Variant report

Variant	esv3417567
Chromosome Location	chr12:50024867-50025196
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:50025180-50025330	GM12867	blood:	n/a	n/a
2	CTCF	chr12:50025180-50025330	WERI-Rb-1	eye:	n/a	n/a
3	CTCF	chr12:50025180-50025330	SAEC	small airway:	n/a	n/a
4	CTCF	chr12:50025180-50025330	GM12874	blood:	n/a	n/a
5	CTCF	chr12:50025180-50025330	HEK293	kidney:	n/a	n/a
6	POLR2A	chr12:50024479-50025167	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:50023976-50031574	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50015886..50019957-chr12:50021996..50025809,6	K562	blood:
2	chr12:50023902..50034192-chr12:50133489..50138270,11	K562	blood:
3	chr12:50023643..50026523-chr12:50135082..50136780,2	MCF-7	breast:
4	chr12:49960687..49963976-chr12:50022315..50025513,4	K562	blood:
5	chr12:50024342..50028618-chr12:50029311..50035232,8	K562	blood:

No data

Variant related genes	Relation type
PRPF40B	TF binding region
ENSG00000110844	chromatin interactions
ENSG00000139644	chromatin interactions
ENSG00000187778	chromatin interactions
ENSG00000161791	chromatin interactions

Extended variants
information (count: 11 )
Associated
traits (count: 69 )

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	rs545994113	chr12:50024912-50024913	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
2	rs7299609	chr12:50024926-50024927	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs531902880	chr12:50024937-50024938	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
4	rs550778402	chr12:50024949-50024950	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
5	rs569048597	chr12:50024975-50024976	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
6	rs561558901	chr12:50025037-50025038	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
7	rs527379154	chr12:50025071-50025072	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
8	rs547219479	chr12:50025088-50025089	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
9	rs200282180	chr12:50025175-50025176	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
10	rs539792661	chr12:50025185-50025186	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
11	rs372638240	chr12:50025191-50025192	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:69)

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
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50017000-50030600	Weak transcription	Fetal Heart	heart
2	chr12:50017200-50025600	Weak transcription	Fetal Lung	lung
3	chr12:50017400-50026600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr12:50017400-50027200	Weak transcription	Gastric	stomach
5	chr12:50017400-50027400	Weak transcription	Lung	lung
6	chr12:50017600-50035600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:50017800-50030600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr12:50017800-50036400	Weak transcription	Colonic Mucosa	Colon
9	chr12:50017800-50042200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr12:50018000-50025000	Weak transcription	Right Ventricle	heart
11	chr12:50018000-50025200	Weak transcription	Brain Hippocampus Middle	brain
12	chr12:50018000-50025200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr12:50018000-50025200	Weak transcription	Fetal Intestine Large	intestine
14	chr12:50018000-50025400	Weak transcription	Brain Substantia Nigra	brain
15	chr12:50018000-50025800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:50018000-50027400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:50018000-50027600	Weak transcription	Aorta	Aorta
18	chr12:50018000-50028400	Weak transcription	Brain Angular Gyrus	brain
19	chr12:50018000-50030400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:50018000-50030400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr12:50018000-50030400	Weak transcription	Right Atrium	heart
22	chr12:50018000-50030600	Weak transcription	Adipose Nuclei	Adipose
23	chr12:50018000-50030600	Weak transcription	Fetal Kidney	kidney
24	chr12:50018000-50030600	Weak transcription	Stomach Mucosa	stomach
25	chr12:50018000-50030800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr12:50018000-50031000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr12:50018000-50031200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:50018000-50031800	Weak transcription	Liver	Liver
29	chr12:50018000-50035400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr12:50018000-50035600	Weak transcription	Left Ventricle	heart
31	chr12:50018000-50035800	Weak transcription	HSMMtube	muscle
32	chr12:50018000-50043000	Weak transcription	Psoas Muscle	Psoas
33	chr12:50018200-50025200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr12:50018200-50025400	Weak transcription	Brain Cingulate Gyrus	brain
35	chr12:50018200-50025400	Weak transcription	Placenta	Placenta
36	chr12:50018200-50025400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr12:50018200-50025600	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr12:50018200-50025600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr12:50018200-50025600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr12:50018200-50025600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr12:50018200-50025600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr12:50018200-50025600	Weak transcription	Ovary	ovary
43	chr12:50018200-50026800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr12:50018200-50030400	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr12:50018200-50030400	Weak transcription	HepG2	liver
46	chr12:50018200-50030800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr12:50018200-50033800	Weak transcription	Esophagus	oesophagus
48	chr12:50018400-50025200	Weak transcription	Fetal Muscle Trunk	muscle
49	chr12:50018400-50025400	Weak transcription	Brain Anterior Caudate	brain
50	chr12:50018400-50025400	Weak transcription	Spleen	Spleen

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