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Table 2 APOE Haplotypes formed by three variants and their association with AD

From: ApoE variant p.V236E is associated with markedly reduced risk of Alzheimer’s disease

APOE Haplotype†

rs429358

rs7412

rs199768005

rs769452

Minor allele frequency (%)

Logistic regression*

p.C112R

p.R158C

p.V236E

p.L28P

Univariate

Multivariate

Base

AA

Base

AA

Base

AA

Base

AA

AD

CON

OR

P

OR

P

ϵ2 allele

T

Cys

t

Cys

T

Val

T

Leu

3.15%

8.50%

0.35 (0.30-0.40)

<2x10−16

0.46 (0.38-0.54)

<2x10−16

ϵ3a allele

T

Cys

C

Arg

T

Val

T

Leu

58.0%

79.0%

0.35 (0.32-0.37)

<2x10−16

1.00 (REF)

REF

ϵ3b allele

T

Cys

C

Arg

c

Glu

T

Leu

0.024%

0.23%

0.11 (0.02-0.36)

2.32x10−03

0.10 (0.02-0.35)

2.16x10−03

ϵ4a allele

C

Arg

C

Arg

T

Val

T

Leu

37.4%

12.3%

5.00 (4.52-5.50)

<2x10−16

4.80 (4.35-5.30)

<2x10−16

ϵ4b allele

C

Arg

C

Arg

T

Val

c

Pro

0.62%

0.26%

2.49 (1.45-4.41)

1.17x10−03

0.91 (0.51-1.66)

0.75

  1. Alleles in uppercase denote a major allele, alleles in lower case denote a minor allele.
  2. *Logistic regression models corrected for sex and age-at-diagnosis, and assume an additive effect.
  3. † Haplotype phasing showed that the minor allele of rs199768005 (p.V236E) is in phase (D’ = 1) with the major alleles at rs429358 and rs7412, indicating that it occurs on the ϵ3 backbone thereby subdividing the ϵ3 haplotype into APOE ϵ3b (minor allele of rs199768005) and APOE ϵ3a (major allele of rs199768005). rs769452 (p.L28P) subdivides ϵ4 into APOE ϵ4b (minor allele of rs769452) and APOE ϵ4a (major allele of rs769452).