Table 2 Associations with Individual Variants outside the APOE region

From: Whole exome sequencing study identifies novel rare and common Alzheimer’s-Associated variants involved in immune response and transcriptional regulation

  

ADSP Discovery Meta

All Replication (ADGC+CHARGE+ADES-FR+FinnAD)

Discovery + All Replication

Name

gene

MAC (EA/CH)

best P

Model (group)

MAC

P Model 1

P Model 2

P Model 0

P Model 1

P Model 2

6:41129252:C:T (R47H)

TREM2

120/0

4.8E-12

0 (EA)

224

1.6E-06

2.7E-06

3.2E-16

2.8E-10

1.6E-10

7:154988675:G:A

AC099552.4

10/0

1.2E-07

2 (EA)

0

NA

NA

1.3E-02

2.0E-07

1.2E-07

7:99971313:T:C (rs2405442)

PILRA

6,219/219

1.7E-07

0 (EA)

22,798

5.3E-05

2.3E-05

9.5E-10

1.1E-06

5.0E-07

20:62729814:C:T (rs148484121)

OPRL1

61/4

5.8E-07

1 (all)

111

3.4E-01

5.6E-01

3.7E-03

1.4E-04

4.5E-04

11:59940599:T:A (rs7232)

MS4A6A

7,540/258

7.7E-07

0 (all)

20,963

1.4E-11

3.1E-09

5.6E-17

3.8E-14

2.6E-11

17:44828931:G:A (rs199533)

NSF

4,238/135

1.3E-06

0 (all)

11,120

2.5E-01

1.4E-02

2.1E-04

1.6E-02

1.9E-04

14:106235767:C:T (rs77307099)

IGHG3

6,200/176

1.9E-06

0 (all)

721

4.0E-01

3.5E-01

1.4E-06

1.3E-04

7.9E-05

14:106235766:G:A (rs78376194)

IGHG3

6,202/176

1.9E-06

0 (all)

719

4.2E-01

3.6E-01

1.5E-06

1.4E-04

8.5E-05

6:15638035:C:T (rs77460377)

DTNBP1

16/3

1.9E-06

2 (all)

35

8.5E-01

8.7E-01

8.7E-02

5.2E-03

3.0E-03

6:33041297:G:A (rs112178281)

HLA-DPA1

10/0

2.9E-06

1 (EA)

6

7.5E-01

9.2E-01

1.4E-01

2.1E-05

2.0E-05

11:59945745:T:C (rs12453)

MS4A6A

8,265/258

3.2E-06

0 (EA)

23,420

4.7E-11

3.0E-08

1.4E-15

6.0E-13

1.2E-09

3:195506101:T:A

MUC4

38/6

3.8E-06

1 (all)

0

NA

NA

3.0E-04

3.8E-06

8.1E-06

10:88446985:T:C (rs76615432)

LDB3

760/62

5.0E-06

1 (CH)

2,303

5.3E-01

5.9E-01

7.0E-01

6.3E-01

6.4E-01

19:1047507:AGGAGCAG:A

ABCA7

67/0

4.3E-06

0 (EA)

11

8.8E-02

9.7E-02

2.4E-04

1.6E-02

1.7E-02

14:106236128:T:A (rs12890612)

IGHG3

6,395/369

4.5E-06

0 (all)

1,473

8.5E-02

7.5E-02

9.8E-07

8.0E-05

6.4E-05

7:99799845:T:A (rs104395)

STAG3

5,248/248

5.5E-06

0 (EA)

15,948

3.0E-03

1.2E-03

8.8E-07

1.2E-04

4.0E-05

  1. Table shows variants with P < 6.1 × 10−6 in EA, CH, or combined strata in the discovery sample. Exome-wide significant results (P < 3.1 × 10−7) and suggestive results which improved in meta analysis of discovery + replication data are highlighted in bold. Results without variation data in the replication datasets are indicated in italics
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