For all probes present on the Illumina HT12 array, a systematic search for sequence polymorphisms was undertaken, using the HapMap database as reference (Release 27; Phase II+III, Feb09, on NCBI B36 assembly and dbSNP b126). Among the 2,477 genes whose expression was associated with cis eSNPs, 173 (7%) were probed by one or several polymorphic sequences (180 probes) (Table S1). For 32 of these probes, the HapMap SNP was present on the Affymetrix array used in this study and for 41 other probes, the HapMap SNP had one or several perfect proxies on the array. For those eQTLs, we cannot exclude the possibility of an artefactual association due to a differential binding of the probe to its target sequence.
