Variant report

Variant	esv2577852
Chromosome Location	chr12:64376290-64377762
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	FOS	chr12:64377337-64377483	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr12:64377318-64377508	MCF10A-Er-Src	breast:	n/a	n/a
3	FOS	chr12:64377302-64377487	MCF10A-Er-Src	breast:	n/a	n/a
4	FOSL2	chr12:64377096-64377585	MCF-7	breast:	n/a	n/a
5	GATA3	chr12:64377653-64377870	T-47D	breast:	n/a	n/a
6	POLR2A	chr12:64377077-64377189	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:64373746..64376340-chr12:64376425..64378945,3	MCF-7	breast:
2	chr12:64311041..64313819-chr12:64377499..64379764,2	MCF-7	breast:
3	chr12:64376417..64378425-chr12:64384160..64386437,2	K562	blood:

Variant related genes	Relation type
SRGAP1	TF binding region
ENSG00000196935	chromatin interactions

Extended variants
information (count: 67 )
Associated
traits (count: 80 )

Variant overlapped rSNPs/rCNVs (count:67 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs536367741	chr12:64376290-64376291	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs556486403	chr12:64376294-64376295	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs569961620	chr12:64376384-64376385	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs539274679	chr12:64376394-64376395	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs185706112	chr12:64376422-64376423	Weak transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs188792434	chr12:64376509-64376510	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs35618652	chr12:64376539-64376540	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs144267207	chr12:64376541-64376542	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs181683350	chr12:64376571-64376572	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs138855146	chr12:64376586-64376587	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs369294877	chr12:64376610-64376611	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs185368661	chr12:64376612-64376613	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs543170069	chr12:64376614-64376615	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs79366960	chr12:64376623-64376624	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs76455374	chr12:64376628-64376629	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs546067269	chr12:64376665-64376666	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs559715228	chr12:64376702-64376703	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs565218273	chr12:64376704-64376705	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs12302441	chr12:64376774-64376775	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs190228888	chr12:64376776-64376777	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs181244256	chr12:64376777-64376778	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs547400024	chr12:64376781-64376782	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs148872536	chr12:64376812-64376813	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs12371171	chr12:64376822-64376823	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
25	rs530169717	chr12:64376857-64376858	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs550011558	chr12:64376885-64376886	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs185833505	chr12:64376955-64376956	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs77404452	chr12:64376972-64376973	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs552439743	chr12:64376996-64376997	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs4445733	chr12:64377022-64377023	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs191037515	chr12:64377062-64377063	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs535010126	chr12:64377080-64377081	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs183668203	chr12:64377094-64377095	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs574935315	chr12:64377097-64377098	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs12296441	chr12:64377100-64377101	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs143623989	chr12:64377125-64377126	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs12316287	chr12:64377169-64377170	Weak transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
38	rs370867226	chr12:64377200-64377201	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs569407125	chr12:64377263-64377264	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs377254596	chr12:64377317-64377318	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
41	rs189218973	chr12:64377369-64377370	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs148059779	chr12:64377371-64377372	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs538884413	chr12:64377399-64377400	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs60432456	chr12:64377467-64377468	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
45	rs146290805	chr12:64377472-64377473	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs558707565	chr12:64377479-64377480	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs138337536	chr12:64377480-64377481	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs530665177	chr12:64377498-64377499	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs550240103	chr12:64377522-64377523	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs369768202	chr12:64377533-64377534	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:80)

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
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
Breast cancer	17899364	CNVD
Colorectal cancer	16272173	CNVD
Glioblastoma multiforme	17387387	CNVD
liposarcomas	17372913	CNVD
Non-small cell lung cancer	24170126	CNVD
Cancer	16751803	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	21785460	CNVD
small cell lung cancer	20016488	CNVD
Melanoma	18172304	CNVD
Glioblastoma multiforme	21390271	CNVD
Cancer	20164919	CNVD
Leukemia	18628472	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
Metanephric adenoma	20802469	CNVD
Follicular lymphoma	18703704	CNVD
Acute myeloid leukemia	21251322	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Multiple myeloma	16616336	CNVD
Lung cancer	16773561	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Mental retardation	17220210	CNVD
Osteopoikilosis	17220210	CNVD
short stature	17220210	CNVD
Burkitt''s lymphoma	20823134	CNVD
abnormal development	18461090	CNVD
Breast cancer	21364760	CNVD
Prostate cancer	18632612	CNVD
Myelofibrosis	22110671	CNVD
Heart disease	21282601	CNVD
Ovarian neoplasms	16753589	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Breast cancer	16620391	CNVD

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64312400-64385000	Weak transcription	Aorta	Aorta
2	chr12:64362600-64385600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr12:64362800-64377600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr12:64362800-64378800	Weak transcription	Pancreas	Pancrea
5	chr12:64362800-64396000	Weak transcription	Psoas Muscle	Psoas
6	chr12:64364200-64376800	Weak transcription	HSMMtube	muscle
7	chr12:64364200-64385800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr12:64365000-64383000	Weak transcription	Stomach Mucosa	stomach
9	chr12:64365800-64378600	Weak transcription	Fetal Intestine Small	intestine
10	chr12:64365800-64379400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr12:64366400-64383600	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr12:64370800-64384400	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr12:64371800-64385800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr12:64372000-64383200	Weak transcription	Fetal Kidney	kidney
15	chr12:64372400-64376600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:64372400-64382000	Weak transcription	HSMM	muscle
17	chr12:64372800-64376400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr12:64372800-64376400	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr12:64372800-64380600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:64373600-64376600	Weak transcription	Osteobl	bone
21	chr12:64373800-64383000	Weak transcription	HMEC	breast
22	chr12:64374000-64376400	Weak transcription	Ovary	ovary
23	chr12:64374000-64376800	Weak transcription	NH-A	brain
24	chr12:64374000-64377000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:64374000-64377200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr12:64374200-64376400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr12:64374400-64377600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr12:64374400-64377800	Weak transcription	NHEK	skin
29	chr12:64374400-64379000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr12:64374600-64376400	Weak transcription	A549	lung
31	chr12:64374600-64378600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:64375000-64377200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:64375200-64377000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:64375200-64377200	Enhancers	NHLF	lung
35	chr12:64375400-64376400	Weak transcription	Brain Germinal Matrix	brain
36	chr12:64375400-64377000	Enhancers	Brain Anterior Caudate	brain
37	chr12:64375400-64377200	Enhancers	Colon Smooth Muscle	Colon
38	chr12:64375400-64377200	Enhancers	Fetal Brain Female	brain
39	chr12:64375400-64383200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr12:64375600-64376800	Weak transcription	Stomach Smooth Muscle	stomach
41	chr12:64375600-64378800	Weak transcription	Fetal Muscle Leg	muscle
42	chr12:64375600-64383200	Weak transcription	Fetal Lung	lung
43	chr12:64375600-64384600	Weak transcription	Hela-S3	cervix
44	chr12:64375800-64377200	Enhancers	NHDF-Ad	bronchial
45	chr12:64375800-64385600	Weak transcription	Adipose Nuclei	Adipose
46	chr12:64376000-64377200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:64376000-64377200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr12:64376200-64376800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:64376200-64377000	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr12:64376200-64377200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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