Variant report

Variant	nsv520245
Chromosome Location	chr19:39844176-39850102
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:13)
LncRNA
region (count:0)
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	BACH1	chr19:39846773-39847257	K562	blood:	n/a	n/a
2	CHD2	chr19:39847309-39847468	K562	blood:	n/a	n/a
3	CTCF	chr19:39845760-39845910	GM12866	blood:	n/a	n/a
4	CUX1	chr19:39847187-39847372	K562	blood:	n/a	n/a
5	E2F6	chr19:39847316-39847588	K562	blood:	n/a	n/a
6	ELF1	chr19:39847188-39847557	K562	blood:	n/a	n/a
7	EP300	chr19:39846875-39847600	K562	blood:	n/a	n/a
8	HDAC2	chr19:39846784-39847270	K562	blood:	n/a	n/a
9	HMGN3	chr19:39847134-39847550	K562	blood:	n/a	n/a
10	IRF1	chr19:39846895-39847973	K562	blood:	n/a	chr19:39847336-39847350 chr19:39847229-39847239 chr19:39847281-39847288 chr19:39847225-39847239
11	IRF1	chr19:39847207-39847549	K562	blood:	n/a	chr19:39847336-39847350 chr19:39847229-39847239 chr19:39847281-39847288 chr19:39847225-39847239
12	JUND	chr19:39846880-39847009	K562	blood:	n/a	n/a
13	JUND	chr19:39847280-39847489	K562	blood:	n/a	n/a
14	MAFF	chr19:39846793-39847119	K562	blood:	n/a	n/a
15	MAFK	chr19:39846795-39847096	K562	blood:	n/a	n/a
16	MAX	chr19:39847241-39847579	K562	blood:	n/a	n/a
17	MAX	chr19:39847063-39847967	K562	blood:	n/a	n/a
18	MAX	chr19:39847270-39847903	K562	blood:	n/a	n/a
19	MAZ	chr19:39847209-39847553	K562	blood:	n/a	n/a
20	MAZ	chr19:39849613-39849618	Hela-S3	cervix:	n/a	n/a
21	MXI1	chr19:39847226-39847748	K562	blood:	n/a	n/a
22	MYC	chr19:39847404-39847474	K562	blood:	n/a	n/a
23	MYC	chr19:39847213-39847800	K562	blood:	n/a	n/a
24	MYC	chr19:39846798-39847979	K562	blood:	n/a	n/a
25	MYC	chr19:39846761-39847935	K562	blood:	n/a	n/a
26	MYC	chr19:39847366-39847393	K562	blood:	n/a	n/a
27	POLR2A	chr19:39847805-39847832	K562	blood:	n/a	n/a
28	POLR2A	chr19:39847030-39847212	HepG2	liver:	n/a	n/a
29	POLR2A	chr19:39847295-39847834	K562	blood:	n/a	n/a
30	POLR2A	chr19:39846261-39846268	K562	blood:	n/a	n/a
31	POLR2A	chr19:39847692-39847693	MCF-7	breast:	n/a	n/a
32	POLR2A	chr19:39847201-39847798	K562	blood:	n/a	n/a
33	POLR2A	chr19:39847216-39847631	SK-N-MC	brain:	n/a	n/a
34	POLR2A	chr19:39846296-39846410	K562	blood:	n/a	n/a
35	POLR2A	chr19:39847370-39847688	MCF-7	breast:	n/a	n/a
36	POLR2A	chr19:39845868-39845904	GM12878	blood:	n/a	n/a
37	POLR2A	chr19:39846892-39846945	MCF-7	breast:	n/a	n/a
38	POLR2A	chr19:39846114-39846124	K562	blood:	n/a	n/a
39	POLR2A	chr19:39845685-39845756	K562	blood:	n/a	n/a
40	POLR2A	chr19:39845638-39845696	HepG2	liver:	n/a	n/a
41	POLR2A	chr19:39846086-39846089	K562	blood:	n/a	n/a
42	POLR2A	chr19:39848782-39849206	HepG2	liver:	n/a	n/a
43	POLR2A	chr19:39847795-39847836	HUVEC	blood vessel:	n/a	n/a
44	POLR2A	chr19:39845620-39845627	K562	blood:	n/a	n/a
45	POLR2A	chr19:39845923-39846397	SK-N-MC	brain:	n/a	n/a
46	POLR2A	chr19:39847786-39847945	HepG2	liver:	n/a	n/a
47	POLR2A	chr19:39847121-39847717	K562	blood:	n/a	n/a
48	POLR2A	chr19:39846829-39846832	MCF-7	breast:	n/a	n/a
49	POLR2A	chr19:39845321-39845380	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr19:39846915-39846962	HepG2	liver:	n/a	n/a

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39849660..39851695-chr19:39853601..39855209,2	K562	blood:
2	chr19:39847929..39849448-chr19:39964068..39965681,2	K562	blood:
3	chr19:39848912..39851365-chr19:39874735..39877110,2	K562	blood:
4	chr19:39845858..39848835-chr19:39849881..39851532,2	K562	blood:
5	chr19:39849513..39851836-chr19:39891478..39893245,2	K562	blood:
6	chr19:39846643..39848442-chr19:39897327..39899339,2	MCF-7	breast:
7	chr19:39848354..39851253-chr19:39867092..39868739,2	K562	blood:
8	chr19:39844628..39846175-chr19:39896261..39898794,2	MCF-7	breast:
9	chr19:39848239..39850464-chr19:39853560..39855951,2	MCF-7	breast:
10	chr19:39845356..39848788-chr19:39900821..39905638,4	MCF-7	breast:
11	chr19:39845453..39848424-chr19:39895764..39898971,3	K562	blood:
12	chr19:39840535..39845164-chr19:39896257..39899085,6	K562	blood:
13	chr19:39843827..39847459-chr19:39858082..39862141,4	MCF-7	breast:

No data

Variant related genes	Relation type
SAMD4B	TF binding region
ENSG00000241983	chromatin interactions
ENSG00000128016	chromatin interactions
ENSG00000179134	chromatin interactions
ENSG00000090924	chromatin interactions

Extended variants
information (count: 211 )
Associated
traits (count: 66 )

Variant overlapped rSNPs/rCNVs (count:211 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs30454	chr19:39844176-39844177	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs73546072	chr19:39844192-39844193	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs547912522	chr19:39844272-39844273	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
4	rs545844696	chr19:39844273-39844274	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
5	rs557851314	chr19:39844275-39844276	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
6	rs573066588	chr19:39844303-39844304	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
7	rs540411036	chr19:39844328-39844329	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs562169511	chr19:39844368-39844369	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs529584704	chr19:39844370-39844371	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs543423518	chr19:39844392-39844393	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs557395458	chr19:39844402-39844403	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs562462518	chr19:39844404-39844405	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
13	rs193294110	chr19:39844425-39844426	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs551475195	chr19:39844490-39844491	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
15	rs116292444	chr19:39844524-39844525	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs28370340	chr19:39844534-39844535	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
17	rs56190851	chr19:39844549-39844550	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs8102194	chr19:39844567-39844568	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs538134704	chr19:39844568-39844569	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
20	rs376741246	chr19:39844580-39844581	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
21	rs57920235	chr19:39844586-39844587	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
22	rs569204066	chr19:39844626-39844627	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
23	rs539462894	chr19:39844661-39844662	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
24	rs368940075	chr19:39844731-39844732	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
25	rs557763739	chr19:39844739-39844740	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
26	rs182842590	chr19:39844760-39844761	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
27	rs538105491	chr19:39844782-39844783	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
28	rs540372061	chr19:39844933-39844934	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
29	rs187480742	chr19:39845010-39845011	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
30	rs552030951	chr19:39845017-39845018	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
31	rs574159146	chr19:39845136-39845137	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
32	rs373318951	chr19:39845185-39845186	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
33	rs563062835	chr19:39845199-39845200	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
34	rs532924653	chr19:39845202-39845203	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
35	rs372073709	chr19:39845243-39845244	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
36	rs200807990	chr19:39845245-39845246	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
37	rs33936530	chr19:39845246-39845247	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
38	rs111501657	chr19:39845247-39845248	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
39	rs34023838	chr19:39845272-39845273	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
40	rs545008798	chr19:39845274-39845275	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
41	rs560219914	chr19:39845321-39845322	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
42	rs62119688	chr19:39845323-39845324	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs143486675	chr19:39845344-39845345	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
44	rs374047980	chr19:39845476-39845477	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
45	rs535439647	chr19:39845511-39845512	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
46	rs30453	chr19:39845544-39845545	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs542126423	chr19:39845548-39845549	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
48	rs62119689	chr19:39845550-39845551	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs539586781	chr19:39845614-39845615	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
50	rs111756700	chr19:39845672-39845673	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a

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
Thoracic aortic aneurysm	21092924	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Autism	22495311	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Ductal carcinoma	22052326	CNVD
Pleomorphic liposarcoma	18784837	CNVD
Congenital nephrotic syndrome	18421352	CNVD
Astrocytoma	17934521	CNVD
Leukemia	17361228	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Breast cancer	21858162	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
Salivary gland adenoid cystic carcinoma	17545515	CNVD
Disorders of sex development	21048976	CNVD
Ovarian cancer	22174824	CNVD
Breast cancer	16608533	CNVD
Neuroblastoma	18923191	CNVD
Breast cancer	21364760	CNVD
Invasive pancreatic ductal carcinoma	18765526	CNVD
Rhabdomyosarcoma	16790082	CNVD
Chordoma	18071362	CNVD
Urothelial carcinoma	21177765	CNVD
small cell lung cancer	20016488	CNVD
Wilms tumour	21544195	CNVD
Mental retardation	19951919	CNVD
19q13.11 deletion syndrome	22378287	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	21045282	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Ovarian neoplasms	16753589	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Metanephric adenoma	20802469	CNVD
Acute myeloid leukemia	16864856	CNVD
Lung cancer	21569311	CNVD
Bladder cancer	21909424	CNVD
Medulloblastoma	16783165	CNVD
Breast cancer	21509527	CNVD
Gastric cancer	18160780	CNVD
Hepatocellular carcinoma	16750200	CNVD
Basal cell lymphoma	19029149	CNVD
Breast cancer	20409316	CNVD
Diffuse large b-cell lymphoma	19029149	CNVD
Multiple myeloma	16616336	CNVD
Renal cell carcinoma	18765545	CNVD
Acute myeloid leukemia	20729466	CNVD
Lung cancer	18438408	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

Chromatin state (count:249 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39834200-39846600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:39834200-39859200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr19:39834400-39844600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr19:39834400-39845400	Weak transcription	Fetal Kidney	kidney
5	chr19:39834400-39849200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr19:39834800-39847400	Weak transcription	Small Intestine	intestine
7	chr19:39834800-39852800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr19:39834800-39852800	Strong transcription	Fetal Muscle Trunk	muscle
9	chr19:39834800-39880000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:39835000-39844600	Weak transcription	Stomach Mucosa	stomach
11	chr19:39835000-39846000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr19:39835600-39853600	Strong transcription	Placenta	Placenta
13	chr19:39835800-39880200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr19:39835800-39880200	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr19:39836000-39847600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr19:39836200-39880400	Strong transcription	Primary T cells from cord blood	blood
17	chr19:39836400-39862600	Strong transcription	Duodenum Mucosa	Duodenum
18	chr19:39836600-39845600	Weak transcription	Aorta	Aorta
19	chr19:39836600-39845800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr19:39836600-39864000	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr19:39836600-39880400	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr19:39836600-39880400	Strong transcription	Fetal Brain Female	brain
23	chr19:39836800-39846000	Weak transcription	Pancreas	Pancrea
24	chr19:39836800-39852000	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr19:39836800-39852600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr19:39837400-39846400	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr19:39837400-39880000	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr19:39837600-39863600	Strong transcription	Fetal Intestine Small	intestine
29	chr19:39837800-39854400	Strong transcription	Fetal Stomach	stomach
30	chr19:39837800-39855400	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr19:39838000-39851800	Strong transcription	Liver	Liver
32	chr19:39838000-39880000	Strong transcription	Brain Germinal Matrix	brain
33	chr19:39838200-39858200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr19:39838200-39858200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr19:39838200-39862600	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr19:39838400-39853200	Strong transcription	A549	lung
37	chr19:39838600-39852600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr19:39838600-39880400	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr19:39838800-39845800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr19:39838800-39880200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr19:39839000-39857600	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr19:39839000-39858200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr19:39839200-39846000	Weak transcription	Right Ventricle	heart
44	chr19:39839200-39851800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr19:39839200-39852600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr19:39839200-39853400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr19:39839200-39879200	Strong transcription	Dnd41	blood
48	chr19:39839800-39847400	Weak transcription	Fetal Heart	heart
49	chr19:39840000-39844600	Weak transcription	Hela-S3	cervix
50	chr19:39841000-39852600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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