Table 3.
Colocalization analysis results for selected genes.
| Gene expression | eGFRcrea association | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Locus ID | Signal ID | Gene | PP_H4 | rsid | EA | OA | BETA | P | FDR | BETA | P | PPA |
| Expression in tubule-interstitial tissue | ||||||||||||
| k4.1 | 1 | GALNTL5 | 0.987 | rs10224210 | C | T | 0.67 | 1.0E-05 | 0.011 | −0.0078 | 2.9E-139 | 0.50 |
| k21.2 | 2 | TFDP2 | 0.001 | rs58436159 | T | C | −0.58 | 1.1E-05 | 0.012 | −0.0051 | 1.6E-23 | 0.13 |
| k27.1 | 1 | SLC6A13 | 0.995 | rs11062102 | C | T | −0.29 | 3.4E-07 | 6.6E-04 | −0.0041 | 2.3E-47 | 0.47 |
| k88 | 1 | TPPP | 0.996 | rs434215 | A | G | 0.57 | 7.4E-06 | 0.0087 | −0.0039 | 6.4E-26 | 0.93 |
| k99.1 | 1 | PPDPF | 0.995 | rs2314639 | T | C | −0.47 | 1.0E-10 | 4.6E-07 | −0.0035 | 5.0E-17 | 0.07 |
| k191.2 | 2 | YY1AP1 | 0.993 | rs4971092 | T | C | −0.73 | 2.9E-05 | 0.025 | −0.0027 | 1.0E-10 | 0.83 |
| n95.1 | 1 | CPXM1 | 0.158 | rs6084184 | A | G | −0.43 | 5.1E-04 | 0.19 | −0.0019 | 2.0E-08 | 0.07 |
| Expression in glomerular tissue | ||||||||||||
| k4.1 | 1 | GALNTL5 | 0.033 | rs10224210 | C | T | 0.15 | 0.44 | 0.99 | −0.0078 | 2.9E-139 | 0.50 |
| k21.2 | 2 | TFDP2 | 0.035 | rs2203002 | T | C | 0.22 | 0.0976 | 0.94 | −0.0051 | 1.2E-23 | 0.14 |
| k27.1 | 1 | SLC6A13 | 0.039 | rs11062102 | C | T | −0.11 | 0.12 | 0.95 | −0.0041 | 2.3E-47 | 0.47 |
| k88 | 1 | TPPP | 0.043 | rs434215 | A | G | 0.19 | 0.21 | 0.97 | −0.0039 | 6.4E-26 | 0.93 |
| k99.1 | 1 | PPDPF | 0.998 | rs72629024 | G | C | −0.46 | 4.9E-07 | 0.0023 | −0.0036 | 3.5E-18 | 0.85 |
| k191.2 | 2 | YY1AP1 | 0.164 | rs4971092 | T | C | 0.30 | 0.037 | 0.90 | −0.0027 | 1.0E-10 | 0.83 |
| n95.1 | 1 | CPXM1 | 0.731 | rs6084180 | T | C | −0.87 | 1.9E-09 | 1.8E-05 | −0.002 | 1.3E-08 | 0.82 |
For the seven genes with small 99% credible sets (<= 5 variants, among 23 highlighted genes from Table 2) that contain significant eQTLs in kidney tissue, we here show results from colocalization analysis between eGFRcrea association signals (n = 1,004,040) and gene expression signals for two types of kidney tissues from NEPTUNE (tubule-interstitial and glomerular tissue, n = 187). PP_H4 is the posterior probability of positive colocalization41. We also show the respective credible set variant with the smallest P value for gene expression and its association estimates for gene expression (NEPTUNE data) and eGFRcrea (GWAS data) (EA: effect allele, OA: other allele, BETA: genetic effect per EA, P: two-sided association P value based on Wald test, FDR: false-discovery-rate, PPA: posterior probability of association from variant-based fine-mapping). Locus/Signal ID: Identifier of identified locus/signal (“n” novel, “k” known; first integer indicating the locus, second integer the signal within the locus). Marked in bold are positive colocalizations (PP_H4 ≥80%) and significant eQTLs (FDR <5%).