5-rs246024

Bulk expression

chr5:140,954,367 · index rs246024 · GWAS p = 5.0×10⁻¹⁰

Colocalization evidence (best PP4 per channel)

Bulk expression

0.90

coloc-SuSiE

0.94

Single-cell

0.53

Fetal eQTL

0.92

Splicing

0.47

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: 0.097
CS mass in adult regulatory chromatin: 0.093
Best bulk-eQTL gene: ENSG00000250120
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 (34)

Gene	Tier	Chain score	CpG	CpG–TSS dist	Direct eQTL PP4
NDUFA2	high	0.98	cg06503255	26 kb	0.41
HARS2	high	0.98	cg06503255	18 kb	0.42
PCDHB9	high	0.97	cg19875535	536 kb	0.25
PCDHA3	high	0.97	cg06503255	127 kb	0.89
PCDHA7	high	0.97	cg12890750	116 kb	0.51
PCDHA2	high	0.97	cg12890750	76 kb	0.61
ZMAT2	high	0.97	cg12890750	20 kb	0.31
TMCO6	high	0.97	cg19875535	12 kb	0.51
PCDHAC1	high	0.97	cg27080348	124 kb	0.90
CYSTM1	high	0.97	cg12890750	544 kb	0.16
PCDHB10	high	0.97	cg12890750	474 kb	0.07
PCDHA4	high	0.96	cg13017022	100 kb	0.07
SRA1	high	0.96	cg06503255	115 kb	0.20
PCDHA10	high	0.96	cg25613667	191 kb	0.90
PCDHA13	high	0.95	cg07379832	156 kb	0.00
PCDHA9	high	0.95	cg07379832	121 kb	0.01
PCDHB7	high	0.95	cg23500537	132 kb	0.30
PCDHB16	high	0.95	cg23500537	–	0.38
PCDHA8	high	0.95	cg23500537	199 kb	0.69
PCDHA6	high	0.95	cg25984996	109 kb	0.19
PCDHA11	high	0.94	cg07379832	143 kb	0.67
PCDHB14	high	0.94	cg23356309	258 kb	0.10
PCDHB8	high	0.94	cg07379832	452 kb	0.08
PCDHA12	high	0.94	cg07379832	149 kb	0.07
PCDHGB2	high	0.94	cg23500537	320 kb	0.14
PCDHB2	high	0.93	cg12890750	376 kb	0.12
CD14	high	0.93	cg27080348	169 kb	0.20
PCDHB3	high	0.91	cg25984996	382 kb	0.14
IK	high	0.90	cg11935114	180 kb	0.36
PCDHB5	high	0.89	cg27080348	333 kb	0.06
HARS	high	0.88	cg06503255	18 kb	0.78
WDR55	high	0.86	cg24076884	303 kb	0.39
PCDHB11	suggestive	0.72	cg02004851	372 kb	0.07
PCDHA5	suggestive	0.72	cg15923943	182 kb	0.51

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.