Variant report

Variant	esv3692830
Chromosome Location	chr4:98625497-98669243
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	chr4:97091475..97092009-chr4:98641981..98642501,2	MCF-7	breast:
2	chr4:98641928..98642827-chr4:98905748..98906362,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TSPAN5-3	chr4:98633850-98633965	NONHSAT097477

Extended variants
information (count: 262 )
Associated
traits (count: 79 )

Variant overlapped rSNPs/rCNVs (count:262 , 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	rs376773252	chr4:98633851-98633852	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
2	rs150068765	chr4:98633897-98633898	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
3	rs17026871	chr4:98633911-98633912	Inactive region	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs149202445	chr4:98633962-98633963	Inactive region	lncRNA	n/a	Overlapped CNVs	n/a
5	rs576712610	chr4:98640806-98640807	Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs544102635	chr4:98640818-98640819	Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs17026893	chr4:98640825-98640826	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs529508545	chr4:98640830-98640831	Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs541500401	chr4:98640909-98640910	Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs559849470	chr4:98640964-98640965	Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs186998408	chr4:98640980-98640981	Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs111967565	chr4:98641005-98641006	Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs570429661	chr4:98641006-98641007	Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs531466551	chr4:98641043-98641044	Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs147892566	chr4:98641076-98641077	Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs568134371	chr4:98641109-98641110	Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs192341942	chr4:98641116-98641117	Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs554295410	chr4:98641151-98641152	Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs141374583	chr4:98641178-98641179	Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs34503459	chr4:98641185-98641186	Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs182156338	chr4:98641217-98641218	Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs150348827	chr4:98641250-98641251	Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs562889510	chr4:98641278-98641279	Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs543727796	chr4:98641288-98641289	Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs559239256	chr4:98641315-98641316	Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs556050883	chr4:98641410-98641411	Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs573879637	chr4:98641424-98641425	Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs541267567	chr4:98641456-98641457	Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs17026896	chr4:98641463-98641464	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs527337349	chr4:98641501-98641502	Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs545504553	chr4:98641638-98641639	Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs563893553	chr4:98641665-98641666	Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs567488157	chr4:98641722-98641723	Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs537999341	chr4:98641734-98641735	Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs373574507	chr4:98641744-98641745	Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs186689034	chr4:98641768-98641769	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs529093932	chr4:98641788-98641789	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs547660789	chr4:98641798-98641799	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs113994771	chr4:98641800-98641801	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs539905599	chr4:98641808-98641809	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs549733541	chr4:98641901-98641902	Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs11728887	chr4:98641952-98641953	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs569926743	chr4:98642001-98642002	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs370250687	chr4:98642026-98642027	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs145120357	chr4:98642033-98642034	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs555776100	chr4:98642050-98642051	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs149107197	chr4:98642084-98642085	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs143165442	chr4:98642111-98642112	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs112580450	chr4:98642129-98642130	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs148198685	chr4:98642137-98642138	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:79)

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
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
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Melanoma	18172304	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Breast cancer	17603634	CNVD
Hepatocellular carcinoma	16750200	CNVD
Myxofibrosarcoma	16751306	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Parkinson disease	18923514	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Cancer	21183584	CNVD
Breast cancer	16272173	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
Adenoid cystic carcinoma	18698036	CNVD
Lung cancer	19208797	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	21785460	CNVD
Myelodysplastic syndrome	21251322	CNVD
Lung cancer	18438408	CNVD
Cancer	22429812	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Autism	18414403	CNVD
primary effusion lymphomas	17116491	CNVD
small cell lung cancer	20016488	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17133270	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Colorectal cancer	20459617	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Hirschsprung''s Disease	21712996	CNVD
Congenital anomalies of the kidney and urinary tract	20505237	CNVD
Breast cancer	17393978	CNVD
Ovarian cancer	21720365	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Esophageal cancer	21851588	CNVD
Cancer	19907438	CNVD
Prostate cancer	16573809	CNVD
Multiple myeloma	16616336	CNVD
Myelofibrosis	22110671	CNVD
Schizophrenia	19197363	CNVD
Melanoma	20688739	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:98640800-98642000	Enhancers	Pancreatic Islets	Pancreatic Islet
2	chr4:98641200-98642400	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr4:98641400-98642600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:98641600-98642200	Enhancers	Fetal Intestine Small	intestine
5	chr4:98641600-98642600	Enhancers	Dnd41	blood
6	chr4:98641600-98643800	Enhancers	HUVEC	blood vessel
7	chr4:98641800-98642000	Enhancers	Brain Hippocampus Middle	brain
8	chr4:98642000-98642400	Flanking Active TSS	Brain Hippocampus Middle	brain
9	chr4:98642000-98642600	Enhancers	Brain Angular Gyrus	brain
10	chr4:98642000-98642800	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr4:98642200-98642600	Enhancers	Brain Anterior Caudate	brain
12	chr4:98642200-98642600	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr4:98642400-98642600	Active TSS	Brain Hippocampus Middle	brain
14	chr4:98642600-98643200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:98642800-98643600	Enhancers	Pancreatic Islets	Pancreatic Islet
16	chr4:98643200-98643400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:98654400-98657400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr4:98657400-98657600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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