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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