Cohen’s h for detection of disease association with rare genetic variants

BMC Genomics

Table 5 Proportions of SNPs with mild, moderate, and large effect for CAD GWAS data

Type of	No. of	Mild effect (%)		Moderate effect (%)		Large effect (%)
SNPs	SNPs	OR	Cohen’s h	OR	Cohen’s h	OR	Cohen’s h
Common	360839	99.453	99.936	0.546	0.063	0.001	0.001
Rare	52220	69.772	73.416	23.932	26.505	6.296	0.079

The respective thresholds of ORs for mild, moderate and large effect at common SNPs were |log(OR)|≦log(1.2), log(1.2) < |log(OR)|≦log(1.5), and |log(OR)| > log(1.5), whereas Cohen’s h had respective thresholds of |h|≦0.075, 0.075 < |h|≦0.15, and |h| > 0.15. The respective thresholds of ORs for mild, moderate and large effect at rare SNPs were |log(OR)|≦log(1.5), log(1.5) < |log(OR)|≦log(2), and |log(OR)| > log(2), whereas Cohen’s h had respective thresholds of |h|≦0.05, 0.05 < |h|≦0.1, and |h| > 0.1.

ISSN: 1471-2164