Regions with multiple SNPs selected by GCTA (cojo-slct) using TOPMed multipopulation reference panel for LD
| Region . | Genes in region . | SNP . | CPTID . | refA . | freq_geno . | bJ . | bJ_se . | pJ . | LD_r . | SNP consequence . |
|---|---|---|---|---|---|---|---|---|---|---|
| 14 | RGS12; HGFAC; DOK7 | rs3748034 | chr4:3444364:G:T | T | 0.121 | 0.025 | 0.004 | 1.56E-10 | −0.086 | Missense (HGFAC) |
| rs16844401 | chr4:3447925:G:A | A | 0.059 | 0.045 | 0.005 | 4.01E-17 | 0.029 | Missense (HGFAC) | ||
| rs36205397 | chr4:3468877:A:G | G | 0.533 | 0.018 | 0.003 | 3.06E-10 | 0.000 | Intronic (DOK7) | ||
| 16 | FGB; FGG | rs2227401 | chr4:154565229:C:T | T | 0.176 | 0.093 | 0.003 | 2.14E-165 | −0.028 | Intronic (FGB) |
| rs6054 | chr4:154568456:C:T | T | 0.004 | −0.385 | 0.022 | 2.21E-67 | −0.011 | Missense (FGB) | ||
| rs2066874 | chr4:154608429:T:C | C | 0.008 | −0.294 | 0.030 | 4.02E-22 | −0.010 | Intronic (FGG) | ||
| rs148685782 | chr4:154611883:G:C | C | 0.003 | −0.805 | 0.024 | 2.88E-237 | −0.020 | Missense (FGG) | ||
| rs28577061 | chr4:154614588:T:C | C | 0.046 | −0.089 | 0.013 | 1.96E-12 | −0.030 | Intergenic | ||
| rs149748987 | chr4:154618106:T:C | C | 0.007 | −0.179 | 0.015 | 2.96E-32 | 0.090 | Intergenic | ||
| rs6536024 | chr4:154622217:T:C | C | 0.478 | −0.029 | 0.003 | 5.10E-25 | 0.000 | Intergenic | ||
| 18 | PDLIM4; SLC22A4; SLC22A5; IRF1; IL5; RAD50 | rs549687735 | chr5:132297674:G:A | A | 0.032 | 0.079 | 0.012 | 1.52E-10 | 0.157 | Intronic (SLC22A4) |
| rs145432904 | chr5:132454828:C:T | T | 0.030 | 0.082 | 0.007 | 3.99E-32 | −0.100 | Intronic (IRF1-AS1) | ||
| rs2706383 | chr5:132456710:G:A | A | 0.235 | −0.065 | 0.003 | 1.95E-80 | 0.000 | Intronic (IRF1-AS1) | ||
| rs2706339 | chr5:132464413:G:T | T | 0.236 | −0.065 | 0.003 | 9.23E-81 | −0.100 | Intronic (IRF1-AS1) | ||
| rs79480807 | chr5:132465298:G:A | A | 0.029 | 0.082 | 0.007 | 2.16E-32 | 0.000 | Intronic (IRF1-AS1) | ||
| 44 | RAB37; SLC9A3R1; NAT9 | rs4789661 | chr17:74429020:G:A | A | 0.635 | −0.030 | 0.004 | 3.49E-14 | 0.526 | Intergenic |
| rs1868057 | chr17:74720763:C:G | G | 0.628 | 0.039 | 0.004 | 7.41E-21 | 0.000 | Intronic (RAB37) | ||
| 45 | SOCS3 | rs11077357 | chr17:78347520:G:C | C | 0.761 | 0.023 | 0.004 | 9.10E-11 | −0.010 | Intergenic |
| rs938351 | chr17:78403323:C:T | T | 0.602 | 0.018 | 0.003 | 2.32E-10 | 0.000 | Intronic (PGS1) | ||
| 48 | HPN; HPN-AS1 | rs1672981 | chr19:35056147:T:C | C | 0.916 | 0.034 | 0.005 | 1.94E-10 | 0.021 | Intergenic (HPN) |
| rs2239943 | chr19:35539605:T:C | C | 0.597 | −0.017 | 0.003 | 1.76E-09 | 0.000 | Intergenic (GAPDHS) |
| Region . | Genes in region . | SNP . | CPTID . | refA . | freq_geno . | bJ . | bJ_se . | pJ . | LD_r . | SNP consequence . |
|---|---|---|---|---|---|---|---|---|---|---|
| 14 | RGS12; HGFAC; DOK7 | rs3748034 | chr4:3444364:G:T | T | 0.121 | 0.025 | 0.004 | 1.56E-10 | −0.086 | Missense (HGFAC) |
| rs16844401 | chr4:3447925:G:A | A | 0.059 | 0.045 | 0.005 | 4.01E-17 | 0.029 | Missense (HGFAC) | ||
| rs36205397 | chr4:3468877:A:G | G | 0.533 | 0.018 | 0.003 | 3.06E-10 | 0.000 | Intronic (DOK7) | ||
| 16 | FGB; FGG | rs2227401 | chr4:154565229:C:T | T | 0.176 | 0.093 | 0.003 | 2.14E-165 | −0.028 | Intronic (FGB) |
| rs6054 | chr4:154568456:C:T | T | 0.004 | −0.385 | 0.022 | 2.21E-67 | −0.011 | Missense (FGB) | ||
| rs2066874 | chr4:154608429:T:C | C | 0.008 | −0.294 | 0.030 | 4.02E-22 | −0.010 | Intronic (FGG) | ||
| rs148685782 | chr4:154611883:G:C | C | 0.003 | −0.805 | 0.024 | 2.88E-237 | −0.020 | Missense (FGG) | ||
| rs28577061 | chr4:154614588:T:C | C | 0.046 | −0.089 | 0.013 | 1.96E-12 | −0.030 | Intergenic | ||
| rs149748987 | chr4:154618106:T:C | C | 0.007 | −0.179 | 0.015 | 2.96E-32 | 0.090 | Intergenic | ||
| rs6536024 | chr4:154622217:T:C | C | 0.478 | −0.029 | 0.003 | 5.10E-25 | 0.000 | Intergenic | ||
| 18 | PDLIM4; SLC22A4; SLC22A5; IRF1; IL5; RAD50 | rs549687735 | chr5:132297674:G:A | A | 0.032 | 0.079 | 0.012 | 1.52E-10 | 0.157 | Intronic (SLC22A4) |
| rs145432904 | chr5:132454828:C:T | T | 0.030 | 0.082 | 0.007 | 3.99E-32 | −0.100 | Intronic (IRF1-AS1) | ||
| rs2706383 | chr5:132456710:G:A | A | 0.235 | −0.065 | 0.003 | 1.95E-80 | 0.000 | Intronic (IRF1-AS1) | ||
| rs2706339 | chr5:132464413:G:T | T | 0.236 | −0.065 | 0.003 | 9.23E-81 | −0.100 | Intronic (IRF1-AS1) | ||
| rs79480807 | chr5:132465298:G:A | A | 0.029 | 0.082 | 0.007 | 2.16E-32 | 0.000 | Intronic (IRF1-AS1) | ||
| 44 | RAB37; SLC9A3R1; NAT9 | rs4789661 | chr17:74429020:G:A | A | 0.635 | −0.030 | 0.004 | 3.49E-14 | 0.526 | Intergenic |
| rs1868057 | chr17:74720763:C:G | G | 0.628 | 0.039 | 0.004 | 7.41E-21 | 0.000 | Intronic (RAB37) | ||
| 45 | SOCS3 | rs11077357 | chr17:78347520:G:C | C | 0.761 | 0.023 | 0.004 | 9.10E-11 | −0.010 | Intergenic |
| rs938351 | chr17:78403323:C:T | T | 0.602 | 0.018 | 0.003 | 2.32E-10 | 0.000 | Intronic (PGS1) | ||
| 48 | HPN; HPN-AS1 | rs1672981 | chr19:35056147:T:C | C | 0.916 | 0.034 | 0.005 | 1.94E-10 | 0.021 | Intergenic (HPN) |
| rs2239943 | chr19:35539605:T:C | C | 0.597 | −0.017 | 0.003 | 1.76E-09 | 0.000 | Intergenic (GAPDHS) |
bJ, joint β; bJ_se, standard error of joint β; CPTID, chromosome:position (b38):allele1: allele 2; freq_geno, frequency of effect allele in reference sample; LD_r, linkage disequilibrium; pJ, joint P value; refA, reference/effect allele.