Variant report

Variant	nsv1054476
Chromosome Location	chr13:53359853-53380149
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	BACH1	chr13:53361003-53361116	H1-hESC	embryonic stem cell:	n/a	n/a
2	CCNT2	chr13:53378360-53378651	K562	blood:	n/a	n/a
3	CEBPB	chr13:53371797-53371876	K562	blood:	n/a	chr13:53371830-53371841 chr13:53371829-53371840
4	CEBPB	chr13:53371689-53372004	HepG2	liver:	n/a	chr13:53371830-53371841 chr13:53371829-53371840
5	CTCF	chr13:53366900-53367050	GM12871	blood:	n/a	n/a
6	CTCF	chr13:53379480-53379630	GM12864	blood:	n/a	n/a
7	E2F4	chr13:53375857-53375964	MCF10A-Er-Src	breast:	n/a	n/a
8	EBF1	chr13:53361724-53362049	GM12878	blood:	n/a	chr13:53361875-53361886 chr13:53361844-53361855
9	EP300	chr13:53360848-53361335	SK-N-SH_RA	brain:	n/a	n/a
10	EP300	chr13:53360861-53361338	SK-N-SH_RA	brain:	n/a	n/a
11	EP300	chr13:53378471-53378757	SK-N-SH_RA	brain:	n/a	n/a
12	EP300	chr13:53378435-53378786	SK-N-SH_RA	brain:	n/a	n/a
13	FOS	chr13:53359672-53360142	MCF10A-Er-Src	breast:	n/a	chr13:53359764-53359775 chr13:53360132-53360142 chr13:53360132-53360142
14	FOS	chr13:53359904-53360237	MCF10A-Er-Src	breast:	n/a	chr13:53360132-53360142 chr13:53360132-53360142
15	FOS	chr13:53360989-53361146	MCF10A-Er-Src	breast:	n/a	chr13:53361072-53361082 chr13:53361071-53361083 chr13:53361073-53361081
16	FOS	chr13:53359829-53360163	MCF10A-Er-Src	breast:	n/a	chr13:53360132-53360142 chr13:53360132-53360142
17	FOXP2	chr13:53372829-53373185	SK-N-MC	brain:	n/a	n/a
18	GATA3	chr13:53378335-53378833	SK-N-SH	brain:	n/a	chr13:53378341-53378350
19	GATA3	chr13:53378212-53378929	SK-N-SH	brain:	n/a	chr13:53378341-53378350
20	JUND	chr13:53360014-53360174	HepG2	liver:	n/a	chr13:53360132-53360142 chr13:53360132-53360142
21	KAP1	chr13:53378265-53378797	HEK293	kidney:	n/a	n/a
22	MAFF	chr13:53361081-53361123	HepG2	liver:	n/a	n/a
23	MAFK	chr13:53363965-53364099	HepG2	liver:	n/a	n/a
24	MAX	chr13:53374443-53374676	H1-hESC	embryonic stem cell:	n/a	chr13:53374445-53374455
25	MYC	chr13:53362380-53362407	H1-hESC	embryonic stem cell:	n/a	n/a
26	NRF1	chr13:53369976-53370004	GM12878	blood:	n/a	n/a
27	POLR2A	chr13:53367428-53368141	H1-neurons	neurons:	n/a	n/a
28	POLR2A	chr13:53361059-53361449	H1-neurons	neurons:	n/a	n/a
29	POLR2A	chr13:53367464-53368140	H1-neurons	neurons:	n/a	n/a
30	POLR2A	chr13:53363252-53363305	MCF-7	breast:	n/a	n/a
31	POLR2A	chr13:53371192-53371788	H1-neurons	neurons:	n/a	n/a
32	POLR2A	chr13:53363253-53363309	Gliobla	brain:	n/a	n/a
33	POLR2A	chr13:53361071-53361419	H1-neurons	neurons:	n/a	n/a
34	POLR2A	chr13:53371211-53371785	H1-neurons	neurons:	n/a	n/a
35	POLR2A	chr13:53372674-53373543	SK-N-MC	brain:	n/a	n/a
36	RAD21	chr13:53360923-53361171	SK-N-SH_RA	brain:	n/a	n/a
37	REST	chr13:53367151-53368432	H1-neurons	neurons:	n/a	chr13:53368274-53368294 chr13:53367955-53367973 chr13:53368274-53368294
38	REST	chr13:53370958-53372086	H1-neurons	neurons:	n/a	n/a
39	REST	chr13:53367526-53368159	H1-neurons	neurons:	n/a	chr13:53367955-53367973
40	REST	chr13:53371198-53371802	H1-neurons	neurons:	n/a	n/a
41	RUNX3	chr13:53378411-53378784	GM12878	blood:	n/a	chr13:53378605-53378614
42	SP1	chr13:53360784-53361390	HCT-116	colon:	n/a	n/a
43	SP1	chr13:53359731-53360436	HCT-116	colon:	n/a	n/a
44	SPI1	chr13:53368715-53369019	HL-60	blood:	n/a	n/a
45	STAT3	chr13:53374166-53374306	MCF10A-Er-Src	breast:	n/a	n/a
46	STAT3	chr13:53368858-53369017	MCF10A-Er-Src	breast:	n/a	n/a
47	STAT3	chr13:53378329-53378529	MCF10A-Er-Src	breast:	n/a	n/a
48	TCF12	chr13:53378399-53378846	SK-N-SH	brain:	n/a	n/a
49	TCF12	chr13:53378418-53378847	SK-N-SH	brain:	n/a	n/a
50	USF1	chr13:53360988-53361163	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:53378011..53379591-chr13:53381360..53382993,2	MCF-7	breast:
2	chr13:53362246..53364630-chr13:53365395..53367188,2	K562	blood:
3	chr13:53362246..53364630-chr13:53365395..53367188,2	K562	blood:

Variant related genes	Relation type
MIR759	TF binding region

Extended variants
information (count: 517 )
Associated
traits (count: 110 )

Variant overlapped rSNPs/rCNVs (count:517 , 50 per page) page: 1 2 3 4 5 6 7 ... 11

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs235789	chr13:53359853-53359854	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs576940567	chr13:53359860-53359861	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs144784558	chr13:53359926-53359927	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs117745298	chr13:53359933-53359934	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs559756661	chr13:53359934-53359935	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs184161170	chr13:53359944-53359945	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs548703986	chr13:53359968-53359969	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs374649444	chr13:53359981-53359982	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs148645492	chr13:53360005-53360006	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs116991382	chr13:53360006-53360007	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs367776604	chr13:53360008-53360009	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs534541537	chr13:53360020-53360021	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs554207681	chr13:53360024-53360025	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs111624609	chr13:53360099-53360100	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs187704378	chr13:53360109-53360110	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs536726518	chr13:53360201-53360202	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs556707892	chr13:53360285-53360286	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs141622309	chr13:53360372-53360373	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs544397300	chr13:53360386-53360387	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs564183804	chr13:53360410-53360411	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs12385882	chr13:53360438-53360439	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs191343090	chr13:53360455-53360456	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs559697228	chr13:53360464-53360465	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs182113944	chr13:53360480-53360481	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs76430609	chr13:53360525-53360526	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs562606989	chr13:53360529-53360530	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs75383278	chr13:53360637-53360638	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs551943029	chr13:53360677-53360678	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs77896303	chr13:53360701-53360702	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs573046468	chr13:53360706-53360707	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs527969499	chr13:53360710-53360711	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs372119518	chr13:53360745-53360746	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs376810889	chr13:53360746-53360747	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs369526335	chr13:53360749-53360750	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs186867	chr13:53360806-53360807	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs567627055	chr13:53360827-53360828	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs187030449	chr13:53360887-53360888	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs464294	chr13:53360911-53360912	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs139066760	chr13:53360926-53360927	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs10454633	chr13:53360934-53360935	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs557928261	chr13:53360943-53360944	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs577443257	chr13:53360956-53360957	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs540103280	chr13:53360960-53360961	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs528240328	chr13:53361030-53361031	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
45	rs549839570	chr13:53361073-53361074	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
46	rs191524313	chr13:53361086-53361087	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
47	rs57111862	chr13:53361117-53361118	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
48	rs184722219	chr13:53361126-53361127	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
49	rs562386239	chr13:53361163-53361164	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
50	rs531434352	chr13:53361164-53361165	Enhancers Weak transcription Bivalent Enhancer	n/a	n/a	Overlapped CNVs	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
Urothelial carcinoma	21177765	CNVD

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:53353800-53361000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr13:53356400-53361000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr13:53357200-53361200	Weak transcription	Brain Angular Gyrus	brain
4	chr13:53357400-53361400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr13:53357600-53361400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr13:53358800-53362000	Enhancers	Brain Cingulate Gyrus	brain
7	chr13:53359200-53361600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr13:53359400-53362000	Enhancers	Brain Anterior Caudate	brain
9	chr13:53359400-53362200	Enhancers	Brain Hippocampus Middle	brain
10	chr13:53359400-53362400	Enhancers	Brain Substantia Nigra	brain
11	chr13:53359600-53360400	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr13:53359600-53361800	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr13:53359600-53362000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr13:53359600-53362200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr13:53359800-53360000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr13:53360000-53360400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr13:53360000-53360400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr13:53360000-53360800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr13:53360000-53362000	Enhancers	HMEC	breast
20	chr13:53360400-53361800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr13:53360800-53362400	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr13:53361000-53361600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr13:53361000-53361800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr13:53361000-53362000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr13:53361000-53362600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr13:53361200-53361800	Enhancers	Brain Angular Gyrus	brain
27	chr13:53361200-53362400	Enhancers	H1 Cell Line	embryonic stem cell
28	chr13:53361400-53361600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr13:53361400-53362000	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr13:53361400-53362400	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr13:53361400-53362600	Enhancers	HUES6 Cell Line	embryonic stem cell
32	chr13:53361600-53362400	Enhancers	H9 Cell Line	embryonic stem cell
33	chr13:53361600-53362400	Enhancers	iPS-18 Cell Line	embryonic stem cell
34	chr13:53361800-53362200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr13:53361800-53362200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr13:53362000-53362600	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr13:53362200-53362400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr13:53362200-53362400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr13:53362400-53362600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr13:53362400-53364200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr13:53362600-53363400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr13:53362600-53364800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr13:53364200-53365000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr13:53364800-53365000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr13:53367400-53367800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr13:53369200-53370200	Enhancers	Brain Germinal Matrix	brain
47	chr13:53369200-53372600	Enhancers	Fetal Brain Male	brain
48	chr13:53369400-53370600	Enhancers	Fetal Brain Female	brain
49	chr13:53370200-53371200	Weak transcription	Brain Germinal Matrix	brain
50	chr13:53370600-53371000	Weak transcription	Fetal Brain Female	brain

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