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Table 1 Nucleotide variants associated with mRNA expression, ribosome occupancy, and protein abundance of HLA-DQA1 and MRPL43a

From: Antagonistic regulatory effects of a single cis-acting expression quantitative trait locus between transcription and translation of the MRPL43 gene

SNP

Positionb

MAF

mRNA expression

Ribosome occupancy

Protein abundance

BETA

P

BETA

P

BETA

P

HLA-DQA1

 g.32637603 T > A

6:32,605,380

0.48

0.842

2.78 × 10−8

0.614

7.15 × 10− 6

0.886

1.50 × 10−7

 g.32639416 T > C

6:32,607,193

0.24

−0.678

7.83 × 10−7

− 0.647

4.48 × 10− 7

− 0.741

6.15 × 10−6

 g.32639504G > A

6:32,607,281

0.36

−0.573

2.87 × 10−6

−0.501

5.75 × 10−6

−0.637

2.72 × 10−6

 g.32640436G > A

6:32,608,213

0.44

−0.687

2.17 × 10−7

−0.537

6.91 × 10−6

−0.692

2.58 × 10−6

 g.32641103G > A

6:32,608,880

0.27

−0.790

7.69 × 10−8

−0.716

1.90 × 10−7

−0.881

7.70 × 10−8

 g.32641737C > A

6:32,609,514

0.48

0.840

3.05 × 10−8

0.607

8.83 × 10−6

0.873

2.24 × 10−7

 g.32644006A > G

6:32,611,783

0.40

−0.628

7.63 × 10−7

− 0.533

3.34 × 10−6

− 0.709

3.91 × 10− 7

 g.32652582C > A

6:32,620,359

0.37

−0.597

1.42 × 10−6

−0.495

9.22 × 10−6

−0.725

1.38 × 10−7

 g.32658175C > A

6:32,625,952

0.47

−0.725

1.48 × 10−7

−0.567

6.87 × 10−6

−0.770

1.07 × 10−6

 g.32658472 T > A

6:32,626,249

0.45

−0.757

2.86 × 10−7

−0.676

6.63 × 10−7

−0.874

4.65 × 10−8

 g.32658813C > A

6:32,626,590

0.48

0.856

3.08 × 10−8

0.632

5.87 × 10−6

0.916

1.19 × 10−7

 g.32661067 T > A

6:32,628,844

0.43

−0.638

9.91 × 10−7

− 0.553

3.24 × 10−6

− 0.649

8.98 × 10− 6

 g.32661176C > A

6:32,628,953

0.39

−0.641

2.82 × 10−7

−0.505

8.44 × 10−6

−0.656

3.23 × 10−6

 g.32662025A > C

6:32,629,802

0.52

0.841

2.62 × 10−8

0.634

3.22 × 10−6

0.904

1.66 × 10−7

 g.32669003G > A

6:32,636,780

0.44

−0.746

2.88 × 10−7

− 0.642

1.60 × 10−6

− 0.848

6.94 × 10−8

 g.32669230G > C

6:32,637,007

0.42

−0.708

5.50 × 10−7

−0.659

4.22 × 10−7

−0.802

1.38 × 10−7

 g.32670046A > G

6:32,637,823

0.40

−0.674

9.23 × 10−7

−0.650

2.83 × 10−7

−0.799

1.11 × 10−7

 g.32670110 T > C

6:32,637,887

0.42

−0.701

5.72 × 10−7

−0.612

2.16 × 10−6

−0.788

2.57 × 10−7

 g.32670309G > A

6:32,638,086

0.41

−0.729

1.59 × 10−7

−0.639

6.07 × 10−7

−0.750

7.31 × 10−7

MRPL43

 g.100983006C > Ac

10:102,742,763

0.47

0.534

9.16 × 10−6

0.748

7.47 × 10−8

−0.577

6.09 × 10−6

 g.100986746C > Gc

10:102,746,503

0.47

0.534

9.16 × 10−6

0.748

7.47 × 10−8

−0.577

6.09 × 10−6

 g.100980514 T > Cc

10:102,740,271

0.47

0.534

9.16 × 10−6

0.748

7.47 × 10−8

−0.577

6.09 × 10−6

  1. aOnly representative nucleotide variants are presented (P < 1 × 10−5)
  2. bChromosome number: chromosomal position in the hg19 version
  3. cThe three nucleotide variants in complete linkage had the lowest P value in one signal
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BMC Genomic Data

ISSN: 2730-6844

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