Table 1. The 24 novel SNPs associated with eGFRcrea in European ancestry individuals.
| SNP ID* | Chr. | Position (bp)† | Locus name‡ | Effect/Non effect allele (EAF) | SNP function§ | Stage 1 (discovery)|| | Stage 2 (replication) | Combined analysis¶ | ||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Beta | P value | Beta | q-value | Beta | P value# | I2 %** | ||||||
| The eight loci whose smallest P value was observed in the ‘no diabetes' group | ||||||||||||
| rs3850625 | 1 | 201,016,296 | CACNA1S | A/G (0.12) | Exonic, nonsyn. SNV | 0.0080 | 2.55E−09 | 0.0071 | 5.46E−03 | 0.0083 | 6.82E−11 | 0 |
| rs2712184 | 2 | 217,682,779 | IGFBP5 | A/C (0.58) | Intergenic | −0.0049 | 1.65E−08 | −0.0055 | 2.06E−03 | −0.0053 | 1.33E−10 | 0 |
| rs9682041 | 3 | 170,091,902 | SKIL | T/C (0.87) | Intronic | −0.0067 | 1.36E−07 | −0.0046 | 2.33E−02 | −0.0068 | 2.58E−08 | 2 |
| rs10513801 | 3 | 185,822,353 | ETV5 | T/G (0.87) | Intronic | 0.0070 | 3.80E−09 | 0.0046 | 1.79E−02 | 0.0072 | 1.03E−09 | 0 |
| rs10994860 | 10 | 52,645,424 | A1CF | T/C (0.19) | UTR5 | 0.0075 | 1.00E−11 | 0.0061 | 5.46E−03 | 0.0077 | 1.07E−12 | 2 |
| rs163160 | 11 | 2,789,955 | KCNQ1 | A/G (0.82) | Intronic | 0.0067 | 9.02E−09 | 0.0050 | 9.89E−03 | 0.0065 | 2.26E−09 | 14 |
| rs164748 | 16 | 89,708,292 | DPEP1 | C/G (0.53) | Intergenic | 0.0047 | 9.92E−09 | 0.0019 | 4.19E−02 | 0.0046 | 1.95E−08 | 17 |
| rs8091180 | 18 | 77,164,243 | NFATC1 | A/G (0.56) | Intronic | −0.0054 | 1.43E−08 | −0.0052 | 5.46E−03 | −0.0060 | 1.28E−09 | 0 |
| The 16 loci whose smallest P value was observed in the ‘overall' group | ||||||||||||
| rs12136063 | 1 | 110,014,170 | SYPL2 | A/G (0.70) | Intronic | 0.0049 | 2.33E−07 | 0.0028 | 2.31E−02 | 0.0045 | 4.71E−08 | 0 |
| rs2802729 | 1 | 243,501,763 | SDCCAG8 | A/C (0.43) | Intronic | −0.0050 | 7.37E−08 | −0.0029 | 2.05E−02 | −0.0046 | 2.20E−08 | 9 |
| rs4667594 | 2 | 170,008,506 | LRP2 | A/T (0.53) | Intronic | −0.0045 | 2.37E−07 | −0.0043 | 5.62E−03 | −0.0044 | 3.52E−08 | 4 |
| rs6795744‡‡ | 3 | 13,906,850 | WNT7A | A/G (0.15) | Intronic | 0.0071 | 9.60E−09 | 0.0019 | 5.15E−02 | 0.0060 | 3.33E−08 | 18 |
| rs228611 | 4 | 103,561,709 | NFKB1 | A/G (0.47) | Intronic | −0.0055 | 4.66E−10 | −0.0060 | 8.91E−04 | −0.0056 | 3.58E−12 | 3 |
| rs7759001 | 6 | 27,341,409 | ZNF204 | A/G (0.76) | ncRNA intronic | −0.0053 | 2.64E−07 | −0.0045 | 9.10E−03 | −0.0051 | 1.75E−08 | 0 |
| rs10277115 | 7 | 1,285,195 | UNCX | A/T (0.23) | Intergenic | 0.0095 | 1.05E−10 | 0.0079 | 9.03E−04 | 0.0090 | 8.72E−14 | 0 |
| rs3750082 | 7 | 32,919,927 | KBTBD2 | A/T (0.33) | Intronic | 0.0049 | 2.52E−07 | 0.0031 | 1.96E−02 | 0.0045 | 3.22E−08 | 2 |
| rs6459680 | 7 | 156,258,568 | RNF32 | T/G (0.74) | Intergenic | −0.0065 | 1.96E−10 | −0.0019 | 4.62E−02 | −0.0055 | 1.07E−09 | 0 |
| rs4014195 | 11 | 65,506,822 | AP5B1 | C/G (0.64) | Intergenic | 0.0061 | 2.19E−11 | 0.0034 | 1.42E−02 | 0.0055 | 1.10E−11 | 0 |
| rs10491967 | 12 | 3,368,093 | TSPAN9 | A/G (0.10) | Intronic | −0.0092 | 3.03E−10 | −0.0106 | 3.93E−04 | −0.0095 | 5.18E−14 | 0 |
| rs7956634 | 12 | 15,321,194 | PTPRO | T/C (0.81) | Intronic | −0.0068 | 2.46E−09 | −0.0069 | 1.51E−03 | −0.0068 | 7.17E−12 | 0 |
| rs1106766 | 12 | 57,809,456 | INHBC | T/C (0.22) | Intergenic | 0.0062 | 4.67E−08 | 0.0058 | 8.79E−03 | 0.0061 | 2.41E−09 | 9 |
| rs11666497 | 19 | 38,464,262 | SIPA1L3 | T/C (0.18) | Intronic | −0.0064 | 8.58E−08 | −0.0041 | 1.53E−02 | −0.0058 | 4.25E−08 | 24 |
| rs6088580 | 20 | 33,285,053 | TP53INP2 | C/G (0.47) | Intergenic | −0.0055 | 7.17E−10 | −0.0027 | 2.31E−02 | −0.0049 | 1.79E−09 | 0 |
| rs17216707 | 20 | 52,732,362 | BCAS1 | T/C (0.79) | Intergenic | −0.0084 | 5.96E−13 | −0.0051 | 6.69E−03 | −0.0077 | 8.83E−15 | 1 |
bp, basepairs; Chr, chromosome; EAF, effect allele frequency; eGFRcrea, eGFR based on serum creatinine; GWAS, genome-wide association studies; SNP, single-nucleotide polymorphism; UTR, untranslated region.
*SNPs are grouped by the stratum where the smallest P value in the discovery and combined analysis was observed. In the ‘no diabetes' group, sample size/number of studies were equal to 118,448/45, 36,433/13 and 154,881/58, in the discovery, replication and combined analyses, respectively. In the ‘overall' group, the numbers for the three analyses were equal to 133,413/48, 42,116/14 and 175,579/62, respectively.
†On the basis of RefSeq genes (build 37).
‡Conventional locus name based on relevant genes in the region as identified by bioinformatic investigation (Supplementary Table 12) or closest gene. A complete overview of the genes in each locus is given in the regional association plots (Supplementary Fig. 4).
§SNP function is derived from NCBI RefSeq genes and may not correspond to the named gene.
||Twice genomic-control (GC) corrected P value from discovery GWAS meta-analysis: at the individual study level and after the meta-analysis.
¶For random-effect estimate, see Supplementary Table 4.
#P value of the meta-analysis of the twice GC-corrected discovery meta-analysis results and replication studies.
**Between-study heterogeneity, as assessed by the I2. Q statistic P value >0.05 for all SNPs, except rs11666497 (SIPA1L3, P value=0.04).
‡‡For this SNP, the conditions for replication were not all met (q-value >0.05 in the replication stage).