Table 2.

44 significantly associated genomic regions in meta-analysis of 135,458 major depression cases and 344,901 controls

Chr	Region (Mb)	SNP	Location-bp	P	A1/2	OR-A1	SE(log)OR)	Frq	Prev	Gene Context
1	8.390–8.895	rs159963	8,504,421	3.2E-08	A/C	0.97	0.0049	0.56	H,S	[RERE]; SLC45A1,100194
1	72.511–73.059	rs1432639	72,813,218	4.6E-15	A/C	1.04	0.0050	0.63	H	NEGR1, −64941
1	73.275–74.077	rs12129573	73,768,366	4.0E-12	A/C	1.04	0.0050	0.37	S	LINC01360, −3486
1	80.785–80.980	rs2389016	80,799,329	1.0E-08	T/C	1.03	0.0053	0.28	H
1	90.671–90.966	rs4261101	90,796,053	1.0E-08	A/G	0.97	0.0050	0.37
1	197.343–197.864	rs9427672	197,754,741	3.1E-08	A/G	0.97	0.0058	0.24		DENND1B, −10118
2	57.765–58.485	rs11682175	57,987,593	4.7E-09	T/C	0.97	0.0048	0.52	H,S	VRK2, −147192
2	156.978–157.464	rs1226412	157,111,313	2.4E-08	T/C	1.03	0.0059	0.79		[LINC01876]; NR4A2,69630; GPD2, −180651
3	44.222–44.997	chr3_44287760_I	44,287,760	4.6E-08	I/D	1.03	0.0051	0.34	T	[TOPAZ1]; TCAIM, −91850; ZNF445,193501
3	157.616–158.354	rs7430565	158,107,180	2.9E-09	A/G	0.97	0.0048	0.58	H	[RSRC1]; LOC100996447,155828; MLF1, −181772
4	41.880–42.189	rs34215985	42,047,778	3.1E-09	C/G	0.96	0.0063	0.24		[SLC30A9]; LINC00682, −163150; DCAF4L1,59294
5	87.443–88.244	chr5_87992715_I	87,992,715	7.9E-11	I/D	0.97	0.0050	0.58	H	LINC00461, −12095; MEF2C,21342
5	103.672–104.092	chr5_103942055_D	103,942,055	7.5E-12	I/D	1.03	0.0048	0.48	C
5	124.204–124.328	rs116755193	124,251,883	7.0E-09	T/C	0.97	0.0050	0.38		LOC101927421, −120640
5	164.440–164.789	rs11135349	164,523,472	1.1E-09	A/C	0.97	0.0048	0.48	H
5	166.977–167.056	rs4869056	166,992,078	6.8E-09	A/G	0.97	0.0050	0.63		[TENM2]
6	27.738–32.848	rs115507122	30,737,591	3.3E-11	C/G	0.96	0.0063	0.18	S	extended MHC
6	99.335–99.662	rs9402472	99,566,521	2.8E-08	A/G	1.03	0.0059	0.24		FBXL4, −170672; C6orf168,154271
7	12.154–12.381	rs10950398	12,264,871	2.6E-08	A/G	1.03	0.0049	0.41		[TMEM106B]; VWDE,105637
7	108.925–109.230	rs12666117	109,105,611	1.4E-08	A/G	1.03	0.0048	0.47
9	2.919–3.009	rs1354115	2,983,774	2.4E-08	A/C	1.03	0.0049	0.62	H	PUM3, −139644; LINC01231, −197814
9	11.067–11.847	rs10959913	11,544,964	5.1E-09	T/G	1.03	0.0057	0.76
9	119.675–119.767	rs7856424	119,733,595	8.5E-09	T/C	0.97	0.0053	0.29		[ASTN2]
9	126.292–126.735	rs7029033	126,682,068	2.7E-08	T/C	1.05	0.0093	0.07		[DENND1A]; LHX2, −91820
10	106.397–106.904	rs61867293	106,563,924	7.0E-10	T/C	0.96	0.0061	0.20	H	[SORCS3]
11	31.121–31.859	rs1806153	31,850,105	1.2E-09	T/G	1.04	0.0059	0.22		[DKFZp686K1684]; [PAUPAR]; ELP4,44032; PAX6, −10596;
12	23.924–24.052	rs4074723	23,947,737	3.1E-08	A/C	0.97	0.0049	0.41		[SOX5]
13	44.237–44.545	rs4143229	44,327,799	2.5E-08	A/C	0.95	0.0091	0.92		[ENOX1]; LACC1, −125620; CCDC122,82689
13	53.605–54.057	rs12552	53,625,781	6.1E-19	A/G	1.04	0.0048	0.44	H	[OLFM4]; LINC01065,80099
14	41.941–42.320	rs4904738	42,179,732	2.6E-09	T/C	0.97	0.0049	0.57		[LRFN5]
14	64.613–64.878	rs915057	64,686,207	7.6E-10	A/G	0.97	0.0049	0.42		[SYNE2]; MIR548H1, −124364; ESR2,7222
14	75.063–75.398	chr14_75356855_I	75,356,855	3.8E-09	D/I	1.03	0.0049	0.49		[DLST]; PROX2, −26318; RPS6KL1,13801
14	103.828–104.174	rs10149470	104,017,953	3.1E-09	A/G	0.97	0.0049	0.49	S	BAG5,4927; APOPT1, −11340
15	37.562–37.929	rs8025231	37,648,402	2.4E-12	A/C	0.97	0.0048	0.57	H
16	6.288–6.347	rs8063603	6,310,645	6.9E-09	A/G	0.97	0.0053	0.65		[RBFOX1]
16	7.642–7.676	rs7198928	7,666,402	1.0E-08	T/C	1.03	0.0050	0.62		[RBFOX1]
16	13.022–13.119	rs7200826	13,066,833	2.4E-08	T/C	1.03	0.0055	0.25		[SHISA9]; CPPED1, −169089
16	71.631–72.849	rs11643192	72,214,276	3.4E-08	A/C	1.03	0.0049	0.41		PMFBP1, −7927; DHX38,67465;
17	27.345–28.419	rs17727765	27,576,962	8.5E-09	T/C	0.95	0.0088	0.92		[CRYBA1]; MYO18A, −69555; NUFIP2,5891
18	36.588–36.976	rs62099069	36,883,737	1.3E-08	A/T	0.97	0.0049	0.42		[MIR924HG]
18	50.358–50.958	rs11663393	50,614,732	1.6E-08	A/G	1.03	0.0049	0.45	O	[DCC]; MIR4528, −148738
18	51.973–52.552	rs1833288	52,517,906	2.6E-08	A/G	1.03	0.0054	0.72		[RAB27B]; CCDC68,50833
18	52.860–53.268	rs12958048	53,101,598	3.6E-11	A/G	1.03	0.0051	0.33	S	[TCF4]; MIR4529, −44853
22	40.818–42.216	rs5758265	41,617,897	7.6E-09	A/G	1.03	0.0054	0.28	H,S	[L3MBTL2]; EP300-AS1, −24392; CHADL,7616

Chr (chromosome) and Region (boundaries in Mb, hg19) are shown, defined by locations of SNPs with P<1×10⁻⁵ and LD r² > 0.1 with the most associated SNP (logistic regression; lowest P-value in region listed not corrected for multiple testing) whose location is given in bp. In three regions a second SNP fulfils the filtering criteria and these were followed up with conditional analyses: Chr1: conditional analysis selects only rs1432639 as significant, with P=2.0×10⁻⁴ for rs12134600 after fitting rs1432639; Chr5, conditional analysis shows two independent associations selecting rs247910 and rs10514301 as the most associated SNPs; and Chr10 conditional analysis selects only rs61867293 with P=8.6×10⁻⁵ for rs1021363 after conditioning on rs61867293. For each of the 47 SNPs, there is at least 1 additional genome-wide significant SNP in the cluster of surrounding SNPs with low P-values. Chromosome X was analyzed but had no findings that met genome-wide significance.

Column labels and abbreviations. A1/2 = the two alleles (or insertion-deletion); A1 was tested for association, and its OR (odds ratio) and SE (standard error) are shown. FreqU = frequency of A1 in controls across all cohorts. Entries in the “Prev” column indicate which of four previous studies identified genome-significant associations in a region. H=Hyde et al.²⁸, 23andMe GWA of self-reported clinical depression (discovery sample overlaps with this paper); O=Okbay et al.¹⁶, meta-analysis of GWA of MDD, depressive symptoms, psychological well-being and neuroticism (includes many PGC29 samples); S=PGC report on 108 schizophrenia-associated loci¹⁹; and C=CHARGE consortium meta-analysis of depressive symptoms¹⁴. Gene context: distances between the Peak SNP and the closest genes are shown. Brackets indicate that the Peak SNP was within that gene. The closest genes upstream (taking strand into account, as a negative number indicating distance in bp between Peak SNP and the nearest gene boundary) and downstream (positive distance in bp) are also shown, if there is a flanking gene within 200 kb. The name of the closest gene is bolded. Note that it is generally not known whether the associated SNPs have biological effects on these or other more distant genes.