Variant report

Variant	rs59945415
Chromosome Location	chr15:75228427-75228428
allele	A/C
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 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	chr15:74906651..74909310-chr15:75228343..75231322,3	K562	blood:
4	chr15:75126487..75129177-chr15:75225564..75229328,3	K562	blood:
5	chr15:75226056..75232063-chr15:75248745..75252832,9	MCF-7	breast:
6	chr15:75196237..75205947-chr15:75227299..75233104,18	K562	blood:
7	chr15:75090885..75095958-chr15:75228068..75231576,5	K562	blood:
8	chr15:75126584..75129177-chr15:75226754..75229328,2	K562	blood:
9	chr15:75133406..75136691-chr15:75228046..75231533,6	MCF-7	breast:
10	chr15:75180021..75183481-chr15:75226759..75230284,3	K562	blood:
11	chr15:75226664..75233309-chr15:75245862..75252227,16	K562	blood:
12	chr15:75199684..75201494-chr15:75226994..75229978,2	MCF-7	breast:
13	chr15:75094337..75095958-chr15:75228176..75229862,2	K562	blood:
14	chr15:75188520..75190057-chr15:75227191..75229624,2	K562	blood:
15	chr15:75131716..75139878-chr15:75227772..75233177,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000198794	Chromatin interaction
ENSG00000140474	Chromatin interaction
ENSG00000103653	Chromatin interaction
ENSG00000260919	Chromatin interaction
ENSG00000178802	Chromatin interaction
ENSG00000178761	Chromatin interaction
ENSG00000178718	Chromatin interaction
ENSG00000179335	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs11072511	0.88[EUR][1000 genomes]
rs11072512	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11072513	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11072514	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1127796	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1130741	0.94[EUR][1000 genomes]
rs1133322	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1133323	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11630592	0.81[EUR][1000 genomes]
rs11630918	0.81[EUR][1000 genomes]
rs11633472	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11638130	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11639413	0.85[EUR][1000 genomes]
rs11854704	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11856413	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11857695	0.91[EUR][1000 genomes]
rs12898539	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12899430	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12899787	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12900662	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12901190	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12902515	0.91[EUR][1000 genomes]
rs12903205	0.92[EUR][1000 genomes]
rs12903370	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12904326	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12904897	0.98[EUR][1000 genomes]
rs12907898	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908365	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12909335	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12911254	0.82[EUR][1000 genomes]
rs12912839	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12913293	0.93[EUR][1000 genomes]
rs12914217	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2044157	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2415251	0.85[EUR][1000 genomes]
rs4643278	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4886608	0.89[EUR][1000 genomes]
rs4886632	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4886636	0.95[EUR][1000 genomes]
rs4886639	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4886640	0.84[EUR][1000 genomes]
rs62029167	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7495664	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7495739	0.93[EUR][1000 genomes]
rs7497026	0.93[EUR][1000 genomes]
rs7497393	0.83[EUR][1000 genomes]
rs8025447	0.95[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
rs59945415	MPI	Cis_1M	lymphoblastoid	RTeQTL
rs59945415	SCAMP5	cis	Artery Tibial	GTEx
rs59945415	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs59945415	SCAMP2	cis	Esophagus Mucosa	GTEx
rs59945415	SCAMP2	cis	Whole Blood	GTEx

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	chr15:75204600-75229200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:75212400-75229600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:75212600-75229200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:75217400-75229400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:75221400-75229800	Weak transcription	Spleen	Spleen
7	chr15:75221600-75228600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr15:75221600-75229200	Weak transcription	Fetal Kidney	kidney
9	chr15:75221600-75229200	Weak transcription	HSMMtube	muscle
10	chr15:75221600-75229400	Weak transcription	Aorta	Aorta
11	chr15:75221600-75229400	Weak transcription	Ovary	ovary
12	chr15:75221600-75229600	Weak transcription	Gastric	stomach
13	chr15:75221800-75228600	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr15:75221800-75228800	Weak transcription	Fetal Brain Female	brain
15	chr15:75222000-75228600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr15:75222000-75228800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr15:75222000-75228800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr15:75222000-75229200	Weak transcription	NHDF-Ad	bronchial
19	chr15:75222200-75228800	Weak transcription	NHLF	lung
20	chr15:75222200-75229200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr15:75222200-75229200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr15:75222200-75229200	Weak transcription	Brain Substantia Nigra	brain
23	chr15:75222200-75229200	Weak transcription	Esophagus	oesophagus
24	chr15:75222200-75229200	Weak transcription	NH-A	brain
25	chr15:75222400-75229200	Weak transcription	HSMM	muscle
26	chr15:75223000-75229200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr15:75223000-75229400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:75223600-75228600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr15:75223600-75229200	Weak transcription	HMEC	breast
30	chr15:75223800-75228600	Weak transcription	Primary hematopoietic stem cells	blood
31	chr15:75223800-75228600	Weak transcription	Fetal Lung	lung
32	chr15:75223800-75229600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr15:75224000-75229000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr15:75224200-75229200	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr15:75224200-75229200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr15:75224200-75229200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr15:75224200-75229200	Weak transcription	NHEK	skin
38	chr15:75224200-75229400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr15:75224200-75229600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr15:75224400-75228600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr15:75224400-75229200	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr15:75224400-75229200	Weak transcription	HUVEC	blood vessel
43	chr15:75224600-75228600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr15:75224600-75228600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr15:75224600-75229000	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr15:75224600-75229000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr15:75224600-75229200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr15:75224800-75228600	Weak transcription	Fetal Thymus	thymus
49	chr15:75225000-75228800	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr15:75225600-75228600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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