Last updated: 2019-02-18
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Knit directory: rss-gsea/
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| html | f5fd9cd | Xiang Zhu | 2018-10-05 | Build site. |
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Prioritization results are summarized by the following table.
P1: posterior probability that at least one SNP within 100 kb of the transcribed region of a given pathway gene (defined by Chr., Start and End columns) has non-zero effect on the trait of interest;
H-distance: the physical distance, in base pair, between a given pathway gene and its nearest GWAS hit;
Nearest hit: the nearest GWAS hit to a given pathway gene, reported in the corresponding GWAS publication.
The “Inf” values in column H-distance indicate that there is no GWAS hit on the same chromosome as the pathway gene.
Differences between Baseline P1 and Enrichment P1 reflect the influence of enrichment on genetic associations, which can help identify putatively trait-associated genes.
| Gene | Chr. | Start | End | Baseline P1 | Enrichment P1 | H-distance | Nearest hit |
|---|---|---|---|---|---|---|---|
| MTTP | 4 | 100485240 | 100545154 | 0.1415537 | 0.9923219 | Inf | none |
| LIPC | 15 | 58724175 | 58861073 | 0.0163921 | 0.9589340 | Inf | none |
| APOA2 | 1 | 161192083 | 161193418 | 0.0033433 | 0.5842822 | 51373777 | rs629301 |
| P4HB | 17 | 79801034 | 79818544 | 0.0000308 | 0.0081494 | 34409230 | rs7225700 |
| SAR1B | 5 | 133936839 | 133968533 | 0.0027561 | 0.4542058 | 22421764 | rs6882076 |
| LPL | 8 | 19796582 | 19824770 | 0.0066880 | 0.7603627 | 10611436 | rs2126259 |
| HSPG2 | 1 | 22148737 | 22263750 | 0.0052681 | 0.6798969 | 3511983 | rs12027135 |
| SDC1 | 2 | 20400558 | 20425194 | 0.0231079 | 0.9153864 | 838706 | rs1367117 |
| LDLRAP1 | 1 | 25870076 | 25895377 | 0.0419188 | 0.8828886 | 94343 | rs12027135 |
| APOA1 | 11 | 116706469 | 116708338 | 0.7034787 | 0.9995003 | 57552 | rs964184 |
| APOC3 | 11 | 116700624 | 116703787 | 0.9998878 | 1.0000000 | 51707 | rs964184 |
| APOA4 | 11 | 116691418 | 116694011 | 0.9998877 | 1.0000000 | 42501 | rs964184 |
| APOC2 | 19 | 45449239 | 45452822 | 1.0000000 | 1.0000000 | 26293 | rs4420638 |
| APOA5 | 11 | 116660086 | 116663136 | 1.0000000 | 1.0000000 | 11169 | rs964184 |
| APOE | 19 | 45409039 | 45412650 | 1.0000000 | 1.0000000 | 10296 | rs4420638 |
| APOB | 2 | 21224301 | 21266945 | 1.0000000 | 1.0000000 | 0 | rs1367117 |
| LDLR | 19 | 11200038 | 11244506 | 1.0000000 | 1.0000000 | 0 | rs6511720 |
─ Session info ──────────────────────────────────────────────────────────
setting value
version R version 3.5.2 (2018-12-20)
os macOS Mojave 10.14.3
system x86_64, darwin15.6.0
ui X11
language (EN)
collate en_US.UTF-8
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tz America/Los_Angeles
date 2019-02-18
─ Packages ──────────────────────────────────────────────────────────────
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[1] /Library/Frameworks/R.framework/Versions/3.5/Resources/library