Variant report

Variant	esv2545161
Chromosome Location	chr19:39624402-39625800
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:14)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39624651..39625632-chr19:39641254..39641826,3	MCF-7	breast:
2	chr19:39624660..39625575-chr19:39641363..39642260,4	MCF-7	breast:
3	chr19:39622591..39626006-chr19:39627126..39631368,3	MCF-7	breast:
4	chr19:39622646..39624803-chr19:39656922..39658959,2	MCF-7	breast:
5	chr19:39340180..39342670-chr19:39622996..39625120,2	MCF-7	breast:
6	chr19:39624151..39625876-chr19:39627199..39629585,2	K562	blood:
7	chr19:39621851..39624607-chr19:39667898..39670113,3	MCF-7	breast:
8	chr19:39619372..39620875-chr19:39624285..39626260,2	K562	blood:
9	chr19:39622616..39624773-chr19:39692455..39694487,2	K562	blood:
10	chr19:39624966..39625536-chr19:39678054..39678776,2	MCF-7	breast:
11	chr19:39615259..39630637-chr19:39640467..39653924,38	MCF-7	breast:
12	chr19:39618750..39620262-chr19:39623192..39625353,2	K562	blood:
13	chr19:39622898..39624850-chr19:39631546..39633915,2	MCF-7	breast:
14	chr19:39624644..39625575-chr19:39641363..39642260,6	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: 77 )
Associated
traits (count: 68 )

Variant overlapped rSNPs/rCNVs (count:77 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs139864774	chr19:39624425-39624426	Enhancers Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs561221814	chr19:39624442-39624443	Enhancers Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs538414155	chr19:39624482-39624483	Enhancers Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs185999296	chr19:39624483-39624484	Enhancers Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs16973211	chr19:39624490-39624491	Enhancers Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
6	rs539050902	chr19:39624491-39624492	Enhancers Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs145499838	chr19:39624527-39624528	Enhancers Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs540161943	chr19:39624554-39624555	Enhancers Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs374653569	chr19:39624579-39624580	Enhancers Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs190066883	chr19:39624580-39624581	Enhancers Weak transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs573520592	chr19:39624643-39624644	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs116450736	chr19:39624663-39624664	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs562273558	chr19:39624678-39624679	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs371758066	chr19:39624683-39624684	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs545031963	chr19:39624688-39624689	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs181349019	chr19:39624726-39624727	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs527239063	chr19:39624736-39624737	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs549721554	chr19:39624737-39624738	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs185760577	chr19:39624746-39624747	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs531975200	chr19:39624754-39624755	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs187624276	chr19:39624776-39624777	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs4803208	chr19:39624790-39624791	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
23	rs571760227	chr19:39624798-39624799	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs140967386	chr19:39624809-39624810	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs191072072	chr19:39624816-39624817	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs514968	chr19:39624818-39624819	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs183706818	chr19:39624841-39624842	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs189144721	chr19:39624876-39624877	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs191159498	chr19:39624904-39624905	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs371380521	chr19:39624914-39624915	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs111838807	chr19:39624919-39624920	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs544051451	chr19:39624926-39624927	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs150143891	chr19:39624928-39624929	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs577726057	chr19:39624933-39624934	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs544780251	chr19:39624945-39624946	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs145549337	chr19:39624953-39624954	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs73549585	chr19:39624959-39624960	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
38	rs562667822	chr19:39624967-39624968	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs140434205	chr19:39624975-39624976	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs369884723	chr19:39624983-39624984	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs145543617	chr19:39624988-39624989	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs550436595	chr19:39624996-39624997	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs367837753	chr19:39625006-39625007	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs532690314	chr19:39625010-39625011	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs137903987	chr19:39625020-39625021	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs566129536	chr19:39625023-39625024	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs140796471	chr19:39625065-39625066	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs200000910	chr19:39625076-39625077	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs187661988	chr19:39625102-39625103	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs4803209	chr19:39625208-39625209	Enhancers Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance

Variant related diseases (count:68)

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
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:169 , 50 per page) page: 1 2 3 4

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	chr19:39617200-39624800	Enhancers	Left Ventricle	heart
4	chr19:39617400-39659800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr19:39617600-39625600	Enhancers	Spleen	Spleen
6	chr19:39617600-39627600	Enhancers	Fetal Heart	heart
7	chr19:39617800-39624600	Enhancers	Stomach Mucosa	stomach
8	chr19:39617800-39625000	Enhancers	Ovary	ovary
9	chr19:39617800-39625200	Enhancers	Pancreas	Pancrea
10	chr19:39617800-39627200	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr19:39617800-39628600	Enhancers	Placenta	Placenta
12	chr19:39617800-39630200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr19:39617800-39641600	Weak transcription	Thymus	Thymus
14	chr19:39618000-39624600	Enhancers	Fetal Muscle Leg	muscle
15	chr19:39618200-39628400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr19:39618400-39624600	Enhancers	Fetal Muscle Trunk	muscle
17	chr19:39618400-39626800	Weak transcription	NHEK	skin
18	chr19:39618400-39646600	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr19:39620000-39627200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr19:39620000-39630000	Weak transcription	HepG2	liver
21	chr19:39620200-39625000	Enhancers	Lung	lung
22	chr19:39620400-39624600	Enhancers	Esophagus	oesophagus
23	chr19:39620400-39624800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr19:39620600-39626800	Enhancers	Fetal Intestine Large	intestine
25	chr19:39621000-39624600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr19:39621000-39624800	Enhancers	Placenta Amnion	Placenta Amnion
27	chr19:39621000-39627200	Enhancers	Fetal Lung	lung
28	chr19:39621000-39628400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr19:39621200-39624600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr19:39621400-39624800	Enhancers	Gastric	stomach
31	chr19:39621400-39625200	Enhancers	Duodenum Mucosa	Duodenum
32	chr19:39621400-39628000	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr19:39621600-39624800	Enhancers	iPS-20b Cell Line	embryonic stem cell
34	chr19:39621600-39624800	Enhancers	Primary hematopoietic stem cells	blood
35	chr19:39621600-39624800	Enhancers	Colon Smooth Muscle	Colon
36	chr19:39621600-39624800	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr19:39621600-39624800	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr19:39621600-39625000	Enhancers	H1 Cell Line	embryonic stem cell
39	chr19:39621600-39627800	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr19:39621800-39624800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr19:39621800-39624800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr19:39621800-39627400	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr19:39622000-39624600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr19:39622200-39625000	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr19:39622200-39627200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr19:39622200-39628200	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr19:39622400-39624600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr19:39622400-39624600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr19:39622400-39627000	Weak transcription	Small Intestine	intestine
50	chr19:39622400-39629000	Weak transcription	NH-A	brain

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