Skip to main content

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.