http://www.hl7.org/fhir/2018May/extension-observation-geneticsphaseset.html easily describes how a set of sequences (not necessarily variants) can be grouped according to being in chromosomal phase with one another (cis, on the same molecule). This is useful for my use case.

I don't see how this can be done in the current IG.

allele-phase in described variant doesn't do it as far as I can tell. If it can, I need to see an example.

Calling the phase-set a haplotype of sequences is technically correct, but seems awkward, especially since our domain talks about haplotypes in a whole gene level (eg describing whether two gene level alleles are on the same molecule. Is it possible to describe haplotypes of haplotypes?

In the end, I need to see examples of this.