All of the risk SNPs listed in Table 1 were analyzed using UCSC Genome Browser data or other bioinformatics analysis software (e.g., FuncPred from http://snpinfo.niehs.nih.gov/snpinfo/snpfunc.htm) to see whether they were located in the transcription factor binding sites (TFBS), within methylated CpG islands, within copy number variations (CNVs) or in exonic splicing silencer (ESS) or enhance (ESE). These locations were helpful for us to predict whether these SNPs were potentially functional. Additionally, Polyphen (19) was applied to predict whether these risk SNPs affected the protein function or structure, and MFOLD (20) was applied to predict whether these risk SNPs altered the secondary RNA structure.
