Table 2 Independent genome-wide significant loci. Independent SNPs, which had genome-wide significant associations with a Biomarker PC in either main effect, sex-stratified or sex interaction models. See also Supplementary Tables for fine-mapping and replication analyses of the PC5 signal near GRIN2D

Tau pathology/Degeneration (PC1)

 rs140169162

17:30886881

Intron

MYO1D

G

0.98

0.69

0.64

0.19

8.6E−04

−0.02

0.26

9.4E−01

1.61

0.30

4.9E−08

0.84

0.23

3.0E−04

Aβ Pathology (PC2)

 rs1638675

10:119178376

Intergenic

-

A

0.57

0.89

−0.08

0.05

7.1E−02

−0.33

0.07

1.0E−06

0.18

0.06

4.2E−03

0.50

0.09

3.5E−08

 rs12972156

19:45387459

Intron

APOE

C

0.74

0.98

0.43

0.05

9.5E−20

0.46

0.07

6.9E−11

0.39

0.07

2.3E−09

−0.04

0.09

6.5E−01

 rs157582

19:45396219

Intron

APOE

C

0.65

1.00

0.37

0.04

9.5E−18

0.40

0.06

2.6E−10

0.33

0.06

3.5E−08

−0.05

0.09

5.6E−01

 rs10119

19:45406673

3′-UTR

APOE

G

0.60

0.95

0.34

0.04

6.4E−15

0.43

0.06

4.9E−11

0.29

0.06

2.6E−06

−0.12

0.09

1.5E−01

 rs429358

19:45411941

Exon

APOE

T

0.70

0.99

0.50

0.04

1.3E−29

0.55

0.06

1.2E−17

0.44

0.06

4.3E−12

−0.09

0.09

3.0E−01

 rs75627662

19:45413576

Intergenic

APOE

C

0.71

0.98

0.35

0.05

1.2E−13

0.38

0.07

4.4E−08

0.31

0.07

2.7E−06

−0.05

0.09

6.2E−01

 rs157595

19:45425460

Intergenic

APOE

A

0.33

0.96

0.28

0.05

1.6E−09

0.28

0.07

7.1E−05

0.24

0.06

2.3E−04

0.00

0.09

9.8E−01

 rs111789331

19:45427125

Intergenic

APOE

T

0.73

0.95

0.45

0.05

8.3E−21

0.46

0.07

1.7E−10

0.45

0.07

1.6E−11

0.02

0.09

8.0E−01

Injury/Inflammation (PC3)

 rs114211800

5:158973225

Intron

LOC105377684

G

0.98

0.91

−0.74

0.17

7.2E−06

−1.23

0.22

1.7E−08

−0.11

0.26

6.9E−01

1.07

0.34

1.5E−03

 rs2302634

7:12270770

Intron

TMEM106B

T

0.58

1.00

0.26

0.04

1.3E−09

0.34

0.06

3.2E−08

0.18

0.06

2.9E−03

−0.16

0.09

6.2E−02

 rs56194026

15:74831534

Intergenic

ARID3B

C

0.92

0.90

−0.03

0.08

7.2E−01

−0.50

0.12

1.6E−05

0.41

0.12

5.3E−04

0.90

0.16

4.7E−08

Non-AD Inflammation (PC4)

 rs7551263

1:203150756

Intron

CHI3L1

T

0.84

0.99

−0.33

0.06

6.0E−09

−0.30

0.08

8.7E−05

-0.40

0.09

3.1E−06

0.07

0.12

5.5E−01

 rs10399931

1:203156080

Intergenic

CHI3L1

T

0.24

0.98

−0.39

0.05

5.7E−17

−0.36

0.07

2.7E−07

−0.45

0.07

1.0E−11

−0.12

0.09

1.9E−01

 rs12670437

7:76390507

Intergenic

-

G

0.98

0.87

−0.49

0.15

9.9E−04

−1.20

0.22

2.4E−08

0.20

0.21

3.3E−01

1.24

0.32

1.2E−04

 rs145791381

9:24796757

Intergenic

-

T

0.98

0.93

−1.01

0.18

2.7E−08

−1.27

0.21

2.7E−09

−0.41

0.36

2.6E−01

NA

NA

NA

 rs16974493

13:110307768

Intergenic

-

T

0.97

0.98

0.59

0.14

1.5E−05

0.18

0.22

4.2E−01

0.97

0.17

2.2E−08

0.77

0.27

5.2E−03

 rs150326618

14:52641990

Intergenic

-

G

0.98

0.80

0.57

0.17

9.8E−04

0.09

0.24

7.2E−01

1.39

0.25

2.6E−08

1.13

0.35

1.3E−03

Non-AD Synaptic Functioning (PC5)

 rs275844

19:48884949

Intergenic

GRIN2D

G

0.88

0.93

−0.30

0.07

9.6E−06

−0.39

0.10

4.0E−05

−0.20

0.10

4.2E−02

0.22

0.14

1.1E−01

 rs8111684

19:48947326

3′-UTR

GRIN2D

G

0.26

1.00

0.19

0.05

9.8E−05

0.24

0.07

8.4E−04

0.12

0.07

7.9E−02

0.11

0.10

2.9E−01

 rs3107911

19:48964305

Intron

GRIN2D

C

0.15

0.96

0.31

0.06

5.0E−07

0.38

0.09

8.7E−06

0.21

0.09

2.0E−02

0.17

0.13

1.7E−01