Variant report

Variant	esv20580
Chromosome Location	chr4:3599322-3601832
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:3597398..3599572-chr4:3602811..3604906,3	K562	blood:
2	chr4:3597553..3600117-chr4:3602844..3606284,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRPAP1-5	chr4:3600844-3601755	NONHSAT094890
2	lnc-LRPAP1-5	chr4:3600324-3600789	NONHSAT094890

Extended variants
information (count: 284 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:284 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs78864323	chr4:3599387-3599388	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
2	rs10025237	chr4:3599392-3599393	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	mRNA abundance
3	rs386670733	chr4:3599397-3599398	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs73201189	chr4:3599398-3599399	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
5	rs553229634	chr4:3599405-3599406	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs572949085	chr4:3599406-3599407	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs544961402	chr4:3599423-3599424	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs565237158	chr4:3599427-3599428	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs575664800	chr4:3599432-3599433	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs543266274	chr4:3599436-3599437	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs73201191	chr4:3599449-3599450	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs10025260	chr4:3599450-3599451	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
13	rs529076849	chr4:3599451-3599452	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs549342252	chr4:3599463-3599464	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs559674191	chr4:3599466-3599467	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs528105609	chr4:3599471-3599472	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs79008342	chr4:3599475-3599476	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs67770740	chr4:3599476-3599477	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs111383316	chr4:3599481-3599482	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs28514933	chr4:3599512-3599513	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs571277747	chr4:3599513-3599514	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs147419596	chr4:3599531-3599532	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs80195723	chr4:3599539-3599540	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs550389846	chr4:3599543-3599544	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs567877185	chr4:3599544-3599545	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs28645995	chr4:3599545-3599546	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs74920127	chr4:3599547-3599548	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs73201193	chr4:3599594-3599595	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
29	rs28495149	chr4:3599595-3599596	ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs573153917	chr4:3599649-3599650	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
31	rs111281030	chr4:3599655-3599656	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
32	rs538668552	chr4:3599658-3599659	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
33	rs558876116	chr4:3599661-3599662	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
34	rs575531286	chr4:3599662-3599663	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
35	rs113367688	chr4:3599681-3599682	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
36	rs73201196	chr4:3599683-3599684	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
37	rs62273028	chr4:3599697-3599698	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
38	rs73201199	chr4:3599713-3599714	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
39	rs542806460	chr4:3599720-3599721	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
40	rs62273029	chr4:3599738-3599739	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
41	rs112850639	chr4:3599754-3599755	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
42	rs62273030	chr4:3599763-3599764	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
43	rs73201200	chr4:3599765-3599766	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
44	rs73201202	chr4:3599784-3599785	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
45	rs73203104	chr4:3599788-3599789	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
46	rs564931224	chr4:3599810-3599811	ZNF genes & repeats Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs62273031	chr4:3599866-3599867	ZNF genes & repeats Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs550698428	chr4:3599867-3599868	ZNF genes & repeats Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs28719511	chr4:3599883-3599884	ZNF genes & repeats Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs28457729	chr4:3599887-3599888	ZNF genes & repeats Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:57)

Disease	PMID	Source
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
T-cell prolymphocytic leukemia	19278963	CNVD
Urothelial carcinoma	21177765	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Schizophrenia	21399695	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Breast cancer	21509527	CNVD
Ependymoma	20639864	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Lung cancer	18438408	CNVD
Schizophrenia	23813976	CNVD

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3595600-3600200	Weak transcription	Fetal Heart	heart
2	chr4:3595800-3599400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:3595800-3603400	Weak transcription	Right Atrium	heart
4	chr4:3597000-3604200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr4:3597000-3608000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
6	chr4:3597200-3599400	Enhancers	Fetal Brain Male	brain
7	chr4:3597400-3601200	ZNF genes & repeats	H9 Cell Line	embryonic stem cell
8	chr4:3598600-3607600	ZNF genes & repeats	Fetal Stomach	stomach
9	chr4:3598800-3601000	ZNF genes & repeats	Spleen	Spleen
10	chr4:3599200-3599600	Flanking Active TSS	HepG2	liver
11	chr4:3599400-3599800	Weak transcription	Fetal Brain Male	brain
12	chr4:3599400-3599800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
13	chr4:3599400-3601000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:3599600-3599800	Enhancers	HepG2	liver
15	chr4:3599600-3600400	Enhancers	Brain Anterior Caudate	brain
16	chr4:3599600-3601000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:3599800-3600600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:3599800-3600600	Enhancers	Fetal Brain Female	brain
19	chr4:3599800-3601800	ZNF genes & repeats	Fetal Brain Male	brain
20	chr4:3600000-3600400	Enhancers	Brain Cingulate Gyrus	brain
21	chr4:3600000-3600400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr4:3600000-3600800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
23	chr4:3600000-3601600	ZNF genes & repeats	Fetal Lung	lung
24	chr4:3600000-3604200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr4:3600200-3600600	ZNF genes & repeats	Fetal Heart	heart
26	chr4:3600200-3600800	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr4:3600200-3601000	ZNF genes & repeats	Gastric	stomach
28	chr4:3600200-3601400	ZNF genes & repeats	Esophagus	oesophagus
29	chr4:3600200-3601600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:3600200-3601600	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr4:3600200-3602200	ZNF genes & repeats	Pancreas	Pancrea
32	chr4:3600400-3601000	ZNF genes & repeats	Fetal Kidney	kidney
33	chr4:3600400-3601600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
34	chr4:3600600-3601400	Weak transcription	Fetal Brain Female	brain
35	chr4:3600800-3601000	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
36	chr4:3601000-3601200	Weak transcription	Spleen	Spleen
37	chr4:3601200-3601400	Enhancers	Spleen	Spleen
38	chr4:3601400-3601600	Enhancers	Fetal Brain Female	brain
39	chr4:3601400-3601600	Flanking Active TSS	Spleen	Spleen
40	chr4:3601600-3602000	Bivalent Enhancer	Placenta	Placenta
41	chr4:3601600-3602000	Active TSS	Spleen	Spleen
42	chr4:3601600-3611600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin

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