Last updated: 2018-10-05

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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
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 information

Session info -------------------------------------------------------------
 setting  value                       
 version  R version 3.5.1 (2018-07-02)
 system   x86_64, darwin15.6.0        
 ui       X11                         
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       America/Los_Angeles         
 date     2018-10-05                  
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