Table 1.

Novel variants associated with eGFRcrea in EA participants from single-variant analysis in stage 1 meeting chip-wide significance (P<3.7×10−7) and associations in stage 2 and combined analysis

LocusadbSNPIDChrPositionbVariation (Substitution)Stage 1cStage 2dCombined
A1/A2 (A1 AF)β (SEM)P ValueI2β (SEM)1-sided Pβ (SEM)P ValueProp Var Exp (%)
PPM1Jrs346117281113255456c.639G>T (L213F)A/C (0.13)−0.0103 (0.0013)1.2E-1413.2−0.0059 (0.0023)4.7E-03−0.0092 (0.0011)3.3E-160.05
EDEM3rs784442981184672098c.2236C>T (P746S)A/G (0.02)−0.0183 (0.0034)5.2E-0815.3−0.0225 (0.0055)1.8E-05−0.0195 (0.0029)1.5E-110.03
ACP1rs115537462272203c.129C>T (T95l)T/C (0.35)−0.0049 (0.0009)2.0E-0720.7−0.0032 (0.0016)2.2E-02−0.0045 (0.0008)1.0E-080.02
ORC4ers23073942148716428c.233A>G (N78S)C/T (0.32)−0.0058 (0.0010)6.8E-0914.3−0.0025 (0.0016)6.0E-02−0.0049 (0.0009)8.4E-090.03
SPEGrs557605162220354108c.8191A>G (R2731G)G/A (0.33)0.0059 (0.0009)4.8E-100.50.0054 (0.0016)3.7E-040.0058 (0.0008)1.7E-130.04
EYA4rs94936276133789728c.829G>A (G223S)A/G (0.31)0.0061 (0.0010)2.3E-100.00.0049 (0.0016)1.4E-030.0058 (0.0009)1.4E-110.04
CYP1A1rs24722971575027880intergenicT/C (0.24)0.0057 (0.0010)7.0E-080.00.0059 (0.0017)3.2E-040.0058 (0.0009)3.0E-110.03
ATXN2Lrs80494391628837515intronicC/T (0.40)0.0048 (0.0009)1.3E-077.10.0045 (0.0016)1.8E-030.0047 (0.0008)1.2E-090.03
  • A1, effect allele; A2, non-effect allele; A1 AF, effect allele frequency; Chr, chromosome; Prop Var Exp, proportion of variance in ln(eGFRcrea) explained.

  • a Loci are named according to the closest gene on the basis of the position of the lead SNP for new loci.

  • b Position is reported in UCSC Genome Browser build hg19.

  • c Sample size for stage 1 analysis: n=111,666.

  • d Sample size for stage 2 analysis: n=48,343.

  • e This variant reached chip-wide significance (P<3.7×10−7) in the stage 1 samples but did not meet validation criteria in stage 2.