Variant report

Variant	nsv580025
Chromosome Location	chr19:52890176-52895885
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:59)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:5)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:59 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr19:52894420-52894570	A549	lung:	n/a	n/a
2	CTCF	chr19:52894500-52894650	GM12873	blood:	n/a	n/a
3	CTCF	chr19:52894431-52894651	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr19:52894499-52894557	GM12891	blood:	n/a	n/a
5	CTCF	chr19:52894500-52894650	HCT-116	colon:	n/a	n/a
6	CTCF	chr19:52894400-52894550	GM12872	blood:	n/a	n/a
7	CTCF	chr19:52894500-52894650	GM12878	blood:	n/a	n/a
8	CTCF	chr19:52894408-52894733	K562	blood:	n/a	n/a
9	CTCF	chr19:52894496-52894667	Medullo	brain:	n/a	n/a
10	CTCF	chr19:52894420-52894570	BE2_C	brain:	n/a	n/a
11	CTCF	chr19:52894361-52894646	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr19:52894497-52894653	GM13977	blood:	n/a	n/a
13	CTCF	chr19:52894520-52894670	HCPEpiC	choroid plexus:	n/a	n/a
14	CTCF	chr19:52894325-52894649	K562	blood:	n/a	n/a
15	CTCF	chr19:52894520-52894670	HCFaa	heart:	n/a	n/a
16	CTCF	chr19:52894480-52894630	GM06990	blood:	n/a	n/a
17	CTCF	chr19:52894475-52894649	HepG2	liver:	n/a	n/a
18	CTCF	chr19:52894500-52894650	Caco-2	colon:	n/a	n/a
19	CTCF	chr19:52894450-52894614	K562	blood:	n/a	n/a
20	CTCF	chr19:52894480-52894630	HBMEC	blood vessel:	n/a	n/a
21	CTCF	chr19:52894668-52894670	Medullo	brain:	n/a	n/a
22	CTCF	chr19:52894460-52894610	HMF	breast:	n/a	n/a
23	CTCF	chr19:52894460-52894610	NB4	blood:	n/a	n/a
24	CTCF	chr19:52894460-52894610	HPF	lung:	n/a	n/a
25	CTCF	chr19:52894500-52894650	MCF-7	breast:	n/a	n/a
26	CTCF	chr19:52894480-52894630	Hela-S3	cervix:	n/a	n/a
27	CTCF	chr19:52894520-52894670	Hela-S3	cervix:	n/a	n/a
28	CTCF	chr19:52894440-52894590	WERI-Rb-1	eye:	n/a	n/a
29	CTCF	chr19:52894522-52894611	HepG2	liver:	n/a	n/a
30	CTCF	chr19:52894484-52894692	K562	blood:	n/a	n/a
31	CTCF	chr19:52894500-52894650	K562	blood:	n/a	n/a
32	CTCF	chr19:52894508-52894598	GM12892	blood:	n/a	n/a
33	CTCF	chr19:52894480-52894630	HCPEpiC	choroid plexus:	n/a	n/a
34	CTCF	chr19:52894422-52894730	GM12878	blood:	n/a	n/a
35	CTCF	chr19:52894435-52894625	H1-hESC	embryonic stem cell:	n/a	n/a
36	CTCF	chr19:52894560-52894710	GM12871	blood:	n/a	n/a
37	CTCF	chr19:52894516-52894528	MCF-7	breast:	n/a	n/a
38	CTCF	chr19:52894460-52894610	HEK293	kidney:	n/a	n/a
39	CTCF	chr19:52894480-52894630	HepG2	liver:	n/a	n/a
40	CTCF	chr19:52894480-52894630	K562	blood:	n/a	n/a
41	E2F6	chr19:52893359-52893709	H1-hESC	embryonic stem cell:	n/a	n/a
42	EBF1	chr19:52892154-52892346	GM12878	blood:	n/a	n/a
43	POLR2A	chr19:52894402-52894441	ProgFib	skin:	n/a	n/a
44	POLR2A	chr19:52893477-52893500	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr19:52892949-52892966	H1-hESC	embryonic stem cell:	n/a	n/a
46	POLR2A	chr19:52890893-52890897	K562	blood:	n/a	n/a
47	RAD21	chr19:52894394-52894757	H1-hESC	embryonic stem cell:	n/a	n/a
48	RAD21	chr19:52894408-52894688	HepG2	liver:	n/a	n/a
49	RAD21	chr19:52894485-52894636	K562	blood:	n/a	n/a
50	RAD21	chr19:52894314-52894744	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:52893005..52896642-chr19:52900305..52903556,3	MCF-7	breast:
2	chr19:52875265..52876916-chr19:52889763..52892567,2	MCF-7	breast:
3	chr19:52894785..52896519-chr19:52899562..52901653,2	MCF-7	breast:
4	chr19:52894967..52896731-chr19:52899629..52901485,2	K562	blood:

(count:5 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF83-1	chr19:52892272-52892556	ENSG00000269834.1
2	lnc-ZNF83-1	chr19:52892095-52896456	ENSG00000246015
3	lnc-ZNF83-1	chr19:52892095-52894826	ENSG00000269834.1
4	lnc-ZNF83-1	chr19:52892095-52892698	NONHSAT067540
5	lnc-ZNF83-1	chr19:52892095-52893679	ENSG00000246015

No data

Variant related genes	Relation type
ENSG00000269834	TF binding region
ENSG00000269834	chromatin interactions
ENSG00000167555	chromatin interactions
ULBP2	miRNA target sites
BMP1	miRNA target sites

Extended variants
information (count: 262 )
Associated
traits (count: 66 )

Variant overlapped rSNPs/rCNVs (count:262 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs34830840	chr19:52890186-52890187	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs139511606	chr19:52890280-52890281	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs571641083	chr19:52890333-52890334	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs371780367	chr19:52890406-52890407	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs187784987	chr19:52890423-52890424	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs529815160	chr19:52890429-52890430	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs377222252	chr19:52890438-52890439	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs12978111	chr19:52890454-52890455	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
9	rs569421732	chr19:52890464-52890465	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs111410636	chr19:52890482-52890483	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs554789110	chr19:52890487-52890488	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs372801518	chr19:52890521-52890522	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs530423643	chr19:52890573-52890574	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs375428120	chr19:52890625-52890626	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs548452114	chr19:52890631-52890632	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs567094401	chr19:52890632-52890633	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs369822878	chr19:52890656-52890657	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs10646059	chr19:52890706-52890707	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs533638183	chr19:52890713-52890714	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs558256646	chr19:52890770-52890771	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs570095484	chr19:52890784-52890785	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs567881441	chr19:52890806-52890807	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs6509634	chr19:52890829-52890830	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
24	rs75663652	chr19:52890839-52890840	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs368902127	chr19:52890846-52890847	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs7252317	chr19:52890847-52890848	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs372650803	chr19:52890859-52890860	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs192203717	chr19:52890921-52890922	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs540716550	chr19:52890941-52890942	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs565344747	chr19:52890962-52890963	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs553298769	chr19:52890986-52890987	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs7252251	chr19:52891000-52891001	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	mRNA abundance
33	rs544233909	chr19:52891074-52891075	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs370970110	chr19:52891079-52891080	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs11479315	chr19:52891088-52891089	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs79139201	chr19:52891099-52891100	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs80159476	chr19:52891101-52891102	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs12151000	chr19:52891119-52891120	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	mRNA abundance
39	rs71180454	chr19:52891152-52891153	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs547274671	chr19:52891159-52891160	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs77186273	chr19:52891166-52891167	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs137941698	chr19:52891195-52891196	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs560289459	chr19:52891196-52891197	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs12985587	chr19:52891260-52891261	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs552367884	chr19:52891261-52891262	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs558879398	chr19:52891281-52891282	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs34983741	chr19:52891289-52891290	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
48	rs537560524	chr19:52891293-52891294	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs549504243	chr19:52891336-52891337	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs10415459	chr19:52891366-52891367	ZNF genes & repeats Strong transcription Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance

Variant related diseases (count:66)

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
Hodgkin''s lymphoma	18641027	CNVD
Myelofibrosis	22110671	CNVD
Gastric adenocarcinoma	19115996	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Adrenocortical carcinoma	18281524	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Lung cancer	18438408	CNVD
Basal cell lymphoma	19029149	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Ovarian cancer	21781307	CNVD
Neuroblastoma	20406844	CNVD
Cancer	20164920	CNVD
Melanoma	17363583	CNVD
Breast cancer	21785460	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:159 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52876200-52890600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr19:52876200-52890600	ZNF genes & repeats	Fetal Lung	lung
3	chr19:52876200-52890800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:52876200-52890800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
5	chr19:52876200-52890800	ZNF genes & repeats	Liver	Liver
6	chr19:52876200-52893400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
7	chr19:52876200-52893800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr19:52876200-52894000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr19:52876200-52894000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr19:52876200-52894200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:52876200-52895000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
12	chr19:52876400-52890600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
13	chr19:52876400-52891000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr19:52877400-52893800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
15	chr19:52877800-52894200	ZNF genes & repeats	Adipose Nuclei	Adipose
16	chr19:52879000-52890600	ZNF genes & repeats	Colon Smooth Muscle	Colon
17	chr19:52879600-52890400	ZNF genes & repeats	Brain Germinal Matrix	brain
18	chr19:52880200-52890600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr19:52880400-52893800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
20	chr19:52882000-52890600	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
21	chr19:52885800-52890600	ZNF genes & repeats	Osteobl	bone
22	chr19:52885800-52890800	ZNF genes & repeats	Brain Hippocampus Middle	brain
23	chr19:52886000-52893400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr19:52886600-52890600	ZNF genes & repeats	Rectal Smooth Muscle	rectum
25	chr19:52886600-52890600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
26	chr19:52888000-52897600	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr19:52888600-52891200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr19:52888600-52891400	Weak transcription	Thymus	Thymus
29	chr19:52888600-52892800	Weak transcription	Right Ventricle	heart
30	chr19:52888600-52898600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr19:52888800-52890200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr19:52888800-52891200	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr19:52888800-52891800	Weak transcription	NH-A	brain
34	chr19:52888800-52894600	ZNF genes & repeats	Fetal Stomach	stomach
35	chr19:52889000-52890200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr19:52889000-52891200	Weak transcription	Placenta	Placenta
37	chr19:52889000-52891400	Weak transcription	HSMMtube	muscle
38	chr19:52889000-52891600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr19:52889000-52891800	Weak transcription	Brain Substantia Nigra	brain
40	chr19:52889000-52891800	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr19:52889000-52892600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr19:52889000-52892800	Weak transcription	HSMM	muscle
43	chr19:52889000-52897600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr19:52889000-52898200	Weak transcription	Brain Angular Gyrus	brain
45	chr19:52889000-52898200	Weak transcription	Brain Anterior Caudate	brain
46	chr19:52889200-52900800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr19:52889400-52892600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr19:52889600-52891800	Weak transcription	Brain Cingulate Gyrus	brain
49	chr19:52889600-52891800	Weak transcription	Fetal Kidney	kidney
50	chr19:52889800-52891400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links