Variant report

Variant	esv3330796
Chromosome Location	chr12:50473061-50473412
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	REST	chr12:50473339-50474125	ECC-1	luminal epithelium:	n/a	chr12:50473629-50473637
2	REST	chr12:50473351-50474121	ECC-1	luminal epithelium:	n/a	chr12:50473629-50473637

No.	Distal block	Cell Line	Cell type
1	chr12:50472028..50474859-chr12:50477717..50480636,3	MCF-7	breast:
2	chr12:50465539..50467962-chr12:50472151..50474107,2	K562	blood:
3	chr12:50450867..50453197-chr12:50472058..50474772,2	MCF-7	breast:
4	chr12:50471856..50474200-chr12:50488886..50490561,2	K562	blood:
5	chr12:50471491..50474468-chr12:50505629..50507284,2	K562	blood:
6	chr12:50466696..50474949-chr12:50474970..50481457,17	MCF-7	breast:

Variant related genes	Relation type
ASIC1	TF binding region
ENSG00000110881	chromatin interactions
ENSG00000178449	chromatin interactions
ENSG00000272368	chromatin interactions
ENSG00000066117	chromatin interactions

Extended variants
information (count: 18 )
Associated
traits (count: 72 )

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs548126686	chr12:50473084-50473085	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
2	rs11169267	chr12:50473101-50473102	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs73121534	chr12:50473120-50473121	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
4	rs573713407	chr12:50473144-50473145	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
5	rs542622708	chr12:50473145-50473146	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
6	rs558522561	chr12:50473152-50473153	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
7	rs528164227	chr12:50473193-50473194	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
8	rs150515728	chr12:50473210-50473211	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
9	rs367986248	chr12:50473214-50473215	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
10	rs545044558	chr12:50473217-50473218	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
11	rs182488798	chr12:50473231-50473232	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
12	rs530699744	chr12:50473234-50473235	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
13	rs550475015	chr12:50473303-50473304	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
14	rs567210050	chr12:50473332-50473333	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
15	rs529280067	chr12:50473346-50473347	Weak transcription Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
16	rs7305558	chr12:50473377-50473378	Weak transcription Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
17	rs566207395	chr12:50473394-50473395	Weak transcription Strong transcription	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
18	rs534817408	chr12:50473406-50473407	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:72)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Seminomas	18059402	CNVD
Wilms tumour	21544195	CNVD
Esophageal cancer	21851588	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Ewing''s sarcoma	21437220	CNVD
Testicular germ cell tumor	18059402	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Neurodevelopmental disorder	22521361	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	18194544	CNVD
Breast cancer	21949216	CNVD
Carcinoma ex pleomorphic adenoma	18828159	CNVD
Acute myeloid leukemia	16864856	CNVD
Cancer	21637783	CNVD
Glioblastoma multiforme	21080181	CNVD
Renal cell carcinoma	19461508	CNVD
Burkitt''s lymphoma	18698080	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	19960244	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Hirschsprung''s Disease	21712996	CNVD
Lissencephaly	21572526	CNVD
Lung cancer	18438408	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	19602461	CNVD
Breast cancer	17899364	CNVD
Colorectal cancer	16272173	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Adenoid cystic carcinoma	18332873	CNVD
Breast cancer	21364760	CNVD
Prostate cancer	18632612	CNVD
Follicular lymphoma	20505157	CNVD
Hepatocellular carcinoma	16750200	CNVD
Melanoma	18172304	CNVD
Metanephric adenoma	20802469	CNVD
Glioblastoma multiforme	17387387	CNVD
liposarcomas	17372913	CNVD
Non-small cell lung cancer	24170126	CNVD
Cancer	16751803	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Bladder cancer	21909424	CNVD
Multiple myeloma	16616336	CNVD
Intracranial aneurysm	16715129	CNVD
Breast cancer	17661082	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	21785460	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Intracranial ependymoma	16609018	CNVD
Cancer	17160897	CNVD
Melanoma	20877625	CNVD
Cancer	20164919	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50458200-50478200	Weak transcription	Thymus	Thymus
2	chr12:50464400-50478200	Weak transcription	Fetal Heart	heart
3	chr12:50464400-50478200	Weak transcription	Right Atrium	heart
4	chr12:50464800-50474800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:50464800-50478200	Weak transcription	Colon Smooth Muscle	Colon
6	chr12:50464800-50478200	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr12:50464800-50478200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:50464800-50478400	Weak transcription	Primary T cells from cord blood	blood
9	chr12:50466800-50474800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:50469400-50474400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:50469400-50474800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr12:50469400-50474800	Weak transcription	Right Ventricle	heart
13	chr12:50469400-50478200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:50469400-50478200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr12:50469400-50478200	Weak transcription	Fetal Brain Male	brain
16	chr12:50469600-50474400	Weak transcription	K562	blood
17	chr12:50469600-50474600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr12:50469600-50474800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:50469600-50477000	Strong transcription	Fetal Brain Female	brain
20	chr12:50469600-50477600	Weak transcription	HMEC	breast
21	chr12:50469600-50478200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:50469600-50478200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:50469600-50478200	Weak transcription	Brain Angular Gyrus	brain
24	chr12:50469600-50478200	Weak transcription	Brain Anterior Caudate	brain
25	chr12:50469600-50478200	Weak transcription	Fetal Lung	lung
26	chr12:50469600-50478200	Weak transcription	Stomach Smooth Muscle	stomach
27	chr12:50469800-50473600	Weak transcription	Fetal Intestine Small	intestine
28	chr12:50469800-50476000	Weak transcription	Colonic Mucosa	Colon
29	chr12:50469800-50478200	Weak transcription	Gastric	stomach
30	chr12:50470000-50473400	Weak transcription	Fetal Intestine Large	intestine
31	chr12:50470000-50473400	Weak transcription	HepG2	liver
32	chr12:50470000-50478200	Weak transcription	Liver	Liver
33	chr12:50470600-50474600	Strong transcription	Fetal Stomach	stomach
34	chr12:50471200-50474000	Strong transcription	Brain Hippocampus Middle	brain
35	chr12:50471200-50476200	Strong transcription	Brain Germinal Matrix	brain
36	chr12:50471400-50477600	Weak transcription	GM12878-XiMat	blood
37	chr12:50471600-50474800	Strong transcription	Cortex derived primary cultured neurospheres	brain
38	chr12:50471800-50474800	Strong transcription	Brain Inferior Temporal Lobe	brain
39	chr12:50472000-50473600	Strong transcription	Fetal Muscle Leg	muscle
40	chr12:50472200-50475600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr12:50472600-50478000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:50472600-50478200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:50473400-50475800	Enhancers	HepG2	liver
44	chr12:50473400-50478200	Enhancers	Fetal Intestine Large	intestine

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