I'm having a plink file (ped map format) which I have subset for a list of SNPs and now I want to know with which genes these SNPs are related.

I did as the website suggested,

    plink --file mydata --assoc

so the `plink.assoc` file was created as should be, but then when I run

    plink --noweb --gene-report plink.assoc --gene-list glist-hg18

the `plink.range.report` file which should contain what I want, is empty.

I have manually checked and confirmed that for at least one SNP there is one corresponding gene.

When I run 

    plink --noweb --gene-report plink.assoc --gene-list glist-hg18 --gene-report-empty

which is the opposite command, it contains all the genes of the glist-hg18 file.

At this point I am unable to think of a solution.
Can you check whether the latest PLINK 1.90 build has the same problem? (Note that it does not support the undocumented `--gene-report-empty` flag.) (Edit: oops, this should not have been an answer, but hopefully it will lead to one in short order.)