Variant report

Variant	nsv1048842
Chromosome Location	chr13:54381146-54401841
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	EP300	chr13:54395604-54396376	T-47D	breast:	n/a	chr13:54395651-54395665 chr13:54395851-54395861 chr13:54395655-54395664
2	ESR1	chr13:54395738-54395970	T-47D	breast:	n/a	n/a
3	FAM48A	chr13:54381574-54381731	GM12878	blood:	n/a	n/a
4	FOS	chr13:54400913-54401166	MCF10A-Er-Src	breast:	n/a	chr13:54401096-54401105 chr13:54401096-54401104 chr13:54401097-54401104
5	FOXA1	chr13:54396204-54396547	T-47D	breast:	n/a	n/a
6	FOXA1	chr13:54395660-54396140	T-47D	breast:	n/a	n/a
7	FOXA1	chr13:54395678-54396069	T-47D	breast:	n/a	n/a
8	GATA3	chr13:54388352-54388617	T-47D	breast:	n/a	n/a
9	GATA3	chr13:54395763-54396039	T-47D	breast:	n/a	n/a
10	GATA3	chr13:54396064-54396556	T-47D	breast:	n/a	n/a
11	GATA3	chr13:54398289-54398468	SH-SY5Y	brain:	n/a	n/a
12	GATA3	chr13:54395678-54396602	T-47D	breast:	n/a	n/a
13	GATA3	chr13:54390049-54390416	T-47D	breast:	n/a	n/a
14	JUND	chr13:54401041-54401166	HepG2	liver:	n/a	chr13:54401096-54401105 chr13:54401096-54401104 chr13:54401094-54401105 chr13:54401097-54401104
15	MAFK	chr13:54392210-54392413	HepG2	liver:	n/a	n/a
16	MAX	chr13:54397022-54397175	NB4	blood:	n/a	chr13:54397114-54397124 chr13:54397116-54397125 chr13:54397115-54397126 chr13:54397114-54397127 chr13:54397114-54397127 chr13:54397115-54397125 chr13:54397112-54397127 chr13:54397114-54397127 chr13:54397118-54397125 chr13:54397115-54397126
17	MYC	chr13:54381794-54381864	NB4	blood:	n/a	n/a
18	NFYA	chr13:54381215-54381341	GM12878	blood:	n/a	n/a
19	POLR2A	chr13:54381514-54381533	MCF10A-Er-Src	breast:	n/a	n/a
20	POLR2A	chr13:54385873-54385963	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr13:54385526-54385633	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr13:54396677-54396681	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr13:54389171-54389253	ProgFib	skin:	n/a	n/a
24	POLR2A	chr13:54393439-54393625	MCF10A-Er-Src	breast:	n/a	n/a
25	STAT3	chr13:54396027-54396087	MCF10A-Er-Src	breast:	n/a	n/a
26	STAT3	chr13:54386676-54386774	MCF10A-Er-Src	breast:	n/a	n/a
27	STAT3	chr13:54399648-54399739	MCF10A-Er-Src	breast:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OLFM4-3	chr13:54389554-54389628	ENSG00000261517.1

Variant related genes	Relation type
LINC00558	TF binding region

Extended variants
information (count: 349 )
Associated
traits (count: 112 )

Variant overlapped rSNPs/rCNVs (count:349 , 50 per page) page: 1 2 3 4 5 6 7

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs114144655	chr13:54381146-54381147	Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs145218885	chr13:54381166-54381167	Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs149135429	chr13:54381169-54381170	Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs528244452	chr13:54381200-54381201	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs990157	chr13:54381248-54381249	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs568151589	chr13:54381256-54381257	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs530655736	chr13:54381294-54381295	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs201914246	chr13:54381306-54381307	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs373265024	chr13:54381324-54381325	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs550572503	chr13:54381343-54381344	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs142476323	chr13:54381353-54381354	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs554115032	chr13:54381371-54381372	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs185245400	chr13:54381392-54381393	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs567695282	chr13:54381472-54381473	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs553588495	chr13:54381494-54381495	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs567053109	chr13:54381508-54381509	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs535648539	chr13:54381539-54381540	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs116739052	chr13:54381567-54381568	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs575315763	chr13:54381670-54381671	Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs146872648	chr13:54381716-54381717	Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs28435472	chr13:54381805-54381806	Flanking Active TSS Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs140703827	chr13:54381806-54381807	Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs113365125	chr13:54381817-54381818	Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs540271672	chr13:54381830-54381831	Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs74346044	chr13:54381844-54381845	Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs528434805	chr13:54381895-54381896	Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs542029687	chr13:54381903-54381904	Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs576680491	chr13:54381912-54381913	Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs545729997	chr13:54381935-54381936	Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs561891893	chr13:54381950-54381951	Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs530747123	chr13:54381951-54381952	Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs550658610	chr13:54381970-54381971	Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs559324766	chr13:54381973-54381974	Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs570461260	chr13:54381983-54381984	Flanking Active TSS Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs1031654	chr13:54382035-54382036	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
36	rs546323840	chr13:54382082-54382083	Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs567139601	chr13:54382102-54382103	Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs548481601	chr13:54382112-54382113	Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs145814316	chr13:54382132-54382133	Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs549289910	chr13:54382136-54382137	Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs7995039	chr13:54382214-54382215	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs138380626	chr13:54382215-54382216	Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs372792615	chr13:54382217-54382218	Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs534218877	chr13:54382230-54382231	Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs10161977	chr13:54382254-54382255	Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs112957598	chr13:54382288-54382289	Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs140201228	chr13:54382289-54382290	Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs370001123	chr13:54382327-54382328	Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs534190321	chr13:54382339-54382340	Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs529764732	chr13:54382357-54382358	Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:112)

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
Acute lymphoblastic leukemia	21339820	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:54380600-54381600	Enhancers	Fetal Heart	heart
2	chr13:54380800-54381200	Enhancers	Fetal Lung	lung
3	chr13:54381200-54381600	Weak transcription	Fetal Lung	lung
4	chr13:54381600-54382000	Flanking Active TSS	Fetal Heart	heart
5	chr13:54381600-54382600	Enhancers	Fetal Lung	lung
6	chr13:54382000-54382600	Enhancers	Fetal Heart	heart
7	chr13:54390600-54390800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr13:54390800-54391000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr13:54391000-54391200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr13:54391200-54391600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr13:54391600-54396400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr13:54395000-54396000	Enhancers	Fetal Heart	heart
13	chr13:54395200-54396600	Enhancers	Fetal Brain Male	brain
14	chr13:54395400-54395800	Enhancers	Brain Substantia Nigra	brain
15	chr13:54395400-54396600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr13:54395600-54396200	Active TSS	Stomach Smooth Muscle	stomach
17	chr13:54395600-54396400	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr13:54395800-54396000	Active TSS	Brain Substantia Nigra	brain
19	chr13:54395800-54396400	Active TSS	Brain Angular Gyrus	brain
20	chr13:54395800-54396400	Active TSS	Brain Anterior Caudate	brain
21	chr13:54395800-54396400	Active TSS	Brain Hippocampus Middle	brain
22	chr13:54395800-54396400	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr13:54395800-54396600	Active TSS	Brain Cingulate Gyrus	brain
24	chr13:54395800-54396600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr13:54396000-54396400	Bivalent/Poised TSS	Brain Substantia Nigra	brain
26	chr13:54396000-54396400	Flanking Active TSS	Fetal Heart	heart
27	chr13:54396400-54396600	Flanking Active TSS	Brain Angular Gyrus	brain
28	chr13:54396400-54397200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr13:54396400-54397200	Enhancers	Fetal Heart	heart
30	chr13:54396800-54397000	Bivalent Enhancer	Brain Substantia Nigra	brain
31	chr13:54397200-54398200	Weak transcription	Fetal Heart	heart
32	chr13:54398200-54398400	Enhancers	Fetal Heart	heart

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