Table 2.

Genetic markers that showed significant genome-wide association with plasma protein N-glycans in the discovery cohort and the follow-up study comprising children with recent-onset type 1 diabetes and unaffected children from the family-based DanDiabKids registry

Glycan/Gene					Discovery cohort (N=1105)					Follow-up study (N=455)		General European population [18] (N=4802)
Glycan	Glycan structure	Locus	Candidate gene	SNP	N	OA, MA (MAF)	R2	p	β (SE)	p	β (SE)	p
GP29	A3G3S3	2: 135,014,116	MGAT5	rs2460382	1044	A, G (0.21)	0.04	3.14 × 10−11	0.01 (0.002)	2.27 × 10−2	0.01 (0.003)	a5.95 × 10−17
GP19	Man9	19: 6,713,262	C3	rs1047286	1033	G, A (0.20)	0.04	2.43 × 10−11	−0.03 (0.005)	b8.66 × 10−4	−0.04 (0.012)	Association not reportedc
GP19	Man9	19: 6,710,782	C3	rs2230203	1045	C, A (0.18)	0.04	4.15 × 10−11	−0.03 (0.005)	8.66 × 10−4	−0.04 (0.012)	Association not reportedc
GP6	FA2[6]BG1	22: 39,843,409	MGAT3	rs5757678	1045	A, G (0.27)	0.04	1.48 × 10−11	0.08 (0.012)	8.63 × 10−7	0.11 (0.021)	d7.98 × 10−10
GP6	FA2[6]BG1	22: 39,844,793	MGAT3	rs5757680	1034	G, A (0.26)	0.04	2.21 × 10−11	0.08 (0.012)	1.35 × 10−6	0.10 (0.021)	d7.98 × 10−10

Significant associations from the largest GWAS on plasma protein N-glycans comprising 4802 participants from the general European population [18] were searched for the same glycan–SNP association, or SNPs in LD (R²>0.5) with the SNP identified in this study, and the same direction of effect estimates (either increasing or decreasing with the same allele), and their p value is included in this table. Associations identified in this study and not previously reported in the general European population are presented in this table with ‘Association not reported’. Locus information is presented as ‘chromosome number: locus start’. The results are reported for GRCh Build 37, and alleles are aligned to the TOP strand. The β coefficient is reported for the minor allele and expressed as the relative glycan abundance (%)

^aResults are reported for rs1257220 (R²=0.98 with rs2460382)

^bResults are reported for rs2230203 (R²=0.85 with rs1047286)

^cIn the general European population, GP19 was exclusively associated with the chromosome 6 SNP rs3115663 near the PRRC2A gene located in the HLA class III region

^dResults are reported for rs909674 (R²=0.91 with rs5757678, R²=0.91 with rs5757680)

N, sample size; OA, other allele; MA, minor allele; MAF, minor allele frequency; R², percentage of explained glycan variance; F, core fucose α1,6-linked to the inner GlcNAc; Manx, number (x) of mannose residues on core GlcNAcs; Ax, number of antenna (GlcNAc) on the trimannosyl core; A2, biantennary N-glycan; A3, triantennary N-glycan; A2[6], galactose linked on the antenna of the α1,6 mannose; B, bisecting GlcNAc β1,4-linked to β1,4-mannose; Gx, number (x) of linked galactose residues on antenna; Sx, number (x) of sialic acid residues linked to galactose