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

Srinivas, Lekshmy; Vellichirammal, Neetha N.; Alex, Ann Mary; Nair, Chandrasekharan; Nair, Indu V.; Banerjee, Moinak

doi:10.1186/s12974-016-0569-8

Journal of Neuroinflammation

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

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

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ISSN: 1742-2094

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