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. 2013 Feb 6;8(2):e54812. doi: 10.1371/journal.pone.0054812

Table 2. MixMAP results in GLGC for IBC array loci with evidence for single SNP LDL-C association.

Position Single SNP p-values
Locus‡ Chr Start Stop Gene Name‡ Single SNP*1 MixMAP*2 # of SNPs Min Median Max
LDLRAP9 1 25568422 25749764 RHCE + - 4 3.10E-10 2.07E-05 1.98E-003
1 25762009 25767440 LDLRAP1 +a - 5 6.38E-05 3.17E-04 3.59E-002
PCSK9 1 55267951 55304223 PCSK9 + + 34 1.93E-28 1.22E-05 0.8714
ANGPTL3 1 62704220 62822181 DOCK7 + - 3 2.16E-17 3.17E-17 8.62E-017
1 62827868 62845701 ANGPTL3 + - 6 1.43E-17 0.18 0.973
SORT1 1 109745416 109745601 PSMA5 + - 2 1.56E-12 – 8.78E-011
1 109590236 109623689 CELSR2 + + 23 9.70E−171 2.31E-29 0.7796
1 109622442 109630036 PSRC1 + + 7 4.93E-164 1.44E-08 0.3477
1 109633806 109650249 MYBPHL + + 10 7.89E-28 1.68E-12 0.07608
1 109652649 109742656 SORT1 + + 28 1.63E-23 1.14E-12 0.8676
APOB 2 21052397 21165196 APOB + + 49 4.48E-114 7.51E-18 0.9401
ABCG5/8 2 43921795 43958429 ABCG8 + + 21 1.73E-47 0.001336 0.9203
2 43893343 43924284 ABCG5 - + 25 8.14E-08 0.07115 0.4809
RAB3GAP1† 2 136262314 136307216 LCT - + 11 1.13E-05 5.36E-05 0.6756
HMGCR 5 74667257 74693036 HMGCR + + 11 5.12E-45 5.70E-13 0.7414
74711473 74793312 COL4A3BP + + 9 2.90E-35 2.07E-12 0.4902
TIMD4† 5 155681482 156120506 SGCDc - + 66 3.38E-07 0.113065 0.8402
5 156445860 156469146 HAVCR2c - + 11 0.003134 0.009268 0.5286
HFE 6 26196869 26204727 HFE + - 8 6.07-10 5.92E-03 6.64E-001
HLA 6 32512043 32535726 HLA-DRA + + 13 7.28E-13 0.01082 0.7028
6 31469689 31498389 MICA - + 20 2.60E-06 0.011105 0.6733
6 31644203 31652541 LTA - + 18 0.0002275 0.01893 0.9282
6 32000620 32025519 C2 - + 14 3.97E-05 0.041215 0.4409
6 32899566 32917826 TAP2 - + 25 4.81E-07 0.116 0.8873
LPA 6 160810340 160838285 LPAL2 - + 9 2.38E-06 0.0008496 0.6485
6 160873025 161011583 LPA + + 29 1.36E-15 1.36E-05 0.9738
NPC1L1 7 44519763 44551551 NPC1L1 + + 14 4.93E-11 7.35E-05 0.9729
TRIB1 8 126506812 126573908 TRIB1 + + 49 2.83E-29 7.98E-10 0.9683
ABO 9 135197039 135229220 SURF1 + - 5 1.57E-12 1.60E-02 1.49E-001
9 135121293 135145180 ABO + + 15 4.60E-21 0.0003062 0.01966
ABCA1 9 106585724 107556417 ABCA1 +b + 121 1.12E-07 0.2582 0.979
FADS1-2-3 11 61305135 61361791 FADS1 + + 9 1.75E-21 8.41E-21 0.0006352
11 61353788 61389758 FADS2 + - 6 2.12E-20 5.75E-04 7.88E-001
11 61398293 61420267 FADS3 + - 7 8.80E-10 3.72E-04 6.20E-001
APOA5-A4-C3-A1 11 116024949 116145447 BUD13 + + 6 4.21E-99 4.91E-06 0.05234
11 116152068 116168917 ZNF259 + + 9 1.47E-26 4.01E-09 0.8141
11 116157417 116170289 APOA5 + + 6 2.32E-16 7.16E-09 0.04245
11 116172547 116202948 APOA4 + - 8 1.97E-08 0.069 0.732
11 116212611 116233487 APOA1 + - 12 1.18E-09 4.12E-03 0.839
11 116230513 116233840 APOC3 - - 2 7.93E-03 – 0.665
BRAP† 12 110368991 110368991 SH2B3 + - 1 1.73E-09 – –
12 110714419 110731337 ALDH2 + + 7 5.42E-09 5.92E-06 0.4789
12 110971201 110971201 C12orf30 + - 1 6.89E-09 – –
HNF1A† 12 119890027 119923981 TCF1 + + 13 3.61E-15 0.03823 0.437
CETP 16 55548996 55576893 CETP + + 44 1.64E-12 0.003372 0.942
HPR 16 70640155 70671503 HPR + - 6 1.75E-22 1.35E-05 2.84E-001
LDLR 19 10663792 10663792 ILF3c + - 1 2.01E-14 – –
19 11024562 11024562 SMARCA4 + - 1 1.74E-25 – –
19 11063306 11103658 LDLR + + 28 4.28E-117 6.98E-10 0.5643
CILP2 19 19185443 19329924 NCAN + + 12 1.42E-19 0.06043 0.5713
19 19324032 19366087 KIAA0892 + - 5 1.78E-15 5.68E-04 3.58E-001
19 19515117 19524850 CILP2 + - 5 5.99E-21 0.506 0.631
19 19526643 19584215 PBX4 + - 7 2.52E-18 6.89E-02 4.81E-001
19 19580840 19619190 EDG4 + - 7 1.02E-17 0.065 0.051
APOE-C1-C2 19 49929652 49944944 BCL3 + + 6 4.21E-99 4.91E-06 0.05234
19 50021054 50021054 BCAM + - 1 6.18E-63 – –
19 50043777 50074877 PVRL2 + + 16 5.11E-67 1.05E-08 0.6158
19 50081014 50119488 APOE + + 8 3.76E-110 2.67E-07 0.9906
19 50100676 50100676 TOMM40 + - 1 3.76E-110 – –
19 50139001 50145079 APOC4 + - 5 1.08E-72 6.08E-03 0.458
19 50139018 50149020 APOC2 + - 7 2.56E-10 0.074 0.652
TOP1† 20 39225477 39230879 PLCG1 + - 2 5.99E-15 – 0.764

For the 31827 SNPs in 2960 genes interrogated in Global Lipids Genetic Consortium (GLGC) summary data [1], MixMAP detects 36 genes in 21 of 26 loci detected by single SNP analysis in GLGC. Coverage of genes detected by both approaches is higher, while the median p-value is generally lower, than that of genes detected by single SNP analysis alone. ‡Genes were assigned to a locus identified in the GLGC [1] if SNPs in that gene were within 500 Kb of or had linkage disequilibrium (LD) Inline graphic with the top SNP at a GLGC genome wide significant locus. †Genes designated at genome wide significant locus in GLGC were not directly interrogated in IBC array data; Inline graphic Inline graphic indicates corresponding gene detected and – indicates corresponding gene not detected; Inline graphicgenome wide significant threshold (Inline graphic); Inline graphicBonferroni correction based on the number of genes (Inline graphic); Inline graphicGene is significant based on Single SNP approach in [1] (Table 1) but significant SNP is not included in IBC array under study; Inline graphicThis gene is significant based on single SNP approach for TC and HDL in GLGC [1] (Table 1) and conditionally associated with LDL (Table 6 Supp); Inline graphicLimited LD (Inline graphic) detected; however, assigned to same locus due to physical proximity (Inline graphicKb) and/or multiple candidate genes in the region. These may represent signal for LDL-C independent of the established GLGC locus.