Variant report

Variant	esv21302
Chromosome Location	chr4:54375399-54378966
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	ARID3A	chr4:54378099-54378285	HepG2	liver:	n/a	n/a
2	BATF	chr4:54378843-54379161	GM12878	blood:	n/a	chr4:54378987-54378995 chr4:54378973-54378984
3	BATF	chr4:54378808-54379131	GM12878	blood:	n/a	chr4:54378987-54378995 chr4:54378973-54378984
4	BHLHE40	chr4:54378185-54378291	HepG2	liver:	n/a	n/a
5	GATA3	chr4:54375897-54376051	SH-SY5Y	brain:	n/a	n/a
6	IKZF1	chr4:54378921-54379060	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:54378239..54380309-chr4:54383066..54385489,2	MCF-7	breast:
2	chr4:54375519..54377286-chr4:54400053..54402800,2	K562	blood:

Variant related genes	Relation type
LNX1	TF binding region

Extended variants
information (count: 128 )
Associated
traits (count: 100 )

Variant overlapped rSNPs/rCNVs (count:128 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs370694474	chr4:54375402-54375403	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs554638972	chr4:54375405-54375406	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs6841529	chr4:54375414-54375415	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs6824775	chr4:54375486-54375487	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs34040981	chr4:54375607-54375608	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs187183592	chr4:54375635-54375636	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs139204809	chr4:54375662-54375663	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs116520234	chr4:54375699-54375700	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs565172143	chr4:54375701-54375702	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs530744369	chr4:54375730-54375731	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs530752376	chr4:54375816-54375817	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs190908412	chr4:54375827-54375828	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs182342017	chr4:54375855-54375856	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs529713430	chr4:54375936-54375937	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs35325403	chr4:54375952-54375953	Weak transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs376318327	chr4:54376163-54376164	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs186916452	chr4:54376171-54376172	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs566611267	chr4:54376213-54376214	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs12501431	chr4:54376220-54376221	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs1435224	chr4:54376243-54376244	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs386674435	chr4:54376269-54376270	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs68134111	chr4:54376270-54376271	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs115506292	chr4:54376324-54376325	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs574445811	chr4:54376331-54376332	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs539617517	chr4:54376383-54376384	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs555064889	chr4:54376411-54376412	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs557910653	chr4:54376416-54376417	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs116337493	chr4:54376463-54376464	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs191335609	chr4:54376465-54376466	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs149969546	chr4:54376493-54376494	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs4864768	chr4:54376506-54376507	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs183210363	chr4:54376533-54376534	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs544128275	chr4:54376576-54376577	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs561211745	chr4:54376606-54376607	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs529703321	chr4:54376654-54376655	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs546652545	chr4:54376680-54376681	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs188224933	chr4:54376681-54376682	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs560266099	chr4:54376694-54376695	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs4864769	chr4:54376709-54376710	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs552266236	chr4:54376736-54376737	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs144132490	chr4:54376811-54376812	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs4864770	chr4:54376820-54376821	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs139830610	chr4:54376823-54376824	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs4864771	chr4:54376828-54376829	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs143139952	chr4:54376850-54376851	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs553779855	chr4:54376920-54376921	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs146701117	chr4:54376949-54376950	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs570191398	chr4:54376976-54376977	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs140269130	chr4:54377020-54377021	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs192920543	chr4:54377044-54377045	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:100)

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
Hodgkin''s lymphoma	17606441	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
Cancer	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
Chronic lymphocytic leukemia	21546498	CNVD
Glioblastoma multiforme	21569311	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
Glioblastoma multiforme	21525872	CNVD
Glioblastoma multiforme	19115005	CNVD
Wilms tumour	21544195	CNVD
Cancer	20164919	CNVD
Gastrointestinal stromal cancer	17527083	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Gastrointestinal stromal cancer	17209131	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Glioblastoma multiforme	21138945	CNVD

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54343000-54385600	Weak transcription	Fetal Brain Female	brain
2	chr4:54343200-54376800	Weak transcription	Brain Anterior Caudate	brain
3	chr4:54347600-54401800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr4:54355200-54378600	Weak transcription	Fetal Brain Male	brain
5	chr4:54362800-54376000	Weak transcription	Brain Angular Gyrus	brain
6	chr4:54363200-54384200	Weak transcription	Esophagus	oesophagus
7	chr4:54363800-54384000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr4:54366600-54384200	Weak transcription	Pancreas	Pancrea
9	chr4:54368000-54376600	Weak transcription	Ovary	ovary
10	chr4:54372800-54388400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr4:54373200-54375600	Enhancers	NHDF-Ad	bronchial
12	chr4:54373200-54375800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr4:54373400-54375400	Enhancers	Stomach Mucosa	stomach
14	chr4:54374000-54375400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:54374400-54376600	Weak transcription	Fetal Muscle Leg	muscle
16	chr4:54374400-54376800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr4:54374400-54399000	Weak transcription	Fetal Intestine Large	intestine
18	chr4:54374400-54421000	Weak transcription	Duodenum Mucosa	Duodenum
19	chr4:54374600-54375400	Enhancers	HSMM	muscle
20	chr4:54374600-54375400	Enhancers	HSMMtube	muscle
21	chr4:54374600-54376800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr4:54374600-54377800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:54374800-54375400	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr4:54374800-54377000	Enhancers	Osteobl	bone
25	chr4:54374800-54377600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr4:54374800-54393600	Weak transcription	Placenta	Placenta
27	chr4:54375000-54375400	Enhancers	Muscle Satellite Cultured Cells	--
28	chr4:54375000-54375600	Weak transcription	Fetal Stomach	stomach
29	chr4:54375000-54375800	Weak transcription	Right Atrium	heart
30	chr4:54375000-54376200	Weak transcription	NHLF	lung
31	chr4:54375000-54376400	Weak transcription	Aorta	Aorta
32	chr4:54375000-54376400	Weak transcription	Liver	Liver
33	chr4:54375000-54376800	Weak transcription	Psoas Muscle	Psoas
34	chr4:54375000-54378000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:54375000-54393600	Weak transcription	Gastric	stomach
36	chr4:54375000-54398800	Weak transcription	Fetal Intestine Small	intestine
37	chr4:54375200-54375400	Bivalent Enhancer	HepG2	liver
38	chr4:54375200-54377000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr4:54375400-54376200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr4:54375400-54376200	Weak transcription	HSMMtube	muscle
41	chr4:54375400-54376800	Weak transcription	HSMM	muscle
42	chr4:54375400-54377200	Weak transcription	Stomach Mucosa	stomach
43	chr4:54375600-54376200	Weak transcription	NHDF-Ad	bronchial
44	chr4:54375800-54377600	Enhancers	Right Atrium	heart
45	chr4:54376000-54376200	Enhancers	Brain Angular Gyrus	brain
46	chr4:54376200-54376400	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr4:54376200-54376600	Weak transcription	Brain Angular Gyrus	brain
48	chr4:54376200-54377600	Enhancers	NHDF-Ad	bronchial
49	chr4:54376200-54378200	Enhancers	HSMMtube	muscle
50	chr4:54376400-54376600	Enhancers	NHLF	lung

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