Table 3 Summary of top variants in the APOA5 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

BUD13

11

116748173..116772987

rs6589565

116,769,521

7.3E-445

yes

8

TG, HDL-C

ZPR1

11

116773799..116788023

rs10750096

116,786,072

3.4E-451

no

NA

TG, HDL-C, TG:HDL-C

APOA5

11

116789367..116792420

rs651821

116,791,863

1.4E-919

no

9

TG, HDL-C, TG:HDL-C

APOA4

11

116820700..116823304

rs5104

116,821,618

1.1E-235

no

8, 11

TG, HDL-C, TG:HDL-C

APOC3

11

116829907..116833072

rs5128

116,832,924

2.8E-152

yes

6

TG, HDL-C

APOA1

11

116835751..116837622

rs12718464

116,836,685

3.1E-39

yes

2, 6, 7, 10

TG, HDL-C, BMI

SIK3

11

116843402..117098428

rs6589574

116,859,922

1.2E-112

no

1, 2, 5, 6, 8, 10

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

PAFAH1B2

11

117144287..117178173

rs7925256

117,174,619

8.0E-75

yes

5, 9

TG, HDL-C, BMI

SIDT2

11

117178743..117197442

rs6589603

117,185,123

1.1E-59

yes

1, 2, 3, 4, 6, 9, 10, 11

TG, HDL-C

TAGLN

11

117199294..117207465

rs12970

117,203,393

6.1E-40

yes

4, 8, 9

TG, HDL-C

PCSK7

11

117204337..117232073

rs236911

117,214,554

5.3E-56

no

1, 2, 7, 11

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

RNF214

11

117232671..117286454

rs200694867

117,244,658

6.3E-28

yes

NA

TG, HDL-C

BACE1

11

117285698..117316256

rs3741288

117,315,499

4.2E−12

yes

2

TG, HDL-C

CEP164

11

117321778..117413266

rs11216364

117,355,903

1.2E-34

no

5, 10

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

DSCAML1a

11

117427772..117817514

rs7115491

117,424,434

8.6E-17

no

NA

TG, HDL-C, TG:HDL-C

TAD

CHR

Interval (b38)

--

--

--

--

--

--

pancreas

11

116760000..119360000

--

--

--

--

--

--

hippocampus

11

116760000..117200000

--

--

--

--

--

--

hippocampus

11

117200000..118960000

--

--

--

--

--

--

liver

11

116720000..117200000

--

--

--

--

--

--

liver

11

117360000..118120000

--

--

--

--

--

--

  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 (http://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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