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Table 3 Replication data of 16 SNPs significantly associated with renal traits on the FHS 100 K chip in 8,717 white participants at ARIC visit 4.

From: Genome-wide association study for renal traits in the Framingham Heart and Atherosclerosis Risk in Communities Studies

SNP

Gene

Strand

Alleles*

MAF

FHS

ARIC

  

FHS/ARIC

 

FHS

ARIC

Trait List†

Trait

GEE p-value

FBAT p-value

GLM p-value

Selected for low p-value only

rs4553158

MIER1

-/+

A/G

0.13(C)

0.17(G)

1,2,3,4

CKD

4.3xe-4

0.739

0.749

       

cys

0.006

0.432

--

       

eGFR

0.003

0.914

0.300

rs6831700

WDR19

-/+

G/T

0.34(C)

0.33(G)

1

CKD

0.004

0.001

0.361

       

cys

0.344

0.005

--

       

eGFR

0.034

0.001

0.472

rs2419912

(BC047601)

+/+

T/C

0.49(C)

0.46(C)

1

CKD

0.002

0.144

0.044

       

cys

0.003

0.030

--

       

eGFR

9.4xe-5

0.342

0.026

rs2228210

HIVEP1

+/+

A/G

0.29(G)

0.36(G)

1,2,3

CKD

0.017

0.007

0.805

ns cSNP

      

cys

0.003

0.027

--

       

eGFR

2.3xe-4

0.005

0.520

rs10509132

ANK3

+/+

G/T

0.45(G)

0.48(G)

1,2,3

CKD

0.009

0.855

0.609

       

cys

0.002

0.002

--

       

eGFR

0.002

0.031

0.349

rs1613631

KRT84

-/+

T/G

0.2(C)

0.20(G)

1,2,3

CKD

0.048

0.002

0.360

       

cys

0.177

0.009

--

       

eGFR

0.013

0.003

0.169

rs6495446

MTHFS

+/+

C/T

0.24(T)

0.27(T)

1,2,3

CKD

0.003

0.429

0.001

       

cys

0.006

0.149

--

       

eGFR

0.001

0.167

0.043

rs2827732

gene desert

-/+

C/A

0.19(T)

0.16(A)

1,2,3

CKD

0.001

0.004

0.403

       

cys

0.002

4.9 × 10-4

--

       

eGFR

0.002

0.025

0.806

Selected as a candidate

rs2061063

FRAS1

-/-

G/C

0.33(G)

0.35(G)

2

CKD

0.009

0.015

0.149

       

cys

0.402

0.790

--

       

eGFR

0.009

0.018

0.719

rs4835136

NR3C2

-/+

C/T

0.36(A)

0.37(T)

2,5

CKD

0.003

0.002

0.380

       

cys

0.971

0.260

--

       

eGFR

0.001

0.001

0.920

rs1743955

SGK1

-/+

T/C

0.42(A)

0.39(T)

3

CKD

0.707

0.459

0.164

       

cys

0.096

0.004

--

       

eGFR

0.006

0.007

0.889

rs4148686

CFTR

-/+

C/G

0.17(C)

0.20(G)

4

CKD

1.1xe-4

0.209

0.543

       

cys

0.914

0.291

--

       

eGFR

0.060

0.555

0.353

rs3779748

EYA1

+/+

T/C

0.32(C)

0.33(C)

3

CKD

0.128

0.826

0.882

       

cys

0.008

0.435

--

       

eGFR

0.006

0.593

0.788

rs1455177

BC047388

+/-

C/G

0.45(C)

0.45(G)

6

CKD

0.113

0.494

0.208

 

(GLIS3)

     

cys

6.0xe-4

0.045

--

       

eGFR

0.059

0.669

0.404

rs10520688

IQGAP1

+/-

T/C

0.15(C)

0.14(G)

3

CKD

0.043

0.837

0.020

       

cys

0.004

0.608

--

       

eGFR

0.003

0.82

0.674

rs2839235

PCNT

+/+

T/C

0.14(C)

0.13(C)

3,5

CKD

0.028

0.134

0.848

       

cys

0.016

0.006

--

       

eGFR

1.6xe-5

0.055

0.827

  1. The upper part of the table contains the SNPs selected for replication based on a low p-value (<0.01) for association with all of the 3 kidney traits in FHS, while the lower part of the table contains the SNPs that were selected for their location in a candidate gene.
  2. *Polymorphic nucleotides (alleles) are listed with respect to the (+) strand relative to the human reference sequence with the nucleotide in the reference sequence listed first; strand information refers to this reference sequence. †Trait lists: 1: all 3 traits, 2: CKD&eGFR, 3: cys&eGFR, 4: CKD, 5: eGFR, 6: cys. Statistical significance for replication was determined a priori at p = 0.00625 for SNPs selected based on p-value and 0.05 for SNPs selected as candidates. P-values shown for ARIC are derived from all participants not missing any covariates (n = 8,717), sample size varies slightly due to missing individual SNPs. Annotation based on USCS Genome Browser, assembly March 2006 (NCBI Build 36.1). Gene names in italics indicate the SNP is located in the gene, parentheses indicate proximity to a gene or mRNA, SNPs more than 400 kb away from the closest known gene or mRNA are defined as located in a gene desert. Abbreviations: MAF: minor allele frequency, GEE: generalized estimating equation, FBAT: family-based association test, GLM: generalized linear model, CKD: chronic kidney disease, cys: cystatin C, eGFR: estimated glomerular filtration rate, ns cSNP: non-synonymous coding SNP.
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BMC Medical Genetics

ISSN: 1471-2350

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