Dataset Open Access
Genetic variation influencing DNA methylation provides new insights into the molecular pathways regulating genomic function - Selected Supplementary Tables
Johann S Hawe; Rory Wilson; Katharina Schmid; Li Zhou; Lakshmi Lakshmanan; Benjamin C Lehne; William R Scott; Matthias Wielscher; Yik Weng Yew; Clemens Baumbach; Dominic P Lee; Eirini Marouli; Manon Bernard; Liliane Pfeiffer; Pamela Matías-García; Matias I Autio; Stephane Bourgeois; Christian Herder; Ville Karhunen; Thomas Meitinger; Holger Prokisch; Wolfgang Rathmann; Michael Roden; Sylvain Sebert; Jean Shin; Konstantin Strauch; Weihua Zhang; Wilson LW Tan; Stefanie M. Hauck; Juliane Merl-Pham; Harald Grallert; Eudes GV Barbosa; MuTHER Consortium; Thomas Illig; Annette Peters; Tomas Paus; Zdenka Pausova; Panos Deloukas; Roger SY Foo; Marjo-Riitta Jarvelin; Jaspal S Kooner; Marie Loh; Matthias Heinig; Christian Gieger; Melanie Waldenberger; John C Chambers
Selected Supplementary Tables - ST5, 7, 8 and 9
Supplementary Table 5. Cosmopolitan results. Cosmopolitan SNP-CpG associations identified through genome-wide association amongst Europeans and South Asians.
Supplementary Table 7. Cross-tissue replication. Results for further testing of the 11,165,559 cosmopolitan SNP-CpG associations identified (by genome-wide association in blood), in 4 isolated white cell subsets (CD4+ lymphocytes, CD8+ lymphocytes, monocytes and neutrophils), in adipocytes isolated from subcutaneous adipose tissue or visceral adipose tissue, and in whole adipose tissue.
Supplementary Table 8. Conditional analysis. Results of conditional analysis to identify SNPs independently associated with each of the ~360K CpG sites tested.
Supplementary Table 9. Sentinel SNPs and CpGs. Results of R2 pruning and locus merging to identify discrete genetic and methylation loci that are associated, and their respective sentinel SNPs and sentinel CpG sites.
Other files (e.g. annotation files and 'intermediate' processing files) referenced in our code are also provided.
| Name | Size | |
|---|---|---|
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allele_frequencies_kora.rds
md5:705a6d1dc8a4227fdc38ba7683a22b94 |
169.6 MB | Download |
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allele_frequencies_kora_epic.rds
md5:549af5ec3c0e4a3ce441acc43b358471 |
164.3 MB | Download |
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allele_frequencies_lolipop.rds
md5:bf0822fc29ad4449d1c5fbc4a6e4e432 |
193.6 MB | Download |
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cis-cosmopairs_combined_151216.RData
md5:67c66ff41021890fc15c5a88ff349afc |
1.6 GB | Download |
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cosmo-cpgs.txt
md5:1c755d12a130dd33e37d2d0ce70666fb |
777.8 kB | Download |
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cosmo-snps.txt
md5:31bb3f44201745bb5db0d1a50449226c |
28.5 MB | Download |
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cosmopairs_combined_151216.RData
md5:c53d28eb4d301c32503c3ee3f1f0d019 |
1.8 GB | Download |
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cpg_annotation_both_arrays.tsv
md5:66a71859a8d795cb09eca7648068ceab |
97.3 MB | Download |
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cpg_annotation_kora.rds
md5:2253bd10d570b88e765e71dcb4a058aa |
9.9 MB | Download |
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cpg_annotation_kora_epic.rds
md5:0f526c73aaa634b40710ab7916f8fdd6 |
24.2 MB | Download |
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cpg_annotation_lolipop.rds
md5:f77c02a751cc82333f387564eed37ee4 |
9.7 MB | Download |
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cpg_base_annotation_kora_epic.rds
md5:d7bd65c5df1cf25d67b7cb50b4de1c03 |
149.8 MB | Download |
|
cpgs2include.RData
md5:73e0c2ec13cf6b7bb780a9cd01308848 |
4.4 MB | Download |
|
enrichment_epigenetic_state_weighted_annotation_all_cpgs.RData
md5:dba6e001257beaddc7f1cfcc4b043e7e |
6.7 MB | Download |
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epigenetic_state_annotation_weighted_snps.rds
md5:400f24885c6cf8b6074c826a42a764ed |
64.0 MB | Download |
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hic_merged_gte3.txt
md5:9e13cfce22521817b3bbd4bfd0125e6f |
9.6 MB | Download |
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measured-cpgs.txt
md5:6c93fcdffa31509fe042b484264cfd9d |
5.3 MB | Download |
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PCHiC_peak_matrix_cutoff5.tsv
md5:3d99b90b54296c08e4f128055562e1bc |
250.6 MB | Download |
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sentinel_pairs_r02_110417.RData
md5:f4ab21c68a191ba296ee6fe6fd94916c |
12.0 MB | Download |
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sentinels_with_trans_epic.tsv
md5:81902b57cda59acd0d18420bcec2142e |
608.4 kB | Download |
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snps2include.RData
md5:f5dfbbd102d816c569b9d241bce35fa1 |
109.9 MB | Download |
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st5_cosmopolitan_meQTL_results.txt
md5:e771ee1a0404ab699dffac465aba64ee |
3.2 GB | Download |
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st7_cross_tissue_replication_of_meQTL.txt
md5:6051c1ac0bc1d5e5c9a882ad20ccecfb |
5.4 GB | Download |
|
st8_conditional_analysis.txt
md5:ab22c85f61e087dc939657bbb379e08f |
17.8 MB | Download |
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TADs_merged.bed
md5:1eede6d786c10ef9fa924e068eca2b6d |
875.1 kB | Download |
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tfbs_granges.RData
md5:992896ac6ee031060ac66177e9896aa1 |
355.1 MB | Download |
|
transpairs_r02_110117_converted_1MB.txt
md5:d0e38b870227c314fa91eacf03dc06cd |
784.9 kB | Download |
| All versions | This version | |
|---|---|---|
| Views | 1,115 | 1,058 |
| Downloads | 3,088 | 3,007 |
| Data volume | 6.7 TB | 6.7 TB |
| Unique views | 964 | 935 |
| Unique downloads | 555 | 550 |
- Publication date:
- October 1, 2021
- DOI:
-
- Published in:
- Nature Genetics:.
- License (for files):
- Creative Commons Attribution 4.0 International