Table 1

Novel loci associated with T2D from the combination of 1000G-imputed GWAS meta-analysis (stage 1) and Metabochip follow-up (stage 2)

Locus name*Stage 1Stage 2Stage 1 + stage 2
Chr:positionSNV†EA/ NEAEAFOR (95% CI)P valueChr:positionSNV‡r2 with lead SNVEA/ NEAEAFOR (95% CI)P valueOR (95% CI)¢P value
ACSL14:185708807rs60780116T/C0.841.09 (1.06–1.13)7.38 × 10−84:185714289rs19965460.62G/T0.861.08 (1.03–1.13)5.60 × 10−41.09 (1.06–1.12)1.98 × 10−10
HLA-DQA16:32594309rs9271774C/A0.741.10 (1.06–1.14)3.30 × 10−76:32594328rs92717750.91T/C0.801.08 (1.03–1.13)7.59 × 10−41.09 (1.06–1.12)1.11 × 10−9
SLC35D36:137287702rs6918311A/G0.531.07 (1.04–1.10)6.67 × 10−76:137299152rs44077330.92A/G0.521.05 (1.02–1.08)1.63 × 10−31.06 (1.04–1.08)6.78 × 10−9
MNX17:157027753rs1182436C/T0.801.08 (1.05–1.12)8.30 × 10−77:157031407rs11823970.92G/T0.851.06 (1.02–1.11)4.38 × 10−31.08 (1.05–1.10)1.71 × 10−8
ABO9:136155000rs635634T/C0.181.08 (1.05–1.12)3.59 × 10−79:136154867rs4958280.83T/G0.201.06 (1.01–1.10)1.23 × 10−21.08 (1.05–1.10)2.30 × 10−8
PLEKHA110:124186714rs2292626C/T0.501.09 (1.06–1.11)1.75 × 10−1210:124167512rs24210160.99C/T0.501.05 (1.02–1.08)2.30 × 10−31.07 (1.05–1.09)1.51 × 10−13
HSD17B1211:43877934rs1061810A/C0.281.08 (1.05–1.11)5.29 × 10−911:43876435rs37365050.92G/A0.301.05 (1.01–1.08)4.82 × 10−31.07 (1.05–1.09)3.95 × 10−10
MAP3K1111:65364385rs111669836A/T0.251.07 (1.04–1.10)7.43 × 10−711:65365171rs112272341.00T/G0.241.05 (1.01–1.08)8.77 × 10−31.06 (1.04–1.09)4.12 × 10−8
NRXN314:79945162rs10146997G/A0.211.07 (1.04–1.10)4.59 × 10−614:79939993rs171092560.98A/G0.211.07 (1.03–1.11)1.27 × 10−41.07 (1.05–1.09)2.27 × 10−9
CMIP16:81534790rs2925979T/C0.301.08 (1.05–1.10)2.72 × 10−816:81534790rs29259791.00T/C0.311.05 (1.02–1.08)3.06 × 10−31.07 (1.04–1.09)2.27 × 10−9
ZZEF117:4014384rs7224685T/G0.301.07 (1.04–1.10)2.00 × 10−717:3985864rs80688040.95A/G0.311.07 (1.03–1.11)4.11 × 10−41.07 (1.05–1.09)3.23 × 10−10
GLP2R17:9780387rs78761021G/A0.341.07 (1.05–1.10)5.49 × 10−817:9791375rs176760670.87C/T0.311.03 (1.00–1.07)3.54 × 10−21.06 (1.04–1.08)3.04 × 10−8
GIP17:46967038rs79349575A/T0.511.07 (1.04–1.09)2.61 × 10−717:47005193rs155630.78G/A0.541.04 (1.01–1.07)2.09 × 10−21.06 (1.03–1.08)4.43 × 10−8
  • *The nearest gene is listed; this does not imply this is the biologically relevant gene. †Lead SNV types: all map outside transcripts except rs429358 (missense variant) and rs1061810 (3′ untranslated region). ‡Stage 2: proxy SNV (r2 > 0.6 with stage 1 lead SNV) was used when no stage 1 SNV was available. ¢The meta-analysis OR is aligned to the stage 1 SNV risk allele. Chr, chromosome; EA, effect allele; EAF, effect allele frequency; NEA, noneffect allele.