Variant report

Variant	esv3330470
Chromosome Location	chr19:40818568-40819008
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40818000..40820409-chr19:40826750..40828476,2	MCF-7	breast:
2	chr19:40817646..40819198-chr19:40820756..40822692,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PLD3-3	chr19:40818459-40819345	NONHSAT066371

Variant related genes	Relation type
ENSG00000160392	chromatin interactions

Extended variants
information (count: 12 )
Associated
traits (count: 65 )

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs558203067	chr19:40818615-40818616	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
2	rs553508055	chr19:40818648-40818649	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs543856201	chr19:40818658-40818659	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
4	rs574702396	chr19:40818659-40818660	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
5	rs563847856	chr19:40818685-40818686	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs184478478	chr19:40818686-40818687	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
7	rs66623822	chr19:40818690-40818691	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs575927928	chr19:40818721-40818722	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
9	rs118071752	chr19:40818814-40818815	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
10	rs139728899	chr19:40818819-40818820	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
11	rs142051598	chr19:40818925-40818926	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
12	rs112647943	chr19:40818971-40818972	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:65)

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
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
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
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
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
Genital abnormality	22378287	CNVD
Hypospadia	22378287	CNVD
Ovarian clear cell carcinoma	19293255	CNVD
Astrocytoma	22246337	CNVD
Anaplastic thyroid cancer	18753363	CNVD
Pleomorphic liposarcoma	18784837	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40792000-40826200	Weak transcription	Hela-S3	cervix
2	chr19:40792200-40821400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr19:40792200-40821400	Weak transcription	Fetal Intestine Small	intestine
4	chr19:40793000-40821400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr19:40793000-40822000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr19:40793200-40820600	Weak transcription	HSMM	muscle
7	chr19:40793200-40820800	Weak transcription	Dnd41	blood
8	chr19:40793200-40822000	Weak transcription	Fetal Stomach	stomach
9	chr19:40793800-40821800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr19:40800400-40826400	Weak transcription	Brain Angular Gyrus	brain
11	chr19:40800800-40822000	Weak transcription	Brain Hippocampus Middle	brain
12	chr19:40802800-40828000	Weak transcription	NH-A	brain
13	chr19:40803000-40822000	Weak transcription	Lung	lung
14	chr19:40803800-40822000	Weak transcription	Primary T cells from cord blood	blood
15	chr19:40807600-40822200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:40808800-40822000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr19:40809000-40822000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr19:40810400-40820600	Weak transcription	K562	blood
19	chr19:40810600-40825800	Weak transcription	Adipose Nuclei	Adipose
20	chr19:40810600-40829800	Weak transcription	NHDF-Ad	bronchial
21	chr19:40810800-40826200	Weak transcription	HMEC	breast
22	chr19:40811200-40821800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr19:40811200-40821800	Weak transcription	Liver	Liver
24	chr19:40811200-40822200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr19:40811200-40822200	Weak transcription	Thymus	Thymus
26	chr19:40811200-40826000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr19:40811400-40826600	Weak transcription	NHEK	skin
28	chr19:40811600-40826600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr19:40811800-40820600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr19:40811800-40822200	Weak transcription	Brain Cingulate Gyrus	brain
31	chr19:40811800-40822200	Weak transcription	A549	lung
32	chr19:40811800-40826400	Weak transcription	Brain Substantia Nigra	brain
33	chr19:40811800-40826600	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr19:40811800-40826600	Weak transcription	Fetal Lung	lung
35	chr19:40811800-40831600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr19:40813200-40822000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr19:40814200-40821800	Weak transcription	Placenta	Placenta
38	chr19:40814600-40824400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr19:40815400-40832800	Weak transcription	Fetal Brain Male	brain
40	chr19:40815600-40826000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr19:40815800-40824400	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr19:40816000-40822000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr19:40816200-40820400	Weak transcription	Fetal Heart	heart
44	chr19:40816400-40824200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr19:40817000-40818600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr19:40817200-40825800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr19:40817400-40827400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr19:40817600-40827200	Weak transcription	Primary hematopoietic stem cells	blood
49	chr19:40817800-40822000	Weak transcription	Spleen	Spleen
50	chr19:40818000-40818600	Enhancers	Primary hematopoietic stem cells short term culture	blood

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