492	6	31486158	6:31486158	GT	G	0.245	0.197	(0.018)	7.1 × 10−27	intergenic	PPIAP9
EBV	ZEBRA	7197	6	32637772	rs9274728	A	G	0.718	− 0.315	(0.018)	4.7 × 10−67	intergenic	HLA-DQB1
HHV6	IE1A	6077	7	139985625	rs2429218	T	C	0.615	0.106	(0.019)	1.4 × 10−8	downstream	RP5-1136G2.1
HHV7	U14	7481	6	32602665	rs139299944	C	CT	0.655	0.114	(0.017)	1.5 × 10−11	intronic	HLA-DQA1
			11	118767564	rs75438046	G	A	0.970	0.280	(0.049)	1.3 × 10−8	3′-UTR	CXCR5 / BCL9L
			17	45794706	rs1808192	A	G	0.331	− 0.099	(0.017)	9.8 × 10−9	intergenic	TBKBP1
HSV1	1gG	5468	6	32627852	rs1130420	G	A	0.583	− 0.122	(0.019)	2.5 × 10−10	3′-UTR	HLA-DQB1
			10	91189187	rs11203123*	A	C	0.988	0.512	(0.093)	3.9 × 10−8	intergenic	SLC16A12
VZV	gE/Ig1	7289	6	32623193	rs9273325	G	A	0.831	− 0.232	(0.021)	8.2 × 10−28	intergenic	HLA-DQB1
BKV	VP1	7523	19	49206462	rs681343	C	T	0.491	− 0.125	(0.016)	4.7 × 10−15	synonymous	FUT2
JCV	VP1	4471	6	32589842	rs9271525	G	A	0.163	− 0.318	(0.031)	3.9 × 10−24	intergenic	HLA-DQA1
MCV	VP1	5219	3	18238783	rs776170649	CT	C	0.790	− 0.134	(0.024)	1.7 × 10−8	intergenic	LOC339862
			5	138865423	rs7444313	G	A	0.263	0.169	(0.021)	2.4 × 10−15	intergenic	TMEM173
			6	32429277	rs9268847	A	G	0.750	− 0.195	(0.022)	2.4 × 10−19	intronic	HLA-DRB9

¹VZV antigens gE and gI were co-loaded onto the same Luminex bead set

²Regression coefficients were estimated per 1 standard deviation increase in normalized MFI value z-scores with adjustment for age at enrollment, sex, body mass index, socioeconomic status (Townsend deprivation index), the presence of any autoimmune conditions, genotyping array, serology assay date, quality control flag, and the top 10 genetic ancestry principal components

*Multi-allelic variants: rs67886110 (G/T and G/C) and rs11203123 (A/C and A/AC)