Variant report

Variant	rs56011263
Chromosome Location	chr4:702972-702973
allele	C/T
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:701950..703734-chr4:716320..717930,2	K562	blood:
2	chr4:698332..701237-chr4:701746..703364,2	K562	blood:
3	chr4:701224..703407-chr4:720806..724106,3	K562	blood:
4	chr4:697549..703820-chr4:770860..775722,9	K562	blood:
5	chr4:700770..703438-chr4:730148..732108,2	K562	blood:
6	chr4:674123..676409-chr4:700716..703557,3	K562	blood:
7	chr4:682326..684833-chr4:700614..702994,2	MCF-7	breast:
8	chr4:671675..674589-chr4:702337..705311,3	MCF-7	breast:
9	chr4:687290..688821-chr4:702192..704645,2	MCF-7	breast:
10	chr4:700678..704217-chr4:710705..714201,3	MCF-7	breast:
11	chr4:674123..675815-chr4:701035..703606,2	K562	blood:
12	chr4:666295..671517-chr4:698228..703248,8	MCF-7	breast:
13	chr4:702491..704848-chr4:710046..712151,2	K562	blood:
14	chr4:701349..702978-chr4:774069..776105,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000169026	Chromatin interaction
ENSG00000169020	Chromatin interaction
ENSG00000248416	Chromatin interaction
ENSG00000249592	Chromatin interaction
ENSG00000185619	Chromatin interaction
ENSG00000215375	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs13126245	0.82[AMR][1000 genomes]
rs35734242	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs55948606	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011715	chr4:43860-823487	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv532702	chr4:72447-755236	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv1005224	chr4:507005-900281	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Strong transcription Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv536976	chr4:507005-900281	Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv822425	chr4:540105-1413799	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	108 gene(s)	inside rSNPs	diseases
6	esv2757916	chr4:603208-931354	Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	esv2759217	chr4:603208-931354	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv878247	chr4:607202-925149	Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
9	nsv530490	chr4:614355-1399150	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
10	nsv593206	chr4:625962-735150	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	esv1829397	chr4:655939-1041957	Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
12	nsv829834	chr4:665477-775524	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
13	nsv593209	chr4:686563-747810	Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv870115	chr4:692811-733794	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56011263	RP11-440L14.1	cis	Whole Blood	GTEx
rs56011263	PCGF3	cis	Whole Blood	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:700000-704400	Enhancers	Fetal Brain Male	brain
2	chr4:700400-703000	Enhancers	Primary B cells from peripheral blood	blood
3	chr4:700400-703400	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr4:700400-703600	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr4:701000-703000	Enhancers	Fetal Heart	heart
6	chr4:701000-703200	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr4:701000-704000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:701000-704000	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr4:701000-705800	Weak transcription	Fetal Kidney	kidney
10	chr4:701200-703000	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr4:701200-703000	Active TSS	HSMM	muscle
12	chr4:701200-703200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr4:701200-703200	Weak transcription	A549	lung
14	chr4:701200-703400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr4:701200-703600	Enhancers	Left Ventricle	heart
16	chr4:701200-703600	Enhancers	Lung	lung
17	chr4:701200-703600	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr4:701200-704400	Enhancers	Right Atrium	heart
19	chr4:701200-704600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr4:701200-713400	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr4:701200-713400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr4:701200-714600	Weak transcription	NHDF-Ad	bronchial
23	chr4:701200-724400	Weak transcription	Aorta	Aorta
24	chr4:701400-703000	Genic enhancers	Fetal Stomach	stomach
25	chr4:701400-703000	Enhancers	Gastric	stomach
26	chr4:701400-703200	Weak transcription	Osteobl	bone
27	chr4:701400-703400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr4:701400-704200	Enhancers	Right Ventricle	heart
29	chr4:701400-705000	Enhancers	Pancreas	Pancrea
30	chr4:701400-705200	Strong transcription	Fetal Intestine Small	intestine
31	chr4:701400-714000	Weak transcription	HMEC	breast
32	chr4:701400-715200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
33	chr4:701400-724400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr4:701400-724800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr4:701600-716800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr4:701800-703200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr4:701800-703400	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr4:701800-703600	Enhancers	Duodenum Mucosa	Duodenum
39	chr4:701800-705000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr4:702000-703000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr4:702000-703000	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
42	chr4:702000-703400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr4:702000-703400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr4:702000-703600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr4:702000-703600	Genic enhancers	Cortex derived primary cultured neurospheres	brain
46	chr4:702000-704000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr4:702000-704000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
48	chr4:702000-704400	Genic enhancers	Fetal Muscle Leg	muscle
49	chr4:702000-704400	Enhancers	Small Intestine	intestine
50	chr4:702000-705000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links