Variant report

Variant	rs3751623
Chromosome Location	chr15:52575321-52575322
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52573228..52575829-chr15:52858890..52861430,2	MCF-7	breast:
2	chr15:52567021..52571873-chr15:52572571..52576998,5	MCF-7	breast:
3	chr15:52562655..52564480-chr15:52574878..52577754,2	MCF-7	breast:
4	chr15:52552685..52555324-chr15:52573608..52576301,2	MCF-7	breast:
5	chr15:52541572..52560373-chr15:52569752..52591000,64	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221052	Chromatin interaction
ENSG00000128833	Chromatin interaction
ENSG00000128989	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11854890	1.00[JPT][hapmap]
rs3751621	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4238390	1.00[JPT][hapmap]

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:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52524400-52579400	Weak transcription	Small Intestine	intestine
2	chr15:52550000-52579200	Weak transcription	Fetal Kidney	kidney
3	chr15:52553200-52575400	Strong transcription	Rectal Mucosa Donor 31	rectum
4	chr15:52554800-52582200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr15:52555000-52585000	Weak transcription	Left Ventricle	heart
6	chr15:52555200-52580600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr15:52555400-52575800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr15:52555800-52575800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr15:52555800-52576400	Weak transcription	Hela-S3	cervix
10	chr15:52556000-52587000	Weak transcription	Brain Hippocampus Middle	brain
11	chr15:52557000-52575800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:52558200-52575400	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr15:52558800-52579400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:52559400-52580600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:52561400-52580600	Weak transcription	Spleen	Spleen
16	chr15:52564400-52575800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:52565800-52587000	Weak transcription	Right Atrium	heart
18	chr15:52567200-52575800	Strong transcription	Fetal Intestine Small	intestine
19	chr15:52568600-52576400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr15:52568600-52579400	Weak transcription	Stomach Mucosa	stomach
21	chr15:52568800-52580000	Weak transcription	Colonic Mucosa	Colon
22	chr15:52570800-52580800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr15:52571200-52581000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr15:52571200-52585800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr15:52571200-52587000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr15:52571400-52580600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr15:52571400-52580600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr15:52571600-52579200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr15:52571600-52579200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr15:52572200-52575800	Enhancers	Pancreas	Pancrea
31	chr15:52572200-52577600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr15:52572400-52577000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr15:52572800-52579800	Weak transcription	Fetal Muscle Trunk	muscle
34	chr15:52573200-52575600	Weak transcription	Lung	lung
35	chr15:52573400-52575400	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr15:52573400-52576600	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr15:52573800-52575800	Strong transcription	Esophagus	oesophagus
38	chr15:52573800-52575800	Enhancers	HepG2	liver
39	chr15:52574000-52575400	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr15:52574000-52580200	Weak transcription	Right Ventricle	heart
41	chr15:52574400-52575400	Weak transcription	Liver	Liver
42	chr15:52574400-52579200	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr15:52574400-52580400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr15:52574600-52575400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr15:52574600-52587000	Weak transcription	Brain Anterior Caudate	brain
46	chr15:52574800-52576000	Enhancers	Fetal Heart	heart
47	chr15:52575000-52576600	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr15:52575000-52577400	Weak transcription	Fetal Intestine Large	intestine
49	chr15:52575000-52577800	Weak transcription	Gastric	stomach
50	chr15:52575000-52579400	Weak transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links