Variant report

Variant	rs4886608
Chromosome Location	chr15:75164530-75164531
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:75163746..75165751-chr15:75191304..75195509,4	K562	blood:
2	chr15:75162469..75167536-chr15:75180880..75184902,6	K562	blood:
3	chr15:75164429..75167842-chr15:75196018..75198435,3	K562	blood:
4	chr15:75163901..75170368-chr15:75180139..75184021,10	K562	blood:
5	chr15:75163277..75165219-chr15:75166368..75168466,2	MCF-7	breast:
6	chr15:75129767..75136088-chr15:75163908..75167881,8	K562	blood:
7	chr15:75134049..75139648-chr15:75161531..75167020,13	MCF-7	breast:
8	chr15:75163895..75166026-chr15:75315159..75317542,2	MCF-7	breast:
9	chr15:75073135..75075746-chr15:75163972..75165852,2	K562	blood:
10	chr15:75163351..75167012-chr15:75180238..75185061,13	MCF-7	breast:
11	chr15:75163342..75166719-chr15:75180364..75184673,7	MCF-7	breast:
12	chr15:75161914..75167776-chr15:75191644..75199761,13	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000178761	Chromatin interaction
ENSG00000178802	Chromatin interaction
ENSG00000140474	Chromatin interaction
ENSG00000138621	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000260483	Chromatin interaction
ENSG00000260824	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11072511	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11072512	0.92[EUR][1000 genomes]
rs11072513	0.82[EUR][1000 genomes]
rs11072514	0.83[EUR][1000 genomes]
rs1127796	0.92[EUR][1000 genomes]
rs1130741	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1133322	0.89[EUR][1000 genomes]
rs1133323	0.81[EUR][1000 genomes]
rs11630918	0.87[EUR][1000 genomes]
rs11633472	0.85[EUR][1000 genomes]
rs11638130	0.84[EUR][1000 genomes]
rs11854704	0.90[EUR][1000 genomes]
rs11856413	0.84[EUR][1000 genomes]
rs11857695	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12898539	0.86[EUR][1000 genomes]
rs12899430	0.86[EUR][1000 genomes]
rs12899787	0.89[EUR][1000 genomes]
rs12900662	0.96[EUR][1000 genomes]
rs12901190	0.81[EUR][1000 genomes]
rs12902515	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12903205	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12903370	0.83[EUR][1000 genomes]
rs12904326	0.82[EUR][1000 genomes]
rs12904897	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12907898	0.91[EUR][1000 genomes]
rs12908365	0.89[EUR][1000 genomes]
rs12909335	0.82[EUR][1000 genomes]
rs12911254	0.89[EUR][1000 genomes]
rs12912839	0.83[EUR][1000 genomes]
rs12913293	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12914217	0.83[EUR][1000 genomes]
rs4643278	0.96[EUR][1000 genomes]
rs4886632	0.97[EUR][1000 genomes]
rs4886636	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4886639	0.83[EUR][1000 genomes]
rs59945415	0.89[EUR][1000 genomes]
rs62029167	0.90[EUR][1000 genomes]
rs7495664	0.83[EUR][1000 genomes]
rs7495739	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7497026	0.87[EUR][1000 genomes]
rs7497393	0.88[EUR][1000 genomes]
rs8025447	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS 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	46 gene(s)	inside rSNPs	diseases
2	nsv904381	chr15:75108636-75242155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv827386	chr15:75161362-75166473	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	n/a
4	nsv827388	chr15:75161362-75169121	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4886608	SCAMP5	cis	Artery Tibial	GTEx
rs4886608	ULK3	cis	Whole Blood	GTEx
rs4886608	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs4886608	SCAMP2	cis	Whole Blood	GTEx
rs4886608	SCAMP2	cis	Esophagus Mucosa	GTEx
rs4886608	MPI	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75137000-75164800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr15:75146000-75164800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:75146600-75164600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr15:75147000-75164800	Weak transcription	Ovary	ovary
5	chr15:75147200-75164800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:75156000-75164800	Enhancers	Fetal Intestine Large	intestine
7	chr15:75157800-75164600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr15:75158000-75165000	Enhancers	Spleen	Spleen
9	chr15:75158200-75164600	Enhancers	Pancreas	Pancrea
10	chr15:75158200-75165000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:75158400-75164800	Enhancers	Liver	Liver
12	chr15:75159000-75164600	Weak transcription	Osteobl	bone
13	chr15:75159200-75164800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr15:75160600-75164800	Enhancers	Fetal Thymus	thymus
15	chr15:75160800-75164600	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr15:75161000-75164600	Weak transcription	A549	lung
17	chr15:75161400-75164800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr15:75161600-75165400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr15:75161800-75164800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr15:75162000-75164800	Enhancers	Psoas Muscle	Psoas
21	chr15:75162400-75164600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr15:75162400-75164800	Enhancers	Fetal Heart	heart
23	chr15:75162400-75164800	Enhancers	Right Atrium	heart
24	chr15:75162600-75164600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr15:75162600-75164600	Weak transcription	Gastric	stomach
26	chr15:75162800-75164600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr15:75162800-75164600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr15:75162800-75164600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr15:75163200-75164600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr15:75163200-75164600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:75163200-75164600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr15:75163200-75164600	Enhancers	HepG2	liver
33	chr15:75163200-75164800	Weak transcription	Fetal Kidney	kidney
34	chr15:75163400-75164600	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr15:75163400-75164600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr15:75163400-75164600	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr15:75163400-75164600	Enhancers	Primary B cells from cord blood	blood
38	chr15:75163400-75164600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr15:75163400-75164600	Weak transcription	NHLF	lung
40	chr15:75163400-75164800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
41	chr15:75163400-75164800	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr15:75163600-75164600	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr15:75163600-75164600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr15:75163600-75164600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr15:75163600-75164600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr15:75163600-75164600	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr15:75163600-75164600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr15:75163600-75164600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr15:75163600-75164600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr15:75163600-75164600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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