So I'm wondering if estrogen is off, would that affect PEMT expression?
There is an oestrogen response element in the promoter of PEMT, so oestrogen can increase production of this enzyme.
The result is that premenopausal women are protected from the deleterious effects of a low choline diet, compared with men and post-menopausal women.
Note that if dietary choline is adequate, oestrogen gives no particular advantage where PEMT is concerned.
As for PEMT SNPs, as far as I am aware, of the three you list, only rs7946 has been characterised as affecting PEMT activity. The change to the protein does reduce activity of the enzyme though the effect does not seem to be dramatic. There is an increased risk of developing NAFLD, but having the SNP doesn't necessarily mean that this will occur.
The other two SNPs you list I think appeared in small association studies which may or may not mean anything.
As for the Livewello templates, these are just lists of SNPs that people have put together - they don't necessarily mean anything and in the case of PEMT, apparently they don't.
On the oestrogen response of PEMT, a relatively recent
study has identified two SNPs in linkage disequilibrium which affect the capacity of oestrogen to regulate PEMT.
rs12325817, in the promoter region of the gene near the oestrogen response element, appears to have the actual effect. The presence of the variant C allele interferes with oestrogen binding to the response element and hence abrogates the protective effect of oestrogen for pre-menopausal women.
Post menopausal women with this SNP are more susceptible to choline deficiency, but as might be expected, men are not affected.
Other genes affect susceptibility to choline deficiency.
Here is a paper looking at relevant SNPs. Again note that the effects are relevant in face of inadequate dietary choline. If this is sufficient, the SNPs are not relevant (to choline metabolism at least - they might have other significance).
ETA
Here is another study from a slightly different angle, looking at the effect of SNPs in folate-related pathways which increase need for choline.