Table 1 Prioritized genes from the MR analysis on MetaBrain eQTLs for brain-related outcomes

From: Brain expression quantitative trait locus and network analyses reveal downstream effects and putative drivers for brain-related diseases

Outcome

Gene

SNP

WR (SE)

P

CT

Outcome

Gene

SNP

WR (SE)

P

CT

AD

CR1

rs679515

0.15 (0.01)

1.40 x 10-23

OLI

MS

ZNF746

rs1046140

-0.57 (0.11)

8.29 x 10-08

 

AD

SLC39A13

rs3740688

-0.22 (0.03)

1.13 x 10-10

 

MS

MAST3

rs112188874

0.56 (0.10)

9.74 x 10-08

 

AD

TSPAN14

rs1902660

0.12 (0.02)

4.73 x 10-09

 

MS

MYNN

rs9866116

-0.43 (0.08)

1.22 x 10-07

 

AD

APH1B

rs117618017

0.17 (0.03)

1.05 x 10-08

 

PD

KANSL1

rs199451

-0.25 (0.03)

3.35 x 10-19

EX

AD

PRSS36

rs78924645

-0.09 (0.02)

1.63 x 10-08

 

PD

CD38

rs4698412

-0.24 (0.03)

6.99 x 10-14

AST

AD

INPP5D

rs7569598

0.32 (0.06)

1.74 x 10-08

 

PD

HSD3B7

rs11150600

-0.46 (0.07)

1.90 x 10-10

MIC

AD

ZNF668

rs2359612

0.26 (0.05)

1.00 x 10-07

 

PD

SETD1A

rs35733741

-0.67 (0.11)

2.43 x 10-09

EX

AD

ACE

rs4291

-0.10 (0.02)

1.39 x 10-07

 

PD

RAB29

rs708723

0.21 (0.04)

1.03 x 10-08

 

ALS

SCFD1

rs229243

0.17 (0.02)

5.56 x 10-15

 

PD

SCARB2

rs7697073

0.29 (0.05)

6.54 x 10-08

 

ALS

G2E3

rs229244

-0.24 (0.03)

4.23 x 10-13

 

SCZ

PPP1R18

rs9265954

0.48 (0.05)

1.11 x 10-19

 

ALS

MOBP

rs6772037

0.29 (0.05)

1.10 x 10-08

 

SCZ

HIST1H4K

rs13217285

0.63 (0.07)

1.40 x 10-18

 

BD

DCLK3

rs9834970

-0.32 (0.04)

4.79 x 10-14

 

SCZ

MICB

rs204999

-0.37 (0.05)

1.82 x 10-15

 

BD

HAPLN4

rs17216041

0.21 (0.04)

4.44 x 10-09

 

SCZ

FTCDNL1

rs2949006

-0.16 (0.02)

7.97 x 10-14

OLI

BD

GNL3

rs7646741

0.19 (0.03)

1.07 x 10-08

 

SCZ

GPANK1

rs7773668

0.24 (0.03)

2.56 x 10-13

 

BD

LMAN2L

rs58361269

-0.24 (0.04)

1.78 x 10-08

 

SCZ

FURIN

rs4702

-0.23 (0.03)

2.55 x 10-12

 

MDD

NEGR1

rs7531118

0.03 (0.00)

4.07 x 10-12

 

SCZ

SF3B1

rs788018

0.21 (0.03)

6.97 x 10-11

 

MDD

SLC12A5

rs9074

0.02 (0.00)

8.03 x 10-08

 

SCZ

MDK

rs35324223

-0.29 (0.05)

2.23 x 10-10

 

FTD

BTNL2

rs9268863

0.75 (0.12)

2.20 x 10-10

 

SCZ

THOC7

rs832190

-0.14 (0.02)

6.19 x 10-10

NEU

JME

HSD3B7

rs11150600

0.04 (0.01)

3.96 x 10-09

MIC

SCZ

CNTN4

rs17194427

0.26 (0.04)

9.19 x 10-10

 

MS

TTC34

rs10797438

-0.43 (0.05)

2.06 x 10-15

 

SCZ

TAOK2

rs4788200

0.44 (0.07)

1.05 x 10-09

 

MS

SLC12A5

rs9074

0.44 (0.06)

5.15 x 10-13

 

SCZ

PCCB

rs696520

-0.12 (0.02)

1.12 x 10-09

OLI

MS

MPV17L2

rs1044821

-0.51 (0.07)

7.57 x 10-12

 

SCZ

ATG13

rs12574668

-0.29 (0.05)

1.23 x 10-09

 

MS

TSPAN31

rs10877011

0.48 (0.07)

5.13 x 10-11

 

SCZ

ASPHD1

rs12919683

-0.23 (0.04)

1.33 x 10-09

OLI

MS

CYP24A1

rs2248137

0.13 (0.02)

7.81 x 10-11

EX + NEU

SCZ

TMEM219

rs9925102

0.30 (0.05)

1.87 x 10-09

 

MS

EEF1AKMT3

rs10877013

-0.13 (0.02)

8.99 x 10-11

MIC

SCZ

DOC2A

rs12921996

0.27 (0.05)

1.97 x 10-09

 

MS

NPEPPS

rs4239163

0.43 (0.07)

1.14 x 10-10

 

SCZ

PLEKHO1

rs11577346

-0.35 (0.06)

1.97 x 10-09

 

MS

AVIL

rs10877018

0.34 (0.05)

1.57 x 10-10

 

SCZ

INO80E

rs3814880

0.11 (0.02)

2.47 x 10-09

 

MS

TSFM

rs11172335

0.16 (0.02)

1.57 x 10-10

NEU

SCZ

GNL3

rs7646741

0.15 (0.03)

3.46 x 10-09

 

MS

PPM1F

rs240064

-0.36 (0.06)

3.58 x 10-10

 

SCZ

SNAP91

rs2022265

0.23 (0.04)

6.34 x 10-09

 

MS

CCDC155

rs2288481

-0.58 (0.09)

9.33 x 10-10

 

SCZ

TM6SF2

rs2905432

0.26 (0.05)

7.06 x 10-09

 

MS

CLECL1

rs7306304

-0.16 (0.03)

1.58 x 10-09

MIC

SCZ

KCTD13

rs11150575

0.39 (0.07)

9.30 x 10-09

 

MS

RNFT1

rs180534

-0.30 (0.05)

2.14 x 10-09

 

SCZ

VPS45

rs2319280

-0.27 (0.05)

1.17 x 10-08

 

MS

TRAF3

rs3803286

0.26 (0.04)

8.03 x 10-09

 

SCZ

CACNA1I

rs7288420

0.32 (0.06)

1.22 x 10-08

 

MS

IL7

rs2717538

-0.15 (0.03)

1.46 x 10-08

EX

SCZ

GATAD2A

rs12975119

-0.12 (0.02)

1.34 x 10-08

 

MS

RGS1

rs3011685

-0.47 (0.08)

1.54 x 10-08

 

SCZ

KMT2E

rs35601145

0.29 (0.05)

1.64 x 10-08

 

MS

IFITM1

rs6421983

0.49 (0.09)

1.78 x 10-08

MIC

SCZ

ZNF823

rs72986630

0.19 (0.03)

4.14 x 10-08

 

MS

IFITM3

rs34481144

-0.30 (0.05)

2.34 x 10-08

 

SCZ

PTPRU

rs267700

-0.19 (0.03)

4.28 x 10-08

EX

MS

TBX6

rs3809627

0.20 (0.04)

3.25 x 10-08

 

SCZ

RERE

rs301792

0.16 (0.03)

4.99 x 10-08

 

MS

ABCB9

rs1790116

0.47 (0.09)

3.55 x 10-08

 

SCZ

GLYCTK

rs6445358

0.19 (0.04)

7.22 x 10-08

 

MS

TYMP

rs131795

-0.25 (0.05)

6.20 x 10-08

 

SCZ

ATP13A1

rs7245672

0.30 (0.06)

1.08 x 10-07

 

MS

SCO2

rs131794

0.33 (0.06)

6.20 x 10-08

 

SCZ

CLCN3

rs72696657

0.24 (0.05)

1.14 x 10-07

 
  1. Harmonized eQTL and GWAS SNP effects and single-SNP Wald ratio-effect (WR) estimates are reported for all genes with Wald ratio effects at P < 1.865 × 10−7. Brain-trait outcomes have been abbreviated as follows: BD, bipolar disorder; MDD, major depressive disorder (broad depression category); FTD, frontotemporal dementia; JME, juvenile myoclonic epilepsy. The cell types (CT) with which the eQTL significantly interacts (BH-FDR < 0.05) are abbreviated as follows: AST, astrocytes; EX, excitatory neurons; MIC, microglia; NEU, other neuron; and OLI, oligodendrocytes. This table is a subset of Supplementary Table 12.
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