Validation of genotype imputation in Southeast Asian populations and the effect of single nucleotide polymorphism annotation on imputation outcome

Table 1 Squared correlation of allele frequencies and chi-square P-values from SNPs in different regions

Region	Squared correlation (r²) of minor allele frequency		Squared correlation (r²) p-value from chi-square
Region	Before post-imputation QC	After post-imputation QC	Before post-imputation QC	After post-imputation QC
Coding region	0.868	0.997	0.387	0.813
Complex region	0.817	0.991	0.267	0.782
Intergenic region	0.864	0.996	0.328	0.789
Intron region	0.863	0.995	0.340	0.784
UTR region	0.830	0.991	0.303	0.756

ISSN: 1471-2350