Variant report

Variant	rs17541016
Chromosome Location	chr15:52513210-52513211
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52505434..52507299-chr15:52513137..52515697,2	MCF-7	breast:
2	chr15:52469037..52470714-chr15:52511840..52513591,2	MCF-7	breast:
3	chr15:52509233..52510844-chr15:52512535..52515103,2	K562	blood:
4	chr15:52513190..52514784-chr15:52519152..52521403,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128833	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs16964760	0.84[TSI][hapmap]
rs17540546	1.00[CEU][hapmap]
rs3751610	0.95[ASN][1000 genomes]
rs4776020	0.92[TSI][hapmap]
rs55676113	0.88[ASN][1000 genomes]
rs74015635	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52473200-52513600	Weak transcription	Rectal Smooth Muscle	rectum
2	chr15:52479800-52532800	Weak transcription	Brain Angular Gyrus	brain
3	chr15:52489200-52520800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr15:52489200-52523800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:52495600-52519000	Strong transcription	HepG2	liver
6	chr15:52497400-52514600	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr15:52497400-52535600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr15:52497800-52549000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr15:52499000-52515600	Weak transcription	Left Ventricle	heart
10	chr15:52500000-52519000	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr15:52501600-52519000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:52501600-52532600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr15:52501800-52528000	Weak transcription	Fetal Heart	heart
14	chr15:52502000-52519200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr15:52502000-52523800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr15:52502400-52520200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:52502600-52519000	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr15:52502800-52517800	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr15:52503200-52519200	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr15:52505400-52526800	Weak transcription	Right Ventricle	heart
21	chr15:52505600-52525600	Weak transcription	Brain Hippocampus Middle	brain
22	chr15:52505600-52549200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr15:52506000-52516400	Weak transcription	Spleen	Spleen
24	chr15:52506400-52514600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:52506400-52548800	Weak transcription	Fetal Kidney	kidney
26	chr15:52508600-52518800	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr15:52508600-52519000	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr15:52509000-52516000	Strong transcription	Sigmoid Colon	Sigmoid Colon
29	chr15:52509000-52516400	Strong transcription	Fetal Muscle Leg	muscle
30	chr15:52509000-52516400	Strong transcription	Fetal Stomach	stomach
31	chr15:52509000-52519000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
32	chr15:52509000-52519000	Strong transcription	Duodenum Mucosa	Duodenum
33	chr15:52509000-52519200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr15:52509400-52537200	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr15:52509800-52514600	Weak transcription	Lung	lung
36	chr15:52509800-52521800	Weak transcription	Psoas Muscle	Psoas
37	chr15:52509800-52526800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr15:52510400-52516600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr15:52510600-52514400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr15:52510600-52519800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr15:52510600-52521000	Weak transcription	Stomach Mucosa	stomach
42	chr15:52510600-52525600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr15:52511000-52513600	Weak transcription	Adipose Nuclei	Adipose
44	chr15:52511200-52518400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr15:52511600-52513600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr15:52511800-52514200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr15:52511800-52514200	Weak transcription	Gastric	stomach
48	chr15:52511800-52514400	Weak transcription	Brain Anterior Caudate	brain
49	chr15:52511800-52514600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr15:52511800-52514600	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links