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Table 5 Statistically Significant SNPs Identified in Patients with Any Tuberculosis (Pulmonary or Extrapulmonary) vs. PPD + Controls

From: Novel human genetic variants associated with extrapulmonary tuberculosis: a pilot genome wide association study

SNP

Rank

P-value

MAF in any TB

MAF in PPD +

Odds Ratio

Chromosome

Gene

Closest Gene

Distance to Gene

rs1989565

1

0.0004

0.1702

0.4074

0.2984

14

MARK3

---

---

rs10490266

2

0.0005

0.125

0.3661

0.2474

2

AC007317.1

  

rs1518350

3

0.0006

0.4688

0.2143

3.235

6

---

SLC35F1

29,253bp

rs2107005

4

0.0008

0.2917

0.5804

0.2977

4

RP11-556L14.2

---

---

rs509423

5

0.0008

0.1064

0.3039

0.2727

4

RP11-440N4

---

---

rs968079

6

0.0009

0.587

0.3163

3.071

9

PTPRD

---

---

  1. Empirical P - value cutoff from permutation testing = 0.0009
  2. The p - value reported is the raw value
  3. MAF = Minor Allele Frequency
  4. TB = Pulmonary or extrapulmonary tuberculosis
  5. PPD + = Purified protein derivative positive
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BMC Research Notes

ISSN: 1756-0500

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