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Table 4 Highlights of conditional analyses of the MHC region in LOMG.

From: Genome-Wide Association Study of Late-Onset Myasthenia Gravis: Confirmation of TNFRSF11A and Identification of ZBTB10 and Three Distinct HLA Associations

Conditioning

HLA-A: 29510630-30465978

Class III: 30466879-31763744

Class II: 31765860-33005932

Lowest residual P value

Variant

Position

Lowest residual P value

Variant

Position

Lowest residual P value

Variant

Position

None

1.00 × 10−11

rs150881176

29947740

4.11 × 10−12

rs2071591

31515799

3.13 × 10 −17

rs111945767

32517045

rs111945767

2.24 × 10 −8

rs150881176

29947740

1.17 × 10−7

6:31534010:D

31534010

7.91 × 10−4

rs204887

32029226

DRB1

3.26 × 10 −8

rs150881176

29947740

8.33 × 10−7

rs2071596

31506691

5.58 × 10−5

rs9501624

32399286

DQA1

1.78 × 10 −8

rs150881176

29947740

1.77 × 10−7

rs2256974

31555392

1.11 × 10−3

rs147008997

32447598

DQB1

1.84 × 10 −9

rs115207654

29942293

7.19 × 10−8

rs2071591

31515799

9.52 × 10−8

DQA1_AA107_I

32609806

HLA-A

1.16 × 10−4

rs1632958

29688643

2.40 × 10−10

rs2071591

31515799

7.02 × 10 −16

rs111945767

32517045

HLA-B

2.82 × 10−8

rs150881176

29947740

3.17 × 10−8

rs116706902

31529335

6.85 × 10 −13

rs111938555

32509707

HLA-C

6.99 × 10−8

rs150881176

29947740

2.68 × 10−6

rs2071591

31515799

3.75 × 10 −12

rs112780983

32511348

DRB1, HLA-A, Class III SNP

2.55 × 10−3

rs1632958

29688643

4.15 × 10 −4

rs138758805

31533722

1.57 × 10 −5

rs9501624

32399286

DQA1, HLA-A, Class III SNP

2.18 × 10−3

6:30014294:I

30014294

2.16 × 10 −3

rs12665489

31507987

2.96 × 10−3

chr6:31834138

31834138

DQA1, HLA-A, HLA-C

2.52 × 10−3

6:30014294:I

30014294

4.20 × 10 −5

rs2071596

31506691

4.08 × 10−3

rs28732173

32071010

DRB1_AA11, A_AA70, Class III SNP

2.34 × 10 −4

rs150881176

29947740

7.05 × 10−4

rs12665489

31507987

2.19 × 10−4

rs114053271

32535948

DQA1_AA75, DQA1_AA130, A_AA70, Class III SNP

5.42 × 10 −4

rs114705891

29990708

1.57 × 10−3

rs12665489

31507987

3.12 × 10−3

rs6907185

31844684

DQA1 AA75, DQA1 AA130, A_AA70, A_AA152, Class III SNP

1.95 × 10 −3

rs150881176

29947740

2.06 × 10−3

rs12665489

31507987

3.40 × 10−3

rs143832718

32287072

  1. The most significant P value for each condition is shown for each of the three regions with signal peaks (Figure 5). The most significant P value for each condition (row) is shown in bold. Gray shading indicates where the signal has been attenuated above P = 5 × 10−5. The class III SNP included in the conditioning is rs2071596, but nearly equivalent results are obtained with rs6929796 or rs2256974. For some of the AAs indicated in this table, others gave nearly identical results: 130A was in complete LD with 41K, and 75I was in nearly complete LD with AAs at multiple positions (40, 47, 50, 51, 53, 107, 156, 161, 163, and 175). For these studies, conditioning was performed using all HLA antigens for each gene that had nominally significant P values (P < 0.05). For AAs, we individually conditioned on each AA (in DQA1, DRB1 and HLA-A) that had nominal P values <0.001. Results are for those AAs with the strongest attenuation of the association signals.
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Molecular Medicine

ISSN: 1528-3658