Variant report

Variant	nsv541800
Chromosome Location	chr13:63704346-63826462
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	chr13:63818314-63818408	HepG2	liver:	n/a	n/a
2	ARID3A	chr13:63740419-63740523	HepG2	liver:	n/a	n/a
3	ATF2	chr13:63758870-63759176	H1-hESC	embryonic stem cell:	n/a	n/a
4	BACH1	chr13:63805105-63805108	H1-hESC	embryonic stem cell:	n/a	n/a
5	BRCA1	chr13:63778099-63778105	GM12878	blood:	n/a	n/a
6	CEBPB	chr13:63773504-63773772	IMR90	lung:	n/a	chr13:63773593-63773604
7	CEBPB	chr13:63783763-63784090	IMR90	lung:	n/a	n/a
8	CEBPB	chr13:63772326-63772639	IMR90	lung:	n/a	n/a
9	CEBPB	chr13:63722264-63722588	HepG2	liver:	n/a	chr13:63722425-63722436
10	CEBPB	chr13:63733024-63733236	HepG2	liver:	n/a	chr13:63733111-63733122
11	CEBPB	chr13:63773680-63773782	H1-hESC	embryonic stem cell:	n/a	n/a
12	CEBPB	chr13:63758997-63759239	H1-hESC	embryonic stem cell:	n/a	n/a
13	CEBPB	chr13:63711527-63711846	HepG2	liver:	n/a	chr13:63711684-63711695
14	CEBPB	chr13:63711510-63711861	IMR90	lung:	n/a	chr13:63711684-63711695
15	CEBPB	chr13:63764919-63765289	Hela-S3	cervix:	n/a	n/a
16	CEBPB	chr13:63740261-63740628	IMR90	lung:	n/a	chr13:63740443-63740452 chr13:63740441-63740454 chr13:63740441-63740452
17	CEBPB	chr13:63740269-63740585	HepG2	liver:	n/a	chr13:63740443-63740452 chr13:63740441-63740454 chr13:63740441-63740452
18	CEBPB	chr13:63711555-63711746	H1-hESC	embryonic stem cell:	n/a	chr13:63711684-63711695
19	CEBPB	chr13:63773594-63773780	HepG2	liver:	n/a	n/a
20	CEBPB	chr13:63776742-63776947	A549	lung:	n/a	n/a
21	CHD1	chr13:63731225-63731227	GM12878	blood:	n/a	n/a
22	CHD2	chr13:63758862-63759125	H1-hESC	embryonic stem cell:	n/a	n/a
23	CHD2	chr13:63741881-63742326	H1-hESC	embryonic stem cell:	n/a	n/a
24	CREB1	chr13:63758924-63759192	H1-hESC	embryonic stem cell:	n/a	n/a
25	CREB1	chr13:63758905-63759282	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr13:63737565-63737657	Kidney_OC	kidney:	n/a	n/a
27	CTCF	chr13:63704400-63704550	SAEC	small airway:	n/a	n/a
28	CTCF	chr13:63740480-63740630	BJ	skin:	n/a	n/a
29	CTCF	chr13:63787363-63787434	GM13976	blood:	n/a	n/a
30	E2F4	chr13:63812329-63812341	GM12878	blood:	n/a	n/a
31	E2F4	chr13:63718323-63718340	MCF10A-Er-Src	breast:	n/a	n/a
32	E2F4	chr13:63786637-63786814	MCF10A-Er-Src	breast:	n/a	n/a
33	EP300	chr13:63758907-63759132	H1-hESC	embryonic stem cell:	n/a	n/a
34	EP300	chr13:63764273-63765463	SK-N-SH	brain:	n/a	chr13:63765098-63765107 chr13:63765136-63765144
35	EP300	chr13:63780473-63781051	SK-N-SH	brain:	n/a	n/a
36	EP300	chr13:63758808-63759156	H1-hESC	embryonic stem cell:	n/a	n/a
37	EP300	chr13:63764300-63765232	SK-N-SH_RA	brain:	n/a	chr13:63765098-63765107 chr13:63765136-63765144
38	EP300	chr13:63758686-63759273	SK-N-SH	brain:	n/a	n/a
39	EP300	chr13:63764463-63764904	SK-N-SH_RA	brain:	n/a	n/a
40	EP300	chr13:63764569-63765342	SK-N-SH	brain:	n/a	chr13:63765098-63765107 chr13:63765136-63765144
41	EP300	chr13:63764858-63765188	A549	lung:	n/a	chr13:63765098-63765107 chr13:63765136-63765144
42	ESR1	chr13:63814113-63814327	ECC-1	luminal epithelium:	n/a	chr13:63814219-63814236 chr13:63814220-63814237
43	ESR1	chr13:63761562-63761916	ECC-1	luminal epithelium:	n/a	n/a
44	FAM48A	chr13:63709572-63709744	GM12878	blood:	n/a	n/a
45	FOS	chr13:63764936-63765251	MCF10A-Er-Src	breast:	n/a	chr13:63765097-63765107 chr13:63765098-63765105 chr13:63765097-63765107 chr13:63765097-63765107 chr13:63765098-63765106 chr13:63765098-63765106
46	FOS	chr13:63758907-63759136	MCF10A-Er-Src	breast:	n/a	n/a
47	FOS	chr13:63759023-63759082	MCF10A-Er-Src	breast:	n/a	n/a
48	FOS	chr13:63723420-63723825	HUVEC	blood vessel:	n/a	chr13:63723663-63723674
49	FOS	chr13:63765014-63765250	MCF10A-Er-Src	breast:	n/a	chr13:63765097-63765107 chr13:63765098-63765105 chr13:63765097-63765107 chr13:63765097-63765107 chr13:63765098-63765106 chr13:63765098-63765106
50	FOS	chr13:63710999-63711128	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:120076978..120077828-chr13:63812850..63813372,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PCDH20-5	chr13:63757234-63757461	XLOC_010639
2	lnc-PCDH20-5	chr13:63768623-63768664	XLOC_010639
3	lnc-PCDH20-5	chr13:63801112-63801189	XLOC_010639

Variant related genes	Relation type
LINC00376	TF binding region

Extended variants
information (count: 2152 )
Associated
traits (count: 96 )

Variant overlapped rSNPs/rCNVs (count:2152 , 50 per page) page: 1 2 3 4 5 6 7 ... 44

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs544070422	chr13:63704381-63704382	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs141491037	chr13:63704396-63704397	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs60853607	chr13:63704449-63704450	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs528421851	chr13:63704453-63704454	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs529253469	chr13:63704512-63704513	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs9539658	chr13:63704532-63704533	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs371475951	chr13:63704575-63704576	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs377240091	chr13:63704602-63704603	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs370218917	chr13:63704606-63704607	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs559839579	chr13:63704677-63704678	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs146188180	chr13:63704684-63704685	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs551947968	chr13:63704746-63704747	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs182500315	chr13:63704771-63704772	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs548140034	chr13:63704803-63704804	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs187548255	chr13:63704810-63704811	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs549233641	chr13:63704813-63704814	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs530581783	chr13:63704829-63704830	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs192319739	chr13:63704842-63704843	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs534562470	chr13:63704856-63704857	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs184525634	chr13:63704857-63704858	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs570949268	chr13:63704910-63704911	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs539062599	chr13:63704930-63704931	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs374946829	chr13:63704932-63704933	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs538330763	chr13:63704946-63704947	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs112202362	chr13:63704969-63704970	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs76224167	chr13:63704994-63704995	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs369298725	chr13:63705027-63705028	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs543669694	chr13:63705033-63705034	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs555986842	chr13:63705138-63705139	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs546224725	chr13:63705158-63705159	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs2175663	chr13:63705178-63705179	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs568688567	chr13:63705231-63705232	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs566110811	chr13:63705247-63705248	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs143094891	chr13:63705253-63705254	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs533403159	chr13:63705268-63705269	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs189170331	chr13:63705270-63705271	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs563797271	chr13:63705277-63705278	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs530688658	chr13:63705303-63705304	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs193077006	chr13:63705339-63705340	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs184548134	chr13:63705443-63705444	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs372901005	chr13:63705458-63705459	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs528362801	chr13:63705580-63705581	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs546523257	chr13:63705592-63705593	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs570888214	chr13:63705600-63705601	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs538267471	chr13:63705621-63705622	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs556604180	chr13:63705702-63705703	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs568869826	chr13:63705740-63705741	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs537605960	chr13:63705753-63705754	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs144332523	chr13:63705812-63705813	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs534487256	chr13:63705896-63705897	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:96)

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
Breast cancer	17133270	CNVD
Myoepithelioma	18604193	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Prostate cancer	16573809	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Paraganglioma	21461997	CNVD
Pheochromocytoma	21461997	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Prostate cancer	17245344	CNVD
Prostate cancer	18632612	CNVD
Colorectal cancer	21586687	CNVD
Small bowel adenocarcinoma	21586687	CNVD
Retinoblastoma	19183342	CNVD
Developmental delay	21147756	CNVD
Melanoma	18172304	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Merkel cell carcinoma	19020549	CNVD
Basal cell lymphoma	17053054	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
lymphocytic leukemia	21291569	CNVD
Multiple myeloma	17550852	CNVD
Breast cancer	21858162	CNVD
Glioblastoma multiforme	21922591	CNVD
Metanephric adenoma	20802469	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Gastric cancer	17908304	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
head and neck squamous cell carcinoma	17671120	CNVD
Colorectal cancer	16774939	CNVD
Adenoid cystic carcinoma	17372589	CNVD
abnormal development	18461090	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Acute myeloid leukemia	20729466	CNVD
Myelofibrosis	22110671	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Bipolar disorder	19114987	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD

Chromatin state (count:195 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:63700200-63706600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr13:63701000-63704800	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr13:63703200-63704600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:63704000-63704600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr13:63704000-63704800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr13:63704400-63704600	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr13:63704800-63705200	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr13:63712200-63712800	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr13:63712800-63713200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr13:63713200-63713600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr13:63713200-63713600	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr13:63720200-63720400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr13:63720400-63720800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr13:63720800-63721000	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr13:63729600-63730000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr13:63735200-63735600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr13:63735200-63735600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr13:63735200-63736400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr13:63738000-63738400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr13:63741200-63741600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr13:63741200-63741600	Enhancers	Fetal Brain Female	brain
22	chr13:63741200-63741800	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr13:63741200-63741800	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr13:63741600-63741800	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr13:63741600-63742000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr13:63741600-63742000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr13:63741600-63742000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr13:63741600-63742000	Weak transcription	Fetal Brain Female	brain
29	chr13:63741600-63742600	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr13:63741600-63742800	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr13:63741800-63742000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr13:63741800-63742000	Active TSS	Osteobl	bone
33	chr13:63741800-63742200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr13:63741800-63742200	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr13:63741800-63742200	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr13:63741800-63742200	Enhancers	Fetal Lung	lung
37	chr13:63741800-63742400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
38	chr13:63741800-63742400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
39	chr13:63741800-63742400	Active TSS	Brain Anterior Caudate	brain
40	chr13:63741800-63742600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr13:63741800-63742600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr13:63741800-63743000	Enhancers	ES-I3 Cell Line	embryonic stem cell
43	chr13:63741800-63743000	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr13:63741800-63743200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr13:63742000-63742200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr13:63742000-63742200	Flanking Active TSS	Osteobl	bone
47	chr13:63742000-63742400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr13:63742000-63742400	Enhancers	Brain Substantia Nigra	brain
49	chr13:63742000-63742600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr13:63742000-63742600	Enhancers	Fetal Brain Female	brain

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