Variant report

Variant	rs7171825
Chromosome Location	chr15:52558247-52558248
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52553415..52555370-chr15:52556618..52558914,2	MCF-7	breast:
2	chr15:52541572..52560373-chr15:52569752..52591000,64	MCF-7	breast:
3	chr15:52536664..52559220-chr15:52576974..52590204,72	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128833	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11070890	1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs11637680	0.85[AFR][1000 genomes]
rs4145157	1.00[AMR][1000 genomes]
rs4238389	1.00[AMR][1000 genomes]
rs4278685	1.00[AMR][1000 genomes]
rs4316698	1.00[AMR][1000 genomes]
rs4497629	1.00[AMR][1000 genomes]
rs4776029	1.00[AMR][1000 genomes]
rs4776033	0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7169177	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7172026	0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8043194	1.00[AMR][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:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52524400-52579400	Weak transcription	Small Intestine	intestine
2	chr15:52549400-52567200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr15:52550000-52579200	Weak transcription	Fetal Kidney	kidney
4	chr15:52550200-52572200	Strong transcription	HepG2	liver
5	chr15:52553000-52562600	Strong transcription	Fetal Intestine Small	intestine
6	chr15:52553200-52575400	Strong transcription	Rectal Mucosa Donor 31	rectum
7	chr15:52554000-52569200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr15:52554800-52582200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr15:52555000-52558400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:52555000-52558400	Weak transcription	Colonic Mucosa	Colon
11	chr15:52555000-52558600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:52555000-52563800	Weak transcription	Placenta	Placenta
13	chr15:52555000-52572800	Weak transcription	Right Ventricle	heart
14	chr15:52555000-52585000	Weak transcription	Left Ventricle	heart
15	chr15:52555200-52567000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr15:52555200-52572800	Weak transcription	Fetal Heart	heart
17	chr15:52555200-52580600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr15:52555400-52558600	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr15:52555400-52558600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr15:52555400-52561400	Strong transcription	Duodenum Mucosa	Duodenum
21	chr15:52555400-52563800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr15:52555400-52572600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:52555400-52574400	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr15:52555400-52575800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr15:52555600-52565000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr15:52555800-52558800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:52555800-52559400	Weak transcription	Liver	Liver
28	chr15:52555800-52559800	Strong transcription	Fetal Intestine Large	intestine
29	chr15:52555800-52560000	Weak transcription	Fetal Muscle Leg	muscle
30	chr15:52555800-52567400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr15:52555800-52568600	Weak transcription	Brain Angular Gyrus	brain
32	chr15:52555800-52573400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr15:52555800-52574000	Weak transcription	Brain Anterior Caudate	brain
34	chr15:52555800-52575800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr15:52555800-52576400	Weak transcription	Hela-S3	cervix
36	chr15:52556000-52558600	Weak transcription	Esophagus	oesophagus
37	chr15:52556000-52561400	Strong transcription	Gastric	stomach
38	chr15:52556000-52570200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr15:52556000-52587000	Weak transcription	Brain Hippocampus Middle	brain
40	chr15:52556200-52558800	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr15:52556200-52559600	Strong transcription	Pancreas	Pancrea
42	chr15:52556400-52558400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:52556400-52558800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr15:52556800-52558600	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr15:52557000-52558400	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr15:52557000-52562400	Strong transcription	Fetal Stomach	stomach
47	chr15:52557000-52572400	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr15:52557000-52575800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr15:52557200-52558600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr15:52557200-52558600	Weak transcription	A549	lung

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