Why do schizophrenia risk loci not colocalize with brain eQTLs?

In plain terms: hundreds of small DNA differences raise the risk of schizophrenia, and nearly all of them sit outside genes rather than inside them. This project asks whether each one works by changing how strongly nearby genes are used in the brain, and tallies how much of the risk map that idea can explain with public data. New to the topic? Start with the reader’s guide.

281 genome-wide significant loci from the PGC3 schizophrenia GWAS^[12], tested for shared causal variants against six molecular channels: bulk expression (14 brain datasets), fine-mapped multi-signal colocalization, single-cell eQTLs (8 cell types), fetal cortex eQTLs, splicing QTLs (17 datasets), and brain DNA methylation QTLs. Click a bar to filter; click any locus for its full evidence card.

32%

loci with any bulk brain eQTL colocalization (PP4 > 0.8)

77%

explained after all six molecular channels (sequential attribution)

loci unexplained by every tested channel

expression-orphan loci with high-confidence gene nominations

Sequential attribution across channels

How to read this figure

What this data is

The 281 schizophrenia risk loci, each tested against six kinds of molecular evidence in a fixed order and credited to the first kind that produced a colocalization at PP4 > 0.8.

How to read it

Bars run left to right in testing order. Each bar’s height is the number of loci newly explained by that channel after everything to its left has had its turn, and the bars stack toward the dashed line at 281. The gray bar is the 65 loci no channel explained. Click a bar to filter the matrix and the table to those loci.

What to take away, and what not to

Bulk brain expression explains 90 of 281 loci (32%); the other five channels raise the total to 216 (77%), with methylation the largest single addition.
Bar heights are not total hit counts: a locus with both splicing and methylation evidence counts under splicing because splicing is tested first.
Explained means a molecular trait shares a causal variant with the GWAS signal, not that the causal gene is identified.

Evidence matrix · best PP4 per locus and channel

Bulk expression

coloc-SuSiE

Single-cell

Fetal eQTL

Splicing

Methylation

How to read this figure

What this data is

One row per locus (281 rows), one column per evidence channel. Each cell shows the best PP4 across all datasets in that channel; the thin left strip carries the locus’s final attribution color.

How to read it

Brighter is stronger, turning light near PP4 0.8 and above. Cells in the background color mean no valid test was possible, which is different from a tested-but-weak dark blue cell. Rows are grouped by attribution in waterfall order, strongest bulk signal first within each group. Hover a cell for its value; click a row to open that locus.

What to take away, and what not to

The methylation column stays dense in the row groups where every expression column goes dark. That contrast is the central observation of the project.
A bright cell says two signals are consistent with one shared variant; it does not name the causal gene. Columns also differ in depth, from 14 bulk datasets to a single methylation meta-analysis.

All loci

281 of 281 loci

Locus	Position	GWAS p ↑	Bulk	coloc-SuSiE	Single-cell	Fetal	Splicing	Methylation	Attribution	Top gene
7-rs58120505	chr7:1.99 Mb	9e-29	0.91	0.55	0.33	0.14	0.10	0.99	Bulk expression	MRM2
10-rs12571643	chr10:102.76 Mb	4e-25	0.34	0.86	0.22	0.12	0.93	1.00	Multi-signal rescue	CNNM2
15-rs4702	chr15:90.88 Mb	6e-25	1.00	1.00	0.99	0.98	0.23	1.00	Bulk expression	FURIN
12-rs1790135	chr12:123.18 Mb	7e-24	0.94	0.93	0.91	0.46	0.92	0.99	Bulk expression	C12orf65
4-rs13107325	chr4:102.27 Mb	3e-23	0.30	0.73	0.17	0.18	0.00	0.97	Methylation	SLC9B1
12-rs4298967	chr12:2.30 Mb	3e-22	0.63	0.11	0.44	0.10	0.06	0.96	Methylation	ENSG00000256769
3-rs2710323	chr3:52.78 Mb	6e-21	0.96	0.98	0.78	0.92	0.99	0.99	Bulk expression	NEK4
2-rs2139054	chr2:57.93 Mb	6e-21	0.45	0.01	0.10	0.38	0.09	0.48	Unexplained	ENSG00000115392
1-rs4950119	chr1:98.03 Mb	2e-20	0.83	0.58	0.31	0.11	0.00	0.96	Bulk expression	ENSG00000117569
7-rs7779548	chr7:137.39 Mb	4e-20	0.80	0.09	0.17	0.55	0.00	0.95	Methylation	ENSG00000228031
8-rs4129585	chr8:142.23 Mb	9e-20	0.68	0.99	0.91	0.23	0.39	1.00	Multi-signal rescue	LY6H
11-rs2902858	chr11:46.50 Mb	5e-19	0.94	0.29	0.47	0.18	0.95	0.97	Bulk expression	MDK
14-rs2190873	chr14:71.96 Mb	7e-19	0.83	0.75	0.81	0.17	0.06	0.98	Bulk expression	PCNX1
1-rs12042444	chr1:73.52 Mb	7e-19	0.30	0.11	0.10	0.22	0.04	0.25	Unexplained	ENSG00000237324
5-rs7709645	chr5:61.44 Mb	8e-19	0.67	0.15	0.78	0.15	0.64	0.85	Methylation	ELOVL7
3-rs71312200	chr3:181.01 Mb	1e-17	0.43	0.97	0.24	0.14	0.09	0.96	Multi-signal rescue	CCDC39
10-rs7893279	chr10:18.46 Mb	1e-17	0.39	0.35	0.30	0.28	0.03	0.97	Methylation	ENSG00000165997
2-rs778371	chr2:232.88 Mb	1e-17	0.34	0.24	0.52	0.29	0.73	0.41	Unexplained	ENSG00000237412
11-rs61902811	chr11:113.50 Mb	8e-17	0.77	0.12	0.42	0.12	0.63	0.99	Methylation	ANKK1
7-rs35274762	chr7:86.78 Mb	1e-16	0.66	0.08	0.20	0.13	0.06	0.98	Methylation	ENSG00000233073
20-rs1006945	chr20:38.83 Mb	1e-16	0.43	0.23	0.68	0.25	0.08	0.98	Methylation	ACTR5
15-rs3813567	chr15:78.64 Mb	1e-16	0.33	0.42	0.42	0.77	0.20	0.96	Methylation	HYKK
12-rs4766428	chr12:110.29 Mb	2e-16	0.81	0.91	0.61	0.90	0.10	0.99	Bulk expression	MVK
1-rs2970610	chr1:43.63 Mb	4e-16	0.67	0.14	0.78	0.51	0.09	0.99	Methylation	MED8
2-rs11680723	chr2:199.95 Mb	5e-16	0.59	0.17	0.87	0.51	0.15	0.99	Single-cell eQTL	FTCDNL1
18-rs55858161	chr18:79.89 Mb	5e-16	0.60	0.33	0.27	0.18	0.28	0.98	Methylation	ENSG00000287879
16-rs9925915	chr16:29.98 Mb	5e-16	0.98	0.97	0.88	0.96	0.97	0.97	Bulk expression	INO80E
19-rs8101499	chr19:19.37 Mb	8e-16	0.94	0.93	0.91	0.20	0.78	0.98	Bulk expression	MAU2
4-rs12498839	chr4:175.81 Mb	9e-16	1.00	1.00	0.17	0.09	1.00	0.68	Bulk expression	ENSG00000249106
1-rs56335113	chr1:29.95 Mb	1e-15	0.31	0.26	0.52	0.36	0.10	0.95	Methylation	PTPRU
2-rs12471454	chr2:199.15 Mb	2e-15	0.63	0.94	0.89	0.55	0.49	0.99	Multi-signal rescue	FTCDNL1
1-rs11587347	chr1:239.04 Mb	4e-15	0.14	0.06	0.08	0.06	0.02	0.24	Unexplained	ENSG00000133019
12-rs61937595	chr12:57.29 Mb	4e-15	0.50	0.93	0.44	0.55	0.14	1.00	Multi-signal rescue	STAC3
15-rs11638554	chr15:84.61 Mb	4e-15	0.92	0.96	0.52	0.83	0.71	0.97	Bulk expression	WDR73
14-rs10873538	chr14:103.79 Mb	5e-15	0.76	0.16	0.50	0.74	0.91	0.98	Splicing	XRCC3
22-rs732381	chr22:39.66 Mb	6e-15	0.70	0.91	0.71	0.13	0.17	1.00	Multi-signal rescue	ENSG00000100399
7-rs7803571	chr7:111.35 Mb	8e-15	0.47	0.08	0.15	0.13	0.61	0.66	Unexplained	ENSG00000287011
3-rs10935184	chr3:136.43 Mb	1e-14	0.95	0.95	0.89	0.41	0.83	0.84	Bulk expression	PCCB
5-rs10035564	chr5:45.25 Mb	1e-14	0.65	–	0.16	0.13	0.44	0.83	Methylation	ENSG00000164588
19-rs7251	chr19:49.66 Mb	2e-14	0.97	0.83	0.84	0.35	0.99	1.00	Bulk expression	IZUMO1
2-rs11693094	chr2:184.74 Mb	2e-14	0.41	0.08	0.35	0.20	0.09	0.25	Unexplained	ENSG00000170396
11-rs4936215	chr11:133.98 Mb	3e-14	0.70	0.21	0.40	0.19	0.71	0.99	Methylation	ENSG00000080854
2-rs12991836	chr2:144.38 Mb	3e-14	0.17	0.07	0.64	0.10	–	0.73	Unexplained	ENSG00000257277
11-rs3016384	chr11:132.70 Mb	5e-14	0.50	0.07	0.06	0.04	0.36	0.86	Methylation	ENSG00000287068
1-rs16851048	chr1:177.31 Mb	5e-14	0.67	0.26	0.46	0.14	0.16	0.71	Unexplained	ENSG00000227579
10-rs17731	chr10:3.78 Mb	5e-14	0.53	0.84	0.20	0.06	0.07	0.97	Multi-signal rescue	ENSG00000228353
5-rs72802887	chr5:152.87 Mb	5e-14	0.71	0.14	0.18	0.13	0.83	0.93	Splicing	NMUR2
8-rs73219806	chr8:26.42 Mb	5e-14	0.94	0.09	0.20	0.08	0.93	0.89	Bulk expression	CHRNA2
18-rs11083369	chr18:29.90 Mb	5e-14	0.07	0.07	0.08	0.05	–	–	Unexplained	ENSG00000134755
15-rs11632947	chr15:61.56 Mb	6e-14	0.25	0.08	0.25	0.12	0.07	0.94	Methylation	ENSG00000182718
13-rs9545047	chr13:79.29 Mb	8e-14	0.97	0.95	0.91	0.81	0.06	0.95	Bulk expression	ENSG00000227676
7-rs2057884	chr7:105.29 Mb	9e-14	0.37	0.07	0.85	0.16	0.32	0.89	Single-cell eQTL	ENSG00000242154
22-rs9607782	chr22:41.19 Mb	1e-13	0.97	0.74	0.73	0.76	0.82	1.00	Bulk expression	ZC3H7B
18-rs9636107	chr18:55.53 Mb	1e-13	0.63	0.25	0.38	0.11	0.71	0.93	Methylation	ENSG00000134046
14-rs12883788	chr14:32.83 Mb	1e-13	0.31	0.07	0.14	0.15	0.05	0.66	Unexplained	ENSG00000100852
2-rs2914983	chr2:197.45 Mb	1e-13	0.95	0.96	0.69	0.77	0.12	0.98	Bulk expression	SF3B1
16-rs12925872	chr16:13.66 Mb	1e-13	0.33	0.28	0.32	0.92	0.13	0.16	Fetal eQTL	ENSG00000103381
2-rs68002929	chr2:145.66 Mb	2e-13	0.11	0.02	0.12	0.07	–	0.23	Unexplained	ENSG00000287115
11-rs893949	chr11:134.43 Mb	2e-13	0.70	0.21	0.41	0.17	0.71	0.99	Methylation	ENSG00000080854
7-rs7807720	chr7:110.43 Mb	3e-13	0.70	0.02	0.18	0.14	0.72	0.66	Unexplained	ENSG00000128512
11-rs12541	chr11:124.75 Mb	4e-13	0.88	0.40	0.17	0.22	0.41	0.99	Bulk expression	OR8B12
1-rs61833239	chr1:243.85 Mb	6e-13	0.35	0.23	0.33	0.20	0.87	0.97	Splicing	AKT3
18-rs715170	chr18:56.13 Mb	1e-12	0.30	0.16	0.17	0.11	0.27	0.93	Methylation	ENSG00000267325
2-rs3770752	chr2:37.35 Mb	1e-12	0.91	0.98	0.76	0.92	0.86	0.97	Bulk expression	NDUFAF7
8-rs73229090	chr8:27.58 Mb	2e-12	0.48	0.21	0.54	0.07	0.03	0.89	Methylation	ENSG00000286804
1-rs2494638	chr1:2.44 Mb	2e-12	0.89	0.37	0.38	0.98	0.13	0.96	Bulk expression	CALML6
9-rs505061	chr9:22.77 Mb	3e-12	0.35	0.14	0.11	0.11	0.00	0.23	Unexplained	ENSG00000099810
6-rs6938026	chr6:43.22 Mb	3e-12	0.95	0.93	0.64	0.22	0.11	0.98	Bulk expression	ENSG00000112659
17-rs959071	chr17:19.24 Mb	3e-12	0.57	0.91	0.57	0.95	0.32	1.00	Multi-signal rescue	FAM83G
11-rs4937935	chr11:134.71 Mb	4e-12	0.70	0.20	0.42	0.17	0.71	0.99	Methylation	ENSG00000080854
7-rs79210963	chr7:24.68 Mb	5e-12	0.44	0.82	0.30	0.11	0.34	0.98	Multi-signal rescue	FAM221A
11-rs77502336	chr11:123.52 Mb	8e-12	0.89	0.73	0.49	0.18	0.45	0.89	Bulk expression	OR8A1
3-rs17194490	chr3:2.51 Mb	8e-12	0.87	0.06	0.13	0.26	0.01	0.22	Bulk expression	ENSG00000144619
4-rs61405217	chr4:169.40 Mb	9e-12	0.56	0.64	0.65	0.41	0.06	0.94	Methylation	NEK1
16-rs9674103	chr16:9.82 Mb	1e-11	0.31	0.09	0.25	0.10	0.06	0.85	Methylation	ENSG00000166669
15-rs2929278	chr15:43.96 Mb	1e-11	0.97	0.94	0.82	0.16	0.92	0.97	Bulk expression	WDR76
8-8-4180090-T-A	chr8:4.32 Mb	1e-11	0.44	0.07	0.12	0.04	0.03	0.46	Unexplained	ENSG00000286934
8-rs4043663	chr8:88.26 Mb	1e-11	0.83	–	0.13	0.39	0.10	0.82	Bulk expression	ENSG00000253553
5-rs187653	chr5:138.55 Mb	1e-11	0.85	0.08	0.72	0.10	0.78	0.90	Bulk expression	ENSG00000131508
3-rs1399551	chr3:80.50 Mb	2e-11	0.13	0.08	0.12	0.09	–	0.97	Methylation	ENSG00000114480
15-rs56282503	chr15:40.27 Mb	2e-11	1.00	0.97	0.77	0.19	0.97	0.99	Bulk expression	ENSG00000230778
8-rs298216	chr8:64.38 Mb	2e-11	0.92	0.28	0.94	0.24	0.11	0.99	Bulk expression	CYP7B1
3-rs4678552	chr3:36.80 Mb	2e-11	0.98	0.15	0.94	0.46	0.04	0.58	Bulk expression	ENSG00000163673
13-rs11619756	chr13:43.75 Mb	2e-11	0.67	0.16	0.18	0.15	0.37	0.96	Methylation	CCDC122
7-rs1593304	chr7:131.94 Mb	3e-11	0.32	0.10	0.59	0.10	0.03	0.85	Methylation	ENSG00000128585
17-rs2696466	chr17:46.21 Mb	3e-11	0.98	0.66	0.91	0.37	0.96	0.98	Bulk expression	ARL17B
3-rs13090130	chr3:162.06 Mb	3e-11	0.24	0.07	0.37	0.27	0.04	0.87	Methylation	ENSG00000213186
11-rs12363019	chr11:24.35 Mb	4e-11	0.26	0.01	0.12	0.12	0.03	0.91	Methylation	ENSG00000187398
12-rs302317	chr12:29.77 Mb	4e-11	0.90	0.26	0.64	0.06	0.12	0.99	Bulk expression	ENSG00000133687
17-rs12943566	chr17:2.25 Mb	4e-11	0.55	0.94	0.79	0.53	0.94	0.96	Multi-signal rescue	MNT
11-rs10767735	chr11:28.62 Mb	5e-11	0.73	0.15	0.16	0.35	0.44	0.99	Methylation	ENSG00000148942
6-rs217310	chr6:83.65 Mb	7e-11	0.89	0.07	0.51	0.47	0.10	0.82	Bulk expression	ENSG00000065609
3-rs6804677	chr3:17.82 Mb	7e-11	0.46	0.50	0.53	0.16	0.38	0.96	Methylation	ENSG00000131374
15-rs2238304	chr15:89.30 Mb	8e-11	0.94	0.21	0.46	0.54	0.98	0.99	Bulk expression	FANCI
5-rs11241041	chr5:109.85 Mb	8e-11	0.29	0.51	0.46	0.14	0.33	0.86	Methylation	ENSG00000112893
13-rs9597388	chr13:56.35 Mb	9e-11	0.20	0.01	0.08	0.09	–	0.16	Unexplained	ENSG00000286709
5-rs7701188	chr5:89.45 Mb	9e-11	0.87	1.00	0.21	0.11	0.16	0.91	Bulk expression	ENSG00000287862
17-rs4793888	chr17:57.66 Mb	1e-10	0.40	0.13	0.21	0.26	0.08	0.83	Methylation	ENSG00000289147
2-rs6430491	chr2:134.08 Mb	1e-10	0.92	0.07	0.37	0.10	0.30	0.97	Bulk expression	ENSG00000152127
4-rs35734242	chr4:0.71 Mb	1e-10	0.56	0.85	0.36	0.21	0.92	0.98	Multi-signal rescue	UVSSA
20-rs6125656	chr20:49.47 Mb	1e-10	0.24	0.20	0.52	0.20	0.08	0.77	Unexplained	ENSG00000203999
1-rs2252865	chr1:8.36 Mb	1e-10	0.95	0.96	0.96	0.16	0.07	0.98	Bulk expression	RERE
14-rs1540840	chr14:99.27 Mb	2e-10	0.31	0.21	0.70	0.08	0.19	0.96	Methylation	ENSG00000182218
2-rs72974238	chr2:224.57 Mb	2e-10	0.96	0.09	0.80	0.06	0.04	0.97	Bulk expression	ENSG00000036257
6-rs9398171	chr6:108.66 Mb	2e-10	0.97	0.95	0.66	0.40	0.18	0.96	Bulk expression	ENSG00000286511
1-rs12138231	chr1:150.14 Mb	2e-10	0.92	0.91	0.59	0.35	0.16	0.96	Bulk expression	RPRD2
8-rs59498392	chr8:38.40 Mb	2e-10	0.88	0.90	0.76	0.88	0.87	0.99	Bulk expression	DDHD2
6-rs12190758	chr6:92.44 Mb	2e-10	0.10	0.06	0.08	0.08	–	0.06	Unexplained	ENSG00000135333
12-rs6538539	chr12:94.80 Mb	3e-10	0.29	0.07	0.20	0.26	0.30	0.09	Unexplained	ENSG00000028203
4-rs1454606	chr4:33.64 Mb	3e-10	0.18	0.04	0.12	–	–	0.92	Methylation	ENSG00000250954
16-rs11076631	chr16:89.81 Mb	3e-10	0.99	0.66	0.75	0.62	0.96	0.99	Bulk expression	DPEP1
11-rs708228	chr11:57.82 Mb	3e-10	0.91	–	0.30	0.34	0.05	0.99	Bulk expression	ZDHHC5
12-rs61952922	chr12:122.08 Mb	3e-10	0.98	0.98	0.95	0.94	0.99	0.99	Bulk expression	C12orf65
17-rs75329315	chr17:1.34 Mb	3e-10	0.50	0.93	0.80	0.32	0.94	0.96	Multi-signal rescue	MNT
13-rs1924378	chr13:37.79 Mb	3e-10	0.40	0.18	0.19	0.06	0.09	0.66	Unexplained	ENSG00000133107
8-rs6471815	chr8:59.79 Mb	3e-10	0.36	0.08	0.24	0.17	0.05	0.87	Methylation	ENSG00000228862
19-rs2387414	chr19:50.53 Mb	4e-10	0.97	0.79	0.85	0.55	0.99	1.00	Bulk expression	FCGRT
1-rs645383	chr1:35.91 Mb	4e-10	0.96	0.09	0.56	0.33	0.12	0.99	Bulk expression	TFAP2E
8-rs10086619	chr8:110.57 Mb	4e-10	0.24	0.07	0.32	0.08	0.06	0.18	Unexplained	ENSG00000253122
1-rs6588168	chr1:65.86 Mb	4e-10	0.46	0.29	0.29	0.08	0.12	0.97	Methylation	AK4
14-rs17571951	chr14:29.55 Mb	4e-10	0.39	0.07	0.16	0.18	0.02	0.80	Methylation	ENSG00000287142
5-rs115037896	chr5:50.25 Mb	5e-10	0.88	0.77	0.74	0.08	0.00	0.15	Bulk expression	ENSG00000170571
1-rs11209828	chr1:71.71 Mb	5e-10	0.40	0.15	0.13	0.15	0.01	0.20	Unexplained	ENSG00000269933
17-rs6504163	chr17:63.47 Mb	5e-10	0.99	1.00	0.46	0.86	0.12	0.46	Bulk expression	ENSG00000159640
5-rs246024	chr5:140.95 Mb	5e-10	0.90	0.94	0.53	0.92	0.47	0.99	Bulk expression	NDUFA2
3-rs167924	chr3:107.66 Mb	5e-10	0.39	0.20	0.16	0.10	0.39	0.99	Methylation	ENSG00000273125
19-rs72986630	chr19:11.74 Mb	6e-10	1.00	1.00	0.67	0.40	0.14	0.92	Bulk expression	ZNF442
4-rs7699241	chr4:165.28 Mb	6e-10	0.11	0.07	0.12	0.11	0.80	0.65	Unexplained	ENSG00000145416
2-rs62152282	chr2:104.37 Mb	6e-10	0.34	0.18	0.17	0.13	0.31	0.96	Methylation	C2orf49
5-rs39967	chr5:58.45 Mb	6e-10	0.17	0.16	0.29	0.08	0.05	0.44	Unexplained	ENSG00000175857
5-rs815609	chr5:154.14 Mb	6e-10	0.56	0.60	0.15	0.24	0.02	0.96	Methylation	GALNT10
10-rs7900775	chr10:104.84 Mb	6e-10	0.60	–	0.81	0.10	0.50	0.85	Single-cell eQTL	GSTO1
1-rs61828917	chr1:173.61 Mb	6e-10	0.99	–	0.84	0.60	0.08	1.00	Bulk expression	SLC9C2
7-rs2944821	chr7:72.33 Mb	6e-10	0.18	0.07	0.51	0.09	0.02	0.94	Methylation	ENSG00000130305
7-rs6461561	chr7:21.43 Mb	7e-10	0.94	0.17	0.41	0.07	0.47	0.45	Bulk expression	ENSG00000105866
10-rs61857878	chr10:91.03 Mb	7e-10	0.46	0.07	0.73	0.10	0.01	0.46	Unexplained	ENSG00000180628
7-rs13233308	chr7:87.62 Mb	8e-10	0.70	0.08	0.20	0.13	0.02	1.00	Methylation	ENSG00000233073
21-rs8134737	chr21:15.07 Mb	8e-10	0.21	0.11	0.56	0.16	0.00	0.16	Unexplained	ENSG00000236471
12-rs2649999	chr12:120.94 Mb	9e-10	0.71	0.85	0.49	0.26	0.42	0.95	Multi-signal rescue	SPPL3
16-rs8048039	chr16:4.45 Mb	9e-10	0.94	0.73	0.60	0.74	0.98	0.99	Bulk expression	MGRN1
14-rs10148671	chr14:29.00 Mb	9e-10	0.41	0.08	0.17	0.16	0.05	0.80	Methylation	ENSG00000287142
4-rs28454198	chr4:79.28 Mb	1e-9	0.61	0.27	0.67	0.15	0.01	0.74	Unexplained	ENSG00000138772
13-rs1545660	chr13:53.88 Mb	1e-9	0.15	–	0.65	0.09	0.01	0.26	Unexplained	ENSG00000279325
1-rs61789527	chr1:96.68 Mb	1e-9	0.29	0.91	0.15	0.07	0.04	0.49	Multi-signal rescue	ENSG00000188641
5-rs252812	chr5:107.40 Mb	1e-9	0.17	0.01	0.82	0.10	0.07	0.95	Single-cell eQTL	ENSG00000151422
6-rs6925079	chr6:64.24 Mb	1e-9	0.14	0.03	0.24	0.08	–	0.94	Methylation	ENSG00000112232
15-rs10906984	chr15:82.70 Mb	1e-9	0.94	0.95	0.47	0.45	0.15	0.80	Bulk expression	ENSG00000182774
9-rs10985811	chr9:98.31 Mb	1e-9	0.59	0.19	0.26	0.10	0.05	0.30	Unexplained	ENSG00000136928
6-rs1856507	chr6:72.45 Mb	1e-9	0.45	0.19	0.46	0.23	0.05	0.72	Unexplained	ENSG00000080007
10-rs2119242	chr10:21.06 Mb	1e-9	0.26	0.01	0.15	0.07	0.00	1.00	Methylation	ENSG00000078403
7-rs1589726	chr7:79.72 Mb	1e-9	0.21	0.09	0.10	0.07	0.07	0.68	Unexplained	ENSG00000135218
12-rs578470	chr12:50.07 Mb	1e-9	0.97	–	0.79	0.28	0.88	0.99	Bulk expression	SPATS2
5-rs72723227	chr5:7.25 Mb	1e-9	0.52	0.11	0.81	0.20	0.02	0.97	Single-cell eQTL	NSUN2
2-rs62183855	chr2:172.09 Mb	2e-9	0.63	0.08	0.21	0.16	0.06	0.99	Methylation	ENSG00000198586
6-rs9322058	chr6:146.42 Mb	2e-9	0.45	0.10	0.30	0.13	0.05	0.95	Methylation	ENSG00000118508
12-rs2686386	chr12:121.20 Mb	2e-9	0.71	0.77	0.49	0.25	0.88	0.96	Splicing	SPPL3
11-rs11227250	chr11:65.67 Mb	2e-9	0.98	0.76	0.97	0.40	0.89	0.99	Bulk expression	RNASEH2C
9-rs13293831	chr9:126.90 Mb	2e-9	0.43	0.21	0.24	0.32	0.20	0.97	Methylation	RPL12
18-rs8084351	chr18:53.20 Mb	2e-9	0.48	–	0.44	0.06	0.19	0.09	Unexplained	ENSG00000187323
4-rs28521069	chr4:117.93 Mb	2e-9	0.81	0.91	0.20	0.09	0.01	0.54	Bulk expression	ENSG00000164100
11-rs10894308	chr11:131.02 Mb	2e-9	0.38	0.67	0.59	0.24	0.07	0.86	Methylation	ENSG00000238117
13-rs9569820	chr13:58.13 Mb	2e-9	0.21	0.06	0.13	0.09	–	0.71	Unexplained	ENSG00000118946
1-rs10157075	chr1:83.74 Mb	3e-9	0.48	0.09	0.28	0.09	0.01	0.09	Unexplained	ENSG00000237076
2-rs1396728	chr2:22.47 Mb	3e-9	0.16	0.09	0.12	0.14	0.00	0.18	Unexplained	ENSG00000223634
16-rs11862968	chr16:68.38 Mb	3e-9	0.91	–	0.40	0.30	0.98	0.98	Bulk expression	NIP7
4-rs356183	chr4:89.70 Mb	3e-9	0.90	–	0.15	0.42	0.20	0.66	Bulk expression	ENSG00000277695
12-rs3764002	chr12:108.22 Mb	3e-9	0.70	0.10	0.15	0.08	0.08	0.27	Unexplained	ENSG00000084112
7-rs35531336	chr7:133.75 Mb	3e-9	0.24	–	0.13	0.11	0.02	0.83	Methylation	ENSG00000155530
12-rs1463209	chr12:39.12 Mb	3e-9	0.22	–	0.82	0.08	0.07	0.74	Single-cell eQTL	ENSG00000175548
5-rs9687282	chr5:139.69 Mb	3e-9	0.98	0.98	0.96	0.78	0.99	0.99	Bulk expression	NDUFA2
14-rs7141857	chr14:84.20 Mb	3e-9	0.08	0.02	0.07	0.06	0.01	0.18	Unexplained	ENSG00000185070
3-rs59971314	chr3:63.93 Mb	3e-9	0.98	0.96	0.30	0.51	0.09	0.97	Bulk expression	ENSG00000163634
4-rs4697446	chr4:24.27 Mb	3e-9	0.34	0.22	0.73	0.17	0.03	0.91	Methylation	ENSG00000152990
2-rs1881046	chr2:155.98 Mb	4e-9	0.74	0.07	0.29	0.06	0.09	0.96	Methylation	ENSG00000162989
8-rs1434281	chr8:102.66 Mb	4e-9	0.41	0.19	0.33	0.29	0.59	0.99	Methylation	ENSG00000236939
1-rs7515363	chr1:200.45 Mb	4e-9	0.84	0.37	0.90	0.21	0.38	0.99	Bulk expression	ZNF281
19-rs3810450	chr19:36.04 Mb	4e-9	0.99	0.33	0.15	0.12	0.08	0.99	Bulk expression	OVOL3
8-rs7464611	chr8:143.85 Mb	4e-9	0.98	0.98	0.92	0.67	0.80	1.00	Bulk expression	SCRIB
2-rs999494	chr2:72.93 Mb	4e-9	0.85	0.95	0.76	0.65	0.35	0.99	Bulk expression	NAT8
15-rs2917627	chr15:34.78 Mb	4e-9	0.39	0.70	0.22	0.41	0.14	0.47	Unexplained	ENSG00000259287
15-rs653765	chr15:58.75 Mb	4e-9	0.91	0.91	0.88	0.25	0.21	0.94	Bulk expression	FAM81A
9-rs2381411	chr9:36.32 Mb	4e-9	0.61	0.31	0.53	0.72	0.49	0.99	Methylation	ENSG00000281649
9-rs498591	chr9:14.51 Mb	5e-9	0.24	0.08	0.19	0.08	0.23	0.07	Unexplained	ENSG00000288876
19-rs322124	chr19:11.29 Mb	5e-9	1.00	1.00	0.68	0.39	0.13	0.76	Bulk expression	ENSG00000197933
19-rs758749	chr19:56.68 Mb	5e-9	0.98	0.99	0.32	0.97	0.96	0.64	Bulk expression	ENSG00000127903
2-rs10173857	chr2:174.09 Mb	6e-9	0.88	–	0.15	0.20	0.06	0.94	Bulk expression	ENSG00000154518
12-rs12315638	chr12:74.95 Mb	6e-9	0.17	0.14	0.15	0.08	0.01	0.39	Unexplained	ENSG00000166006
1-rs3900555	chr1:60.60 Mb	6e-9	0.55	0.86	0.50	0.74	0.77	0.94	Multi-signal rescue	ENSG00000226476
2-rs4672366	chr2:60.16 Mb	6e-9	0.50	0.22	0.33	0.09	0.03	0.97	Methylation	ENSG00000082898
1-rs12126806	chr1:200.99 Mb	7e-9	0.85	0.22	0.91	0.19	0.04	0.99	Bulk expression	ZNF281
13-rs650520	chr13:38.29 Mb	7e-9	0.61	0.17	0.17	0.09	0.13	0.66	Unexplained	ENSG00000120693
8-rs876983	chr8:18.55 Mb	7e-9	0.84	0.13	0.18	0.05	0.04	0.80	Bulk expression	ENSG00000285624
14-rs4903718	chr14:78.18 Mb	8e-9	0.38	0.11	0.29	0.11	0.09	0.85	Methylation	ENSG00000100596
12-rs61924144	chr12:71.87 Mb	8e-9	0.32	0.98	0.23	0.10	0.03	0.83	Multi-signal rescue	TBC1D15
21-rs229362	chr21:20.74 Mb	8e-9	0.97	0.99	0.07	0.05	0.94	0.07	Bulk expression	ENSG00000224924
5-rs34879738	chr5:90.98 Mb	8e-9	0.47	0.43	0.19	0.10	0.83	0.89	Splicing	ENSG00000113356
7-rs2349487	chr7:8.53 Mb	9e-9	0.17	0.24	0.35	0.07	0.08	0.07	Unexplained	ENSG00000219545
5-rs12652777	chr5:156.35 Mb	9e-9	0.19	0.09	0.12	0.07	0.01	0.90	Methylation	ENSG00000254246
2-rs7604885	chr2:161.95 Mb	9e-9	0.22	0.27	0.24	0.17	0.38	0.26	Unexplained	ENSG00000115271
13-rs61973697	chr13:101.37 Mb	1e-8	0.20	0.16	0.67	0.05	0.01	0.27	Unexplained	ENSG00000102452
2-rs7575796	chr2:97.08 Mb	1e-8	1.00	–	0.93	0.16	0.99	0.97	Bulk expression	FAHD2B
1-rs10559	chr1:153.95 Mb	1e-8	0.86	0.98	0.68	0.88	0.89	0.98	Bulk expression	DCST1
17-rs11263770	chr17:36.54 Mb	1e-8	0.98	0.83	0.92	0.01	0.67	0.90	Bulk expression	CCL3
2-rs7599488	chr2:60.49 Mb	1e-8	0.48	0.21	0.32	0.10	0.00	0.97	Methylation	ENSG00000082898
8-rs79445414	chr8:34.01 Mb	1e-8	0.12	0.13	0.12	0.07	0.07	0.74	Unexplained	ENSG00000156687
22-rs6010045	chr22:50.66 Mb	1e-8	0.76	0.89	0.66	0.77	0.91	0.93	Multi-signal rescue	ZBED4
5-rs2914025	chr5:91.69 Mb	1e-8	0.48	0.40	0.18	0.11	0.83	0.43	Splicing	ENSG00000113356
6-rs9390083	chr6:143.33 Mb	1e-8	0.79	0.17	0.20	0.86	0.94	0.14	Fetal eQTL	ENSG00000146416
9-rs6479494	chr9:93.57 Mb	1e-8	0.97	0.99	0.92	0.32	0.94	0.96	Bulk expression	ENSG00000237385
2-rs34181670	chr2:27.80 Mb	1e-8	0.68	–	0.67	0.77	0.45	0.97	Methylation	CGREF1
13-rs9603649	chr13:39.93 Mb	1e-8	0.35	–	0.28	0.23	0.03	0.65	Unexplained	ENSG00000102738
2-rs12476312	chr2:228.12 Mb	1e-8	0.42	0.13	0.23	0.26	0.15	0.90	Methylation	AGFG1
19-rs144821294	chr19:2.16 Mb	1e-8	0.71	0.96	0.80	0.24	0.41	0.94	Multi-signal rescue	PLEKHJ1
1-rs41314284	chr1:226.60 Mb	1e-8	0.15	0.93	0.25	0.14	0.09	0.96	Multi-signal rescue	ENSG00000143768
2-rs2033996	chr2:76.06 Mb	1e-8	0.21	0.44	0.09	0.16	0.01	0.85	Methylation	ENSG00000270996
12-rs10777187	chr12:89.55 Mb	1e-8	0.91	0.95	0.73	0.06	0.03	0.86	Bulk expression	GALNT4
12-rs10861176	chr12:104.24 Mb	1e-8	0.65	0.28	0.36	0.12	0.06	0.97	Methylation	ENSG00000255150
7-rs10243922	chr7:138.92 Mb	2e-8	0.94	0.21	0.26	0.12	0.11	0.99	Bulk expression	KIAA1549
2-rs6546857	chr2:73.61 Mb	2e-8	0.85	0.94	0.76	0.65	0.33	0.99	Bulk expression	NAT8
12-rs1464492	chr12:74.15 Mb	2e-8	0.22	0.28	0.26	0.10	0.12	0.39	Unexplained	ENSG00000257497
6-rs80249955	chr6:68.57 Mb	2e-8	0.16	0.15	0.29	0.22	0.06	0.67	Unexplained	ENSG00000168216
4-rs215483	chr4:23.38 Mb	2e-8	0.31	0.27	0.71	0.21	0.04	0.91	Methylation	ENSG00000152990
16-rs11647188	chr16:82.61 Mb	2e-8	0.14	0.06	0.20	0.08	0.08	0.56	Unexplained	ENSG00000184860
1-rs61786047	chr1:28.71 Mb	2e-8	0.67	0.32	0.22	0.18	0.15	0.98	Methylation	ENSG00000242125
1-rs1023330	chr1:95.12 Mb	2e-8	0.93	0.14	0.32	0.13	0.52	0.61	Bulk expression	ENSG00000152078
18-rs8096175	chr18:4.99 Mb	2e-8	0.25	–	0.24	0.13	0.07	0.09	Unexplained	ENSG00000265487
9-rs2890914	chr9:10.24 Mb	2e-8	0.12	0.10	0.15	0.07	0.02	0.03	Unexplained	ENSG00000270372
13-rs12877581	chr13:73.75 Mb	2e-8	0.27	0.08	0.46	0.06	0.01	0.99	Methylation	ENSG00000102554
9-rs10781248	chr9:74.71 Mb	2e-8	0.22	0.10	0.22	0.06	0.18	0.22	Unexplained	ENSG00000198963
3-rs62291002	chr3:180.46 Mb	2e-8	0.40	0.97	0.23	0.15	0.08	0.96	Multi-signal rescue	CCDC39
14-rs745467	chr14:90.66 Mb	2e-8	0.20	0.19	0.25	0.10	0.04	0.90	Methylation	ENSG00000165914
11-rs12282735	chr11:124.44 Mb	2e-8	0.88	0.25	0.55	0.11	0.42	0.95	Bulk expression	OR8B12
4-rs59518103	chr4:19.90 Mb	2e-8	0.09	0.13	0.17	0.11	0.07	0.09	Unexplained	ENSG00000272995
7-rs6946576	chr7:139.33 Mb	2e-8	0.94	0.10	0.27	0.13	0.19	0.99	Bulk expression	KIAA1549
10-rs7902292	chr10:122.14 Mb	2e-8	0.82	0.47	0.17	0.26	0.45	0.73	Bulk expression	ENSG00000066468
16-rs79478621	chr16:7.70 Mb	2e-8	0.10	0.08	0.11	0.06	0.04	0.84	Methylation	ENSG00000286635
6-rs9390172	chr6:144.58 Mb	2e-8	0.17	–	0.11	0.11	0.02	0.28	Unexplained	ENSG00000152818
7-rs2299409	chr7:104.17 Mb	2e-8	0.69	0.14	0.66	0.30	0.50	0.94	Methylation	RELN
12-rs513022	chr12:99.17 Mb	2e-8	0.42	0.24	0.15	0.21	0.38	0.81	Methylation	ENSG00000139354
12-rs61928076	chr12:53.34 Mb	2e-8	0.38	–	0.28	0.10	0.06	0.99	Methylation	KRT6C
18-rs337718	chr18:72.11 Mb	3e-8	0.13	0.14	0.19	0.05	0.08	0.01	Unexplained	ENSG00000141668
6-rs9487653	chr6:111.50 Mb	3e-8	0.38	–	0.67	0.65	0.87	0.95	Splicing	ENSG00000173214
9-rs6478858	chr9:129.04 Mb	3e-8	0.78	–	0.48	0.72	0.95	0.92	Splicing	ENDOG
3-rs7648272	chr3:177.07 Mb	3e-8	0.22	0.10	0.33	0.09	0.00	0.97	Methylation	ENSG00000231310
4-rs13117857	chr4:37.25 Mb	3e-8	0.50	1.00	0.10	0.46	0.21	0.99	Multi-signal rescue	ENSG00000174145
6-rs9470670	chr6:11.99 Mb	3e-8	0.65	0.15	0.19	0.89	0.08	0.58	Fetal eQTL	ENSG00000111845
6-rs117178087	chr6:96.02 Mb	3e-8	0.14	0.76	0.15	0.07	0.03	0.59	Unexplained	ENSG00000287578
10-rs2812599	chr10:33.75 Mb	3e-8	0.12	0.13	0.31	0.10	0.04	0.98	Methylation	ENSG00000229327
6-rs221618	chr6:105.02 Mb	3e-8	0.83	0.78	0.84	0.46	0.97	0.88	Bulk expression	ENSG00000203809
8-rs6989793	chr8:9.89 Mb	3e-8	0.62	0.31	0.65	0.11	0.57	0.93	Methylation	XKR6
7-rs62479287	chr7:126.25 Mb	3e-8	0.13	–	0.06	0.07	0.04	0.57	Unexplained	ENSG00000179603
11-rs12224032	chr11:113.04 Mb	3e-8	0.90	0.13	0.43	0.12	0.06	0.99	Bulk expression	ANKK1
16-rs244908	chr16:58.63 Mb	3e-8	0.94	0.94	0.93	0.81	0.95	0.96	Bulk expression	SETD6
2-rs345906	chr2:8.55 Mb	3e-8	0.44	0.07	0.21	0.08	0.10	0.79	Unexplained	ENSG00000235665
7-rs7811528	chr7:2.66 Mb	3e-8	0.90	0.55	0.34	0.17	0.24	0.99	Bulk expression	MRM2
3-rs11129383	chr3:30.06 Mb	3e-8	0.12	–	0.07	0.06	0.00	0.98	Methylation	ENSG00000163513
17-rs3909258	chr17:20.04 Mb	3e-8	0.58	0.60	0.58	0.96	0.32	0.99	Fetal eQTL	GRAPL
6-rs9341835	chr6:63.42 Mb	3e-8	0.11	0.02	0.24	0.07	0.08	0.94	Methylation	ENSG00000112232
4-rs2905625	chr4:104.52 Mb	3e-8	0.11	–	0.14	0.07	0.04	0.65	Unexplained	ENSG00000245384
11-rs1144403	chr11:104.81 Mb	3e-8	0.75	–	0.45	0.11	0.01	0.30	Unexplained	ENSG00000204397
6-rs7773962	chr6:130.26 Mb	3e-8	0.71	–	0.22	0.28	0.05	0.87	Methylation	ENSG00000164484
10-rs10995239	chr10:62.63 Mb	3e-8	0.15	0.49	0.19	0.07	0.07	0.98	Methylation	ENSG00000228566
1-rs11122119	chr1:6.71 Mb	4e-8	0.50	–	0.47	0.19	0.04	0.98	Methylation	ENSG00000270035
12-rs11064369	chr12:6.76 Mb	4e-8	0.85	0.21	0.36	0.35	0.84	0.96	Bulk expression	ENSG00000285770
9-rs72761691	chr9:131.91 Mb	4e-8	0.18	–	0.22	0.16	0.06	0.38	Unexplained	ENSG00000130717
4-rs7681616	chr4:142.89 Mb	4e-8	0.29	–	0.21	0.05	0.64	0.99	Methylation	GYPA
7-rs12671608	chr7:153.83 Mb	4e-8	0.16	0.07	0.08	0.06	0.01	0.35	Unexplained	ENSG00000286461
11-rs4923457	chr11:27.63 Mb	4e-8	0.42	0.09	0.14	0.38	0.12	0.98	Methylation	ENSG00000148942
9-rs1319017	chr9:82.12 Mb	4e-8	0.39	0.85	0.08	0.11	0.00	0.21	Multi-signal rescue	ENSG00000165105
2-rs11685270	chr2:193.06 Mb	4e-8	0.11	–	0.09	0.11	0.04	0.86	Methylation	ENSG00000225539
2-rs35026989	chr2:155.06 Mb	4e-8	0.36	0.06	0.32	0.07	0.06	0.29	Unexplained	ENSG00000287900
1-rs61838368	chr1:147.49 Mb	4e-8	0.41	0.55	0.29	0.36	0.07	0.23	Unexplained	ENSG00000234283
14-rs221902	chr14:71.13 Mb	4e-8	0.79	0.82	0.76	0.15	0.11	0.98	Multi-signal rescue	ENSG00000100731
22-rs76365544	chr22:43.75 Mb	4e-8	0.29	0.32	0.17	0.15	0.11	0.78	Unexplained	ENSG00000230922
17-rs2189336	chr17:5.42 Mb	5e-8	0.94	–	0.88	0.64	0.89	0.97	Bulk expression	MIS12
3-rs77174383	chr3:45.28 Mb	5e-8	0.70	0.18	0.20	0.14	0.06	0.68	Unexplained	ENSG00000163820
4-rs982012	chr4:155.30 Mb	5e-8	0.63	–	0.23	0.08	0.91	0.46	Splicing	ENSG00000164116
7-rs3923569	chr7:71.30 Mb	5e-8	0.79	0.11	0.57	0.15	0.18	0.83	Methylation	ENSG00000272843
17-rs7225476	chr17:80.59 Mb	5e-8	0.77	–	0.35	0.52	0.42	0.99	Methylation	FSCN2
12-rs10777341	chr12:91.86 Mb	5e-8	0.22	0.03	0.30	0.11	0.00	0.83	Methylation	ENSG00000133639
5-rs12514660	chr5:64.43 Mb	5e-8	0.89	0.85	0.28	0.07	0.08	0.99	Bulk expression	ENSG00000164197

How to read this table

What this data is

Every locus with its best PP4 per channel, its attribution, and a top gene: the chained nomination where one exists, otherwise the best bulk eQTL gene.

How to read it

Click a column header to sort; type in the box to search by locus, rsID, or gene. A dash means no valid test in that channel. Values at or above 0.8 are shown in bold gold. Locus IDs link to the full evidence card.

What to take away, and what not to

Sorting by the Methylation column shows how many loci have their only strong evidence there.
PP4 values are not comparable measures of importance across channels; sample sizes and numbers of tested traits differ widely between them.