Variant report

Variant	nsv1009297
Chromosome Location	chr4:58053516-58098616
allele	n/a
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:5)
LncRNA
region (count:23)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:58061801..58064588-chr4:58070107..58072268,2	K562	blood:
2	chr4:58056446..58057481-chr4:58169186..58169817,3	MCF-7	breast:
3	chr4:58047640..58050466-chr4:58055836..58057973,2	K562	blood:
4	chr4:58061801..58064588-chr4:58070107..58072268,2	K562	blood:
5	chr4:58029500..58030425-chr4:58077363..58078281,2	K562	blood:

(count:23 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-POLR2B-1	chr4:58070644-58070759	ENSG00000245067.2
2	lnc-POLR2B-1	chr4:58070644-58070759	XLOC_003547
3	lnc-POLR2B-1	chr4:58067299-58068163	XLOC_003547
4	lnc-POLR2B-1	chr4:58071240-58071627	XLOC_003547
5	lnc-POLR2B-1	chr4:58067952-58067986	XLOC_003547
6	lnc-POLR2B-1	chr4:58070307-58070759	XLOC_003547
7	lnc-POLR2B-1	chr4:58067299-58067381	XLOC_003547
8	lnc-POLR2B-1	chr4:58054336-58054485	ENSG00000245067.2
9	lnc-POLR2B-1	chr4:58067584-58067986	XLOC_003547
10	lnc-POLR2B-1	chr4:58067299-58067986	ENSG00000245067.2
11	lnc-POLR2B-1	chr4:58071240-58071676	XLOC_003547
12	lnc-POLR2B-1	chr4:58069674-58069736	XLOC_003547
13	lnc-POLR2B-1	chr4:58071240-58071465	ENSG00000245067.2
14	lnc-POLR2B-1	chr4:58070644-58070759	ENSG00000245067.2
15	lnc-POLR2B-1	chr4:58069401-58069761	NONHSAT096554
16	lnc-POLR2B-1	chr4:58067299-58067381	XLOC_003547
17	lnc-POLR2B-1	chr4:58071240-58071590	XLOC_003547
18	lnc-POLR2B-1	chr4:58054431-58054485	XLOC_003547
19	lnc-POLR2B-1	chr4:58071240-58071676	ENSG00000245067.2
20	lnc-POLR2B-1	chr4:58070644-58070759	XLOC_003547
21	lnc-POLR2B-1	chr4:58067299-58067381	ENSG00000245067.2
22	lnc-POLR2B-1	chr4:58071240-58071464	NONHSAT096544
23	lnc-POLR2B-1	chr4:58070644-58070740	NONHSAT096554

No data

Variant related genes	Relation type
SPATS2	miRNA target sites
INSIG1	miRNA target sites
INSIG2	miRNA target sites
TMX3	miRNA target sites
HAUS3	miRNA target sites

Extended variants
information (count: 1746 )
Associated
traits (count: 89 )

Variant overlapped rSNPs/rCNVs (count:1746 , 50 per page) page: 1 2 3 4 5 6 7 ... 35

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs34285935	chr4:58053539-58053540	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs55823928	chr4:58053602-58053603	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs535798289	chr4:58053618-58053619	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs538699043	chr4:58053644-58053645	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
5	rs185338425	chr4:58053664-58053665	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs557425588	chr4:58053721-58053722	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs6857279	chr4:58053743-58053744	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs541742418	chr4:58053755-58053756	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs534543848	chr4:58053771-58053772	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs557967448	chr4:58053772-58053773	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs577877871	chr4:58053798-58053799	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs76528505	chr4:58053821-58053822	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs563536256	chr4:58053834-58053835	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs79595098	chr4:58053845-58053846	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs542605366	chr4:58053852-58053853	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs6857528	chr4:58053877-58053878	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs528177658	chr4:58053885-58053886	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs572584780	chr4:58053901-58053902	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs551157422	chr4:58053924-58053925	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs539978174	chr4:58053930-58053931	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs190244695	chr4:58053973-58053974	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs533301218	chr4:58054008-58054009	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs550069853	chr4:58054036-58054037	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs570002562	chr4:58054054-58054055	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs372295140	chr4:58054076-58054077	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs535525191	chr4:58054085-58054086	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs549337488	chr4:58054091-58054092	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs60029672	chr4:58054157-58054158	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs535133154	chr4:58054158-58054159	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs148250295	chr4:58054170-58054171	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs540501411	chr4:58054179-58054180	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
32	rs11945297	chr4:58054196-58054197	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs537234117	chr4:58054200-58054201	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs368140930	chr4:58054272-58054273	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs192601293	chr4:58054283-58054284	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs573860555	chr4:58054318-58054319	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs201212323	chr4:58054329-58054330	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs372073934	chr4:58054350-58054351	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
39	rs542294795	chr4:58054383-58054384	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
40	rs184935115	chr4:58054402-58054403	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
41	rs189100680	chr4:58054433-58054434	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
42	rs560336388	chr4:58054541-58054542	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs544704572	chr4:58054560-58054561	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs564595677	chr4:58054608-58054609	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
45	rs180943255	chr4:58054633-58054634	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
46	rs375101154	chr4:58054653-58054654	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
47	rs186243043	chr4:58054665-58054666	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
48	rs79994849	chr4:58054666-58054667	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
49	rs35950951	chr4:58054671-58054672	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
50	rs529574324	chr4:58054677-58054678	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:89)

Disease	PMID	Source
Gastrointestinal stromal cancer	16982739	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Glioblastoma multiforme	21080181	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Chordoma	21602918	CNVD
HIV/AIDS	22032296	CNVD
Medulloblastoma	21979893	CNVD
Neuroblastoma	18923191	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Breast cancer	21858162	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
lymphocytic leukemia	21291569	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Non-small cell lung cancer	21829676	CNVD
Melanoma	22183965	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Lung cancer	18438408	CNVD
Renal cell carcinoma	18194544	CNVD
Breast cancer	17603634	CNVD
Glioblastoma multiforme	21922591	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Parkinson disease	21956041	CNVD
Mental retardation	20522426	CNVD
delayed speech	20522426	CNVD
growth disorder	20522426	CNVD
Hepatocellular carcinoma	16750200	CNVD
Myxofibrosarcoma	16751306	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Acute myeloid leukemia	20729466	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Parkinson disease	18923514	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Cancer	21183584	CNVD
Breast cancer	16272173	CNVD
Glioblastoma multiforme	19435819	CNVD
Multiple myeloma	16616336	CNVD
Colorectal cancer	19359472	CNVD
Malignant mesothelioma	18160781	CNVD
Medulloblastoma	18056178	CNVD
Multiple myeloma	17077331	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
4q-syndrome	17576883	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Colorectal cancer	20709793	CNVD
Muscular dystrophy	21149563	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Liposarcoma	21253554	CNVD
Oligodendroglial tumors	17285580	CNVD
Cervical cancer	21062161	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma multiforme	22286061	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Ovarian neoplasms	16753589	CNVD
Metanephric adenoma	20802469	CNVD
Breast cancer	16608533	CNVD
Glioblastoma	17504929	CNVD
Glioblastoma	16823502	CNVD
Melanoma	16908931	CNVD
Glioblastoma	20031968	CNVD
Medulloblastoma	19270706	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Olfactory neuroblastoma	18408657	CNVD
Basal cell lymphoma	19029149	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Rhabdomyosarcoma	16790082	CNVD
Gastrointestinal stromal cancer	17438095	CNVD
Colorectal cancer	16272173	CNVD
Lung cancer	19208797	CNVD
small cell lung cancer	20016488	CNVD
Wilms tumour	21544195	CNVD
Glioblastoma multiforme	21138945	CNVD
Breast cancer	21785460	CNVD
Cancer	22183965	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:266 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:58047400-58059600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr4:58048600-58059600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr4:58049000-58059400	Weak transcription	Brain Angular Gyrus	brain
4	chr4:58049200-58059200	Weak transcription	Brain Substantia Nigra	brain
5	chr4:58050200-58054200	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr4:58050400-58054600	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr4:58051200-58057000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr4:58051400-58053600	Weak transcription	Brain Anterior Caudate	brain
9	chr4:58051400-58054200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:58051600-58053600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:58051600-58053600	Weak transcription	Brain Hippocampus Middle	brain
12	chr4:58051800-58054000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:58051800-58054200	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr4:58051800-58054200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr4:58052000-58054200	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr4:58052000-58054200	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr4:58052200-58053600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:58052200-58054200	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr4:58052200-58054400	Enhancers	HMEC	breast
20	chr4:58052400-58053600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr4:58052400-58053600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr4:58052400-58054600	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr4:58052600-58053600	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr4:58052600-58054200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr4:58052600-58054400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr4:58052600-58054400	Enhancers	NHEK	skin
27	chr4:58052800-58058200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr4:58052800-58060400	Weak transcription	Aorta	Aorta
29	chr4:58053000-58054800	Enhancers	H1 Cell Line	embryonic stem cell
30	chr4:58053400-58053800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr4:58053400-58053800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr4:58053400-58054000	Enhancers	Brain Cingulate Gyrus	brain
33	chr4:58053600-58054000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
34	chr4:58053600-58054000	Enhancers	Brain Anterior Caudate	brain
35	chr4:58053600-58054000	Enhancers	Brain Hippocampus Middle	brain
36	chr4:58053600-58054200	Enhancers	H9 Cell Line	embryonic stem cell
37	chr4:58053600-58054200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr4:58053600-58054200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr4:58053600-58054200	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr4:58053800-58054000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:58053800-58054000	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:58054000-58055400	Weak transcription	Brain Anterior Caudate	brain
43	chr4:58054000-58057200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr4:58054000-58057400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
45	chr4:58054000-58057800	Weak transcription	Brain Hippocampus Middle	brain
46	chr4:58054000-58059400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr4:58054200-58054400	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr4:58054200-58054800	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr4:58054200-58056400	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr4:58054200-58056600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links