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. 2022 Jun 8;2(6):100140. doi: 10.1016/j.xgen.2022.100140

Table 2.

Lead SNPs for the top ten loci per latent factor from multivariate association analyses

Lead SNP CHR:BP A1 A2 MAF Z p Nearest gene Function CADD RDB
F1 (depressive symptoms, manic symptoms, psychotic symptoms, major depressive disorder, and bipolar II disorder)
rs30266 5:103972357 G A 0.32 −7.83 4.94 × 10−15 RP11-6N13.1 ncRNA intronic 2.275 N/A
rs148682985 6:29288001 G A 0.03 −7.66 1.93 × 10−14 DDX6P1 intergenic 2.643 5
rs9586 3:49213637 C T 0.02 7.46 8.80 × 10−14 KLHDC8B UTR3 11.63 N/A
rs28656217 4:42099424 T C 0.16 7.30 2.85 × 10−13 SLC30A9 intergenic 4.861 6
rs67526282 18:53471187 T C 0.33 −7.04 1.97 × 10−12 RP11-397A16.3 intergenic 7.656 6
rs7934649 11:113372671 C T 0.36 −6.53 6.50 × 10−11 DRD2 intergenic 1.426 7
rs17410557 18:50776391 T C 0.38 −6.04 1.52 × 10−9 DCC intronic 4.502 7
rs3807866 7:12250378 G A 0.40 −6.03 1.69 × 10−9 TMEM106B upstream 7.544 N/A
rs184262 3:12134740 A G 0.15 6.02 1.77 × 10−9 SYN2 ncRNA intronic 6.559 7
rs2696673 17:44315803 A C 0.22 −6.01 1.89 × 10−9 RP11-259G18.2 intergenic 3.3 N/A
F2 (bipolar I disorder, schizoaffective disorder, and schizophrenia)
rs7746199 6:27261324 C T 0.17 9.34 9.95 × 10−21 POM121L2 intronic 0.879 1f
rs9834970 3:36856030 T C 0.49 −7.96 1.67 × 10−15 TRANK1 intergenic 11.17 4
rs12764899 10:104635103 G A 0.23 7.95 1.82 × 10−15 C10orf32-ASMT:AS3MT intronic 1.133 7
rs4298967 12:2408194 A G 0.34 7.92 2.37 × 10−15 CACNA1C intronic 10.73 5
rs6461049 7:2017445 C T 0.44 −7.15 8.80 × 10−13 MAD1L1 intronic 0.914 5
rs12902973 15:85105982 G C 0.28 7.04 1.89 × 10−12 UBE2Q2P1 ncRNA intronic 1.808 7
rs4380187 2:185811940 A C 0.45 6.86 6.95 × 10−12 ZNF804A intergenic 2.923 7
rs2535627 3:52845105 T C 0.50 6.63 3.36 × 10−11 ITIH4 intergenic 5.307 N/A
rs1198588 1:98552832 A T 0.23 −6.62 3.65 × 10-11 NFU1P2 intergenic 1.829 3a
rs11693528 2:200736507 C G 0.18 −6.60 4.18 × 10−11 AC073043.1 ncRNA intronic 2.344 6

Results for all lead SNPs are presented in Tables S2A and S2B. Lead SNPs refer to approximately independent lead SNPs identified via FUMA. CHR:BP refers to genomic location of the lead SNP, specifically the chromosome and base pair location on that chromosome. A1 and A2 refer to the alleles for that SNP. MAF, minor allele frequency; CADD, Combined Annotation Dependent Depletion score; RDB, RegulomeDB score.