Table 3 Conditional genome-wide association study results.

From: Genome-wide association study of prostate-specific antigen levels identifies novel loci independent of prostate cancer

Chrom

Position

Genes

SNP

Allele

Kaiser Permanente NHW non-cases (n=28,503)

Replication meta-analysis ( n =11,825)

Combined meta-analysis ( n =40,328)

     

Allele Frequency

β† (× 102)

P -value

β† (× 102)

P -value

β† (× 102)

P -value

Previous PCa/PSA GWAS Hits

3q23

141,133,450

ZBTB38R1

rs1991431

A/G

0.43

3.8

5.5 × 10−9

3.6

0.0011

3.7

2.5 × 10−11

S/N

8p21.2

23,466,984

SLC25A37R1

rs4614003

A/G

0.3

4.9

3.0 × 10−12

5.3

6.10 × 10−5

5

1.0 × 10−15

S/N

8q24.21

128,342,866

8q24/MYCR1

rs17464492

A/G

0.71

4.1

6.9 × 10−9

3.7

0.0055

4.0.

1.5 × 10−10

S*/N

10p12.1

28,094,419

ARMC4R1

rs2492906

G/C

0.79

4

3.2 × 10−7

3.0

0.0092

3.7

1.3 × 10−8

N/N

10q26.12

122,674,849

WDR11-FGFR2R1

rs200367988

A/G

0.33

5.9

1.2 × 10−17

3.0

0.0064

5.1

4.7 × 10−18

L*/L

10q26.13

123,185,303

WDR11-FGFR2R3

rs10749415

A/G

0.95

11.6

7.9 × 10−16

12.0

2.10 × 10−10

11.7

9.1 × 10−25

L/L

19q13.33

51,349,090

KLK3R4

rs266849

A/G

0.79

5.8

4.4 × 10−13

5.4

1.60 × 10−5

5.7

4.0 × 10−17

S/S

19q13.33

51,352,937

KLK3R3

rs266868

G/A

0.71

5.1

4.0 × 10−13

3.3

0.0034

4.6

1.4 × 10−14

L/S

19q13.33

51,354,397

KLK3R1

rs11665748

A/G

0.65

7.8

1.4 × 10−30

11.9

1.50 × 10−27

9

3.1 × 10−54

S/S

19q13.33

51,361,382

KLK3R2

rs61752561

G/A

0.97

18.6

1.4 × 10−24

10.2

0.011

17.2

2.4 × 10−25

L/L

19q13.33

51,373,279

KLK2R6

rs2739472

C/T

0.56

3.3

1.9 × 10−7

3.6

9.3 × 10−4

3.4

7.8 × 10−10

L*/L

19q13.33

51,380,110

KLK2R5

rs6070

T/A

0.65

4

4.9 × 10−9

6.8

1.20 × 10−9

4.8

4.2 × 10−16

L/S

Xp22.2

16,830,673

TXLNGR1

rs5969745

T/C

0.60

3.1

4.6 × 10−11

2.6

0.0012

3

2.7 × 10−13

N*/N

  1. L, previously identified locus; N, novel locus; NHW, non-Hispanic White; PCa, prostate cancer; PSA, prostate-specific antigen; S, previously identified SNP; SNP, single-nucleotide polymorphism.
  2. The replication samples for these conditional analyses are restricted to the other KP samples (that is, all KP samples except the non-Hispanic white non-cases). Listed SNPs have association P<5 × 10−8 in combined meta-analysis of all KP samples, P<5 × 10−7 in KP non-Hispanic white non-cases, and P<0.10 in Kaiser replication studies and with same direction of effect. A total of 23 conditional hits were tested for replication. Single nucleotide polymorphisms (SNPs) associated with prostate specific antigen (PSA) levels from conditional analyses that adjust for other significantly associated SNPs (Table 2). Full details of conditional models given in Supplementary Tables 1–3.
  3. *, ** Associated with PCa in our study adjusting for PSA: *P<0.00125, **0.00125<P<0.05.
  4. R1Conditional round 1, conditioning on: rs6662386, rs4951018, rs9306895, rs13395387, rs2556375, rs35350834, rs56935123, rs10023685, rs37004, rs74786629, rs6920449, rs10486567, rs13272392, rs12676621, rs10505477, rs6478343, rs59482735, rs116940348, rs10993994, rs10886902, rs4378355, rs12285347, rs11067228, rs202346, rs8023057, rs9921192, rs62046493, rs7213911, rs11263761, rs151059257, rs11084596, rs17632542, rs55891214, rs16980679, rs6627995, rs10855058, rs13441059.
  5. R2Conditional round 2: R1, rs111862174, rs1991431, rs906496, rs4614003, rs17464492, rs2492906, rs200367988, rs74922337, rs9596300, rs11665748, rs5969745.
  6. R3Conditional round 3: R2, rs58235267, rs4871796, rs4752569, rs66624999, rs61752561.
  7. R4Conditional round 4: R3, rs10749415, rs12429206, rs266868.
  8. R5Conditional round 5: R4, rs147520802, rs266849.
  9. R6Conditional round 6: R5, rs6070.
  10. †Change in log-transformed PSA per PSA-increasing allele.
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