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Table 1 Information about the 37 SNPs in the eight genes

From: Patterns of linkage disequilibrium and haplotype distribution in disease candidate genes

SNP

Gene

dbSNP accession

polymor phisma

Domain

Distanceb

Frequency (%)c

Forward Primer

Reverse Primer

1

APOE

ss12568587

G-C

5' UTR

 

35.7

TCCCCAGGAGCCGGTGA

CCCCAAGCCCGACCCC

2

APOE

ss12568609

G-A

Intron 2

1,277

39.9

CCTCAGGTGATCTGCCCGTTTC

ACTCCTGGGCTCAAGTGATCCTC

3

APOE

ss12568607

T-C

Exon 4

1,497

14.9

CGGGCACGGCTGTCCAA

CGAGCATGGCCTGCACCTC

4

APOE

ss12568612

C-T

Exon 4

138

8.7

GCTGCGTAAGCGGCTCC

GCGGCCCTGTTCCACC

5

COL1A1

ss12568606

G-T

5' UTR

 

15.4

GCACCCTGCCCTAGACCAC

CCTAGTGCCAGCGACTGCA

6

COL1A1

ss12568597

G-T

Intron 1

3,543

18.8

CCAATCAGCCGCTCCCATTC

CATCGGGAGGGCAGGCTC

7

COL1A1

ss12568598

G-T

Exon 8

2,365

0.0

GGAAGACTGGGATGAGGGCA

GGCTCGCCAGGCTCACC

8

COL1A1

ss12568584

G-A

Exon 45

9,862

1.9

CTCAGCCTTCCCTGGCCAA

AGGCGGAAGTTCCATTGGCATC

9

ER-α

ss12568579

A-G

Exon 1

 

48.4

TTGAGCTGCGGACGGTTCA

CGCCGGTTTCTGAGCCTTC

10

ER-α

ss12568596

T-C

Intron 1

34,258

44.9

TGGGATTCCAGGCATGAACCAC

TGGCGTCGATTATCTGAATTTGGCC

11

ER-α

ss12568619

G-A

Intron 3

66,110

25.7

CCCAGAAACAAGTCATCTGCTATTGACA

GTAACAAAAGGTTAACAATGGTTAGCCC

12

ER-α

ss12568618

G-C

Exon 4

36,077

21.8

ACAGCCTGGCCTTGTCCC

CAGGTTGGTCAGTAAGCCCATCA

13

ER-α

ss12568585

G-A

Intron 4

39,074

9.8

GATCAATGAAGTGGGTCTTGAAAAACCAA

GGTGACAAGCTGGAAATCTAAGCTTCA

14

ER-α

ss12568605

G-A

Intron 6

83,068

11.9

GGAACGGCCCTTGGAAATTGTAAA

CTGCCTACAGAATACAGTCAGCCA

15

ER-α

ss12568617

G-A

Exon 8

32,431

20.3

TCGCATTCCTTGCAAAAGTATTACATCAC

CAAGCAAATGAATGGCCACTCATCTAGAAA

16

LEPR

ss12568615

A-G

Exon 4

 

29.0

AGATTTAAGTTGTCTTGCATGCCACC

TTAAGCCCAGCATCCATTAGCTATTCTTTC

17

LEPR

ss12568604

G-C

Exon 14

3,013

18.2

GAGTAATTGGAGCAATCCAGCCTACA

GCTTCAGCCACTGTACATCTTAGCTC

18

LEPR

ss12568614

G-A

Exon 20

62,803

35.3

GCCACGCTGATCAGCAACTC

CCCTTGACTTGTCAGTCAAAAGCAC

19

PTHR1

ss12568589

G-A

Intron 1

 

0.1

GACTTACATTAGGATTCAAGGTTACTGCCA

GGGACGCAAGCCTGAGTCC

20

PTHR1

ss12568592

A-G

Intron 2

4,250

39.8

GCAGAACCCTAAGGGCTTGTCA

GGCGGGACCCAGGATACA

21

PTHR1

ss12568591

C-T

Intron 8

5,436

37.4

CGAGCCTCAATTCAGGTGAATCTAACC

CCCGCCCCAAGTGGAACA

22

PTHR1

ss12568588

G-A

Intron 10

1,912

39.7

CCTTGAGCCCTTGGTTTTCCTTTC

GCTCCGGGAACAAAAAGTGGATCA

23

PTHR1

ss12568590

G-A

Exon 13

1,246

38.0

CTACAAGGCTCAAATTGCCCCAAA

TTGGCGTCCACTACATTGTCTTCA

24

TGF-β1

ss12568613

C-T

5' UTR

 

31.1

GGGCCCAGTTTCCCTATCTGTAAA

CTGGGCCACCGTCCTCATC

25

TGF-β1

ss12568603

+C/-C

Intron 4

12,354

2.1

CCACGCCCCACTTATCTATCCC

GGAAAGGCCGGTTCATGCCA

26

TGF-β1

ss12568593

C-T

Exon 5

83

0.8

CAGGCTACAAGGCTCACCTGAA

GGTTCACTACCGGCCGC

27

TGF-β1

ss12568602

C-T

Intron 5

9,644

27.4

GGCTTGTCTTAAGCATTGCGTGAAATTAA

GTACAGCTGCCGCACGC

28

UCP3

ss12568601

C-T

5' UTR

 

26.5

CACTGCCCTCACCAGCCA

GTGAGTCCTGCCACGGCA

29

UCP3

ss12568600

G-A

Exon 2

2,122

0.0

GCCCTAAAGGGACTGGGCA

GAAAGGTAACGAGGTCAGCAAAACA

30

UCP3

ss12568595

T-C

Exon 3

809

25.8

TGATTCCCGTAACATCTGGACTTTCATC

CTGCCTAAATCCCCTTAGCAGAAAAAAAAA

31

UCP3

ss12568580

T-C

Exon 5

1,712

44.7

CCTAACAGGAACTTTGCCCAACATCA

TCCACGGAGTTCTGGGTTCC

32

UCP3

ss12568599

C-T

Exon 7

2,996

0.0

CCTAACAGGAACTTTGCCCAACATCA

TCCACGGAGTTCTGGGTTCC

33

VDR

ss12568583

G-A

5' UTR

 

28.1

CAGCATGCCTGTCCTCAGC

CCAGTACTGCCAGCTCCCA

34

VDR

ss12568581

C-T

Exon 2

4,818

37.3

TGGCCCTGGCACTGACTC

GGCACGTTCCGGTCAAAGTC

35

VDR

ss12568582

C-T

Exon 4

21,590

0.0

GGACAGTCTGCGGCCCA

CCCTACTCCCTGGGCCC

36

VDR

ss12568610

G-A

Intron 8

11,470

41.9

GTGCCCCTCACTGCCCTTA

CCTCAAATAACAGGAATGTTGAGCCCA

37

VDR

ss12568608

T-C

Exon 9

1,078

40.8

GGGCCAGGCAGTGGTATCAC

AGGTCGGCTAGCTTCTGGATCA

  1. a: Minor alleles are given in italic. b: Distance from the previous SNP within each gene in the unit of bp. c: Frequency of minor allele