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Table 1 Summary information about the studied SNPs

From: Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and osteoporosis

SNPa

Geneb

Namec

dbSNP Accession

Mutationd

Domain

Minor allele frequency

Forward primer

Reverse primer

1

APOE

 

ss12568587

G-C

5' UTR

0.357

TCCCCAGGAGCCGGTGA

CCCCAAGCCCGACCCC

2

APOE

 

ss12568609

G-A

Intron 2

0.399

CCTCAGGTGATCTGCCCGTTTC

ACTCCTGGGCTCAAGTGATCCTC

3

APOE

 

ss12568607

T-C

Exon 4

0.149

CGGGCACGGCTGTCCAA

CGAGCATGGCCTGCACCTC

4

APOE

 

ss12568612

C-T

Exon 4

0.087

GCTGCGTAAGCGGCTCC

GCGGCCCTGTTCCACC

5

COL1α1

 

ss12568606

G-T

5' UTR

0.154

GCACCCTGCCCTAGACCAC

CCTAGTGCCAGCGACTGCA

6

COL1α1

Sp1

ss12568597

G-T

Intron 1

0.188

CCAATCAGCCGCTCCCATTC

CATCGGGAGGGCAGGCTC

7

COL1α1

 

ss12568598

G-T

Exon 8

0.000

GGAAGACTGGGATGAGGGCA

GGCTCGCCAGGCTCACC

8

COL1α1

 

ss12568584

G-A

Exon 45

0.019

CTCAGCCTTCCCTGGCCAA

AGGCGGAAGTTCCATTGGCATC

9

ER-α

 

ss12568579

A-G

Exon 1

0.484

TTGAGCTGCGGACGGTTCA

CGCCGGTTTCTGAGCCTTC

10

ER-α

Pvu II

ss12568596

T-C

Intron 1

0.449

TGGGATTCCAGGCATGAACCAC

TGGCGTCGATTATCTGAATTTGGCC

11

ER-α

 

ss12568619

G-A

Intron 3

0.257

CCCAGAAACAAGTCATCTGCTATTGACA

TGTAACAAAAGGTTAACAATGGTTAGCCC

12

ER-α

 

ss12568618

G-C

Exon 4

0.218

ACAGCCTGGCCTTGTCCC

CAGGTTGGTCAGTAAGCCCATCA

13

ER-α

 

ss12568585

G-A

Intron 4

0.098

GATCAATGAAGTGGGTCTTGAAAAACCAA

GGTGACAAGCTGGAAATCTAAGCTTCA

14

ER-α

 

ss12568605

G-A

Intron 6

0.119

GGAACGGCCCTTGGAAATTGTAAA

CTGCCTACAGAATACAGTCAGCCA

15

ER-α

 

ss12568617

G-A

Exon 8

0.203

TCGCATTCCTTGCAAAAGTATTACATCAC

CAAGCAAATGAATGGCCACTCATCTAGAAA

16

IL-6

 

ss12568616

C-G

5' UTR

0.434

GGGCAGAATGAGCCTCAGACATC

GACATGCCAAAGTGCTGAGTCACTAATA

17

IL-6

 

ss12568586

A-T

Exon 4

0.005

CCTCCACTGCAAAGGATTTATTCAACA

CATGTCCTGCAGCCACTGGTTC

18

LEPR

 

ss12568615

A-G

Exon 4

0.290

AGATTTAAGTTGTCTTGCATGCCACC

TTAAGCCCAGCATCCATTAGCTATTCTTTC

19

LEPR

 

ss12568604

G-C

Exon 14

0.182

GAGTAATTGGAGCAATCCAGCCTACA

GCTTCAGCCACTGTACATCTTAGCTC

20

LEPR

 

ss12568614

G-A

Exon 20

0.353

GCCACGCTGATCAGCAACTC

CCCTTGACTTGTCAGTCAAAAGCAC

21

PTHR1

 

ss12568589

G-A

Intron 1

0.001

GACTTACATTAGGATTCAAGGTTACTGCCA

GGGACGCAAGCCTGAGTCC

22

PTHR1

 

ss12568592

A-G

Intron 2

0.398

GCAGAACCCTAAGGGCTTGTCA

GGCGGGACCCAGGATACA

23

PTHR1

 

ss12568591

C-T

Intron 8

0.374

CGAGCCTCAATTCAGGTGAATCTAACC

CCCGCCCCAAGTGGAACA

24

PTHR1

 

ss12568588

G-A

Intron 10

0.397

CCTTGAGCCCTTGGTTTTCCTTTC

GCTCCGGGAACAAAAAGTGGATCA

25

PTHR1

 

ss12568590

G-A

Exon 13

0.380

CTACAAGGCTCAAATTGCCCCAAA

TTGGCGTCCACTACATTGTCTTCA

26

TGF-β1

 

ss12568613

C-T

5' UTR

0.311

GGGCCCAGTTTCCCTATCTGTAAA

CTGGGCCACCGTCCTCATC

27

TGF-β1

 

ss12568603

+C/-C

Intron 4

0.021

CCACGCCCCACTTATCTATCCC

GGAAAGGCCGGTTCATGCCA

28

TGF-β1

 

ss12568593

C-T

Exon 5

0.008

CAGGCTACAAGGCTCACCTGAA

GGTTCACTACCGGCCGC

29

TGF-β1

 

ss12568602

C-T

Intron 5

0.274

GGCTTGTCTTAAGCATTGCGTGAAATTAA

GTACAGCTGCCGCACGC

30

TNFR2

 

ss12568594

T-C

5' UTR

0.000

TGCACTCGGCCTGTTTAGACTC

CTGTTCATCTGCCCCCTGCC

31

TNFR2

 

ss12568611

T-G

Exon 6

0.198

AGCCACCCCAGCCACTC

GCTTGGAGCAGTGCTGGGTTC

32

UCP3

 

ss12568601

C-T

5' UTR

0.265

CACTGCCCTCACCAGCCA

GTGAGTCCTGCCACGGCA

33

UCP3

 

ss12568600

G-A

Exon 2

0.000

GCCCTAAAGGGACTGGGCA

GAAAGGTAACGAGGTCAGCAAAACA

34

UCP3

 

ss12568595

T-C

Exon 3

0.258

TGATTCCCGTAACATCTGGACTTTCATC

CTGCCTAAATCCCCTTAGCAGAAAAAAAAA

35

UCP3

 

ss12568580

T-C

Exon 5

0.447

CCTAACAGGAACTTTGCCCAACATCA

TCCACGGAGTTCTGGGTTCC

36

UCP3

 

ss12568599

C-T

Exon 7

0.000

CCTAACAGGAACTTTGCCCAACATCA

TCCACGGAGTTCTGGGTTCC

37

VDR

 

ss12568583

G-A

5' UTR

0.281

CAGCATGCCTGTCCTCAGC

CCAGTACTGCCAGCTCCCA

38

VDR

Fok I

ss12568581

C-T

Exon 2

0.373

TGGCCCTGGCACTGACTC

GGCACGTTCCGGTCAAAGTC

39

VDR

 

ss12568582

C-T

Exon 4

0.000

GGACAGTCTGCGGCCCA

CCCTACTCCCTGGGCCC

40

VDR

Bsm I

ss12568610

G-A

Intron 8

0.419

GTGCCCCTCACTGCCCTTA

CCTCAAATAACAGGAATGTTGAGCCCA

41

VDR

Taq I

ss12568608

T-C

Exon 9

0.408

GGGCCAGGCAGTGGTATCAC

AGGTCGGCTAGCTTCTGGATCA

  1. aDesignation in the present study. bAbbreviations: APOE, apolipoprotein E; COL1α1, collagen type I α1; ER-α, estrogen receptor-α; IL-6, interleukin-6; LEPR, leptin receptor; PTHR1, parathyroid hormone (PTH)/PTH-related peptide receptor type 1; TGF-α1, transforming growth factor-ß1; TNFR2, tumor necrosis factor receptor 2; UCP3, uncoupling protein 3; VDR, vitamin D (1,25-dihydroxyvitamin D3) receptor. cCommon name. dMinor alleles are given in bold.