Table 3.

p values of replicated SNPs conditional on nearby T1D-associated HLA genes in addition to DRB1 and DQB1

Block	SNP ID	SNP Pos	p
CA trend test conditional ona:			DR - DQ - A
	rs1619379	29893214	0.4107
	rs3873283	30040979	0.5397
	rs379221	30058119	0.1085
	rs916570	30174010	0.4594
	rs1116221	30179309	0.4687

Block	SNP ID	SNP Pos	p
CA trend test conditional ona:			DR - DQ - B	DR - DQ - C
1	rs3094663 b	31215066	3.18 × 10−3b	2.57 × 10−3b
	rs3130503 c	31245144	0.0199c	0.0120
	rs3094609 c	31273545	0.0246c	3.13 × 10−3b
	rs3134782 c	31305612	0.0259c	2.52 × 10−3b
	rs3132499 c	31315899	0.0388c	5.88 × 10−3b
2	rs3130542 c	31340090	7.68 × 10−3b	0.0135c
	rs2394953 c	31341332	0.0107c	0.0217c
	rs2844621	31349516	7.05 × 10−3b	0.0515c
3	rs7381988 b	31354682	9.84 × 10−3b	2.36 × 10−3b
	rs7382297 c	31355046	0.0480c	7.69 × 10−3b
	rs2523619 b	31426123	5.74 × 10−4	3.21 × 10−5b

Block	SNP ID	SNP Pos	p
MH test conditional ond			DR - DQ - DPB1	DR - DQ - DPA1
4	rs2281390	33167647	0.0108b	3.08 × 10−3b
	rs6457721	33215729	0.3820	4.12 × 10−8
	rs721394	33225796	0.2711	1.20 × 10−8
	rs9380350	33234843	0.2349	9.80 × 10−9
	rs9368757	33236355	0.2741	8.86 × 10−9
	rs9380351	33237724	0.2937	1.11 × 10−8

^aUsing combined dataset of 4,225 cases and 2,771 controls

^bSNPs or p values that pass the LD-adjusted 5% Bonferroni’s significance level. SNPs showing novel associations are highlighted in bold

^cSNPs or p values that pass the 5% FDR criterion

^dUsing T1DGC dataset of 3,350 case and 2,233 control haplotypes