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Table 4 Comparison with the prior literature

From: Genome-wide association with select biomarker traits in the Framingham Heart Study

Gene

rs number previous reports

# Affy SNPs within 60 kb

rs ID Affy SNPs

Chr

D'

r2

Distance Associated SNP

MAF

FBAT p-value

GEE p-value

IL6

rs1800795

= -174G/C

7

rs6461667

7

1

0.82

30098

0.36

0.09

0.66

MCP1

rs1024611

13

rs10491109

17

1

0.04

30762

0.15

0.048

0.13

   

rs1080327

 

1

0.96

11878

0.25

0.78

0.35

   

rs1860181

 

0.92

0.27

37799

0.45

0.04

0.11

   

rs1860182

 

0.92

0.27

37649

0.45

0.046

0.11

   

rs3815341

 

1

0.02

34637

0.05

0.001

0.50

CRP average 2,6,7

rs1205

37

rs1446959

1

0.56

0.12

75429

0.39

0.86

0.002

   

rs1891187

 

0.39

0.05

53180

0.33

0.30

0.02

   

rs2808629

 

1

1

5437

0.34

4.8*105

3.2*10-8

   

rs2794520

 

1

1

3417

0.34

4.3*10-5

2.8*10-8

   

rs4131568

 

0.63

0.12

39823

0.30

0.004

0.001

 

rs1417938

 

rs1446959

 

0.5

0.16

77382

0.39

0.86

0.002

   

rs1891187

 

0.29

0.07

55133

0.33

0.30

0.02

   

rs2808629

 

1

0.25

7390

0.34

4.8*10-5

3.2*10-8

   

rs2794520

 

1

0.25

5370

0.34

4.3*10-5

2.8*10-8

   

rs4131568

 

1

0.83

37870

0.30

0.004

0.001

   

rs1446959

 

0.66

0.03

72832

0.39

0.86

0.002

 

rs3093077

 

rs1891187

 

0.47

0.02

50583

0.33

0.30

0.02

   

rs2808629

 

1

0.03

2840

0.34

4.8*10-5

3.2*10-8

   

rs2794520

 

1

0.03

820

0.34

4.3*10-5

2.8*10-8

   

rs4131568

 

1

0.03

42420

0.30

0.004

0.001

   

rs1446959

 

0.51

0.17

90106

0.39

0.86

0.002

 

rs3116653

 

rs1891187

 

0.31

0.08

67857

0.33

0.30

0.02

   

rs2808629

 

1

0.25

20114

0.34

4.8*10-5

3.2*10-8

   

rs2794520

 

1

0.25

18094

0.34

4.3*10-5

2.8*10-8

   

rs4131568

 

1

0.83

25146

0.30

0.004

0.001

  1. Displayed are SNPs that are either in the highest LD (r2) with previously reported SNPs or that have an FBAT or GEE p-value < 0.05.
  2. For bilirubin concentrations in Framingham study unrelated participants we previously reported significant linkage to chromosome 2q telomere [39] and a significant association to a TA repeat UGT1A1, there were no association between bilirubin concentrations and 1 SNP within 30 kb (rs741159) + 2 more SNPs within 50 kb (rs726017 and rs6752792). The previously reported UGT1A1 variant is not a SNP and therefore not in HapMap; we have no LD information and cannot assess whether the association previous reported is also present in the current sample. ICAM1on chromosome 19 has 3 reported SNPs in literature (rs1799969, rs5491, rs5498), but there were no Affymetrix SNPs within 60 KB of the gene.
  3. CCL2[Other associated SNPs: rs2857654, rs1024610, rs2857657 are NOT in HapMap, so no LD information was available.
  4. CRP2 SNPs are in perfect LD with rs1205. The previously reported triallelic SNP rs3091244 is not in HapMap. CRP association was previously reported in Framingham unrelated participants [32].