Variant report

Variant	nsv976117
Chromosome Location	chr13:53051476-53058376
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	CTCF	chr13:53056165-53056313	HUVEC	blood vessel:	n/a	n/a
2	CTCF	chr13:53056159-53056365	A549	lung:	n/a	n/a
3	CTCF	chr13:53052519-53052553	GM20000	blood:	n/a	n/a
4	CTCF	chr13:53054946-53054986	Kidney_OC	kidney:	n/a	n/a
5	CTCF	chr13:53056172-53056300	Hela-S3	cervix:	n/a	n/a
6	CTCF	chr13:53056183-53056321	GM12878	blood:	n/a	n/a
7	CTCF	chr13:53051466-53051551	GM20000	blood:	n/a	n/a
8	CTCF	chr13:53056182-53056322	K562	blood:	n/a	n/a
9	FOSL2	chr13:53051203-53051544	HepG2	liver:	n/a	n/a
10	IRF1	chr13:53055283-53055541	K562	blood:	n/a	chr13:53055383-53055400 chr13:53055385-53055396 chr13:53055382-53055395 chr13:53055361-53055368 chr13:53055383-53055395 chr13:53055395-53055408 chr13:53055397-53055407 chr13:53055381-53055398 chr13:53055376-53055396 chr13:53055395-53055409 chr13:53055382-53055395 chr13:53055384-53055398 chr13:53055384-53055395 chr13:53055380-53055394 chr13:53055382-53055395 chr13:53055393-53055407 chr13:53055382-53055396 chr13:53055381-53055395 chr13:53055382-53055395 chr13:53055384-53055394
11	MYC	chr13:53057535-53057557	K562	blood:	n/a	n/a
12	MYC	chr13:53057413-53057531	K562	blood:	n/a	n/a
13	NR3C1	chr13:53053433-53053710	A549	lung:	n/a	n/a
14	NR3C1	chr13:53053332-53053649	A549	lung:	n/a	n/a
15	POLR2A	chr13:53052824-53052846	K562	blood:	n/a	n/a
16	POLR2A	chr13:53052072-53052363	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr13:53052251-53052498	K562	blood:	n/a	n/a
18	POLR2A	chr13:53051681-53052027	HepG2	liver:	n/a	n/a
19	POLR2A	chr13:53053597-53053997	MCF-7	breast:	n/a	n/a
20	POLR2A	chr13:53050696-53054441	K562	blood:	n/a	n/a
21	POLR2A	chr13:53051553-53051656	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr13:53052916-53053013	HepG2	liver:	n/a	n/a
23	POLR2A	chr13:53052788-53053816	SK-N-MC	brain:	n/a	n/a
24	POLR2A	chr13:53052093-53053509	MCF-7	breast:	n/a	n/a
25	POLR2A	chr13:53052013-53052255	SK-N-SH	brain:	n/a	n/a
26	POLR2A	chr13:53051160-53051781	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr13:53054885-53055100	MCF-7	breast:	n/a	n/a
28	POLR2A	chr13:53051210-53051553	K562	blood:	n/a	n/a
29	POLR2A	chr13:53054316-53054355	ProgFib	skin:	n/a	n/a
30	POLR2A	chr13:53052017-53052025	MCF-7	breast:	n/a	n/a
31	POLR2A	chr13:53054543-53054626	MCF-7	breast:	n/a	n/a
32	POLR2A	chr13:53051486-53051514	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr13:53051375-53051542	GM12891	blood:	n/a	n/a
34	POLR2A	chr13:53051691-53051700	K562	blood:	n/a	n/a
35	POLR2A	chr13:53053341-53053421	HUVEC	blood vessel:	n/a	n/a
36	POLR2A	chr13:53054182-53054697	SK-N-MC	brain:	n/a	n/a
37	POLR2A	chr13:53051278-53051575	PFSK-1	brain:	n/a	n/a
38	POLR2A	chr13:53053980-53054166	MCF10A-Er-Src	breast:	n/a	n/a
39	POLR2A	chr13:53051054-53051997	MCF-7	breast:	n/a	n/a
40	POLR2A	chr13:53053816-53053917	Hela-S3	cervix:	n/a	n/a
41	POLR2A	chr13:53051571-53052137	HepG2	liver:	n/a	n/a
42	POLR2A	chr13:53051237-53051840	PFSK-1	brain:	n/a	n/a
43	POLR2A	chr13:53053137-53053217	K562	blood:	n/a	n/a
44	POLR2A	chr13:53053432-53053542	HUVEC	blood vessel:	n/a	n/a
45	POLR2A	chr13:53053443-53053643	GM12878	blood:	n/a	n/a
46	POLR2A	chr13:53051467-53051809	GM12891	blood:	n/a	n/a
47	POLR2A	chr13:53052523-53052791	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr13:53051578-53051579	K562	blood:	n/a	n/a
49	POLR2A	chr13:53051409-53051778	SK-N-MC	brain:	n/a	n/a
50	POLR2A	chr13:53051714-53051839	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:53049275..53051586-chr13:53052175..53054640,2	MCF-7	breast:
2	chr13:53049275..53051586-chr13:53052175..53054640,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-VPS36-1	chr13:53058296-53058419	XLOC_010621

Variant related genes	Relation type
TPTE2P3	TF binding region
ENSG00000244471	TF binding region

Extended variants
information (count: 241 )
Associated
traits (count: 110 )

Variant overlapped rSNPs/rCNVs (count:241 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs566401302	chr13:53051480-53051481	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs376142298	chr13:53051522-53051523	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs4396422	chr13:53051526-53051527	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs144202309	chr13:53051535-53051536	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs548813304	chr13:53051609-53051610	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs9526927	chr13:53051627-53051628	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
7	rs144413900	chr13:53051639-53051640	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs560315286	chr13:53051646-53051647	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs181201769	chr13:53051656-53051657	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs148792366	chr13:53051725-53051726	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs12863221	chr13:53051743-53051744	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs142417866	chr13:53051772-53051773	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs558236861	chr13:53051781-53051782	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs572021228	chr13:53051867-53051868	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs540887114	chr13:53051875-53051876	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs542808740	chr13:53051908-53051909	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs144302411	chr13:53051951-53051952	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs151292548	chr13:53051998-53051999	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs574288050	chr13:53052050-53052051	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs562681594	chr13:53052056-53052057	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs543592420	chr13:53052057-53052058	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs563781865	chr13:53052087-53052088	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs74087311	chr13:53052089-53052090	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs531456331	chr13:53052098-53052099	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs546195858	chr13:53052127-53052128	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs111314611	chr13:53052165-53052166	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs559744567	chr13:53052178-53052179	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs528800378	chr13:53052179-53052180	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs548898772	chr13:53052206-53052207	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs34127234	chr13:53052223-53052224	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs116777464	chr13:53052268-53052269	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs564312416	chr13:53052307-53052308	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs531119580	chr13:53052412-53052413	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs549637081	chr13:53052442-53052443	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs569752970	chr13:53052487-53052488	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs370961360	chr13:53052488-53052489	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs558530487	chr13:53052493-53052494	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs374401680	chr13:53052523-53052524	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs367850404	chr13:53052529-53052530	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs565290487	chr13:53052533-53052534	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs371571016	chr13:53052570-53052571	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs375027956	chr13:53052573-53052574	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs368209447	chr13:53052636-53052637	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs186153597	chr13:53052659-53052660	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs543626062	chr13:53052677-53052678	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs371925726	chr13:53052689-53052690	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs546613123	chr13:53052707-53052708	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs577276881	chr13:53052711-53052712	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs201426625	chr13:53052756-53052757	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs7319583	chr13:53052821-53052822	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:110)

Disease	PMID	Source
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	21080181	CNVD
HIV/AIDS	22032296	CNVD
Prostate cancer	16705090	CNVD
High-proliferative meningiomas	17937814	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Autism	22495311	CNVD
Chordoma	21602918	CNVD
Bladder cancer	21949216	CNVD
Acute myeloid leukemia	16864856	CNVD
Burkitt''s lymphoma	18698080	CNVD
Cancer	21637783	CNVD
Medulloblastoma	21979893	CNVD
Chronic lymphocytic leukemia	21518781	CNVD
colon cancer	17210682	CNVD
Endometrial cancer	22040021	CNVD
Colorectal cancer	20709793	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	17387387	CNVD
Hepatocellular carcinoma	22174799	CNVD
Ovarian cancer	20844748	CNVD
Colorectal cancer	19359472	CNVD
Intracranial aneurysm	19064780	CNVD
Breast cancer	19287154	CNVD
Acute myeloid leukemia	18379011	CNVD
Human rectal carcinomas	16397240	CNVD
Olfactory neuroblastoma	18408657	CNVD
Multiple myeloma	17077331	CNVD
Ependymoma	16718352	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Squamous cell cancer	20885788	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Thyroid cancer	19087340	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Ovarian cancer	22174824	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Colorectal cancer	16774939	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17133270	CNVD
Myoepithelioma	18604193	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Prostate cancer	16573809	CNVD
Prostate cancer	18632612	CNVD
Paraganglioma	21461997	CNVD
Pheochromocytoma	21461997	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Prostate cancer	19242612	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Prostate cancer	17245344	CNVD
Colorectal cancer	21586687	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Retinoblastoma	19183342	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Developmental delay	21147756	CNVD
Melanoma	18172304	CNVD
Hepatocellular carcinoma	16750200	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	17053054	CNVD
Multiple myeloma	19135901	CNVD
Autism	18414403	CNVD
Neurocytoma	17123091	CNVD
Central neurocytomas	17123091	CNVD
Prostate cancer	16461572	CNVD
Merkel cell carcinoma	19020549	CNVD
Lung cancer	18438408	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
lymphocytic leukemia	21291569	CNVD
Multiple myeloma	17550852	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Breast cancer	21858162	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Acute myeloid leukemia	21251322	CNVD
Acute myeloid leukemia	17237825	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Breast cancer	16272173	CNVD
Glioblastoma multiforme	21922591	CNVD
Metanephric adenoma	20802469	CNVD
Acute myeloid leukemia	20729466	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Congenital anomalies of the kidney and urinary tract	20467480	CNVD
Gastric cancer	17908304	CNVD
Breast cancer	18852474	CNVD
Myelofibrosis	22110671	CNVD
craniofacial dysmorphism	21918468	CNVD
Glioblastoma multiforme	22286061	CNVD
Glioblastoma multiforme	21750150	CNVD
Breast cancer	17603634	CNVD
Cancer	21183584	CNVD
Breast cancer	17393978	CNVD
Splenic marginal zone lymphoma	18492102	CNVD
Liposarcoma	21253554	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
early-passage human iPS cells	21368824	CNVD

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53030200-53052600	Weak transcription	Spleen	Spleen
2	chr13:53030200-53053800	Weak transcription	Small Intestine	intestine
3	chr13:53030400-53055800	Weak transcription	Lung	lung
4	chr13:53030600-53052400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr13:53030600-53052800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr13:53032600-53052200	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr13:53033800-53051600	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr13:53034200-53052000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr13:53034400-53054400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr13:53036000-53052600	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr13:53036800-53053000	Weak transcription	Brain Germinal Matrix	brain
12	chr13:53037600-53052000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr13:53038000-53053200	Weak transcription	Brain Angular Gyrus	brain
14	chr13:53038200-53051800	Strong transcription	Dnd41	blood
15	chr13:53038200-53055400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr13:53039200-53051600	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr13:53039800-53052800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr13:53041000-53052000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr13:53041200-53052200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr13:53041200-53053200	Weak transcription	Fetal Stomach	stomach
21	chr13:53041400-53052600	Weak transcription	Placenta	Placenta
22	chr13:53042800-53054400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr13:53043000-53052800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr13:53043200-53052400	Weak transcription	Fetal Heart	heart
25	chr13:53043600-53052800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr13:53044600-53051800	Strong transcription	HMEC	breast
27	chr13:53045400-53051600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr13:53045400-53051600	Strong transcription	Fetal Intestine Large	intestine
29	chr13:53045600-53051800	Strong transcription	NH-A	brain
30	chr13:53045800-53051600	Strong transcription	Fetal Thymus	thymus
31	chr13:53045800-53052000	Strong transcription	HSMM	muscle
32	chr13:53046200-53051800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr13:53047200-53052800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr13:53047200-53053000	Weak transcription	Thymus	Thymus
35	chr13:53048000-53051600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr13:53048600-53053200	Weak transcription	Fetal Intestine Small	intestine
37	chr13:53049200-53052600	Weak transcription	GM12878-XiMat	blood
38	chr13:53049400-53051600	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr13:53049400-53053000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr13:53049400-53054000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr13:53049600-53052400	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr13:53049600-53053000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr13:53049600-53054000	Weak transcription	Liver	Liver
44	chr13:53049800-53052800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr13:53050000-53051600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr13:53050000-53051600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr13:53050000-53051600	Weak transcription	Adipose Nuclei	Adipose
48	chr13:53050000-53051600	Weak transcription	Ovary	ovary
49	chr13:53050000-53052400	Weak transcription	HSMMtube	muscle
50	chr13:53050000-53052600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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