[ensembl-dev] RsIDs consistently fail with variation API, v83

[Johanne Håøy Horn]

Hello,

Thank you for your help!

I have a list of ~2300 SNPs which I expanded with max_snp_distance(500_000). The API is at v84, and I have hg38 as my chromosome. It took longer, as expected, and I got more variants in LD. However, I still got a max distance of 100KB. I find this a bit suspicious, and believe this is probably due to a technicality rather than the fact that none of my SNPs have LD further away than 100K. Either my code has some bug, or I use the Ensembl API wrong. Could you please help me find out how to get distances > 100K?

I attach my code, a file of the tag SNPs I have expanded, and some histograms with different r2 to show the distribution of distances. The file of the actual expanded LD SNPs is large, ~45MB, but I can send it if you want to take a look. The plots are inline images, let me know if you cannot see them. The x axis are the distances between a tagSNP and a variant in LD. Especially the plot where r2 is 0, makes it quite clear a cutoff at 100k is present. Such a defined threshold seems more human than biological.

The max distances with the different r2 is as follows:
r2 = 0: max distance of 100,000
Number of expanded SNPs in LD: 931,299

r2 = 0.5: max distance of 99,998
Number of expanded SNPs in LD: 146,881

r2 = 0.7: max distance of 99,994
Number of expanded SNPs in LD: 88,862

r2 = 0.8: max distance of 99,986
Number of expanded SNPs in LD: 67,744

r2 = 0.9: max distance of 99,986
Number of expanded SNPs in LD: 50,025

r2  = 1: max distance of 99,986
Number of expanded SNPs in LD: 28,046

Inline plots:
r2 = 0:
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