Variant report

Variant	rs1873379
Chromosome Location	chr15:75498744-75498745
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:75498147-75499158	GM12892	blood:	n/a	n/a
2	POLR2A	chr15:75496957-75499106	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr15:75498249-75499053	GM18505	blood:	n/a	n/a
4	POLR2A	chr15:75498287-75499009	GM19193	blood:	n/a	n/a
5	POLR2A	chr15:75496856-75499164	GM12892	blood:	n/a	n/a
6	POLR2A	chr15:75498321-75499124	HL-60	blood:	n/a	n/a
7	POLR2A	chr15:75490585-75499135	GM12878	blood:	n/a	n/a
8	POLR2A	chr15:75497998-75499191	GM12878	blood:	n/a	n/a
9	POLR2A	chr15:75496927-75499167	GM12891	blood:	n/a	n/a
10	POLR2A	chr15:75498572-75498821	A549	lung:	n/a	n/a
11	POLR2A	chr15:75497875-75499173	GM12892	blood:	n/a	n/a
12	POLR2A	chr15:75498091-75499046	GM12891	blood:	n/a	n/a
13	POLR2A	chr15:75497766-75498929	GM12891	blood:	n/a	n/a
14	POLR2A	chr15:75498005-75509029	GM12878	blood:	n/a	n/a
15	POLR2A	chr15:75489631-75513671	GM12878	blood:	n/a	n/a
16	POLR2A	chr15:75498732-75498749	GM12878	blood:	n/a	n/a
17	POLR2A	chr15:75498588-75498835	Hela-S3	cervix:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75314737..75326433-chr15:75490770..75500610,30	K562	blood:
2	chr15:75312886..75327225-chr15:75491522..75500922,36	K562	blood:
3	chr15:75314704..75323577-chr15:75491522..75500562,29	MCF-7	breast:
4	chr15:75334055..75342899-chr15:75492444..75498798,20	K562	blood:
5	chr15:75314427..75332274-chr15:75491598..75502885,56	MCF-7	breast:
6	chr15:75490684..75493339-chr15:75497415..75499804,2	K562	blood:
7	chr15:75331603..75340227-chr15:75492938..75499942,15	K562	blood:

No data

Variant related genes	Relation type
C15orf39	TF binding region
ENSG00000167173	Chromatin interaction
ENSG00000260483	Chromatin interaction
ENSG00000138621	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs1009194	0.80[CEU][hapmap]
rs11634836	1.00[CEU][hapmap]
rs11636245	0.94[CEU][hapmap];0.89[EUR][1000 genomes]
rs12442583	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904383	chr15:75382542-75520378	Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	esv1796196	chr15:75389382-75531124	Weak transcription Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1039713	chr15:75394213-75674389	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
4	nsv1037713	chr15:75401213-75665304	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
5	nsv1053212	chr15:75428467-75534408	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv833056	chr15:75452947-75614590	Enhancers Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv904384	chr15:75493823-75520378	Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv569995	chr15:75493823-75537475	Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv569996	chr15:75493823-75540491	Active TSS Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	nsv904385	chr15:75493823-75546700	Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
11	nsv482859	chr15:75493899-75688451	Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1873379	SCAMP5	cis	Artery Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75495800-75500000	Weak transcription	Brain Germinal Matrix	brain
2	chr15:75496200-75506000	Weak transcription	Fetal Brain Female	brain
3	chr15:75496400-75498800	Weak transcription	Small Intestine	intestine
4	chr15:75496400-75500400	Weak transcription	Right Atrium	heart
5	chr15:75496400-75504000	Weak transcription	HSMMtube	muscle
6	chr15:75496400-75506000	Weak transcription	Psoas Muscle	Psoas
7	chr15:75496600-75499600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:75496600-75499600	Weak transcription	HSMM	muscle
9	chr15:75496600-75501600	Weak transcription	Brain Substantia Nigra	brain
10	chr15:75496600-75506600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr15:75496800-75500400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr15:75496800-75507200	Weak transcription	NH-A	brain
13	chr15:75497200-75500200	Weak transcription	Brain Anterior Caudate	brain
14	chr15:75497600-75498800	Weak transcription	Colon Smooth Muscle	Colon
15	chr15:75497600-75498800	Weak transcription	HMEC	breast
16	chr15:75497600-75499000	Genic enhancers	Primary monocytes fromperipheralblood	blood
17	chr15:75497600-75499200	Strong transcription	Fetal Intestine Small	intestine
18	chr15:75497600-75499400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr15:75497600-75499400	Weak transcription	Osteobl	bone
20	chr15:75497600-75499600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr15:75497600-75500200	Weak transcription	NHDF-Ad	bronchial
22	chr15:75497600-75500400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr15:75497600-75500600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr15:75497600-75501000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr15:75497600-75501200	Weak transcription	Brain Angular Gyrus	brain
26	chr15:75497600-75501400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr15:75497600-75501400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr15:75497600-75501600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr15:75497600-75507000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr15:75497800-75499400	Weak transcription	Liver	Liver
31	chr15:75497800-75499600	Genic enhancers	Stomach Smooth Muscle	stomach
32	chr15:75497800-75499800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr15:75497800-75499800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr15:75497800-75499800	Genic enhancers	HepG2	liver
35	chr15:75497800-75500200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr15:75497800-75500200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr15:75497800-75500400	Strong transcription	Dnd41	blood
38	chr15:75497800-75500600	Weak transcription	Fetal Heart	heart
39	chr15:75497800-75501200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr15:75497800-75501400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr15:75497800-75501800	Strong transcription	Fetal Thymus	thymus
42	chr15:75497800-75502200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
43	chr15:75497800-75504200	Strong transcription	Hela-S3	cervix
44	chr15:75497800-75505200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:75497800-75506400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr15:75498000-75498800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr15:75498000-75499400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr15:75498000-75499800	Weak transcription	Brain Hippocampus Middle	brain
49	chr15:75498000-75500200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr15:75498000-75500400	Strong transcription	Rectal Mucosa Donor 29	rectum

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