Prioritization results of high-density lipoprotein & Lipid digestion, mobilization and transport

Last updated: 2018-10-06

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Rmd	8c88dc6	Xiang Zhu	2018-10-06	wflow_publish(“analysis/hdl2010_path3093.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
CUBN	10	16865965	17171816	0.2406825	0.9994505	Inf	none
ABCG1	21	43619799	43717354	0.0142198	0.8869822	Inf	none
MGLL	3	127407909	127542051	0.0107509	0.7681549	Inf	none
ABHD5	3	43732375	43764217	0.0075172	0.6293175	Inf	none
PNLIPRP1	10	118350490	118368686	0.0046938	0.5561547	Inf	none
AMN	14	103388993	103397179	0.0069808	0.5555097	Inf	none
PNLIPRP2	10	118380465	118404654	0.0045243	0.5475144	Inf	none
PNLIP	10	118305428	118327367	0.0046319	0.5423388	Inf	none
FABP6	5	159614374	159665729	0.0048792	0.5549469	106316349	rs6450176
SAR1B	5	133936839	133968533	0.0016990	0.2720344	80638814	rs6450176
FABP1	2	88422501	88427650	0.0055362	0.5770968	67197220	rs1042034
PRKACB	1	84543745	84704181	0.0096699	0.7435945	44515565	rs4660293
PRKACG	9	71627445	71629039	0.0059514	0.6143190	36035262	rs1883025
FABP5	8	82192718	82197012	0.0049761	0.4998743	34402187	rs2293889
FABP9	8	82370618	82373758	0.0194732	0.6549818	34225441	rs2293889
FABP4	8	82390732	82395473	0.0181394	0.6139685	34203726	rs2293889
FABP12	8	82437281	82443550	0.0159355	0.5895221	34155649	rs2293889
ALB	4	74269972	74287129	0.0026427	0.3505016	28901580	rs13107325
NPC1L1	7	44552134	44580914	0.0041557	0.4703797	28401960	rs17145738
CEL	9	135937365	135947248	0.0072240	0.6401437	28273064	rs1883025
PLIN1	15	90207598	90222648	0.0031923	0.4235168	26810731	rs2652834
ABCG8	2	44066103	44105605	0.0065822	0.6574766	22840822	rs1042034
ABCG5	2	44039611	44065958	0.0068908	0.6631670	22814330	rs1042034
APOA2	1	161192083	161193418	0.0083531	0.7145047	20975467	rs1689800
HSPG2	1	22148737	22263750	0.0040563	0.5210218	17764430	rs4660293
FABP2	4	120238405	120243316	0.1152144	0.9849063	17049696	rs13107325
FABP7	6	123100646	123105219	0.0036182	0.4847385	16724447	rs605066
CAV1	7	116164839	116201239	0.0043034	0.5168359	14232145	rs4731702
LDLRAP1	1	25870076	25895377	0.0006044	0.1071723	14132803	rs4660293
A2M	12	9220304	9268558	0.0000000	0.0000000	11205200	rs7134375
FABP3	1	31838100	31845923	0.0062248	0.5271911	8182257	rs4660293
PPP1CB	2	28974614	29025806	0.0075204	0.5365480	7749333	rs1042034
PPP1CA	11	67165652	67169376	0.0031469	0.3983433	5542512	rs174601
P4HB	17	79801034	79818544	0.0000509	0.0095303	3423552	rs4082919
PRKACA	19	14202500	14228559	0.0011522	0.1925645	2855007	rs737337
MTTP	4	100485240	100545154	0.0059346	0.5958281	2643555	rs13107325
LIPE	19	42905666	42931578	0.0012356	0.2054058	2491368	rs4420638
BMP1	8	22022653	22069839	0.0035904	0.4754862	2178431	rs12678919
CLPS	6	35762760	35765102	0.0026278	0.3828265	1209963	rs2814944
PPP1CC	12	111157613	111180783	0.0088115	0.5327792	1157420	rs7134594
APOF	12	56754355	56756583	0.0021271	0.3086031	1087466	rs3741414
SDC1	2	20400558	20425194	0.1054414	0.9591638	800087	rs1042034
LDLR	19	11200038	11244506	0.9646380	0.9999992	102987	rs737337
APOA1	11	116706469	116708338	1.0000000	1.0000000	57552	rs964184
APOC3	11	116700624	116703787	1.0000000	1.0000000	51707	rs964184
LCAT	16	67973787	67978015	0.0025836	1.0000000	45745	rs16942887
APOA4	11	116691418	116694011	1.0000000	1.0000000	42501	rs964184
LIPC	15	58724175	58861073	1.0000000	1.0000000	40809	rs1532085
APOC2	19	45449239	45452822	1.0000000	1.0000000	26293	rs4420638
LPL	8	19796582	19824770	1.0000000	1.0000000	19452	rs12678919
PLTP	20	44527259	44541003	1.0000000	1.0000000	13012	rs6065906
APOA5	11	116660086	116663136	1.0000000	1.0000000	11169	rs964184
APOE	19	45409039	45412650	1.0000000	1.0000000	10296	rs4420638
CETP	16	56995835	57017756	1.0000000	1.0000000	2511	rs3764261
LPA	6	160952515	161087407	0.8566843	0.9999007	2410	rs1084651
SCARB1	12	125262174	125348519	1.0000000	1.0000000	581	rs838880
ABCA1	9	107543283	107690527	1.0000000	1.0000000	0	rs1883025
APOB	2	21224301	21266945	0.9999999	1.0000000	0	rs1042034

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     2018-10-06

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Prioritization results of high-density lipoprotein & Lipid digestion, mobilization and transport

Xiang Zhu

2018-10-05

Table legends

Analysis results

Session information