Table 2 Distinct signals at loci suggestively associated with glycemic traits FG and FI in TOPMed, P < 5 × 10−8.

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

SLC30A8

8:117179236:C:T

C

rs35859536

2.5KB downstream

0.74

1.0 × 10−9

0.03

0.01

 
 

8:117258547:C:Tb

T

rs542965166

Intronic

0.001

1.9 × 10−6

0.50

0.11

rs35859536

APOB

2:21074277:A:G

A

rs478588

30KB upstream

0.29

2.9 × 10−9

0.03

0.01

 

TCF7L2

10:112998590:C:T

T

rs7903146

Intronic

0.25

2.0 × 10−8

0.03

0.01

 

ADCY5

3:123335923:A:C

A

rs72964564

Intronic

0.80

2.8 × 10−8

0.03

0.01

 

HS/L

HS6ST3

13:96407609:A:G

G

rs1328056

Intronic

0.02

3.6 × 10−8

0.33

0.06

 

CTD-2199C04.4

5:10169711:T:C

C

rs13361160

Intergenic

0.45

3.1 × 10−8

0.10

0.02

 

Fasting insulin

Pooled

PTPRT

20:42752773:G:A

A

rs185250851

Intronic

0.002

2.1 × 10−8

0.30

0.05

 
 

20:43230137:C:Tb

T

rs78618809

Intergenic

0.02

5.9 × 10−6

0.08

0.02

rs185250851

ROBO1

3:79812347:C:A

C

rs539973028

44KB upstream

0.99

4.7 × 10−8

0.51

0.09

 

EU

LINC00704, LINC00705

10:4656482:GAAAAT:G

G

rs775018107

ncRNA intronic

0.002

4.5 × 10−8

0.33

0.06

 

Samoan

RP11/IGSF11

3:118656074:T:Gc

G

rs117592405

ncRNA intronic

0.01

3.3 × 10−8

0.80

0.14

 
  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 for association at significance level P < 1 × 10−5 and MAC > 20 after conditional analysis.
  4. cThis signal was not replicated (Supplementary Table 7).
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