Variant report

Variant	nsv823473
Chromosome Location	chr6:30920117-30921002
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:30919991..30921780-chr6:30922637..30925077,3	K562	blood:
2	chr6:30887250..30888956-chr6:30920094..30923079,2	MCF-7	breast:
3	chr6:30914358..30916014-chr6:30920897..30922627,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SFTA2-3	chr6:30920138-30920308	NONHSAT108705
2	lnc-SFTA2-3	chr6:30920844-30920981	ENSG00000233529.1

Variant related genes	Relation type
ENSG00000233529	chromatin interactions
ENSG00000137411	chromatin interactions

Extended variants
information (count: 32 )
Associated
traits (count: 121 )

Variant overlapped rSNPs/rCNVs (count:32 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs143551263	chr6:30920123-30920124	Weak transcription Active TSS Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs3132580	chr6:30920124-30920125	Weak transcription Active TSS Strong transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance disease
3	rs570008856	chr6:30920146-30920147	Weak transcription Active TSS Strong transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
4	rs537037983	chr6:30920170-30920171	Weak transcription Active TSS Strong transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
5	rs140721086	chr6:30920172-30920173	Weak transcription Active TSS Strong transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
6	rs183461489	chr6:30920180-30920181	Weak transcription Active TSS Strong transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
7	rs267600946	chr6:30920183-30920184	Weak transcription Active TSS Strong transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
8	rs367931222	chr6:30920192-30920193	Weak transcription Active TSS Strong transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
9	rs371574542	chr6:30920209-30920210	Weak transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
10	rs188616708	chr6:30920264-30920265	Weak transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
11	rs370719305	chr6:30920298-30920299	Weak transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
12	rs553252346	chr6:30920308-30920309	Weak transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
13	rs112101060	chr6:30920351-30920352	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs542065683	chr6:30920396-30920397	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs571542804	chr6:30920397-30920398	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs141734710	chr6:30920407-30920408	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs531143923	chr6:30920524-30920525	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs554361563	chr6:30920558-30920559	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs370644456	chr6:30920707-30920708	Weak transcription Bivalent/Poised TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs77087190	chr6:30920755-30920756	Weak transcription Bivalent/Poised TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs202063234	chr6:30920757-30920758	Weak transcription Bivalent/Poised TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs267600947	chr6:30920765-30920766	Weak transcription Bivalent/Poised TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs373014829	chr6:30920770-30920771	Weak transcription Bivalent/Poised TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs375547718	chr6:30920772-30920773	Weak transcription Bivalent/Poised TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs150597131	chr6:30920774-30920775	Weak transcription Bivalent/Poised TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs565830437	chr6:30920804-30920805	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs2240804	chr6:30920890-30920891	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
28	rs375340956	chr6:30920907-30920908	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
29	rs368001626	chr6:30920910-30920911	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
30	rs548442389	chr6:30920918-30920919	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
31	rs2240803	chr6:30920957-30920958	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers	Chromatin interactive region lncRNA	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
32	rs537375797	chr6:30920977-30920978	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:121)

Disease	PMID	Source
Acute lymphoblastic leukemia	22237106	CNVD
Follicular lymphoma	20505157	CNVD
Glioblastoma multiforme	21080181	CNVD
Ewing''s sarcoma	21437220	CNVD
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
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
Acute myeloid leukemia	20729466	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	21858162	CNVD
Lung cancer	18438408	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
Cancer	20164919	CNVD
Melanoma	18172304	CNVD
Breast cancer	22844521	CNVD
HIV/AIDS	22844521	CNVD
Ovarian cancer	22844521	CNVD
Prostate cancer	22844521	CNVD
Psoriasis	22844521	CNVD
Rheumatoid arthritis	22844521	CNVD
Sclerosis systemic	22844521	CNVD
Systemic lupus erythematosus	22844521	CNVD
Breast cancer	22522925	CNVD
Ovarian cancer	21781307	CNVD
Breast cancer	21552322	CNVD
Immune disease	21076436	CNVD
Autoimmune disease	19135723	CNVD
Systemic lupus erythematosus	17953491	CNVD
Recurrent Infections	22737222	CNVD
Systemic lupus erythematosus	21904924	CNVD
Ependymoma	19289631	CNVD
Gestational infection	22844521	CNVD
Head circumference	22844521	CNVD
Infertility	22844521	CNVD
Recurrent birth weight diabetes	22844521	CNVD
Obesity	22844521	CNVD
Recurrent pregnancy loss	22844521	CNVD
Intellectual disability	21811512	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Congenital anomalies of the kidney and urinary tract	18694510	CNVD
Nasopharyngeal cancer	22815911	CNVD
Hepatocellular carcinoma	16750200	CNVD
Basal cell lymphoma	21115979	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Autism	22495311	CNVD
Cancer	16790693	CNVD
Cervical cancer	21062161	CNVD
Breast cancer	21785460	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Systemic lupus erythematosus	17503323	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Urothelial carcinoma	18382360	CNVD
Cancer	21183584	CNVD
Hodgkin''s lymphoma	17606441	CNVD
small cell lung cancer	20016488	CNVD
Renal cell carcinoma	18765545	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Gastric cancer	17908304	CNVD
Metanephric adenoma	20802469	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Schizophrenia	19571808	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Neuroblastoma	16790693	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
abnormal development	18461090	CNVD
Melanoma	17363583	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	16397240	CNVD
Retinoblastoma	22278416	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Systemic lupus erythematosus	20877625	CNVD
Cleidocranial dysplasia	18696259	CNVD
Holoprosencephaly	21359414	CNVD
Liposarcoma	21253554	CNVD
Uveal melanoma	20484589	CNVD
Fibroblasts	20926602	CNVD
Breast cancer	21364760	CNVD
Systemic lupus erythematosus	19279649	CNVD
Retinoblastoma	16790693	CNVD
Acute myocardial infarction	18032375	CNVD
Renal cell carcinoma	19150565	CNVD
Systemic lupus erythematosus	19591781	CNVD
Attention deficit hyperactivity disorder	19287146	CNVD
Autism	19287146	CNVD
Erythema nodosum in leprosy	19287146	CNVD
Henoch-schoenlein purpura	19287146	CNVD
Liver cirrhosis	19287146	CNVD
Systemic lupus erythematosus	19287146	CNVD
Congenital adrenal hyperplasia	18478071	CNVD
Systemic lupus erythematosus	19287147	CNVD
Osteosarcoma	16790693	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30913600-30922800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr6:30915400-30923000	Weak transcription	Gastric	stomach
3	chr6:30918800-30920200	Strong transcription	Stomach Mucosa	stomach
4	chr6:30919400-30923000	Weak transcription	Right Atrium	heart
5	chr6:30919600-30921000	Enhancers	GM12878-XiMat	blood
6	chr6:30919800-30920200	Active TSS	Brain Substantia Nigra	brain
7	chr6:30920200-30922800	Weak transcription	Brain Substantia Nigra	brain
8	chr6:30920200-30922800	Weak transcription	Stomach Mucosa	stomach
9	chr6:30920600-30921000	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
10	chr6:30920800-30921000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:30920800-30921000	Enhancers	Ovary	ovary
12	chr6:30920800-30921000	Enhancers	Spleen	Spleen
13	chr6:30921000-30922400	Weak transcription	Ovary	ovary
14	chr6:30921000-30922600	Weak transcription	GM12878-XiMat	blood

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