Colocalization evidence (best PP4 per channel)
Bulk expression
0.96
coloc-SuSiE
0.98
Single-cell
0.78
Fetal eQTL
0.92
Splicing
0.99
Methylation
0.99
Vertical line marks the PP4 = 0.8 threshold.
How to read these bars
What this data is
The strongest colocalization between this locus’s GWAS signal and each evidence channel, taking the best PP4 across every dataset in the channel.
How to read it
Bars fill toward 1. Solid bars pass the 0.8 threshold used sitewide; faded bars fall short; a dash means no dataset in the channel yielded a valid test here, usually because too few variants were shared between the studies. Treat a passing bar as evidence that the GWAS signal and that molecular trait plausibly share one causal variant, not as proof that the trait causes the disease.
Fine-mapping and annotation
- GWAS credible sets (SuSiE)
- 1
- CS mass in fetal regulatory chromatin
- 0.022
- CS mass in adult regulatory chromatin
- 0.022
- Best bulk-eQTL gene
- ENSG00000163938
- Best single-cell type
- Inhibitory neurons
- External
- UCSC browser ↗
What these annotations mean
Reading guide
Credible sets come from SuSiE fine-mapping of the GWAS: each is the smallest set of variants 95% likely to contain the causal variant for one independent signal, so a count above one means this locus carries multiple signals. The two chromatin numbers give the fraction of credible-set probability falling in regulatory chromatin (enhancer or promoter states) of fetal versus adult brain; a high fetal value beside a low adult one hints at a developmental window. The best bulk gene and best single-cell type are the strongest direct expression matches, listed even when they fall below threshold.
Gene nominations via methylation chain (21)
| Gene | Tier | Chain score | CpG | CpG–TSS dist | Direct eQTL PP4 |
|---|---|---|---|---|---|
| NEK4 | high | 0.99 | cg14845053 | 529 kb | 0.46 |
| GNL3 | high | 0.99 | cg14845053 | 439 kb | 0.96 |
| GLYCTK | high | 0.99 | cg14845053 | 45 kb | 0.75 |
| PBRM1 | high | 0.98 | cg14845053 | 444 kb | 0.09 |
| PPM1M | high | 0.98 | cg11156132 | 953 kb | 0.48 |
| RFT1 | high | 0.96 | cg01966117 | 636 kb | 0.06 |
| TKT | high | 0.95 | cg11156132 | 57 kb | 0.13 |
| STIMATE | high | 0.95 | cg11156132 | 302 kb | 0.14 |
| ITIH4 | high | 0.93 | cg00748718 | 418 kb | 0.05 |
| PRKCD | high | 0.91 | cg01966117 | 661 kb | 0.11 |
| SFMBT1 | high | 0.90 | cg19033906 | 452 kb | 0.18 |
| NISCH | high | 0.88 | cg14845053 | 213 kb | 0.09 |
| GLT8D1 | high | 0.83 | cg01966117 | 211 kb | 0.15 |
| ITIH3 | high | 0.81 | cg11156132 | 404 kb | 0.27 |
| TNNC1 | suggestive | 0.79 | cg01966117 | 41 kb | 0.12 |
| SPCS1 | suggestive | 0.78 | cg01966117 | 210 kb | 0.57 |
| DNAH1 | suggestive | 0.78 | cg07507251 | 217 kb | 0.15 |
| TLR9 | suggestive | 0.72 | cg01966117 | 256 kb | 0.00 |
| NT5DC2 | suggestive | 0.69 | cg07507251 | 2 kb | 0.37 |
| TWF2 | suggestive | 0.60 | cg00150837 | 449 kb | 0.12 |
| BAP1 | suggestive | 0.53 | cg01966117 | 84 kb | 0.34 |
How to read these nominations
Reading guide
Each row is a methylation chain: the GWAS signal colocalizes with a CpG’s methylation signal, and the same methylation signal colocalizes with this gene’s expression in independent data. The chain score is the weaker of the two links, and the tier bands it (high means at least 0.8). CpG-to-TSS distance is a plausibility check, since regulatory contacts weaken with distance, and the direct eQTL PP4 column shows what direct expression testing said at this locus. Nominations are ranked hypotheses for follow-up, not confirmed target genes.