Variant report

Variant	rs4886639
Chromosome Location	chr15:75227949-75227950
allele	A/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	chr15:75180806..75183670-chr15:75227670..75231591,7	K562	blood:
2	chr15:75227655..75229943-chr15:75305697..75307723,2	MCF-7	breast:
3	chr15:75126487..75129177-chr15:75225564..75229328,3	K562	blood:
4	chr15:75226056..75232063-chr15:75248745..75252832,9	MCF-7	breast:
5	chr15:75196237..75205947-chr15:75227299..75233104,18	K562	blood:
6	chr15:75126584..75129177-chr15:75226754..75229328,2	K562	blood:
7	chr15:75180021..75183481-chr15:75226759..75230284,3	K562	blood:
8	chr15:75226664..75233309-chr15:75245862..75252227,16	K562	blood:
9	chr15:75199684..75201494-chr15:75226994..75229978,2	MCF-7	breast:
10	chr15:75188520..75190057-chr15:75227191..75229624,2	K562	blood:
11	chr15:75226234..75228164-chr15:75247599..75249841,2	K562	blood:
12	chr15:75131716..75139878-chr15:75227772..75233177,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000178761	Chromatin interaction
ENSG00000178718	Chromatin interaction
ENSG00000178802	Chromatin interaction
ENSG00000198794	Chromatin interaction
ENSG00000140474	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11072511	0.82[EUR][1000 genomes]
rs11072512	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11072513	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11072514	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1127796	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1130741	0.88[EUR][1000 genomes]
rs1133322	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1133323	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11633472	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11638130	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11639413	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11854704	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11856413	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11857695	0.85[EUR][1000 genomes]
rs12898539	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12899430	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12899787	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12900662	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12901190	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12902515	0.85[EUR][1000 genomes]
rs12903205	0.86[EUR][1000 genomes]
rs12903370	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12904326	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12904897	0.92[EUR][1000 genomes]
rs12907898	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12908365	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12909335	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12912839	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12913293	0.87[EUR][1000 genomes]
rs12914217	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2044157	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2415251	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4643278	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4886608	0.83[EUR][1000 genomes]
rs4886632	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4886636	0.89[EUR][1000 genomes]
rs4886640	0.84[EUR][1000 genomes]
rs59945415	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62029167	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7495664	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7495739	0.87[EUR][1000 genomes]
rs7497026	0.87[EUR][1000 genomes]
rs7497393	0.80[EUR][1000 genomes]
rs8025447	0.89[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4886639	SCAMP2	cis	Whole Blood	GTEx
rs4886639	SCAMP5	cis	Artery Tibial	GTEx
rs4886639	SCAMP2	cis	Esophagus Mucosa	GTEx
rs4886639	SCAMP2	Cis_1M	lymphoblastoid	RTeQTL
rs4886639	COX5A	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75199600-75229400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:75204000-75228400	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr15:75204600-75229200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:75212400-75229600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:75212600-75229200	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr15:75217400-75229400	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr15:75221400-75229800	Weak transcription	Spleen	Spleen
8	chr15:75221600-75228000	Weak transcription	Fetal Brain Male	brain
9	chr15:75221600-75228600	Weak transcription	Stomach Smooth Muscle	stomach
10	chr15:75221600-75229200	Weak transcription	Fetal Kidney	kidney
11	chr15:75221600-75229200	Weak transcription	HSMMtube	muscle
12	chr15:75221600-75229400	Weak transcription	Aorta	Aorta
13	chr15:75221600-75229400	Weak transcription	Ovary	ovary
14	chr15:75221600-75229600	Weak transcription	Gastric	stomach
15	chr15:75221800-75228600	Weak transcription	Cortex derived primary cultured neurospheres	brain
16	chr15:75221800-75228800	Weak transcription	Fetal Brain Female	brain
17	chr15:75222000-75228200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:75222000-75228600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr15:75222000-75228800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr15:75222000-75228800	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr15:75222000-75229200	Weak transcription	NHDF-Ad	bronchial
22	chr15:75222200-75228200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr15:75222200-75228800	Weak transcription	NHLF	lung
24	chr15:75222200-75229200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:75222200-75229200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr15:75222200-75229200	Weak transcription	Brain Substantia Nigra	brain
27	chr15:75222200-75229200	Weak transcription	Esophagus	oesophagus
28	chr15:75222200-75229200	Weak transcription	NH-A	brain
29	chr15:75222400-75229200	Weak transcription	HSMM	muscle
30	chr15:75223000-75229200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr15:75223000-75229400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr15:75223600-75228600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr15:75223600-75229200	Weak transcription	HMEC	breast
34	chr15:75223800-75228200	Weak transcription	Primary B cells from peripheral blood	blood
35	chr15:75223800-75228600	Weak transcription	Primary hematopoietic stem cells	blood
36	chr15:75223800-75228600	Weak transcription	Fetal Lung	lung
37	chr15:75223800-75229600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:75224000-75228000	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr15:75224000-75228000	Weak transcription	Lung	lung
40	chr15:75224000-75228200	Weak transcription	Osteobl	bone
41	chr15:75224000-75229000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr15:75224200-75228200	Weak transcription	Rectal Smooth Muscle	rectum
43	chr15:75224200-75229200	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr15:75224200-75229200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr15:75224200-75229200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr15:75224200-75229200	Weak transcription	NHEK	skin
47	chr15:75224200-75229400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr15:75224200-75229600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr15:75224400-75228600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr15:75224400-75229200	Weak transcription	H1 Cell Line	embryonic stem cell

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