Variant report

Variant	esv3397575
Chromosome Location	chr12:25258310-25260858
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	ATF2	chr12:25260702-25261368	GM12878	blood:	n/a	n/a
2	ATF2	chr12:25260821-25261321	GM12878	blood:	n/a	n/a
3	BATF	chr12:25260848-25261197	GM12878	blood:	n/a	n/a
4	BCLAF1	chr12:25260730-25261237	GM12878	blood:	n/a	n/a
5	CUX1	chr12:25260813-25261244	GM12878	blood:	n/a	n/a
6	EBF1	chr12:25260823-25261257	GM12878	blood:	n/a	n/a
7	EP300	chr12:25260844-25261298	GM12878	blood:	n/a	n/a
8	EP300	chr12:25259804-25260169	SK-N-SH_RA	brain:	n/a	n/a
9	FOXM1	chr12:25260802-25261331	GM12878	blood:	n/a	n/a
10	GATA3	chr12:25259853-25260186	SK-N-SH	brain:	n/a	n/a
11	IKZF1	chr12:25260648-25261270	GM12878	blood:	n/a	n/a
12	IRF4	chr12:25260774-25261264	GM12878	blood:	n/a	n/a
13	IRF4	chr12:25260803-25261219	GM12878	blood:	n/a	n/a
14	JUND	chr12:25260713-25261275	GM12878	blood:	n/a	n/a
15	JUND	chr12:25260331-25261327	GM12878	blood:	n/a	n/a
16	MAFK	chr12:25258880-25258926	HepG2	liver:	n/a	n/a
17	MAZ	chr12:25258942-25258944	HepG2	liver:	n/a	n/a
18	MEF2A	chr12:25260773-25261349	GM12878	blood:	n/a	chr12:25261322-25261343
19	MTA3	chr12:25260773-25261354	GM12878	blood:	n/a	n/a
20	NFATC1	chr12:25260770-25261353	GM12878	blood:	n/a	n/a
21	NFATC1	chr12:25260759-25261341	GM12878	blood:	n/a	n/a
22	NFIC	chr12:25260804-25261374	GM12878	blood:	n/a	n/a
23	NFIC	chr12:25260651-25261602	GM12878	blood:	n/a	n/a
24	PBX3	chr12:25259813-25260213	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr12:25260304-25264528	GM12891	blood:	n/a	n/a
26	POLR2A	chr12:25259389-25259395	GM12878	blood:	n/a	n/a
27	POLR2A	chr12:25258419-25259090	GM12878	blood:	n/a	n/a
28	POLR2A	chr12:25259740-25262661	GM12878	blood:	n/a	n/a
29	RCOR1	chr12:25260447-25261263	GM12878	blood:	n/a	n/a
30	RUNX3	chr12:25260757-25261362	GM12878	blood:	n/a	n/a
31	RUNX3	chr12:25260744-25261192	GM12878	blood:	n/a	n/a
32	SPI1	chr12:25260730-25261312	GM12891	blood:	n/a	n/a
33	SPI1	chr12:25260817-25261258	GM12891	blood:	n/a	n/a
34	SPI1	chr12:25260651-25261642	GM12878	blood:	n/a	n/a
35	SPI1	chr12:25260847-25261260	GM12878	blood:	n/a	n/a
36	STAT1	chr12:25260798-25260998	GM12878	blood:	n/a	n/a
37	STAT5A	chr12:25260720-25261206	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000258449	TF binding region

Extended variants
information (count: 92 )
Associated
traits (count: 104 )

Variant overlapped rSNPs/rCNVs (count:92 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs567842519	chr12:25258317-25258318	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs538194887	chr12:25258334-25258335	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs140106794	chr12:25258351-25258352	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs578243439	chr12:25258388-25258389	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs539457253	chr12:25258456-25258457	Strong transcription Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs17327547	chr12:25258458-25258459	Strong transcription Weak transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs572858008	chr12:25258497-25258498	Strong transcription Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs188338998	chr12:25258501-25258502	Strong transcription Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs540320189	chr12:25258524-25258525	Strong transcription Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs555314778	chr12:25258527-25258528	Strong transcription Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs113724903	chr12:25258574-25258575	Strong transcription Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs377577636	chr12:25258578-25258579	Strong transcription Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
13	rs59012229	chr12:25258583-25258584	Strong transcription Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs573765887	chr12:25258614-25258615	Strong transcription Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs544129622	chr12:25258659-25258660	Strong transcription Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs562462508	chr12:25258727-25258728	Strong transcription Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs533022550	chr12:25258740-25258741	Strong transcription Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs545010653	chr12:25258755-25258756	Strong transcription Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
19	rs78365939	chr12:25258776-25258777	Strong transcription Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
20	rs543258484	chr12:25258786-25258787	Strong transcription Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs1497265	chr12:25258824-25258825	Strong transcription Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs59014784	chr12:25258901-25258902	Strong transcription Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs377537124	chr12:25258906-25258907	Strong transcription Weak transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs859149	chr12:25258918-25258919	Strong transcription Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs368564471	chr12:25258990-25258991	Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs192593778	chr12:25259019-25259020	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs183077448	chr12:25259023-25259024	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs531956172	chr12:25259066-25259067	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs550365007	chr12:25259068-25259069	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs571981730	chr12:25259070-25259071	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs75609224	chr12:25259079-25259080	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs557834434	chr12:25259105-25259106	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs74713322	chr12:25259136-25259137	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs142258134	chr12:25259157-25259158	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs370105788	chr12:25259212-25259213	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs373818053	chr12:25259217-25259218	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs144823382	chr12:25259224-25259225	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs368630014	chr12:25259225-25259226	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs187371555	chr12:25259262-25259263	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs149376086	chr12:25259275-25259276	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs371142806	chr12:25259289-25259290	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs543989136	chr12:25259345-25259346	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs200296649	chr12:25259357-25259358	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs573624721	chr12:25259371-25259372	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs374156417	chr12:25259409-25259410	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs201202846	chr12:25259420-25259421	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs368474067	chr12:25259424-25259425	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs369628640	chr12:25259437-25259438	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs371612812	chr12:25259492-25259493	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs859148	chr12:25259497-25259498	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:104)

Disease	PMID	Source
Malignant germ cell tumour	17285132	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Melanoma	18172304	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Myxofibrosarcoma	16751306	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Wilms tumour	21544195	CNVD
Squamous cell cancer	21044232	CNVD
Acute myeloid leukemia	16864856	CNVD
T-cell acute lymphoblastic leukemia	20065082	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Endometrial cancer	22040021	CNVD
Colorectal cancer	20709793	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Testicular cancer	18059402	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Seminomas	18059402	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
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
Acute lymphoblastic leukemia	21248843	CNVD
Ewing''s sarcoma	17952124	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	21858162	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Myelodysplastic syndrome	21251322	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Acute myeloid leukemia	21251322	CNVD
Breast cancer	17133270	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Acute myeloid leukemia	20729466	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	16397240	CNVD
Neurodevelopmental disorder	22521361	CNVD
Intracranial aneurysm	16715129	CNVD
Breast cancer	21509527	CNVD
Autism	22102821	CNVD
Follicular lymphoma	18703704	CNVD
Lung cancer	18438408	CNVD
Lung cancer	21911935	CNVD
Breast cancer	22048815	CNVD
Malignant peripheral nerve sheath tumor	19844265	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	16272173	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Heart disease	21282601	CNVD
Ovarian cancer	20844748	CNVD
Lung cancer	17925434	CNVD
Non-small cell lung cancer	21829676	CNVD
Ovarian neoplasms	16753589	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
Gastric cancer	24379144	CNVD
Gastric cancer	19545448	CNVD
Lung cancer	20031968	CNVD
Lung adenocarcinoma	19525976	CNVD
Lung adenocarcinoma	19826477	CNVD
Lung cancer	19525976	CNVD
Lung cancer	19826477	CNVD
Non-small cell lung cancer	19451690	CNVD
Non-small cell lung cancer	17504988	CNVD
Bipolar disorder	19114987	CNVD
Lung cancer	19671679	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Breast cancer	21364760	CNVD
Lung cancer	21569311	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Lung adenocarcinoma	17982442	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Ovarian cancer	21720365	CNVD
Cancer	17699850	CNVD
Ovarian cancer	17699850	CNVD
Cancer	20164920	CNVD
Gastric cancer	22315472	CNVD
Adenocarcinoma	19001599	CNVD
Non-small cell lung cancer	19001599	CNVD
Pancreatic cancer	20981101	CNVD
Squamous cell cancer	19001599	CNVD
Acute lymphoblastic leukemia	21680795	CNVD
Lung adenocarcinoma	18379350	CNVD
Lung cancer	18379350	CNVD
Ovarian cancer	22174824	CNVD
Pancreatic cancer	21811562	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:25209400-25264400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:25210000-25262800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr12:25215000-25265000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:25230000-25264600	Strong transcription	Fetal Thymus	thymus
5	chr12:25232200-25263600	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr12:25238600-25263000	Weak transcription	Left Ventricle	heart
7	chr12:25238600-25265200	Weak transcription	Lung	lung
8	chr12:25242800-25262200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr12:25243000-25259200	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr12:25246400-25264000	Weak transcription	Ovary	ovary
11	chr12:25247400-25258400	Strong transcription	Primary T cells from cord blood	blood
12	chr12:25248400-25262800	Strong transcription	Primary T cells fromperipheralblood	blood
13	chr12:25248600-25258600	Strong transcription	Primary hematopoietic stem cells	blood
14	chr12:25248600-25264400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr12:25248800-25258400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr12:25248800-25259200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr12:25249200-25261800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr12:25251800-25274600	Weak transcription	Pancreas	Pancrea
19	chr12:25252200-25264000	Weak transcription	Spleen	Spleen
20	chr12:25252400-25260400	Weak transcription	Adipose Nuclei	Adipose
21	chr12:25253200-25262800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr12:25254000-25260200	Strong transcription	Primary B cells from peripheral blood	blood
23	chr12:25254200-25259800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr12:25254200-25260400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr12:25254200-25263600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr12:25254200-25263800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr12:25254200-25263800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:25254400-25260600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr12:25255600-25260400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr12:25255800-25260200	Weak transcription	Thymus	Thymus
31	chr12:25255800-25261400	Weak transcription	Small Intestine	intestine
32	chr12:25255800-25262400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr12:25256000-25260400	Weak transcription	Liver	Liver
34	chr12:25256000-25265200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr12:25256800-25262600	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr12:25257000-25264800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr12:25257400-25258600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr12:25257400-25264800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr12:25257600-25259800	Weak transcription	GM12878-XiMat	blood
40	chr12:25257800-25260400	Weak transcription	Primary T helper cells PMA-I stimulated	--
41	chr12:25258000-25259800	Weak transcription	Primary B cells from cord blood	blood
42	chr12:25258000-25259800	Weak transcription	Dnd41	blood
43	chr12:25258400-25258600	Weak transcription	Primary T cells from cord blood	blood
44	chr12:25258400-25260000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr12:25258600-25258800	Strong transcription	Primary T cells from cord blood	blood
46	chr12:25258600-25259800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr12:25258600-25262200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr12:25258800-25260000	Weak transcription	Primary T cells from cord blood	blood
49	chr12:25259000-25263200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr12:25259200-25260000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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