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Table 1 List of cytokine candidate genes and their selected polymorphisms

From: Pro-inflammatory cytokines and their epistatic interactions in genetic susceptibility to schizophrenia

Gene

Locus

SNP

rs id

GMAF

Alleles

Genotyping method

Location

Predicted functional effect

IL1A

2q13

−889G>A

rs1800587

0.2786

G/A

TaqMan AD (C_9546481_20)a

Promoter

TFBS, splicing (ESE or ESS)

IL1B

2q13

+3954 C>T, Phe105Phe

rs1143634

0.1328

C/T

PCR-RFLP

Exon 4

sSNP, splicing (ESE or ESS)

  

−31T>C

rs1143627

0.4724

C/T

PCR-RFLP

Promoter

TFBS

  

−511C>T

rs16944

0.4906

T/C

PCR-RFLP

Promoter

TFBS

IL1RN

2q13

(86)n VNTR

rs2234663

 

1/2

PCR FLP

Intron 2

Regulatory protein-binding sites

IL4

5q31.1

−590C>T

rs2243250

0.4698

C/T

PCR-RFLP

Promoter

TFBS

  

−33C>T

rs2070874

0.4012

C/T

TaqMan AD (C_16176215_10)a

Promoter

TFBS

IL6

7p21

−597G>A

rs1800797

0.1382

G/A

PCR-RFLP

Promoter

TFBS

  

−572G>C

rs1800796

0.3139

G/C

PCR-RFLP

Promoter

TFBS

  

−174G>C

rs1800795

0.1412

G/C

PCR-RFLP

Promoter

TFBS

IL10

1q31

−592A>C

rs1800872

0.4349

T/G

PCR-RFLP

Promoter

TFBS

  

−819C>T

rs1800871

0.4347

G/A

KASPar assay

Promoter

TFBS

  

−1082G>A

rs1800896

0.2722

T/C

KASPar assay

Promoter

TFBS

IL3

5q31.1

rs31400T>C

rs31400

0.4581

T/C

TaqMan AD (C_3141153_10)a

Promoter

Promoter/regulatory region

  

rs31480C>T

rs31480

0.2883

C/T

TaqMan AD (C_2397270_10)a

Promoter

TFBS

  

rs40401C>T, Ser27Pro

rs40401

0.4195

C/T

TaqMan AD (C_2397269_30)a

Exon 1

nsSNP, benign

TNFA

6p21.3

−308G>A

rs1800629

0.0903

G/A

KASPar assay

Promoter

TFBS

  

−238G>A

rs361525

0.0609

G/A

KASPar assay

Promoter

TFBS

IFNG

12q24.1

+3232A>G

rs2069718

0.3832

A/G

TaqMan AD (C_15799728_10)a

Intron 3

–

  

+874A>T

rs2430561

0.2802

A/T

KASPar assay

Intron 1

NFKB binding site

TGFB1

19q13.2

+915G>C, Arg25Pro

rs1800471

0.0483

G/C

KASPar assay

Exon 1

nsSNP, benign

  

+869A>G, Leu10Pro

rs1800470

0.4547

A/G

TaqMan AD (C_22272997_10)a

Exon 1

nsSNP

  

−509C>T

rs1800469

0.368

C/T

KASPar assay

Promoter

TFBS

  1. TFBS transcription factor binding site, ESE exonic splicing enhancer, ESS exonic splicing silencer, sSNP synonymous SNP, nsSNP nonsynonymous SNP, GMAF global minor allele frequency
  2. aTaqMan allelic discrimination accession numbers