<div dir="ltr">Hi devs,<div><br></div><div>When looking for proxy snps of rs7707921, the snp rs17243791 does not show up:</div><div><br></div><div><a href="https://rest.ensembl.org/ld/homo_sapiens/rs7707921/1000GENOMES:phase_3:CEU?window_size=500;d_prime=0;r2=0.8">https://rest.ensembl.org/ld/homo_sapiens/rs7707921/1000GENOMES:phase_3:CEU?window_size=500;d_prime=0;r2=0.8</a><br></div><div><br></div><div>But if I ask for their linkage disequilibrium explicitly:</div><div><br></div><div><a href="https://rest.ensembl.org/ld/homo_sapiens/pairwise/rs7707921/rs17243791?population_name=1000GENOMES:phase_3:CEU;d_prime=0;r2=0">https://rest.ensembl.org/ld/homo_sapiens/pairwise/rs7707921/rs17243791?population_name=1000GENOMES:phase_3:CEU;d_prime=0;r2=0</a><br></div><div><br></div><div>I can see that they are indeed in LD with an r^2 of 0.920 (above the 0.8 threshold used above).</div><div><br></div><div>The two snps are 215,400 bp away from each other, which is below the 250k up/downstream threshold, i.e. window_size=500.</div><div><br></div><div>Any clue?</div><div><br></div><div>Many thanks in advance, Ramiro Magno</div></div>