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S-LDSC

Stratified Linkage Disequilibrium Score Regression (S-LDSC)1 was applied to summary statistics from the UK BioBank GWAS of migraine23.

Reference Data Sources

This analysis used standard reference datasets recommended and preprocessed by the authors of the S-LDSC method:

Results

GTEx and Franke lab tissue expression data

No tissues reached significance after multiple test correction in this analysis, but the plot of the findings, and those findings with the lowest p-values are presented below.

Name Coefficient Coefficient_P_value Reject Null
A11.443.Erythroid.Cells 1.93042e-09 0.00135639 False
A07.231.114.Arteries 2.06079e-09 0.00377676 False
A10.165.114.830.750.Subcutaneous.Fat 1.38947e-09 0.0107585 False
Uterus 1.39761e-09 0.022005 False
Artery_Tibial 1.29389e-09 0.0246144 False
Artery_Coronary 1.19152e-09 0.0298192 False
A10.165.114.830.500.750.Subcutaneous.Fat..Abdominal 1.08925e-09 0.0374019 False
A05.360.319.679.690.Myometrium 1.08187e-09 0.0446265 False
Fallopian_Tube 1.12642e-09 0.0482797 False
Cervix_Endocervix 1.04014e-09 0.0496349 False

Roadmap chromatin data

Reference data generated by Finucane et al.1 from the Roadmap Epigenetics Project was used in S-LDSC. No tissues were significant, but the findings with the ten lowest p values are shown below.

Name Coefficient Coefficient_P_value Reject Null
Stomach_Smooth_Muscle__H3K4me3 4.68039e-08 0.000252115 False
Ovary__H3K27ac 3.30793e-08 0.000320663 False
Aorta_ENTEX__H3K4me1 1.30506e-08 0.00048254 False
Aorta__H3K27ac 4.37318e-08 0.000693232 False
Brain_Dorsolateral_Prefrontal_Cortex__H3K4me3 6.21303e-08 0.000696467 False
Colon_Smooth_Muscle__H3K4me1 1.73213e-08 0.000718577 False
Aorta_ENTEX__H3K27ac 1.29581e-08 0.00120846 False
Ganglion_Eminence_derived_primary_cultured_neurospheres__H3K4me3 6.19777e-08 0.00170215 False
Artery-Coronary_ENTEX__H3K4me3 5.29013e-08 0.00191323 False
Stomach_Smooth_Muscle__H3K4me1 1.76338e-08 0.00206621 False

ImmGen data

In the ImmGen dataset, there were no significant cell types. The most significant cell type is shown below.

Name Coefficient Coefficient_P_value Reject Null
DN.SLN.v2 1.44288e-09 0.0101024 False

Corces et al. ATAC-seq data

There were no significant hematopoietic-related cell types in the Corces ATAC-seq dataset. The most significant cell type is shown below.

Name Coefficient Coefficient_P_value Reject Null
MPP 9.67243e-09 0.147218 False

Cahoy and GTEx-Brain data

There were no significant cell types when analyzing the neurological cell types in the Cahoy dataset using S-LDSC. The most significant cell type is shown below.

Name Coefficient Coefficient_P_value Reject Null
Astrocyte 6.62339e-10 0.171121 False

Similarly, there were no significant tissues when testing the GTEx brain tissues using S-LDSC. The most significant tissue is shown below.

Name Coefficient Coefficient_P_value Reject Null
Brain_Caudate_(basal_ganglia) 3.93733e-10 0.247229 False

  1. Hilary K Finucane, Yakir A Reshef, Verneri Anttila, Kamil Slowikowski, Alexander Gusev, Andrea Byrnes, Steven Gazal, Po-Ru Loh, Caleb Lareau, Noam Shoresh, and others. Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types. Nature Genetics, 50(4):621–629, 2018. URL: https://pmc.ncbi.nlm.nih.gov/articles/PMC5896795/. ↩↩

  2. UK Biobank Whole-Genome Sequencing Consortium and others. Whole-genome sequencing of 490,640 UK Biobank participants. Nature, 645(8081):692, 2025. URL: https://www.nature.com/articles/s41586-025-09272-9. ↩

  3. GWAS Catalog - Study: GCST90473326. [Accessed 25-05-2026]. URL: https://www.ebi.ac.uk/gwas/studies/GCST90473326. ↩