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Table 1 Results of analyzing Dataset A with aff2sv and snpStats

From: affy2sv: an R package to pre-process Affymetrix CytoScan HD and 750K arrays for SNP, CNV, inversion and mosaicism calling

NameAFFY NamedbSNP CHR Position P value MAFNijmegen MAFToronto
S-3KHLT rs2445906 8 87901 7.995824e-10 0.4402516 0.35731132
S-3FEKM rs12429439 13 516673 7.957754e-08 0.2156250 0.09953162
S-3TIFM rs62459010 7 688240 1.007604e-07 0.1957831 0.08313253
S-3QSBZ rs4243640 14 650233 1.317467e-07 0.4108280 0.25768322
S-3XDND --- 1 510137 2.857901e-07 0.1027778 0.03154206
S-4FNLK rs4239595 19 547436 3.786156e-07 0.2225806 0.10352941
S-4LWCG rs60081206 1 483264 3.804457e-07 0.1655844 0.06721698
S-4HMDR rs10868728 9 752489 3.880796e-07 0.4024390 0.25817757
S-3FSKC rs12402205 1 510072 5.298163e-07 0.1027778 0.03271028
S-3KMMG --- 1 510066 5.298163e-07 0.1027778 0.03271028
  1. Top 10 significant SNPs obtained from the GWAS Toronto vs. Nijmegen (Dataset A) using a complete set of 429 .CEL files from Affymetrix CytoScan HD