Variant report

Variant	rs60279448
Chromosome Location	chr15:52525904-52525905
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:52521390..52524844-chr15:52525282..52528513,3	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11070886	1.00[EUR][1000 genomes]
rs11070890	0.84[ASN][1000 genomes]
rs17650476	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59060156	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs59211915	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61367038	1.00[AMR][1000 genomes]
rs61551630	1.00[AMR][1000 genomes]
rs6493548	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7165256	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7180204	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv904220	chr15:52485024-52526507	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	esv1851383	chr15:52501831-52534344	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	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
7	nsv1537	chr15:52502246-52537067	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	esv2637818	chr15:52524720-52526349	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52479800-52532800	Weak transcription	Brain Angular Gyrus	brain
2	chr15:52497400-52535600	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr15:52497800-52549000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr15:52501600-52532600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr15:52501800-52528000	Weak transcription	Fetal Heart	heart
6	chr15:52505400-52526800	Weak transcription	Right Ventricle	heart
7	chr15:52505600-52549200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr15:52506400-52548800	Weak transcription	Fetal Kidney	kidney
9	chr15:52509400-52537200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr15:52509800-52526800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr15:52512800-52534000	Weak transcription	Colonic Mucosa	Colon
12	chr15:52514000-52539400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr15:52516000-52549400	Weak transcription	Left Ventricle	heart
14	chr15:52516200-52526400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr15:52516800-52528200	Weak transcription	Spleen	Spleen
16	chr15:52517400-52526800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr15:52517400-52527000	Weak transcription	Brain Anterior Caudate	brain
18	chr15:52518600-52526800	Weak transcription	Gastric	stomach
19	chr15:52518800-52526200	Weak transcription	Fetal Muscle Leg	muscle
20	chr15:52519000-52526200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr15:52519000-52527000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr15:52519000-52528200	Weak transcription	Duodenum Mucosa	Duodenum
23	chr15:52520200-52533800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr15:52521400-52526800	Weak transcription	Liver	Liver
25	chr15:52521600-52530400	Weak transcription	Fetal Intestine Large	intestine
26	chr15:52521600-52531400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr15:52522400-52526800	Weak transcription	Lung	lung
28	chr15:52522400-52531400	Weak transcription	Stomach Mucosa	stomach
29	chr15:52523400-52528600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr15:52523400-52530000	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr15:52523400-52530400	Strong transcription	HepG2	liver
32	chr15:52523400-52532400	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr15:52523400-52532600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:52523400-52548600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr15:52523600-52530000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
36	chr15:52523800-52527000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr15:52523800-52527200	Enhancers	Primary T cells from cord blood	blood
38	chr15:52523800-52528600	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr15:52523800-52528600	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr15:52523800-52530000	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr15:52524000-52526600	Weak transcription	Fetal Intestine Small	intestine
42	chr15:52524000-52526800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr15:52524000-52528000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr15:52524400-52526200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr15:52524400-52579400	Weak transcription	Small Intestine	intestine
46	chr15:52524600-52526200	Enhancers	NHEK	skin
47	chr15:52524600-52528600	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr15:52524600-52530000	Strong transcription	HUES64 Cell Line	embryonic stem cell
49	chr15:52524800-52526000	Enhancers	HSMMtube	muscle
50	chr15:52524800-52526200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links