Variant report

Variant	rs4238389
Chromosome Location	chr15:52543181-52543182
allele	C/G/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	chr15:52542990..52545987-chr15:52943389..52945907,2	MCF-7	breast:
2	chr14:90778941..90780629-chr15:52542772..52544408,2	MCF-7	breast:
3	chr15:52534831..52539766-chr15:52540408..52545106,6	MCF-7	breast:
4	chr15:52538818..52541921-chr15:52541930..52545867,4	K562	blood:
5	chr15:52536445..52539563-chr15:52540903..52544563,5	K562	blood:
6	chr15:52541572..52560373-chr15:52569752..52591000,64	MCF-7	breast:
7	chr15:52542793..52545085-chr15:52889244..52891733,2	MCF-7	breast:
8	chr15:52542795..52546643-chr15:52859589..52862742,4	MCF-7	breast:
9	chr15:52536664..52559220-chr15:52576974..52590204,72	MCF-7	breast:

No data

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

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11070891	0.91[AFR][1000 genomes]
rs4145157	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4278685	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4316698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4497629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4776029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4776032	0.91[AFR][1000 genomes]
rs4776033	1.00[AMR][1000 genomes]
rs7169177	1.00[AMR][1000 genomes]
rs7171825	1.00[AMR][1000 genomes]
rs7172026	1.00[AMR][1000 genomes]
rs7175945	0.91[AFR][1000 genomes]
rs8043194	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9920688	0.85[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	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:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52497800-52549000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:52505600-52549200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:52506400-52548800	Weak transcription	Fetal Kidney	kidney
4	chr15:52516000-52549400	Weak transcription	Left Ventricle	heart
5	chr15:52523400-52548600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:52524400-52579400	Weak transcription	Small Intestine	intestine
7	chr15:52525800-52554000	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr15:52526000-52548800	Weak transcription	Brain Hippocampus Middle	brain
9	chr15:52526200-52548200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr15:52527400-52548200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:52528000-52548800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr15:52528000-52548800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr15:52528600-52549600	Weak transcription	Right Ventricle	heart
14	chr15:52531600-52548600	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr15:52532000-52549000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr15:52533800-52543200	Strong transcription	Rectal Mucosa Donor 31	rectum
17	chr15:52533800-52543200	Strong transcription	HepG2	liver
18	chr15:52533800-52543600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr15:52533800-52543600	Strong transcription	Pancreas	Pancrea
20	chr15:52533800-52544400	Strong transcription	HUES6 Cell Line	embryonic stem cell
21	chr15:52533800-52544400	Strong transcription	Fetal Intestine Small	intestine
22	chr15:52533800-52546000	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr15:52533800-52548600	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr15:52533800-52548800	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr15:52534400-52543800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr15:52534400-52548200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr15:52534400-52548800	Weak transcription	Primary T cells from cord blood	blood
28	chr15:52535800-52549400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr15:52536200-52553600	Weak transcription	Lung	lung
30	chr15:52536200-52553800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr15:52536600-52548800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr15:52536600-52548800	Weak transcription	Brain Anterior Caudate	brain
33	chr15:52536600-52549000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr15:52536800-52549000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr15:52537200-52549200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:52537600-52548800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr15:52537800-52543600	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr15:52538000-52554600	Weak transcription	Colonic Mucosa	Colon
39	chr15:52538800-52546400	Weak transcription	Adipose Nuclei	Adipose
40	chr15:52539200-52546400	Weak transcription	Spleen	Spleen
41	chr15:52539600-52544800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr15:52539600-52545800	Weak transcription	Esophagus	oesophagus
43	chr15:52539600-52553400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr15:52539800-52548800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr15:52539800-52548800	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr15:52540000-52544800	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr15:52540000-52545000	Weak transcription	Duodenum Mucosa	Duodenum
48	chr15:52540000-52548400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr15:52540000-52553800	Weak transcription	Rectal Smooth Muscle	rectum
50	chr15:52540200-52544400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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