Table 1 The five independent variants after meta-analysis in the discovery cohorts

From: Fine mapping the CETP region reveals a common intronic insertion associated to HDL-C

      

After meta-analysis

 

After GCTA analysis

Marker name

Chr

Position

EA

Type

Freq

βa

S.e. β

P value

Freq geno

β Ja

S.e. β j

P valueJ

rs12920974

16

56,993,025

T

SNP

0.271

−1.748

0.096

1.41E−74

0.281

−1.806

0.139

2.40E−38

rs34065661

16

56,995,935

G

SNP

0.058

7.203

0.560

7.04E−38

0.020

6.782

0.582

2.23E−31

rs5817082

16

56,997,349

CA

INDEL

0.285

−2.869

0.098

8.95E−187

0.305

−4.286

0.172

1.55E−137

rs4587963

16

56,997,369

A

SNP

0.240

−0.972

0.101

5.25E−22

0.261

−2.014

0.165

2.11E−34

rs7499892

16

57,006,590

T

SNP

0.209

−3.384

0.107

2.94E−218

0.245

−2.083

0.150

1.31E−43

  1. Abbreviations: EA, effect allele—the allele for which the effect on HDL-C is estimated; Freq, the frequency of reference allele in the discovery cohorts; Freqgeno, the frequency of the variant within the reference panel.
  2. aβ is the effect of the effect allele. βj is the effect of the effect allele after joint analysis of all selected variants by GCTA.
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