Variant report

Variant	nsv1062264
Chromosome Location	chr19:56496803-56538729
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	BHLHE40	chr19:56538297-56538378	K562	blood:	n/a	n/a
2	CEBPB	chr19:56527867-56528017	K562	blood:	n/a	chr19:56527886-56527897
3	CEBPB	chr19:56527810-56527996	A549	lung:	n/a	chr19:56527886-56527897 chr19:56527850-56527861
4	CEBPB	chr19:56502244-56502561	Hela-S3	cervix:	n/a	n/a
5	CEBPB	chr19:56527761-56527969	Hela-S3	cervix:	n/a	chr19:56527886-56527897 chr19:56527850-56527861
6	CEBPB	chr19:56527760-56528021	HepG2	liver:	n/a	chr19:56527886-56527897 chr19:56527850-56527861
7	CTCF	chr19:56504857-56504894	Pancreas_OC	pancreas:	n/a	n/a
8	CTCF	chr19:56530979-56531030	Medullo	brain:	n/a	n/a
9	CTCF	chr19:56520034-56520087	Kidney_OC	kidney:	n/a	n/a
10	CTCF	chr19:56531964-56532032	Kidney_OC	kidney:	n/a	n/a
11	CTCF	chr19:56537300-56537450	WI-38	lung:	n/a	n/a
12	E2F6	chr19:56497992-56498199	K562	blood:	n/a	chr19:56498040-56498049
13	EGR1	chr19:56497934-56498235	K562	blood:	n/a	chr19:56498094-56498104 chr19:56498092-56498106 chr19:56498095-56498104 chr19:56498003-56498027 chr19:56498094-56498104
14	EGR1	chr19:56497924-56498156	K562	blood:	n/a	chr19:56498094-56498104 chr19:56498092-56498106 chr19:56498095-56498104 chr19:56498003-56498027 chr19:56498094-56498104
15	EP300	chr19:56502699-56502871	K562	blood:	n/a	n/a
16	GABPA	chr19:56504804-56504951	HepG2	liver:	n/a	n/a
17	GABPA	chr19:56504811-56504948	HepG2	liver:	n/a	n/a
18	GATA3	chr19:56502149-56502576	MCF-7	breast:	n/a	n/a
19	GATA3	chr19:56502152-56502603	MCF-7	breast:	n/a	n/a
20	GATA3	chr19:56502167-56502656	SK-N-SH	brain:	n/a	n/a
21	MAFF	chr19:56538326-56538429	HepG2	liver:	n/a	n/a
22	MAFF	chr19:56526189-56526488	HepG2	liver:	n/a	chr19:56526320-56526338
23	MAFK	chr19:56526211-56526460	IMR90	lung:	n/a	chr19:56526322-56526337
24	MAFK	chr19:56526158-56526495	HepG2	liver:	n/a	chr19:56526322-56526337
25	MAFK	chr19:56526176-56526464	HepG2	liver:	n/a	chr19:56526322-56526337
26	MAX	chr19:56527210-56527384	NB4	blood:	n/a	n/a
27	MAX	chr19:56497954-56498399	HCT-116	colon:	n/a	chr19:56498092-56498101 chr19:56498094-56498103 chr19:56498092-56498102 chr19:56498091-56498102 chr19:56498092-56498101 chr19:56498275-56498285 chr19:56498092-56498101
28	MAX	chr19:56497891-56498323	K562	blood:	n/a	chr19:56498092-56498101 chr19:56498094-56498103 chr19:56498092-56498102 chr19:56498091-56498102 chr19:56498092-56498101 chr19:56498275-56498285 chr19:56498092-56498101
29	MAX	chr19:56497873-56498385	MCF-7	breast:	n/a	chr19:56498092-56498101 chr19:56498094-56498103 chr19:56498092-56498102 chr19:56498091-56498102 chr19:56498092-56498101 chr19:56498275-56498285 chr19:56498092-56498101
30	MAX	chr19:56497993-56498180	K562	blood:	n/a	chr19:56498092-56498101 chr19:56498094-56498103 chr19:56498092-56498102 chr19:56498091-56498102 chr19:56498092-56498101 chr19:56498092-56498101
31	MYC	chr19:56512508-56512616	GM12878	blood:	n/a	n/a
32	MYC	chr19:56498039-56498042	MCF-7	breast:	n/a	n/a
33	MYC	chr19:56498041-56498128	MCF-7	breast:	n/a	chr19:56498092-56498101 chr19:56498094-56498103 chr19:56498092-56498102 chr19:56498091-56498102 chr19:56498092-56498101 chr19:56498092-56498101
34	MYC	chr19:56498044-56498141	MCF-7	breast:	n/a	chr19:56498092-56498101 chr19:56498094-56498103 chr19:56498092-56498102 chr19:56498091-56498102 chr19:56498092-56498101 chr19:56498092-56498101
35	MYC	chr19:56497692-56497733	MCF-7	breast:	n/a	n/a
36	POLR2A	chr19:56510304-56510306	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chr19:56521363-56521455	GM12878	blood:	n/a	n/a
38	POLR2A	chr19:56523701-56523812	GM12878	blood:	n/a	n/a
39	POLR2A	chr19:56538121-56538381	K562	blood:	n/a	n/a
40	POLR2A	chr19:56511550-56511580	ProgFib	skin:	n/a	n/a
41	POLR2A	chr19:56516986-56517065	MCF-7	breast:	n/a	n/a
42	POLR2A	chr19:56537762-56537834	K562	blood:	n/a	n/a
43	POLR2A	chr19:56535979-56536076	A549	lung:	n/a	n/a
44	PRDM1	chr19:56527061-56527443	Hela-S3	cervix:	n/a	chr19:56527250-56527265
45	RCOR1	chr19:56502746-56502837	K562	blood:	n/a	n/a
46	REST	chr19:56527066-56527481	SK-N-SH	brain:	n/a	n/a
47	REST	chr19:56526916-56527549	K562	blood:	n/a	n/a
48	REST	chr19:56531415-56531724	K562	blood:	n/a	n/a
49	REST	chr19:56527144-56527434	HepG2	liver:	n/a	n/a
50	REST	chr19:56530712-56531055	PFSK-1	brain:	n/a	chr19:56530924-56530933 chr19:56530918-56530938 chr19:56530918-56530938 chr19:56530918-56530938 chr19:56530919-56530937 chr19:56530918-56530932

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:56510965-56511015	NH-A	brain:	n/a
2	chr19:56510833-56510883	HRE	kidney:	n/a
3	chr19:56511149-56511199	HepG2	liver:	n/a
4	chr19:56510892-56510942	NH-A	brain:	n/a
5	chr19:56510965-56511015	NHBE	bronchial:	n/a
6	chr19:56510833-56510883	K562	blood:	n/a
7	chr19:56510965-56511015	T-47D	breast:	n/a
8	chr19:56499348-56499398	HRE	kidney:	n/a
9	chr19:56510200-56510250	CMK	blood:	n/a
10	chr19:56510200-56510250	HCT-116	colon:	n/a
11	chr19:56510965-56511015	GM19239	blood:	n/a
12	chr19:56510892-56510942	SKMC	muscle:	n/a
13	chr19:56510200-56510250	AG10803	skin:	n/a
14	chr19:56511149-56511199	GM12878	blood:	n/a
15	chr19:56499348-56499398	AG09309	skin:	n/a
16	chr19:56511149-56511199	HMEC	breast:	n/a
17	chr19:56511149-56511199	MCF-7	breast:	n/a
18	chr19:56510892-56510942	U87	brain:	n/a
19	chr19:56499348-56499398	MCF-7	breast:	n/a
20	chr19:56510892-56510942	GM12891	blood:	n/a
21	chr19:56510965-56511015	GM12891	blood:	n/a
22	chr19:56510200-56510250	HepG2	liver:	n/a
23	chr19:56499348-56499398	HCT-116	colon:	n/a
24	chr19:56510965-56511015	HIPEpiC	eye:	n/a
25	chr19:56510833-56510883	SK-N-MC	brain:	n/a
26	chr19:56510965-56511015	HCF	heart:	n/a
27	chr19:56510892-56510942	AG04450	lung:	fetal
28	chr19:56511149-56511199	PANC-1	pancreas:	n/a
29	chr19:56510965-56511015	ovcar-3	ovarian:	n/a
30	chr19:56510892-56510942	SK-N-SH_RA	brain:	n/a
31	chr19:56511149-56511199	HCM	heart:	n/a
32	chr19:56511149-56511199	ovcar-3	ovarian:	n/a
33	chr19:56511149-56511199	PFSK-1	brain:	n/a
34	chr19:56510833-56510883	SK-N-SH_RA	brain:	n/a
35	chr19:56510965-56511015	HL-60	blood:	n/a
36	chr19:56511149-56511199	Hela-S3	cervix:	n/a
37	chr19:56510200-56510250	NHDF-neo	bronchial:	n/a
38	chr19:56511149-56511199	Jurkat	blood:	n/a
39	chr19:56510833-56510883	ovcar-3	ovarian:	n/a
40	chr19:56511149-56511199	HNPCEpiC	eye:	n/a
41	chr19:56510965-56511015	A549	lung:	n/a
42	chr19:56510833-56510883	NT2-D1	testis:	n/a
43	chr19:56499348-56499398	LNCaP	prostate:	n/a
44	chr19:56499348-56499398	HEEpiC	esophagus:	n/a
45	chr19:56510200-56510250	HPAEpiC	pulmonary alveolar:	n/a
46	chr19:56499348-56499398	NB4	blood:	n/a
47	chr19:56499348-56499398	GM19239	blood:	n/a
48	chr19:56510892-56510942	LNCaP	prostate:	n/a
49	chr19:56510200-56510250	Caco-2	colon:	n/a
50	chr19:56499348-56499398	U87	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:56532441..56535023-chr19:56626628..56629336,2	K562	blood:
2	chr19:56538350..56540357-chr19:56542809..56545691,2	K562	blood:
3	chr19:56538480..56540946-chr19:56548359..56549987,2	K562	blood:
4	chr19:56537372..56539980-chr19:56548359..56550687,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF787-1	chr19:56526602-56527706	ucscGeneNc_uc002pwe_1
2	lnc-ZNF787-1	chr19:56528857-56529011	ucscGeneNc_uc002pwe_1
3	lnc-ZNF787-1	chr19:56533954-56534208	ucscGeneNc_uc002pwe_1
4	lnc-ZNF787-1	chr19:56529257-56529370	ucscGeneNc_uc002pwe_1
5	lnc-ZNF787-1	chr19:56532304-56532600	ucscGeneNc_uc002pwe_1
6	lnc-ZNF787-1	chr19:56535081-56535219	ucscGeneNc_uc002pwe_1
7	lnc-ZNF787-1	chr19:56532996-56533274	ucscGeneNc_uc002pwe_1

Variant related genes	Relation type
NLRP5	TF binding region
NLRP5	CpG island

Extended variants
information (count: 516 )
Associated
traits (count: 69 )

Variant overlapped rSNPs/rCNVs (count:516 , 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	rs140616957	chr19:56496804-56496805	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs549084042	chr19:56496806-56496807	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs577038857	chr19:56496813-56496814	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs376609087	chr19:56496821-56496822	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs55905529	chr19:56496883-56496884	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs8102420	chr19:56496916-56496917	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs576028308	chr19:56496990-56496991	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs306463	chr19:56497077-56497078	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs116545229	chr19:56497091-56497092	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs142944826	chr19:56497117-56497118	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs563753688	chr19:56497145-56497146	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs306462	chr19:56497148-56497149	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs549711155	chr19:56497152-56497153	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs575676131	chr19:56497164-56497165	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs306461	chr19:56497226-56497227	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs528543358	chr19:56497239-56497240	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs551464931	chr19:56497241-56497242	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs571748222	chr19:56497269-56497270	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs10406992	chr19:56497304-56497305	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs557399093	chr19:56497408-56497409	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs370332708	chr19:56497450-56497451	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs139701680	chr19:56497519-56497520	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs535229954	chr19:56497603-56497604	ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs540007599	chr19:56497641-56497642	ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs372284071	chr19:56497646-56497647	ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs572004537	chr19:56497657-56497658	ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs534712998	chr19:56497663-56497664	ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
28	rs368782329	chr19:56497665-56497666	ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
29	rs114671992	chr19:56497667-56497668	ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs200122897	chr19:56497671-56497672	ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs201343610	chr19:56497673-56497674	ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
32	rs199644371	chr19:56497678-56497679	ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
33	rs377116498	chr19:56497694-56497695	ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs143343122	chr19:56497695-56497696	ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
35	rs200906659	chr19:56497696-56497697	ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
36	rs567081249	chr19:56497697-56497698	ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
37	rs557486552	chr19:56497733-56497734	ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
38	rs368983447	chr19:56497748-56497749	ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
39	rs577541147	chr19:56497751-56497752	ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
40	rs369821189	chr19:56497770-56497771	ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
41	rs445526	chr19:56497778-56497779	ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs570720036	chr19:56497786-56497787	ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs10409739	chr19:56497794-56497795	ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
44	rs143870298	chr19:56497809-56497810	ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs55637278	chr19:56497810-56497811	ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs563359340	chr19:56497811-56497812	ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs62130170	chr19:56497812-56497813	ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs62130171	chr19:56497814-56497815	ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs62130172	chr19:56497816-56497817	ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs529552004	chr19:56497817-56497818	ZNF genes & repeats Bivalent/Poised TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:69)

Disease	PMID	Source
Myelodysplastic syndrome	17634407	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Chordoma	21602918	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Cancer	21637783	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Ovarian cancer	21720365	CNVD
Cancer	20164919	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Ductal carcinoma	22052326	CNVD
Congenital nephrotic syndrome	18421352	CNVD
Astrocytoma	17934521	CNVD
Leukemia	17361228	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Breast cancer	17603634	CNVD
Glioma	21971842	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Endometrial cancer	22040021	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Oligodendroglial tumors	17285580	CNVD
renal disease	20603712	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Chordoma	18071362	CNVD
Urothelial carcinoma	21177765	CNVD
Metanephric adenoma	20802469	CNVD
Acute myeloid leukemia	16864856	CNVD
Bladder cancer	21909424	CNVD
Medulloblastoma	16783165	CNVD
Acute myeloid leukemia	20729466	CNVD
Ovarian cancer	22174824	CNVD
Multiple myeloma	16616336	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Wilms tumour	21544195	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Congenital anomalies of the kidney and urinary tract	18852474	CNVD
Glioblastoma multiforme	17002787	CNVD
Cervical cancer	21062161	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Prostate cancer	16573809	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Lung cancer	18438408	CNVD
Colorectal cancer	16272173	CNVD
Ovarian cancer	21781307	CNVD
Neuroblastoma	20406844	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
T-cell acute lymphoblastic leukemia	19406988	CNVD
Alzheimer''s disease	22166940	CNVD
Heart disease	21282601	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Glioblastoma multiforme	21922591	CNVD
Non-syndromic sensorineural hearing loss	18496225	CNVD
Basal cell lymphoma	19029149	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Breast cancer	20409316	CNVD
Breast cancer	22522925	CNVD
early-passage human iPS cells	21368824	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Melanoma	20877625	CNVD

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56496200-56497600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr19:56496400-56497600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr19:56497600-56498000	Bivalent/Poised TSS	Breast Myoepithelial Primary Cells	Breast
4	chr19:56497600-56498200	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr19:56497600-56498200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
6	chr19:56497800-56498200	ZNF genes & repeats	Pancreas	Pancrea
7	chr19:56502400-56502800	Enhancers	Hela-S3	cervix
8	chr19:56504600-56504800	Active TSS	HSMM	muscle
9	chr19:56504600-56504800	Weak transcription	HSMMtube	muscle
10	chr19:56504600-56505000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
11	chr19:56504600-56505000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
12	chr19:56504600-56505000	ZNF genes & repeats	NHEK	skin
13	chr19:56504800-56505000	Enhancers	HSMMtube	muscle
14	chr19:56504800-56505200	Flanking Active TSS	HSMM	muscle
15	chr19:56504800-56505600	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
16	chr19:56504800-56505600	Active TSS	GM12878-XiMat	blood
17	chr19:56505000-56505800	Weak transcription	HSMMtube	muscle
18	chr19:56519000-56519400	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
19	chr19:56521200-56521600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr19:56521400-56521600	Bivalent/Poised TSS	Hela-S3	cervix
21	chr19:56538000-56540200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
22	chr19:56538200-56538800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:56538400-56538600	Bivalent/Poised TSS	Hela-S3	cervix
24	chr19:56538600-56539200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links