In conclusion, the APOM SNP frequencies and the LD structure reported in this study of Hong Kong Chinese population will facilitate future population genetics studies. While our results did not support an association between APOM and T2D susceptibility in Hong Kong Chinese, subgroup analyses found SNP as well as haplotype associations between APOM and metabolic traits in T2D. Bioinformatics/molecular analyses revealed the cryptic nature of exon 5 responsible for the expression of a novel transcript APOM5, predominantly in liver and kidney. The activity of APOM5 on modifying cellular cholesterol content revealed another layer of regulation underlying the expression and function of APOM. (Mus musculus; chr17) , rat (Rattus norvegicus; chr20), cow (Bos Taurus; chr23) and dog (Canis familiaris; chr12) genes are shown. Conserved sequences were defined as coding exons (blue), The Evolutionary Conserved Regions (ECRs) were indicated by pink lines (on top of the panel for each species) with a default value of 70%. The human APOM was depicted as a horizontal blue line above the graph, with strand/transcriptional orientation indicated by arrows. APOM coding exons were shown as blue boxes along the line, while untranslated regions (UTR) were indicated as yellow boxes. Peaks within the conservation profile which corresponded to these five exons of APOM were similarly coloured within the plot. Peaks within the conservation profile that did not correspond to transcribed sequences were highlighted in red colour. Regions of transposable elements and simple repeats were highlighted in green color. Figure S5 Computer-predicted transcription factor interaction sites in nucleotide sequences spanning SNPs rs707922(G+1837T) and rs707921(C+1871A). This figure is generated by the MATCH program. Top panel: The transcription factors predicted to interact with the nucleotide sequences spanning the major allele of SNPs rs707922 (G allele) and rs707921 (the C allele). Bottom panel: The transcription factors predicted to interact with the nucleotide sequences spanning the minor allele of SNPs rs707922 (the T allele) and rs707921 (the A allele). The predicted transcription factors are marked by blue text with scores of matrix match indicated in parentheses. The locations and orientations of the binding sites for these predicted transcription factors are marked by black horizontal dashed lines with arrows. Highlighted in pink boxes are allele-specific transcription factors (PAX6 and AREB6 for rs707922-T; HNF4 and OCT1 for rs707921-A) and their corresponding binding sites. The vertical dashed lines indicate the locations of SNPs rs707922 and rs707921. The precise nucleotide positions of SNP rs707922 and rs707921 are also highlighted with grey boxes in the DNA sequences represented by red colored text. (TIFF)