Table 1.
Serum lipid-associated loci with eQTL annotations
| Chr | rsid | Major allele and minor allele (minor allele frequency) | Position (hg19) | Associated traits | eGene | eQTL signal (Subcutaneous adipose) | eQTL signal (Liver) | |||
|---|---|---|---|---|---|---|---|---|---|---|
| P_MuTHER | P_GTEx (V4) | P_U_of _C | P_U_of _W | P_Merck | ||||||
| 2 | rs12622106 | C>T (0.44) | 20883561 | HDL-C, LDL-C | C2orf43 | 5.10E-36 | 9.90E-10 | |||
| 2 | rs2834578 | T>C (0.36) | 36059609 | TC, LDL-C | CLIC6 | 2.50E-47 | 8.50E-07 | |||
| 2 | rs2076673 | G>C (0.41) | 36124860 | TC, LDL-C | APOL5 | 2.60E-06 | 2.40E-03 | 4.10E-03 | ||
| 4 | rs1680074 | G>A (0.48) | 1279621 | TG, HDL-C | CTBP1 | 8.60E-06 | 3.00E-02 | 3.50E-02 | ||
| 5 | rs17772583 | A>G (0.43) | 131953510 | TG, TC | RAD50 | <1.0E-16 | 6.50E-06 | 4.60E-03 | ||
| 7 | rs1880118 | G>C (0.19) | 6435220 | TC, HDL-C | DAGLB | 1.00E-04 | 2.20E-12 | |||
| 10 | rs532473 | G>A (0.34) | 27669655 | TC, LDL-C | PTCHD3 | 8.40E-41 | 2.50E-09 | |||
| 10 | rs224045 | T>C (0.42) | 64525547 | TG, TC | ADO | 3.30E-03 | 1.70E-03 | 3.10E-06 | ||
| 12 | rs7296841 | A>C (0.23) | 112444109 | TG, TC | TMEM116 | 8.90E-16 | 1.30E-05 | 3.70E-05 | ||
| 12 | rs11831480 | G>T (0.12) | 132554702 | TG, LDL-C | DDX51 | <1.0E-16 | 2.60E-02 | 5.50E-03 | ||
| 13 | rs2296347 | T>G (0.43) | 52728423 | TG, TC | NEK3 | 6.20E-10 | 3.30E-02 | 1.40E-05 | ||
| 15 | rs1077834 | T>C (0.40) | 58723479 | TG, TC, HDL-C | LIPC | 7.60E-08 | 7.10E-03 | 2.50E-04 | ||
| 17 | rs2286590 | G>A (0.21) | 74683666 | TC, HDL-C | MXRA7 | 1.60E-14 | 2.30E-11 | |||
| 19 | rs3786505 | G>A (0.49) | 45490570 | TC, LDL-C | APOC4 | <1.0E-16 | 9.10E-04 | 1.50E-03 | ||
In the discovery stage, genotype–phenotype associations were performed for SNPs with eQTL annotations either in subcutaneous adipose tissue or in liver tissues. Fourteen eQTLs associated with at least two lipid components are shown in Table 1
The minor allele is considered as the effect allele in analysis
U of C an eQTL study from the University of Chicago, U of W an eQTL study from the University of Washington, Merck an eQTL study from Merck, Chr chromosome, hg19: Human Genome version 19, also known as GRCh37, eGene the gene that has a significant eQTL acting upon it, TC total cholesterol, TG triglyceride, HDL-C high-density lipoprotein cholesterol, LDL-C low-density lipoprotein cholesterol