Table 3.
Comparison of fine-mapping results between JAM single trait and flashfm multi-trait fine mapping
| Region (Nearest genes) | Trait | JAM CS99 size | flashfm CS99 size | Size Reduction (%) | JAM top SNPs | JAM MPP of top SNPs | flashfm top SNPs | flashfm MPP of Top SNPs | LD (r2) between JAM & flashfm top SNPs |
|---|---|---|---|---|---|---|---|---|---|
| 16:56889590-57089590(CETP, HERPUD1) | HDL | 24 | 24 | 0 | >10 | all >0.9 | >10 | all >0.9 | 1 |
| LDL | 5 | 2 | 60 | rs247616 | 0.501 | rs183130 | 0.999 | 0.992 | |
| TC | 24 | 23 | 4.2 | rs1801706 | 0.925 | rs1801706 | 0.983 | 1 | |
| TG | 7 | 2 | 71.4 | rs4783961 | 0.332 | rs183130 | 0.999 | 0.470 | |
| 16:71465787-71665787(CHSY4, ZNF19, TAT) | HDL | 8 | 4 | 50 | rs78302875 | 0.406 | rs78302875 | 0.920 | 1 |
| LDL | 43 | 33 | 23.3 |
rs77223082 rs144454811 rs72799815 rs72799820 |
all >0.9 |
rs77223082 rs144454811 rs72799815 rs72799820 |
all >0.9 | 1 | |
| TC | 21 | 20 | 4.8 |
rs115532837 rs57422486 rs78302875 rs144454811 rs116408331 rs72799815 rs72799820 |
all >0.9 |
rs115532837 rs57422486 rs78302875 rs144454811 rs116408331 rs72799815 rs72799820 |
all >0.9 | 1 | |
| 21:46753876-46975775(SLC19A1, COL18A1) | HDL | 18 | 16 | 11.1 | rs116386571 | 0.863 | rs116386571 | 0.999 | 1 |
| TC | 16 | 2 | 87.5 | rs77974343 | 0.275 | rs116386571 | 0.989 | 0.686 | |
| TG | 17 | 8 | 52.9 | rs116386571 | 1.0 | rs116386571 | 1.0 | 1 |
CS99 size; 99 credible set size, MPP marginal posterior probability of causality.