Prioritization results of low-density lipoprotein & Chylomicron-mediated lipid transport

Last updated: 2018-10-05

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File	Version	Author	Date	Message
Rmd	782d641	Xiang Zhu	2018-10-05	wflow_publish(“analysis/ldl2010_path1698.Rmd”)

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

devtools::session_info()

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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Prioritization results of low-density lipoprotein & Chylomicron-mediated lipid transport

Xiang Zhu

2018-10-05

Table legends

Analysis results

Session information