Variant report

Variant	rs62260708
Chromosome Location	chr3:47553806-47553807
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:47553798-47554532	K562	blood:	n/a	n/a
2	POLR2A	chr3:47553380-47555576	K562	blood:	n/a	n/a
3	POLR2A	chr3:47553774-47555628	K562	blood:	n/a	n/a
4	POLR2A	chr3:47552940-47555595	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:47553702-47555668	PFSK-1	brain:	n/a	n/a
6	NR2F2	chr3:47553046-47555690	K562	blood:	n/a	n/a
7	HEY1	chr3:47553390-47555623	K562	blood:	n/a	n/a
8	CBX3	chr3:47553092-47555580	K562	blood:	n/a	n/a
9	TBP	chr3:47553689-47555539	K562	blood:	n/a	n/a
10	POLR2A	chr3:47553796-47555586	Raji	blood:	n/a	n/a
11	POLR2A	chr3:47553792-47555692	SK-N-MC	brain:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:47537303..47543925-chr3:47549598..47557776,11	K562	blood:
2	chr3:47465805..47469012-chr3:47553458..47556919,3	K562	blood:
3	chr3:47553592..47556395-chr3:47843645..47846155,3	K562	blood:
4	chr3:47323574..47325560-chr3:47553415..47554938,2	MCF-7	breast:
5	chr3:47419982..47424786-chr3:47552828..47558423,7	K562	blood:
6	chr3:47515849..47519127-chr3:47552237..47555413,3	MCF-7	breast:
7	chr3:47514858..47522453-chr3:47552535..47558710,16	K562	blood:
8	chr3:47462410..47464482-chr3:47553675..47556809,5	MCF-7	breast:
9	chr3:47552778..47555538-chr3:47843986..47845971,3	MCF-7	breast:
10	chr3:47553771..47557534-chr3:47822005..47824702,4	K562	blood:
11	chr3:47422121..47423963-chr3:47552042..47554328,2	K562	blood:
12	chr3:47552921..47556395-chr3:47844042..47846639,3	K562	blood:
13	chr3:47517000..47518898-chr3:47553503..47555286,3	MCF-7	breast:
14	chr3:47421047..47423962-chr3:47553797..47559192,6	MCF-7	breast:
15	chr3:47516853..47519140-chr3:47552540..47554804,2	K562	blood:
16	chr3:47462501..47465704-chr3:47552223..47556756,6	MCF-7	breast:

No data

Variant related genes	Relation type
ELP6	TF binding region
ENSG00000173473	Chromatin interaction
ENSG00000114648	Chromatin interaction
ENSG00000271161	Chromatin interaction
ENSG00000114650	Chromatin interaction
ENSG00000076201	Chromatin interaction
ENSG00000272110	Chromatin interaction
ENSG00000088727	Chromatin interaction
ENSG00000260236	Chromatin interaction
ENSG00000132153	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs17784714	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62260713	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6800588	0.81[EUR][1000 genomes]
rs73081211	0.82[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47538400-47554000	Weak transcription	Stomach Mucosa	stomach
2	chr3:47541400-47554000	Weak transcription	Right Atrium	heart
3	chr3:47545800-47554000	Weak transcription	Colon Smooth Muscle	Colon
4	chr3:47546000-47554000	Weak transcription	Psoas Muscle	Psoas
5	chr3:47546000-47554000	Weak transcription	Small Intestine	intestine
6	chr3:47550000-47554000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:47551800-47554000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr3:47552400-47554000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:47552600-47554000	Weak transcription	Esophagus	oesophagus
10	chr3:47552600-47554000	Weak transcription	Ovary	ovary
11	chr3:47552800-47554000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:47552800-47554000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr3:47552800-47554000	Enhancers	Fetal Brain Male	brain
14	chr3:47553000-47554000	Enhancers	Primary T cells fromperipheralblood	blood
15	chr3:47553000-47554000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:47553000-47554000	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr3:47553000-47554000	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr3:47553000-47554000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr3:47553000-47554200	Enhancers	Fetal Heart	heart
20	chr3:47553000-47555600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr3:47553200-47554000	Enhancers	Primary B cells from peripheral blood	blood
22	chr3:47553200-47554000	Enhancers	Primary T cells from cord blood	blood
23	chr3:47553200-47554000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:47553200-47554000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
25	chr3:47553200-47554000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr3:47553200-47554000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:47553200-47554000	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr3:47553200-47554000	Enhancers	Brain Substantia Nigra	brain
29	chr3:47553200-47554000	Enhancers	Placenta	Placenta
30	chr3:47553200-47554000	Enhancers	Gastric	stomach
31	chr3:47553200-47554000	Enhancers	Left Ventricle	heart
32	chr3:47553200-47554000	Enhancers	Rectal Mucosa Donor 31	rectum
33	chr3:47553200-47554400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:47553400-47554000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr3:47553400-47554000	Enhancers	Liver	Liver
36	chr3:47553400-47554000	Enhancers	Brain Hippocampus Middle	brain
37	chr3:47553400-47554000	Enhancers	Lung	lung
38	chr3:47553400-47554000	Enhancers	Sigmoid Colon	Sigmoid Colon
39	chr3:47553400-47554200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:47553400-47554200	Flanking Active TSS	HUVEC	blood vessel
41	chr3:47553400-47554200	Flanking Active TSS	NHEK	skin
42	chr3:47553400-47555600	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr3:47553400-47555600	Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr3:47553600-47554000	Enhancers	Primary B cells from cord blood	blood
45	chr3:47553600-47554000	Enhancers	Primary hematopoietic stem cells	blood
46	chr3:47553600-47554000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:47553600-47554000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr3:47553600-47554000	Weak transcription	Fetal Lung	lung
49	chr3:47553600-47554000	Flanking Active TSS	Fetal Stomach	stomach
50	chr3:47553600-47554000	Enhancers	Placenta Amnion	Placenta Amnion

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