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. Author manuscript; available in PMC: 2023 Jan 1.
Published in final edited form as: Biol Psychiatry. 2021 Mar 23:S0006-3223(21)01139-2. doi: 10.1016/j.biopsych.2021.02.972

Table 1. Single-disorder and Cross-disorder Autosomal SNP-by-sex interaction results.

Cross-disorder and within-disorder meta-analyses were carried out using METAL, incorporating cohort-level summary statistics from PLINK. Listed are SNPs with interaction p-values < 1×10−6 in SCZ, BIP, (r)MDD, and cross-disorder. Loci were clumped using ‘plink --bfile 1kgp_ref_file --clump metal_output --clump-p1 1e-4 --clump-p2 1e-4 --clump-r2 0.6 --clump-kb 3000’. Extended results (p < 1×10−4), including eQTL data for the variants highlighted in this table, and including secondary extended model statistics, are available in Supplementary Table 6.

SNP CHR BP A1/
A2		 Freq1
MAF		 Compartment Gene
(Distance in kb)		 N Cases
(%Female)		 N Controls
(%Female)		 BetaGxS
(SE)		 pGxS (pext) BetaF
(SE)		 pF BetaM
(SE)		 pM ZFM pFM
Schizophrenia (European only)
rs11665282 18 33767479 A/G 0.69
0.31		 UTR5 MOCOS 21,581
(35.18%)		 24,250
(48.62%)		 −0.156
(0.030)		 1.48E-7
(2.53E-5)		 −0.081
(0.023)		 3.98E-4 0.072
(0.019)		 2.16E-4 −5.09 3.50E-7
rs12445424 16 87063374 A/G 0.26
0.26		 intergenic LINC02188 (291.9);
LINC02181 (280.2)		 29,467
(36.04%)		 34,519
(48.33%)		 0.140
(0.028)		 3.52E-7
(2.28E-4)		 0.097
(0.021)		 5.80E-6 −0.050
(0.018)		 4.67E-3 5.30 1.19E-7
Schizophrenia (European + East Asian)
rs11665282 18 33767479 A/G 0.69
0.31		 UTR5 MOCOS 22,060
(35.39%)		 24,674
(48.26%)		 −0.149
(0.03)		 3.74E-7
(4.46E-5)		 −0.077
(0.023)		 6.74E-4 0.070
(0.019)		 2.53E-4 −4.96 6.89E-7
Bipolar Disorder
rs12341335 9 25649145 T/C 0.90
0.10		 intergenic TUSC1 (27.2) 7,730
(57.72%)		 13,635
(51.28%)		 0.373
(0.072)		 2.29E-7
(7.91E-7)		 0.176
(0.048)		 2.59E-4 −0.201
(0.054)		 2.11E-4 5.20 2.03E-7
rs17651437 2 106055684 T/C 0.52
0.48		 upstream FHL2 16,365
(60.18%)		 28,140
(50.75%)		 0.155
(0.031)		 3.72E-7
(1.04E-5)		 0.079
(0.020)		 9.97E-5 −0.069
(0.023)		 3.08E-3 4.79 1.63E-6
Major Depressive Disorder
rs9428240 1 118831676 T/C 0.59
0.41		 intergenic SPAG17 (103.8) 14,232
(68.63%)		 21,846
(50.63%)		 −0.181
(0.035)		 1.64E-7
(3.31E-7)		 −0.087
(0.022)		 6.41E-5 0.094
(0.028)		 8.41E-4 −5.08 3.70E-7
rs147515485 17 40182099 T/C 0.02
0.02		 intronic ZNF385C 31,149
(61.17%)		 35,385
(50.89%)		 −0.472
(0.094)		 4.61E-7
(4.76E-6)		 −0.190
(0.060)		 1.55E-3 0.303
(0.074)		 4.39E-5 −5.17 2.39E-7
Recurrent Major Depressive Disorder
rs61138090 1 118832069 D/I2 0.59
0.41		 intergenic SPAG17 (104.2) 7,685
(70.59%)		 15,976
(51.71%)		 −0.240
(0.046)		 1.40E-7
(−)		 −0.109
(0.028)		 1.03E-4 0.142
(0.038)		 2.08E-4 −5.28 1.30E-7
Cross-Disorder SCZ-BIP-MDD (European only)
rs7302529 12 77321581 T/C 0.26
0.26		 intergenic CSRP2 (48.8);
E2F7 (93.4)		 34,638
(51.36%)		 34.696
(50.15%)		 0.145
(0.028)		 1.60E-7
(5.35E-7)		 0.087
(0.019)		 5.09E-6 −0.051
(0.020)		 1.15E-2 4.98 6.51E-7
rs73033497 7 2910659 A/T 0.86
0.14		 intergenic GNA12 (26.7);
CARD11 (35.0)		 14,916
(49.21%)		 17,547
(47.81%)		 0.246
(0.050)		 8.82E-7
(2.24E-6)		 0.116
(0.036)		 1.09E-3 −0.128
(0.035)		 2.69E-4 4.89 1.03E-6
Cross-Disorder SCZ-BIP-MDD (European + East Asian)
rs7914279 10 122161890 T/G 0.89
0.11		 intergenic MIR4682 (44.3);
PLPP4 (54.6)		 78,640
(49.95%)		 71.790
(49.70%)		 0.146
(0.029)		 6.39E-7
(4.78E-6)		 0.064
(0.020)		 1.86E-3 −0.077
(0.021)		 2.27E-4 4.82 1.43E-6
rs73033497 7 2910659 A/T 0.86
0.14		 intergenic GNA12 (26.7);
CARD11 (35.0)		 14,916
(49.21%)		 17,547
(47.81%)		 0.246
(0.050)		 8.82E-7
(2.24E-6)		 0.116
(0.036)		 1.09E-3 −0.128
(0.035)		 2.69E-4 4.89 1.03E-6
rs7302529 12 77321581 T/C 0.25
0.25		 intergenic CSRP2 (48.8);
E2F7 (93.4)		 35,114
(50.69%)		 36,707
(50.72%)		 0.133
(0.027)		 9.37E-7
(2.69E-6)		 0.082
(0.019)		 1.35E-5 −0.044
(0.020)		 2.37E-2 4.64 3.51E-6
Cross-Disorder SCZ-BIP-rMDD (European only)
rs73033497 7 2910659 A/T 0.86
0.14		 intergenic GNA12 (26.7);
CARD11 (35.0)		 13,497
(47.22%)		 14,619
(48.26%)		 0.267
(0.054)		 6.22E-7
(2.22E-6)		 0.142
(0.039)		 2.55E-4 −0.129
(0.037)		 4.89E-4 5.05 4.37E-7
rs7302529 12 77321581 T/C 0.26
0.26		 intergenic CSRP2 (48.8);
E2F7 (93.4)		 31,541
(49.75%)		 31,377
(50.42%)		 0.144
(0.029)		 7.43E-7
(2.32E-6)		 0.094
(0.020)		 4.48E-6 −0.048
(0.021)		 2.13E-2 4.86 1.18E-6
Cross-Disorder SCZ-BIP-rMDD (European + East Asian)
rs8040598 15 71857368 A/G 0.86
0.14		 intronic THSD4 41,001
(45.92%)		 43,732
(50.94%)		 0.183
(0.036)		 3.90E-7
(8.25E-7)		 0.084
(0.026)		 1.18E-3 −0.093
(0.025)		 2.18E-4 4.89 9.90E-7
rs73033497 7 2910659 A/T 0.86
0.14		 intergenic GNA12 (26.7);
CARD11 (35.0)		 13,497
(47.22%)		 14,619
(48.26%)		 0.267
(0.054)		 6.22E-7
(2.22E-6)		 0.142
(0.039)		 2.55E-4 −0.129
(0.037)		 4.89E-4 5.05 4.37E-7

Abbreviations: SNP, Variant rs ID; pGxS; p-value for GxS interaction in combined PGC + iPSYCH datasets (p-value for secondary extended model, pext, in parentheses); CHR, Chromosome; BP, Base Pair Position; A1/A2, Allele 1/Allele 2; Freq1, Frequency of Allele 1; MAF, Minor Allele Frequency; BetaGxS, Beta (Standard Error) for GxS interaction; BetaF (SE), Beta (Standard Error) for female-stratified association; pF, p-value for female-stratified association; BetaM, Beta (Standard Error) for male-stratified association; pM, p-value for male-stratified association; ZFM, Z-score heterogeneity females-males; pFM, p-value heterogeneity females-males