Difference between variant and gene pages

Dear Open Target Community,

My study is interested in the association between the variant 6_41161514_C_T and TREM2. The variant’s page suggests a high V2G score, the influential effect, and a short distance between them. However, the gene’s page doesn’t describe the variant at all. Could anyone help explain the difference, please?

Best regards,
Tzu-Hao Kuo

The gene page only shows variants which are lead or tags of an associated locus. Although the PheWAS plot shows strong associations with Alzheimer’s disease with p-value below 1e-20 (study ID: GCST90012877). This variant is very rare (0.25% in European), which would explain why none of the finemapped loci of this study in the region contain it. As the l2g scores are computed based on the credible sets of the loci, different variant sets lead to different prediction.

Take a look at the regional plot of the study, where your variant of interest is on the middle top:

That’s so detailed! Many thanks.