Prioritization results of adult human height & Endochondral ossification

Last updated: 2019-02-18

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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 3.5.2 (2018-12-20)
 os       macOS Mojave 10.14.3        
 system   x86_64, darwin15.6.0        
 ui       X11                         
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       America/Los_Angeles         
 date     2019-02-18                  

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[1] /Library/Frameworks/R.framework/Versions/3.5/Resources/library

Prioritization results of adult human height & Endochondral ossification

Xiang Zhu

2018-10-05

Table legends

Analysis results