Table 3. Most associated HLA variants of different diseases and correlation with expression levels of HLA Class II genes.

Disease	SNP GWAS [ref.]	Gene	Transcripts	r Value	p Value	RiskAllele	Risk AlleleFrequency
UC	rs9268853 [35]	DQA2	ENST00000374940	0.728	4.33E-11	T	0.66
		DQB1	ENST00000399074	−0.637	4.41E-08
	rs2395185 [36]	DQA2	ENST00000374940	0.728	4.33E-11	G	0.61
		DQB1	ENST00000399084	−0.637	4.41E-08
IBD	rs477515 [34]	DQB1	ENST00000399082	0.591	6.50E-07	G	0.69
		DQA1	ENST00000374940	−0.708	2.41E-10
T1D	rs9272346 [33]	DQB1	ENST00000399082	0.629	7.30E-08	G	0.61
		DQB1	ENST00000399074	0.809	6.00E-15
		DQB1	ENST00000399084	0.85	<E-15
		DQA1	ENST00000395364	0.803	1.20E-14
		DQA1	ENST00000343139	0.769	7.27E-13
SLE	rs9271100 [37]	DRB1	ENST00000360004	0.731	3.22E-11	T	0.14
		DQB1	ENST00000399084	0.621	1.17E-07
MS	rs3135388 [29]	DQB1	ENST00000399065	−0.647	2.34E-08	A	0.22
		DRB5	ENST00000374975	−0.728	4.40E-11
		DRB1	ENST00000360004	−0.702	3.98E-10
IgA deficiency	rs9271366 [40]	DQB1	ENST00000399065	0.647	2.34E-08	A	0.85
		DRB5	ENST00000374975	0.728	4.40E-11
		DRB1	ENST00000360004	0.702	3.98E-10
Asthma	rs9272346 [39]	DQB1	ENST00000399082	0.629	7.30E-08	G	0.61
		DQB1	ENST00000399074	0.809	6.00E-15
		DQB1	ENST00000399084	0.85	<E-15
		DQA1	ENST00000395364	0.803	1.20E-14
		DQA1	ENST00000343139	0.769	7.27E-13

Diseases: Type 1 diabetes (T1D), inflammatory bowel disease (IBD), ulcerative colitis (UC), systemic lupus erythematosus (SLE), asthma, IgA deficiency and multiple sclerosis (MS). SNP GWAS indicate the most associated variant detected by GWAS, references in brackets. Transcripts are with Ensembl nomenclature. r values (correlation coefficient) and p-values from Spearman correlation test.