Table 1 Association results of eight independent variants of NPC genetic susceptibility in discovery, validation, and combined phases.

From: Nasopharyngeal carcinoma MHC region deep sequencing identifies HLA and novel non-HLA TRIM31 and TRIM39 loci

Variants

Locus

Markers

in LD

EA/OA

MAF

Discovery (n = 3047)

Validation (n = 2642)

Combined (n = 5689)

Conditional analysis

OR

(95% CI)

P

OR

(95% CI)

P

OR

(95% CI)

P

P

rs9391681

intergenic

RPP21*

HLA-E

HLA-A*02:0714,16,17,

HLA-Aaa-C9911

C/T

0.17/0.23/0.12

2.30

(2.00–2.64)

1.73E−31

1.90

(1.64–2.21)

3.68e−17

2.11

(1.90–2.33)

1.50e−46

–

HLA-A amino acid Q62

HLA-A

HLA-A*11:017,10,11,

rs28605807

P/Ab

0.33/0.26/0.39

0.54

(0.48–0.61)

1.35E−26

0.58

(0.51–0.65)

7.11e−19

0.56

(0.51–0.61)

6.27e−44

1.68e−24

rs2523589

HLA-B

rs9405084a

G/T

0.30/0.24/0.35

0.56

(0.50–0.63)

1.05E−23

0.62

(0.55–0.70)

4.15e−14

0.59

(0.54–0.64)

1.77e−36

3.26e−19

HLA-B*55:02

HLA-B

–

P/Ab

0.018/0.0047/0.031

0.13

(0.070–0.23)

1.99E−11

0.18

(0.10–0.32)

4.81e−09

0.15

(0.10–0.23)

3.59e−19

8.79e−14

rs2517664

TRIM31

rs1116222, rs2844796a

T/C

0.030/0.014/0.046

0.27

(0.19–0.39)

7.77E−13

0.31

(0.21–0.45)

1.66e−09

0.29

(0.22–0.37)

6.38e−21

2.55e−12

rs9265975

HLA-B

rs24982077

A/G

0.10/0.072/0.13

0.46

(0.39–0.55)

4.41E−17

0.56

(0.47–0.68)

1.15e−09

0.51

(0.45–0.58)

6.77e−25

1.61e−09

rs9461780

HLA-DQA1

–

T/C

0.071/0.049/0.091

0.51

(0.42–0.62)

2.81E−11

0.55

(0.44–0.70)

6.85e−07

0.52

(0.45–0.61)

4.38e−17

2.60e−14

rs117495548

TRIM39/

TRIM39-RPP21

rs148603250a

G/A

0.020/0.0094/0.030

0.36

(0.24–0.54)

8.56E−07

0.27

(0.16–0.43)

1.19e−07

0.31

(0.23–0.43)

4.53e−13

2.24e−06

  1. P < 1.69e10-5 after Bonferroni correction considering 2967 significant common variants.
  2. OR and P of the combined data set and P of conditional analysis are bolded.
  3. EA effect allele, OA other allele, P present allele, Ab absent allele for locus with multiple alleles, MAF minor allele frequency for combined data set/case/control, conditional analysis forward conditional logistic regression model with gender- and age-adjusted, OR odds ratio, P P-value.
  4. aPutative functional annotated SNPs in tight LD with the previously unreported independent signals observed in the current NPC study.
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