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Table 1 Association significance between the TF binding-disrupting SNPs and gene expression in the human brain tissues(at least four brain eQTL datasets)

From: Functional genomic analysis delineates regulatory mechanisms of GWAS-identified bipolar disorder risk variants

SNP

Gene

CMCa

LIBD2(DLPFC) a

LIBD2(Hippo) a

xQTLa

Brain(GTEx) c

P value

FDR

P value

FDR

P value

FDR

P value

FDRb

P value

rs2071507

GLT8D1

2.02E-08

2.80E-06

2.83E-06

1.86E-04

NA

NA

1.30E-03

4.69E-02

0.000030( Brain - Nucleus accumbens (basal ganglia))

rs2071507

NEK4

1.25E-12

3.32E-10

4.63E-08

4.39E-06

2.93E-06

2.76E-04

2.68E-04

1.28E-02

0.000005(Brain - Cerebellar Hemisphere);

rs3862386

PACS1

2.30E-12

6.51E-10

9.28E-09

9.95E-07

NA

NA

3.69E-10

5.78E-08

7.0e-7( Brain - Cortex);0.000044( Brain - Frontal Cortex (BA9));

rs2251219

NEK4

5.00E-16

2.01E-13

3.71E-17

1.15E-14

8.40E-12

2.07E-09

1.14E-06

1.00E-04

9.9e-7( Brain - Cerebellar Hemisphere);0.0000062(Brain - Cerebellum)

rs6591201

PACS1

5.69E-06

5.67E-04

7.98E-05

3.56E-03

1.93E-05

1.46E-03

4.51E-09

6.05E-07

0.0000010(Brain - Cortex);0.0000044(Brain - Frontal Cortex (BA9));

rs2270448

PACS1

3.66E-09

6.71E-07

1.54E-06

1.08E-04

NA

NA

5.76E-12

1.14E-09

3.9e-7(Brain - Cortex);0.0000068(Brain - Frontal Cortex (BA9));0.000016(Brain - Hypothalamus)

rs10896081

PACS1

2.21E-12

6.29E-10

9.13E-08

8.21E-06

NA

NA

6.60E-10

9.97E-08

0.0000004(Brain - Cortex);0.000030(Brain - Frontal Cortex (BA9));

  1. aBrain tissues from the dorsolateral prefrontal cortex (DLPFC) were used in the CommonMind Consortium (CMC) (N=467), the xQTL map of the human brains (xQTL) (N=494) and the Lieber Institute for Brain Development (LIBD2) brain eQTL (N=551). bThe FDR were calculate by R function p.adjust(). cFDR value is not available for GTEx eQTL data, but GTEx provided genome-wide empirical P-value threshold for each gene that calculated under FDR=0.05, all the GTEx eQTL P values listed here had passed the P-value threshold (FDR < 0.05)