Variant report

Variant	esv3431259
Chromosome Location	chr12:57111616-57111814
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:41)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:41 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr12:57111548-57111863	GM12878	blood:	n/a	n/a
2	EP300	chr12:57111556-57111748	GM12878	blood:	n/a	n/a
3	HEY1	chr12:57111470-57111835	K562	blood:	n/a	n/a
4	HEY1	chr12:57111571-57111955	HepG2	liver:	n/a	n/a
5	HEY1	chr12:57111540-57111862	HepG2	liver:	n/a	n/a
6	HEY1	chr12:57111440-57112682	K562	blood:	n/a	n/a
7	POLR2A	chr12:57109094-57117058	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr12:57110895-57113126	GM12892	blood:	n/a	n/a
9	POLR2A	chr12:57111677-57111876	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr12:57109177-57115890	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr12:57109486-57115298	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr12:57111499-57111774	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr12:57109356-57117115	GM12878	blood:	n/a	n/a
14	POLR2A	chr12:57111525-57111912	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr12:57111493-57112758	GM12891	blood:	n/a	n/a
16	POLR2A	chr12:57111481-57111877	GM12892	blood:	n/a	n/a
17	POLR2A	chr12:57109111-57113222	GM12892	blood:	n/a	n/a
18	POLR2A	chr12:57111528-57111788	A549	lung:	n/a	n/a
19	POLR2A	chr12:57109422-57111685	K562	blood:	n/a	n/a
20	POLR2A	chr12:57111363-57112218	GM12891	blood:	n/a	n/a
21	POLR2A	chr12:57109230-57111658	K562	blood:	n/a	n/a
22	POLR2A	chr12:57109233-57116354	PANC-1	pancreas:	n/a	n/a
23	POLR2A	chr12:57111735-57112149	Hela-S3	cervix:	n/a	n/a
24	POLR2A	chr12:57111483-57112504	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr12:57111488-57111952	GM12878	blood:	n/a	n/a
26	POLR2A	chr12:57109223-57113587	K562	blood:	n/a	n/a
27	POLR2A	chr12:57109373-57115069	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr12:57109283-57116293	GM12878	blood:	n/a	n/a
29	POLR2A	chr12:57110844-57111688	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr12:57110773-57112301	GM12891	blood:	n/a	n/a
31	POLR2A	chr12:57111468-57111696	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr12:57111326-57114042	GM12892	blood:	n/a	n/a
33	POLR2A	chr12:57111463-57112022	GM12878	blood:	n/a	n/a
34	POLR2A	chr12:57111783-57111806	MCF-7	breast:	n/a	n/a
35	POLR2A	chr12:57111472-57111996	GM12891	blood:	n/a	n/a
36	POU2F2	chr12:57111518-57111793	GM12891	blood:	n/a	n/a
37	RUNX3	chr12:57111285-57111616	GM12878	blood:	n/a	n/a
38	SP1	chr12:57111474-57112143	GM12878	blood:	n/a	n/a
39	SP1	chr12:57111454-57112054	GM12878	blood:	n/a	n/a
40	TCF12	chr12:57111452-57112024	GM12878	blood:	n/a	n/a
41	TCF12	chr12:57111487-57112053	GM12878	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:57111474..57114081-chr12:57143216..57146135,2	MCF-7	breast:
2	chr12:57078008..57083064-chr12:57107591..57112002,6	MCF-7	breast:
3	chr12:56510526..56513327-chr12:57111291..57113363,2	K562	blood:
4	chr12:57079048..57083970-chr12:57107938..57112602,6	K562	blood:
5	chr12:57074578..57085543-chr12:57108746..57121559,55	K562	blood:
6	chr12:57029529..57031708-chr12:57108822..57111712,2	K562	blood:

No data

Variant related genes	Relation type
NACA	TF binding region
ENSG00000025423	chromatin interactions
ENSG00000229117	chromatin interactions
ENSG00000198056	chromatin interactions
ENSG00000110958	chromatin interactions
ENSG00000139641	chromatin interactions
ENSG00000076108	chromatin interactions
ENSG00000135482	chromatin interactions

Extended variants
information (count: 20 )
Associated
traits (count: 93 )

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs12822513	chr12:57111618-57111619	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
2	rs202147060	chr12:57111622-57111623	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
3	rs12822876	chr12:57111636-57111637	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
4	rs528876497	chr12:57111638-57111639	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
5	rs544365247	chr12:57111647-57111648	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
6	rs12822887	chr12:57111672-57111673	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
7	rs535923910	chr12:57111677-57111678	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
8	rs562442625	chr12:57111679-57111680	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
9	rs371075827	chr12:57111687-57111688	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
10	rs533157907	chr12:57111688-57111689	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
11	rs2926746	chr12:57111705-57111706	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	8 gene(s)	Overlapped CNVs	n/a
12	rs367779814	chr12:57111722-57111723	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
13	rs551249413	chr12:57111725-57111726	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
14	rs566775915	chr12:57111726-57111727	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
15	rs527554681	chr12:57111727-57111728	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
16	rs371978815	chr12:57111734-57111735	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
17	rs2958150	chr12:57111746-57111747	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
18	rs111848322	chr12:57111774-57111775	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
19	rs568150891	chr12:57111794-57111795	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
20	rs2926745	chr12:57111810-57111811	Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:93)

Disease	PMID	Source
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
Chronic lymphocytic leukemia	21546498	CNVD
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	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
Lissencephaly	21572526	CNVD
Lung cancer	18438408	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	19602461	CNVD
Breast cancer	17899364	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	21364760	CNVD
Prostate cancer	18632612	CNVD
Metanephric adenoma	20802469	CNVD
Glioblastoma multiforme	17387387	CNVD
liposarcomas	17372913	CNVD
Non-small cell lung cancer	24170126	CNVD
Cancer	16751803	CNVD
Bladder cancer	21909424	CNVD
Intracranial aneurysm	16715129	CNVD
Breast cancer	17661082	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Breast cancer	21785460	CNVD
small cell lung cancer	20016488	CNVD
Hodgkin''s lymphoma	18179710	CNVD
Ewing''s sarcoma	17952124	CNVD
Autism	20531469	CNVD
Rhabdomyosarcoma	16790082	CNVD
Renal cell carcinoma	18765545	CNVD
Urothelial cell carcinoma	18451213	CNVD
Melanoma	18172304	CNVD
Glioblastoma multiforme	21138945	CNVD
Glioblastoma multiforme	21569311	CNVD
Glioblastoma multiforme	21390271	CNVD
Cancer	20164919	CNVD
Breast cancer	21509527	CNVD
Leukemia	18628472	CNVD
Glioblastoma multiforme	22291905	CNVD
Glioblastoma multiforme	19435819	CNVD
Myelofibrosis	22110671	CNVD
Phyllodes tumor	17334353	CNVD
Glaucoma	21310917	CNVD
Breast cancer	16272173	CNVD
Mental retardation	19951919	CNVD
Glaucoma	21447600	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Developmental delay	21267005	CNVD
12q14 microdeletion syndrome	21267005	CNVD
Developmental delay	19277063	CNVD
Dwarfism	19277063	CNVD
Fibroblasts	20926602	CNVD
Follicular lymphoma	18703704	CNVD
Acute myeloid leukemia	21251322	CNVD
Glycogen storage disease	18421352	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Glioblastoma multiforme	20080666	CNVD
Medulloblastoma	19270706	CNVD
Breast cancer	17133270	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:128 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57104000-57114600	Weak transcription	Fetal Brain Male	brain
2	chr12:57104600-57112600	Strong transcription	Fetal Intestine Large	intestine
3	chr12:57104600-57115000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr12:57105200-57112200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr12:57105800-57112200	Weak transcription	Fetal Heart	heart
6	chr12:57107400-57113800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr12:57107800-57112600	Weak transcription	Fetal Kidney	kidney
8	chr12:57108400-57115400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr12:57108600-57117200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr12:57109200-57116200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:57109400-57112000	Strong transcription	Fetal Intestine Small	intestine
12	chr12:57109400-57114800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr12:57109600-57112600	Weak transcription	HUVEC	blood vessel
14	chr12:57109600-57115400	Genic enhancers	Duodenum Smooth Muscle	Duodenum
15	chr12:57109600-57116000	Genic enhancers	Fetal Muscle Leg	muscle
16	chr12:57109600-57117000	Genic enhancers	Primary T cells fromperipheralblood	blood
17	chr12:57109600-57117000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
18	chr12:57109600-57117800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:57109800-57111800	Genic enhancers	Brain Hippocampus Middle	brain
20	chr12:57109800-57113600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr12:57109800-57113600	Genic enhancers	Fetal Muscle Trunk	muscle
22	chr12:57109800-57114400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr12:57109800-57114600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
24	chr12:57109800-57115800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr12:57109800-57117200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr12:57110000-57112600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr12:57110000-57112800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:57110200-57112000	Weak transcription	Fetal Lung	lung
29	chr12:57110200-57112600	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr12:57110200-57112600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr12:57110200-57112600	Weak transcription	Esophagus	oesophagus
32	chr12:57110200-57113200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr12:57110200-57115400	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr12:57110200-57115800	Genic enhancers	Placenta	Placenta
35	chr12:57110200-57116800	Genic enhancers	Fetal Stomach	stomach
36	chr12:57110400-57112000	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr12:57110400-57112600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr12:57110400-57112600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr12:57110400-57112600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:57110400-57112600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr12:57110400-57112600	Weak transcription	Aorta	Aorta
42	chr12:57110400-57112600	Enhancers	Placenta Amnion	Placenta Amnion
43	chr12:57110400-57112600	Weak transcription	Stomach Mucosa	stomach
44	chr12:57110400-57112600	Weak transcription	Hela-S3	cervix
45	chr12:57110400-57112600	Weak transcription	HSMMtube	muscle
46	chr12:57110400-57112600	Weak transcription	K562	blood
47	chr12:57110400-57112800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr12:57110400-57113000	Weak transcription	Gastric	stomach
49	chr12:57110400-57113200	Weak transcription	Brain Angular Gyrus	brain
50	chr12:57110400-57116800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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