Table 2

SNP allele frequencies between cases and controls

Gene

Sequence variation

Detection method

Allele

Allele frequencies (%)

p-value

Controls

Cases

VDR

c.2T > C, Met1Thr

(rs10735810)

FokI

C

153 (64)

90 (62)

T

87 (36)

54 (37)

NS

c.1024+283G > A

(rs1544410)

BsmI

A

90 (38)

45 (31)

G

150 (63)

99 (69)

NS

c.1056T > C, Ile352Ile

(rs731236)

TaqI

C

88 (37)

45 (31)

T

152 (63)

99 (69)

NS

IL6

-174G > C

(rs1800795)

NlaIII

C

126 (52.5)

72 (50)

G

114 (47.5)

72 (50)

NS

CTR

c.1377C > T, Pro463Leu

(rs1801197)

AluI

C

73 (30)

35 (24)

T

167 (70)

109 (76)

NS

COL1A1

c.101+1024G > T

(rs1800012)

Sequencing

G

204 (85)

123 (85)

T

36 (15)

21 (15)

NS

c.1930-14T > C

(rs2696247)

CSGE

C

41 (17)

28 (19)

T

199 (83)

116 (81)

NS

c.3261C > T

(rs2586488)

Eco57I

C

158 (66)

87 (60)

T

82 (34)

57 (40)

NS

COL1A2

c.280-68A > G

(rs406226)

CSGE

A

206 (86)

120 (83)

G

34 (14)

24 (17)

NS

c.1666-41G > A

(rs2301643)

MslI

A

32 (13)

24 (17)

G

208 (87)

120 (83)

NS

c.2350-89ins38bp

(rs3216902)

CSGE

insertion

151 (63)

96 (67)

no ins.

89 (37)

48 (33)

NS

LRP5

c.2007G > A, E644E

(rs2277268)

Sequencing

G

231 (96)

131 (91)

A

9 (4)

13 (9)

0.031¹

c.2074G > A, V667M

(rs4988321)

Sequencing

G

235 (98)

137 (95)

A

5 (2)

7 (5)

NS

c.3432A > G, V1119V

(rs556442)

Sequencing

A

200 (83)

112 (78)

G

40 (17)

32 (22)

NS

c.4064C > T, A1330V

(rs3736228)

Sequencing

C

227 (95)

134 (93)

T

13 (5)

10 (7)

NS

NS = not significant; GenBank Accession numbers COL1A1 NM_000088, COL1A2 NM_000089, VDR NM_000376, LRP5 NM_002335, CTR NM_001742; ¹NS permutation p-value, p = 0.21.

Korvala et al. BMC Genetics 2010 11:95   doi:10.1186/1471-2156-11-95