Table 1. Loci associated with IgG glycosylation.

Each locus is represented by the SNP with the strongest association in the region. Locus, coded by “chromosome: locus start–locus end” (GRCh37); No. of SNPs, maximum number of SNPs independently contributing to trait variation; SNP, variant with the strongest association in the locus; position, position of the SNP on the NCBI (National Center for Biotechnology Information) build 37; EA, allele for which effect estimate is reported; OA, other allele; EAF, frequency of the effect allele; R², sample size weighted average of imputation quality for the SNP with the strongest association in the locus; glycan, glycan associated with the reported SNP; No. of glycans, number of other glycans suggestively or significantly associated with variants in given locus; β, effect estimate for the SNP and glycan with the strongest association in the locus in the discovery; P, P value for the discovery effect estimate; β UPLC repl, effect estimate for the SNP and glycan with the strongest association in the locus in replication; P UPLC repl, P value for the effect estimate in replication. The loci replicated in UPLC replication at P ≤ 0.0019 are in bold. The loci from Lauc et al. (6), Shen et al. (7), and Wahl et al. (8) are in italics.

Locus	Candidate genes	No. of SNPs	SNP	EA	OA	EAF	R2	Glycan	No. of glycans	β	P	β UPLC repl	P UPLC repl
Genome-wide significant
1:25226001-25345011	RUNX3	1	rs10903118	T	C	0.484	0.886	IGP74	13	−0.121	5.14 × 10−13	−0.097	7.93 × 10−4
3:186712711-186738421	ST6GAL1	2	rs7621161	A	C	0.284	0.937	IGP29	27	−0.653	4.65 × 10−276	−0.682	1.55 × 10−111
5:95211647-95347786	ELL2	1	rs7700895	A	T	0.215	0.997	IGP35	4	0.155	1.20 × 10−14	0.097	4.61 × 10−3
5:131026218-131833599	IRF1-SLC22A4	1	rs11748193	A	T	0.399	0.987	IGP2	2	0.110	4.31 × 10−10	0.116	1.31 × 10−4
6:29299390-33883424	HLA region	2	rs3099844	A	C	0.136	0.995	IGP15	13	−0.227	1.12 × 10−13	−0.083	2.28 × 10−1
6:139617590-139636003	TXLNB	1	rs9385856	T	C	0.574	0.977	IGP70	24	0.151	5.05 × 10−19	0.111	1.54 × 10−4
6:143150223-143203591	HIVEP2	1	rs7758383	A	G	0.521	0.952	IGP13	3	0.125	9.61 × 10−14	0.225	1.12 × 10−14
7:6520676-6537913	DAGLB	1	rs6964421	T	C	0.328	0.957	IGP14	7	0.117	5.31 × 10−11	0.000	9.95 × 10−1
7:50325717-50361683	IKZF1	1	rs6421315	C	G	0.383	0.938	IGP62	37	0.192	4.70 × 10−27	0.133	8.97 × 10−6
7:150906453-150969535	ABCF2	1	rs7812088	A	G	0.119	0.981	IGP2	16	−0.250	2.06 × 10−22	−0.269	3.83 × 10−9
8:103538266-103550211	ODF1	1	rs10096810	A	G	0.627	1.000	IGP77	4	−0.110	9.52 × 10−11	−0.074	1.37 × 10−2
9:33041761-33186080	B4GALT1	3	rs10813951	A	G	0.732	0.967	IGP17	30	0.230	8.84 × 10−34	0.156	4.57 × 10−6
9:33205136-33375592	SPINK4	1	rs12341905	A	G	0.896	0.964	IGP53	4	0.168	1.46 × 10−09	0.199	4.99 × 10−5
11:114323627-114450529	NXPE1-NXPE1	1	rs481080	A	G	0.475	0.999	IGP29	3	−0.140	1.05 × 10−16	−0.099	5.28 × 10−4
14:65472891-66284991	FUT8	6	rs11847263	T	G	0.647	0.985	IGP42	16	−0.283	1.13 × 10−58	−0.252	5.93 × 10−17
14:105966019-106002352	TMEM121	1	rs4074453	T	C	0.758	0.996	IGP48	6	−0.218	3.82 × 10−29	−0.299	1.25 × 10−13
16:23397113-23613191	GGA2-COG7	1	rs250555	T	C	0.860	0.961	IGP26	4	−0.155	6.76 × 10−10	−0.044	2.24 × 10−1
17:37903731-38112190	ORMDL3-GSDMB-IKZF3-ZPBP2	1	rs7216389	T	C	0.487	0.999	IGP59	11	0.137	1.17 × 10−15	0.094	1.53 × 10−3
17:43463492-44896083	CRHR1-SPPL2C-MAPT-ARHGAP27	1	rs199456	T	C	0.196	0.984	IGP14	7	0.162	6.76 × 10−14	0.136	9.18 × 10−4
17:45518583-45874272	TBX21	1	rs11651000	A	G	0.150	0.981	IGP59	8	−0.165	2.66 × 10−12	−0.144	4.05 × 10−4
17:79165171-79257880	SLC38A10-CEP131-TEPSIN	1	rs2725391	T	C	0.460	0.974	IGP24	12	0.133	9.91 × 10−16	0.177	1.15 × 10−9
19:5822316-5845974	FUT6	1	rs874232	T	C	0.565	0.971	IGP12	5	0.119	7.85 × 10−13	0.070	2.08 × 10−2
19:19260586-19296217	RFXANK	1	rs7257072	T	C	0.515	0.997	IGP9	12	−0.122	1.59 × 10−13	−0.068	1.97 × 10−2
20:17818141-17833534	MGME1	1	rs2745851	A	G	0.376	0.982	IGP38	10	−0.125	4.61 × 10−13	−0.094	8.82 × 10−3
21:36546756-36665202	RUNX1	1	rs7281587	A	G	0.247	0.998	IGP45	19	−0.144	1.13 × 10−13	−0.171	7.51 × 10−7
22:24093789-24182500	SMARCB1-DELR3-CHCHD10-VPREB3	1	rs17630758	A	G	0.152	0.991	IGP66	25	−0.308	1.20 × 10−41	−0.386	4.94 × 10−23
22:39774448-39860868	MGAT3	1	rs5750830	A	C	0.740	0.965	IGP40	28	−0.344	7.74 × 10−69	−0.363	5.26 × 10−29
Suggestive
1:246854862-246963137	LINC01341	1	rs3795464	A	G	0.383	0.984	IGP73	2	−0.099	1.01 × 10−08
2:100636757-100805273	AC092667.1	1	rs2309748	A	T	0.647	0.993	IGP34	2	−0.105	3.38 × 10−09
17:16820099-16875636	TBC1D27-TNFRSF13B	1	rs4561508	T	C	0.105	0.975	IGP9	2	0.163	5.70 × 10−09
17:56398006-56410041	MIR142	1	rs2526378	A	G	0.549	0.935	IGP31	1	−0.100	4.44 × 10−09
19:1614910-1658699	TCF3	1	rs4807942	T	C	0.878	0.661	IGP68	1	0.154	1.54 × 10−08
20:52170177-52212273	ZNF217	1	rs1555926	T	C	0.789	0.992	IGP11	3	−0.118	6.96 × 10−09