Table 1 Summary of top variants in the GCKR gene cluster exhibiting genome-wide significance for the TyG index, a marker of insulin resistance, identified within the Taiwan Biobank cohort

From: Gene clusters linked to insulin resistance identified in a genome-wide study of the Taiwan Biobank population

GENE

CHR

Interval (b38)

Top SNP

Pos (b38)

Top P

Novel

TWAS

GWAS catalog

DPYSL5

2

26847995..26950351

rs72804857

26,938,608

7.8E-11

no

NA

TG, HDL-C, FG, BMI, TG:HDL-C

MAPRE3

2

26970637..27027219

rs10207573

27,020,067

4.0E-09

no

1, 3

TG, HDL-C, TG:HDL-C

TMEM214

2

27032965..27041694

rs2304713

27,035,893

3.5E-10

yes

NA

NA

AGBL5

2

27050364..27070618

rs70953845

27,064,781

2.1E-10

yes

1, 5

TG

OST4a

2

27070472..27071654

rs4665943

27,073,017

1.8E-08

yes

7

NA

EMILIN1

2

27078615..27086403

rs2304682

27,084,901

1.8E-09

yes

2

NA

KHK

2

27086772..27100762

rs6714547

27,098,338

6.2E-11

yes

2, 8, 9, 10, 11

NA

CGREF1

2

27099353..27119128

rs6746337

27,118,195

2.6E-11

yes

5

TG

ABHD1

2

27123815..27130812

rs4665946

27,125,063

2.3E-21

yes

1, 2, 7, 8

NA

PREB

2

27130756..27134636

rs71401560

27,131,111

1.6E-15

yes

2, 9, 10

NA

PRR30

2

27136848..27139410

rs11121

27,137,019

1.3E-15

yes

NA

TG

TCF23

2

27149004..27156974

rs1275513

27,148,102

7.9E-18

yes

NA

TG

SLC5A6a

2

27199587..27212787

rs74684611

27,191,771

2.3E-21

yes

8

TG, HDL-C

CADa

2

27217369..27243943

rs118130043

27,245,399

3.8E-13

yes

3

TG

TRIM54

2

27282429..27307435

rs189387480

27,292,538

5.9E−12

yes

NA

TG

MPV17

2

27309492..27323097

rs146502189

27,322,314

3.3E-13

yes

8

TG

GTF3C2

2

27325854..27356764

rs201232671

27,348,271

6.4E-14

yes

1

TG

PPM1G

2

27381199..27409591

rs79803862

27,399,271

4.0E-22

yes

6, 8, 9

TG, FG, BMI

NRBP1a

2

27427790..27442259

rs147530299

27,419,228

2.2E-23

yes

5

TG, FG, BMI

IFT172

2

27444377..27489743

rs117414910

27,455,222

1.8E-17

no

1, 10, 11

TG, TG:HDL-C

GCKR

2

27496839..27523684

rs1260326

27,508,073

4.3E-204

no

5, 11

IG, TG, T2D, FG, BMI, TG:HDL-C

SPATA31H1

2

27537386..27582722

rs1919127

27,578,626

6.9E-114

yes

1, 2, 4, 9, 11

NA

ZNF512

2

27583042..27623217

rs12989678

27,598,615

1.3E-115

yes

NA

TG, T2D

GPN1

2

27628247..27651511

rs34502053

27,631,657

7.9E-68

yes

4, 8, 10, 11

TG, BMI

SUPT7L

2

27642568..27663614

rs4666010

27,655,819

9.9E-45

yes

1, 5, 6, 9, 10, 11

NA

SLC4A1AP

2

27663889..27694969

rs13021208

27,678,861

1.6E−57

yes

6, 10

TG

MRPL33

2

27771719..27779733

rs3792252

27,773,064

2.2E-37

yes

2, 8, 9

TG, FG

RBKS

2

27781379..27890387

rs898034

27,867,953

1.5E-38

yes

8, 11

TG

BABAM2

2

27888709..28338901

rs141361525

27,896,053

8.7E-18

yes

1, 2, 11

TG, HDL-C, FG. BMI

TAD

CHR

Interval (b38)

--

--

--

--

--

--

pancreas

2

25920000..27320000

--

--

--

--

--

--

pancreas

2

27680000..28520000

--

--

--

--

--

--

hippocampus

2

25360000..27360000

--

--

--

--

--

--

hippocampus

2

27680000..28480000

--

--

--

--

--

--

liver

2

25920000..27320000

--

--

--

--

--

--

liver

2

27360000..28520000

--

--

--

--

--

--

  1. Tissues in TWAS: 1 = Adipose Subcutaneous; 2 = Adipose Visceral Omentum; 3 = Adrenal Gland; 4 = Brain Cortex; 5 = Brain Hippocampus; 6 = Brain Hypothalamus; 7 = Liver; 8 = Muscle Skeletal; 9 = Pancreas; 10 = Pituitary; 11 = Thyroid. Previous GWASs reported in the NHGRI-EBI GWAS Catalog have identified various phenotypes that reach genome-wide significance (P < 5 × 10−8). Coordinates for TADs were retrieved from the following source (https://3dgenome.fsm.northwestern.edu/publications.html).
  2. AD Alzheimer’s disease, b38 Genome Research Consortium human build 38, BMI body mass index, CHR chromosome, FG fasting glucose, HDL-C high-density lipoprotein cholesterol, IR insulin resistance, NA not available, Pos position, T2D type 2 diabetes, TAD topologically associating domains, TG triglycerides, TG:HDLC the triglyceride to high-density lipoprotein cholesterol ratio, TWAS transcriptome-wide association analysis.
  3. aNearby gene. -- not applicable. This GWAS analysis utilized BOLT-LMM’s mixed linear models with a two-sided chi-square test. The conventional genome-wide significance threshold of P < 5 × 10−8 was applied.
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