be synthetic associations resulting from the contributions of multiple rare SNPs within the PHF3-PTP4A1 region, which need to be identified by sequencing. Third, both PHF3 and PTP4A1 were found to have significant association and functional signals. PHF3 had weaker association signals in AAs and EAs and weaker functional signals in lymphoblastoid cell lines than PTP4A1. However, associations for PHF3 markers were also replicated in the Australian sample. PHF3 had greater evidence of altered RNA secondary structures than PTP4A1. These positive signals might be due to the LD with a single causal locus in PHF3-PTP4A1 region, and this putative causal locus was more likely to be located in PHF3 based on our current evidence, which, again, needs sequencing to confirm. Finally, HapMap JPT and YRI-Children populations also presented functional signals, but the distributions of −log(P) values across the LD block in these two populations were negatively correlated with those in AAs, EAs, Australians, HapMap CHB and CEU-Children. It is likely that, in these two sets of populations, different phases of alleles might be in LD with the same causal allele.
