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Table 1 Functional consequence and prevalence of inflammatory-associated sequence variants

From: The impact of genetic variants in inflammatory-related genes on prostate cancer risk among men of African Descent: a case control study

dbSNPID

Gene

Location functional consequence

NCBI nucleotide change (major > minor allele)

NCBI minor allele frequency (MAF) for African-Americans

NCBI major/major genotype n (%) for African-Americans

NCBI major/minor genotype n (%) for African-Americans

NCBI minor/minor genotype n (%) for African-Americans

Current study nucleotide change (major > minor allele)

Current study MAF n(%) for African-Americans

Current study major/major genotype n (%) for African-Americans

Current study major/minor genotype n (%) for African-Americans

Current study minor/minor genotype n (%) for African-Americans

Overall χ2P-value comparing genotypes from individuals of African Descent as reported in NCBI versus the current study††

rs1058867 ǂ

IL10RB

UTR'3 miRNA

G > A

A = 37.9

26 (42.0)

25 (40.3)

11 (17.7)

G > A

A = 33.9

239 (44.6)

229 (42.9)

67 (12.5)

0.514

rs1071676 ǂ

IL1B

UTR'3 miRNA

G > C

C = 14.6

19 (79.2)

3 (12.5)

2 (8.3)

G > C

C = 16.1

378 (70.7)

142 (26.5)

15 (2.80)

0.106

rs11123902 ǂ

IL1R2

Intron 1

A > C

C = 31.8

10 (45.5)

10 (45.5)

2 (9.10)

A > C

C = 30.7

258 (48.2)

225 (42.1)

52 (9.70)

0.949

rs1126579 ǂ

IL8RB

UTR'3 miRNA

C > T

T = 14.5

46 (74.2)

14 (22.6)

2 (3.20)

G > A

A = 13.8

402 (75.1)

118 (22.1)

15 (2.80)

0.886

rs1143627 ǂ

IL1B

Near gene 5' TFBS

C > T

T = 37.5

12 (50.0)

6 (25.0)

6 (25.0)

G > A

A = 39.6

194 (36.3)

256 (48.2)

83 (15.5)

0.063

rs1143634 ǂ

IL1B

Exon 4 Splicing

C > T

T = 12.9

47 (75.8)

14 (22.6)

1 (1.60)

G > A

A = 15.5

381 (71.2)

142 (26.5)

12 (2.3)

0.833

rs11574752 ǂ

IL8RB

UTR'3 miRNA

G > A

A = 10.4

19 (79.2)

5 (20.8)

0(0.00)

G > A

A = 9.40

435 (81.3)

99 (18.5)

1 (0.20)

0.798

rs11886877

IL1R2

Intron 1

---

---

---

---

---

G > A

A = 35.8

211 (39.4)

265 (49.5)

59 (11.1)

 

rs12135247 ǂǂ

RNASEL

UTR'3 TFBS, miRNA

T > C

C = 16.3

33 (67.3)

16 (32.7)

0 (0.00)

A > G

G = 17.9

368 (68.8)

142 (26.5)

25 (4.70)

0.226

rs12328606 ǂǂ

IL1R2

Near gene 5' TFBS

C > T

T = 11.2

38 (77.6)

11 (22.4)

0 (0.00)

G > A

A = 13.5

405 (75.7)

116 (21.7)

14 (2.60)

0.798

rs1304037 ǂ

IL1A

UTR'3 miRNA

A > G

G = 39.6

8 (33.3)

13 (54.2)

3 (12.5)

A > G

G = 41.1

191 (35.7)

248 (46.4)

96 (17.9)

0.760

rs16944 ǂ

IL1B

Near gene 5' TFBS

A > G

G = 39.0

18 (30.5)

36 (61.0)

5 (8.50)

A > G

G = 45.1

156 (29.2)

275 (51.4)

104 (19.4)

0.108

rs17561 ǂ

IL1A

Exon 4 Splicing, nsSNP, benign

G > T

T = 15.3

44 (71.0)

17 (27.4)

1 (1.60)

C > A

A = 18.6

358 (66.9)

155 (29.0)

22 (4.10)

0.698

rs1799964 ǂ

TNF

Near gene 5' TFBS

T > C

C = 12.9

46 (74.2)

16 (25.8)

0 (0.00)

A > G

G = 16.5

374 (69.9)

145 (27.1)

16 (3.00)

0.492

rs1800587 ǂ

IL1A

UTR'5 TFBS, Splicing

C > T

T = 39.1

9 (39.1)

10 (43.5)

4 (17.4)

G > A

A = 41.8

183 (34.2)

257 (48.0)

95 (17.8)

0.885

rs1800629 ǂ

TNF

Near gene 5' TFBS

G > A

A = 13.7

46 (74.2)

15 (24.2)

1 (1.60)

G > A

A = 16.9

368 (68.8)

153 (28.6)

14 (2.60)

0.752

rs1800871 ǂ

IL10

Near gene 5' TFBS

C > T

T = 36.3

28 (45.2)

23 (37.1)

11 (17.7)

G > A

A = 40.7

188 (35.0)

258 (48.0)

89 (17.0)

0.219

rs1800872 ǂǂ

IL10

Near gene 5' TFBS

A > C

A = 50.0 C = 50.0

5 (21.7)

13 (56.6)

5 (21.7)

C > A

A = 40.7

188 (35.0)

258 (48.0)

89 (17.0)

0.874

rs1800893 ǂ

IL10

Near gene 5' TFBS

G > A

A = 37.1

22 (35.5)

34 (54.8)

6 (9.70)

G > A

A = 36.4

216 (40.4)

248 (46.4)

71 (13.2)

0.419

rs1800896 ǂ

IL10

Near gene 5' TFBS

A > G

G = 40.5

7 (33.3)

11 (52.4)

3 (14.3)

A > G

G = 33.3

243 (45.4)

228 (42.6)

64 (12.0)

0.491

rs2192752 ǂ

IL1R1

Near gene 5' TFBS

A > C

C = 4.80

56 (90.3)

6 (9.70)

0 (0.00)

A > C

C = 5.60

477 (89.1)

56 (10.5)

2 (0.40)

1.000

rs2227532 ǂ

IL8

Near gene 5' TFBS

T > C

C = 9.70

50 (80.6)

12 (19.4)

0 (0.00)

A > G

G = 8.60

448 (83.7)

82 (15.3)

5 (1.00)

0.690

rs2227538 ǂ

IL8

UTR'5 TFBS, Splicing

C > T

T = 17.7

41 (66.1)

20 (32.3)

1 (1.60)

G > A

A = 23.2

323 (60.4)

176 (32.9)

36 (6.70)

0.291

rs2227545 ǂ

IL8

UTR'3 miRNA

A > C

C = 8.70

19 (82.6)

4 (17.4)

0 (0.00)

A > C

C = 8.50

449 (83.9)

81 (15.1)

5 (1.00)

0.812

rs2229113 ǂ

IL10RA

Exon 7 nsSNP, probably damaging

G > A

A = 20.5

14 (63.7)

7 (31.8)

1 (4.50)

G > A

A = 18.8

355 (66.4)

159 (29.7)

21 (3.90)

0.782

rs2834167 ǂ

IL10RB

Exon 2 Splicing, nsSNP, benign

A > G

G = 16.9

44 (71.0)

15 (24.2)

3 (4.80)

A > G

G = 11.0

423 (79.1)

106 (19.8)

6 (1.10)

0.050

rs2856836 ǂ

IL1A

UTR'3 miRNA

T > C

C = 17.4

16 (69.6)

6 (26.1)

1 (4.30)

A > G

G = 18.6

358 (66.9)

155 (29.0)

22 (4.10)

1.000

rs3135932 ǂ

IL10RA

Exon 5 Splicing, nsSNP, benign

A > G

G = 2.10

23 (95.8)

1 (4.20)

0 (0.00)

A > G

G = 2.60

508 (95.0)

26 (4.80)

1 (0.20)

1.000

rs315951 ǂ

IL1RN

UTR'3 miRNA

C > G

G = 47.9

8 (33.3)

9 (37.5)

7 (29.2)

C > G

G = 48.0

144 (26.9)

268 (50.1)

123 (23.0)

0.482

rs3738579 ǂ

RNASEL

UTR'5 TFBS, Splicing

T > C

C = 16.7

14 (66.7)

7 (33.3)

0 (0.00)

A > G

G = 12.3

411 (76.8)

116 (21.7)

8 (1.50)

0.474

rs3917225 ǂ

IL1R1

Near gene 5' TFBS

A > G

G = 12.3

49 (80.3)

9 (14.8)

3 (4.90)

A > G

G = 9.10

438 (81.9)

97 (18.1)

0 (0.00)

0.001

rs4073 ǂ

IL8

Near gene 5' TFBS

A > T

T = 26.6

34 (54.8)

23 (37.1)

5 (8.10)

T > A

A = 20.9

335 (62.6)

176 (32.9)

24 (4.50)

0.262

rs4141134 ǂǂ

IL1R2

Near gene 5'

T > C

C = 11.2

39 (79.6)

9 (18.4)

1 (2.00)

A > G

G = 13.7

399 (74.6)

125 (23.4)

11 (2.00)

0.660

rs4251961 ǂ

IL1RN

Near gene 5' TFBS

T > C

C = 20.2

37 (59.7)

25 (40.3)

0 (0.00)

A > G

G = 17.9

367 (68.6)

145 (27.1)

23 (4.30)

0.035

rs4252243 ǂ

IL10RA

Near gene 5' TFBS

C > T

T = 32.5

9 (45.0)

9 (45.0)

2 (10.0)

G > A

A = 27.5

271 (50.7)

234 (43.7)

30 (5.60)

0.522

rs4674257 ǂǂ

IL8RB

Near gene 5' TFBS

G > A

A = 25.0

14 (58.3)

8 (33.3)

2 (8.30)

G > A

A = 20.1

347 (64.9)

161 (30.10)

27 (5.00)

0.468

rs4674259 ǂ

IL8RB

UTR'5 TFBS

A > G

G = 23.9

12 (52.2)

11 (47.8)

0 (0.00)

A > G

G = 20.0

349 (65.0)

158 (30.0)

28 (5.00)

0.176

rs486907 ǂ

RNASEL

Exon 1 nsSNP, benign

G > A

A = 16.7

16 (66.7)

8 (33.3)

0 (0.00)

G > A

A = 13.2

402 (75.1)

125 (23.4)

8 (1.50)

0.528

rs6726713 ǂǂ

IL1R2

Near gene 5' TFBS

C > T

T = 11.2

38 (77.6)

11 (22.4)

0 (0.00)

G > A

A = 12.1

417 (78.0)

106 (19.8)

12 (2.20)

0.689

rs673 ǂ

TNF

Near gene 5' TFBS

G > A

A = 13.7

45 (72.6)

17 (27.4)

0 (0.00)

G > A

A = 17.4

364 (68.0)

156 (29.2)

15 (2.80)

0.546

rs8178433 ǂ

IL10RB

Near gene 5' TFBS

T > G

G = 12.9

46 (74.2)

16 (25.8)

0 (0.00)

A > C

C = 12.4

408 (76.3)

121 (22.6)

6 (1.10)

0.811

rs949963 ǂ

IL1R1

Near gene 5' TFBS

G > A

A = 31.1

31 (50.8)

22 (36.1)

8 (13.1)

G > A

A = 33.1

249 (46.5)

218 (40.8)

68 (12.7)

0.771

rs9610 ǂ

IL10RA

UTR'3 miRNA

A > G

G = 41.9

20 (32.3)

32 (51.6)

10 (16.1)

A > G

G = 33.9

237 (44.3)

233 (43.5)

65 (12.2)

0.184

rs999788 ǂ

IL10RB

Near gene 5' TFBS

C > T

T = 19.5

40 (67.8)

15 (25.4)

4 (6.80)

G > A

A = 12.4

410 (76.6)

117 (21.9)

8 (1.50)

0.026

  1. The nucleotide change may vary relative to that reported in NCBI depending on whether the genotyping was performed using the sense or anti-sense DNA strand.
  2. ††The chi-square test was used to assess differences in the overall genotype frequencies comparing men of African Descent as reported in NCBI to those in the total population from the current study. P-values generated from the Fisher’s exact test (in italics) were used when expected genotype counts were < 5 for either cases or controls.
  3. Abbreviations: MAF Minor Allele Frequency; UTR untranslated region; TFBS transcription factor binding site; nsSNP non-synonymous coding SNP; miRNA microRNA binding site; NCBI National Center for Biotechnology Information Entrez SNP.
  4. ǂNCBI AFR1 or African American Population Panel.
  5. ǂǂNCBI ASW Population Panel.