5-rs9687282

Bulk expression

chr5:139,686,403 · index rs9687282 · GWAS p = 3.3×10⁻⁹

Colocalization evidence (best PP4 per channel)

Bulk expression

0.98

coloc-SuSiE

0.98

Single-cell

0.96

Fetal eQTL

0.78

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): 2
CS mass in fetal regulatory chromatin: 0.458
CS mass in adult regulatory chromatin: 0.538
Best bulk-eQTL gene: ENSG00000279726
Best single-cell type: Oligodendrocytes
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 (38)

Gene	Tier	Chain score	CpG	CpG–TSS dist	Direct eQTL PP4
NDUFA2	high	0.99	cg06503255	26 kb	0.82
HARS2	high	0.99	cg06503255	18 kb	0.95
PCDHA3	high	0.98	cg06503255	127 kb	0.95
TMCO6	high	0.98	cg06503255	34 kb	0.73
SRA1	high	0.98	cg06503255	115 kb	0.26
PCDHA2	high	0.98	cg16577123	147 kb	0.95
PCDHB9	high	0.97	cg19875535	536 kb	0.93
PCDHA4	high	0.97	cg06503255	133 kb	0.95
PCDHA8	high	0.97	cg03378599	115 kb	0.96
PCDHA7	high	0.97	cg03378599	108 kb	0.79
PCDHA10	high	0.97	cg03378599	130 kb	0.96
ZMAT2	high	0.97	cg03378599	28 kb	0.94
PCDHAC1	high	0.95	cg16577123	279 kb	0.88
PCDHB16	high	0.94	cg06503255	–	0.89
PCDHB14	high	0.93	cg03975922	522 kb	0.91
SIL1	high	0.92	cg13084536	448 kb	0.18
IK	high	0.91	cg26395211	18 kb	0.42
HARS	high	0.89	cg06503255	18 kb	0.95
TMEM173	high	0.87	cg07879474	202 kb	0.17
PCDHB7	high	0.87	cg01063759	447 kb	0.73
CYSTM1	high	0.87	cg01063759	551 kb	0.09
PCDHB10	high	0.87	cg01063759	466 kb	0.84
PCDHB3	high	0.86	cg19875535	449 kb	0.37
PCDHB2	high	0.86	cg01063759	369 kb	0.27
HBEGF	high	0.83	cg00585072	461 kb	0.14
PCDHB5	high	0.83	cg00585072	328 kb	0.70
PCDHB8	high	0.83	cg00585072	370 kb	0.39
CD14	high	0.83	cg00585072	174 kb	0.09
PCDHA9	high	0.83	cg00585072	40 kb	0.55
PCDHA13	high	0.83	cg00585072	75 kb	0.52
PCDHA11	high	0.83	cg00585072	62 kb	0.45
PCDHA12	high	0.83	cg00585072	68 kb	0.27
PCDHA6	high	0.81	cg01063759	102 kb	0.26
PCDHB11	suggestive	0.65	cg06503255	526 kb	0.57
PROB1	suggestive	0.60	cg16049890	392 kb	0.11
DNAJC18	suggestive	0.54	cg00063979	295 kb	0.14
WDR55	suggestive	0.53	cg00585072	143 kb	0.70
CXXC5	suggestive	0.53	cg07879474	37 kb	0.69

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.