Table 4 Summary of fine mapping of replicated loci
From: Transferability and Fine Mapping of genome-wide associated loci for lipids in African Americans
SNP (local SNP if replicated locally) | Haplotype block length (CEU) | Haplotype block length (YRI) | Comment |
|---|---|---|---|
rs10401969 | 96 kb | 88 kb | Â |
rs11869286 | 19 kb | 49 kb | Â |
rs12678919 | 53 kb | Not in block | Higher peak is rs12679834 (p = 0.0010), in same haplotype block as rs12678919 in CEU, not in YRI. (Figure 2) |
rs2081687 | 17 kb | 1 kb | Rs10088541 is a higher peak nearby (p = 7.5 x 10-5). R2 between rs10088541 and index SNP = 0.75 among CEU, but only 0.03 in HUFS. (Figure 3) |
rs2131925 | 298 kb | 201 kb | Â |
rs2972146 (rs2943652) | Â | Â | Index SNP not successfully genotyped or imputed in HUFS: no fine-mapping comparisons possible. |
rs3764261 (rs173539) | Â | Â | Index SNP not successfully genotyped or imputed in HUFS: no fine-mapping comparisons possible. |
rs3764261 (rs1800775) | Â | Â | Index SNP not successfully genotyped or imputed in HUFS: no fine-mapping comparisons possible. |
rs3764261 (rs4783961) | Â | Â | Index SNP not successfully genotyped or imputed in HUFS: no fine-mapping comparisons possible. |
rs4420638 | Not in block | Not in block | Â |
rs629301 | 16 kb | 468 bp | (Figure 4) |
rs7941030 (rs6589939) | 40 kb | Not in block | Higher peak is at SNP rs6589939 (p = 0.005 vs. p = 0.10), which is in the same 40 kb block as the index SNP among CEU. |