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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
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Molecular Medicine

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