Table 2 Association of SNPs in the 9p21.3 locus* with BCP-ALL in HAs and AAs.

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

SNP (rsID)

Position (bp) †

LD ( r2) by population*

HA (NA>10% and NA>YRI)‡ (391 cases and 1,008 controls)

AA (YRI>70%) § (203 cases and 1,363 controls)

  

EUR ‖

MXL

ASW #

OR (95% CI) **

P HA value

OR (95% CI) **

P AA value

      

Unconditional ††

Conditional ‡‡

 

Unconditional ††

Conditional ‡‡

rs78545330

21,995,941

0.77

0.83

0.28

1.51 (1.09–2.09)

0.014

0.014

1.18 (0.92–1.50)

0.185

0.255

rs2811712

21,998,035

0.69

0.83

0.28

1.48 (1.16–1.80)

0.017

0.018

1.15 (0.90–1.40)

0.276

0.329

rs3218018

21,998,139

0.79

0.83

0.86

1.54 (1.08–2.20)

0.017

0.030

1.13 (0.79–1.60)

0.512

0.404

rs3218007

21,999,800

0.77

0.83

0.28

1.47 (1.06–2.03)

0.021

0.023

1.14 (0.89–1.46)

0.288

0.347

rs3218005

22,000,247

0.77

0.83

0.28

1.51 (1.09–2.09)

0.014

0.014

1.14 (0.89–1.47)

0.285

0.342

rs3218002

22,000,841

0.77

0.83

0.28

1.49 (1.08–2.06)

0.016

0.014

1.15 (0.90–1.48)

0.253

0.315

rs2069426

22,006,273

0.79

0.83

0.86

1.51 (1.06–2.16)

0.024

0.035

1.16 (0.82–1.64)

0.409

0.333

rs974336

22,006,348

0.77

0.83

0.30

1.48 (1.07–2.05)

0.017

0.014

1.11 (0.87–1.42)

0.391

0.477

rs2069422

22,008,026

0.70

0.83

0.86

1.47 (1.12–1.82)

0.028

0.042

1.28 (0.92–1.64)

0.179

0.157

rs77920300

22,012,441

0.79

0.83

0.93

1.50 (1.05–2.14)

0.025

0.036

1.12 (0.79–1.58)

0.529

0.401

rs116729641

22,025,432

0.79

0.83

0.86

1.48 (1.04–2.12)

0.029

0.043

1.12 (0.79–1.58)

0.537

0.409

rs77284052

22,025,885

0.79

0.83

0.93

1.48 (1.04–2.12)

0.029

0.043

1.12 (0.79–1.58)

0.533

0.406

rs598664

22,027,551

0.70

0.83

0.93

1.44 (1.02–2.05)

0.038

0.057

1.10 (0.78–1.56)

0.580

0.437

rs662463

22,030,438

0.70

0.83

0.58

1.45 (1.03–2.06)

0.034

0.051

1.55 (1.16–2.06)

0.003

0.002

rs79985856

22,033,824

0.79

0.83

0.93

1.50 (1.05–2.14)

0.026

0.039

1.14 (0.81–1.62)

0.450

0.332

rs79182326

22,034,267

0.69

0.70

0.93

1.41 (1.00–2.00)

0.049

0.073

1.15 (0.81–1.63)

0.425

0.297

rs76213463

22,040,839

0.79

0.83

0.93

1.50 (1.05–2.15)

0.025

0.036

1.17 (0.83–1.63)

0.364

0.292

rs80166549

22,041,155

0.79

0.83

0.93

1.51 (1.05–2.15)

0.024

0.035

1.14 (0.81–1.59)

0.454

0.379

rs1333035

22,044,059

0.69

0.83

0.32

1.41 (1.02–1.94)

0.037

0.032

1.10 (0.87–1.41)

0.427

0.505

rs1333034

22,044,122

0.70

0.83

0.93

1.48 (1.05–2.10)

0.026

0.039

1.12 (0.80–1.57)

0.500

0.413

rs17694555

22,051,295

0.78

0.83

0.11

1.71 (1.31–2.11)

0.008

0.015

1.79 (0.33–3.25)

0.430

0.386

rs17756311

22,053,895

0.77

0.83

1

1.43 (0.99–2.05)

0.055

0.076

1.05 (0.75–1.49)

0.766

0.665

rs74655961

22054164

0.77

0.83

1

1.46 (1.01–2.10)

0.041

0.058

1.14 (0.82–1.60)

0.430

0.355

rs17694572

22,054,356

0.77

0.83

1

1.46 (1.02–2.10)

0.041

0.058

1.11 (0.80–1.56)

0.528

0.445

rs77728904

22,057,530

—

—

—

1.76 (1.21–2.57)

0.003

0.005

1.16 (0.82–1.64)

0.403

0.281

rs115574830

22,059,061

0.87

1

1

1.70 (1.17–2.48)

0.005

0.007

1.26 (0.90–1.76)

0.186

0.120

  1. AA, African Americans; ASW, AA ancestry; BCP-ALL, B-cell precursor acute lymphoblastic leukaemia; CI, confidence interval; EUR, European ancestry; HA, Hispanic Americans; LD, linkage disequilibrium; MXL, Hispanic ancestry; NA, Native Americans; OR, odds ratio; SNP, single-nucleotide polymorphism.
  2. Highlighted are SNPs with the smallest P-values for each stage of the analysis (see Table 1 legend). rs662463 is the only SNP significantly associated with BCP-ALL in AAs (bold).
  3. *Correlation (r2) with rs77728904 in individuals of EUR, MXL and ASW in 1,000 Genomes Phase 1 (ref. 17).
  4. †Physical positions on chromosome 9 are from NCBI build 37/hg19.
  5. ‡HA ancestry defined as >10% NA with % of NA>YRI (African ancestry).
  6. §AA ancestry defined as >70% YRI ancestry.
  7. ‖SNPs in LD (r2>0.60) with rs77728904 and present in the discovery, replication and multi-ethnic analyses.
  8. 1,000 Genomes population of Mexican ancestry from Los Angeles, CA, used as a proxy for HA ancestry.
  9. #1,000 Genomes population of African ancestry in Southwest USA, used as a proxy for AA ancestry.
  10. **OR with 95%CI.
  11. ††Unconditional P-values for listed SNPs.
  12. ‡‡P-values for listed SNPs when conditioned on rs3731217.
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