Table 6.

The genome-wide association studies coronary artery disease risk allele at rs1746048 is associated with higher CXCL12 transcript levels in human tissue: strongest individual probe associations

SNP	Published risk allele, OR for CAD/MI (P-value)	Affymetrix Human Exon 1.0 ST array probeset ID (type of probe)	Affymetrix Human Exon 1.0 ST array exon cluster IDa	Expression data setb	Genotype (n)	Normalized expression value (SD)	P-value*	P-value**
rs1746048	C, 1.17 (10−9)c	3286617 (core, α)	605625	NK	CC (3)	3.72 (0.41)	9.5 × 10−5	0.002
					CT (3)	1.9 (0.44)
					TT (1)	1.5 (0)
		3296619 (core, α)	605625	Liver	CC (25)	5.36 (0.77)	4.8 × 10−5	0.001
					CT (11)	3.71 (0.63)
					TT (1)	3.11 (0)

^aThe exon cluster ID 605625 marks an exon in CXCL12 isoform-α (splice variant 1), but not isoform β.

^bThese data are derived from seven individuals with NK cell expression on Affymetrix Human ST Exon 1.0 Array and genotyped on the Illumina 550kV3 chip. The liver data are derived from 35 individuals with liver tissue expression on Affymetrix Human ST Exon 1.0 Array and genotyped on the Illumina 550kV3 chip. These tissues express CXCL12 isoforms α and β, but not other splice variants.¹⁴

^cData derived from Myocardial Infarction Genetics Consortium Study.³

*P-value derived from non-parametric testing of normalized transcript expression using genotypes 0, 1, and 2 for number of copies of risk alleles.

**P-value after Bonferroni correction (18 probesets tested).