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Table 3 Top repeated occurrences from 52,554 unique SNPs among 56,411 SNP-phenotype associations.

From: An Open Access Database of Genome-wide Association Results

SNPid Repeat assoc. Gene(s) Trait(s) P value range Chr Position Gene size SNP on platforms? Perfect CEU LD proxies on other platforms?
rs4420638 11 APOE/APOC cluster Lipids, Alzheimer's, CAD 1.7E-4 to 1.0E-60 19 50114786 4 kb Affymetrix, Illumina Y
rs599839 8 PSRC1 (near CELSR2, SORT1) Lipids, CAD 2.2E-5 to 1.2E-33 1 109623689 88 kb Affymetrix, Illumina Y
rs693 8 APOB Lipids 6.8E-4 to 1.0E-21 2 21085700 43 kb Affymetrix, Illumina Y
rs17482753 6 LPL Lipids 3.6E-5 to 5.9E-19 8 19876926 29 kb Affymetrix Y
rs780094 6 GCKR Triglycerides, Crohn's 6.0E-3 to 1.0E-15 2 27594741 27 kb Affymetrix, Illumina Y
rs1801282 6 PPARG TypeII, Alzheimer's, Obesity 4.5E-2 to 1.7E-6 3 12368125 146 kb Affymetrix, Illumina Y
rs910049 5 MHC locus (C6orf10) TypeII, TypeI, MS, CAD 7.8E-4 to 3.0E-93 6 32423705 79 kb Affymetrix, Illumina Y
rs2076530 5 MHC locus (BTNL2) MS, TypeI, RA 3.2E-10 to 6.7E-74 6 32471794 12 kb Affymetrix, Illumina Y
rs7901695 5 TCF7L2 TypeII, Waist:Height 2.6E-4 to 1.0E-48 10 114744078 216 kb Affymetrix, Illumina Y
rs7903146 5 TCF7L2 TypeII 5.5E-8 to 1.0E-48 10 114748339 216 kb Illumina N
rs4506565 5 TCF7L2 TypeII, BMI 8.6E-4 to 2.3E-31 10 114746031 216 kb Affymetrix N
rs10503669 5 LPL Lipids 9.1E-4 to 3.9E-22 8 19891970 29 kb Affymetrix Y
rs562338 5 APOB Lipids 2.2E-6 to 5.6E-22 2 21141826 43 kb Affymetrix Y
rs11209026 5 IL23R Crohn's, Psoriasis 4.8E-4 to 6.6E-19 1 67478546 93 kb Affymetrix, Illumina Y
rs8050136 5 FTO BMI, TypeII 9.8E-7 to 7.3E-14 16 52373776 410 kb Affymetrix, Illumina Y
rs9939609 5 FTO BMI, TypeII 1.9E-6 to 9.0E-12 16 52378028 410 kb Affymetrix Y
rs4970834 5 CELSR2 (near SORT1, PSRC1) Lipids, CAD 3.4E-4 to 3.0E-11 1 109616403 26 kb Affymetrix, Illumina Y
rs1111875 5 HHEX TypeII 1.4E-3 to 5.7E-10 10 94452862 6 kb Affymetrix, Illumina Y
rs13266634 5 SLC30A8 TypeII 3.3E-6 to 5.3E-8 8 118253964 42 kb Illumina N
rs968671 5 GABRG3 BMI, Hypertension 3.3E-4 to 2.5E-6 15 25036654 650 kb Affymetrix N
rs7034356 5 RAPGEF1 BMI 3.7E-4 to 1.3E-5 9 133468838 161 kb Affymetrix Y
rs4740294 5 RAPGEF1 BMI 8.3E-4 to 1.3E-5 9 133462842 161 kb Affymetrix Y
rs481843 5 Intergenic (near APO cluster, BUD13) Lipids, Alzheimer's 9.3E-4 to 2.1E-5 11 116031077 - Affymetrix Y
rs2889849 5 PIGU BMI, Lipids 8.8E-4 to 1.9E-4 20 32627938 117 kb Affymetrix, Illumina Y
rs10498015 5 SPAG16 Lipids, Hgt, Wgt 9.7E-4 to 1.2E-4 2 214425824 165 kb Affymetrix, Illumina Y
  1. Highly repeated occurrences of unique SNPs among 56,411 SNP-phenotype associations. We report the presence of these SNPs and whether a perfect proxy LD SNP exists based on the HapMap CEU population, on both Affymetrix and Illumina platforms, and the other platform in the case of a SNP only genotyped on an array from one company. This information was determined using the SNAP tool [33] and demonstrates that signals from a small minority of these SNPs could be missed depending on the platform applied in each case. Underlined entries represent newly recognized loci or phenotype associations.