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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.
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BMC Medical Genomics

ISSN: 1755-8794

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