Variant report

Variant	rs58294763
Chromosome Location	chr15:75299768-75299769
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr15:75299695-75299866	HepG2	liver:	n/a	chr15:75299784-75299795
2	CEBPB	chr15:75299690-75299857	K562	blood:	n/a	chr15:75299784-75299795
3	POLR2A	chr15:75299495-75300076	GM12892	blood:	n/a	n/a
4	RUNX3	chr15:75299216-75299808	GM12878	blood:	n/a	n/a
5	MTA3	chr15:75299253-75299899	GM12878	blood:	n/a	n/a
6	IKZF1	chr15:75299306-75299892	GM12878	blood:	n/a	n/a
7	RUNX3	chr15:75299247-75299822	GM12878	blood:	n/a	n/a
8	NFIC	chr15:75299207-75299890	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:75298103..75301325-chr15:75314824..75318127,4	K562	blood:
2	chr15:75299758..75302262-chr15:75305323..75307805,2	K562	blood:
3	chr15:75299144..75301143-chr15:75314698..75317590,3	MCF-7	breast:

Variant related genes	Relation type
SCAMP5	TF binding region
ENSG00000138621	Chromatin interaction
ENSG00000260483	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs11072519	0.83[AMR][1000 genomes]
rs12591175	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12591994	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12592477	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12593476	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12593542	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12594117	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2289582	0.98[ASN][1000 genomes]
rs2304904	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28394281	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3812943	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3812946	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3816261	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3910748	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55877218	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56828495	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56970592	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58068887	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58403754	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58645417	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59094290	0.99[ASN][1000 genomes]
rs59303424	0.81[ASN][1000 genomes]
rs61166993	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6495135	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6495136	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6495137	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6495138	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6495140	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6495142	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6495146	0.81[ASN][1000 genomes]
rs7163390	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7166105	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7167415	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7168638	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7172065	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7172715	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7172989	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7173218	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7174129	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7177109	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7179097	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7181942	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7182286	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72475969	0.81[ASN][1000 genomes]
rs7342591	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7342601	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73432941	0.80[ASN][1000 genomes]
rs73436579	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73436586	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73438537	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73438554	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73438569	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs74023908	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs74023935	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs74025863	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8031545	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8034149	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8036573	0.99[ASN][1000 genomes]
rs8039433	0.81[ASN][1000 genomes]
rs8040961	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9672926	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9672995	0.98[ASN][1000 genomes]
rs9672996	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9673012	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9788648	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv542435	chr15:75271788-75321117	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs58294763	SCAMP5	cis	Esophagus Mucosa	GTEx
rs58294763	PPCDC	cis	Adipose Subcutaneous	GTEx
rs58294763	SCAMP5	cis	Artery Tibial	GTEx
rs58294763	SCAMP5	cis	Thyroid	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75289000-75315800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:75289400-75305000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr15:75289400-75305000	Weak transcription	Brain Substantia Nigra	brain
4	chr15:75289400-75305600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr15:75289400-75315400	Weak transcription	Fetal Kidney	kidney
6	chr15:75289600-75304000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr15:75289600-75305400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr15:75289800-75304000	Weak transcription	Brain Hippocampus Middle	brain
9	chr15:75290000-75303600	Weak transcription	Brain Angular Gyrus	brain
10	chr15:75290000-75303800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr15:75290000-75304400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:75290000-75304400	Weak transcription	HepG2	liver
13	chr15:75290000-75309400	Weak transcription	Gastric	stomach
14	chr15:75290000-75316000	Weak transcription	Small Intestine	intestine
15	chr15:75290200-75302400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr15:75290400-75304800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr15:75290400-75304800	Weak transcription	Brain Anterior Caudate	brain
18	chr15:75290600-75304400	Weak transcription	Fetal Stomach	stomach
19	chr15:75291400-75305400	Weak transcription	Fetal Brain Male	brain
20	chr15:75292000-75305000	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr15:75292600-75305400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr15:75293000-75304000	Weak transcription	Fetal Intestine Large	intestine
23	chr15:75293200-75315800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr15:75294600-75312200	Weak transcription	Adipose Nuclei	Adipose
25	chr15:75294600-75315600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr15:75296800-75302000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr15:75296800-75303600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr15:75297200-75304600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr15:75297400-75305000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:75297600-75303800	Weak transcription	Fetal Brain Female	brain
31	chr15:75297800-75302000	Weak transcription	Fetal Intestine Small	intestine
32	chr15:75298200-75304000	Weak transcription	Pancreas	Pancrea
33	chr15:75298200-75305600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr15:75299200-75299800	Bivalent Enhancer	Primary B cells from cord blood	blood
35	chr15:75299200-75299800	Flanking Active TSS	GM12878-XiMat	blood
36	chr15:75299200-75300200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr15:75299200-75300200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr15:75299200-75300600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr15:75299200-75300800	Enhancers	Primary hematopoietic stem cells	blood
40	chr15:75299200-75302600	Enhancers	Primary B cells from peripheral blood	blood
41	chr15:75299400-75302400	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr15:75299600-75300200	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr15:75299600-75300200	Strong transcription	Brain Germinal Matrix	brain
44	chr15:75299600-75300200	Genic enhancers	Brain Inferior Temporal Lobe	brain
45	chr15:75299600-75300200	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr15:75299600-75300400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr15:75299600-75302800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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