Last updated: 2024-09-16

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Knit directory: rss-gsea/

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Table legends

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.

Analysis results

Gene Chr. Start End Baseline P1 Enrichment P1 H-distance Nearest hit
CASP3 4 185548850 185570629 0.0410473 0.3426184 62149359 rs45475795
CALM3 19 47104512 47114039 0.0238403 0.2599032 36332571 chr19:10771941
CBLB 3 105377109 105587887 0.0996482 0.6010868 30814173 rs9826828
GBP3 1 89472360 89488549 0.0666986 0.3600171 24889019 rs2476601
IKZF1 7 50344378 50472799 0.3269607 0.9120020 22169392 rs67250450
JUN 1 59246463 59249785 0.0158713 0.1871712 20612584 rs12140275
NFATC3 16 68119269 68263162 0.0267481 0.2565569 17755925 rs13330176
CALM1 14 90863327 90874619 0.0245160 0.2633888 14518218 rs2582532
BATF3 1 212859759 212873327 0.0555358 0.4484060 14219271 rs17668708
CALM2 2 47387221 47403740 0.0596491 0.4168546 13721110 rs34695944
E2F1 20 32263292 32274210 0.0061236 0.0766776 12475041 rs4239702
PTGS2 1 186640944 186649559 0.7361085 0.9798033 11990929 rs17668708
ITCH 20 32951062 33099197 0.0280377 0.3150238 11650054 rs4239702
EGR3 8 22545174 22550815 0.0218336 0.2482249 11203294 rs2736337
IFNG 12 68548550 68553521 0.0323326 0.3327044 10440498 rs1633360
NFATC1 18 77155772 77289323 0.0648569 0.5257250 9611726 rs2469434
PTPRK 6 128289924 128841870 0.0960472 0.6357498 9163645 rs17264332
EGR4 2 73518057 73520829 0.0092396 0.1141007 7919757 rs1858037
TBX21 17 45810610 45823485 0.0285532 0.2854522 7778753 chr17:38031857
FOS 14 75745481 75748937 0.0607553 0.5077550 6985340 rs1950897
MAF 16 79627745 79634622 0.0543748 0.4783299 6384465 rs13330176
EGR1 5 137801181 137805004 0.0118330 0.1432342 6371063 rs657075
POU2F1 1 167190066 167396582 0.5717731 0.9830715 5545808 chr1:161644258
NFATC2 20 50007765 50179168 0.0932253 0.6252816 5258514 rs4239702
CXCL8 4 74606223 74609433 0.0271892 0.2808819 4893539 rs10028001
PPARG 3 12329349 12475855 0.2820428 0.9781047 4571177 rs4452313
PTPN1 20 49126891 49201088 0.0382931 0.3567284 4377640 rs4239702
FOSL1 11 65659692 65667997 0.0215682 0.2420795 4064128 rs968567
JUNB 19 12902310 12904125 0.0203174 0.2148365 2130369 chr19:10771941
SLC3A2 11 62623484 62656355 0.0192871 0.2186758 1027920 rs968567
TNF 6 31543350 31546112 0.0000000 0.0000000 882660 rs9268839
FASLG 1 172628185 172636013 0.1598367 0.5288472 713712 rs2105325
IL4 5 132009373 132018368 0.0202753 0.2077011 579255 rs657075
EGR2 10 64571756 64578927 0.0653783 0.5181729 534875 rs6479800
IL5 5 131877136 131879214 0.0224986 0.2322052 447018 rs657075
PRKCQ 10 6469105 6557111 0.9998743 0.9999988 78655 rs947474
DGKA 12 56324946 56347807 0.0116905 0.9744830 47147 rs773125
CDK4 12 58142003 58146164 0.9936727 0.9656595 33951 rs1633360
IL3 5 131396347 131398896 0.0357833 0.3187039 31222 rs657075
IL2 4 123372625 123377650 0.0195263 0.8700974 21841 rs45475795
CSF2 5 131409485 131411859 0.0357269 0.3147562 18259 rs657075
IRF4 6 391739 411443 0.9904927 0.9996726 14712 rs9378815
CTLA4 2 204732511 204738683 1.0000000 1.0000000 236 rs3087243
GATA3 10 8096667 8117164 0.9999977 0.9999999 0 rs3824660
IL2RA 10 6052657 6104333 0.9999829 0.9999910 0 rs706778 

devtools::session_info()
─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.1 (2024-06-14)
 os       macOS Sonoma 14.6.1
 system   aarch64, darwin20
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/Los_Angeles
 date     2024-09-16
 pandoc   3.1.11 @ /Applications/RStudio.app/Contents/Resources/app/quarto/bin/tools/aarch64/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
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 [1] /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library

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