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. 2011 Mar 11;88(3):294–305. doi: 10.1016/j.ajhg.2011.02.002

Table 2.

Estimated Genetic Variance in the Observed Scale Explained by All SNPs for Two Control Samples in the WTCCC Data

Thresholda No. SNPb Estimatec(SE) LRd p valuee
MAF > 0.01

200 309,040 0.17 (0.11) 2.29 0.07
20 297,198 0.13 (0.11) 1.31 0.13
7 266,534 0.08 (0.11) 0.59 0.22
4 226,165 0.06 (0.11) 0.29 0.30

MAF > 0.05

200 278,564 0.19 (0.11) 3.42 0.03
20 267,043 0.16 (0.10) 2.33 0.06
7 239,614 0.12 (0.10) 1.33 0.12
4 203,698 0.09 (0.10) 0.92 0.17
a

Excluding SNPs with more than the listed number of missing genotypes. Two hundred missing genotypes are approximately equal to a missingness rate of 5% (depending on sample size).

b

After filtering on the basis of SNP missing rate.

c

Estimate of genetic variance proportional to the total phenotypic variance on the observed scale.

d

Likelihood-ratio test statistic.

e

p values were calculated assuming that the LR is distributed as a 50:50 mixture of zero and χ12 under the null hypothesis.