Table 2

The association results of 12 SNPs in the HLA region implicated in LASSO model

SNP^*	A1/A2	BP	LASSO regression coefficient^†	Schizophrenia				Psoriasis				Combined

				Single-variant association^‡				Single-variant association^‡				Single-variant association^‡				Forward stepwise		Backward stepwise

				Fca	Fcn	OR (95% CI)	p value^§	Fca	Fcn	OR (95% CI)	p value^§	Fca	Fcn	OR (95% CI)	p value^§	OR	p value^§	OR	p value^§
rs113778742	T/A	31229552	0.44	0.22	0.19	1.36 (1.05–1.77)	0.021	0.52	0.19	3.17 (2.49–4.03)	8.64E⁻²¹	0.4	0.19	1.90 (1.60–2.25)	1.13E⁻¹³	2.00	5.36E⁻¹⁴	2.14	2.00E⁻¹⁶
rs115328826	A/G	31247270	0.68	0.27	0.24	1.25 (1.01–1.55)	0.043	0.55	0.21	3.35 (2.68–4.18)	1.03E⁻²⁶	0.44	0.22	1.83 (1.58–2.11)	5.77E⁻¹⁶	2.37	2.00E⁻¹⁶	2.43	2.00E⁻¹⁶
rs115798226	T/G	31412271	0.07	0.02	0.01	3.29 (1.40–7.76)	0.006	0.11	0.01	9.09 (5.74–14.40)	5.59E⁻²¹	0.07	0.01	5.64 (3.82–8.32)	2.55E⁻¹⁸	—	—	—	—
rs116129306	C/T	31367874	0.71	0.03	0.01	3.16 (1.48–6.73)	0.003	0.11	0.01	7.64 (4.93–11.83)	9.00E⁻²⁰	0.08	0.01	4.99 (3.47–7.18)	4.16E⁻¹⁸	—	—	3.06	1.37E⁻⁰⁶
rs116743258	A/G	31242174	−0.16	0.41	0.36	1.25 (1.04–1.51)	0.018	0.63	0.34	2.07 (1.72–2.50)	1.03E⁻¹⁴	0.54	0.35	1.47 (1.30–1.66)	1.06E⁻⁰⁹	0.76	3.40E⁻⁰³	0.74	0.002
rs139966987	C/A	31453711	0.06	0.03	0.01	2.14 (1.12–4.09)	0.022	0.14	0.03	7.87 (5.20–11.91)	1.73E⁻²²	0.1	0.02	3.55 (2.57–4.92)	2.12E⁻¹⁴	—	—	—	—
rs141611788	A/G	32515516	−0.29	0.04	0.05	0.46 (0.28–0.85)	0.002	0.044	0.042	0.40 (0.26–0.62)	5.11E⁻⁰⁵	0.041	0.043	0.35 (0.25–0.49)	1.43E⁻⁰⁹	0.67	6.21E⁻⁰³	0.68	0.004
rs141906974	A/T	31098344	0.04	0.4	0.37	1.24 (1.02–1.50)	0.032	0.62	0.37	2.05 (1.67–2.51)	4.07E⁻¹²	0.53	0.37	1.47 (1.28–1.67)	1.43E⁻⁰⁸	—	—	—	—
rs146554817	A/G	30719578	0.11	0.05	0.03	1.67 (1.01–2.77)	0.044	0.13	0.02	6.99 (4.52–10.81)	2.40E⁻¹⁸	0.1	0.03	3.30 (2.38–4.57)	8.10E⁻¹³	—	—	—	—
rs41293883	T/C	31474820	−0.14	0.05	0.03	1.61 (1.05–2.47)	0.029	0.11	0.04	3.22 (2.32–4.46)	2.31E⁻¹²	0.09	0.03	2.17 (1.70–2.78)	8.50E⁻¹⁰	0.68	3.48E⁻⁰²	0.75	0.09
rs41543314	G/A	31322690	0.13	0.02	0.01	4.39 (1.63–11.80)	0.003	0.1	0.01	8.88 (5.52–14.28)	1.93E⁻¹⁹	0.07	0.01	6.00 (3.98–9.04)	1.24E⁻¹⁷	—	—	—	—
rs78439157	T/C	29837158	0.38	0.05	0.03	1.61 (1.01–2.56)	0.045	0.12	0.02	4.74 (3.12–7.21)	3.06E⁻¹³	0.09	0.03	2.66 (1.94–3.64)	9.90E⁻¹⁰	—	—	1.80	8.39E⁻⁰⁵

A1 = effective allele; A2 = alternative allele; BP = physical position; CI = confidence interval; Fca = the effective allele frequency in cases; Fcn = the effective allele frequency in controls; HLA = human leukocyte antigen; OR = odds ratio; SNP = single nucleotide polymorphism.
↵* We built the multivariate regression model using these 12 SNPs. The missing genotypes were imputed as the average values for each SNP.
↵† In the final best LASSO model, the log(λ(min)) = −6.598, log(λ(1se)) = −4.738.
↵‡ Single-variant associate was implemented in “−logistic” function in Plink version 1.07 using the respective first 20 PCs as covariates in each data set.
↵§ Threshold for forward/backward stepwise regression: 0.1.