Variant report

Variant	esv2008944
Chromosome Location	chr19:39624915-39625584
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39624966..39625536-chr19:39678054..39678776,2	MCF-7	breast:
2	chr19:39624644..39625575-chr19:39641363..39642260,6	MCF-7	breast:
3	chr19:39618750..39620262-chr19:39623192..39625353,2	K562	blood:
4	chr19:39340180..39342670-chr19:39622996..39625120,2	MCF-7	breast:
5	chr19:39619372..39620875-chr19:39624285..39626260,2	K562	blood:
6	chr19:39624151..39625876-chr19:39627199..39629585,2	K562	blood:
7	chr19:39624651..39625632-chr19:39641254..39641826,3	MCF-7	breast:
8	chr19:39624660..39625575-chr19:39641363..39642260,4	MCF-7	breast:
9	chr19:39622591..39626006-chr19:39627126..39631368,3	MCF-7	breast:
10	chr19:39615259..39630637-chr19:39640467..39653924,38	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SYCN-1	chr19:39625522-39625844	ENSG00000269172.1

No data

Variant related genes	Relation type
ENSG00000130669	chromatin interactions
ENSG00000104824	chromatin interactions

Extended variants
information (count: 38 )
Associated
traits (count: 67 )

Variant overlapped rSNPs/rCNVs (count:38 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs111838807	chr19:39624919-39624920	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs544051451	chr19:39624926-39624927	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs150143891	chr19:39624928-39624929	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs577726057	chr19:39624933-39624934	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs544780251	chr19:39624945-39624946	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs145549337	chr19:39624953-39624954	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs73549585	chr19:39624959-39624960	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs562667822	chr19:39624967-39624968	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs140434205	chr19:39624975-39624976	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs369884723	chr19:39624983-39624984	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs145543617	chr19:39624988-39624989	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs550436595	chr19:39624996-39624997	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs367837753	chr19:39625006-39625007	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs532690314	chr19:39625010-39625011	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs137903987	chr19:39625020-39625021	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs566129536	chr19:39625023-39625024	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs140796471	chr19:39625065-39625066	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs200000910	chr19:39625076-39625077	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs187661988	chr19:39625102-39625103	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs4803209	chr19:39625208-39625209	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
21	rs567329180	chr19:39625227-39625228	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs116300977	chr19:39625230-39625231	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs534735824	chr19:39625241-39625242	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs11426235	chr19:39625244-39625245	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs143006461	chr19:39625262-39625263	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs34846983	chr19:39625326-39625327	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs369751450	chr19:39625327-39625328	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs141188548	chr19:39625342-39625343	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs539588190	chr19:39625343-39625344	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs542690228	chr19:39625375-39625376	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs560856879	chr19:39625391-39625392	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs529214584	chr19:39625447-39625448	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs191777510	chr19:39625480-39625481	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs544127299	chr19:39625494-39625495	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs150675019	chr19:39625498-39625499	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs532610931	chr19:39625524-39625525	Enhancers Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
37	rs547953460	chr19:39625578-39625579	Enhancers Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
38	rs34110379	chr19:39625583-39625584	Enhancers Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:67)

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
Lung cancer	18438408	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
Breast cancer	22522925	CNVD
Ovarian cancer	21240255	CNVD

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39617000-39630800	Weak transcription	Primary T cells from cord blood	blood
2	chr19:39617000-39635000	Weak transcription	Aorta	Aorta
3	chr19:39617400-39659800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr19:39617600-39625600	Enhancers	Spleen	Spleen
5	chr19:39617600-39627600	Enhancers	Fetal Heart	heart
6	chr19:39617800-39625000	Enhancers	Ovary	ovary
7	chr19:39617800-39625200	Enhancers	Pancreas	Pancrea
8	chr19:39617800-39627200	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr19:39617800-39628600	Enhancers	Placenta	Placenta
10	chr19:39617800-39630200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr19:39617800-39641600	Weak transcription	Thymus	Thymus
12	chr19:39618200-39628400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr19:39618400-39626800	Weak transcription	NHEK	skin
14	chr19:39618400-39646600	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr19:39620000-39627200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr19:39620000-39630000	Weak transcription	HepG2	liver
17	chr19:39620200-39625000	Enhancers	Lung	lung
18	chr19:39620600-39626800	Enhancers	Fetal Intestine Large	intestine
19	chr19:39621000-39627200	Enhancers	Fetal Lung	lung
20	chr19:39621000-39628400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:39621400-39625200	Enhancers	Duodenum Mucosa	Duodenum
22	chr19:39621400-39628000	Enhancers	HUES6 Cell Line	embryonic stem cell
23	chr19:39621600-39625000	Enhancers	H1 Cell Line	embryonic stem cell
24	chr19:39621600-39627800	Enhancers	iPS-15b Cell Line	embryonic stem cell
25	chr19:39621800-39627400	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr19:39622200-39625000	Enhancers	HUES48 Cell Line	embryonic stem cell
27	chr19:39622200-39627200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr19:39622200-39628200	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr19:39622400-39627000	Weak transcription	Small Intestine	intestine
30	chr19:39622400-39629000	Weak transcription	NH-A	brain
31	chr19:39622400-39635200	Weak transcription	Fetal Brain Female	brain
32	chr19:39622600-39639600	Weak transcription	HSMM	muscle
33	chr19:39622800-39626800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr19:39622800-39627400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr19:39623000-39625000	Enhancers	Brain Anterior Caudate	brain
36	chr19:39623000-39635200	Weak transcription	Primary B cells from peripheral blood	blood
37	chr19:39623400-39626800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr19:39623400-39629000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr19:39623400-39646000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr19:39623600-39625000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr19:39623600-39625600	Enhancers	Fetal Intestine Small	intestine
42	chr19:39623600-39626800	Weak transcription	Adipose Nuclei	Adipose
43	chr19:39623600-39627200	Weak transcription	HUVEC	blood vessel
44	chr19:39623600-39630200	Weak transcription	Brain Angular Gyrus	brain
45	chr19:39623800-39627400	Weak transcription	Brain Hippocampus Middle	brain
46	chr19:39623800-39630200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr19:39624000-39625000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr19:39624000-39625200	Enhancers	H9 Cell Line	embryonic stem cell
49	chr19:39624000-39625200	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr19:39624000-39647000	Weak transcription	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links