SZGR2

Summary ?

GeneID	1406
Symbol	CRX
Synonyms	CORD2\|CRD\|LCA7\|OTX3
Description	cone-rod homeobox
Reference	MIM:602225\|HGNC:HGNC:2383\|Ensembl:ENSG00000105392\|HPRD:03748\|Vega:OTTHUMG00000170610
Gene type	protein-coding
Map location	19q13.3
Pascal p-value	0.096
Fetal beta	0.189
DMG	1 (# studies)
eGene	Myers' cis & trans

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
DMG:Wockner_2014	Genome-wide DNA methylation analysis	This dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24).	1

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg19762747	19	48325089	CRX	3.29E-4	-0.534	0.041	DMG:Wockner_2014

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs734994	chr1	30796504	CRX	1406	0.18	trans
rs17108402	chr1	53846252	CRX	1406	0.11	trans
rs17091285	chr1	71957915	CRX	1406	0.01	trans
rs11162132	chr1	76833107	CRX	1406	0.06	trans
rs6688662	chr1	76842132	CRX	1406	0.01	trans
rs12096089	chr1	112349065	CRX	1406	0.11	trans
rs1891733	chr1	164807829	CRX	1406	0	trans
rs12118136	chr1	164812580	CRX	1406	0	trans
rs17392895	chr1	164814782	CRX	1406	0	trans
rs512189	chr1	182632586	CRX	1406	0	trans
rs16849110	chr1	201567374	CRX	1406	0.01	trans
rs6666913	chr1	237092144	CRX	1406	3.167E-8	trans
rs16865199	chr2	6621910	CRX	1406	0.02	trans
rs16865228	chr2	6629622	CRX	1406	0.01	trans
rs16865230	chr2	6630187	CRX	1406	0.01	trans
rs11691188	chr2	6631799	CRX	1406	0.01	trans
rs10209546	chr2	53408320	CRX	1406	3.909E-4	trans
rs3755119	chr2	53957339	CRX	1406	0.01	trans
rs2303604	chr2	71828422	CRX	1406	0.11	trans
rs13401483	chr2	84219167	CRX	1406	0.01	trans
rs260675	chr2	109600118	CRX	1406	5.175E-4	trans
rs7596511	chr2	120010898	CRX	1406	0.09	trans
rs7574824	chr2	130696073	CRX	1406	0.04	trans
rs13403353	chr2	144067716	CRX	1406	0.06	trans
rs10176716	chr2	151596595	CRX	1406	0.03	trans
rs10195263	chr2	151725791	CRX	1406	0.17	trans
rs12694629	chr2	157312146	CRX	1406	0.01	trans
rs10515928	chr2	160074898	CRX	1406	0.02	trans
rs9287785	chr2	160075008	CRX	1406	0.02	trans
rs10490004	chr2	160076139	CRX	1406	0.02	trans
rs11903200	chr2	160076308	CRX	1406	0.02	trans
rs2241023	chr2	160081335	CRX	1406	0.02	trans
rs10490003	chr2	160082889	CRX	1406	0.02	trans
rs3815475	chr2	160114314	CRX	1406	0.15	trans
rs10189317	chr2	160123106	CRX	1406	0.02	trans
rs8179587	chr2	160187588	CRX	1406	0.03	trans
rs3755433	chr2	160269002	CRX	1406	0.18	trans
rs7589313	chr2	174771910	CRX	1406	0.13	trans
rs4453654	chr2	189185130	CRX	1406	0.05	trans
rs7587596	chr2	189361401	CRX	1406	0.11	trans
rs13413644	chr2	189475948	CRX	1406	0.02	trans
rs13397537	chr2	189737534	CRX	1406	0.13	trans
rs17049214	chr3	8545477	CRX	1406	0.13	trans
rs9855575	chr3	15514062	CRX	1406	0.17	trans
rs7646474	chr3	46011068	CRX	1406	0.04	trans
rs2109558	chr3	52501615	CRX	1406	0.18	trans
rs11923953	chr3	64365756	CRX	1406	0	trans
rs17342237	chr3	65072365	CRX	1406	0.11	trans
snp_a-1952572		0	CRX	1406	0.12	trans
rs6548978	chr3	68139529	CRX	1406	0	trans
rs17011179	chr3	73501887	CRX	1406	0.07	trans
rs7609917	chr3	76094301	CRX	1406	5.525E-8	trans
rs2324466	chr3	76100753	CRX	1406	8.455E-12	trans
rs17013713	chr3	76105150	CRX	1406	6.884E-13	trans
rs17013722	chr3	76107656	CRX	1406	8.455E-12	trans
rs17013724	chr3	76107684	CRX	1406	8.455E-12	trans
rs13326424		0	CRX	1406	0.15	trans
rs11127757	chr3	82043061	CRX	1406	0.02	trans
rs7619146	chr3	82098527	CRX	1406	0.03	trans
rs2178316	chr3	82187874	CRX	1406	0.04	trans
rs301930	chr3	97348309	CRX	1406	0.09	trans
rs2705554	chr3	112273545	CRX	1406	0.07	trans
rs7644174	chr3	112722325	CRX	1406	0.06	trans
rs4312656	chr3	115157721	CRX	1406	0	trans
rs9819488	chr3	132544205	CRX	1406	0.14	trans
rs16859029	chr3	146759514	CRX	1406	0.15	trans
rs16854658	chr3	169674405	CRX	1406	0.15	trans
rs16854694	chr3	169701831	CRX	1406	0.14	trans
rs179852	chr3	172328734	CRX	1406	0.01	trans
rs16831155	chr3	173574763	CRX	1406	0.01	trans
rs9882442	chr3	173644484	CRX	1406	0.11	trans
rs16991886	chr4	36048970	CRX	1406	0.04	trans
rs12646252		0	CRX	1406	0.05	trans
rs17148160	chr4	70974564	CRX	1406	0.13	trans
rs1389042	chr4	82973241	CRX	1406	0.03	trans
rs11734196	chr4	102796071	CRX	1406	6.771E-4	trans
rs10212684	chr4	102822506	CRX	1406	4.857E-4	trans
rs7656183	chr4	114600890	CRX	1406	0.07	trans
rs17007390	chr4	124705927	CRX	1406	0	trans
rs681601	chr4	137983010	CRX	1406	0.17	trans
rs6858531	chr4	141053847	CRX	1406	0.05	trans
rs11937178	chr4	148847598	CRX	1406	0	trans
rs11934409	chr4	148848884	CRX	1406	0	trans
rs2605050	chr4	180362144	CRX	1406	0	trans
rs4301163	chr4	187861271	CRX	1406	0.04	trans
rs9986296	chr5	3199318	CRX	1406	1.185E-6	trans
rs2455248	chr5	36478729	CRX	1406	0.14	trans
rs2648734	chr5	52068572	CRX	1406	0.01	trans
rs12658469	chr5	72670113	CRX	1406	0.14	trans
rs17502163	chr5	120026331	CRX	1406	0.1	trans
rs920385	chr5	124490714	CRX	1406	0	trans
rs2895773	chr5	148114635	CRX	1406	0.02	trans
rs10059267	chr5	168676624	CRX	1406	0.01	trans
rs10078402	chr5	168678851	CRX	1406	0.01	trans
rs17077791	chr5	176616523	CRX	1406	0.13	trans
rs2281351	chr6	187343	CRX	1406	0.01	trans
rs9396617	chr6	15924214	CRX	1406	0.07	trans
rs199055	chr6	23490116	CRX	1406	0.15	trans
rs726836	chr6	25843925	CRX	1406	0.14	trans
rs7740062	chr6	27705597	CRX	1406	0.07	trans
rs200470	chr6	27762186	CRX	1406	0.01	trans
rs201005	chr6	27804159	CRX	1406	0.03	trans
rs200955	chr6	27839311	CRX	1406	0.07	trans
rs200959	chr6	27842046	CRX	1406	0.07	trans
rs839777	chr6	27909656	CRX	1406	0.04	trans
rs149898	chr6	27958071	CRX	1406	0.04	trans
rs156741	chr6	27962383	CRX	1406	0.1	trans
rs156742	chr6	27963191	CRX	1406	0.04	trans
rs175955	chr6	28059733	CRX	1406	0.04	trans
rs1225593	chr6	28150518	CRX	1406	0.04	trans
rs195749	chr6	37253745	CRX	1406	1.892E-4	trans
rs4435942	chr6	37694937	CRX	1406	0.09	trans
rs16896683	chr6	43687846	CRX	1406	0	trans
rs16875134	chr6	85489519	CRX	1406	0.01	trans
rs16875178	chr6	85516099	CRX	1406	0.02	trans
rs17073406	chr6	144447390	CRX	1406	0.01	trans
rs7762250	chr6	144475063	CRX	1406	0.02	trans
rs11961018	chr6	145288413	CRX	1406	0.01	trans
rs9497157	chr6	145288521	CRX	1406	0.01	trans
rs9497158	chr6	145288571	CRX	1406	0.11	trans
rs3735131	chr7	2962292	CRX	1406	0.15	trans
rs1005524	chr7	20596813	CRX	1406	0.03	trans
rs17145334	chr7	21808409	CRX	1406	0.01	trans
rs895578	chr7	35410694	CRX	1406	0.11	trans
rs2013491	chr7	91946015	CRX	1406	0.06	trans
rs992435	chr7	97050802	CRX	1406	7.536E-4	trans
rs17159863	chr7	112311225	CRX	1406	0.15	trans
rs12532261	chr7	132264028	CRX	1406	0.04	trans
rs12533690	chr7	132265977	CRX	1406	0.01	trans
rs8190856	chr8	18079123	CRX	1406	0.1	trans
rs16920368	chr8	55392852	CRX	1406	2.314E-4	trans
rs10086973	chr8	61105602	CRX	1406	0.15	trans
rs16927318	chr8	62365911	CRX	1406	1.356E-6	trans
rs348150	chr8	73371619	CRX	1406	0	trans
rs16938220	chr8	73377940	CRX	1406	0	trans
rs7843769	chr8	83608406	CRX	1406	0.01	trans
rs7830923	chr8	83608478	CRX	1406	0.01	trans
rs16910790	chr8	83621808	CRX	1406	0.01	trans
rs16910793	chr8	83621841	CRX	1406	0.01	trans
rs16910802	chr8	83622265	CRX	1406	0.01	trans
rs16910804	chr8	83622540	CRX	1406	0.02	trans
rs1969215	chr8	108644706	CRX	1406	0.1	trans
rs1448721	chr8	136924784	CRX	1406	0.09	trans
rs16908622	chr8	139231604	CRX	1406	0.01	trans
rs4545144	chr8	139689307	CRX	1406	0.01	trans
rs10815658	chr9	7709422	CRX	1406	0.01	trans
rs16910463	chr9	26444298	CRX	1406	0.06	trans
rs180038	chr9	101514415	CRX	1406	0.01	trans
rs4742740	chr9	101524552	CRX	1406	0.01	trans
rs4743277	chr9	101557528	CRX	1406	0.02	trans
rs10119434	chr9	110944789	CRX	1406	0	trans
rs10983187	chr9	119238934	CRX	1406	0	trans
rs7870892	chr9	132533165	CRX	1406	0.2	trans
rs11251091	chr10	2249852	CRX	1406	0.05	trans
rs17274849	chr10	2738293	CRX	1406	0.04	trans
rs11253047	chr10	5259202	CRX	1406	0.12	trans
rs11007809	chr10	30209705	CRX	1406	0.07	trans
rs11193467	chr10	109217296	CRX	1406	0.07	trans
rs7920992	chr10	130402940	CRX	1406	0.06	trans
rs17233214	chr11	21367388	CRX	1406	0.16	trans
rs16911034	chr11	23302320	CRX	1406	0.05	trans
rs10734372	chr11	26090747	CRX	1406	0.1	trans
rs3802783	chr11	27150261	CRX	1406	0.13	trans
rs12224887	chr11	37400374	CRX	1406	0.03	trans
rs721238	chr11	41679262	CRX	1406	0.14	trans
rs1002405	chr11	85572958	CRX	1406	0	trans
rs17148600	chr11	85628826	CRX	1406	0.06	trans
rs956959	chr11	124400687	CRX	1406	0.12	trans
rs11569358	chr12	6553503	CRX	1406	0.04	trans
rs7311343	chr12	21228780	CRX	1406	0.01	trans
rs11177887	chr12	41093631	CRX	1406	0.03	trans
rs2069410	chr12	56364644	CRX	1406	4.634E-13	trans
rs17120736	chr12	58785277	CRX	1406	0.08	trans
rs11115597	chr12	83509142	CRX	1406	0	trans
rs10746278	chr12	83789575	CRX	1406	0.01	trans
rs7979024	chr12	84506011	CRX	1406	0.01	trans
rs11105124	chr12	89375908	CRX	1406	0.01	trans
rs17837122	chr12	92660211	CRX	1406	0.01	trans
rs17021407	chr12	94013807	CRX	1406	0	trans
rs17031683	chr12	102005385	CRX	1406	0.05	trans
rs825045	chr12	102045030	CRX	1406	0.02	trans
rs6539020	chr12	102308189	CRX	1406	0.11	trans
rs4770243	chr13	22662276	CRX	1406	0.03	trans
rs17078563	chr13	23864835	CRX	1406	0.03	trans
rs9670212	chr13	29070572	CRX	1406	7.367E-4	trans
rs17834315	chr13	37991091	CRX	1406	4.518E-8	trans
rs17055627	chr13	38019666	CRX	1406	0.05	trans
rs17072833	chr13	49914392	CRX	1406	0.01	trans
rs575555	chr13	52437620	CRX	1406	0.06	trans
rs11841288	chr13	60215833	CRX	1406	0.01	trans
rs987035	chr13	106274330	CRX	1406	0.02	trans
rs16967008	chr13	106287437	CRX	1406	0.03	trans
rs16975617	chr13	110867407	CRX	1406	0.01	trans
rs17110779	chr14	26599617	CRX	1406	0.06	trans
rs17113537	chr14	43290583	CRX	1406	0.1	trans
rs10498433	chr14	52289530	CRX	1406	0.01	trans
rs17091014	chr14	56562713	CRX	1406	0	trans
rs10483833	chr14	71165243	CRX	1406	0.05	trans
rs1743505	chr14	96143407	CRX	1406	0	trans
rs16939821	chr15	58449860	CRX	1406	0.01	trans
rs16946329	chr15	63324362	CRX	1406	0.01	trans
rs16946913	chr15	63653889	CRX	1406	0	trans
rs7174517	chr15	87256320	CRX	1406	0.05	trans
rs17694187	chr15	91881259	CRX	1406	0.01	trans
rs920567	chr15	98248480	CRX	1406	0.07	trans
rs6598553	chr15	99339208	CRX	1406	0.05	trans
rs962253	chr15	99339832	CRX	1406	0.1	trans
rs2684763	chr15	99365485	CRX	1406	0.1	trans
rs17634236	chr16	5067148	CRX	1406	0.06	trans
rs4786811	chr16	6132786	CRX	1406	0.09	trans
rs17142983	chr16	7294508	CRX	1406	1.584E-4	trans
rs7196563	chr16	7333407	CRX	1406	0.01	trans
rs7191914	chr16	7333464	CRX	1406	0	trans
rs11865410	chr16	7333565	CRX	1406	0	trans
rs8056710	chr16	7447629	CRX	1406	0	trans
rs16972025	chr16	19461881	CRX	1406	0.06	trans
rs12596831	chr16	23385256	CRX	1406	0.07	trans
snp_a-4250222		0	CRX	1406	0.14	trans
rs7195151	chr16	61082370	CRX	1406	0.02	trans
rs6499075	chr16	66387395	CRX	1406	0.14	trans
rs17666993	chr16	72146665	CRX	1406	0.14	trans
rs17667053	chr16	72147430	CRX	1406	0.18	trans
rs7192551	chr16	74750141	CRX	1406	0.08	trans
rs8051077	chr16	75036432	CRX	1406	0.14	trans
rs519507	chr16	88963599	CRX	1406	0.12	trans
rs1391765	chr17	8297465	CRX	1406	0.03	trans
rs17798004	chr18	70665382	CRX	1406	0	trans
rs17736134	chr18	70665805	CRX	1406	1.007E-4	trans
rs2469060	chr18	70673106	CRX	1406	1.007E-4	trans
rs2469009	chr18	70713334	CRX	1406	1.696E-4	trans
rs9962412	chr18	73427437	CRX	1406	0.13	trans
rs9965745	chr18	73429162	CRX	1406	0.09	trans
rs1943200	chr18	73462540	CRX	1406	0.04	trans
rs8110995	chr19	40863841	CRX	1406	0.19	trans
rs2288529	chr19	55665688	CRX	1406	0.09	trans
rs12461195	chr19	55688575	CRX	1406	0.08	trans
rs7344216		0	CRX	1406	0.08	trans
rs4814288	chr20	14186386	CRX	1406	0.08	trans
rs6514759		0	CRX	1406	0	trans
rs409642	chr20	54250273	CRX	1406	2.491E-4	trans
snp_a-2019049		0	CRX	1406	0.07	trans
rs7275460	chr21	41447057	CRX	1406	0.01	trans
rs2837496	chr21	41576838	CRX	1406	0.07	trans
rs2837506	chr21	41581683	CRX	1406	0.07	trans
rs16993271	chr22	34307850	CRX	1406	0.01	trans
rs17003586	chr22	43667457	CRX	1406	0	trans
rs2269667	chr22	43699291	CRX	1406	0	trans
rs6007794	chr22	46685016	CRX	1406	0.01	trans
rs7290732	chr22	46691902	CRX	1406	0	trans
rs5960312	chrX	54576348	CRX	1406	0.13	trans
rs11091332		0	CRX	1406	0.05	trans
rs5961111	chrX	54659538	CRX	1406	0.03	trans
rs5920627	chrX	97385064	CRX	1406	0.01	trans
snp_a-2027825		0	CRX	1406	0.01	trans

Section II. Transcriptome annotation

General gene expression (GTEx)

Gene expression during devlopment (BrainCloud)

Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.

Gene expression of temporal and spatial changes (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
TMEM205	0.66	0.67
PGP	0.65	0.70
UROD	0.65	0.69
GNPTG	0.64	0.63
SNRPN	0.64	0.69
MRPL2	0.63	0.65
THOP1	0.63	0.69
NR1H2	0.63	0.65
ACOT8	0.63	0.69
DHRS11	0.63	0.67

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
THOC2	-0.43	-0.39
AC005035.1	-0.42	-0.39
ZNF326	-0.41	-0.41
CCDC112	-0.40	-0.24
HMGB1	-0.40	-0.38
AC114546.1	-0.40	-0.32
FNBP1L	-0.39	-0.26
PHF14	-0.39	-0.35
AL953897.2	-0.39	-0.30
AC005921.3	-0.39	-0.49

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
RIZ ERYTHROID DIFFERENTIATION APOBEC2	27	19	All SZGR 2.0 genes in this pathway
NGUYEN NOTCH1 TARGETS DN	86	67	All SZGR 2.0 genes in this pathway
NIKOLSKY OVERCONNECTED IN BREAST CANCER	22	19	All SZGR 2.0 genes in this pathway
SENGUPTA EBNA1 ANTICORRELATED	173	85	All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS UP	504	321	All SZGR 2.0 genes in this pathway
PURBEY TARGETS OF CTBP1 AND SATB1 UP	87	52	All SZGR 2.0 genes in this pathway
KUMAR PATHOGEN LOAD BY MACROPHAGES	275	155	All SZGR 2.0 genes in this pathway
KUMAR AUTOPHAGY NETWORK	71	46	All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 2ND EGF PULSE ONLY	1725	838	All SZGR 2.0 genes in this pathway

Gene Page: CRX