Table 1 Results from the meta-analysis of Icelandic and UK GWAS of symptomatic BPH/LUTS and from the the conditional analysis for loci with multiple variants

From: Genome-wide associations for benign prostatic hyperplasia reveal a genetic correlation with serum levels of PSA

Locus

Marker (EA/OA)

Covariate

Annotation/nearby gene(s)

EAF

Phet/I2(%)

Meta-analysis results

OR (95% c.i.)

P-value

2p16.1

rs2556378 (T/G)

rs10180282

Intron variant/BCL11A

0.154

0.37/0

1.12 (1.08, 1.15)

3.4 × 10−12

2p16.1

rs10180282a (T/C)

rs2556378

Intergenic variant/BCL11A

0.456

0.58/0

1.06 (1.03, 1.08)

8.7 × 10−7

5p15.33

rs381949 (A/G)

rs2853677

Intron variant/CLPTM1L

0.415

0.86/0

0.90 (0.88, 0.92)

4.9 × 10−19

5p15.33

rs2853677a (G/A)

rs381949

Intron variant/TERT

0.421

0.44/0

1.09 (1.06, 1.11)

1.7 × 10−12

5q22.1

rs10054105 (G/T)

na

Intergenic variant/STARD4

0.213

0.65/0

0.91 (0.88, 0.93)

3.5 × 10−12

5q31.1

rs677394 (G/C)

na

Intron variant/C5orf66, H2AFY

0.123

0.034/78

0.88 (0.85, 0.92)

2.9 × 10−11

6p22.1

rs200476 (T/A)

na

Intergenic variant/HIST1H2BL

0.162

0.23/30

0.88 (0.85, 0.90)

3.9 × 10−17

10p12.31

rs148678804 (A/G)

rs7906649

Intergenic variant/DNAJC1

0.035

0.17/48

1.27 (1.19, 1.35)

3.0 × 10−14

10p12.31

rs7906649a (G/A)

rs148678804

Intergenic variant/EBLN1

0.286

0.71/0

1.07 (1.04, 1.10)

2.1 × 10−7

10q26.12

rs11199879 (C/T)

rs4548546 and rs2981575

Intergenic variant/FGFR2

0.252

0.021/81

1.14 (1.11, 1.17)

5.7 × 10−23

10q26.12

rs4548546a (T/C)

rs11199879 and rs2981575

Intron variant/WDR11

0.310

0.20/40

1.11 (1.08, 1.13)

2.0 × 10−16

10q26.12

rs2981575a (G/A)

rs11199879 and rs4548546

Intron variant/FGFR2

0.427

0.97/0

0.94 (0.92, 0.96)

6.0 × 10−8

11p15.5

rs72878024 (A/G)

na

Missense variant/ODF3

0.080

0.20/40

0.85 (0.82, 0.89)

1.4 × 10−12

12q24.21

rs2555019 (T/C)

rs8853

Intergenic variant/TBX5

0.456

0.82/0

0.93 (0.91, 0.95)

2.4 × 10−11

12q24.21

rs8853a (C/T)

rs2555019

3-prime UTR variant/TBX3

0.494

0.75/0

1.07 (1.05, 1.10)

1.4 × 10−9

13q14.3

rs1638703 (C/G)

rs6561599

Intron variant/DLEU1

0.256

0.57/0

1.10 (1.07, 1.13)

1.1 × 10−13

13q14.3

rs6561599a (C/G)

rs1638703

Upstream gene variant/RNASEH2B

0.371

1.0/0

0.94 (0.92, 0.96)

1.8 × 10−7

17q12

rs11651052 (A/G)

na

Intron variant/HNF1B

0.470

0.24/29

0.93 (0.91, 0.95)

3.2 × 10−10

18q11.2

rs9958656 (T/C)

rs17670370

Intergenic variant/GATA6

0.430

1.0/0

1.11 (1.08, 1.13)

4.3 × 10−19

18q11.2

rs17670370a (G/T)

rs9958656

Intergenic variant/CTAGE1

0.262

0.24/28

1.07 (1.04, 1.10)

1.6 × 10−7

19q12

rs11084596 (C/T)

na

Intergenic variant/THEG5

0.356

0.34/0

0.88 (0.86, 0.90)

2.1 × 10−24

20q13.33

rs200383755 (C/G)

rs6061244

Missense variant/GATA5

0.0091

0.53/0

0.67 (0.59, 0.77)

3.2 × 10−9

20q13.33

rs6061244a (C/G)

rs200383755

Intron variant/GATA5

0.386

0.16/49

0.94 (0.92, 0.96)

5.7 × 10−8

  1. Shown is the effect allele (EA), the other allele (OA), the simple average effect allele population frequency (EAF), the allelic odds ratio (OR) for the effect allele with upper and lower 95% confidence intervals (c.i.) and the two-sided P-value for association testing between variants and disease, which was performed using the likelihood ratio statistic. Results from the two study groups were combined using a Mantel-Haenszel model (see Methods). Annotation is according to Variant Effect Predictor (VEP). Shown are also the P-value for the heterogeneity (Phet) between the two study groups and the heterogeneity statistic (I2) representing the fraction of variability due to heterogeneity between study groups. rs200383755 had an imputation information score of 0.99 and 0.88 in the Icelandic and UK datasets, respectively. All other markers listed had imputation information score >0.95. Results for markers pertaining to loci with more than one association signal are shown after conditioning on a relevant covariate. Markers at loci with no additional association signal do not have any applicable covariate (na) and the results are the unconditioned association result from the GWAS of symptomatic BPH/LUTS
  2. aMarkers discovered in the conditional analysis
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