Table 3.

Single locus and stepwise results for top ten independent HLA associations

MarkerA	Position	Upstream Gene	Downstream Gene	Within Gene	MAFB	P-value	OR (95%CIC)	Maj/MinD	Stepwise P-value	Stepwise OR (95%CIC)
rs116727542	32421227	8.4kb from HLA-DRA	64kb from HLA-DRB5	-	0.1700	6.15×10−24	0.53 (0.47-0.60)	G/A	1.96×10−18	1.74 (1.54-1.97)
rs9273371	32626565	14kb from HLA-DQA1	675bp from HLA-DQB1	-	0.1000	1.18×10−9	1.61 (1.38-1.87)	C/T	8.43×10−5	1.38 (1.18-1.63)
rs114653103	32668846	34kb from HLA-DQB1	40kb from HLA-DQA2	-	0.1200	7.31×10−15	0.57 (0.49-0.66)	G/T	1.81×10−13	0.50 (0.41-0.60)
rs115253455	33100021	43kb from HLA-DPB1	30kb from COL11A2	-	0.1300	4.68×10−7	0.70 (0.61-0.80)	T/A	4.51×10−7	0.66 (0.56-0.77)
chr6:31996524	31996524	-	-	C4B	0.1700	4.95×10−8	0.71 (0.63-0.80)	C/A	4.87×10−10	0.64 (0.55-0.73)
rs113833333	32594898	37kb from HLA-DRB1	10kb from HLA-DQA1	-	0.4100	2.30×10−5	0.82 (0.74-0.90)	C/T	3.09×10−8	0.74 (0.67-0.82)
rs116427960	31319226	79kb from HLA-C	2.4kb from HLA-B	-	0.0081	8.96×10−7	4.57 (2.49-8.38)	C/T	1.69×10−5	3.17 (1.87-5.35)
rs114904515	29362756	20kb from OR12D3	1.7kb from OR12D2	-	0.1000	1.55×10−6	0.69 (0.60-0.80)	C/T	5.70×10−6	0.67 (0.56-0.79)
rs118044183	30954150	-	-	MUC21	0.1200	3.61×10−6	1.50 (1.27-1.79)	C/T	1.39×10−4	1.39 (1.17-1.64)
rs2736191	31560910	~150bp from NCR3	22kb from AIF1	-	0.3800	7.53×10−7	0.79 (0.71-0.86)	C/G	1.01×10−4	0.81 (0.73-0.90)

^AAll variants within this table have been imputed.

^BCI = Confidence interval

^CMAF = Minor allele frequency

^DMaj/Min = Major allele/Minor allele

Note: Tables are in the order they were identified in the stepwise model. The stepwise results presented in this table are for adjusting for all other variants in the table. For complete results in the HLA region, please refer to Supplementary Table 4.