Datasets:

OpenMed
/

pgc-mdd

CHR int64	SNP string	BP int64	A1 string	A2 string	FRQ_A_301 float64	FRQ_U_226 float64	INFO float64	OR float64	SE float64	P float64	ngt int64	Direction string	HetISqt float64	HetDf int64	HetPVa float64	Nca int64	Nco int64	Neff float64	_source_file string
1	rs647287	14,539,152	A	G	0.669	0.6	0.998	1.24707	0.1505	0.1424	3	+++	0	2	0.4775	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs567880659	17,711,691	D	I	0.836	0.835	0.927	0.93435	0.2111	0.7475	0	--+	0	2	0.6114	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs12123608	14,301,802	A	C	0.841	0.843	0.943	1.07993	0.2054	0.7079	3	+-+	0	2	0.8522	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs57440988	15,879,034	T	C	0.951	0.903	1.05	2.1206	0.2923	0.01011	0	+++	0	2	0.5453	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs150503509	14,519,622	C	T	0.957	0.951	0.977	1.36206	0.331	0.3505	0	--+	0	2	0.3951	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs76162695	25,763,112	T	C	0.988	0.99	0.677	0.88923	0.8155	0.8855	0	-+-	0	2	0.592	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs59163005	10,637,841	D	I	0.752	0.706	0.989	1.2411	0.1635	0.1865	0	+++	0	2	0.5793	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs4646093	15,821,400	C	A	0.383	0.411	1.07	0.87959	0.1472	0.3832	0	+-+	0	2	0.4447	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs141303407	6,697,801	C	T	0.99	0.985	0.803	2.57256	0.8738	0.2795	0	-?-	0	1	0.91	172	181	169.54	AntiDepNonRemissionEAS2021.gz
1	rs3737234	5,964,991	T	C	0.147	0.14	0.927	1.09155	0.2086	0.6746	0	+++	0	2	0.8072	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs148126903	17,657,717	G	A	0.984	0.976	0.836	2.09887	0.5648	0.1893	0	---	0	2	0.6882	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs574319725	9,001,593	D	I	0.882	0.861	0.827	1.17046	0.248	0.5256	0	+-+	0	2	0.9084	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs10916692	20,339,057	A	C	0.738	0.755	0.965	1.03438	0.1764	0.8479	0	-+-	-1.7	2	0.1398	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs12044214	9,369,053	C	T	0.716	0.759	0.998	0.76376	0.1682	0.1092	0	+++	0	2	0.6052	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs17391171	14,008,871	A	T	0.978	0.991	0.516	0.41553	0.9316	0.3458	0	---	0	2	0.86	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs10915664	4,093,700	G	A	0.96	0.959	0.593	1.09439	0.5266	0.8641	0	+-?	0	1	0.6552	259	148	181.66	AntiDepNonRemissionEAS2021.gz
1	rs6681674	5,424,374	T	C	0.94	0.942	0.984	0.63674	0.3238	0.1633	3	-+-	0	2	0.5548	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs76716765	13,841,381	C	T	0.789	0.784	1.03	0.94374	0.1832	0.752	0	+-+	0	2	0.5268	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs6672970	19,118,367	G	A	0.644	0.631	1.02	1.06024	0.1556	0.7071	0	-+-	-1.5	2	0.1393	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs7418584	19,122,151	A	C	0.255	0.288	1.06	0.9081	0.1585	0.5433	0	--+	0	2	0.3803	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs55903004	16,641,236	G	T	0.823	0.81	0.961	0.88029	0.1959	0.5151	0	+++	0	2	0.8972	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs28736783	16,419,415	A	C	0.874	0.882	0.71	0.91494	0.2688	0.741	0	-+-	0	2	0.5166	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs2038878	19,336,726	C	A	0.454	0.431	0.97	1.1184	0.1555	0.4717	0	-+-	-31.9	2	0.2195	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs3790639	10,708,028	G	A	0.973	0.982	0.927	0.73184	0.5147	0.5441	0	-++	-59.7	2	0.2858	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs2206761	15,466,832	C	T	0.385	0.358	0.955	1.20454	0.1596	0.2436	3	-+-	-60.3	2	0.2871	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs7548096	15,339,627	A	G	0.0732	0.0774	0.811	0.95772	0.3112	0.8896	0	-++	0	2	0.6286	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs74770301	14,367,567	C	T	0.878	0.879	0.959	0.99134	0.2309	0.9699	0	-++	0	2	0.4002	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs10907208	5,693,997	A	G	0.375	0.362	0.865	1.23023	0.1626	0.2025	0	+-+	0	2	0.3759	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs139581921	1,609,070	C	T	0.937	0.934	0.763	1.1275	0.3497	0.7315	0	--+	25.2	2	0.06903	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs9430176	11,091,031	G	A	0.776	0.816	0.94	0.72819	0.198	0.1092	0	++-	-48.7	2	0.2605	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs12044831	2,964,397	A	C	0.769	0.802	0.873	0.74662	0.2085	0.1612	0	---	0	2	0.6525	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs114983999	4,751,901	C	T	0.983	0.979	0.514	1.16474	0.7939	0.8477	0	+-?	-199.8	1	0.3172	259	148	181.66	AntiDepNonRemissionEAS2021.gz
1	rs196400	24,837,599	T	C	0.26	0.225	0.987	1.17222	0.1701	0.3503	0	++-	0	2	0.734	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs2032539	9,269,719	T	C	0.523	0.556	1.08	0.74394	0.1453	0.04177	0	---	0	2	0.7062	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs71580204	3,084,866	I	D	0.811	0.797	0.969	1.12086	0.195	0.5584	0	-++	34.2	2	0.04789	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs3935066	900,730	G	A	0.28	0.297	0.991	0.77693	0.1614	0.1179	0	++-	-77.7	2	0.3244	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs523919	18,150,298	A	G	0.305	0.275	0.93	1.11773	0.1677	0.507	0	+--	-31.4	2	0.2182	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs311477	25,409,607	A	G	0.578	0.582	0.974	1.07885	0.1486	0.6093	3	++-	7.1	2	0.1161	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs6671785	14,779,509	T	G	0.766	0.746	0.996	0.98383	0.1805	0.928	0	+-+	39.1	2	0.0374	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs79202759	25,338,370	C	T	0.982	0.982	0.863	0.9111	0.5796	0.8723	0	+-+	0	2	0.6787	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs7550526	3,272,541	G	A	0.553	0.512	0.556	1.20202	0.1966	0.3493	0	+--	-25.5	2	0.2031	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs72862531	14,426,142	G	A	0.984	0.989	0.951	0.97463	0.7439	0.9724	0	+-?	0	1	0.9016	259	148	181.66	AntiDepNonRemissionEAS2021.gz
1	rs4329522	11,452,291	G	A	0.956	0.944	1.04	1.36547	0.3379	0.3565	0	--+	0	2	0.5728	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs35816604	18,430,374	G	C	0.938	0.938	0.837	0.80896	0.3342	0.5258	0	+-+	0	2	0.7309	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs61774184	7,706,303	C	T	0.606	0.609	0.58	0.96899	0.1963	0.8723	0	-+-	0	2	0.4838	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs6664873	18,039,182	C	A	0.153	0.151	1.06	0.84891	0.1981	0.4083	3	+++	0	2	0.7696	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs34017141	7,849,205	D	I	0.736	0.728	0.886	1.07272	0.182	0.6997	0	+-+	19.2	2	0.08404	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs35332894	3,826,626	A	G	0.756	0.727	0.955	0.92876	0.174	0.6711	0	-+-	0	2	0.6645	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs7555966	11,664,772	G	A	0.517	0.431	1	1.45907	0.1516	0.01267	0	---	0	2	0.8412	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs34655486	19,761,894	T	C	0.887	0.858	0.966	1.26301	0.2271	0.304	0	++-	-14.5	2	0.1744	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs742795	17,414,305	C	A	0.576	0.62	0.931	0.83169	0.1545	0.2328	0	+++	0	2	0.7252	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs78013390	12,022,494	C	T	0.763	0.762	0.957	1.2084	0.1751	0.2798	0	---	0	2	0.7189	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs2807336	22,549,666	A	G	0.171	0.232	0.975	0.67963	0.1863	0.03818	0	---	-99.6	2	0.3671	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs185508335	7,818,942	C	G	0.987	0.983	0.518	1.94138	0.9525	0.4861	0	++?	0	1	0.5201	259	148	181.66	AntiDepNonRemissionEAS2021.gz
1	rs2697985	14,133,419	G	C	0.194	0.19	0.943	1.12862	0.1958	0.5365	0	---	0	2	0.7362	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs547995783	12,412,643	T	G	0.971	0.988	0.477	0.16528	1.317	0.1717	0	--?	0	1	0.4626	259	148	181.66	AntiDepNonRemissionEAS2021.gz
1	rs2076612	17,421,956	C	A	0.561	0.603	0.945	0.84815	0.1519	0.278	0	+++	0	2	0.7831	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs75877917	18,132,142	G	A	0.874	0.859	0.733	1.16777	0.2624	0.5546	0	-+-	-81.1	2	0.3314	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs4586003	6,175,087	G	C	0.777	0.751	0.966	1.07272	0.1788	0.6945	0	-+-	0	2	0.437	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs75822390	7,490,405	C	G	0.744	0.82	0.872	0.62164	0.1979	0.01628	0	---	0	2	0.8935	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs7519955	14,453,475	C	G	0.229	0.245	0.919	0.85121	0.1835	0.38	0	+--	0	2	0.412	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs3767150	21,894,214	G	A	0.563	0.498	0.919	1.08264	0.1559	0.6105	2	-+-	0	2	0.819	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs80321184	19,186,936	A	G	0.943	0.945	0.932	0.93735	0.3193	0.8394	0	-+-	0	2	0.7608	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs62652319	5,306,550	T	C	0.261	0.23	0.936	1.37589	0.1776	0.07238	0	+++	0	2	0.7432	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs630542	12,206,866	G	T	0.73	0.713	1.01	0.9981	0.1655	0.9908	3	-++	-24.7	2	0.201	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs117433781	24,495,264	C	T	0.966	0.97	0.754	0.8589	0.4688	0.7456	0	+-+	-2	2	0.1408	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs12141257	20,510,752	T	C	0.604	0.618	0.949	0.99134	0.1554	0.9555	0	+--	27.5	2	0.0635	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs74651861	18,371,530	G	A	0.931	0.918	0.979	1.07702	0.276	0.7881	0	---	0	2	0.7865	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs35933063	14,776,616	D	I	0.624	0.614	0.918	0.73993	0.161	0.06136	0	---	0	2	0.4576	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs56077964	5,137,114	G	A	0.94	0.92	0.545	1.48929	0.3902	0.3073	0	--+	0	2	0.3961	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs56168930	11,037,447	A	G	0.724	0.719	0.966	1.16813	0.1688	0.3573	0	+++	0	2	0.7814	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs537943741	2,037,950	D	I	0.722	0.691	0.543	1.27214	0.2197	0.2734	0	+++	0	2	0.6746	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs7554396	8,223,588	C	T	0.203	0.188	1.08	0.938	0.1738	0.7125	0	+--	0	2	0.7608	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs76233799	21,649,926	C	T	0.904	0.891	0.671	1.31969	0.2971	0.3504	0	+--	-21.1	2	0.1917	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs35136906	3,732,253	I	D	0.457	0.469	0.826	1.05633	0.1709	0.7484	0	+-+	45.2	2	0.026	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs78271619	11,010,177	G	A	0.748	0.767	1.02	0.89297	0.1667	0.4971	0	+-+	13.3	2	0.09958	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs61780165	23,524,370	A	T	0.852	0.779	0.975	1.49302	0.1961	0.04095	0	+++	0	2	0.9771	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs13303198	2,020,905	C	T	0.869	0.867	0.894	1.23195	0.225	0.3538	0	--+	0	2	0.6903	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs56817795	24,016,260	C	G	0.973	0.982	0.777	0.35064	0.6929	0.1304	0	--+	-5.9	2	0.1513	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs143974042	19,387,146	C	T	0.922	0.934	0.861	0.63948	0.3056	0.1434	0	+++	0	2	0.7263	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs12116992	24,369,481	G	A	0.833	0.873	0.976	0.74871	0.2142	0.1766	0	+-+	-80.2	2	0.3296	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs72907441	2,041,053	G	A	0.849	0.86	1.08	0.88135	0.2062	0.5402	0	+-+	56.1	2	0.01047	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs72632938	9,136,404	G	A	0.713	0.654	0.936	1.31943	0.1656	0.09421	0	---	0	2	0.8599	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs7532560	7,433,496	G	A	0.453	0.414	0.992	1.07713	0.1497	0.6196	0	+--	0	2	0.4114	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs2297881	10,397,567	A	G	0.932	0.936	1.01	0.9498	0.2987	0.8631	3	-+-	0	2	0.9396	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs546108223	4,488,212	T	C	0.865	0.875	0.573	0.9462	0.2967	0.8521	0	-+-	0	2	0.506	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs75677049	23,074,504	C	T	0.847	0.869	0.98	0.82399	0.2202	0.3791	0	+--	-32.2	2	0.2203	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs1181871	3,684,321	A	G	0.277	0.327	0.979	0.88728	0.1693	0.48	0	-+-	43	2	0.03002	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs1737618	10,850,844	C	A	0.0256	0.0486	0.771	0.42712	0.5732	0.1378	0	+?+	0	1	0.7438	172	181	169.54	AntiDepNonRemissionEAS2021.gz
1	rs12044299	14,288,119	G	A	0.729	0.684	1.04	1.30944	0.159	0.09	3	---	0	2	0.6577	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs4908581	7,017,985	A	G	0.814	0.812	0.922	1.1012	0.1957	0.6224	3	+++	0	2	0.9244	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs3789528	6,160,609	C	T	0.626	0.625	0.913	0.98955	0.1592	0.9475	0	-++	-5.1	2	0.1491	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs75979929	4,196,825	A	G	0.548	0.532	0.502	1.35703	0.2101	0.1461	0	+++	0	2	0.7514	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs72647128	15,963,908	T	C	0.984	0.944	1.04	2.28439	0.465	0.07565	0	+++	0	2	0.5493	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs74557977	14,049,383	G	T	0.988	0.99	0.976	1.18827	0.7943	0.828	0	+-?	-188.2	1	0.3076	259	148	181.66	AntiDepNonRemissionEAS2021.gz
1	rs80324675	15,502,502	T	G	0.953	0.96	0.924	0.94686	0.3608	0.8798	0	-+-	0	2	0.9062	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs12136469	18,079,812	C	T	0.758	0.703	0.94	1.43118	0.1727	0.03789	0	-+-	-86.5	2	0.3423	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs676643	23,521,340	G	A	0.749	0.758	1.04	1.0001	0.1689	0.9996	0	+-+	0	2	0.7813	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs74813460	11,046,182	G	A	0.937	0.934	0.772	0.88541	0.3357	0.7169	0	+-+	0	2	0.4392	301	226	236.26	AntiDepNonRemissionEAS2021.gz
1	rs12566659	17,604,924	G	A	0.862	0.873	1.01	0.94686	0.2182	0.8023	0	++-	0	2	0.3754	301	226	236.26	AntiDepNonRemissionEAS2021.gz

End of preview. Expand in Data Studio

PGC Major Depressive Disorder — GWAS Summary Statistics

Dataset Description

Genome-wide association study (GWAS) summary statistics for Major Depressive Disorder phenotypes from the Psychiatric Genomics Consortium (PGC).

Each publication is available as a separate subset (config) and can be loaded independently.

Usage

from datasets import load_dataset

# Load a specific GWAS
ds = load_dataset("OpenMed/pgc-mdd", "AntiDepResponse2021")
print(ds)

List all available subsets

from datasets import get_dataset_config_names
print(get_dataset_config_names("OpenMed/pgc-mdd"))

Subsets

Config	Phenotype	Journal	Year	PubMed
`AntiDepResponse2021`	Antidepressant Response	Biol Psychiatry: Global Open Science	2021	Pending
`mdd2013`	Major Depression	Molecular Psychiatry	2013	22472876
`mdd2018`	Major Depression	Nature Genetics	2018	29700475
`mdd2018_noUKBB`	Major Depression (no UK Biobank)	Nature Genetics	2018	29700475
`mdd2021asi`	Major Depression (East Asian)	JAMA Psychiatry	2021	34586374
`mdd2023diverse`	Major Depression (Multi-Ancestry)	Nature Genetics	2023	38177345
`mdd2025`	Major Depression	Cell	2025	39814019
`ppd2023`	Peripartum Depression	American Journal of Psychiatry	2023	37849304

Data Format

All data is stored as Apache Parquet shards (10,000 rows each). Common columns:

Column	Description
`SNP` / `ID`	SNP rsID or variant identifier
`CHR`	Chromosome
`BP` / `POS`	Base-pair position (typically GRCh37/hg19)
`A1`	Effect allele
`A2`	Non-effect allele
`OR` / `BETA`	Odds ratio or effect size
`SE`	Standard error
`P`	P-value
`_source_file`	Original source filename