Table 3.
Effects of spatial eQTL SNPs on genes involved in lipid metabolism (IPA knowledgebase) that are expressed (RPKM > 1.0) in subcutaneous and visceral adipose, skeletal muscles, and pancreas.
| eQTL SNP (rs#) | OR/Beta | OR/Beta direction | Disease/Trait | Trait description¥ | GWAS-mapped gene | CoDeS3D-mapped gene | Effect size# | |||
|---|---|---|---|---|---|---|---|---|---|---|
| Adipose subcut· | Adipose visceral | Skeletal muscle | Pancreas | |||||||
| SNPS: TYPE 2 DIABETES; DISEASE RISK: POSITIVE* | ||||||||||
| 507506 | 0.022 | Decrease | Adiponectin levels | DLG4 | ACADVL | −0.20 | – | – | – | |
| 507506 | 0.022 | Decrease | Adiponectin levels | DLG4 | CLDN7 | −0.36 | −0.44 | −0.56§ | – | |
| 174541 | 0.28 | Increase | Metabolite levels | adrenate | FEN1-FADS1 | FADS1 | – | – | −0.21 | −0.70 |
| 174550 | ND | Fasting glucose-related | FADS1 | FADS1 | – | – | −0.20 | −0.73 | ||
| 7945071 | 3.012 | Increase | Cognitive function | RAVLT | LOC105369486 | FDX1 | – | 0.23 | – | – |
| 2290402 | ND | Type 2 diabetes | AA | TMEM175 | IDUA | – | −0.41 | −0.29 | – | |
| 1515110 | 0.022 | Decrease | Adiponectin levels | LOC646736-LOC105373913 | IRS1 | −0.26 | – | – | – | |
| 2943640 | 1.09 | Type 2 diabetes | LOC646736-LOC105373913 | IRS1 | −0.31 | – | – | – | ||
| 2943641 | 1.19 | Type 2 diabetes and other traits | LOC646736-LOC105373913 | IRS1 | −0.29 | – | – | – | ||
| 925735 | 0.02 | Decrease | Adiponectin levels | LOC105373913-LOC105373915 | IRS1 | −0.27 | – | – | – | |
| 10510110 | 1.05 | Type 2 diabetes | PLEKHA1-LOC105378525 | PLEKHA1 | −0.20 | – | −0.14 | – | ||
| 7493 | 1.06 | Yu-Zhi constitution type in type 2 diabetes | Genotype model | PON2 | PON2 | – | – | −0.28 | −0.37 | |
| SNPS: TYPE 2 DIABETES; DISEASE RISK: NEGATIVE* | ||||||||||
| 849134 | 1.13 | Type 2 diabetes | JAZF1 | JAZF1 | 0.20 | 0.25 | 0.27 | 0.52 | ||
| 849135 | 1.12 | Type 2 diabetes | JAZF1 | JAZF1 | 0.20 | 0.25 | 0.27 | 0.52 | ||
| 864745 | 1.1 | Type 2 diabetes | JAZF1 | JAZF1 | 0.20 | 0.24 | 0.27 | 0.51 | ||
| 2290402 | ND | Type 2 diabetes | AA | TMEM175 | DGKQ | −0.30 | – | – | – | |
| 507506 | 0.022 | Decrease | Adiponectin levels | DLG4 | CTDNEP1 | 0.21 | – | – | – | |
| SNPS: OBESITY; DISEASE RISK: POSITIVE* | ||||||||||
| 2230061 | 0.06 | Decrease | Fat body mass | Adjusted by Lean body mass | CTSS | ARNT | – | 0.19 | – | – |
| 2230061 | 0.06 | Decrease | Fat body mass | Adjusted by Lean body mass | CTSS | CTSS | 0.17 | – | 0.29§ | 0.33 |
| 8050907 | 0.03 | Increase | Obesity-related traits | Total antioxidants | PKD2L1 | HMOX2 | – | – | 0.66 | – |
| 10540 | 0.028 | Increase | Body mass index | EA, men | RNH1 | HRAS | −0.31 | – | −0.24 | – |
| 2176040 | 0.024 | Increase | Body mass index | EA, men | LOC646736-LOC105373913 | IRS1 | −0.29 | – | – | – |
| 4144743 | 0.023 | Increase | Body mass index | EA | MYL4-ITGB3 | ITGB3 | −0.33 | – | −0.31§ | – |
| 1805081 | 1.41 | Obesity | Adults | NPC1 | NPC1 | 0.54 | 0.45 | 0.14 | 0.40 | |
| 1808579 | 0.022 | Increase | Body mass index | EA, women | C18orf8, NPC1 | NPC1 | 0.45 | 0.37 | 0.13 | 0.38 |
| 4888671 | 0.03 | Increase | Obesity-related traits | Folate | NUDT7-VAT1L | NUDT7 | 0.44 | 0.46 | – | 0.58 |
| 11247915 | 0.03 | Increase | Obesity-related traits | Calorimeter activity | ALLC, LOC105373393 | PIGV | – | – | −0.2 | – |
| 10540 | 0.028 | Increase | Body mass index | EA, men | RNH1 | PTDSS2 | −0.36 | −0.43 | −0.36 | – |
| 2650492 | 0.021 | Increase | Body mass index | EA | SBK1 | SULT1A1 | – | – | −0.29 | −0.51 |
| SNPS: OBESITY; DISEASE RISK: NEGATIVE* | ||||||||||
| 17001654 | 0.03 | Increase | Body mass index | SCARB2 | NAAA | 0.35 | – | – | – | |
| 7503807 | 1.04 | Obesity | Overweight | RPTOR | RPTOR | – | – | 0.16 | – | |
The effect size of the eQTL as defined by GTEx. The slope of the linear regression computed as the effect of the alternative allele (ALT) relative to the reference allele (REF) in the human genome reference GRCh37/hg19 (i.e., the eQTL effect allele is the ALT allele).
Gene has expression of RPKM <1 0. RPKM (Reads Per Kilobase of transcript per Million mapped reads) is a measure of the abundance of transcripts in RNA-Seq.
positive variant, increases risk for disease; negative variant, reduces risk for disease; ambiguous variant, risk is unclear.
RAVLT, Rey Auditory-Verbal Learning Task; AA, African-Americans; EA East Asians.