Table 3 |. Size of 99% credible sets of variants for the seven identified signals for Rapid3 or CKDi25.
Shown number of genes overlapping each of the six locus regions (lead variant +/−500kB) and the number of variants in the 99% credible set for each of the seven signals. The credible sets of variants were computed (i) for the two rapid eGFRcrea decline traits (Rapid3 and CKDi25) highlighting the set for the analysis that identified the locus/signal (signals 1.1 to 4 from genome-wide approach, signals 5 and 6 from candidate-based approach) and (ii) for cross-sectional eGFRcrea from CKDGen data as reported previously17.
| Locus/signal no. | Locus name (a) | Identifying trait (b) | Locus region (c) |
No. of variants in
99%credible set (overlap with eGFRcrea sets) |
No. of variants in 99% credible set
(overlap with CKDi25 sets) |
||||
|---|---|---|---|---|---|---|---|---|---|
| Chr | Start | Stop | No. of genes | Rapid3 | CKDi25 | eGFRcrea *** | |||
| 1.1 | [UMOD-PDILT] | Rapid3, CKDi25 | 16 | 19,866,507 | 20,867,645 | 13 | 14 (10) | 13 (11) | 16 (10) |
| 1.2 | [UMOD-PDILT] | CKDi25 2nd | 16 | 19,866,507 | 20,867,645 | s.a. | 1,059 | 1 (1) | 1 (1) |
| 2 | [WDR72] | CKDi25 | 15 | 53,502,606 | 54,502,606 | 1 | 2,931 | 37 (0) | 41 (0) |
| 3 | [PRKAG2] | CKDi25 | 7 | 150,906,788 | 151,906,788 | 14 | 2,671 | 16 (6) | 6 (6) |
| 4 | [OR2S2] | Rapid3 | 9 | 35,437,931 | 36,437,931 | 36 | 2 | 2,573 | NA |
| 5 | [LARP4B] | CKDi25 | 10 | 399,071 | 1,399,071 | 10 | 2,955 | 2,806 | 1 (d) |
| 6 | [GATM] | Rapid3 | 15 | 45,183,795 | 46,183,795 | 17 | 1,438 | 2,493 | 1 (d) |
Chr=Chromosome of locus region, Start/Stop=Start and stop of locus region on GRCh37, s.a.=see above, (a) Nearest gene(s), stated in brackets to distinguish from gene and protein names; (b) Indicates the trait for which the variant was identified with significant association (“CKDi25 2nd” indicating that this is the 2nd independent signal for the CKDi25 trait analysis); (c) Locus region defined as the region of the two lead variants identified for Rapid3 and CKDi25 in [UMOD-PDILT] or for the single lead variant identified for Rapid3 or CKDi25 in the other loci ±500 kB. The CKDi25 2nd signal (signal no. 1.2) is mapped to the [UMOD-PDILT] locus region from signal no. 1.1; (d) For the candidate-based identified loci [LARP4B] and [GATM], the statistics for the credible sets were instable due to the lack of genome-wide significance and yielded extremely wide credible set intervals. Since the CKDi25 or Rapid3 signal was very similar to the signal for cross-sectional eGFRcrea (Supplementary Figure 4E&F), we conducted the bioinformatic follow-up for the credible set variant derived from eGFRcrea previously.