Table 2. Most significant SNP associations in 60 chromosomal regions, by chromosome, from the Discovery analysis.
| Chromosomal region | SNP | Position (build 36/hg18) | Coded Allele | Coded Allele Freq. | OR (95% CI) | P | Gene name (GENCODE) | Location | RegulomeDB* |
|---|---|---|---|---|---|---|---|---|---|
| 1p13.2 | rs116268993 | 115272760 | T | 0.99 | 4.55 (2.07–10.0) | 1.36E-05 | CSDE1 | intronic | 7 |
| 1p34.3 | 34655226:T_TG | 34655226 | R | 0.95 | 2.05 (1.48–2.84)) | 7.35E-06 | |||
| 1p36.13 | rs72655635 | 18794898 | A | 0.83 | 1.40 (1.20–1.64) | 1.24E-05 | 13kb 5' of KLHDC7A | 5 | |
| 1p36.21 | rs6677152 | 14414502 | T | 0.66 | 1.33 (1.16–1.53) | 3.62E-05 | C1orf196 | 6 | |
| 1q31.3 | rs80197301 | 194961694 | G | 0.98 | 2.71 (1.63–4.50) | 3.43E-05 | 134kb 5' of AL357932.1 | 7 | |
| 1q32.2 | rs12403733 | 209784188 | G | 0.97 | 0.49 (0.35–0.69) | 3.65E-05 | CAMK1G | intronic | 4 |
| 2q37.1 | rs74645168 | 233943347 | G | 0.97 | 2.61 (1.63–4.20) | 2.12E-05 | INPP5D | 5 | |
| 3p12.3 | rs7430339 | 79766511 | G | 0.58 | 0.78 (0.71–0.89) | 1.20E-04 | ROBO1 | intronic | 7 |
| 3p21.31 | rs9836993 | 46665120 | A | 0.93 | 0.62 (0.37–0.78) | 5.29E-05 | TDGF1 | intronic | 6 |
| 3p25.2 | rs62246114 | 11948649 | C | 0.66 | 0.78 (0.66–0.88) | 5.46E-05 | 46kb 3' of Metazoa_SRP | 7 | |
| 3q22.1 | rs114398209 | 133638227 | G | 0.94 | 1.78 (1.36–2.33) | 1.46E-05 | 8.8kb 3' of C3orf36 | 6 | |
| 3q25.1 | rs9834244 | 151422581 | G | 0.91 | 0.59 (0.37–0.73) | 8.40E-07 | 29kb 5' of AADACL2 | 7 | |
| 4p16.2 | rs34775372 | 4796443 | C | 0.92 | 1.69 (1.33–2.13) | 6.39E-06 | 65kb 5' of MSX1 | 5 | |
| 4p15.32 | rs1532347 | 15003896 | C | 0.94 | 1.75 (1.33–2.32) | 4.81E-05 | 226bp 5' of AC006296.3 | 4 | |
| 4q23 | rs139005704 | 100974971 | C | 0.99 | 4.03 (1.87–8.68) | 3.06E-05 | RP11-15B17.1 | 6 | |
| 4q31.1 | rs4863620 | 139876605 | A | 0.63 | 1.29 (1.14–1.45) | 2.06E-05 | RP11-371F15.3 | 6 | |
| 4q32.2 | rs11736440 | 163336693 | G | 0.91 | 0.66 (0.55–0.8) | 1.41E-05 | 252kb 5' of FSTL5 | 6 | |
| 5p13.3 | rs253937 | 31655104 | A | 0.89 | 1.51 (1.24–1.83) | 2.19E-05 | PDZD2 | 6 | |
| 5q31.3 | rs169087 | 140283860 | C | 0.97 | 0.48 (0.34–0.67) | 1.35E-05 | PCDHA1 | intronic | 6 |
| 6p23 | rs71564305 | 14108031 | G | 0.96 | 0.43 (0.05–0.63) | 3.21E-06 | 9.8kb 5' of CD83 | 5 | |
| 6q12 | rs112319963 | 66907171 | T | 0.99 | 0.25 (0.13–0.45) | 1.53E-06 | 162kb 5' of AC002485.1 | 7 | |
| 6q15 | rs72915109 | 92335740 | A | 0.91 | 1.51 (1.31–1.85) | 7.20E-05 | 3.9kb 3' of RP3-433F14.3 | 7 | |
| 6q22.31 | rs235701 | 124247963 | C | 0.81 | 1.33 (1.18–1.55) | 2.79E-04 | NKAIN2 | intronic | 7 |
| 6q27 | rs4075454 | 166722486 | T | 0.51 | 0.77 (0.66–0.86) | 4.64E-06 | 549bp 5' of PRR18 | 4 | |
| 7p12.1 | rs4433098 | 52284370 | A | 0.58 | 0.76 (0.64–0.87) | 2.53E-05 | 24kb 5' of RP11-153N17.1 | 6 | |
| 7p12.1 | rs11981322 | 52485878 | T | 0.57 | 0.78 (0.69–0.88) | 4.20E-05 | 94kb 5' of snoU13 | 6 | |
| 7p14.1 | rs7794030 | 38752094 | A | 0.81 | 1.43 (1.29–1.65) | 1.07E-06 | 10kb 3' of VPS41 | 7 | |
| 7p14.1** | rs1468348* | 38767914 | T | 0.80 | 1.39 (1.25–1.6) | 4.72E-06 | VPS41 | intronic | 1f |
| 7q33 | rs59191429 | 137663901 | G | 0.93 | 0.62 (0.38–0.79) | 5.37E-05 | CREB3L2 | intronic | 5 |
| 8p12 | rs6996680 | 32844577 | A | 0.63 | 0.77 (0.65–0.87) | 2.25E-05 | 9.1kb 5' of RP11-11N9.4 | 6 | |
| 8p22 | rs34793944 | 17024449 | A | 0.67 | 1.27 (1.14–1.44) | 2.80E-04 | ZDHHC2 | intronic | 6 |
| 8q21.11 | rs7461712 | 75405213 | C | 0.62 | 1.28 (1.16–1.44) | 3.77E-05 | 4.1kb 3' of GDAP1 | 5 | |
| 8q22.3 | rs12548629# | 104201401 | C | 0.73 | 0.71 (0.58–0.81) | 2.54E-07 | BAALC | intronic | 6 |
| 9p13.3 | 35969579:G_GT | 35969579 | R | 0.77 | 0.74 (0.64–0.85) | 3.49E-05 | |||
| 9p22.2 | rs1618634 | 17962581 | G | 0.99 | 2.69 (2.22–4.32) | 2.84E-05 | 165kb 3' of SH3GL2 | 7 | |
| 9q21.32 | rs13293114 | 85832384 | A | 0.64 | 0.76 (0.64–0.85) | 4.35E-06 | 1.9kb 5' of RP11-439K3.1 | 6 | |
| 9q31.3 | rs60702108 | 113047837 | T | 0.84 | 0.70 (0.54–0.83) | 1.75E-05 | 18kb 3' of TXNDC8 | 6 | |
| 9q34.13 | rs59210554 | 135012819 | A | 0.77 | 1.27 (1.13–1.45) | 5.72E-04 | 25kb 5' of NTNG2 | 5 | |
| 10p12.2 | rs11013837 | 24284651 | T | 0.77 | 1.37 (1.19–1.58) | 6.40E-06 | KIAA1217 | intronic | 6 |
| 10p13 | rs192386529 | 13664943 | A | 0.97 | 0.45 (0.31–0.66) | 2.80E-05 | PRPF18 | intronic | 6 |
| 10q26.3 | rs4751122 | 131583538 | C | 0.59 | 0.78 (0.7–0.88) | 2.88E-05 | RP11-109A6.4 | 5 | |
| 11p15.4 | rs1023996 | 7400790 | G | 0.58 | 1.32 (1.18–1.48) | 2.27E-06 | SYT9 | intronic | 6 |
| 11p15.4 | rs55740932 | 8453025 | C | 0.94 | 1.79 (1.36–2.35) | 1.72E-05 | STK33 | intronic | 5 |
| 11q22.3 | rs965505 | 103739232 | C | 0.81 | 1.37 (1.18–1.6) | 3.55E-05 | RP11-563P16.1 | 5 | |
| 12q22 | rs7302318 | 68094969 | R | 0.85 | 0.70 (0.59–0.83) | 3.17E-05 | CRADD | 3a | |
| 12q24.33 | rs7975553 | 131045130 | G | 0.57 | 0.77 (0.68–0.86) | 5.95E-06 | RIMBP2 | 6 | |
| 16p13.2 | rs73494614 | 9515438 | A | 0.85 | 1.44 (1.23–1.7) | 9.58E-06 | 13kb 3' of RP11-243A14.1 | 7 | |
| 17p13.3 | rs4359482 | 2915699 | A | 0.55 | 1.29 (1.15–1.45) | 1.59E-05 | RAP1GAP2 | intronic | 6 |
| 18q12.2 | rs17659787 | 36600043 | T | 0.71 | 0.75 (0.65–0.85) | 1.31E-05 | 3.7kb 5' of 7SK | 5 | |
| 18q21.1 | rs34007497 | 46451073 | C | 0.54 | 0.78 (0.69–0.87) | 1.26E-05 | SMAD7 | intronic | 4 |
| 19p13.12 | rs3752185 | 14828737 | G | 0.52 | 0.78 (0.66–0.87) | 1.41E-05 | ZNF333 | intronic | 6 |
| 19p13.12** | rs11666622* | 14830568 | T | 0.52 | 0.78 (0.66–0.87) | 1.65E-05 | ZNF333 | 3'-UTR | 6 |
| 19q13.41 | rs162277 | 53030198 | C | 0.79 | 1.41 (1.26–1.63) | 6.95E-06 | 706bp 5' of ZNF808 | 3a | |
| 19q13.42 | rs2217653 | 54223164 | T | 0.73 | 1.31 (1.15–1.5) | 4.30E-05 | 185bp 5' of MIR520D | 5 | |
| 19q13.42 | rs112822051 | 55547043 | C | 0.97 | 2.56 (1.67–3.93) | 3.24E-06 | GP6 | intronic | 7 |
| 20p11.23 | rs113118767 | 19499434 | T | 0.99 | 4.02 (1.99–8.13) | 8.97E-06 | SLC24A3 | intronic | 5 |
| 20q12 | rs6071641 | 37677661 | T | 0.58 | 0.76 (0.63–0.85) | 6.44E-06 | 9.3kb 3' of DHX35 | 6 | |
| 20q12* | rs742276* | 37679849 | G | 0.56 | 0.77 (0.66–0.87) | 8.74E-06 | 11kb 3' of DHX35 | 2b | |
| 20q13.33 | rs6027867 | 59434375 | G | 0.82 | 0.74 (0.58–0.86) | 8.68E-05 | 45kb 5' of RP11-151E14.1 | 7 | |
| 21q22.2 | rs59603367 | 42433821 | T | 0.95 | 0.57 (0.44–0.74) | 3.52E-05 | 80kb 3' of LINC00323 | 7 |
*RegulomeDB [28] scores: 1f, likely to affect binding and linked to expression of a gene target; 2b, likely to affect binding; 3a, less likely to affect binding; 4–6, minimal binding evidence; 7, no data.
**Denotes a potentially functional SNP in Linkage Disequilibrium (r2>0.9) with the SNP with the smallest P-value in the region. Other SNPs in the same genomic regions are listed in Supplementary Table 1 (S1 Table).
#Most significant SNP in the Discovery data