Table 2 Evidence for a shared causal SNP or two distinct causal SNPs between BMI and diabetes shown in five regions.

From: Integrative analysis of Mendelian randomization and Bayesian colocalization highlights four genes with putative BMI-mediated causal pathways to diabetes

Region

N

PP3

PP4

Candidate causal SNP

Chr: position

Gene

Alleles

EAF

B_BMI

P_BMI

B_diabetes

P_diabetes

chr6: 50600724-51065757

472

0.049

0.923

rs987237

6: 50803050

TFAP2B

G/A

0.09

0.044

1.07 × 10−30

0.004

5.67 × 10−8

chr10: 114554779-114958159

447

0.001

0.999

rs7903146

10: 114758349

TCF7L2

T/C

0.25

−0.024

1.10 × 10−12

0.015

3.72 × 10−150

chr16: 53604177-54000907

247

0.026

0.974

rs1558902

16: 53803574

FTO

A/T

0.45

0.084

1.13 × 10−156

0.005

1.67 × 10−22

chr19: 47369753-47761543

386

0.004

0.993

rs3810291

19: 47569003

ZC3H4

A/G

0.63

0.029

6.35 × 10−16

0.003

1.24 × 10−8

chr3: 185324933-186022133

112

1

0.000

rs9816226*

3:185834499

ETV5

A/T

0.15

−0.040

6.03 × 10−24

0.002

2.88 × 10−3

rs1470580

3:185529174

IGF2BP2

A/T

0.29

−0.014

1.03 × 10−4

0.006

7.88 × 10−27

  1. PP4 is the posterior probability of a single causal SNP common to BMI and diabetes in the test region. PP3 denotes the posterior probability of two distinct causal SNPs, one for BMI only and the other for diabetes only. N is the number of SNPs included in the test region. Alleles (effect/reference), effect allele frequency (EAF), estimated coefficient (B) and p-value (P) are summary results from two independent GWASs: BMI from the GIANT study http://portals.broadinstitute.org/collaboration/giant/index.php/GIANT_consortium_data_files#GWAS_Anthropometric_2015_BMI, diabetes from the UK Biobank study http://www.nealelab.is/blog/2017/7/19/rapid-gwas-of-thousands-of-phenotypes-for-337000-samples-in-the-uk-biobank. * The SNP rs9816226 does not lie within a gene. ETV5 is its nearest gene.
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