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
MMP13 11 102813721 102826463 0.4475670 0.9286314 15786772 rs632124
FGFR1 8 38268656 38326352 0.6693504 0.9673366 10740661 rs568610
PLAT 8 42032236 42065194 0.0000000 0.0000000 7348586 rs6988484
PLAU 10 75670862 75677259 0.3871728 0.9962272 5251534 rs1815314
BMPR1A 10 88516396 88684945 0.8754327 0.9988295 4352464 rs2631676
PTH1R 3 46919236 46945289 0.9388569 1.0000000 4126424 rs13088462
GLI3 7 42000547 42276618 0.9981750 0.9999999 3890474 rs6974574
MMP9 20 44637547 44645200 0.5586571 0.9586277 3127064 rs17450430
CST5 20 23856572 23860380 0.0000000 0.0000000 2676313 rs6137287
DDR2 1 162602228 162750255 0.8775772 0.9991192 2202642 rs6688100
PRKACA 19 14202500 14228559 0.9226463 0.9884570 2015889 rs7259684
CALM1 14 90863327 90874619 0.4427005 0.9178998 1552729 rs7154721
COL2A1 12 48366748 48398285 0.7436775 0.9950522 1539725 rs10880969
HDAC4 2 239969864 240322643 0.9825446 0.9999719 1495884 rs4344931
AKT1 14 105235686 105262080 0.9936763 0.9995562 1356912 rs12882130
ADAMTS5 21 28290231 28339439 0.9315165 0.9994099 1081296 rs2829941
CALM3 19 47104512 47114039 0.4173754 0.9094855 1074770 rs2059877
ADAMTS1 21 28208606 28217728 0.9639698 0.9999300 999671 rs2829941
BMP7 20 55743809 55841707 0.8105462 0.9979101 901431 rs1326023
SOX6 11 15987995 16497935 0.9373336 0.9997789 853748 rs757081
HMGCS1 5 43289493 43313595 0.0000000 0.0000000 852577 rs17574650
VEGFA 6 43737946 43754224 0.9771801 0.9998988 785537 rs1040941
ADAMTS4 1 161159538 161168845 0.3619263 0.8765674 759952 rs6688100
CTSV 9 99791959 99801925 0.3825341 0.9998142 590374 rs7870753
CAB39 2 231577557 231685790 0.7829306 0.9989698 582522 rs6733349
ENPP1 6 132129156 132216295 0.9634009 0.9997195 514077 rs7743622
MGP 12 15034115 15038853 0.9907099 0.9990710 513414 rs12228415
CHST11 12 104850692 105155792 0.9939521 0.9999999 505856 rs2164747
FRZB 2 183698002 183731498 0.0000000 0.0000000 478901 rs833152
CALM2 2 47387221 47403740 0.9678946 0.9999988 465936 rs12474201
STAT5B 17 40351195 40428424 0.5032175 0.9929653 424417 rs9766
THRA 17 38218446 38250120 0.9467918 0.9999999 349110 rs584828
NKX3-2 4 13542454 13546114 0.9586002 0.9986497 348363 rs4834927
SCIN 7 12610203 12693228 0.9726120 0.9999799 333681 rs929637
IFT88 13 21141208 21265576 0.0000000 0.0000000 304670 rs1199734
KIF3A 5 132028323 132073265 0.9963992 0.9999103 286095 rs6596075
SPP1 4 88896802 88904563 0.9775060 0.9995442 266771 rs6813055
ALPL 1 21835858 21904905 0.9982074 0.9999996 252547 rs212524
PTH 11 13513601 13517567 0.4115143 0.8479092 235640 rs10766065
SOX9 17 70117161 70122561 0.9999354 0.9999985 193806 rs10083886
IGF1 12 102789645 102874378 0.9999071 1.0000000 188219 rs833706
RUNX3 1 25226002 25291501 0.9999999 1.0000000 181891 rs4601530
TIMP3 22 33196802 33259028 0.9889742 1.0000000 139943 rs2413143
MEF2C 5 88014058 88199922 1.0000000 1.0000000 127860 rs6894139
FGFR3 4 1795039 1810599 0.9768451 1.0000000 101108 rs3958122
CDKN1C 11 2904448 2906995 0.9999996 1.0000000 93717 rs2237886
TGFB1 19 41836812 41859831 1.0000000 1.0000000 62521 rs4803468
SLC38A2 12 46751971 46766645 0.9999770 0.9999999 60378 rs10880969
RUNX2 6 45296054 45518819 1.0000000 1.0000000 51639 rs10948222
FGF2 4 123747863 123819390 0.9998332 0.9999999 16266 rs12513181
GH1 17 61994563 61996198 1.0000000 1.0000000 11300 rs2070776
IHH 2 219919142 219925238 0.9999998 1.0000000 10773 rs12470505
COL10A1 6 116440085 116447296 0.7968700 1.0000000 4146 rs2145357
STAT1 2 191833762 191878976 0.9995340 1.0000000 1100 rs12693589
IGF2 11 2150347 2170833 1.0000000 1.0000000 768 rs4320932
ACAN 15 89346674 89418585 1.0000000 1.0000000 0 rs11633371-rs16942341-rs2280470-rs3817428
BMP6 6 7727011 7881961 1.0000000 1.0000000 0 rs9328445-rs9405356
IGF1R 15 99192761 99507759 1.0000000 1.0000000 0 rs2871865
PTCH1 9 98205264 98279247 1.0000000 1.0000000 0 rs4448343
TGFB2 1 218518676 218617961 1.0000000 1.0000000 0 rs991967
SOX5 12 23685231 24715380 1.0000000 1.0000000 0 rs11047239
SERPINH1 11 75273101 75283849 1.0000000 1.0000000 0 rs606452
PTHLH 12 28111017 28124916 0.9999768 1.0000000 0 rs10492364
FGF18 5 170846667 170884630 1.0000000 1.0000000 0 rs4620037
GHR 5 42423877 42721980 0.0000000 0.0000000 0 rs17574650 

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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