Table 2 Independent loci identified by cortical PAM GWAS

From: Neuropathological correlates and genetic architecture of microglial activation in elderly human brain

PAM region

Ch

Lead SNP

SNP position

A1

A2

Freq (A1)

Beta (A1)

P-value

Genes mapped to locus (combined positional and/or eQTL mapping)

MF

1

rs2997325

83641424

A

T

0.629

−0.0389

1.88E−08

RP11-170N11.1

 

1

rs157864

165383761

T

C

0.1415

0.0443

8.60E−06

RXRG

 

1

rs651691

193958320

T

C

0.5531

0.0317

6.45E−06

 
 

2

rs12623587

232160554

A

C

0.29

−0.0321

6.00E−06

C2orf72, PSMD1, HTR2B, ARMC9

 

3

rs78461316

104858434

T

C

0.0587

0.0749

2.54E−07

 
 

7

rs141219652

70367062

C

T

0.0226

0.1083

8.72E−06

 
 

10

rs61860520

134826645

T

C

0.0543

−0.0719

4.02E−06

TTC40, LINC01166

 

11

rs138662357

92058950

C

A

0.0555

0.074

3.49E−07

NDUFB11P1, FAT3, PGAM1P9

 

13

rs9514523

106927120

T

C

0.1871

−0.0386

9.20E−06

 
 

13

rs9521336

110023731

C

T

0.2146

0.0378

1.96E−06

MYO16-AS1, LINC00399

 

14

rs2105997

107209226

T

A

0.2276

0.0388

8.46E−06

IGHV4-39, HOMER2P1, IGHV4-61, IGHV3-64, IGHV3-66, IGHV1-69, IGHV3-72, IGHV3-73, IGHV3-74

 

15

rs144705301

67855035

C

T

0.0263

0.11

1.74E−07

AAGAB, RPS24P16, MAP2K5, SKOR1

IT

1

rs56267558

21005316

T

G

0.1287

0.0431

6.40E−06

MUL1, CDA, PINK1, PINK1-AS, DDOST, KIF17

 

1

rs113285275

70896319

A

G

0.2344

−0.0328

3.10E−06

HHLA3, CTH

 

1

rs183093970

88454261

G

A

0.0147

0.1535

5.47E−10

 
 

1

rs147836155

113501607

T

C

0.0129

0.1346

2.46E−06

SLC16A1, SLC16A1-AS1

 

2

rs148259393

28713654

G

C

0.0204

0.1038

3.30E−06

PLB1

 

2

rs141418970

40576095

T

G

0.0102

0.1593

4.82E−07

SLC8A1

 

2

rs17018138

80154236

G

C

0.05

0.0588

7.53E−06

CTNNA2

 

2

rs79341575

129133292

C

G

0.0551

0.063

2.75E−06

GPR17

 

2

rs60200364

160708050

A

G

0.0623

0.0555

2.14E−06

BAZ2B, LY75, LY75-CD302, PLA2R1, ITGB6

 

2

rs2348117

201598521

T

G

0.8893

−0.0414

9.76E−06

AOX3P, AOX2P, AC007163.3, PPIL3, RNU6-312P

 

3

rs9289581

139405842

T

G

0.37

0.0271

8.32E−06

NMNAT3

 

4

rs7656795

22398514

T

C

0.8175

−0.037

1.22E−06

GPR125

 

4

rs114105899

23027094

G

A

0.0158

0.1197

8.10E−07

RP11-412P11.1

 

4

rs10011717

86136864

A

G

0.3774

−0.0282

6.09E−06

 
 

4

rs77601419

148249054

T

C

0.015

0.1168

2.22E−06

 
 

7

rs77033896

115513816

A

G

0.0169

0.1262

6.84E−07

TFEC, CAV1

 

8

rs17494322

20673550

G

A

0.075

0.0535

4.18E−06

 
 

11

rs139629925

76144667

G

A

0.0121

0.1347

5.91E−06

RP11-111M22.2, C11orf30, LRRC32

 

11

rs2084308

111051351

T

A

0.028

0.0967

4.29E−07

 
 

13

rs7328235

41998022

T

C

0.9439

−0.0607

6.72E−06

MTRF1, OR7E36P

 

13

rs9567982

48605441

G

A

0.1375

0.0394

3.08E−06

LINC00444, LINC00562, SUCLA2, SUCLA2-AS1, NUDT15, MED4, MED4-AS1, POLR2KP2

 

13

rs117372720

61819169

T

C

0.0149

0.1092

8.97E−06

 
 

13

rs149383020

112585032

A

G

0.0341

0.0787

5.09E−07

 
 

14

rs144434563

91361842

G

A

0.0135

0.1265

6.79E−06

RPS6KA5

 

14

rs137899216

91830706

T

C

0.0277

0.0911

3.06E−06

GPR68, CCDC88C, SMEK1

 

17

rs112645358

66248531

T

C

0.0384

0.069

9.94E−06

KPNA2, LRRC37A16P, AMZ2, ARSG

 

18

rs148222222

65675614

T

C

0.0169

0.1133

1.47E−06

RP11-638L3.1

 

20

rs71336998

5467150

G

A

0.018

0.1266

1.17E−07

LINC00654

  1. Ch chromosome, A1 allele 1 (effect allele), A2 allele 2, eQTL expression quantitative trait loci, Freq allele frequency, IT inferior temporal cortex, MF midfrontal cortex
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