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Table 2 Genome-wide association study single nucleotide polymorphisms that correlate with Δphotoperiod

From: Genetic adaptation of the human circadian clock to day-length latitudinal variations and relevance for affective disorders

SNP

Gene(s)a

Disease

Risk allele

Risk allele frequency decreases with Δphotoperiod

Kendall's correlationPvalueb

Ï„ rankc

FSTrankd

lnRsb ranke

Gene functional connection to circadian rhythm

       

Biaka-Orcadian

Biaka-Maya

CEPH

CHB + JPT

 

rs1930961

LRP5L, ADRBK2

BPD

C

Yes

1.182 × 10-6

0.993

0.996

0.942

0.530

0.700

ADRBK2 (aka GRK3) phosphorylates melanopsin [34]

rs6746896

LMAN2L, CNNM4

BPD

A

Yes

8.421 × 10-7

0.995

0.550

0.350

0.780

0.790

CNNM4 is an RNAi hit (the gene does not appear in Table 1 because the SNP is non-genic)

rs8099939

GRIK5

BPD

T

Yes

6.538 × 10-5

0.956

0.968

0.615

0.960

0.980

-

rs2286492

FAM126A

BPD

G

No

8.521 × 10-5

0.966

0.811

0.000

0.160

0.260

-

rs7570682

TMEM18, POU3F3

BPD

A

Yes

2.320 × 10-4

0.950

0.455

0.004

0.160

0.090

-

rs4075511

KCNS3, RDH14

BPD

A

No

7.345 × 10-9

0.999

0.797

0.156

0.720

0.730

-

rs7319311

COL4A2

BPD and SCZ

A

No

1.083 × 10-4

0.952

0.474

0.319

0.400

0.470

Clock-regulated in mouse cardiomyocytes [35]

rs1124376

KAT2B

BPD and SCZ

G

Yes

3.852 × 10-4

0.950

0.860

0.076

0.880

0.150

Directly interacts with CLOCK and NPAS2 [36]

rs1605834

APOB, KLHL29

BPD and SCZ

C

Yes

2.857 × 10-4

0.950

0.966

0.877

0.350

0.240

-

rs17002034

MKL1

BPD and SCZ

G

Yes

2.322 × 10-5

0.978

0.689

0.000

0.990

0.990

RNAi hit (gene does not appear among selected hits because of heavier Bonferroni correction)

rs589249

CSF3R, GRIK3

SCZ

G

Yes

4.565 × 10-5

0.964

0.996

0.624

1.000

1.000

Grik3 expression is regulated by Clock in the mouse ventral tegmental area [37]

rs7004633

MMP16, RIPK2

SCZ

A

No

1.433 × 10-6

0.992

0.925

0.538

0.260

0.330

-

rs1009080

PTPRU, MATN1

SCZ

G

Yes

2.419 × 10-6

0.988

0.987

0.708

0.900

0.690

-

rs1572299

TLR4, DBC1

SCZ

A

Yes

3.901 × 10-4

0.951

0.950

0.321

1.000

0.200

DBC1 regulates NR1D1 stability [38]

rs892055

RASGRP4

Asperger

nr

na

4.268 × 10-5

0.964

0.603

0.585

0.610

0.420

-

rs9601248

NDFIP2, SPRY2

MDD

C

No

7.198 × 10-5

0.958

0.896

0.085

0.390

0.330

SPRY2 is a direct target of ARNTL in mouse liver [39]

rs8020095

GPHN

Depression

A

Yes

1.273 × 10-4

0.950

0.944

0.504

0.620

0.980

GPHN shows rhythmic expression in mouse SCN [40]

rs12593813

MAP2K5

RLS

A

No

2.066 × 10-5

0.971

0.498

0.175

1.000

0.830

-

  1. aOne gene is reported if the variant is genic, for intergenic SNPs the two flanking protein-coding genes are listed; bKendall's P values for the correlation between allele frequency and Δphotoperiod; cpercentile rank in the distribution of Kendall's correlation coefficients (τ) calculated for minor allele frequency (MAF)-matched SNPs; dFST percentile rank in the distribution of SNPs showing a similar average MAF (calculated over all populations); elnRsb percentile rank; significant values are shown in bold. BPD, bipolar disorder; CEPH, 1000 Genomes Phase I data for Utah Residents with Northern and Western European ancestry; CHB + JPT, 1000 Genomes Phase I data for Han Chinese in Beijing plus Japanese in Tokyo; MDD, major depressive disorder; na, not available; nr, not reported; RLS, restless leg syndrome; SCZ, schizophrenia; SNP, single nucleotide polymorphism.
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Genome Biology

ISSN: 1474-760X

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