Table 1

Polymorphisms in the IRF5 locus screened by functional tests.a

Polymorphism

Position

Gene

Alleles

MAF

Selection criteriab

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

3.8c

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.

Alonso-Perez et al. Arthritis Research & Therapy 2013 15:R82   doi:10.1186/ar4262

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