Table 2. Genome-wide Significant Results (P < 5x10⁻⁸) for IgAD GWAS.

Closest Gene(s)	Varianta	Position (hg19)	Minor Allele	% Frequency in Swedish Sample		P	FDR q values	OR	Type	Immune Diseases Sharing this Locusb
				Cases	Controls
HLA-DQA1 c	rs116041786	6:32602396	C	14.4	38.7	3.3e–92	1.0e–87	0.38	Intergenic	Celiac Graves’ IBD Sjögren’sd
IFIH1	rs1990760	2:163124051	G	29.3	37.3	3.7e–15	2.7e–12	0.70	Missense	T1D SLE Psoriasis Vitiligoe
PVT1	rs11299600	8:129204573	1 bp deletion	18.9	25.3	4.3e–11	2.4e–8	0.73	Intergenic	RAf
ATG13 – AMBRA1	rs4565870	11:46349869	C	28.9	23.6	6.7e–10	3.5e–7	1.38	Intergenic
AHI1	rs7773987	6:135707486	C	51.3	44.6	8.4e–10	4.3e–7	1.30	Intron	MS
CLEC16A	rs34069391	16:11161214	1 bp insertion	14.3	19.6	1.4e–09	6.9e–7	0.71	Intron	T1D MS PBCg

^aPeak variants were imputed, except for IFIH1 and CLEC16A, which were genotyped in all but the Czech cohort. Three loci had suggestive association in our previous GWAS: PVT1 (P = 4x10⁻⁶), DGKZ (P = 2x10⁻⁶) and CLEC16A (P = 2x10⁻⁷).

^bAutoimmune diseases reporting a genome-wide significant variant (P < 5x10⁻⁸) in Immunobase and the GWAS Catalog (see URLs) with at least a modest effect (OR ≥ 1.1) in the same direction as IgAD results and on the same haplotype as a peak IgAD variant (r² > 0.45).¹² IBD, inflammatory bowel disease; MS, multiple sclerosis; SLE, systemic lupus erythematosus; PBC, primary biliary cirrhosis; RA, rheumatoid arthritis; T1D, type 1 diabetes.

^cGenetic association of IgAD with HLA class II is well-established, particularly with HLA-DQB1*02:01 and HLA-DRB1*01:02 and the highly protective HLA-DRB1*15:01 allele.⁶ Few of the cases (2.1%) were carrying two copies of rs116041786*C (versus 15.7% of controls).

^dMS, RA, SLE, T1D, vitiligo, allergy and asthma also have some associations reported at this locus.

^eIBD is also associated with this locus.

^fMS, celiac disease, eczema and allergy also have some associations reported at this locus.

^gCeliac disease and asthma also have some associations reported at this locus.