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Table 3 Top associated markers based on imputed allelic frequencies

From: An empirical evaluation of imputation accuracy for association statistics reveals increased type-I error rates in genome-wide associations

SNP

CHR

Position

Empiric

Imputed

MAF(emp)

MAF(imp)

STATUS

rs2000816

11

84151075

0,2382

1,57E-30

0,50

0,49

Discordant

rs4143896

14

41379353

0,4551

1,06E-19

0,50

0,49

Discordant

rs4982270

14

34950569

0,0853

5,72E-17

0,50

0,49

Discordant

rs10152907

15

52679008

0,3110

2,30E-15

0,50

0,50

Discordant

rs12900200

15

99971327

0,0394

2,80E-15

0,49

0,49

Discordant

rs35143

16

63543734

0,8364

3,62E-15

0,50

0,49

Discordant

rs2572406

8

11129662

0,0291

6,78E-15

0,49

0,48

Discordant

rs2996005

1

217884996

0,0010

5,61E-14

0,48

0,48

Discordant

rs696891

5

60940318

0,4430

9,85E-14

0,50

0,49

Discordant

rs4506565

10

114746031

6,02E-13

1,38E-12

0,35

0,35

Concordant

  1. The column "Position" refers to the chromosomal position of the marker based on the reference genome (Hg18). The columns Empiric and Imputed organize the observed p values for the association with the diabetes phenotype based on directly genotyped and imputed allelic frequencies, respectively. The columns MAF(emp) and MAF(imp) refers to the minor allele frequency determined by allelic frequencies determined by direct genotyping (emp) and imputed (imp). The column STATUS describes if there is a concordance between association statistics based on allelic frequencies determined by both measures using a pre defined stringent significance threshold (10 -8).