Variant report

Variant	rs564504819
Chromosome Location	chr4:568748-568749
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F6	chr4:568697-569379	H1-hESC	embryonic stem cell:	n/a	chr4:568834-568843
2	POLR2A	chr4:568373-568989	SK-N-MC	brain:	n/a	n/a
3	REST	chr4:568516-569842	PFSK-1	brain:	n/a	chr4:569243-569263 chr4:569243-569263 chr4:569178-569198 chr4:569813-569826 chr4:569681-569691 chr4:569251-569261 chr4:569244-569262 chr4:569243-569252 chr4:569243-569263 chr4:569248-569257 chr4:569249-569263 chr4:568592-568605 chr4:569728-569741 chr4:569246-569259 chr4:568580-568593 chr4:569243-569256 chr4:569731-569744
4	MAX	chr4:568444-568978	H1-hESC	embryonic stem cell:	n/a	chr4:568550-568560 chr4:568884-568891 chr4:568549-568557
5	MAX	chr4:568478-569455	H1-hESC	embryonic stem cell:	n/a	chr4:568550-568560 chr4:568884-568891 chr4:568549-568557
6	POLR2A	chr4:568722-570035	H1-neurons	neurons:	n/a	n/a
7	ZNF143	chr4:568741-568840	H1-hESC	embryonic stem cell:	n/a	n/a
8	REST	chr4:568696-569858	PFSK-1	brain:	n/a	chr4:569243-569263 chr4:569243-569263 chr4:569178-569198 chr4:569813-569826 chr4:569681-569691 chr4:569251-569261 chr4:569244-569262 chr4:569243-569252 chr4:569243-569263 chr4:569248-569257 chr4:569249-569263 chr4:569728-569741 chr4:569246-569259 chr4:569243-569256 chr4:569731-569744

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PIGG-1	chr4:562509-568807	l_2577_chr4:560751-568807_brain

Variant related genes	Relation type
ENSG00000273238	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 0)

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	esv2830422	chr4:72247-681939	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
3	nsv532703	chr4:72447-614414	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv931097	chr4:72447-683874	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	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
6	nsv532704	chr4:85040-628550	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
7	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
8	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
9	nsv878245	chr4:509178-694613	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	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
11	esv1796312	chr4:560701-569738	Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
12	esv3420187	chr4:567777-570825	Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
13	esv3436442	chr4:568052-571400	Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
14	esv3358052	chr4:568427-571250	Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:567200-572200	Active TSS	Brain Angular Gyrus	brain
2	chr4:567400-568800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:567400-569000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr4:567600-570800	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr4:568200-568800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
6	chr4:568200-568800	Bivalent Enhancer	Fetal Brain Male	brain
7	chr4:568200-568800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr4:568200-569000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr4:568200-569200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
10	chr4:568200-569200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:568200-569400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr4:568200-569400	Bivalent Enhancer	Spleen	Spleen
13	chr4:568200-570800	Active TSS	Brain Anterior Caudate	brain
14	chr4:568400-568800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr4:568400-568800	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
16	chr4:568400-568800	Bivalent Enhancer	Right Ventricle	heart
17	chr4:568400-569000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr4:568400-569000	Bivalent Enhancer	Ovary	ovary
19	chr4:568400-569400	Enhancers	Primary hematopoietic stem cells	blood
20	chr4:568400-569400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
21	chr4:568400-569600	Bivalent Enhancer	Esophagus	oesophagus
22	chr4:568400-571600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
23	chr4:568600-568800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
24	chr4:568600-568800	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:568600-568800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
26	chr4:568600-568800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
27	chr4:568600-568800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
28	chr4:568600-568800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr4:568600-568800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr4:568600-568800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr4:568600-568800	Bivalent Enhancer	Colonic Mucosa	Colon
32	chr4:568600-568800	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
33	chr4:568600-568800	Bivalent/Poised TSS	Fetal Brain Female	brain
34	chr4:568600-568800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
35	chr4:568600-568800	Enhancers	Right Atrium	heart
36	chr4:568600-568800	Enhancers	Stomach Smooth Muscle	stomach
37	chr4:568600-569000	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr4:568600-569400	Bivalent Enhancer	Left Ventricle	heart
39	chr4:568600-569600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
40	chr4:568600-569600	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr4:568600-569600	Bivalent Enhancer	Lung	lung
42	chr4:568600-569800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr4:568600-569800	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:568600-569800	Enhancers	Gastric	stomach
45	chr4:568600-570800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
46	chr4:568600-571200	Enhancers	Pancreas	Pancrea
47	chr4:568600-571400	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr4:568600-571800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
49	chr4:568600-571800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell

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