Table 1 Potential causal variants in APOE and the surrounding region identified by CAVIAR analysis

From: Non-coding variability at the APOE locus contributes to the Alzheimer’s risk

SNP

BP

Gene

EA

Beta

SE

Z-value

p-value

TF binding

EAF in NC (Mainland/HK/ADNI/ADC/LOAD)

rs11668861

19:45380970

PVRL2

T

−0.39

0.12

−3.28

1.0E−03

Yes

0.78/0.79/0.55/0.53/0.54

rs6859

19:45382034

PVRL2

G

−0.40

0.11

−3.54

3.9E−04

Yes

0.69/0.71/0.43/0.42/0.42

rs3852860

19:45382966

PVRL2

T

−0.36

0.12

−3.03

2.4E−03

Yes

0.76/0.77/0.59/0.58/0.59

rs3852861

19:45383061

PVRL2

T

−0.34

0.12

−2.87

4.1E−03

Yes

0.76/0.77/0.59/0.58/0.59

rs429358

19:45411941

APOE

C

0.91

0.14

6.44

1.2E−10

No

0.11/0.11/0.14/0.14/0.21

rs12721046

19:45421254

APOC1

A

0.87

0.14

6.44

1.2E−10

No

0.13/0.09/0.13/0.13/0.17

rs12721051

19:45422160

APOC1

G

0.87

0.14

6.43

1.3E−10

Yes

0.13/0.09/0.17/0.17/0.22

rs56131196

19:45422846

APOC1

A

0.87

0.14

6.45

1.1E−10

No

0.13/0.09/0.19/0.17/0.22

rs4420638

19:45422946

APOC1

G

0.85

0.13

6.34

2.4E−10

No

0.13/0.09/0.19/0.17/0.22

  1. Note: CAVIAR analysis results for the major causal variants, defined as a posterior probability ≥ 10%, with a summary for variants frequency in normal control participants from each studied cohort. Regions with transcription factor-binding events annotated by the ENCODE database are marked as “yes” in the “TF binding” column. The last column displayed the effective allele frequencies of corresponding variants in the normal control populations of given cohorts accordingly
  2. BP base position in GRCh37 annotation, Gene nearest genes, EA effect allele, Beta effect size, SE standard error, TF transcription factor, EAF effect allele frequency, NC normal controls
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