Variant report

Variant	rs4238390
Chromosome Location	chr15:52585305-52585306
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52584377..52586164-chr15:52849893..52851751,2	MCF-7	breast:
2	chr15:52548134..52549154-chr15:52584600..52585596,7	MCF-7	breast:
3	chr15:52548220..52549072-chr15:52585130..52585678,2	MCF-7	breast:
4	chr15:52584512..52586382-chr15:52971188..52973757,2	MCF-7	breast:
5	chr15:52536664..52559220-chr15:52576974..52590204,72	MCF-7	breast:
6	chr15:52541572..52560373-chr15:52569752..52591000,64	MCF-7	breast:
7	chr15:52583678..52585995-chr15:52615862..52618102,2	MCF-7	breast:
8	chr15:52584393..52589074-chr15:52819513..52822265,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000047346	Chromatin interaction
ENSG00000128989	Chromatin interaction
ENSG00000128833	Chromatin interaction
ENSG00000197535	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11854890	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12907067	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12907952	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35982476	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3751621	1.00[JPT][hapmap]
rs3751623	1.00[JPT][hapmap]
rs4442751	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4776034	0.84[AMR][1000 genomes]
rs55845575	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56071450	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57506065	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62015972	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][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	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

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52556000-52587000	Weak transcription	Brain Hippocampus Middle	brain
2	chr15:52565800-52587000	Weak transcription	Right Atrium	heart
3	chr15:52571200-52585800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr15:52571200-52587000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr15:52574600-52587000	Weak transcription	Brain Anterior Caudate	brain
6	chr15:52580400-52587000	Weak transcription	Right Ventricle	heart
7	chr15:52581000-52587200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr15:52581200-52587000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr15:52581400-52585800	Weak transcription	Fetal Intestine Small	intestine
10	chr15:52582200-52586800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr15:52582400-52585400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr15:52582400-52585400	Weak transcription	Colonic Mucosa	Colon
13	chr15:52582400-52585400	Weak transcription	Lung	lung
14	chr15:52582400-52586400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr15:52582400-52586400	Weak transcription	Hela-S3	cervix
16	chr15:52582400-52586600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr15:52582400-52586800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr15:52582400-52586800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr15:52582400-52587000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:52582400-52587200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr15:52583200-52585400	Genic enhancers	Pancreas	Pancrea
22	chr15:52583400-52586000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:52583600-52587000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr15:52583800-52585400	Weak transcription	Spleen	Spleen
25	chr15:52583800-52587000	Weak transcription	Fetal Kidney	kidney
26	chr15:52584400-52585400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:52584400-52585400	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr15:52584400-52586000	Enhancers	Fetal Muscle Leg	muscle
29	chr15:52584400-52586400	Genic enhancers	HepG2	liver
30	chr15:52584800-52585400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr15:52584800-52585800	Enhancers	Stomach Mucosa	stomach
32	chr15:52584800-52586200	Genic enhancers	Gastric	stomach
33	chr15:52584800-52586800	Enhancers	Primary B cells from peripheral blood	blood
34	chr15:52584800-52586800	Enhancers	A549	lung
35	chr15:52585000-52585400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr15:52585000-52585600	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr15:52585000-52585800	Weak transcription	Brain Angular Gyrus	brain
38	chr15:52585000-52585800	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr15:52585000-52586200	Genic enhancers	Esophagus	oesophagus
40	chr15:52585000-52586200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
41	chr15:52585000-52586400	Enhancers	Duodenum Mucosa	Duodenum
42	chr15:52585000-52586600	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr15:52585200-52586200	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr15:52585200-52586400	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:52585200-52586400	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr15:52585200-52586800	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr15:52585200-52586800	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr15:52585200-52586800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr15:52585200-52586800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr15:52585200-52587000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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