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Table 3 MetS SNP association with phenotypes and their gene annotation at 14q13 QTL

From: A comprehensive analysis of adiponectin QTLs using SNP association, SNP cis-effects on peripheral blood gene expression and gene expression correlation identified novel metabolic syndrome (MetS) genes with potential role in carcinogenesis and systemic inflammation

Variant Minor allele MAF -LOG(p) Associated phenotypes Nearest gene Location Annotation
rs1955850 G 0.33 2.95 Weight NOVA1 intergenic post-transcription regulation
rs2332524 G 0.10 2.87 Height STXBP6 intergenic exocytosis
rs1955850 G 0.33 3.75 BMI NOVA1 intergenic post-transcription regulation
rs6574794 A 0.06 3.08 WC NOVA1 intergenic post-transcription regulation
rs1956993 C 0.09 2.92 HC AKAP6 intergenic signal transduction
rs17096124 G 0.03 3.81 WHR PRKD1 intron signal transduction
rs8007613 G 0.28 2.88 Fatkg NPAS3 intron Transcription regulation
rs41449149 T 0.07 3.45 Fatpct PRKD1 intergenic signal transduction
rs1111533 C 0.05 3.53 Leankg NPAS3 intron Transcription regulation
rs41449149 T 0.07 3.55 Leanpct PRKD1 intergenic signal transduction
rs10137682 G 0.37 3.35 SubQF NPAS3 intron Transcription regulation
rs12888531 C 0.06 3.59 VF SLC25A21 intron solute carrier
rs10137682 G 0.37 3.39 TAF NPAS3 intron Transcription regulation
rs11623278 G 0.46 4.16 RQ AKAP6 intergenic signal transduction
rs11161057 A 0.42 3.42 REE MIR548AI intergenic mircoRNA
rs10137682 G 0.37 3.50 REE/weight NPAS3 intron Transcription regulation
rs17414154 A 0.05 3.43 REE/Lean AKAP6 intron signal transduction
rs17112354 A 0.08 2.95 FG BC148262/MIR4307/LOC100505967/NOVA1 intergenic cDNA clone/mircoRNA/non coding RNA/paraneoplastic disease antigens
rs2105274 G 0.39 3.40 FI NOVA1 intergenic paraneoplastic disease antigens
rs1626390 C 0.11 3.48 IGR EGLN3 intergenic Transcription regulation
rs2105274 G 0.39 3.47 HOMA NOVA1 intergenic paraneoplastic disease antigens
rs1951758 T 0.36 3.21 SI MIR4307 / LOC100505967 / NOVA1 intergenic mircoRNA/non-coding RNA/paraneoplastic disease antigens
rs17114954 A 0.04 3.32 SG MIR548AI downstream mircoRNA
rs8012040 G 0.46 3.53 AIR BC148262 /LOC100505967/ NOVA1 intergenic cDNA clone / non coding RNA/paraneoplastic disease antigens
rs10483452 C 0.27 3.82 DI PPP2R3C intron signal transduction
rs8006023 A 0.05 4.60 TG NPAS3 intron transcription regulation
rs8004607 C 0.10 4.44 TC NPAS3 intron transcription regulation
rs712300 C 0.26 4.09 LDL-c EGLN3 intergenic transcription regulation
rs8004607 C 0.10 3.71 cal. LDL-c NPAS3 intron transcription factor
rs10136818 T 0.02 3.63 HDL-c STXBP6 intergenic exocytosis
rs12886242 G 0.12 2.61 HMED NPAS3 intron Transcription regulation
rs17103757 G 0.05 3.84 LMEDn BRMS1L intergenic transcription regulation
rs847501 C 0.35 3.29 LDLppd BRMS1L intergenic transcription regulation
rs10134570 C 0.02 3.83 BMED NPAS3 intron Transcription regulation
rs1951039 A 0.45 4.26 sBP STXBP6/NOVA1 intergenic exocytosis/paraneoplastic disease antigens
rs10498306 C 0.13 4.17 dBP MIR548AI/PRKD1 intergenic microRNA/signal transduction
rs8007613 G 0.28 3.04 Pulse NPAS3 intron Transcription regulation
rs9322942 A 0.33 3.43 Adiponectin SRP54 intron signal recognition particle 54kDal
rs17427680 C 0.05 3.12 Leptin G2E3 intergenic protein sorting
rs1440983 A 0.04 3.64 TNF-alpha PRKD1 intergenic signal transduction
rs11849533 C 0.17 3.67 IL-1B NPAS3 intron Transcription regulation
rs17406989 T 0.09 2.87 IL-6 NPAS3 intron Transcription regulation
  1. SNPs within 1 LOD reduction from the linkage peak were tested for associations against the 42 phenotypes. Annotated genes and their known function were derived from the NCBI build 36 human genome assembly. Annotations were determined at the position and within 250kb up- and downstream of the associated SNP. Data shown in column “-Log10(p)” are levels of the highest association. SNP associations that exceed statistical QTL-specific significance threshold are bolded.