Table 1 Summary of association analysis results with an X-chromosome-wide significant signal.

From: X‐chromosome-wide association study for Alzheimer’s disease

        

Main analysis

Sex-adjusted

Varianta

Model

Meta-analysis

Positionb

Genec

Inactivation statusd

Minor/major allele

MAFe

ORf

95% CI

p value

I2

ORf

95% CI

p value

I2

Common variants (MAF > 0.01)

 rs4364769

r-XCI

AD-proxy

5,462,201

NLGN4X (Xp22.32)

Variable

T/G

0.12

1.079

1.048–1.110

2.55 × 10−7

0

1.074

1.043–1.107

1.52 × 10−6

0.0

 rs5933929

11,916,372

FRMPD4

Inactive

C/A

0.38

0.952

0.935–0.970

1.98 × 10−7

0

0.951

0.933–0.969

2.01 × 10−7

0.0

 rs5972406

excluding biobanks

31,546,147

DMD

Inactive

A/G

0.08

1.143

1.083–1.207

1.16 × 10−6

0

1.131

1.066–1.200

4.38 × 10−5

0.0

 rs191195705

AD-proxy

122,643,733

GRIA3 (Xq25)

NA

A/C

0.11

0.925

0.896–0.954

7.09 × 10−7

12.3

0.922

0.894–0.952

6.71 × 10−7

10.5

Rare variants (MAF ≤ 0.01)

 rs189139822

r-XCI

AD-Diagnosed

54,307,465

WNK3

Inactive

A/G

9.70 × 10−3

1.481

1.263–1.735

1.29 × 10−6

0

1.475

1.251–1.739

3.67 × 10−6

29.7

e-XCI

9.10 × 10−3

1.343

1.192–1.513

1.20 × 10−6

15.2

    

 rs771148434

r-XCI

AD-proxy

69,290,372

PJA1

Inactive

G/A

8.00 × 10−4

3.107

1.967–4.910

1.18 × 10−6

0

3.185

1.986–5.109

1.54 × 10−6

0.0

 rs1326297223

AD-Diagnosed

86,293,721

DACH2

Variable

A/T

2.10 × 10−3

2.281

1.629–3.192

1.56 × 10−6

0

2.642

1.758–3.970

2.91 × 10−6

0.0

  1. p values are two-sided raw p values derived from a fixed-effect meta-analysis.
  2. CI confidence interval, OR odds ratio, MAF minor allele frequency.
  3. aReference single-nucleotide polymorphism (SNP) (rs) number, according to dbSNP build 153.
  4. bGRCh38 assembly.
  5. cNearest protein-coding gene according to GENCODE release 45.
  6. dFrom Tukiainen et al. [13].
  7. eWeighted average MAF across all discovery studies.
  8. fApproximate OR calculated with respect to the minor allele.
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