As mentioned above, rs805264, rs707922, and rs707921 are located within the same LD block. Therefore, in the subsequent haplotype analysis, rs707922 was used to 'tag' the three SNPs. Haplotype construction was conducted for rs707922(G+1837T) with other independent SNPs rs805297(C-1065A) and rs9404941(T-855C). Four haplotypes (A-T-G, C-C-G, C-T-G, and C-T-T) accounting for 99.9% of all possible haplotypes were detected in our Hong Kong Chinese population (Supplementary  Table S3 ). No significant association was found between these haplotypes with T2D. Homozygous C-T-T was significantly associatiated with elevated TC, LDL-C and HbA1c in T2D patients (p,0.0125, Supplementary Table S4 ). Figure S3) . SNPs rs707922 (G+1837T) and rs707921 (C+1871A) which associated with plasma levels of TC, LDL-C and apoM in T2D patients fell within the evolutionary conserved region. Figure 1 (top panel) illustrated the cross-species sequence conservation of the rs707922-and rs707921-flanking region. BLAST search using this conserved sequence as the template returned unique human EST clones BI757556 (human brain) and AA975560.1 (human kidney) which are likely other APOM transcripts. The Ensembl Browser also displayed three APOM transcripts (APOM1: Ensembl-ENST00000375916, APOM2: Ensembl-ENST00000375920 and APOM3: Ensembl-ENST00000375918). 4.2. Molecular cloning of APOM transcripts. Since the sequences of EST clones BI757556 and AA975560.1 were different than the known APOM transcripts, we proceeded with cloning alternative transcripts of APOM. A novel transcript, designated APOM5, was identified by 59 RACE and 39 RACE. As shown in Figure 1 , the 39 end of APOM5 was identical to the 39 end of APOM3. The 59 end, however, was similar to that of the vulgate APOM transcript (designated APOM1) except that the transcription start site of APOM5 was 21 nucleotides downstream that of the APOM1. The full-length sequence of APOM5 is provided in Supplementary Figure S4 . It is important to note that the two SNPs rs707922(G+1837T) and rs707921(C+1871A) associated with metabolic traits in T2D are located to the exon 5 of APOM5. On the contrary, when reference to the vulgate APOM1 transcript, rs707921 and rs707922 are located to intron 5. These observations support the cryptic nature of exon 5 of the gene. 