Table 2.
Novel X chromosome lipid-associated loci
| RSID | Position in chromosome X (hg19) | EA/NEA | Annotation (closest gene) |
Associated trait | EAF | N | Effect size (SE) from METAL |
Ancestry and GC corrected p-value from MR-MEGA | Sex difference p-value |
|---|---|---|---|---|---|---|---|---|---|
| rs35143646 | 2,856,155 | T/C | Missense (ARSL) | LDL-C | 0.6352 | 1,038,070 |
0.0115 (0.0014) |
1.83x10− 16 | 0.1791 |
| TC | 0.6449 | 1,100,310 |
0.0091 (0.0014) |
1.47x10− 14 | 0.08484 | ||||
| nonHDL-C | 0.6822 | 712,983 |
0.0112 (0.0017) |
2.08x10− 11 | 0.5294 | ||||
| rs5934507 | 8,917,206 | G/A | Intergenic (FAM9B) | HDL-C | 0.274 | 1,158,000 | − 0.0076 (0.0012) | 9.99x10− 10 | 5.83x10− 4 |
| rs191084933 | 14,133,208 | G/A | Intergenic (GEMIN8) | HDL-C | 0.0055 | 1,052,630 |
0.0694 (0.0101) |
5.20x10− 10 | 0.3272 |
| rs7888119 | 16,813,128 | T/C | Intronic (TXLNG) | HDL-C | 0.546 | 1,158,000 |
0.0114 (0.0012) |
1.47x10− 20 | 0.2212 |
| rs2230488 | 20,204,461 | T/G | Synonymous (RPS6KA3) | LDL-C | 0.1772 | 1,135,110 | − 0.0143 (0.0015) | 6.90x10− 18 | 0.9297 |
| TC | 0.1745 | 1,237,380 | − 0.0114 (0.0014) | 4.68x10− 12 | 0.8906 | ||||
| rs6527977 | 20,322,238 | A/C | Intergenic (RPS6KA3) | nonHDL-C | 0.1602 | 789,200 | − 0.0147 (0.0020) | 3.06x10− 10 | 0.7000 |
| rs12012576 | 21,813,178 | G/A | Intergenic (SMPX) | TG | 0.3103 | 1,160,340 | − 0.0072 (0.0012) | 4.88x10− 8 | 0.4558 |
| rs6609434 | 46,636,767 | C/A | Intergenic (SLC9A7) | HDL-C | 0.4959 | 767,051 |
0.0060 (0.0014) |
4.25x10− 8 | 0.9035 |
| rs113957181 | 49,848,600 | A/C | Intronic (CLCN5) | HDL-C | 0.0566 | 452,268 | − 0.0297 (0.0047) | 1.39x10− 9 | 0.1896 |
| rs782397956 | 53,993,589 | T/C | Intronic (PHF8) | HDL-C | 0.2050 | 621,342 | − 0.0009 (0.0021) | 2.65x10− 15 | 0.2585 |
| rs72305711 | 55,981,911 | T/TTA | Intronic (RP13-188A5.1) | HDL-C | 0.1111 | 534,967 | − 0.0167 (0.0033) | 2.22x10− 22 | 0.03202 |
| rs5914559 | 56,139,739 | G/T | Intergenic (KLF8) | TG | 0.6697 | 738,155 | − 0.0131 (0.0016) | 4.44x10− 16 | 0.3224 |
| rs5964416 | 64,368,487 | A/C | Intergenic (ZC4H2) | HDL-C | 0.0924 | 614,283 | − 0.0316 (0.0016) | 2.68x10− 11 | 0.1478 |
| rs5965342 | 66,204,144 | T/C | Intergenic (EDA2R) | HDL-C | 0.2037 | 745,721 | − 0.0212 (0.0020) | 1.20x10− 29 | 0.02050 |
| rs505520 | 66,258,914 | C/A | Intergenic (EDA2R) | TG | 0.2191 | 750,415 |
0.0217 (0.0019) |
2.91x10− 30 | 0.004371 |
| rs771540123 | 67,967,645 | A/G | Intergenic (STARD8) | nonHDL-C | 0.0027 | 15,311 |
− 0.0202 (0.115) |
1.61x10− 9 | NA |
| rs5937000 | 70,047,788 | C/T | Intronic (TEX11) | HDL-C | 0.4515 | 796,971 |
0.0075 (0.0013) |
9.55x10− 9 | 0.02603 |
| rs5938008 | 74,496,225 | C/T | Intronic (UPRT) | HDL-C | 0.9167 | 1,072,550 |
0.0174 (0.003) |
1.24x10− 8 | 0.7235 |
| rs1802288 | 99,890,204 | T/C | Missense (TSPAN6) | LDL-C | 0.1665 | 714,113 |
0.0159 (0.0019) |
1.42x10− 16 | 0.9642 |
| TC | 0.1684 | 753,479 |
0.0128 (0.0018) |
2.49x10− 10 | 0.8646 | ||||
| rs139144471 | 117,829,694 | G/T | Intergenic (DOCK11) | HDL-C | 0.0876 | 1,098,540 | − 0.0121 (0.0022) | 1.16x10− 8 | 0.1111 |
| rs6648533 | 122,804,678 | C/T | Intronic (THOC2) | HDL-C | 0.299 | 1,106,090 | − 0.0100 (0.0013) | 2.24x10− 12 | 0.4516 |
| rs5929738 | 135,265,287 | C/A | Intronic (FHL1) | HDL-C | 0.4679 | 970,330 |
0.0071 (0.0011) |
3.21x10− 10 | 0.4197 |
| rs5975692 | 135,266,089 | G/A | Intronic (FHL1) | TG | 0.465 | 1,138,740 | − 0.0084 (0.0011) | 7.87x10− 12 | 0.9215 |
| rs2070826 | 153,582,198 | C/T | Intronic (FLNA) | HDL-C | 0.1427 | 1,141,020 |
0.0170 (0.0017) |
6.65x10− 26 | 0.08671 |
| rs11593 | 153,627,145 | C/A | Intronic (RPL10) | TG | 0.1586 | 1,143,360 | − 0.0166 (0.0017) | 5.76x10− 21 | 0.8695 |
| rs7886627 | 153,679,609 | G/A | Intergenic (FAM50A) | nonHDL-C | 0.1214 | 771,706 | − 0.0147 (0.0022) | 9.26x10− 9 | 0.06819 |
| rs1050828 | 153,764,217 | T/C | Missense (G6PD) | LDL-C | 0.0113 | 744,968 | − 0.0514 (0.0061) | 2.54x10− 15 | 0.6533 |
| rs762517 | 153,764,734 | A/G | Intronic (G6PD) | TC | 0.0142 | 798,600 | − 0.0480 (0.0057) | 5.26x10− 16 | 0.7594 |
EA Effect allele, NEA Non-effect allele, EAF Effect allele frequency, N Number of samples, SE Standard error of the effect size, GC Genomic control, LDL-C Low-density lipoprotein cholesterol, TC Total cholesterol, HDL-C High-density lipoprotein cholesterol, TG Triglycerides