Table 1. Novel/missed and refined variants from 1000 genomes imputation-based analysis.

Type	Trait	Lead SNP in present study (association Pa)	Chromosome band	Gene	MAF	Estimated R2 b	Alleles	Odds ratio (95% CI)	Lead SNP in original Study (association P, LDc, physical distance, conditional Pd)	Nearest SNP in literature (association P, LDc, physical distance, conditional Pd)
Missed	T1D	rs61839660 P=5.1 × 10−9 (1.8 × 10−8)	10p15	IL2RA intron 7	0.09	0.87 (0.90)	C->T	1.60 (1.44–1.76)	NA	rs1225130718 (P=2.9 × 10−5; LD=0.74 (0.38) 28.8 kb Pcon=3.7 × 10−5)
Missed	T2D	rs7018475 P=2.5 × 10−8 (6.1 × 10−8)	9p21	CDKN2B -128 kb	0.24	0.79 (0.85)	T->G	0.74 (0.64–0.85)	NA	rs1075728220 (P=2.7 × 10−3; LD=0.97 (0.41) 3.7 kb Pcon=3.7 × 10−7) rs1081166119, 20 (P=7.1 × 10−4; LD=0.50 (0.02) 3.6 kb Pcon=1.5 × 10−7) Pcon=0.5e
Refined	CD	rs11209026 P=4.2 × 10−21 (1.1 × 10−17)	1p31	IL23R exon 9	0.06	0.90 (0.91)	G->A	3.18 (2.91–3.44)	rs11805303 (P=5.8 × 10−12; LD=0.57 (0.01) 30.4 kb Pcon=7.6 × 10−17)	rs1146580422 (P=7.7 × 10−20; LD=1.0 (0.88) 3.4 kb Pcon=7.9 × 10−3)
Refined	T1D	rs1265564 P=1.0 × 10−16 (1.1 × 10−16)	12q24	CUX2 intron 4	0.48	0.87 (0.92)	A->C	0.69 (0.60–0.78)	rs17696736 (P=1.5 × 10−14; LD=0.43 (0.18) 778.4 kb Pcon=5.3 × 10−6)	rs318450418 (P=1.4 × 10−14; LD=0.74 (0.47) 176.2 kb Pcon=1.1 × 10−4)

Abbreviations: CD: Crohns's disease; T1D: type 1 diabetes; T2D: type 2 diabetes.

^aThe first value is based on MACH/MACH2DAT and the value in brackets is based on BEAGLE/PLINK.

^bImputation quality (estimated R²) based on MaCH and Beagle (values in brackets).

^cLD between lead SNP reported in this study and SNP in this column based on the same version of the 1000 genomes data, measured by D-prime (R²).

^dConditional P-value of the lead SNP reported in this study conditioned on SNP in this column.

^eConditional P-value of the lead SNP on the two-SNP (rs10757282 and rs10811661) haplotype.