Table 3. Significant variants associated with anxiety disorder risk when conditioning on brain volume GWAS.

The chromosome (Chr) and base pair (BP) are given in h19b37 coordinates. The Effect in Brain and Effect in AD (anxiety disorders) are both given in terms of the effect allele (EA). The non-effect allele (NEA) is also shown. The allele frequency (Freq) corresponds to the effect allele. Tagging SNP corresponds to the most significant variant in a given LD block (if different from the SNP chosen based on clumping in the brain volume GWAS).

a) Factor score dataset

Brain volume

SNP

Chr

BP

EA

NEA

Freq

Nearest Gene

Distance to Gene

Effect in Brain (SE)

P-value in Brain

Effect in AD (SE)

P-value in AD

q-value

Amygdala

rs77520376

4

30993011

A

G

0.089

PCDH7

Intronic variant

16.172 (4.67)

0.0005369

0.038 (0.009)

3.21×10−5

0.0281

Hippocampus

rs78587286

6

14266689

T

C

0.096

CD83

129kb

36.86 (7.88)

2.87×10−6

0.0246 (0.008)

0.001954

0.0293

Putamen

rs56242606

7

12421909

T

C

0.922

VWDE

Intronic variant

33.199 (11.91)

0.005299

−0.0417 (0.009)

6.2×10−6

0.0402

b) Case control dataset

Brain volume

SNP

Chr

BP

EA

NEA

Freq

Nearest Gene

Distance to Gene

Effect in Brain (SE)

P-value in Brain

Effect in AD (SE)

P-value in AD

q-value

Hippocampus

rs28373923

16

88815473

A

G

0.075

PIEZOl

Intronic variant

−31.994 (12.04)

7.89×10−3

0.4193 (0.091)

4.56×10−6

0.0317

Pallidum

rs12751736

1

21851462

A

G

0.288

ALPL

Intronic variant

8.669 (2.14)

5.1×10−5

0.108 (0.03)

0.0003394

0.0414

Thalamus

rs2740360

17

629309

T

C

0.439

FAM57A

6kb

16.946 (7.01)

1.57×10−2

0.1696 (0.033)

3.81×10−7

0.0101