Table 2

Top Discovery hits from the GUARDIAN Consortium, ordered by trait

SNPChrPosition*GeneAllelesRAFTraitβP value
rs2302063193150418GNA15A/C0.336MCRI−0.297.31E-08
rs16020844128843480MFSD8G/A0.041SI + M8.975.20E-07
rs89623222732877MYT1L/TSSC1T/C0.291SI + M−5.281.26E-06
rs671944222722295MYT1L/TSSC1A/G0.184SI + M−5.031.53E-06
rs1978648243371542HAAO/ZFP36L2/THADA§T/C0.324SI0.205.31E-07
rs8965981574036629C15orf59A/G0.116SI0.375.83E-07
rs48871401574046663C15orf59/TBC1D21G/T0.139SI0.316.91E-08
rs196701680147187HMGN3/LCA5C/T0.132SI−0.351.37E-06
rs104924941374920186KLF12/LINC00347A/C0.240M−22.025.04E-07
rs116830872227586606LOC646736/IRS1G/A0.412M20.547.42E-07
rs108309631192708710MTNR1BG/C0.220AIRg−2.765.23E-12
rs13871531192673828FAT3/MTNR1B#T/C0.220AIRg−2.552.21E-09
rs2206734620694884CDKAL1**T/C0.198AIRg−2.051.02E-06
rs38475541192668826FAT3/MTNR1B††A/G0.341AIRg−1.641.08E-06
rs9368222620686996CDKAL1‡‡A/C0.264AIRg−1.461.28E-06
rs68038033180116563PEX5L/TTC14C/T0.003AIRg17.531.64E-06
rs108309631192708710MTNR1BG/C0.230DI−3.401.03E-11
rs13871531192673828FAT3/MTNR1B#T/C0.220DI−3.201.32E-09
rs21494231336772381CCDC169-SOHLH2; SOHLH2G/A0.315DI2.183.67E-07
rs38125709139275204SNAPC4A/C0.461DI−1.871.72E-06
rs5230793187615862BCL6/LPPT/C0.069SG0.251.53E-07
rs780093227742603GCKR§§T/C0.341SG0.141.12E-06
rs7883381950778543MYH14C/T0.287SG−0.171.66E-06
  • Independent signals (r2 < 0.80) with evidence of association (P < 2.00 × 10−6) with the nearest annotated RefSeq genes listed. Chr, chromosome; RAF, reference allele frequency.

  • *Build hg19.

  • †Reference allele/other allele.

  • §Previously identified T2D locus (THADA rs7578597, r2 = 0.0079).

  • ‖Previously identified T2D locus (IRS1 rs2943641, r2 = 0.04).

  • ¶Previously identified T2D locus (MTNR1B rs1387153, r2 = 0.69).

  • #Previously identified T2D locus (MTNR1B rs1387153).

  • **Previously identified T2D locus (CDKAL1 rs7754840, r2 = 0.42).

  • ††Previously identified T2D locus (MTNR1B rs1387153, r2 = 0.54).

  • ‡‡Previously identified T2D locus (CDKAL1 rs7754840, r2 = 0.72).

  • §§Previously identified T2D locus (GCKR rs780094, r2 = 0.98).