Variant report

Variant	esv3497672
Chromosome Location	chr12:377422-384887
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:371632..373367-chr12:383696..385601,2	MCF-7	breast:
2	chr12:371815..373339-chr12:375834..377443,2	K562	blood:
3	chr12:371815..374343-chr12:375834..377592,4	K562	blood:
4	chr12:378409..380462-chr12:383368..386178,2	MCF-7	breast:
5	chr12:381899..384416-chr12:386819..388918,2	K562	blood:
6	chr12:381899..385111-chr12:386819..388918,3	K562	blood:
7	chr12:378409..380462-chr12:383368..386178,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KDM5A-1	chr12:383120-386289	ENSG00000261799.1

No data

Variant related genes	Relation type
ENSG00000010379	chromatin interactions

Extended variants
information (count: 296 )
Associated
traits (count: 82 )

Variant overlapped rSNPs/rCNVs (count:296 , 50 per page) page: 1 2 3 4 5 6

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs566611512	chr12:377448-377449	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs533866608	chr12:377546-377547	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs79653077	chr12:377554-377555	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs139683484	chr12:377590-377591	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs187456093	chr12:377608-377609	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs193270458	chr12:377706-377707	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs565721873	chr12:377720-377721	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs566753773	chr12:377727-377728	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs527290964	chr12:377768-377769	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs370797522	chr12:377775-377776	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs577837556	chr12:377791-377792	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs184601894	chr12:377855-377856	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
13	rs545234056	chr12:377889-377890	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
14	rs560079452	chr12:377894-377895	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
15	rs526282	chr12:377904-377905	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
16	rs116158154	chr12:377916-377917	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
17	rs371990568	chr12:377933-377934	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
18	rs114671349	chr12:377941-377942	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
19	rs529217436	chr12:377950-377951	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
20	rs554511782	chr12:377957-377958	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
21	rs550685780	chr12:377998-377999	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
22	rs115126993	chr12:378018-378019	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs117852751	chr12:378045-378046	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs551994042	chr12:378046-378047	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs567020117	chr12:378059-378060	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs533893351	chr12:378066-378067	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs549062451	chr12:378087-378088	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs200963919	chr12:378089-378090	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs567351242	chr12:378096-378097	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs189242852	chr12:378159-378160	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs797755	chr12:378195-378196	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs7976420	chr12:378218-378219	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs797756	chr12:378228-378229	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs371802110	chr12:378233-378234	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs797757	chr12:378237-378238	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs540345362	chr12:378243-378244	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs192237524	chr12:378298-378299	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs555010552	chr12:378329-378330	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs561883136	chr12:378353-378354	Weak transcription Bivalent Enhancer Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs149330943	chr12:378406-378407	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
41	rs544644011	chr12:378416-378417	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
42	rs562733883	chr12:378418-378419	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
43	rs533690920	chr12:378442-378443	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
44	rs567321484	chr12:378455-378456	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
45	rs560680554	chr12:378464-378465	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
46	rs527920646	chr12:378471-378472	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
47	rs7959713	chr12:378495-378496	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs567414420	chr12:378520-378521	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
49	rs573438351	chr12:378524-378525	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a
50	rs368892553	chr12:378573-378574	Weak transcription Enhancers Bivalent Enhancer	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:82)

Disease	PMID	Source
Cancer	20164920	CNVD
Myelofibrosis	22110671	CNVD
Non-syndromic sensorineural hearing loss	19587683	CNVD
Glaucoma	21310917	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Malignant peripheral nerve sheath tumor	19844265	CNVD
Squamous cell cancer	19607727	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Hepatocellular carcinoma	16750200	CNVD
Breast cancer	17133270	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Mental retardation	17847001	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
abnormal development	18461090	CNVD
Ovarian cancer	20844748	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Medulloblastoma	16968546	CNVD
Ovine squamous-cell carcinoma	17599052	CNVD
T-cell acute lymphoblastic leukemia	20065082	CNVD
Breast cancer	22032731	CNVD
Cancer	21183584	CNVD
Myxofibrosarcoma	16751306	CNVD
Non-small cell lung cancer	21829676	CNVD
Ovarian neoplasms	16753589	CNVD
Prostate cancer	21965145	CNVD
Acute myeloid leukemia	16864856	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Disorders of sex development	21048976	CNVD
Glioblastoma multiforme	21080181	CNVD
Liposarcoma	21253554	CNVD
Prostate cancer	19156837	CNVD
Emphysema	19352772	CNVD
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Malignant germ cell tumour	17285132	CNVD
Melanoma	18172304	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Wilms tumour	21544195	CNVD
Squamous cell cancer	21044232	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	19960244	CNVD
Endometrial cancer	22040021	CNVD
Colorectal cancer	20709793	CNVD
Breast cancer	21264507	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
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
small cell lung cancer	20016488	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Breast cancer	21364760	CNVD
Developmental delay	21147756	CNVD
Acute lymphoblastic leukemia	21248843	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Ewing''s sarcoma	17952124	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Acute myeloid leukemia	20729466	CNVD
Breast cancer	21858162	CNVD
Breast cancer	21509527	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21785460	CNVD
Autism	22495309	CNVD
Ovarian cancer	21720365	CNVD
Myelodysplastic syndrome	21251322	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Cancer	20164919	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:187 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:372000-379200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:372400-393600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr12:373200-378600	Weak transcription	Placenta	Placenta
4	chr12:373200-391200	Weak transcription	Lung	lung
5	chr12:373200-393600	Weak transcription	A549	lung
6	chr12:373200-401400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:373600-387800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:373600-388200	Weak transcription	HSMM	muscle
9	chr12:373800-393000	Weak transcription	Thymus	Thymus
10	chr12:374200-389800	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr12:375400-388000	Weak transcription	Primary T cells from cord blood	blood
12	chr12:376400-377800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:376600-391000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:376800-378200	Enhancers	Brain Cingulate Gyrus	brain
15	chr12:376800-378800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
16	chr12:376800-393800	Weak transcription	Fetal Kidney	kidney
17	chr12:377000-377600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr12:377000-377600	Bivalent Enhancer	Fetal Brain Male	brain
19	chr12:377000-377800	Active TSS	Pancreatic Islets	Pancreatic Islet
20	chr12:377000-378000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:377000-378000	Enhancers	Brain Inferior Temporal Lobe	brain
22	chr12:377000-378000	Enhancers	Brain Substantia Nigra	brain
23	chr12:377000-378200	Enhancers	Brain Angular Gyrus	brain
24	chr12:377000-378200	Enhancers	Ovary	ovary
25	chr12:377000-378600	Enhancers	Fetal Heart	heart
26	chr12:377200-377600	Enhancers	HepG2	liver
27	chr12:377200-377800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr12:377200-377800	Enhancers	Liver	Liver
29	chr12:377200-377800	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr12:377200-378000	Enhancers	Esophagus	oesophagus
31	chr12:377200-378000	Enhancers	Right Ventricle	heart
32	chr12:377200-378000	Enhancers	HSMMtube	muscle
33	chr12:377200-378200	Enhancers	Left Ventricle	heart
34	chr12:377200-379000	Enhancers	Fetal Muscle Leg	muscle
35	chr12:377200-379000	Enhancers	Right Atrium	heart
36	chr12:377200-392400	Weak transcription	Osteobl	bone
37	chr12:377400-377600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:377400-378000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:377400-378000	Enhancers	Brain Anterior Caudate	brain
40	chr12:377400-378000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr12:377400-378400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr12:377400-378600	Weak transcription	Brain Germinal Matrix	brain
43	chr12:377400-378800	Bivalent Enhancer	Fetal Lung	lung
44	chr12:377400-382200	Weak transcription	Small Intestine	intestine
45	chr12:377400-391200	Weak transcription	Adipose Nuclei	Adipose
46	chr12:377400-393800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr12:377600-377800	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr12:377600-377800	Enhancers	Gastric	stomach
49	chr12:377600-378000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:377600-378000	Bivalent Enhancer	Fetal Brain Female	brain

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