Variant report

Variant	nsv518217
Chromosome Location	chr4:102040091-102042049
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	chr4:102039346..102042301-chr4:102044157..102045962,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 73 )

Variant overlapped rSNPs/rCNVs (count:55 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs12639641	chr4:102040091-102040092	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs76524671	chr4:102040110-102040111	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs201507463	chr4:102040114-102040115	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs533055846	chr4:102040117-102040118	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs79047093	chr4:102040118-102040119	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs144032622	chr4:102040223-102040224	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs150542754	chr4:102040230-102040231	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs111291392	chr4:102040237-102040238	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs543898142	chr4:102040291-102040292	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs149677799	chr4:102040338-102040339	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs542225312	chr4:102040372-102040373	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs554550671	chr4:102040373-102040374	Enhancers Weak transcription Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs376278775	chr4:102040426-102040427	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
14	rs189205507	chr4:102040460-102040461	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs540175975	chr4:102040489-102040490	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs564721607	chr4:102040530-102040531	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs532201093	chr4:102040586-102040587	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs35274938	chr4:102040611-102040612	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs563594766	chr4:102040653-102040654	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs201479922	chr4:102040658-102040659	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs377701668	chr4:102040660-102040661	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs6819038	chr4:102040662-102040663	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs533709211	chr4:102040666-102040667	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs549063123	chr4:102040724-102040725	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs111848231	chr4:102040800-102040801	Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs546566799	chr4:102040911-102040912	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs145467402	chr4:102040919-102040920	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs556748633	chr4:102040958-102040959	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs576588985	chr4:102040975-102040976	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs528787939	chr4:102040986-102040987	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs547354207	chr4:102041047-102041048	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs571847456	chr4:102041070-102041071	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs142592315	chr4:102041112-102041113	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs144948887	chr4:102041146-102041147	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs187560128	chr4:102041205-102041206	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs6820738	chr4:102041236-102041237	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs377559692	chr4:102041384-102041385	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs370502484	chr4:102041407-102041408	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs536392061	chr4:102041442-102041443	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs554257375	chr4:102041464-102041465	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs572213722	chr4:102041467-102041468	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs572830775	chr4:102041534-102041535	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs533811185	chr4:102041600-102041601	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs6532920	chr4:102041621-102041622	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs191117147	chr4:102041622-102041623	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs115831156	chr4:102041638-102041639	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs562708430	chr4:102041652-102041653	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs141788721	chr4:102041674-102041675	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs183991405	chr4:102041717-102041718	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs561113988	chr4:102041850-102041851	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:73)

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
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
Cancer	21183584	CNVD
primary effusion lymphomas	17116491	CNVD
small cell lung cancer	20016488	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17133270	CNVD
T-cell prolymphocytic leukemia	19278963	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
Prostate cancer	16573809	CNVD
Multiple myeloma	16616336	CNVD
Melanoma	20688739	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	16397240	CNVD
Acute myeloid leukemia	18000384	CNVD

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:102025000-102048200	Weak transcription	Left Ventricle	heart
2	chr4:102025600-102049200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr4:102026000-102046400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr4:102026200-102068600	Weak transcription	Primary T cells from cord blood	blood
5	chr4:102026400-102046000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr4:102029600-102046600	Weak transcription	Primary B cells from cord blood	blood
7	chr4:102029800-102046200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr4:102030200-102046000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr4:102030200-102049200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr4:102030400-102049600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:102032600-102046400	Weak transcription	Psoas Muscle	Psoas
12	chr4:102034200-102044400	Weak transcription	Primary B cells from peripheral blood	blood
13	chr4:102036200-102040200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr4:102036200-102040400	Weak transcription	Brain Substantia Nigra	brain
15	chr4:102036400-102040200	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr4:102036600-102040200	Enhancers	Brain Anterior Caudate	brain
17	chr4:102036600-102046400	Weak transcription	Colon Smooth Muscle	Colon
18	chr4:102036600-102048000	Weak transcription	Small Intestine	intestine
19	chr4:102036600-102049600	Weak transcription	Fetal Intestine Small	intestine
20	chr4:102037400-102044400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr4:102037800-102043000	Weak transcription	A549	lung
22	chr4:102037800-102043000	Weak transcription	HepG2	liver
23	chr4:102037800-102047800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr4:102037800-102048400	Weak transcription	HMEC	breast
25	chr4:102039200-102040200	Enhancers	Brain Cingulate Gyrus	brain
26	chr4:102039200-102040600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:102039200-102041000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr4:102039400-102040200	Enhancers	Brain Hippocampus Middle	brain
29	chr4:102039400-102041000	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr4:102039600-102040200	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr4:102039800-102040200	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr4:102039800-102040600	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr4:102039800-102041000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr4:102039800-102041000	Enhancers	Brain Angular Gyrus	brain
35	chr4:102039800-102048000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr4:102040000-102040400	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr4:102040000-102040800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr4:102040000-102040800	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr4:102040200-102040400	Flanking Active TSS	Brain Anterior Caudate	brain
40	chr4:102040200-102040600	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr4:102040200-102040600	Enhancers	iPS-18 Cell Line	embryonic stem cell
42	chr4:102040200-102040600	Flanking Active TSS	Brain Cingulate Gyrus	brain
43	chr4:102040200-102040600	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr4:102040200-102040600	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr4:102040400-102040600	Enhancers	Brain Substantia Nigra	brain
46	chr4:102040400-102040800	Active TSS	Brain Anterior Caudate	brain
47	chr4:102040600-102041000	Enhancers	Brain Cingulate Gyrus	brain
48	chr4:102040600-102041000	Enhancers	Brain Hippocampus Middle	brain
49	chr4:102040600-102043000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr4:102040600-102043600	Weak transcription	Brain Substantia Nigra	brain

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