sorry...didn't attach full view from HapMap...these are the ones not genotyped related to the other image

If you have the genotype and family informations of your cohort you can operate the LD analysis without matching the HapMap map file using PLINK or INTERSNP. I would reccomend you to use PLINK (you can find more information about LD calculations here: http://pngu.mgh.harvard.edu/~purcell/plink/ld.shtml) because it works really well for such kind of analyses.

First; I have not yet tried the options you mention...

I have only genotyped one of the SNPs in my cohort and I want to know if there is LD between this SNP and another one I haven't genotyped and furthermore, has no data on CEU population (nor any other) in HapMap.

I suppose it Is not possible to get information about LD with the programs you talk about? Or am I wrong?

I don't know what your purpose is, but all these SNPs are likely to be very high LD as they are very few bp apart. Generally, LD is fairly closely related to bp distance, although it varies by location (recombination hotspots, etc.). If you can't find an actual estimate, you might look at neighboring SNPs that ARE in Hapmap and assume that the LD is higher for SNPs that are closer together in that region.

Thanks James Farnham.

My purpose: I've found an association between a SNP I've genotyped and the chance of response to certain treatment in my cohort.

Another study has found association between another SNP and response to the same kind of treatment (in another cohort, of course)

I want to give an estimate/figure of LD between these two SNPs, but the one SNP from the other study isn't in HapMap -

therefore can I find these kind of data in another database? (1000 genomes project, etc?)

(I have looked at LD values to SNPs at either side of the one without data, as you suggest, and will use the argument you also present)

Thanks