Dienekes points me to a provisional open access paper, Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping. Here’s the conclusion:
There were small but significant differences in measures of genetic diversity between
AJ [Ashkenazi Jewish] and CEU [Utah whites from the HapMap sample]. Analysis of genome-wide LD structure revealed a greater number of haplotype blocks which tended to be smaller in AJ. There was essentially no difference in global LD decay between AJ and CEU, although there was a tendency for faster decay of nearby SNPs and slower decay of intermediate distance SNPs in the AJ. These data are more consistent with the AJ as an older, larger population than CEU, and would suggest that, depending on regional differences in LD structure, AJ populations may not always provide an advantage for whole-genome association mapping.
The image above left illustrates the differentiation between 102 Ashkanezi Jews and 60 gentile Northern Europeans (a Mormon sample from Utah) along the first two principle components of genetic variation. Obviously there are average genetic differences between gentiles and Jews, as evidenced by the different prevalence of some diseases and so forth. I am intrigued by the result of a larger older population, though I’m not sure if I want to read too much into it. Do remember though that long term effective population is the harmonic mean, which means that one generation of an incredible bottleneck can have a disproportionate impact. For more of the same, see Discerning the Ancestry of European Americans in Genetic Association Studies.