Table 6.
Regions with top models chosen by stepwise (SW), independent fine-mapping and Flashfm where there is a noticeable reduction in SNP group sizes and/or PP of top model.
| Region | Trait | Stepwise Model | Independent | Flashfm | Change by Flashfm | |||
|---|---|---|---|---|---|---|---|---|
| Model (Group Size) | PP | Model (Group Size) | PP | PP gain | Group reduction | |||
| 1:55517883-55674945 (PCSK9,USP24) | LDL | rs11804420/A | A:rs45613943 (4) | 0.5 | A: rs45613943 (3) | 0.63 | 0.13 | A = 25% |
| TC | rs11804420/A | A:rs45613943 (4) | 0.6 | A:rs45613943 (3) | 0.76 | 0.12 | ||
| 2:62716187-62887884 (TMEM17) | ALP | rs13403582/B | B:rs7580494 (8) | 0.66 | B:rs6750204 (5) | 0.73 | 0.07 | J = 0 B = 38% |
| PLT | rs765799086/J | J:rs765799086 (1) | 0.46 | B + J J:rs765799086 (1) | 0.62 | 0.16 | ||
| 15:58718136-58742605 (LIPC) | HDL | rs1800588/G | G:rs8033940 (5) | 0.42 | G:rs1800588 (4) | 0.52 | 0.10 | A = 20% |
| TG | rs1077835/G | G:rs8033940 (5) | 0.56 | G:rs1800588 (4) | 0.66 | 0.10 | ||
| 16:441156-557188 (LOC100134368, NME4, DECR2, RAB11FIP3) | MCV | rs75167983/L + rs150717215/C + rs147633052/A |
L + C + A + B L:rs144739959 (4) C:rs150717215 (2) A:rs147633052 (14) B:rs116567883 (1) |
0.42 |
L + C + A + B L:rs75167983 (1) C:rs150717215 (2) A = rs147633052 (14) B = rs116567883 (1) |
0.46 | 0.04 |
L = 75% C = 0 A = 0 B = 0 D = 0 |
| MCH | rs75167983/L + rs150717215/C + rs147633052/A + rs116567883/B. | L + C + A + B | 0.15 | L + C + A + B | 0.26 | 0.11 | ||
|
L + C + A + B + D D:rs553374841 (2) |
0.15 |
L + C + A + B + D D = rs553374841 (2) |
0.16 | 0.01 | ||||
| Bilirubin | L = rs75167983 | L = rs144739959 (4) | 0.45 | L = rs75167983 (1) | 0.63 | 0.18 | ||
| 19:45380937-45441453 (NECTIN2, TOMM40, APOE, APOC1, APOC1P1) | LDL |
rs7412/B + rs34215622/V + rs61357706/E + rs429358/L + rs367640607/D2 |
E + L + B + V + D2 E:rs113152469 (5) L:rs429358 (1) B:rs61679753 (2) V:rs34215622 (1) D2:rs367640607 (2) |
0.41 |
E + L + B + V + D2 E:rs113152469 (5) L:rs429358 (1) B:rs7412 (1) V:rs34215622 (1) D2:rs367640607 (2) |
0.40 | 0.00 |
B = 50% E2 = 25% E = 0 L = 0 V = 0 D2 = 0 |
| TC |
rs7412/B + rs34215622/V + rs429358/L |
E + L + B + V | 0.26 | E + L + B + V | 0.41 | 0.15 | ||
| E + L + B + V + D2 | 0.25 | E + L + B + V + D2 | 0.31 | 0.06 | ||||
| TG |
rs12721054/I + rs5112/X |
E + I + Y + E2 I = rs12721054 (1) Y = rs7260330 (3) E2 = rs12721051 (4) |
0.42 |
E + I + X + E2 I = rs12721054 (1) X = rs5112 (1) E2 = rs12721051 (3) |
0.63 | 0.21 | ||
| HDL | rs75627662/A | A = rs75627662 (1) | 0.38 | B = rs7412 (1) | 0.42 | 0.03 | ||
Each row summarises results for a single region, defined by chromosome, start and end base-pair position and nearby gene(s). Each cell lists the SNP groups in a model; model A+B indicates all 2-SNP models with one SNP from group A and one SNP from group B. The number of SNPs in each group is given in brackets beside each group in the model. Here we list a representative SNP from each group; rs IDs are from build GRCh37/hg19. The SNPs belonging to each group and their functional annotations are given in Supplementary Data 1.22.