Table 1 Twenty-eight novel loci identified in the genome-wide meta-analysis of kidney stone disease

From: Integrative genome-wide analyses identify novel loci associated with kidney stones and provide insights into its genetic architecture

CHR

Position

Lead SNP

EA/NEA

EAF

OR (95% CI)

P

Gene

Replication

1

150958836

rs267733

A/G

0.845

0.92 (0.89–0.95)

2.07×10−8

ANXA9

5.17×10−3 (rs7551686)

1

186651932

rs113831804

A/T

0.022

1.24 (1.16–1.33)

1.09×10−9

PACERR

9.64×10−4 (rs7516899)*

1

205724302

rs823121

A/G

0.438

1.07 (1.05–1.09)

3.48×10−9

SLC41A1

7.56×10−6 (rs41264867)*

1

220082150

rs884127

A/G

0.404

0.92 (0.9–0.95)

8.93×10−12

SLC30A10

3.00×10−4 (rs77145552)*

3

48861058

rs200495345

A/AT

0.943

1.3 (1.22–1.39)

2.67×10−15

PRKAR2A

2.09×10−1 (rs3895736)

3

51100168

rs191107165

A/G

0.048

0.77 (0.71–0.83)

6.55×10−11

DOCK3

3.23×10−5 (rs72964039)*

3

52124388

rs138789058

T/C

0.065

0.84 (0.79–0.89)

8.01×10−10

POC1A

3.23×10−5 (rs72964039)*

4

3744294

rs440318

A/G

0.547

0.94 (0.92–0.96)

2.68×10−8

ADRA2C

1.22×10−3 (rs35867127)*

4

77505067

rs28454965

A/G

0.504

0.93 (0.91–0.96)

1.37×10−9

SHROOM3

2.97×10−4 (rs7664160)*

4

115498457

rs71606723

A/T

0.717

0.9 (0.88–0.93)

3.45×10−16

UGT8

5.13×10−4 (rs9884467)*

5

51165567

rs55672774

T/C

0.362

1.08 (1.05–1.1)

9.31×10−11

ISL1

6.00×10−5 (rs184643180)*

6

32107851

rs3134962

A/G

0.155

0.9 (0.87–0.93)

1.51×10−11

PRRT1

9.37×10−8 (rs4947328)*

6

43804571

rs729761

T/G

0.296

1.08 (1.06–1.11)

1.79×10−10

VEGFA

1.25×10−4 (rs137924211)*

6

50786008

rs2206271

A/T

0.318

1.08 (1.05–1.11)

9.70×10−11

TFAP2B

1.08×10−5 (rs11961359)*

6

101161812

rs1039031

A/G

0.494

1.07 (1.04–1.09)

5.98×10−9

ASCC3

1.09×10−3 (rs12210312)*

7

142605221

rs4252512

T/C

0.985

0.78 (0.71–0.85)

1.88×10−8

TRPV5

1.05×10−2 (rs11520897)

9

71172306

rs12376362

A/C

0.823

1.09 (1.06–1.12)

8.00×10−9

TMEM252

4.22×10−3 (rs71503670)

9

97585477

rs150891531

T/C

0.086

0.88 (0.84–0.91)

8.73×10−10

AOPEP

7.05×10−7 (rs10993151)*

10

9280394

rs17486892

T/C

0.773

1.08 (1.05–1.11)

1.90×10−8

TCEB1P3

2.08×10−4 (rs1243417)*

10

90142203

rs11202736

A/T

0.680

0.93 (0.91–0.95)

2.47×10−9

RNLS

1.90×10−5 (rs11203100)*

13

96175396

rs57719175

A/G

0.400

0.93 (0.91–0.95)

2.05×10−10

CLDN10

4.58×10−4 (rs61152555)*

15

48500263

rs34819316

A/G

0.005

0.54 (0.43–0.67)

4.59×10−8

SLC12A1

2.52×10−4 (rs117970606)*

15

85719783

rs10852147

T/G

0.319

1.07 (1.04–1.09)

4.35×10−8

PDE8A

4.69×10−3 (rs4887181)

16

88549264

rs55637647

C/G

0.650

0.93 (0.91–0.95)

6.50×10−10

ZFPM1

3.68×10−7 (rs8054971)*

17

44025888

rs242559

A/C

0.808

0.92 (0.89–0.94)

4.22×10−9

MAPT

2.11×10−4 (rs197923)*

19

4335513

rs58169740

T/G

0.683

1.07 (1.05–1.1)

6.74×10−9

STAP2

3.55×10−4 (rs58659609)*

19

46181392

rs1800437

C/G

0.227

0.92 (0.9–0.95)

1.02×10−9

GIPR

5.72×10−5 (rs187967034)*

19

53357172

rs7259073

T/C

0.916

1.13 (1.08–1.18)

3.02×10−8

ZNF468

1.09×10−3 (rs11667654)*

  1. The lead SNP is the variant with the smallest P value within each locus. The gene is the nearby protein-coding gene to the lead SNP.
  2. EA effect allele, NEA non-effect allele, EAF frequency of the effect allele, OR Odds ratio, CI confidence interval.
  3. *suggests the variant with the smallest P value at each novel locus in Japanese population passed the significant threshold (0.05/28).
Back to article page