Table 3. Association results for SPP1 (chromosome 4) for the rare variant analysis.
| (A) Association results of aggregated variant testing | |||||||
| Model | Gene | Burden test | SKAT test | No of SNPs aggregated | Total MAC | Cumulative MAF of SNPs | |
| p-value | Beta (SE) | p-value | |||||
| adjusted for age, sex, log(eGFR), log(UACR) | SPP1 | 1.36E-03 | -0.31 (0.10) | 2.51E-08 | 7 | 59.03 | 6.05E-03 |
| Same as above plus 2 replicated common SNPs* | SPP1 | 1.50E-03 | -0.30 (0.10) | 9.43E-08 | 7 | 59.03 | 6.05E-03 |
| (B) Association results of single variant analysis for aggregated variants | |||||||
| Model | Variant | Position (GRCh37) | MAF | Beta (SE) | p-value | Exonic effect (CADD) | |
| adjusted for age, sex, log(eGFR), log(UACR) | rs139555315 | 88901197 | 1.54E-03 | -1.20 (0.19) | 2.54E-10 | splicing (23.7) | |
| rs140258871 | 88901249 | 1.95E-03 | 0.24 (0.17) | 1.62E-01 | nonsynonymous (NA) | ||
| rs138638879 | 88902774 | 7.18E-04 | -0.18 (0.28) | 5.18E-01 | nonsynonymous (26.8) | ||
| rs7435825 | 88903774 | 3.08E-04 | 0.04 (0.42) | 9.17E-01 | nonsynonymous (12.8) | ||
| rs149833253 | 88903825 | 3.08E-04 | -0.45 (0.42) | 2.85E-01 | nonsynonymous (8.8) | ||
| rs146563765 | 88903899 | 1.02E-03 | -0.10 (0.23) | 6.83E-01 | nonsynonymous (4.2) | ||
| rs4660 | 88904005 | 2.05E-04 | -0.52 (0.52) | 3.22E-01 | nonsynonymous (9.8) | ||
MAC: minor allele count; MAF: minor allele frequency; NA: not available
* rs10011284, rs4253311. Statistical significant association p-values are marked in bold (aggregated variant testing: p-value<1.4E-06, single variant analysis: p-value<5.0E-08. Exonic effects: source dbNSFP v.2.0.