Table 1 Results of the IgA GWAS. For each locus, the table reports the cytogenic location, the candidate gene along with its function, the total number of associated glycan traits (either measured glycopeptides or derived trait), as well as the fraction, expressed as a percentage, of replicated glycan associations in QMDiab (% Replicated), the strongest associated SNP, along with the effect allele (EA, the minor allele), the other allele (OA), and the effect allele frequency (EAF) in TwinsUK. For each lead SNP within the locus, we report the glycan trait showing the strongest association, along with its GWAS summary statistics, i.e., the association effect size (β), standard error (SE) and p-value (P) in both TwinsUK and QMDiab. We further report whether the locus is associated with either N- or O-glycans in TwinsUK (N/O glyc), as well as information on previous GWAS (identified as [PMID]) reporting associations within the locus for the N-glycome (Glycosylation measurements) or relevant traits or disease (Phenotypic trait/Disease), as extracted from the GWAS Catalog

3:186705790–186782999

ST6GAL1

Sialyltransferase

20

LAGC_A2S

rs6764279

A

C

28.4

-0.489

0.032

2.90 × 10⁻⁴⁹

N

IgG [29535710, 23382691, 28878392, 35332118, 32128391]

Total plasma [31163085]

IgA nephropathy [26028593]

 −0.459

0.073

8.80 × 10⁻¹⁰

42

5:95221337–95310985

ELL2

Transcription regulator

4

TPL_H5N5F1S2

rs11744881

T

A

25.3

-0.241

0.035

8.10 × 10⁻¹²

N

IgG [28878392]

Multiple myeloma [26007630, 27363682]

 −0.314

0.086

3.10 × 10⁻⁴

25

7:7194680–7290732

C1GALT1

Galactosyltransferase

10

HYT_H3N5F0S2

rs10246303

T

A

40.4

-0.297

0.032

1.30 × 10⁻²⁰

O

Serum galactose-deficient IgA1 levels in IgA nephropathy [33593824];

Lung function (FEV1/FVC) [30804560, 28166213]

-0.388

0.071

1.05 × 10⁻⁷

75

7:150906453–150954562

ABCF2

Transporter

3

HYT_H3N5F0S1

rs113810201

G

A

11.5

-0.376

0.050

1.00 × 10⁻¹³

N/O

IgG [23382691, 32128391, 35332118]

Multiple myeloma [27363682, 33875642]

 −0.072

0.148

6.29 × 10⁻¹

0

8:134509215–134535985

ST3GAL1

Sialyltransferase

23

HYT_H4N5F0S1

rs6995270

C

T

49.9

-0.396

0.032

3.20 × 10⁻³³

O

-0.507

0.068

1.20 × 10⁻¹²

89

9:33119241–33180813

B4GALT1

Galactosyltransferase

6

TPL_H5N4F1S2

rs3780480

T

G

25.3

-0.315

0.035

5.50 × 10⁻¹⁹

N

IgG [29535710, 23382691, 28878392, 32128391]

Total plasma [31163085]

 −0.172

0.078

2.95 × 10⁻²

0

9:101364062–101570336

GALNT12

N-acetylgalactosaminyltransferase

5

HYT_H4N6F0S2

rs1137654

T

A

9.3

-0.551

0.058

4.30 × 10⁻²¹

O

 −0.451

0.323

1.64 × 10⁻¹

0

14:105966605–106019014

TMEM121

Transmembrane protein

2

SES_H4N5F1S1

rs61983272

C

G

33.1

0.298

0.042

2. × 10⁻¹²

N

IgG [35332118, 28878392, 32128391]

NA

17:79217478–79268562

SLC38A10-CEP131-TEPSIN-NDUFAF8

5

HYT_H4N6F0S4

rs2659005

T

C

43.4

0.206

0.031

4.00 × 10⁻¹¹

O

IgG [32128391, 23382691]

 0.076

0.075

3.10 × 10⁻¹

0

22:24135043–24179922

SMARCB1

Chromatin remodelling

4

TPL_H5N4F1S1

rs9624334

C

G

13.5

0.301

0.045

3.80 × 10⁻¹¹

N

IgG [29535710, 23382691, 28878392, 35332118, 32128391]

Total plasma [31163085]

0.210

0.120

8.10 × 10⁻²

0

22:39775156–39874314

MGAT3

N-acetylglucosaminyltransferase

5

LAGC_A2B

rs5757682

T

G

25.0

0.293

0.035

6.60 × 10⁻¹⁷

N

IgG [29535710, 23382691, 32128391, 28878392, 35332118]

Factor VIII or von Willebrand factor [35285134, 30586737]

0.294

0.079

2.29 × 10⁻⁴

100