Variant report

Variant	rs4514621
Chromosome Location	chr15:52583153-52583154
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52580770..52583438-chr15:52859904..52862559,3	MCF-7	breast:
2	chr15:52581350..52585067-chr15:52859210..52861594,5	MCF-7	breast:
3	chr15:52582266..52584692-chr15:52609132..52611411,2	MCF-7	breast:
4	chr15:52580244..52584410-chr15:52619433..52625902,7	MCF-7	breast:
5	chr15:52581186..52583538-chr15:52625731..52628644,3	MCF-7	breast:
6	chr15:52536664..52559220-chr15:52576974..52590204,72	MCF-7	breast:
7	chr15:52578087..52583541-chr15:52969803..52973267,6	MCF-7	breast:
8	chr15:52541572..52560373-chr15:52569752..52591000,64	MCF-7	breast:
9	chr15:52309835..52312480-chr15:52580964..52583747,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000259438	Chromatin interaction
ENSG00000128989	Chromatin interaction
ENSG00000128833	Chromatin interaction
ENSG00000069956	Chromatin interaction
ENSG00000047346	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10851510	1.00[CEU][hapmap]
rs10851511	1.00[CEU][hapmap]
rs11070890	1.00[CEU][hapmap];0.84[JPT][hapmap]
rs12594710	0.93[GIH][hapmap]
rs17650476	1.00[YRI][hapmap]
rs17707198	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3794551	0.84[JPT][hapmap];1.00[MEX][hapmap]
rs4432216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4496072	1.00[CEU][hapmap]
rs4774617	1.00[CEU][hapmap]
rs4776031	1.00[CEU][hapmap]
rs59056894	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59060156	1.00[AFR][1000 genomes]
rs59211915	0.89[AFR][1000 genomes]
rs61367038	1.00[AFR][1000 genomes]
rs7165256	0.84[JPT][hapmap]
rs7172236	1.00[CEU][hapmap]
rs8025608	0.84[JPT][hapmap]

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	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4514621	SLCO2A1	trans	brain	seeQTL
rs4514621	KLK1	trans	brain	seeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52555000-52585000	Weak transcription	Left Ventricle	heart
2	chr15:52556000-52587000	Weak transcription	Brain Hippocampus Middle	brain
3	chr15:52565800-52587000	Weak transcription	Right Atrium	heart
4	chr15:52571200-52585800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr15:52571200-52587000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:52574600-52587000	Weak transcription	Brain Anterior Caudate	brain
7	chr15:52575000-52585000	Weak transcription	Fetal Stomach	stomach
8	chr15:52579600-52583200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr15:52580400-52587000	Weak transcription	Right Ventricle	heart
10	chr15:52581000-52587200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr15:52581200-52583200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:52581200-52583400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:52581200-52583400	Weak transcription	Spleen	Spleen
14	chr15:52581200-52587000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr15:52581400-52585800	Weak transcription	Fetal Intestine Small	intestine
16	chr15:52581600-52583200	Enhancers	GM12878-XiMat	blood
17	chr15:52581600-52585000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:52581800-52583800	Enhancers	Stomach Mucosa	stomach
19	chr15:52581800-52584200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:52582000-52584000	Enhancers	HepG2	liver
21	chr15:52582200-52583800	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr15:52582200-52584400	Weak transcription	Fetal Muscle Leg	muscle
23	chr15:52582200-52585000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr15:52582200-52585000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr15:52582200-52586800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr15:52582400-52583200	Weak transcription	Primary B cells from peripheral blood	blood
27	chr15:52582400-52583200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr15:52582400-52583200	Weak transcription	Pancreas	Pancrea
29	chr15:52582400-52583800	Enhancers	A549	lung
30	chr15:52582400-52584400	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr15:52582400-52584400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr15:52582400-52584400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:52582400-52584400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr15:52582400-52584800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr15:52582400-52584800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr15:52582400-52584800	Weak transcription	Gastric	stomach
37	chr15:52582400-52585000	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr15:52582400-52585000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr15:52582400-52585400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
40	chr15:52582400-52585400	Weak transcription	Colonic Mucosa	Colon
41	chr15:52582400-52585400	Weak transcription	Lung	lung
42	chr15:52582400-52586400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr15:52582400-52586400	Weak transcription	Hela-S3	cervix
44	chr15:52582400-52586600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr15:52582400-52586800	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr15:52582400-52586800	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr15:52582400-52587000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:52582400-52587200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr15:52582600-52584600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
50	chr15:52583000-52583600	Enhancers	Esophagus	oesophagus

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