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. Author manuscript; available in PMC: 2018 Apr 30.
Published in final edited form as: Nat Genet. 2017 Oct 30;49(12):1758–1766. doi: 10.1038/ng.3977

Table 1.

Protein-altering variants at novel loci associated with lipid levels

Chromosome:position (hg19) rs ID Alleles (reference/alternative) Gene Protein change N Frequency alternative allele Trait P value Beta SE
Total Cholesterol
2:101627925 rs1062062 C/T TBC1D8 p.Gly954Arg 292898 0.12 TC 1×10−7 −0.021 0.0040
4:69343287 rs976002 A/G TMPRSS11E p.Tyr303Cys 293961 0.23 TC
LDL-C		 5×10−20
3×10−12 		0.029,
0.023		 0.0031,
0.0033
4:155489608 rs6054 C/T FGB p.Pro206Leu 307997 0.0038 TC
TG		 5×10−12
3×10−11 		0.14,
0.14		 0.021,
0.021
9:5073770 rs77375493 G/T JAK2 p.Val617Phe 188412 0.0011 TC
LDL-C		 1×10−11
2×10−9 		−0.32,
−0.30		 0.047,
0.049
9:117166246 rs2274159 A/G DFNB31 p.Val400Ala 319677 0.48 TC 2×10−7 0.013 0.0026
17:8216468 rs871841 T/C ARHGEF15 p.Leu277Pro 298725 0.52 TC 2×10−8 0.015 0.0026
19:18304700 rs874628 A/G MPV17L2 p.Met72Val 319677 0.26 TC 2×10−7 0.015 0.0029
LDL Cholesterol
1:155106227 rs4745 A/T EFNA1 p.Asp137Val 291361 0.49 LDL-C 5×10−8 −0.015 0.0027
4:187120211 rs13146272 C/A CYP4V2 p.Gln259Lys 295826 0.62 LDL-C 1×10−7 −0.015 0.0027
5:176520243 rs351855 G/A FGFR4 p.Gly388Arg 233058 0.29 LDL-C 4×10−8 −0.018 0.0033
9:139368953 rs3812594 G/A SEC16A p.Arg1039Cys 293723 0.24 LDL-C 2×10−8 −0.018 0.0031
10:118397971 rs10885997 A/G PNLIPRP2 p.Gln387Arg 258146 0.41 LDL-C 9×10−8 0.015 0.0029
10:124610027 rs1891110 G/A FAM24B p.Pro2Leu 295826 0.55 LDL-C
TC		 8×10−15
2×10−13 		0.021,
0.019		 0.0026,
0.0025
12:72179446 rs61754230 C/T RAB21 p.Ser224Phe 292762 0.015 LDL-C 1×10−7 0.057 0.011
14:94844947 rs28929474 C/T SERPINA1 p.Glu366Lys 290263 0.015 LDL-C
TC		 4×10−14
6×10−14 		0.081,
0.078		 0.011,
0.010
17:26694861 rs704 G/A VTN p.Thr400Met 295826 0.49 LDL-C
TC		 6×10−16
1×10−8 		0.021,
0.015		 0.0026,
0.0025
19:42584958 rs201596848 C/T ZNF574 p.Arg734Cys 273744 0.0014 LDL-C 5×10−12 −0.255 0.037
Triglycerides
2:202122995 rs3769823 A/G CASP8 p.Lys14Arg 295956 0.69 TG 1×10−9 0.017 0.0028
5:131008194 rs26008 T/C FNIP1 p.Gln620Arg 305699 0.92 TG 5×10−9 −0.028 0.0048
10:52573772 rs41274050 C/T A1CF p.Gly398Ser 299984 0.0072 TG
TC		 4×10−11
1×10−7 		0.10,
0.08		 0.015, 0.015
13:45970147 rs138358301 A/G SLC25A30 p.Phe280Leu 301087 0.0035 TG 3×10−11 0.15 0.022
15:40751555 rs3803357 C/A BAHD1 p.Gln298Lys 305699 0.55 TG 1×10−10 −0.017 0.0026
17:17409560 rs7946 C/T PEMT p.Val212Met 304420 0.67 TG 1×10−8 −0.016 0.0029
20:56140439 rs41302559 G/A PCK1 p.Arg483Gln 299984 0.0021 TG 9×10−8 −0.154 0.029
22:17625915 rs35665085 G/A CECR5 p.Thr149Met 302582 0.050 TG 5×10−8 0.032 0.0059
HDL Cholesterol
2:272203 rs11553746 C/T ACP1 p.Thr95Ile 313148 0.33 HDL-C 5×10−8 0.015 0.0027
2:54482553 rs17189743 G/A TSPYL6 p.Arg246Cys 314415 0.029 HDL-C 2×10−7 0.040 0.0076
2:179309165 rs75862065 G/A PRKRA p.Pro116Leu 105490 0.29 HDL-C 2×10−7 0.026 0.0050
3:48229366 rs146179438 C/A CDC25A p.Gln25His 288306 0.020 HDL-C 3×10−11 −0.063 0.0095
5:176637576 rs28932178 T/C NSD1 p.Ser457Pro 310567 0.17 HDL-C 8×10−9 0.020 0.0035
11:64031241 rs35169799 C/T PLCB3 p.Ser778Leu 314415 0.060 HDL-C
TG		 4×10−13,
3×10−12 		−0.039,
0.038		 0.0054,
0.0055
11:68703959 rs622082 A/G IGHMBP2 p.Thr671Ala 316391 0.31 HDL-C 6×10−10 −0.017 0.0028
16:4755108 rs78074706 G/A ANKS3 p.Arg286Trp 315298 0.022 HDL-C 1×10−9 −0.053 0.0087
16:69385641 rs76116020 A/G TMED6 p.Phe6Leu 310822 0.033 HDL-C 7×10−9 −0.041 0.0071
17:40257163 rs2074158 T/C DHX58 p.Gln425Arg 244331 0.19 HDL-C 1×10−7 −0.020 0.0038