Table 1 Association of SNPs in the 9p21.3 locus* with BCP-ALL in individuals of European ancestry.

From: A variant at 9p21.3 functionally implicates CDKN2B in paediatric B-cell precursor acute lymphoblastic leukaemia aetiology

SNP rsID †

Position (bp) ‡

LD ( r2)§

Alleles ‖

Discovery meta-analysis (1,210 cases and 4,144 controls)

Replication (977 cases and 1,399 controls)

Combined

    

OR (95% CI)*

P -value

P het

I2 (%)#

OR (95% CI)*

P -value

OR (95% CI)*

P -value

     

Unconditional **

Conditional ††

   

Unconditional **

Conditional ††

 

Unconditional **

Conditional ††

rs78545330

21,995,941

0.77

A/T

1.58 (1.34–1.86)

6.04 × 10−8

1.06 × 10−6

0.480

0

1.57 (1.31–1.89)

1.19 × 10−6

1.84 × 10−5

1.58 (1.39–1.78)

3.44 × 10−13

8.37 × 10−11

rs2811712

21,998,035

0.69

G/A

1.43 (1.22–1.68)

8.91 × 10−6

1.09 × 10−4

0.202

37.5

1.52 (1.34–1.69)

3.89 × 10−6

7.60 × 10−5

1.47 (1.31–1.65)

1.66 × 10−10

3.40 × 10−8

rs3218018

21,998,139

0.79

G/T

1.59 (1.34–1.88)

9.39 × 10−8

1.42 × 0−6

0.548

0

1.58 (1.31–1.91)

1.74 × 10−6

4.76 × 10−5

1.59 (1.40–1.80)

7.68 × 10−13

2.85 × 10−10

rs3218007

21,999,800

0.77

T/C

1.57 (1.33–1.84)

9.04 × 10−8

1.49 × 10−6

0.498

0

1.57 (1.31–1.88)

1.37 × 10−6

2.23 × 10−5

1.57 (1.39–1.77)

5.86 × 10−13

1.42 × 10−10

rs3218005

22,000,247

0.77

C/T

1.57 (1.33–1.84)

9.05 × 10−8

1.50 × 10−6

0.498

0

1.57 (1.31–1.88)

1.37 × 10−6

2.23 × 10−5

1.57 (1.39–1.77)

5.87 × 10−13

1.42 × 10−10

rs3218002

22,000,841

0.77

A/G

1.57 (1.33–1.85)

8.65 × 10−8

1.45 × 10−6

0.491

0

1.57 (1.31–1.88)

1.37 × 10−6

2.23 × 10−5

1.57 (1.39–1.77)

5.62 × 10−13

1.38 × 10−10

rs2069426

22,006,273

0.79

T/G

1.59 (1.34–1.88)

9.47 × 10−8

1.42 × 10−6

0.545

0

1.58 (1.31–1.90)

2.23 × 10−6

5.85 × 10−5

1.58 (1.39–1.80)

9.93 × 10−13

3.52 × 10−10

rs974336

22,006,348

0.77

T/C

1.57 (1.33–1.85)

7.67 × 10−8

1.25 × 10−6

0.514

0

1.60 (1.33–1.92)

4.18 × 10−7

7.52 × 10−6

1.58 (1.40–1.79)

1.58 × 10−13

4.17 × 10−11

rs2069422

22,008,026

0.70

G/T

1.44 (1.22–1.69)

1.33 × 10−5

1.45 × 10−4

0.240

30.0

1.52 (1.33–1.70)

6.53 × 10−6

1.91 × 10−4

1.47 (1.30–1.66)

4.02 × 10−10

1.05 × 10−7

rs77920300

22,012,441

0.79

T/C

1.60 (1.35–1.89)

4.26 × 10−8

6.50 × 10−7

0.583

0

1.57 (1.30–1.89)

2.43 × 10−6

6.26 × 10−5

1.59 (1.40–1.80)

4.95 × 10−13

1.78 × 10−10

rs116729641

22,025,432

0.79

A/G

1.61 (1.36–1.90)

2.84 × 10−8

4.49 × 10−7

0.614

0

1.57 (1.30–1.89)

2.31 × 10−6

5.83 × 10−5

1.59 (1.40–1.80)

3.16 × 10−13

1.17 × 10−10

rs77284052

22,025,885

0.79

T/C

1.61 (1.36–1.90)

2.82 × 10−8

4.46 × 10−7

0.618

0

1.57 (1.30–1.89)

2.31 × 10−6

5.83 × 10−5

1.59 (1.40–1.80)

3.14 × 10−13

1.16 × 10−10

rs598664

22,027,551

0.70

C/T

1.46 (1.25–1.72)

3.46 × 10−6

4.19 × 10−5

0.287

19.9

1.51 (1.26–1.81)

7.91 × 10−6

2.21 × 10−4

1.48 (1.32–1.67)

1.21 × 10−10

3.47 × 10−8

rs662463

22,030,438

0.70

A/G

1.46 (1.24–1.71)

3.71 × 10−6

4.43 × 10−5

0.288

19.7

1.50 (1.25–1.79)

1.16 × 10−5

3.03 × 10−4

1.48 (1.31–1.66)

1.87 × 10−10

4.97 × 10−8

rs79985856

22,033,824

0.79

T/C

1.61 (1.37–1.91)

2.03 × 10−8

3.29 × 10−7

0.657

0

1.56 (1.30–1.89)

2.86 × 10−6

7.22 × 10−5

1.59 (1.41–1.80)

2.84 × 10−13

1.08 × 10−10

rs79182326

22,034,267

0.69

T/C

1.45 (1.24–1.70)

4.30 × 10−6

5.47 × 10−5

0.303

16.3

1.45 (1.21–1.73)

4.72 × 10−5

1.00 × 10−3

1.45 (1.29–1.63)

8.33 × 10−10

1.96 × 10−7

rs76213463

22,040,839

0.79

A/G

1.62 (1.37–1.91)

1.68 × 10−8

2.76 × 10−7

0.636

0

1.56 (1.29–1.88)

3.70 × 10−6

8.62 × 10−5

1.59 (1.40–1.80)

3.08 × 10−13

1.11 × 10−10

rs80166549

22,041,155

0.79

G/A

1.62 (1.37–1.91)

1.67 × 10−8

2.74 × 10−7

0.635

0

1.56 (1.29–1.88)

3.70 × 10−6

8.62 × 10−5

1.59 (1.40–1.80)

3.06 × 10−13

1.10 × 10−10

rs1333035

22,044,059

0.69

G/A

1.46 (1.25–1.71)

1.78 × 10−6

2.50 × 10−5

0.238

30.2

1.50 (1.26–1.78)

6.87 × 10−6

1.42 × 10−4

1.48 (1.31–1.66)

5.45 × 10−11

1.36 × 10−8

rs1333034

22,044,122

0.70

C/T

1.47 (1.25–1.72)

2.93 × 10−6

3.58 × 10−5

0.307

15.3

1.50 (1.26–1.80)

9.04 × 10−6

2.34 × 10−4

1.48 (1.32–1.67)

1.17 × 10−10

3.14 × 10−8

rs17694555

22,051,295

0.78

G/A

1.61 (1.35–1.92)

1.61 × 10−7

2.24 × 10−6

0.458

0

1.59 (1.40–1.78)

1.85 × 10−6

4.28 × 10−5

1.60 (1.41–1.82)

1.40 × 10−12

4.08 × 10−10

rs17756311

22,053,895

0.77

A/G

1.63 (1.37–1.94)

3.95 × 10−8

7.00 × 10−7

0.531

0

1.57 (1.30–1.90)

2.92 × 10−6

5.74 × 10−5

1.60 (1.41–1.82)

5.66 × 10−13

1.81 × 10−10

rs74655961

22,054,164

0.77

G/A

1.64 (1.38–1.95)

2.90 × 10−8

5.16 × 10−7

0.557

0

1.55 (1.28–1.87)

5.85 × 10−6

1.11 × 10−4

1.60 (1.40–1.82)

8.63 × 10−13

2.71 × 10−10

rs17694572

22,054,356

0.77

A/G

1.63 (1.37–1.94)

2.89 × 10−8

4.98 × 10−7

0.526

0

1.54 (1.28–1.87)

6.87 × 10−6

1.28 × 10−4

1.59 (1.40–1.81)

1.01 × 10−12

3.02 × 10−10

rs77728904

22,057,530

—

C/A

1.71 (1.42–2.05)

1.02 × 10−8

1.25 × 10−7

0.687

0

1.74 (1.42–2.12)

6.28 × 10−8

1.59 × 10−6

1.72 (1.50–1.97)

3.32 × 10−15

9.34 × 10−13

rs115574830

22,059,061

0.87

A/T

1.61 (1.35–1.92)

7.09 × 10−8

8.60 × 10−7

0.574

0

1.55 (1.28–1.88)

8.34 × 10−6

1.38 × 10−4

1.58 (1.39–1.80)

2.83 × 10−12

5.32 × 10−10

  1. AA, African American; BCP-ALL, B-cell precursor acute lymphoblastic leukaemia; CI, confidence interval; GWAS, genome-wide association study; LD, linkage disequilibrium; OR, odds ratio; SNP, single-nucleotide polymorphism.
  2. Highlighted are SNPs with the smallest P-values for each part of the analysis (rs77728904 in blue for the discovery GWAS, the replication analysis and the combined analysis; rs662463 in green for AA in the multi-ethnic analysis).
  3. *OR with 95% CI.
  4. †SNPs in LD (r2EUR>0.60 in 1,000 Genomes Phase 1 (ref. 17) from HaploReg24) with rs77728904 (rs115939893 and rs72654280 were not included, because they were not present in the replication and multi-ethnic analyses; all SNPs in r2EUR>0.2 are listed in Supplementary Table 4).
  5. ‡Physical positions on chromosome 9 are from NCBI build 37/hg19.
  6. §LD (r2) with the index SNP (rs77728904).
  7. ‖Minor/major allele.
  8. Cochran’s test of heterogeneity in the studies comprising the discovery meta-analysis.
  9. #Percentage of variation in the meta-analysis due to heterogeneity.
  10. **Unconditional P-values for listed SNPs.
  11. ††P values for listed SNPs when conditioned on rs3731217.
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