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Table 2 Cross-population association results.

From: In search of causal variants: refining disease association signals using cross-population contrasts

 

EA SAMPLE ONLY

AA SAMPLE ONLY

PRIMARY ANALYSIS OF THE COMBINED SAMPLE

SNP

p-value1

Odds ratio

(95%

confidence

interval)

p-value1

Odds ratio

(95%

confidence

interval)

Primary2

p-value

EA

Population

-specific

odds

ratio3

AA

Population

-specific

odds

ratio3

P-value,

population-by

-genotype term

(heterogeneity)

rs17483548

        

rs17405217

        

rs17483721

        

rs2656052

0.0147

0.71 (0.539, 0.935)

0.9737

1.004 (0.793, 1.272)

0.04656

0.7074

1.0008

0.06031

rs7181486

        

rs17483929

        

rs17484235

        

rs9788721

0.0031

0.662 (0.505, 0.870)

0.4084

1.108 (0.868, 1.415)

0.008229

0.6619

1.1045

0.005783

rs8034191

0.0052

0.679 (0.518, 0.891)

0.7846

1.046 (0.756, 1.449)

0.01903

0.6797

1.0389

0.04839

rs10519203

0.0035

0.667 (0.509, 0.875)

0.8629

1.022 (0.795, 1.315)

0.01312

0.6679

1.0208

0.02396

rs8031948

        

rs931794

        

rs2036527

0.0062

0.683 (0.520, 0.897)

0.5081

0.906 (0.677, 1.213)

0.01797

0.6837

0.9048

0.1676

rs17486278

0.0032

0.663 (0.504, 0.871)

0.3669

0.884 (0.676, 1.155)

0.007876

0.6616

0.8848

0.1356

rs7180002

        

rs951266

0.0051

0.677 (0.515, 0.890)

0.8252

0.952 (0.617, 1.469)

0.01777

0.6761

0.9512

0.1894

rs16969968

0.0033

0.664 (0.505, 0.873)

0.2397

0.729 (0.430, 1.235)

0.006299

0.6636

0.7313

0.7479

rs1051730

0.0036

0.666 (0.507, 0.876)

0.6663

0.913 (0.604, 1.380)

0.01135

0.6636

0.9149

0.2016

rs1317286

0.0044

0.675 (0.515, 0.884)

0.9011

0.982 (0.736, 1.311)

0.01586

0.6745

0.9830

0.06096

rs12914385

        

rs17487223

        
  1. The SNPs correlated with rs16969968 on chromosome 15 (r2 ≥ 0.8 in HapMap CEU) are sorted by genomic position. The heterogeneity test results are given in the rightmost column.
  2. 1One-degree of freedom test as described in methods.
  3. 2 Two-degree of freedom test as described in methods.
  4. 3 Population-specific odds ratio for the effect of one copy of the minor allele, from the combined analysis as defined in the methods.