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. 2019 Nov 15;10:5175. doi: 10.1038/s41467-019-13145-x

Table 1.

SNPs significantly associated with kidney stone disease at trans-ethnic meta-analysis

Cha SNP Positionb Annc EAd NEAe EAFf INFOg ORh Pi Candidate gene
1 rs10917002 21836340 I T C UKj 0.11 0.997 1.18 (1.12–1.25) 3.60 × 10–9 ALPL†
BJk 0.38 0.998 1.09 (1.04–1.15) 5.83 × 10−5
MAl − − 1.13 (1.09–1.17) 3.45 × 10−11
2 rs780093 27742603 I T C UKj 0.38 1 1.08 (1.04–1.12) 3.60 × 10−5 GCKR
BJk 0.56 0.997 1.14 (1.09–1.18) 1.10 × 10−8
MAl − − 1.10 (1.08–1.13) 1.31 × 10−13
2 rs13003198* 234257105 IG T C UKj 0.39 0.997 1.10 (1.06–1.14) 6.50 × 10−8 DGKD
BJk 0.25 0.98 1.12 (1.06–1.18) 1.09 × 10−5
MAl − − 1.11 (1.07–1.14) 3.89 × 10−11
4 rs1481012* 89039082 I G A UKj 0.11 0.994 1.12 (1.06–1.18) 4.30 × 10−5 ABCG2
BJk 0.30 0.994 1.11 (1.05–1.17) 1.50 × 10−5
MAl − − 1.11 (1.07–1.16) 2.79 × 10−8
5 rs56235845 176798040 S G T UKj 0.33 0.986 1.16 (1.12–1.20) 9.10 × 10−15 SLC34A1
BJk 0.31 0.87 1.18 (1.12–1.25) 1.88 × 10−11
MAl − − 1.16 (1.13–1.20) 2.64 × 10−21
6 rs1155347 39146230 IG C T UKj 0.22 0.975 1.12 (1.07–1.17) 2.60 × 10−7 KCNK5
BJk 0.16 0.925 1.16 (1.08–1.24) 1.33 × 10−6
MAl − − 1.13 (1.09–1.17) 8.54 × 10−11
6 rs77648599* 160624115 I G T UKj 0.03 0.992 1.33 (1.21–1.47) 5.50 × 10−9 SLC22A2
BJk 0.04 0.739 1.22 (1.06–1.44) 1.89 × 10−3
MAl − − 1.30 (1.20–1.42) 5.39 × 10−10
7 rs12539707* 27626165 I T C UKj 0.30 0.999 1.13 (1.08–1.17) 6.30 × 10−10 HIBADH
BJk 0.09 0.789 1.10 (1.01–1.21) 0.0268
MAl − − 1.12 (1.08-1.16) 1.09 × 10–10
7 rs12666466 30916430 I G C UKj 0.03 0.994 1.22 (1.11-1.34) 5.00 × 10–5 AQP1
BJk 0.12 0.989 1.17 (1.08-1.26) 2.80 × 10–6
MAl − − 1.19 (1.12–1.26) 3.26 × 10−8
11 rs4529910 111243102 I T G UKj 0.27 0.998 1.07 (1.02–1.11) 1.40 × 10−3 POU2AF
BJk 0.59 0.999 1.12 (1.08–1.16) 3.94 × 10−7
MAl − − 1.09 (1.06–1.12) 4.25 × 10−10
13 rs1037271 42779410 I C T UKj 0.39 0.995 1.11 (1.07–1.15) 2.50 × 10−8 DGKH†
BJk 0.55 0.936 1.20 (1.15–1.24) 7.49 × 10−15
MAl − − 1.15 (1.12–1.18) 1.29 × 10−24
15 rs578595 53997089 I C A UKj 0.46 0.996 1.09 (1.05–1.13) 2.50 × 10−6 WDR72
BJk 0.69 0.996 1.11 (1.06–1.15) 2.25 × 10−5
MAl − − 1.09 (1.07–1.12) 6.26 × 10−11
16 rs77924615 20392332 I A G UKj 0.20 0.980 1.13 (1.08–1.18) 1.80 × 10−8 UMOD
BJk 0.22 0.984 1.17 (1.10–1.24) 2.80 × 10−9
MAl − − 1.14 (1.10–1.19) 1.14 × 10−13
16 rs889299* 23381914 I G A UKj 0.76 1 1.10 (1.05–1.14) 8.20 × 10−6 SCNN1B
BJk 0.66 0.895 1.09 (1.04–1.14) 9.39 × 10−4
MAl − − 1.09 (1.06–1.13) 1.55 × 10−8
17 rs1010269 59448945 I G A UKj 0.83 0.981 1.08 (1.03–1.14) 7.10 × 10−4 BCAS†
BJk 0.56 0.87 1.17 (1.12–1.22) 4.82 × 10−11
MAl − − 1.13 (1.10–1.17) 3.71 × 10−15
17 rs4793434* 70352537 I G C UKj 0.50 0.993 1.09 (1.05–1.13) 1.50 × 10−6 SOX9
BJk 0.32 0.983 1.09 (1.04–1.15) 2.04 × 10−4
MAl − − 1.09 (1.06–1.12) 4.52 × 10−9
19 rs3760702 14588237 IG A G UKj 0.33 0.994 1.08 (1.05–1.13) 1.40 × 10−5 GIPC1
BJk 0.25 0.971 1.14 (1.08–1.20) 3.78 × 10−7
MAl − − 1.09 (1.07–1.13) 1.98 × 10−9
20 rs17216707 52732362 IG T C UKj 0.81 0.961 1.17 (1.12–1.22) 9.90 × 10−12 CYP24A1
BJk 0.92 0.766 1.24 (1.15–1.34) 5.90 × 10−6
MAl − − 1.19 (1.14–1.23) 7.82 × 10−18
21 rs12626330 37835982 I G C UKj 0.49 0.980 1.16 (1.12–1.20) 5.80 × 10−17 CLDN14
BJk 0.39 0.981 1.12 (1.07–1.18) 2.77 × 10−7
MAl − − 1.15 (1.12–1.18) 7.24 × 10−21
22 rs13054904* 23410918 I A T UKj 0.26 0.999 1.15 (1.11–1.20) 3.30 × 10−12 BCR
BJk 0.02 0.967 1.05 (0.91–1.26) 0.505
MAl − − 1.14 (1.10-1.19) 4.49 × 10–12

aChromosome. bBased on NCBI Genome Build 37 (hg19). cAnnotation, I denotes an intronic position, IG an intergenic position, and S a splice site position. dThe effect allele. eThe alternate (non-effect) allele. fThe effect allele frequency in the study population. gThe imputation quality score. hOdds ratio (95% confidence intervals). OR > 1 indicative of increased risk with effect allele. ip values less than the genome-wide significance threshold of 5.0 × 10−8 are shown in bold italics. jUK Biobank, cohort 6536 cases and 388,508 controls. kBiobank Japan, cohort 5587 cases and 28,870 controls. lTrans-ethnic meta-analysis. *Loci not previously reported to associate with kidney stone disease in GWAS. †These three variants showed nominally significant heterogeneity in effects between the two populations (Q value p < 0.05)