N = 10 individual SNPs at six genes were significantly associated with gene expression signal, three genes exhibited significant association to gene expression in the single additive model, and three genes exhibited one or more statistically significant haplotype partitions (Table 3, Figure 1, Additional file 3).
This SNP was included in a FL high-risk FDFT1 haplotype (p = 1.6×10−3, q = 6.4×10−2, Table 3), though the p-value was no more significant for the haplotype than for the rs1047643 SNP association.
The majority of global association tests were more significant than individual haplotype results for our five top genes.
Because of the modeling of any possible distinct haplotypes, the multiallelic model will have more power for detecting significant haplotypes and their imprinting effects than biallelic models.
Our association results are consistent with that study, and we were able to show a more significant effect with a haplotype analysis that included a second SNP, rs5029306, 70.5 kb upstream in intron 3.
Testing of haplotypes consisting of five adjacent SNPs did not reveal any haplotype that was more significant than the corresponding individual SNPs (data not shown).
In addition to single SNP association, we furthermore report two previously undescribed SCH-associated four-marker haplotypes on 7q36.1 region encompassing HERG1, that were more significant than unique significant SNP (the at-risk haplotype A-A-A-T and the protective haplotype C-A-C-G).
In Japanese population, the haplotype association was more significant than those of respective SNPs (Tables 2 and 3).
In region 3, the most significant two-marker haplotype (rs2736107/rs2735940) is more significant than rs2736107 alone, again supporting the existing of either two independent signals or a partially correlated untested causal variant.
The haplotype analysis also suggests a possible combined effect of SNPs in regions 2 and 3; the T/T haplotype of rs28353676/ rs7449190 is more significant than single marker effect of rs28353676.
