Table 2 Overview of Top Association and Linkage Results for MeanLDL-C, MeanHDL-C, and MeanTG
From: A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study
2a. Top 25 SNPs for association with MeanLDL-C, MeanHDL-C, or MeanTG based on the lowest p values of the GEE tests | ||||||
|---|---|---|---|---|---|---|
Phenotype | SNP rs ID* | Chr | Physical location (bp) | GEE P-value | FBAT P-value | gene (IN or NEAR) |
MeanLDL-C | rs287474 | 13 | 68173961 | 6.3*10-9 | 1.4*10-8 | Â |
MeanLDL-C | rs287354 | 13 | 68137953 | 3.4*10-8 | 6.8*10-8 | Â |
MeanHDL-C | rs524802 | 19 | 42138787 | 7.6*10-7 | 0.04 | Â |
MeanHDL-C | rs505717 | 19 | 42122156 | 1.2*10-6 | 0.07 | ZNF345 |
MeanHDL-C | rs544543 | 19 | 42122663 | 2.5*10-6 | 0.07 | Â |
MeanTG | rs7007075 | 8 | 138168448 | 7.7*10-6 | 0.004 | Â |
MeanHDL-C | rs3734678 | 6 | 107639853 | 8.2*10-6 | 0.009 | C6orf210 |
MeanLDL-C | rs10488824 | 11 | 81678287 | 1.4*10-5 | 0.03 | Â |
MeanTG | rs2142136 | 10 | 89753050 | 1.5*10-5 | 0.06 | BC005821| PTEN |
MeanLDL-C | rs1555173 | 6 | 85121177 | 1.7*10-5 | 0.09 | Â |
MeanHDL-C | rs688933 | 9 | 70902713 | 1.8*10-5 | 0.38 | TRPM3| AJ505026| AL136545 |
MeanTG | rs314474 | 11 | 11482634 | 1.8*10-5 | 0.09 | AB094146| IGSF4| BC047021 |
MeanHDL-C | rs966376 | 18 | 27086836 | 2.1*10-5 | 0.07 | Â |
MeanHDL-C | rs4459845 | 3 | 127400326 | 2.3*10-5 | 0.005 | ALDH1L1| CR749807 |
MeanTG | rs220840 | 11 | 114826173 | 2.5*10-5 | 0.09 | AB094146| IGSF4| BC047021 |
MeanHDL-C | rs3850301 | 14 | 58150885 | 2.8*10-5 | 8.6*10-4 | BX161433| DACT1 |
MeanLDL-C | rs1317538 | 6 | 73706132 | 3.0*10-5 | 0.02 | BC050689| KCNQ5 |
MeanHDL-C | rs7021834 | 9 | 71123639 | 3.0*10-5 | 0.003 | AL136545 |
MeanLDL-C | rs504527 | 1 | 34142701 | 3.2*10-5 | 0.007 | CSMD2 |
MeanHDL-C | rs10488779 | 11 | 79494759 | 3.6*10-5 | 0.07 | Â |
MeanLDL-C | rs2415621 | 14 | 40114277 | 3.8*10-5 | 0.005 | Â |
MeanHDL-C | rs10508518 | 10 | 17081479 | 3.9*10-5 | 0.09 | CUBN |
MeanLDL-C | rs1245058 | 1 | 69760085 | 4.1*10-5 | 0.004 | LRRC7 |
MeanHDL-C | rs10488780 | 11 | 79490000 | 4.4*10-5 | 0.06 | Â |
MeanHDL-C | rs541326 | 9 | 70936505 | 4.5*10-5 | 0.39 | TRPM3| AJ505026| AL136545 |
2b. Top 25 SNPs for association with MeanLDL-C, MeanHDL-C, or MeanTG based on the lowest p values of the FBAT tests | ||||||
Phenotype | SNP rs ID* | Chr | Physical location (bp) | GEE P-value | FBAT P-value | gene (IN or NEAR) |
MeanLDL-C | rs287474 | 13 | 68173961 | 1.4*10-8 | 6.3*10-9 | Â |
MeanLDL-C | rs287354 | 13 | 68137953 | 6.8*10-8 | 3.4*10-8 | Â |
MeanTG | rs1449866 | 3 | 144359331 | 1.8*10-5 | 0.002 | CHST2| AK131346 |
MeanTG | rs10506354 | 12 | 57759034 | 2.2*10-5 | 0.007 | Â |
MeanTG | rs10494989 | 1 | 211576634 | 2.4*10-5 | 4.7*10-4 | AY552981| AK123409| KCNK2 |
MeanTG | rs2371978 | 12 | 57759239 | 2.4*10-5 | 0.01 | Â |
MeanHDL-C | rs10495594 | 2 | 12280997 | 5.1*10-5 | 1.8*10-4 | Â |
MeanHDL-C | rs10495593 | 2 | 12279945 | 5.1*10-5 | 1.8*10-4 | Â |
MeanLDL-C | rs1411931 | 1 | 37451967 | 5.8*10-5 | 0.03 | Â |
MeanLDL-C | rs10516433 | 4 | 99800704 | 7.7*10-5 | 0.03 | TSPAN5 |
MeanHDL-C | rs2182114 | 1 | 111496269 | 8.2*10-5 | 0.07 | CHI3L2 |
MeanTG | rs1835353 | 2 | 124880057 | 8.3*10-5 | 0.02 | CNTNAP5| AK056528 |
MeanLDL-C | rs10516434 | 4 | 99802493 | 8.6*10-5 | 0.03 | TSPAN5 |
MeanLDL-C | rs10507755 | 13 | 68355991 | 1.1*10-4 | 1.6*10-4 | Â |
MeanLDL-C | rs6853079 | 4 | 99800789 | 1.3*10-4 | 0.06 | TSPAN5 |
MeanHDL-C | rs1508116 | 2 | 41437773 | 1.3*10-4 | 0.07 | Â |
MeanLDL-C | rs10518072 | 4 | 71271418 | 1.4*10-4 | 0.05 | APIN| C4orf7| CSN3 |
MeanTG | rs715260 | 4 | 9804415 | 1.5*10-4 | 0.002 | WDR1 |
MeanTG | rs7784056 | 7 | 77762038 | 1.6*10-4 | 0.12 | AB014605| MAGI2 |
MeanHDL-C | rs6505623 | 18 | 1115057 | 1.6*10-4 | 0.006 | Â |
MeanHDL-C | rs1541296 | 18 | 59173095 | 1.6*10-4 | 0.02 | FVT1 |
MeanHDL-C | rs6821328 | 4 | 54058427 | 1.7*10-4 | 0.02 | SCFD2 |
MeanTG | rs1501572 | 9 | 2894794 | 1.7*10-4 | 1.1*10-4 | Â |
MeanTG | rs4684343 | 3 | 2366098 | 1.8*10-4 | 0.24 | CNTN4 |
MeanTG | rs225634 | 6 | 142518312 | 1.9*10-4 | 2.4*10-4 | C6orf55 |
2c. Magnitude and Location of Peak LOD scores > 2.0 for MeanLDL-C, MeanHDL-C, and MeanTG | ||||||
Phenotype | Exam | Chr | Physical location (Mb) | Maximum LOD | LOD-1.5 Interval | LOD+1.5 Interval |
MeanHDL-C | 1–7 | 7 | 33485983 | 3.30 | 27810820 | 36074331 |
MeanLDL-C | 1–7 | 9 | 94130181 | 2.83 | 88057135 | 98516033 |
MeanTG | 1–7 | 1 | 153444389 | 2.73 | 151582274 | 155505440 |
MeanLDL-C | 1–7 | 3 | 196384998 | 2.12 | 187706181 | 199138789 |