Table 1 Summary statistics of identified rare coding variants.

From: Whole-genome sequencing reveals novel ethnicity-specific rare variants associated with Alzheimer’s disease

Variant

Allele 1/2

Gene

Stage (n)

No. of subjects

A1 frequency

*P

Case

Control

Case

Control

 

rs752176038

A/G

FAM126A

Discovery (933)

139

794

0.022

0.00063

6.12 × 10−5

   

Replication (2827)

1596

1231

0.0078

0.0069

1.00

   

Combined (3760)

1735

2025

0.0089

0.0044

0.032

rs537717672

T/C

ZFHX4

Discovery (927)

137

790

0.026

0.0019

1.09 × 10−4

   

Replication (2826)

1596

1230

0.0038

0.0061

0.24

   

Combined (3753)

1733

2020

0.0055

0.0045

0.62

rs17109924

C/T

LGR5

Discovery (932)

138

794

0.025

0.0019

1.10 × 10−4

   

Replication (2822)

1596

1226

0.0060

0.0045

0.58

   

Combined (3754)

1734

2020

0.0075

0.0035

0.024

rs11541286

C/T

ZFC3H1

Discovery (932)

138

794

0.025

0.0019

1.10 × 10−4

   

Replication (2829)

1599

1230

0.0059

0.0045

0.58

   

Combined (3761)

1737

2024

0.0075

0.0035

0.024

rs146006146

T/C

OR51G1

Discovery (933)

139

794

0.032

0.0044

1.28 × 10−4

   

Replication (2798)

1585

1213

0.0091

0.0054

0.036

   

Combined (3731)

1724

2007

0.011

0.0050

1.36 × 10−3

rs190260914

A/T

OR4X2

Discovery (933)

139

794

0.014

0

4.75 × 10−4

   

Replication (2822)

1596

1226

0.0038

0.0024

0.48

   

Combined (3755)

1735

2020

0.0046

0.0015

0.017

rs1470808145

G/C

ARHGEF4

Discovery (933)

139

794

0.014

0

4.75 × 10−4

   

Replication (2832)

1601

1231

0.0022

0.0028

0.79

   

Combined (3765)

1740

2025

0.0032

0.0017

0.24

rs749072077

T/C

PRUNE2

Discovery (933)

139

794

0.014

0

4.75 × 10−4

   

Replication (2829)

1601

1228

0.00062

0.0016

0.41

   

Combined (3762)

1740

2022

0.0017

0.00099

0.53

rs55867815

T/G

MLKL

Discovery (932)

138

794

0.029

0.0044

4.91 × 10−4

   

Replication (2827)

1598

1229

0.0084

0.011

0.41

   

Combined (3759)

1736

2023

0.010

0.0081

0.39

  1. Bold font indicates statistical significance in both datasets.
  2. A1 allele 1.
  3. *P values were obtained from Fisher’s exact tests.
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