Table 1 Independent variants with a genome-wide significant (P < 5 × 10−8) association with broad depression, probable major depressive disorder (MDD), or International Classification of Diseases (ICD)-coded MDD in the UK Biobank

From: Addendum: Genome-wide association study of depression phenotypes in UK Biobank identifies variants in excitatory synaptic pathways

     

UK Biobank

23andMe

Meta-analysis

Phenotype

Chr

Marker name

Position

A1/A2

Freq

Info

log OR (St Err)

P -value

Gene ± 10 kb

log OR (St Err)

P -value

log OR (St Err)

P -value

Direction

Broad depression

1

rs10127497

67050144

T/A

0.138

1.00

0.044 (0.0077)

1.26 × 10−8

SGIP1

0.0098 (0.0086)

0.257

0.029 (0.0058)

5.70 × 10−7

++

1

rs6699744

72825144

T/A

0.612

1.00

0.040 (0.0055)

1.64 × 10−13

—

0.0328 (0.0064)

2.68 × 10−7

0.0372 (0.0042)

9.76 × 10−19

++

1

rs6424532

73664022

A/G

0.486

1.00

0.029 (0.0053)

3.74 × 10−8

—

0.0233 (0.006)

1.14 × 10−4

0.0267 (0.004)

4.10 × 10−11

++

1

rs7548151

177026983

A/G

0.084

1.00

0.056 (0.0095)

3.77 × 10−9

ASTN1

0.006 (0.0104)

0.560

0.0339 (0.0071)

1.97 × 10−6

++

5

rs40465

103981726

G/T

0.332

1.00

0.035 (0.0056)

4.37 × 10−10 

RP11-6N13.1

0.0193 (0.0064)

2.63 × 10−3

0.0285 (0.0043)

3.53 × 10−11

++

6

rs3132685

29945949

A/G

0.130

1.00

−0.059 (0.0081)

2.48 × 10−13

—

−0.0249 (0.0099)

0.0115

−0.0459 (0.0063)

4.87 × 10−13

−−

6

rs112348907

73587953

G/A

0.296

1.00

0.033 (0.0058)

1.44 × 10−8

—

−0.0004 (0.0067)

0.950

0.019 (0.0045)

2.06 × 10−5

+−

7

rs3807865

12250402

A/G

0.412

1.00

0.037 (0.0054)

6.81 × 10−12

TMEM106B

0.019 (0.0061)

0.002

0.0293 (0.0041)

8.79 × 10−13

++

7

rs2402273

117600424

C/T

0.409

1.00

0.032 (0.0054)

1.88 × 10−9

—

0.0093 (0.0061)

0.130

0.0226 (0.0041)

3.97 × 10−8

++

9

rs263575

17033840

A/G

0.460

1.00

−0.030 (0.0053)

2.36 × 10−8

—

−0.0157 (0.0061)

9.45 × 10−3

−0.0238 (0.0041)

4.51 × 10−9

−−

10

rs1021363

106610839

G/A

0.642

1.00

−0.032 (0.0055)

1.02 × 10−8

SORCS3

−0.031 (0.0063)

9.34 × 10−7

−0.0314 (0.0042)

1.04 × 10−13

−−

11

rs10501696

88748162

G/A

0.499

0.99

−0.036 (0.0054)

6.42 × 10−11

GRM5

−0.0251 (0.0066)

1.49 × 10−4

−0.0315 (0.0043)

1.55 × 10−13

−−

13

rs9530139

31847324

T/C

0.195

1.00

−0.040 (0.0067)

2.59 × 10−9

B3GLCT

−0.0075 (0.0078)

0.338

−0.0265 (0.0052)

2.77 × 10−7

−−

15

rs28541419

88945878

G/C

0.231

1.00

−0.035 (0.0064)

2.82 × 10−8

—

−0.0029 (0.0073)

0.688

−0.0218 (0.0049)

7.75 × 10−6

−−

Probable MDD

2

rs10929355

15398964

G/T

0.456

1.00

−0.053 (0.0090)

5.89 × 10−9

NBAS

−0.0078 (0.0061)

0.199

−0.0221 (0.0051)

1.62 × 10−5

−−

7

rs5011432

12268668

C/A

0.412

1.00

0.051 (0.0091)

2.10 × 10−8

TMEM106B

0.022 (0.0061)

3.15 × 10−4

0.0313 (0.0052)

1.47 × 10−9

++

ICD-coded MDD

7

rs1554505

1983929

A/G

0.752

1.00

0.114 (0.0191)

2.73 × 10−9

MAD1L1

0.017 (0.007)

0.015

0.0291 (0.0068)

1.63 × 10−5

++

  1. The UK Biobank results are from logistic regression analyses in PLINK of variants identified as genome-wide significant using BGENIE. Variants were examined within the 23andMe association analysis of depression4 to obtain their reported P-values and determine whether their effect was in the same direction as UK Biobank. The allele frequency (Freq) is for the A1 allele within UK Biobank, with the effect size (Log OR) and standard error (St. err.) reported for the A1 allele within UK Biobank, 23andMe and the meta-analysis. The chromosome (Chr) and basepair position is given for the GRCh37 assembly. Imputation accuracy (Info) score of UK Biobank was calculated based on the sample analysed
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