Variant report

Variant	nsv528327
Chromosome Location	chr4:87677257-87679642
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GTF2F1	chr4:87678212-87678322	K562	blood:	n/a	n/a
2	MYC	chr4:87678966-87678968	MCF10A-Er-Src	breast:	n/a	n/a
3	MYC	chr4:87678585-87678614	MCF10A-Er-Src	breast:	n/a	n/a
4	POLR2A	chr4:87678176-87678283	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
PTPN13	TF binding region

Extended variants
information (count: 69 )
Associated
traits (count: 81 )

Variant overlapped rSNPs/rCNVs (count:69 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs1035191	chr4:87677257-87677258	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs371957133	chr4:87677258-87677259	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs562899140	chr4:87677339-87677340	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs180727402	chr4:87677349-87677350	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs28545322	chr4:87677353-87677354	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs558336463	chr4:87677382-87677383	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs142333808	chr4:87677394-87677395	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs61160693	chr4:87677397-87677398	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs570144217	chr4:87677673-87677674	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs537202810	chr4:87677791-87677792	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs144702442	chr4:87677808-87677809	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs368210852	chr4:87677847-87677848	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs570793291	chr4:87677859-87677860	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs535012477	chr4:87677888-87677889	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs553272403	chr4:87677903-87677904	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs138588469	chr4:87677906-87677907	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs186366421	chr4:87677988-87677989	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs114011166	chr4:87677999-87678000	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs149308537	chr4:87678043-87678044	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs561874889	chr4:87678078-87678079	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs575341492	chr4:87678086-87678087	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs5860036	chr4:87678099-87678100	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs144552920	chr4:87678189-87678190	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs564342788	chr4:87678222-87678223	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs1038290	chr4:87678243-87678244	Weak transcription Strong transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
26	rs540507154	chr4:87678280-87678281	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
27	rs377128120	chr4:87678290-87678291	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
28	rs371704824	chr4:87678296-87678297	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
29	rs2006842	chr4:87678426-87678427	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
30	rs530076621	chr4:87678427-87678428	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs148443464	chr4:87678438-87678439	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs563626996	chr4:87678475-87678476	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs12510802	chr4:87678527-87678528	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs552472373	chr4:87678647-87678648	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs539753404	chr4:87678652-87678653	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs534902032	chr4:87678659-87678660	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs375735882	chr4:87678675-87678676	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs546847589	chr4:87678746-87678747	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs72665791	chr4:87678787-87678788	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs550060385	chr4:87678797-87678798	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs553723143	chr4:87678847-87678848	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs189251145	chr4:87678863-87678864	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs181640283	chr4:87678864-87678865	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs539550696	chr4:87678878-87678879	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs542129918	chr4:87678915-87678916	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs557910434	chr4:87678929-87678930	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs573041639	chr4:87679066-87679067	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs186922712	chr4:87679100-87679101	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs555655092	chr4:87679144-87679145	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs574030906	chr4:87679183-87679184	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:81)

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
lymphocytic leukemia	21291569	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
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
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
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Myelodysplastic syndrome	21251322	CNVD
Multiple myeloma	17550852	CNVD
Lung cancer	18438408	CNVD
Chronic lymphocytic leukemia	18922857	CNVD
Cancer	22429812	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Autism	18414403	CNVD
primary effusion lymphomas	17116491	CNVD
Olfactory neuroblastoma	18408657	CNVD
small cell lung cancer	20016488	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17133270	CNVD
Colorectal cancer	20459617	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87631200-87712200	Weak transcription	Aorta	Aorta
2	chr4:87635200-87737400	Weak transcription	Fetal Brain Male	brain
3	chr4:87636400-87683800	Weak transcription	Stomach Smooth Muscle	stomach
4	chr4:87639200-87688000	Weak transcription	Fetal Intestine Large	intestine
5	chr4:87639400-87739200	Weak transcription	A549	lung
6	chr4:87641800-87683400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr4:87642200-87692600	Weak transcription	NH-A	brain
8	chr4:87642400-87735800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr4:87642600-87692400	Weak transcription	Colon Smooth Muscle	Colon
10	chr4:87642600-87697600	Weak transcription	Brain Angular Gyrus	brain
11	chr4:87642600-87719200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr4:87644600-87680600	Weak transcription	NHLF	lung
13	chr4:87650400-87677400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:87655600-87704400	Weak transcription	Hela-S3	cervix
15	chr4:87661600-87680400	Weak transcription	Brain Substantia Nigra	brain
16	chr4:87661600-87680600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr4:87661600-87683200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:87661600-87710200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr4:87661600-87711400	Weak transcription	Brain Germinal Matrix	brain
20	chr4:87661600-87712000	Weak transcription	Esophagus	oesophagus
21	chr4:87661600-87737800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr4:87661800-87683000	Weak transcription	Fetal Stomach	stomach
23	chr4:87661800-87683200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr4:87661800-87683800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:87661800-87708000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr4:87661800-87712000	Weak transcription	Fetal Intestine Small	intestine
27	chr4:87661800-87728800	Weak transcription	Pancreas	Pancrea
28	chr4:87663000-87683600	Weak transcription	Fetal Brain Female	brain
29	chr4:87663000-87711400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr4:87665000-87692400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr4:87668000-87679400	Weak transcription	Osteobl	bone
32	chr4:87669200-87690800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr4:87671800-87713000	Weak transcription	HSMMtube	muscle
34	chr4:87672000-87683600	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr4:87672000-87689000	Weak transcription	Brain Cingulate Gyrus	brain
36	chr4:87672000-87712200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr4:87672200-87683600	Weak transcription	Fetal Kidney	kidney
38	chr4:87672600-87683600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr4:87672600-87683800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr4:87672800-87679800	Weak transcription	Adipose Nuclei	Adipose
41	chr4:87672800-87679800	Weak transcription	Brain Anterior Caudate	brain
42	chr4:87672800-87680600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr4:87672800-87683000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr4:87672800-87690600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr4:87672800-87710000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr4:87672800-87712000	Weak transcription	Lung	lung
47	chr4:87673000-87678600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr4:87673000-87683200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr4:87673000-87687400	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr4:87673200-87680000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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