Genome-wide SNP data for LCLs

Expression array data were obtained for all 174 lymphoblastoid cell lines (LCLs) as previously described [17 (link)]. Illumina HumanHap550K and 510S BeadChips, which assayed 561,298 and 493,750 SNPs, respectively, were used to obtain genome-wide SNP data for these LCLs [23 (link)]. Genotyping was performed in the Genotype Shared Resource (GSR) at the Mayo Clinic, Rochester, MN. We also obtained publicly available Affymetrix SNP Array 6.0 Chip SNP data which involved 643,600 SNPs unique to the Affymetrix SNP array for the same cell lines. After quality control (QC), SNPs with call rates <0.95, Hardy-Weinberg Equilibrium (HWE) P values < 0.001, or MAFs <5% were excluded, as were DNA samples with call rates <0.95. A total of 1,348,798 SNPs that passed QC were used to perform the association studies.