Variant report

Variant	esv3332928
Chromosome Location	chr5:53176220-53178243
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	FOXA1	chr5:53175745-53176275	HepG2	liver:	n/a	n/a
2	POLR2A	chr5:53177358-53177977	K562	blood:	n/a	n/a
3	POLR2A	chr5:53176718-53176966	K562	blood:	n/a	n/a
4	POLR2A	chr5:53176573-53176649	K562	blood:	n/a	n/a
5	POLR2A	chr5:53177715-53178147	K562	blood:	n/a	n/a
6	POLR2A	chr5:53176503-53176838	K562	blood:	n/a	n/a
7	SPI1	chr5:53178220-53178554	HL-60	blood:	n/a	chr5:53178463-53178476

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARL15-4	chr5:53176123-53176881	ENSG00000272416.1

Variant related genes	Relation type
ENSG00000272416	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 88 )

Variant overlapped rSNPs/rCNVs (count:59 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs370139239	chr5:53176228-53176229	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
2	rs6860378	chr5:53176232-53176233	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs571201595	chr5:53176296-53176297	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
4	rs541006085	chr5:53176298-53176299	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
5	rs114303660	chr5:53176299-53176300	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
6	rs530321840	chr5:53176323-53176324	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
7	rs542067502	chr5:53176325-53176326	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
8	rs563861421	chr5:53176401-53176402	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
9	rs2407068	chr5:53176402-53176403	Weak transcription Enhancers	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
10	rs549817910	chr5:53176404-53176405	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
11	rs557810207	chr5:53176459-53176460	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
12	rs532165177	chr5:53176462-53176463	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
13	rs77734459	chr5:53176501-53176502	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
14	rs566024110	chr5:53176506-53176507	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
15	rs536503172	chr5:53176509-53176510	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
16	rs554813013	chr5:53176541-53176542	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
17	rs569798332	chr5:53176573-53176574	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
18	rs577445994	chr5:53176596-53176597	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
19	rs184578425	chr5:53176743-53176744	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
20	rs373752189	chr5:53176789-53176790	Weak transcription Enhancers	lncRNA	n/a	Overlapped CNVs	n/a
21	rs559039419	chr5:53176834-53176835	Enhancers Weak transcription	lncRNA	n/a	Overlapped CNVs	n/a
22	rs202155065	chr5:53176942-53176943	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs141665178	chr5:53176944-53176945	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs577251702	chr5:53176952-53176953	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
25	rs376903567	chr5:53177068-53177069	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs527323312	chr5:53177194-53177195	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs567071962	chr5:53177223-53177224	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs377138944	chr5:53177231-53177232	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs189411501	chr5:53177233-53177234	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs541069319	chr5:53177255-53177256	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs115162642	chr5:53177327-53177328	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs574797502	chr5:53177331-53177332	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs182235968	chr5:53177345-53177346	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs139546099	chr5:53177399-53177400	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs186026927	chr5:53177412-53177413	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs544614836	chr5:53177426-53177427	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs568310748	chr5:53177428-53177429	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs189332045	chr5:53177508-53177509	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs565030094	chr5:53177509-53177510	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs532242000	chr5:53177517-53177518	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs547418734	chr5:53177544-53177545	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs565638752	chr5:53177553-53177554	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs57693952	chr5:53177597-53177598	Enhancers Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs75852552	chr5:53177598-53177599	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs61356213	chr5:53177606-53177607	Enhancers Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs9292030	chr5:53177648-53177649	Enhancers Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs114962680	chr5:53177651-53177652	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs375927284	chr5:53177657-53177658	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
49	rs570974806	chr5:53177774-53177775	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs572065316	chr5:53177822-53177823	Enhancers Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:88)

Disease	PMID	Source
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Metanephric adenoma	20802469	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Medulloblastoma	21979893	CNVD
Phyllodes tumor	17334353	CNVD
Malaria	21533027	CNVD
Renal cell carcinoma	19461508	CNVD
Colorectal cancer	21645411	CNVD
Gastric cancer	22152101	CNVD
Oesophago-gastric ulcer	22152101	CNVD
Ovarian cancer	21781307	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Cancer	20164919	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Multiple myeloma	17550852	CNVD
Thoracic aortic aneurysm	21092924	CNVD
DNA damage stimulus	22844521	CNVD
DNA repair	22844521	CNVD
Breast cancer	21785460	CNVD
Spinal muscular atrophy	22422766	CNVD
Spinal muscular atrophy	22558076	CNVD
Spinal muscular atrophy	21320981	CNVD
Spinal muscular atrophy	21762474	CNVD
Cancer	16751803	CNVD
Autism	22495311	CNVD
Intellectual disability	22102821	CNVD
Prostate cancer	21965145	CNVD
Cancer	21183584	CNVD
Ovarian cancer	20844748	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Breast cancer	17603634	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Melanoma	18172304	CNVD
Glioma	20126413	CNVD
Non-small cell lung cancer	21829676	CNVD
Breast cancer	22032731	CNVD
Esophageal cancer	20955586	CNVD
Congenital anomalies of the kidney and urinary tract	18694510	CNVD
Breast cancer	17393978	CNVD
Cancer	21359685	CNVD
adenomatous polyposis	22470819	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Acute myeloid leukemia	20729466	CNVD
Cancer	22429812	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Liposarcoma	21253554	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Breast cancer	21858162	CNVD
Hepatocellular carcinoma	16750200	CNVD
Leukemia	17361228	CNVD
Myelodysplastic syndrome	18508791	CNVD
5q-syndrome	17576883	CNVD
Gastric cancer	17908304	CNVD
Lung cancer	16740712	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Lung cancer	18438408	CNVD
Urothelial carcinoma	21177765	CNVD
Acute myeloid leukemia	21251322	CNVD
Breast cancer	21364760	CNVD
Oral cancer	21386901	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Bladder cancer	21909424	CNVD
Esophageal adenocarcinoma	19417022	CNVD
Barrett''s syndrome	19417022	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Lung cancer	21911935	CNVD
Breast cancer	17133270	CNVD
Breast cancer	19602461	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Renal cell carcinoma	18194544	CNVD

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:53166800-53176800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:53169600-53178000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:53170200-53177600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:53170200-53181800	Weak transcription	Spleen	Spleen
5	chr5:53173600-53178000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr5:53173600-53178000	Weak transcription	NHLF	lung
7	chr5:53173600-53178400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr5:53173800-53178400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr5:53173800-53178400	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr5:53173800-53178600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr5:53173800-53227800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr5:53174000-53177400	Weak transcription	NHDF-Ad	bronchial
13	chr5:53174000-53178200	Weak transcription	Osteobl	bone
14	chr5:53174200-53177600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr5:53174200-53178600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:53174200-53186400	Weak transcription	Left Ventricle	heart
17	chr5:53174400-53211000	Weak transcription	K562	blood
18	chr5:53175200-53176600	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr5:53175400-53176600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr5:53175400-53176600	Enhancers	HepG2	liver
21	chr5:53175400-53183400	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr5:53175400-53186400	Weak transcription	Primary T cells from cord blood	blood
23	chr5:53175800-53176600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:53175800-53177400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:53176000-53176800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr5:53176000-53177600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:53176000-53178000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr5:53176000-53178400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr5:53176000-53187200	Weak transcription	Esophagus	oesophagus
30	chr5:53176200-53177200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr5:53176200-53177400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr5:53176200-53177400	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr5:53176200-53177400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr5:53176200-53177600	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr5:53176600-53177200	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr5:53176600-53177600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr5:53176600-53180800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr5:53176600-53189000	Weak transcription	Fetal Intestine Large	intestine
39	chr5:53176600-53190400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr5:53176800-53179200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr5:53176800-53181000	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr5:53177000-53212800	Weak transcription	Fetal Intestine Small	intestine
43	chr5:53177200-53177400	Enhancers	H9 Cell Line	embryonic stem cell
44	chr5:53177200-53178800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
45	chr5:53177200-53180800	Enhancers	HUES64 Cell Line	embryonic stem cell
46	chr5:53177400-53178000	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr5:53177400-53178600	Enhancers	iPS-20b Cell Line	embryonic stem cell
48	chr5:53177400-53178800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr5:53177400-53179200	Enhancers	NHDF-Ad	bronchial
50	chr5:53177400-53179400	Enhancers	H1 Cell Line	embryonic stem cell

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