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. Author manuscript; available in PMC: 2019 Mar 1.
Published in final edited form as: Genet Epidemiol. 2017 Nov 26;42(2):146–155. doi: 10.1002/gepi.22093

Table 2.

Haplotypes and their frequencies used for conducting simulation studies in scenario where underlying causal SNP is untyped and is assumed to be imputed based on neighboring genotyped SNPs. “U” and “T” indicate the untyped and typed SNP positions, respectively.

MAF*=0.3, R2 = 0.8# MAF*=0.05, R2 = 0.5#
UTTTT Frequency UTTTT Frequency
10011 0.2530 00111 0.3800
10101 0.0128 01110 0.2350
10111 0.0342 01111 0.2900
00101 0.2374 11001 0.0456
00111 0.2233 11111 0.0044
01110 0.2393 00001 0.0450

MAF, minor allele frequency.

*

Minor allele frequency of the untyped causal SNP.

#

Obtained by fitting multivariate regression of genotype at the causal SNP on the genotypes of the neghboring SNPs.