SZGR2

Summary ?

GeneID	10590
Symbol	SCGN
Synonyms	CALBL\|DJ501N12.8\|SECRET\|SEGN\|setagin
Description	secretagogin, EF-hand calcium binding protein
Reference	MIM:609202\|HGNC:HGNC:16941\|Ensembl:ENSG00000079689\|HPRD:10211\|Vega:OTTHUMG00000014409
Gene type	protein-coding
Map location	6p22.3-p22.1
Pascal p-value	2.853E-4
Fetal beta	2.617
eGene	Myers' cis & trans

Gene in Data Sources

Gene set name	Method of gene set	Description
CV:GWASdb	Genome-wide Association Studies	GWASdb records for schizophrenia
CV:PGCnp	Genome-wide Association Study	GWAS
GSMA_I	Genome scan meta-analysis	Psr: 0.033

Section I. Genetics and epigenetics annotation

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs1325252	chr1	34431772	SCGN	10590	0.02	trans
rs17392743	chr1	54764240	SCGN	10590	0.04	trans
rs2297760	chr1	152487033	SCGN	10590	0.15	trans
rs16823145	chr1	184397914	SCGN	10590	0	trans
rs10494876	chr1	206610117	SCGN	10590	0.19	trans
rs12405921	chr1	206695730	SCGN	10590	0.09	trans
rs17187394	chr1	208569242	SCGN	10590	0.06	trans
rs17025528	chr1	216043152	SCGN	10590	0.04	trans
rs17572651	chr1	218943612	SCGN	10590	7.845E-4	trans
rs1934584	chr1	245971711	SCGN	10590	0.05	trans
rs16829545	chr2	151977407	SCGN	10590	1.277E-18	trans
rs7584986	chr2	184111432	SCGN	10590	0.01	trans
rs6741060	chr2	217169088	SCGN	10590	3.826E-5	trans
rs17060743	chr3	59445697	SCGN	10590	0.02	trans
rs9861691	chr3	95639191	SCGN	10590	0.18	trans
rs16853287	chr3	142984245	SCGN	10590	0.18	trans
rs7635430	chr3	180152035	SCGN	10590	0.04	trans
rs16882010	chr4	11453741	SCGN	10590	0.01	trans
rs16878852	chr4	27115684	SCGN	10590	9.517E-7	trans
rs17572822	chr4	27123560	SCGN	10590	0.03	trans
rs2407220	chr4	152193824	SCGN	10590	0.01	trans
rs17028403	chr4	152943625	SCGN	10590	0.06	trans
rs1480540	chr4	171103335	SCGN	10590	0.02	trans
rs3111196	chr5	54402889	SCGN	10590	0.05	trans
rs17762315	chr5	76807576	SCGN	10590	2.248E-7	trans
rs7729096	chr5	76835927	SCGN	10590	0.15	trans
rs443095	chr5	79362549	SCGN	10590	0.1	trans
rs3777174	chr5	95280552	SCGN	10590	0	trans
rs6893788	chr5	95335085	SCGN	10590	0	trans
rs10515234	chr5	95336330	SCGN	10590	0	trans
snp_a-2174305		0	SCGN	10590	0.03	trans
rs17452260	chr5	107607108	SCGN	10590	0	trans
rs887375	chr5	126458125	SCGN	10590	0.15	trans
rs11955168	chr5	131956906	SCGN	10590	0.02	trans
rs13360496		0	SCGN	10590	0.05	trans
rs9340817	chr6	152175105	SCGN	10590	0.18	trans
rs10271456	chr7	25498908	SCGN	10590	0.01	trans
rs3857726	chr7	25503390	SCGN	10590	0.01	trans
rs9969299	chr7	25513687	SCGN	10590	0.01	trans
rs7777722	chr7	26488550	SCGN	10590	0.09	trans
rs10253181	chr7	26563022	SCGN	10590	0.04	trans
rs12706918	chr7	80266147	SCGN	10590	0.02	trans
rs6467660	chr7	136132857	SCGN	10590	0.11	trans
rs17079498	chr8	3018343	SCGN	10590	0.07	trans
rs10505367	chr8	120591463	SCGN	10590	0.02	trans
rs2305128	chr8	120599486	SCGN	10590	0.02	trans
rs6583554	chr8	143022152	SCGN	10590	0.18	trans
rs11139334	chr9	84209393	SCGN	10590	0.01	trans
rs7041027	chr9	126744530	SCGN	10590	0.09	trans
rs10122864	chr9	134991712	SCGN	10590	0.19	trans
rs1009138	chr9	135000607	SCGN	10590	0.17	trans
rs11254048	chr10	6729510	SCGN	10590	0.2	trans
rs17140456	chr10	6730309	SCGN	10590	0.11	trans
rs2935286	chr10	34332326	SCGN	10590	0.02	trans
rs2393316	chr10	59333070	SCGN	10590	8.251E-5	trans
rs11185824	chr10	91393711	SCGN	10590	0.01	trans
rs1902708	chr10	98004531	SCGN	10590	0.14	trans
rs11190310	chr10	101659518	SCGN	10590	0	trans
rs11190338	chr10	101713253	SCGN	10590	0.01	trans
rs17124813	chr10	110347464	SCGN	10590	0.11	trans
rs1335014	chr10	130004943	SCGN	10590	0.05	trans
rs12289208	chr11	125224267	SCGN	10590	8.569E-4	trans
rs749881	chr11	125224856	SCGN	10590	0.01	trans
rs11061703	chr12	1436977	SCGN	10590	0.03	trans
rs2638324		0	SCGN	10590	0.05	trans
rs12315969	chr12	67498529	SCGN	10590	0.02	trans
rs1526959	chr12	79753789	SCGN	10590	0	trans
rs1547161	chr13	30552900	SCGN	10590	0.12	trans
rs7337967	chr13	53519044	SCGN	10590	0.14	trans
rs4112777	chr13	99281457	SCGN	10590	0.07	trans
rs10498433	chr14	52289530	SCGN	10590	0.03	trans
rs17108303	chr14	79305092	SCGN	10590	0.07	trans
rs17111984	chr14	95881425	SCGN	10590	0.1	trans
rs16955618	chr15	29937543	SCGN	10590	1.447E-20	trans
rs17711752	chr16	34436184	SCGN	10590	0.13	trans
rs12597471	chr16	53678428	SCGN	10590	0.14	trans
rs2270919	chr16	58150942	SCGN	10590	0.09	trans
rs3809597	chr16	58163518	SCGN	10590	0.01	trans
rs11076222	chr16	58239497	SCGN	10590	0.02	trans
rs11873184	chr18	1584081	SCGN	10590	0.17	trans
rs12458173	chr18	31430166	SCGN	10590	0.17	trans
rs2000894	chr18	57219161	SCGN	10590	0.15	trans
rs6046863	chr20	20423018	SCGN	10590	0.01	trans
rs1041786	chr21	22617710	SCGN	10590	2.52E-4	trans
rs16986332	chrX	10958354	SCGN	10590	0.03	trans
rs3829726	chrX	72666188	SCGN	10590	0.03	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.

No co-expressed genes in brain regions

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005509	calcium ion binding	NAS		10811645
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0008150	biological_process	ND		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005576	extracellular region	IEA		-
GO:0005737	cytoplasm	NAS		10811645
GO:0016020	membrane	IEA		-
GO:0031410	cytoplasmic vesicle	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
SABATES COLORECTAL ADENOMA DN	291	176	All SZGR 2.0 genes in this pathway
CERVERA SDHB TARGETS 1 DN	38	22	All SZGR 2.0 genes in this pathway
XU GH1 AUTOCRINE TARGETS UP	268	157	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL DN	701	446	All SZGR 2.0 genes in this pathway
MIKKELSEN IPS HCP WITH H3 UNMETHYLATED	80	50	All SZGR 2.0 genes in this pathway
MIKKELSEN MEF HCP WITH H3K27ME3	590	403	All SZGR 2.0 genes in this pathway
HOELZEL NF1 TARGETS DN	115	73	All SZGR 2.0 genes in this pathway
ROLEF GLIS3 TARGETS	37	29	All SZGR 2.0 genes in this pathway

Gene Page: SCGN