Variant report

Variant	rs62016466
Chromosome Location	chr15:52500672-52500673
allele	A/G
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52466781..52469103-chr15:52500146..52502200,2	MCF-7	breast:
2	chr15:52455479..52456330-chr15:52500106..52501199,5	MCF-7	breast:
3	chr15:52470561..52473090-chr15:52500221..52502576,3	MCF-7	breast:
4	chr15:52455491..52456419-chr15:52500266..52500940,3	K562	blood:
5	chr15:52271043..52273593-chr15:52500641..52502378,2	MCF-7	breast:
6	chr15:52483314..52485035-chr15:52498952..52501032,2	MCF-7	breast:
7	chr15:52475538..52476921-chr15:52500216..52501095,4	MCF-7	breast:
8	chr15:52477215..52477900-chr15:52500295..52500830,2	MCF-7	breast:
9	chr15:52216346..52217850-chr15:52500229..52502926,2	MCF-7	breast:
10	chr15:52499920..52501518-chr15:52503207..52505042,2	MCF-7	breast:
11	chr15:52475319..52476508-chr15:52500260..52501551,7	MCF-7	breast:
12	chr15:52473218..52475845-chr15:52500048..52503534,3	MCF-7	breast:
13	chr15:52486663..52491950-chr15:52497424..52502756,7	MCF-7	breast:
14	chr15:52274239..52275037-chr15:52500239..52501186,3	MCF-7	breast:
15	chr15:52498552..52502035-chr15:52503246..52505472,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000138594	Chromatin interaction
ENSG00000259577	Chromatin interaction
ENSG00000069966	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs16964751	1.00[AMR][1000 genomes]
rs16964760	1.00[AMR][1000 genomes]
rs16964764	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17540546	0.94[AMR][1000 genomes]
rs17540734	0.93[AMR][1000 genomes]
rs17612637	1.00[AMR][1000 genomes]
rs17612796	1.00[AMR][1000 genomes]
rs2231289	1.00[AMR][1000 genomes]
rs35581121	1.00[AMR][1000 genomes]
rs41277704	0.94[AMR][1000 genomes]
rs41277706	0.94[AMR][1000 genomes]
rs41277712	0.87[AMR][1000 genomes]
rs4776006	1.00[AMR][1000 genomes]
rs4776018	0.87[AMR][1000 genomes]
rs4776019	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62016465	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7168334	1.00[AMR][1000 genomes]
rs7181736	1.00[AMR][1000 genomes]
rs74015635	0.83[AMR][1000 genomes]
rs8024846	0.94[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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

No data

Chromatin state (count:69 , 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	chr15:52473600-52512400	Weak transcription	Primary B cells from cord blood	blood
3	chr15:52475800-52505600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:52479800-52532800	Weak transcription	Brain Angular Gyrus	brain
5	chr15:52484200-52503200	Weak transcription	Lung	lung
6	chr15:52484400-52503800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr15:52486000-52505800	Weak transcription	Psoas Muscle	Psoas
8	chr15:52487400-52505200	Weak transcription	Thymus	Thymus
9	chr15:52488600-52509800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr15:52488800-52505600	Weak transcription	Fetal Kidney	kidney
11	chr15:52489200-52520800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:52489200-52523800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr15:52490400-52503000	Weak transcription	Brain Hippocampus Middle	brain
14	chr15:52495600-52519000	Strong transcription	HepG2	liver
15	chr15:52496000-52500800	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr15:52496000-52505000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr15:52496200-52501600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr15:52496200-52505400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:52497200-52505200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr15:52497400-52501000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr15:52497400-52503000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:52497400-52505000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr15:52497400-52509400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr15:52497400-52510400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:52497400-52514600	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr15:52497400-52535600	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr15:52497600-52501600	Weak transcription	Fetal Muscle Trunk	muscle
28	chr15:52497600-52502800	Weak transcription	Adipose Nuclei	Adipose
29	chr15:52497600-52503200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr15:52497600-52503200	Weak transcription	Esophagus	oesophagus
31	chr15:52497600-52503200	Weak transcription	Fetal Intestine Small	intestine
32	chr15:52497600-52503200	Weak transcription	Fetal Muscle Leg	muscle
33	chr15:52497600-52503200	Weak transcription	Spleen	Spleen
34	chr15:52497600-52503400	Weak transcription	Fetal Intestine Large	intestine
35	chr15:52497600-52503600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr15:52497600-52503600	Weak transcription	Primary T cells from cord blood	blood
37	chr15:52497600-52503600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr15:52497600-52503600	Weak transcription	Colonic Mucosa	Colon
39	chr15:52497600-52504000	Weak transcription	Right Ventricle	heart
40	chr15:52497600-52508800	Weak transcription	Stomach Mucosa	stomach
41	chr15:52497800-52549000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr15:52498400-52500800	Enhancers	HUVEC	blood vessel
43	chr15:52498400-52503000	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr15:52498600-52502000	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr15:52498800-52501200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr15:52498800-52501800	Enhancers	Primary monocytes fromperipheralblood	blood
47	chr15:52499000-52501200	Weak transcription	Fetal Stomach	stomach
48	chr15:52499000-52501200	Weak transcription	Gastric	stomach
49	chr15:52499000-52501800	Enhancers	Primary hematopoietic stem cells short term culture	blood
50	chr15:52499000-52502800	Weak transcription	H9 Cell Line	embryonic stem cell

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