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%).

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