| | | |
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)
|
- 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
- Bolding indicate genome wide significant observation at 99% level of significance. Underline indicate significant odds ratio
- adenotes annotation of SNP to the two closest flanking genes