Table 2.

Psoriasis associations from stepwise meta-analysis of the extended MHC region for two studies of South Asian ancestry

Stepa	Variantb	chr6 positionc	Alleles		Risk allele frequency		Association at entry into model		Association in final full model		Vg
			Riskd	Nonrisk	Cases	Controls	OR (95% CI)	p value	OR (95% CI)	p value
1	HLA-C∗06	31238192	C∗06	other	0.3361	0.1012	5.80 (5.02–6.71)	6.7 × 10−124	4.68 (3.99–5.50)	1.3 × 10−78	0.04822
2	rs2428489	31352972	C, T	A	NA	NA	NA	8.2 × 10−15	NA	9.6 × 10−16	0.01001
			C	other	0.4094	0.2654	1.41 (1.26–1.58)	2.1 × 10−9	1.64 (1.45–1.85)	1.8 × 10−15	NA
			T	other	0.0840	0.1044	0.71 (0.87–1.29)	1.4 × 10−4	1.06 (0.87–1.29)	0.57	NA
			other	A	0.4934	0.3697	ref	ref	ref	ref	NA
3	rs2442752	31351764	T	C	0.6508	0.5154	1.39 (1.23–1.56)	8.8 × 10−8	1.39 (1.23–1.57)	8.8 × 10−8	0.00576
4	rs139451799	32454479	–	other	0.2295	0.2532	1.46 (1.26–1.69)	3.3 × 10−7	1.43 (1.23–1.65)	1.6 × 10−6	0.00521
5	rs9260313	29916885	T	C	0.6593	0.5341	1.29 (1.16–1.44)	3.4 × 10−6	1.29 (1.16–1.44)	3.4 × 10−6	0.00345

Abbreviations: chr6, chromosome 6; CI, confidence interval; NA, not applicable; OR, odds ratio; ref, reference; V_g, variance in liability explained by the genetic variant.⁷²

^aRound of stepwise regression analysis.

^bVariant notes: variant ID is build 151 dbSNP rsID when applicable; HLA-C∗06 is one biallelic split from a decomposed set of 14 classical 1-field HLA-C alleles; the stepwise-selected variant for triallelic indel rs139451799 is one of its biallelic splits with − versus A+G alleles.

^cBase pair position in hg19 human reference; for classical HLA proteins the position of the center of the coding unit is given; for indels (all of which are insertions into the reference sequence), the position immediately before the insertion point is given.

^dRisk allele is based on final full regression model.