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Table 1 Summary of T1D association results for the case-control collection

From: Evidence of association with type 1 diabetes in the SLC11A1 gene region

    

Allele or genotype

frequency N (%)

   

Variant

[Synonym]

Location

Number of

cases

Number of

controls

Allele or

genotype

in cases

in controls

OR

(95% C.I.)

P-value

rs4674297 G > A

8502

10071

A

3710 (21.82)

4682 (23.25)

0.91

(0.86-0.96)

1.57 × 10-4

5' of SLC11A1

        

within MGC50811 (aka C2orf62)

  

G/G

5210 (61.28)

5945 (59.03)

1.00

(reference)

 
   

G/A

2874 (33.80)

3570 (35.45)

0.91

(0.86-0.97)

 

P HWE = 0.050

  

A/A

418 (4.92)

556 (5.52)

0.84

(0.74-0.96)

 

Microsatellite (GT)n 3 > 2

7697

7371

2

3999 (25.98)

4010 (27.20)

0.94

(0.89-0.99)

0.016

Promoter

        
   

3*/3*

4195 (54.50)

3913 (53.09)

1.00

(reference)

 
   

3*/2

3005 (39.04)

2906 (39.42)

0.96

(0.89-1.03)

 

P HWE = 0.697

  

2/2

497 (6.46)

552 (7.49)

0.85

(0.74-0.97)

 

rs7573065 C > T

5649

6233

T

647 (5.73)

732 (5.87)

0.97

(0.87-1.09)

0.662

[-237 C->T]

        

Promoter

  

C/C

5018 (88.83)

5518 (88.53)

1.00

(reference)

 
   

C/T

615 (10.89)

698 (11.20)

0.97

(0.86-1.09)

 

P HWE = 0.303

  

T/T

16 (0.28)

17 (0.27)

1.00

(0.50-2.00)

 

rs2276631 C > T

5578

6048

T

2933 (26.29)

3331 (27.54)

0.93

(0.87-0.99)

0.016

[274 [C/T]]

        

Exon 3

  

C/C

2998 (53.75)

3153 (52.13)

1.00

(reference)

 
   

C/T

2227 (39.92)

2459 (40.66)

0.94

(0.87-1.02)

 

P HWE = 0.144

  

T/T

353 (6.33)

436 (7.21)

0.84

(0.72-0.98)

 

rs3731865 G > C

8787

10611

C

4691 (26.69)

6116 (28.82)

0.90

(0.86-0.94)

1.55 × 10-6

[469 +14 [G/C]; INT4]

        

Intron 4

  

G/G

4713 (53.64)

5401 (50.90)

1.00

(reference)

 
   

G/C

3457 (39.34)

4304 (40.56)

0.91

(0.86-0.97)

 

P HWE = 0.242

  

C/C

617 (7.02)

906 (8.54)

0.78

(0.69-0.87)

 

rs2279015 G > A

5549

5872

A

4312 (38.85)

4658 (39.66)

0.96

(0.91-1.02)

0.205

[1465-85 [A/G]]

        

Intron 13

  

G/G

2060 (37.12)

2142 (36.48)

1.00

(reference)

 
   

G/A

2666 (48.04)

2802 (47.72)

1.00

(0.92-1.08)

 

P HWE = 0.817

  

A/A

823 (14.83)

928 (15.80)

0.92

(0.82-1.03)

 

rs17235409 G > A

5498

6062

A

241 (2.19)

216 (1.78)

1.28

(1.06-1.55)

0.010

[D543N]

        

Exon 15

  

G/G

5259 (95.65)

5849 (96.49)

1.00

(reference)

 
   

G/A

237 (4.31)

210 (3.46)

1.31

(1.08-1.59)

 

P HWE = 0.430

  

A/A

2 (0.04)

3 (0.05)

0.72

(0.12-4.37)

 

rs17235416 TGTG> del

8463

9835

del

312 (1.84)

299 (1.52)

1.22

(1.04-1.44)

0.015

[1729+55del4 [TGTG]; 3'UTR]

        

3'UTR

  

TGTG/TGTG

8153 (96.34)

9539 (96.99)

1.00

(reference)

 
   

TGTG/del

308 (3.64)

293 (2.98)

1.24

(1.05-1.46)

 

P HWE = 0.624

  

del/del

2 (0.02)

3 (0.03)

0.69

(0.11-4.20)

 

rs1059823 A > G

5,605

6,137

ND

ND

ND

ND

 

ND

[1801+86[A/G]]

        

3'UTR

        

P HWE = 0.001

        

rs1809231 C > G

5643

6151

G

4870 (43.15)

5399 (43.89)

0.97

(0.92-1.02)

0.028**

3' intergenic region

        
   

C/C

1783 (31.60)

1959 (31.85)

1.00

(reference)

 
   

C/G

2850 (50.51)

2985 (48.53)

1.04

(0.96-1.14)

 

P HWE = 0.249

  

G/G

1010 (17.90)

1207 (19.62)

0.91

(0.82-1.01)

 
  1. Association of alleles and genotypes were tested using single locus logistic regression.
  2. * Rare microsatellite alleles (with frequency <0.1%) were combined with the common allele 3. ** The multiplicative allelic effects model was an appropriate model for all variants (P > 0.05), except for rs1809231 C>G where a genotype effects model was required (P = 0.019). [P HWE = Hardy- Weinberg equilibrium in controls; OR = odds ratio; 95% C.I. = 95% confidence intervals; ND = not done.]
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BMC Medical Genetics

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