Variant report

Variant	esv3356673
Chromosome Location	chr4:562152-566350
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:560744..563501-chr4:564361..568313,3	K562	blood:
2	chr4:564165..566404-chr4:569838..571549,2	K562	blood:
3	chr4:565489..567950-chr4:568759..571284,3	MCF-7	breast:
4	chr4:564200..566117-chr4:572319..574456,3	K562	blood:
5	chr4:560447..562765-chr4:571972..574666,2	MCF-7	breast:

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	chromatin interactions

Extended variants
information (count: 207 )
Associated
traits (count: 60 )

Variant overlapped rSNPs/rCNVs (count:207 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs534775476	chr4:562154-562155	Bivalent Enhancer Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs181638852	chr4:562158-562159	Bivalent Enhancer Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs535528970	chr4:562191-562192	Bivalent Enhancer Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs33972056	chr4:562200-562201	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs201948554	chr4:562234-562235	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs185956748	chr4:562239-562240	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs567469471	chr4:562245-562246	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs78518952	chr4:562308-562309	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs374331304	chr4:562323-562324	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs543724634	chr4:562345-562346	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs561874299	chr4:562362-562363	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs189981299	chr4:562363-562364	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs540679442	chr4:562365-562366	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs574341162	chr4:562383-562384	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs559363670	chr4:562410-562411	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs532883757	chr4:562444-562445	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs35309205	chr4:562447-562448	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs551088282	chr4:562503-562504	Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs570693430	chr4:562509-562510	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
20	rs531825607	chr4:562525-562526	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
21	rs541702030	chr4:562537-562538	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
22	rs183034359	chr4:562541-562542	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
23	rs560449770	chr4:562631-562632	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
24	rs568666258	chr4:562648-562649	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
25	rs535802543	chr4:562684-562685	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
26	rs187688267	chr4:562707-562708	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
27	rs566150900	chr4:562730-562731	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
28	rs115630353	chr4:562789-562790	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
29	rs558317777	chr4:562801-562802	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
30	rs190953510	chr4:562818-562819	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
31	rs576295222	chr4:562823-562824	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
32	rs368432885	chr4:562856-562857	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
33	rs543255603	chr4:562875-562876	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
34	rs71602476	chr4:562892-562893	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
35	rs75226863	chr4:562902-562903	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
36	rs556872620	chr4:562932-562933	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
37	rs527583725	chr4:562961-562962	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
38	rs575144868	chr4:562968-562969	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
39	rs4501163	chr4:562973-562974	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
40	rs532796340	chr4:562976-562977	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
41	rs188026639	chr4:562987-562988	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
42	rs545481889	chr4:563021-563022	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
43	rs563087192	chr4:563064-563065	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
44	rs371433625	chr4:563067-563068	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
45	rs374750794	chr4:563068-563069	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
46	rs28758469	chr4:563080-563081	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
47	rs568704213	chr4:563086-563087	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
48	rs549308867	chr4:563119-563120	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
49	rs529583991	chr4:563173-563174	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
50	rs73074226	chr4:563192-563193	Weak transcription	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:60)

Disease	PMID	Source
Myelofibrosis	22110671	CNVD
Wolf-Hirschhorn syndrome	21549014	CNVD
Breast cancer	21806811	CNVD
Wolf-Hirschhorn syndrome	22283845	CNVD
Wolf-Hirschhorn syndrome	16773131	CNVD
Mental retardation	16773131	CNVD
Wolf-Hirschhorn syndrome	22470819	CNVD
Wolf-Hirschhorn syndrome	18541967	CNVD
sporadic birth defects	19047251	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Retinitis pigmentosa	18421352	CNVD
Wolf-Hirschhorn syndrome	19259404	CNVD
Bladder cancer	19242612	CNVD
Breast cancer	19242612	CNVD
Congenital anomalies of the kidney and urinary tract	19242612	CNVD
abnormal development	18461090	CNVD
Olfactory neuroblastoma	18408657	CNVD
Wilms tumour	21544195	CNVD
Melanoma	20688739	CNVD
Colorectal cancer	16272173	CNVD
Non-syndromic sensorineural hearing loss	20606397	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17603634	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	17533364	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Cancer	21637783	CNVD
Melanoma	21693616	CNVD
Squamous cell cancer	21044232	CNVD
Colorectal cancer	20709793	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Non-small cell lung cancer	21044232	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	17387387	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Cervical cancer	21062161	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Neuroblastoma	18923191	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	17142309	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Developmental delay	21147756	CNVD
Urothelial carcinoma	21177765	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Lung cancer	18438408	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:561600-562200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:561800-562200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:562200-563800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:563800-564000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr4:563800-564400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:563800-564400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:564000-564400	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:564200-564400	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr4:564200-564400	Enhancers	Brain Inferior Temporal Lobe	brain
10	chr4:564400-564800	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:564400-565800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr4:564600-564800	Bivalent Enhancer	Placenta	Placenta
13	chr4:565600-565800	Bivalent Enhancer	Fetal Brain Female	brain
14	chr4:565600-567200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr4:565800-566200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:565800-566200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:565800-566200	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
18	chr4:565800-566200	ZNF genes & repeats	Gastric	stomach
19	chr4:565800-567000	Enhancers	Brain Angular Gyrus	brain
20	chr4:565800-567800	Bivalent Enhancer	Fetal Brain Male	brain
21	chr4:566000-566200	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr4:566200-568600	Weak transcription	Gastric	stomach

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