Variant report

Variant	rs549097612
Chromosome Location	chr4:571801-571802
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	KAP1	chr4:571118-572058	HEK293	kidney:	n/a	chr4:571445-571454
2	SUZ12	chr4:571267-572780	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTBP2	chr4:570834-571856	H1-hESC	embryonic stem cell:	n/a	n/a
4	REST	chr4:568983-572510	H1-neurons	neurons:	n/a	chr4:569243-569263 chr4:569243-569263 chr4:570373-570386 chr4:569178-569198 chr4:569813-569826 chr4:569681-569691 chr4:570404-570417 chr4:571320-571333 chr4:570810-570820 chr4:569251-569261 chr4:569244-569262 chr4:569243-569252 chr4:571381-571394 chr4:569243-569263 chr4:570817-570830 chr4:569248-569257 chr4:569249-569263 chr4:571378-571391 chr4:569728-569741 chr4:569246-569259 chr4:569243-569256 chr4:569731-569744
5	POLR2A	chr4:570768-572264	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:570799..573548-chr4:580234..582794,2	MCF-7	breast:
2	chr4:560309..561984-chr4:571273..573145,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PDE6B-1	chr4:570957-572108	ENSG00000256961
2	lnc-PDE6B-1	chr4:571079-572650	NONHSAT094567
3	lnc-PDE6B-1	chr4:571582-574077	NONHSAT094572
4	lnc-PDE6B-1	chr4:571576-571933	NONHSAT094574

Variant related genes	Relation type
ENSG00000273238	TF binding region

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

Variant overlapped rSNPs/rCNVs (count:13 , 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	esv1815184	chr4:568928-575087	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
12	esv1816544	chr4:568928-575087	Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
13	esv3339025	chr4:569577-572125	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:567200-572200	Active TSS	Brain Angular Gyrus	brain
2	chr4:568800-572000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
3	chr4:570200-572200	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
4	chr4:570200-572800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr4:570200-573200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr4:570400-572200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr4:570600-572000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
8	chr4:570800-572200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
9	chr4:570800-572200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
10	chr4:571000-572400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr4:571200-572000	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:571200-572000	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
13	chr4:571200-572200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr4:571200-572400	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr4:571200-572600	Weak transcription	Pancreas	Pancrea
16	chr4:571200-573600	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr4:571400-572000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
18	chr4:571400-572000	Bivalent Enhancer	Right Ventricle	heart
19	chr4:571400-572400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr4:571400-572800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
21	chr4:571600-572000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
22	chr4:571600-572000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
23	chr4:571600-572200	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:571600-572200	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
25	chr4:571600-572200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
26	chr4:571600-572200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
27	chr4:571600-572400	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:571600-572600	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr4:571600-572600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr4:571600-572800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr4:571800-572000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
32	chr4:571800-572000	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:571800-572000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr4:571800-572000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr4:571800-572000	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
36	chr4:571800-572000	Bivalent Enhancer	HepG2	liver
37	chr4:571800-572000	Bivalent Enhancer	HSMMtube	muscle
38	chr4:571800-572000	Bivalent Enhancer	NHEK	skin
39	chr4:571800-572200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr4:571800-572200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
41	chr4:571800-572200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
42	chr4:571800-572200	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr4:571800-572200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
44	chr4:571800-572400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
45	chr4:571800-572800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr4:571800-572800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
47	chr4:571800-573000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr4:571800-573400	Bivalent/Poised TSS	Brain Anterior Caudate	brain
49	chr4:571800-573800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:571800-574000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell

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