Identification of three new cis-regulatory IRF5 polymorphisms: in vitro studies

Table 1 Polymorphisms in the IRF5 locus screened by functional tests.^a

Polymorphism	Position	Gene	Alleles	MAF	Selection criteria^b	EMSA	Reporter
rs4731530	128562578	5' IRF5	C > T	39.9	Hap	-
rs6950728	128565661	5' IRF5	G > A	30.9	r² = 0.97	-
rs11982901	128566754	5' IRF5	C > T	31.6	r² = 0.97	-
rs4728141	128567032	5' IRF5	C > T	49.5	Hap	-
rs13245639	128567810	5' IRF5	C > T	31.6	r² = 0.97	+	+
rs729302	128568960	5' IRF5	A > C	31.1	r² = 1.0	-
rs729068	128569561	5' IRF5	C > T	31.1	r² = 0.9	-
rs12706860	128570026	5' IRF5	C > G	33.7	r² = 0.83	+	+
rs7808659	128570238	5' IRF5	C > A	30.4	r² = 0.9	-
rs754284	128571478	5' IRF5	C > G	31.6	r² = 0.87	-
rs4728142	128573967	5' IRF5	G > A	47.8	Hap	-
rs7801838	128573994	5' IRF5	C > T	28.9	r² = 0.73	-
rs3778754	128575552	5' IRF5	G > C	48.9	Hap	+	-
rs11269962	128575812	5' IRF5	ins > del	48.9	RNA-seq	+	+
rs3757388	128576023	5' IRF5	A > G	33.3	Hap	-
rs3757387	128576086	5' IRF5	T > C	49.4	Hap	-
rs3757385	128577304	5' IRF5	G > T	33.3	Hap	-
rs3807135	128577617	5' IRF5	C > T	33.0	Hap	-
CGGGG indel	128577931	5' IRF5	del > ins	48.4	Known cis-eQTL	+	+
rs3807307	128579202	IRF5	C > T	47.8	Hap	+	-
rs3823536	128579666	IRF5	A > G	47.8	Hap	-
rs3778753	128580042	IRF5	G > A	47.8	Hap	-
rs3778752	128580047	IRF5	T > G	47.8	Hap	-
rs3778751	128580048	IRF5	T > A	47.8	Hap	-
rs3807306	128580680	IRF5	T > G	45.7	Hap/microarray	-
rs17424179	128657995	TPNO3	G > A	3.8^c	Microarray	+	-

^aThe polymorphisms' genomic position, relation to genes, alleles, minor allele frequency (MAF), criteria of selection and results of the electrophoretic mobility shift assay (EMSA) and reporter gene assays are shown. ^bSelection criteria were hap = concordance of the minor allele with the minor allele of rs729302 in most haplotypes; r² = level of genotype correlation with rs729302; RNA-seq = polymorphism most associated with RNA-seq data; microarray = specially associated single-nucleotide polymorphisms in microarray expression analysis. ^cFrequency from HapMap (Hap) CEPH (Utah residents with ancestry from northern and western Europe: CEU) individuals. eQTL = expression quantitative trait loci.

ISSN: 1478-6362