Table 1 Distinct signals at loci significantly associated with glycemic traits FG and FI in TOPMed, P < 1 × 10−9.

From: Whole genome sequence association analysis of fasting glucose and fasting insulin levels in diverse cohorts from the NHLBI TOPMed program

Trait

Population

Nearest gene

MarkerIDa

EA

rsID

Annotation

EAF

P-value

Beta

SE

Conditioned on

Fasting glucose

Pooled

MTNR1B

11:92975544:C:G

G

rs10830963

Intronic

0.24

9.1 × 10−46

0.07

0.01

 
 

11:92884161:G:Ab

G

rs73560545

intronic

0.83

5.7 × 10−6

0.03

0.01

rs10830963

G6PC2

2:168906638:T:C

C

rs560887

Intronic

0.82

6.8 × 10−37

0.07

0.01

 
 

2:168900420:A:Gb

A

rs540524

2KB upstream

0.66

9.9 × 10−14

0.04

0.01

rs560887

 

2:168907981:T:C c

T

rs2232326

Missense

0.99

5.0 × 10−6

0.15

0.03

rs560887, rs540524

GCK

7:44189469:C:T

T

rs1799884

2KB upstream

0.18

3.9 × 10−28

0.06

0.01

 

GCKR

2:27508073:T:C

C

rs1260326

Missense

0.65

6.1 × 10−21

0.04

0.01

 

FOXA2

20:22581688:A:AG

A

rs3833331

3′ UTR

0.85

5.4 × 10−10

0.04

0.01

 

Fasting insulin

Pooled

GCKR

2:27508073:T:C

C

rs1260326

Missense

0.67

7.2 × 10−13

0.03

0.01

 
  1. EA effect allele, EAF effect allele frequency, EU European, HS/L Hispanic/Latinx.
  2. aChromosome, position(Hg38), reference allele, alternative allele of the genetic variant with the lowest P-value and highest posterior probability representing a distinct association at a locus.
  3. bIndicates secondary signal.
  4. cIndicates tertiary signal for association at significance level P < 1 × 10−5 and MAC > 20 after conditional analysis.
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