Resolving the polymorphism-in-probe problem is critical for correct interpretation of expression QTL studies.

Nucleic Acids Res · 2013 · PMC3627570 · PMID 23435227

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highly significantP -value = 8 × 10 − 31actually significant

The hit SNP is in high LD with this common 2-base pair deletion (labelled as chr17:44102741:D in 1000 Genomes or as rs67759530 in dbSNP) within the probe ( r 2 = 0.91, minor allele frequency = 23%), giving rise to a highly significant association in the Illumina HT12 data set ( P -value = 8 × 10 − 31 ).

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