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
| Locusa | dbSNPID | Chr | Positionb | Variation (Substitution) | Stage 1c | Stage 2d | Combined | ||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| A1/A2 (A1 AF) | β (SEM) | P Value | I2 | β (SEM) | 1-sided P | β (SEM) | P Value | Prop Var Exp (%) | |||||
| PPM1J | rs34611728 | 1 | 113255456 | c.639G>T (L213F) | A/C (0.13) | −0.0103 (0.0013) | 1.2E-14 | 13.2 | −0.0059 (0.0023) | 4.7E-03 | −0.0092 (0.0011) | 3.3E-16 | 0.05 |
| EDEM3 | rs78444298 | 1 | 184672098 | c.2236C>T (P746S) | A/G (0.02) | −0.0183 (0.0034) | 5.2E-08 | 15.3 | −0.0225 (0.0055) | 1.8E-05 | −0.0195 (0.0029) | 1.5E-11 | 0.03 |
| ACP1 | rs11553746 | 2 | 272203 | c.129C>T (T95l) | T/C (0.35) | −0.0049 (0.0009) | 2.0E-07 | 20.7 | −0.0032 (0.0016) | 2.2E-02 | −0.0045 (0.0008) | 1.0E-08 | 0.02 |
| ORC4e | rs2307394 | 2 | 148716428 | c.233A>G (N78S) | C/T (0.32) | −0.0058 (0.0010) | 6.8E-09 | 14.3 | −0.0025 (0.0016) | 6.0E-02 | −0.0049 (0.0009) | 8.4E-09 | 0.03 |
| SPEG | rs55760516 | 2 | 220354108 | c.8191A>G (R2731G) | G/A (0.33) | 0.0059 (0.0009) | 4.8E-10 | 0.5 | 0.0054 (0.0016) | 3.7E-04 | 0.0058 (0.0008) | 1.7E-13 | 0.04 |
| EYA4 | rs9493627 | 6 | 133789728 | c.829G>A (G223S) | A/G (0.31) | 0.0061 (0.0010) | 2.3E-10 | 0.0 | 0.0049 (0.0016) | 1.4E-03 | 0.0058 (0.0009) | 1.4E-11 | 0.04 |
| CYP1A1 | rs2472297 | 15 | 75027880 | intergenic | T/C (0.24) | 0.0057 (0.0010) | 7.0E-08 | 0.0 | 0.0059 (0.0017) | 3.2E-04 | 0.0058 (0.0009) | 3.0E-11 | 0.03 |
| ATXN2L | rs8049439 | 16 | 28837515 | intronic | C/T (0.40) | 0.0048 (0.0009) | 1.3E-07 | 7.1 | 0.0045 (0.0016) | 1.8E-03 | 0.0047 (0.0008) | 1.2E-09 | 0.03 |
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.