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Table 1 New genome-wide significant loci identified in this study (a total of 17 novel risk loci)

From: Genome-wide association study followed by trans-ancestry meta-analysis identify 17 new risk loci for schizophrenia

Genomic locusa Lead SNP Chr Pos A1/A2(MAb) MAF_Ac MAF_Ud P ORe Nearby gene(s)f
1 rs7192086 16 13061611 T/A(T) 0.32 0.28 4.92 × 10−08 1.22 SHISA9
2 rs57016637 22 30992925 G/C(G) 0.20 0.16 2.33 × 10−11 1.34 SF3A1, CCDC157, RNF215, SEC14L2, MTFP1, SEC14L3, SEC14L6, GAL3ST1, PES1, TCN2, SLC35E4, DUSP18, OSBP2, MORC2
3 rs115487049 2 76297343 A/T(A) 0.042 0.036 4.72 × 1008 1.07 SUCLA2P2
4 rs10178509 2 236792838 T/C(T) 0.39 0.42 1.08 × 1008 0.95 AGAP1
5 rs1426271 3 188187250 A/G(G) 0.35 0.33 3.23 × 1008 0.95 LPP
6 rs2911914 4 37820679 T/G(T) 0.25 0.27 2.12 × 1008 0.95 PGM2
7 rs6848123 4 80203425 A/C(C) 0.14 0.16 1.17 × 1008 1.05 NAA11
8 rs319227 5 146245762 A/C(A) 0.33 0.30 6.11 × 1009 1.05 PPP2R2B
9 rs12202107 6 130598623 T/C(C) 0.42 0.45 2.51 × 1008 1.05 SAMD3,TMEM200A
10 rs9386072 6 144859509 A/T(A) 0.43 0.47 1.01 × 1008 0.93 UTRN
11 rs2106747 7 23911499 A/G(G) 0.40 0.42 3.36 × 1008 1.05 TRA2A, FAM221A, STK31
12 rs492430 7 100313099 T/G(T) 0.065 0.058 2.26 × 1008 1.07 ACTL6B, GNB2, GIGYF1, POP7, EPO
13 rs59761926 9 10238178 T/C(T) 0.37 0.39 3.02 × 1009 0.95 PTPRD
14 rs7301566 12 50581647 T/C(T) 0.099 0.091 2.91 × 1008 1.06 ASIC1, SMARCD1, GPD1, COX14, CERS5, LIMA1
15 rs6563592 13 38814939 T/G(G) 0.31 0.30 2.13 × 1008 0.95 LINC00571
16 rs2099108 14 81675420 C/G(G) 0.45 0.47 2.67 × 1008 1.05 GTF2A1,STON2
17 rs6100546 20 58252407 T/C(C) 0.079 0.076 2.79 × 1008 0.94 PHACTR3
  1. a The new loci identified in our Han Chinese cohort are shown in bold. b minor allele of our Chinese samples. c minor allele frequency in our Chinese cases. d minor allele frequency in our Chinese controls. e Odds ratio is based on A1; f The nearby genes were defined with FUMA. FUMA firstly identified the SNPs that were in LD (r2 > 0.6) with independent lead SNPs. And these SNPs were further used to identify the nearby genes by FUMA with default parameters (posMapWindowSize = 10 kb). More details about defining nearby genes can be found in FUMA website: https://fuma.ctglab.nl/tutorial#parameters