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Table 2 Summary results for identified risk loci pair overlaps

From: Enrichment of B cell receptor signaling and epidermal growth factor receptor pathways in monoclonal gammopathy of undetermined significance: a genome-wide genetic interaction study

    

Discovery set

Replication set

Gene1

Chr1

Gene2

Chr2

SNP1 (Risk allele)

Position (hg19,bp)

MAF

SNP2 (Risk allele)

Position (hg19,bp)

MAF

WZ P-value

OR (95% CI)

SNP1 (Risk allele)

Position (hg19,bp)

MAF

SNP2 (Risk allele)

Position (hg19,bp)

MAF

WZ P value

OR (95% CI)

TNC

9q33.1

CRYL1

13q12.11

rs10118040 (T)

117,879,414

0.40

rs7337130 (C)

21,021,343

0.31

6.91E-11

2.64 (1.91–3.65)

rs1330368 (A)

117,821,026

0.48

rs7337231 (G)

20,896,618

0.49

2.48E-08

1.05 (0.96–1.14)

SETBP1

18q12.3

PREX1

20q13.13

rs12959213 (C)

42,769,020

0.41

rs6066791 (T)

47,251,687

0.26

7.07E-11

2.39 (1.75–3.25)

rs11082429 (G)

42,743,790

0.44

rs170536 (A)

46,878,722

0.32

4.25E-08

1.01 (0.93–1.09)

SETBP1

18q12.3

PREX1

20q13.13

rs12959213 (C)

42,769,020

0.41

rs6066791 (T)

47,251,687

0.26

7.07E-11

2.39 (1.75–3.25)

rs1376230 (T)

42,703,052

0.35

rs6063251 (C)

47,015,157

0.43

6.37E-07

1.03 (0.94–1.11)

ERBB4

2q34

RORA

15q22.2

rs1546717 (G)

212,902,339

0.10

rs1159814 (A)

61,431,996

0.41

9.07E-11

5.03 (2.89–8.77)

rs6745249 (G)

213,130,571

0.48

rs974065 (A)

60,952,440

0.34

1.06E-10

1.13 (1.04–1.22)

PARK2

6q26

C14orf177

14q32.2

rs6455744 (T)

162,060,468

0.38

rs7359146 (C)

99,084,602

0.14

1.12E-10

2.92 (1.96–4.33)

rs6927285 (G)

162,010,329

0.43

rs8022922 (A)

98,987,292

0.44

1.23E-14

1.06 (0.98–1.14)

ETNK1

12p12.1

TMC2

20p13

rs2467112 (C)

23,071,644

0.19

rs1028441 (T)

2,600,186

0.24

1.20E-10

3.24 (2.12–4.95)

rs7313039 (C)

23,091,130

0.47

rs6050256 (T)

2,554,907

0.48

2.04E-07

1.05 (0.97–1.14)

aLOC646784 / HFM1

1p22.2

LOC647259

13q21.1

rs674135 (G)

91,675,675

0.26

rs4146191 (A)

62,872,965

0.47

1.44E-10

2.61 (1.89–3.60)

rs7416823 (T)

157,386,394

0.31

rs428328 (C)

63,110,606

0.41

2.24E-09

1.05 (0.96–1.13)

ERBB4

2q34

PTPRD

9p23

rs1437919 (A)

212,110,840

0.23

rs10978043 (G)

9,860,402

0.19

2.64E-10

3.38 (2.19–5.22)

rs6747637 (G)

212,406,789

0.45

rs4427223 (A)

10,663,815

0.48

7.35E-14

1.01 (0.93–1.09)

AUTS2

7p11.22

HS6ST3

13q32.1

rs1011780 (A)

70,124,648

0.28

rs9556582 (G)

97,040,531

0.46

2.68E-10

2.40 (1.75–3.29)

rs10267303 (T)

70,082,913

0.47

rs12876541 (C)

97,304,003

0.44

3.33E-08

1.06 (0.97–1.14)

SETBP1

18q12.3

PREX1

20q13.13

rs12959213 (C)

42,769,020

0.41

rs4810836 (T)

47,228,931

0.25

3.04E-10

2.40 (1.75–3.25)

rs11082429 (G)

42,743,790

0.44

rs170536 (A)

46,878,722

0.32

4.25E-08

0.98 (0.90–1.06)

SETBP1

18q12.3

PREX1

20q13.13

rs12959213 (C)

42,769,020

0.41

rs4810836 (T)

47,228,931

0.25

3.04E-10

2.40 (1.75–3.25)

rs1376230 (T)

42,703,052

0.35

rs6063251 (C)

47,015,157

0.43

6.37E-07

0.97 (0.89–1.05)

CNTN4

3p26.3

FAM19A1

3p14.1

rs2619566 (C)

2,624,938

0.12

rs1032376 (A)

68,317,975

0.19

3.28E-10

4.66 (2.71–8.02)

rs1499133 (C)

2,952,214

0.41

rs7610023 (T)

68,123,731

0.40

4.14E-09

1.05 (0.97–1.14)

CNTN4

3p26.3

FAM19A1

3p14.1

rs2619566 (G)

2,624,938

0.12

rs1032376 (A)

68,317,975

0.19

3.28E-10

4.66 (2.71–8.02)

rs1178491 (G)

2,342,825

0.36

rs6549098 (A)

68,323,280

0.40

2.83E-08

0.98 (0.90–1.06)

TNC

9q33.1

CRYL1

9q33.1

rs2071520 (T)

117,880,792

0.32

rs7337130 (C)

21,021,343

0.31

3.50E-10

2.80 (1.99–3.15)

rs1330368 (A)

117,821,026

0.48

rs7337231 (G)

20,896,618

0.49

2.48E-08

0.96 (0.89–1.04)

CSMD1

8p23.2

LOC392301

9q13

rs1700112 (G)

4,097,418

0.41

rs410684 (A)

31,673,588

0.42

3.84E-10

2.16 (1.62–2.87)

rs2740939 (C)

3,872,513

0.48

rs7853053 (T)

32,211,402

0.49

2.04E-16

1.04 (0.95–1.12)

CSMD1

8p23.2

LOC392301

9q13

rs1700112 (G)

4,097,418

0.41

rs410684 (A)

31,673,588

0.42

3.84E-10

2.16 (1.62–2.87)

rs2740929 (C)

3,879,918

0.49

rs7853053 (T)

32,211,402

0.49

3.81E-10

1.04 (0.95–1.12)

ERBB4

2q34

LOC729802

9p23

rs1437919 (A)

212,110,840

0.23

rs7851513 (G)

9,842,176

0.19

3.92E-10

3.10 (2.05–4.69)

rs6747637 (G)

212,406,789

0.45

rs4427223 (A)

10,663,815

0.48

7.35E-14

0.92 (0.85–0.99)

KHDRBS3

8q24.23

KSR2

12q24.23

rs4909494 (C)

136,646,548

0.46

rs10774941 (T)

118,037,655

0.27

4.22E-10

2.51 (1.83–3.45)

rs16905387 (G)

136,539,132

0.42

rs7972142 (A)

118,211,046

0.44

3.97E-13

1.05 (0.96–1.13)

SETBP1

18q12.3

PREX1

20q13.13

rs12959213 (C)

42,769,020

0.41

rs6095212 (T)

47,233,383

0.25

4.25E-10

2.39 (1.75–3.25)

rs11082429 (G)

42,743,790

0.44

rs170536 (A)

46,878,722

0.32

4.25E-08

1.04 (0.96–1.12)

SETBP1

18q12.3

PREX1

20q13.13

rs12959213 (C)

42,769,020

0.41

rs6095212 (T)

47,233,383

0.25

4.25E-10

2.39 (1.75–3.25)

rs1376230 (T)

42,703,052

0.35

rs6063251 (C)

47,015,157

0.43

6.37E-07

1.03 (0.95–1.11)

MAN1A1

6q22.31

FRMD4A

10p13

rs808034 (A)

119,467,743

0.39

rs789761 (C)

14,137,678

0.48

4.72E-10

0.46 (0.34–0.61)

rs1295392 (G)

119,676,177

0.45

rs751498 (A)

13,929,130

0.47

1.25E-09

1.05 (0.96–1.14)

BNC2

9p22.3

CDH13

16q23.3

rs7867771 (T)

16,314,909

0.28

rs11149564 (C)

83,441,027

0.44

4.82E-10

2.20 (1.62–3.00)

rs1415471 (A)

16,656,653

0.44

rs7194615 (G)

82,769,498

0.44

1.07E-08

1.02 (0.94–1.09)

DAOA

13q33.2

TOM1L1

17q22

rs5012127 (G)

105,119,100

0.17

rs4793773 (A)

52,646,414

0.27

4.89E-10

2.81 (1.88–4.02)

rs3015345 (A)

105,860,621

0.45

rs8070668 (G)

52,991,636

0.38

6.06E-10

1.05 (0.97–1.14)

  1. Risk allele is the allele corresponding to which the test is performed and the odds ratio is calculated. Frequency of risk allele pair is tested against controls. SNP1 and SNP2 are the two SNP candidates of a pair from each population; gene1 and gene2are the corresponding genes annotated to SNP1 and SNP2, respectively. WZ p-value is Wellek Ziegler test p-value. OR, interaction odds ratio; MAF, minor allele frequency; bp, base pair; hg19, human genome build 19; CI, confidence interval
  2. Bolding indicate genome wide significant observation at 99% level of significance. Underline indicate significant odds ratio
  3. adenotes annotation of SNP to the two closest flanking genes