Variant report

Variant	esv3384217
Chromosome Location	chr12:48497934-48498463
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CHD1	chr12:48498455-48498794	GM12878	blood:	n/a	n/a
2	CTCF	chr12:48498420-48498570	SK-N-SH_RA	brain:	n/a	n/a
3	EBF1	chr12:48498443-48498569	GM12878	blood:	n/a	n/a
4	FOXA1	chr12:48498332-48498648	T-47D	breast:	n/a	n/a
5	FOXA1	chr12:48498418-48498752	T-47D	breast:	n/a	n/a
6	GABPA	chr12:48497980-48498037	HepG2	liver:	n/a	n/a
7	GABPA	chr12:48497981-48498059	HepG2	liver:	n/a	n/a
8	GATA3	chr12:48498329-48498678	T-47D	breast:	n/a	n/a
9	GATA3	chr12:48498292-48498831	MCF-7	breast:	n/a	n/a
10	HCFC1	chr12:48498126-48501600	Hela-S3	cervix:	n/a	n/a
11	HDAC2	chr12:48498347-48498821	MCF-7	breast:	n/a	chr12:48498689-48498703
12	HDAC2	chr12:48498308-48498820	MCF-7	breast:	n/a	chr12:48498689-48498703
13	MAX	chr12:48498313-48498768	MCF-7	breast:	n/a	n/a
14	NRF1	chr12:48498224-48498312	H1-hESC	embryonic stem cell:	n/a	n/a
15	NRF1	chr12:48498369-48498561	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:48498334-48501462	GM12891	blood:	n/a	n/a
17	POLR2A	chr12:48498219-48498732	GM12892	blood:	n/a	n/a
18	POLR2A	chr12:48498418-48501460	GM18505	blood:	n/a	n/a
19	RELA	chr12:48498308-48500398	GM12878	blood:	n/a	chr12:48499466-48499475 chr12:48499466-48499475
20	WRNIP1	chr12:48498305-48498641	GM12878	blood:	n/a	n/a
21	ZNF217	chr12:48498360-48498735	MCF-7	breast:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48490196..48492740-chr12:48498056..48500665,3	MCF-7	breast:
2	chr12:48495831..48503326-chr12:48548997..48555180,8	K562	blood:
3	chr12:48496389..48500489-chr12:48511491..48515053,4	K562	blood:
4	chr12:48492802..48495479-chr12:48497432..48499214,2	K562	blood:
5	chr12:48497586..48502171-chr12:48511099..48514258,8	MCF-7	breast:
6	chr12:48492914..48496557-chr12:48498180..48501677,4	MCF-7	breast:
7	chr12:48497572..48499249-chr12:48549769..48551418,2	MCF-7	breast:
8	chr12:48496939..48501728-chr12:48549612..48553634,6	MCF-7	breast:
9	chr12:48497262..48501671-chr12:48511273..48513832,5	K562	blood:

No data

Variant related genes	Relation type
SENP1	TF binding region
PFKM	TF binding region
ENSG00000258051	chromatin interactions
ENSG00000079387	chromatin interactions
ENSG00000152556	chromatin interactions
ENSG00000177981	chromatin interactions

Extended variants
information (count: 27 )
Associated
traits (count: 70 )

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs537097277	chr12:48497976-48497977	Weak transcription Enhancers Active TSS	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
2	rs550944451	chr12:48497981-48497982	Weak transcription Enhancers Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
3	rs71747947	chr12:48498018-48498019	Weak transcription Active TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
4	rs58280906	chr12:48498019-48498020	Weak transcription Active TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
5	rs371498257	chr12:48498021-48498022	Weak transcription Active TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
6	rs375125817	chr12:48498022-48498023	Weak transcription Active TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
7	rs374589255	chr12:48498023-48498024	Weak transcription Active TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
8	rs371520806	chr12:48498037-48498038	Weak transcription Active TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
9	rs201941972	chr12:48498038-48498039	Weak transcription Active TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
10	rs200544796	chr12:48498045-48498046	Weak transcription Active TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
11	rs185381451	chr12:48498066-48498067	Weak transcription Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
12	rs567431325	chr12:48498068-48498069	Weak transcription Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
13	rs540611266	chr12:48498075-48498076	Weak transcription Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
14	rs201482953	chr12:48498095-48498096	Weak transcription Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
15	rs536317964	chr12:48498136-48498137	Weak transcription Active TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
16	rs555157416	chr12:48498162-48498163	Weak transcription Active TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
17	rs571943534	chr12:48498199-48498200	Weak transcription Active TSS Enhancers Flanking Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
18	rs142884965	chr12:48498209-48498210	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
19	rs529325760	chr12:48498257-48498258	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
20	rs577857075	chr12:48498260-48498261	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
21	rs11168408	chr12:48498327-48498328	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region	6 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
22	rs563225742	chr12:48498358-48498359	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
23	rs10875743	chr12:48498413-48498414	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	6 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
24	rs190586705	chr12:48498428-48498429	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
25	rs542712497	chr12:48498438-48498439	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
26	rs10875744	chr12:48498440-48498441	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	6 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
27	rs528726654	chr12:48498441-48498442	Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Enhancers	TF binding region Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:70)

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
T-cell prolymphocytic leukemia	17713554	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
Malignant peripheral nerve sheath tumor	18522746	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
Anaplastic thyroid cancer	18753363	CNVD
Breast cancer	21785460	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Intracranial ependymoma	16609018	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:268 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48432200-48498400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:48453000-48498200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr12:48468600-48498400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr12:48468800-48498200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:48475000-48498200	Weak transcription	Psoas Muscle	Psoas
6	chr12:48476800-48498400	Weak transcription	Fetal Brain Male	brain
7	chr12:48477200-48498200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:48477400-48498400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:48479400-48498200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr12:48479400-48498200	Weak transcription	Brain Angular Gyrus	brain
11	chr12:48479400-48498400	Weak transcription	Aorta	Aorta
12	chr12:48479600-48498000	Weak transcription	NHEK	skin
13	chr12:48480400-48498200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr12:48482800-48498200	Weak transcription	NHDF-Ad	bronchial
15	chr12:48483000-48498200	Weak transcription	NH-A	brain
16	chr12:48483000-48498400	Weak transcription	HSMMtube	muscle
17	chr12:48483200-48498200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:48483200-48498200	Weak transcription	HepG2	liver
19	chr12:48483200-48498400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr12:48483200-48499200	Weak transcription	Small Intestine	intestine
21	chr12:48483400-48498200	Weak transcription	NHLF	lung
22	chr12:48484800-48498200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr12:48485000-48498200	Weak transcription	Spleen	Spleen
24	chr12:48486200-48499000	Weak transcription	Gastric	stomach
25	chr12:48488000-48498200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr12:48488200-48498200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr12:48488200-48498200	Weak transcription	Lung	lung
28	chr12:48488200-48498200	Weak transcription	Pancreas	Pancrea
29	chr12:48488200-48498400	Weak transcription	Brain Substantia Nigra	brain
30	chr12:48488200-48499200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:48488400-48498200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr12:48488400-48498400	Weak transcription	Right Ventricle	heart
33	chr12:48489000-48498200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr12:48489600-48498400	Weak transcription	Left Ventricle	heart
35	chr12:48489600-48499000	Weak transcription	Esophagus	oesophagus
36	chr12:48489800-48498200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:48489800-48498200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr12:48489800-48498200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr12:48489800-48498400	Weak transcription	Thymus	Thymus
40	chr12:48490000-48498400	Weak transcription	Colonic Mucosa	Colon
41	chr12:48490200-48498200	Weak transcription	Brain Germinal Matrix	brain
42	chr12:48490200-48498200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr12:48490200-48498200	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr12:48490200-48498200	Weak transcription	HUVEC	blood vessel
45	chr12:48490600-48499000	Weak transcription	Ovary	ovary
46	chr12:48491400-48498200	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr12:48491400-48498200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr12:48491400-48498200	Weak transcription	Fetal Intestine Large	intestine
49	chr12:48491600-48498000	Weak transcription	HMEC	breast
50	chr12:48491600-48498200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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