Variant report

Variant	esv3378001
Chromosome Location	chr6:53603388-53603557
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	chr6:53603213..53606013-chr6:53606213..53607991,3	MCF-7	breast:
2	chr17:56708938..56710691-chr6:53601479..53604353,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLHL31-2	chr6:53603240-53603794	NONHSAT113194

Variant related genes	Relation type
ENSG00000212195	chromatin interactions

Extended variants
information (count: 11 )
Associated
traits (count: 76 )

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs547483892	chr6:53603395-53603396	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
2	rs570538421	chr6:53603402-53603403	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs533206598	chr6:53603404-53603405	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
4	rs561185895	chr6:53603410-53603411	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
5	rs185276384	chr6:53603419-53603420	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs370996682	chr6:53603449-53603450	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
7	rs531692158	chr6:53603492-53603493	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
8	rs368239987	chr6:53603495-53603496	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
9	rs190188211	chr6:53603498-53603499	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
10	rs543229299	chr6:53603522-53603523	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
11	rs10456164	chr6:53603537-53603538	Weak transcription Enhancers	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance

Variant related diseases (count:76)

Disease	PMID	Source
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Leukemia	21518781	CNVD
Cancer	21637783	CNVD
Facial dysmorphism	22105932	CNVD
Medulloblastoma	21979893	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Endometrial cancer	22040021	CNVD
Acute myeloid leukemia	16864856	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Bladder cancer	19088036	CNVD
Wilms tumour	21544195	CNVD
Uveal melanoma	21693616	CNVD
Biliary cancer	19435499	CNVD
Malaria	21533027	CNVD
Retinoblastoma	19183342	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	21858162	CNVD
Ewing''s sarcoma	17952124	CNVD
Autism	21448237	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Autism	22495311	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Urothelial carcinoma	18382360	CNVD
Cancer	21183584	CNVD
Hodgkin''s lymphoma	17606441	CNVD
small cell lung cancer	20016488	CNVD
Gastric cancer	17908304	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Neuroblastoma	16790693	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Osteosarcoma	16790693	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Lung cancer	18438408	CNVD
Neuroblastoma	18923191	CNVD
Breast cancer	17603634	CNVD
Neurocytoma	17123091	CNVD
Systemic lupus erythematosus	17503323	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Breast cancer	16608533	CNVD
Melanoma	18172304	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Neuroblastoma	19686582	CNVD
Neuroblastoma	17289879	CNVD
Breast cancer	17899364	CNVD
Breast cancer	17133270	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma multiforme	22286061	CNVD
Colorectal cancer	16912164	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	21364760	CNVD

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53596000-53605600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:53597200-53604000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:53599800-53606200	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr6:53600000-53605800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:53600800-53603600	Enhancers	Dnd41	blood
6	chr6:53600800-53606200	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr6:53601000-53606000	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr6:53601000-53606200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr6:53601200-53605800	Weak transcription	Primary T cells from cord blood	blood
10	chr6:53601200-53605800	Weak transcription	Thymus	Thymus
11	chr6:53601200-53606000	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr6:53601200-53606000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr6:53601200-53606000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr6:53601200-53606000	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr6:53601200-53606200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr6:53601600-53638000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr6:53601800-53603400	Enhancers	Fetal Intestine Large	intestine
18	chr6:53601800-53603400	Enhancers	HepG2	liver
19	chr6:53601800-53603600	Enhancers	Fetal Intestine Small	intestine
20	chr6:53601800-53613400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:53602000-53603600	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr6:53602200-53606400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr6:53602200-53614800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr6:53602600-53603400	Enhancers	Fetal Thymus	thymus
25	chr6:53602600-53603600	Enhancers	Placenta	Placenta
26	chr6:53602800-53605800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr6:53603000-53608800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr6:53603000-53608800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:53603200-53608000	Weak transcription	NHEK	skin
30	chr6:53603200-53609000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:53603400-53605200	Weak transcription	Fetal Intestine Large	intestine
32	chr6:53603400-53605600	Weak transcription	HepG2	liver
33	chr6:53603400-53605800	Weak transcription	Fetal Thymus	thymus

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