Variant report

Variant	esv1007948
Chromosome Location	chr4:160484245-160492870
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RAPGEF2-5	chr4:160485093-160485299	expReg_chr4_8078_+

Extended variants
information (count: 300 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:300 , 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	rs79627241	chr4:160484308-160484309	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs545685317	chr4:160484313-160484314	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs979909	chr4:160484376-160484377	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs575936221	chr4:160484392-160484393	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs143548116	chr4:160484395-160484396	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs371164609	chr4:160484396-160484397	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs186217619	chr4:160484415-160484416	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs138431879	chr4:160484437-160484438	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs190692033	chr4:160484461-160484462	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs559094624	chr4:160484523-160484524	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs552785678	chr4:160484566-160484567	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs528275269	chr4:160484574-160484575	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs572688958	chr4:160484582-160484583	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs143891855	chr4:160484598-160484599	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs571198250	chr4:160484644-160484645	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs537396389	chr4:160484703-160484704	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs147246076	chr4:160484715-160484716	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs567288511	chr4:160484743-160484744	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs535930218	chr4:160484769-160484770	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs76968468	chr4:160484782-160484783	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs573425963	chr4:160484790-160484791	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs557533266	chr4:160484797-160484798	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs533411404	chr4:160484861-160484862	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs575828452	chr4:160484902-160484903	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs56336757	chr4:160484905-160484906	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs561094034	chr4:160484914-160484915	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs574798523	chr4:160484916-160484917	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs370721559	chr4:160484928-160484929	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs73859188	chr4:160484947-160484948	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs560223254	chr4:160484987-160484988	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs532511896	chr4:160485003-160485004	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs374878232	chr4:160485008-160485009	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs11321530	chr4:160485095-160485096	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
34	rs397995978	chr4:160485102-160485103	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
35	rs201057696	chr4:160485103-160485104	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
36	rs551157752	chr4:160485115-160485116	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
37	rs141585050	chr4:160485116-160485117	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
38	rs11944945	chr4:160485140-160485141	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs139399676	chr4:160485144-160485145	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
40	rs567120245	chr4:160485160-160485161	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
41	rs368045715	chr4:160485204-160485205	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
42	rs371811217	chr4:160485243-160485244	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
43	rs546676719	chr4:160485310-160485311	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs180737687	chr4:160485342-160485343	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs4691576	chr4:160485391-160485392	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs559182323	chr4:160485404-160485405	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs368735851	chr4:160485412-160485413	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs11945017	chr4:160485488-160485489	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs538129336	chr4:160485545-160485546	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs112547168	chr4:160485582-160485583	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:82)

Disease	PMID	Source
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
Breast cancer	21858162	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Gastric cancer	21586687	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17603634	CNVD
Acute lymphoblastic leukemia	20067559	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
Oral squamous cell carcinoma	17134496	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
Metanephric adenoma	20802469	CNVD
Breast cancer	16608533	CNVD
Lung cancer	19208797	CNVD
Wilms tumour	21544195	CNVD
Lung cancer	18438408	CNVD
Cancer	22429812	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
primary effusion lymphomas	17116491	CNVD
Breast cancer	16272173	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17133270	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Congenital anomalies of the kidney and urinary tract	20505237	CNVD
Breast cancer	17393978	CNVD
Esophageal cancer	21851588	CNVD
Testicular germ cell tumor	18059402	CNVD
Ovarian cancer	22174824	CNVD
Olfactory neuroblastoma	18408657	CNVD
Breast cancer	21785460	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Hodgkin''s lymphoma	17606441	CNVD
small cell lung cancer	20016488	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Ewing''s sarcoma	17952124	CNVD
Breast cancer	21633010	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Cancer	20581869	CNVD
Myelofibrosis	22110671	CNVD
Chronic lymphocytic leukemia	18922857	CNVD
Glioblastoma multiforme	22286061	CNVD
Breast cancer	20409316	CNVD
Basal cell lymphoma	17053054	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	20164919	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Breast cancer	21364760	CNVD
Schizophrenia	19805367	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:160479600-160506800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr4:160484200-160484400	Enhancers	Fetal Intestine Small	intestine
3	chr4:160484200-160486400	Enhancers	Fetal Intestine Large	intestine
4	chr4:160484600-160486000	Weak transcription	Fetal Intestine Small	intestine
5	chr4:160485200-160485400	Enhancers	Pancreas	Pancrea
6	chr4:160485400-160486200	Weak transcription	Pancreas	Pancrea
7	chr4:160485400-160486400	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr4:160485600-160486000	Active TSS	Rectal Mucosa Donor 29	rectum
9	chr4:160486000-160486200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
10	chr4:160486000-160486400	Enhancers	Liver	Liver
11	chr4:160486000-160486400	Enhancers	Fetal Intestine Small	intestine
12	chr4:160486200-160486400	Enhancers	Pancreas	Pancrea
13	chr4:160486400-160487200	Weak transcription	Pancreas	Pancrea
14	chr4:160487200-160487400	Enhancers	Pancreas	Pancrea

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