Variant report

Variant	esv3482051
Chromosome Location	chr12:4388628-4389430
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	POLR2A	chr12:4388618-4393839	GM18526	blood:	n/a	n/a
2	POLR2A	chr12:4385126-4393865	K562	blood:	n/a	n/a
3	POLR2A	chr12:4389104-4389678	K562	blood:	n/a	n/a
4	POLR2A	chr12:4388886-4389692	GM12892	blood:	n/a	n/a
5	POLR2A	chr12:4388548-4388863	GM12892	blood:	n/a	n/a
6	POLR2A	chr12:4388901-4388928	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:4385965-4389349	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr12:4388436-4393945	GM12892	blood:	n/a	n/a
9	POLR2A	chr12:4384783-4393854	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:4377522-4393821	GM19099	blood:	n/a	n/a
11	POLR2A	chr12:4388767-4388833	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr12:4385697-4406476	GM12892	blood:	n/a	n/a
13	POLR2A	chr12:4389093-4389098	K562	blood:	n/a	n/a
14	POLR2A	chr12:4388983-4390182	GM12892	blood:	n/a	n/a
15	POLR2A	chr12:4388513-4400468	GM19193	blood:	n/a	n/a
16	POLR2A	chr12:4377597-4393888	GM12891	blood:	n/a	n/a
17	POLR2A	chr12:4388751-4389934	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr12:4389085-4400803	GM18951	blood:	n/a	n/a
19	POLR2A	chr12:4377513-4404672	GM12878	blood:	n/a	n/a
20	POLR2A	chr12:4388506-4391070	SK-N-MC	brain:	n/a	n/a
21	POLR2A	chr12:4388672-4391133	PFSK-1	brain:	n/a	n/a
22	POLR2A	chr12:4378383-4393977	GM12878	blood:	n/a	n/a
23	POLR2A	chr12:4388932-4391099	GM12878	blood:	n/a	n/a
24	POLR2A	chr12:4388969-4393842	GM18505	blood:	n/a	n/a
25	POLR2A	chr12:4389367-4391080	K562	blood:	n/a	n/a
26	POLR2A	chr12:4388948-4389720	GM12891	blood:	n/a	n/a
27	POLR2A	chr12:4388589-4388874	GM12878	blood:	n/a	n/a
28	POLR2A	chr12:4388888-4389102	K562	blood:	n/a	n/a
29	POLR2A	chr12:4389424-4389839	GM12878	blood:	n/a	n/a
30	POLR2A	chr12:4388414-4408317	GM12878	blood:	n/a	n/a
31	POLR2A	chr12:4386676-4402492	PFSK-1	brain:	n/a	n/a
32	WRNIP1	chr12:4388645-4389569	GM12878	blood:	n/a	n/a
33	ZC3H11A	chr12:4388919-4388987	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:3967810..3970791-chr12:4389057..4391827,2	MCF-7	breast:

Variant related genes	Relation type
CCND2-AS1	TF binding region
CCND2-AS2	TF binding region

Extended variants
information (count: 37 )
Associated
traits (count: 76 )

Variant overlapped rSNPs/rCNVs (count:37 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs536601421	chr12:4388639-4388640	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
2	rs146765819	chr12:4388662-4388663	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
3	rs372912015	chr12:4388663-4388664	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
4	rs570122412	chr12:4388701-4388702	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
5	rs373965197	chr12:4388714-4388715	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
6	rs537675030	chr12:4388715-4388716	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
7	rs542206444	chr12:4388733-4388734	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
8	rs140375230	chr12:4388744-4388745	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
9	rs577902991	chr12:4388756-4388757	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
10	rs57236600	chr12:4388764-4388765	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
11	rs540146036	chr12:4388785-4388786	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
12	rs187728335	chr12:4388801-4388802	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
13	rs193147781	chr12:4388846-4388847	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
14	rs145648142	chr12:4388855-4388856	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
15	rs560888742	chr12:4388860-4388861	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
16	rs375799911	chr12:4388877-4388878	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
17	rs28714286	chr12:4388889-4388890	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
18	rs185702252	chr12:4388890-4388891	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
19	rs74894572	chr12:4388899-4388900	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
20	rs4372527	chr12:4388914-4388915	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
21	rs545323707	chr12:4388941-4388942	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
22	rs75618424	chr12:4388977-4388978	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
23	rs74645081	chr12:4389034-4389035	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer	TF binding region	2 gene(s)	Overlapped CNVs	n/a
24	rs548110911	chr12:4389076-4389077	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer	TF binding region	2 gene(s)	Overlapped CNVs	n/a
25	rs141836854	chr12:4389144-4389145	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer	TF binding region	2 gene(s)	Overlapped CNVs	n/a
26	rs11063072	chr12:4389158-4389159	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer	TF binding region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs373168899	chr12:4389171-4389172	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer	TF binding region	2 gene(s)	Overlapped CNVs	n/a
28	rs550129530	chr12:4389183-4389184	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer	TF binding region	2 gene(s)	Overlapped CNVs	n/a
29	rs570100616	chr12:4389190-4389191	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer	TF binding region	2 gene(s)	Overlapped CNVs	n/a
30	rs189016964	chr12:4389196-4389197	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer	TF binding region	2 gene(s)	Overlapped CNVs	n/a
31	rs150232091	chr12:4389197-4389198	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer	TF binding region	2 gene(s)	Overlapped CNVs	n/a
32	rs571423161	chr12:4389214-4389215	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS	TF binding region	2 gene(s)	Overlapped CNVs	n/a
33	rs533711519	chr12:4389250-4389251	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs553667340	chr12:4389261-4389262	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs3217813	chr12:4389364-4389365	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs542242388	chr12:4389365-4389366	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs78238815	chr12:4389406-4389407	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:76)

Disease	PMID	Source
Ovarian cancer	20844748	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Breast cancer	17133270	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Medulloblastoma	16968546	CNVD
Ovine squamous-cell carcinoma	17599052	CNVD
Hepatocellular carcinoma	16750200	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
Chronic lymphocytic leukemia	21670202	CNVD
Breast cancer	21364760	CNVD
Acute lymphoblastic leukemia	21248843	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Breast cancer	21858162	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Breast cancer	21785460	CNVD
Myelodysplastic syndrome	21251322	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164919	CNVD
lymphocytic leukemia	21291569	CNVD
Acute myeloid leukemia	20729466	CNVD
Adenocarcinoma	19607727	CNVD
Squamous cell cancer	19607727	CNVD
Epilepsy	21858020	CNVD
Colorectal cancer	19359472	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Breast cancer	21509527	CNVD
Chordoma	18071362	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:151 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4384400-4390600	Weak transcription	Gastric	stomach
2	chr12:4385000-4390000	Transcr. at gene 5' and 3'	Cortex derived primary cultured neurospheres	brain
3	chr12:4385200-4390800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr12:4385200-4390800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
5	chr12:4385200-4391000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
6	chr12:4385400-4388800	Genic enhancers	Primary hematopoietic stem cells	blood
7	chr12:4385400-4400000	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
8	chr12:4385400-4404400	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
9	chr12:4385600-4389400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:4385600-4389600	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
11	chr12:4385600-4390000	Genic enhancers	HSMM	muscle
12	chr12:4385600-4390400	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr12:4385600-4390600	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:4385600-4390800	Genic enhancers	Colonic Mucosa	Colon
15	chr12:4385600-4390800	Genic enhancers	Fetal Lung	lung
16	chr12:4385600-4391000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:4385600-4391400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr12:4385600-4400600	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr12:4385800-4390400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:4385800-4390600	Genic enhancers	Placenta Amnion	Placenta Amnion
21	chr12:4385800-4398400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr12:4386000-4390200	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:4386000-4393600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr12:4386000-4400000	Genic enhancers	Fetal Stomach	stomach
25	chr12:4386000-4404600	Genic enhancers	Primary T cells fromperipheralblood	blood
26	chr12:4386200-4389200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr12:4386200-4389600	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr12:4386200-4389600	Genic enhancers	Duodenum Smooth Muscle	Duodenum
29	chr12:4386200-4390200	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr12:4386200-4390400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr12:4386200-4390800	Enhancers	Skeletal Muscle Female	skeletal muscle
32	chr12:4386200-4393200	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr12:4386200-4403000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr12:4386200-4404200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
35	chr12:4386200-4404800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
36	chr12:4386400-4389000	Genic enhancers	Rectal Smooth Muscle	rectum
37	chr12:4386400-4393800	Transcr. at gene 5' and 3'	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:4386600-4389200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr12:4386600-4389600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:4386600-4389800	Genic enhancers	NHEK	skin
41	chr12:4386600-4390200	Genic enhancers	Colon Smooth Muscle	Colon
42	chr12:4386600-4390600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:4386600-4390800	Genic enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr12:4386600-4393200	Weak transcription	Brain Substantia Nigra	brain
45	chr12:4386600-4393200	Weak transcription	Thymus	Thymus
46	chr12:4386600-4395000	Strong transcription	Primary B cells from peripheral blood	blood
47	chr12:4386600-4400000	Genic enhancers	Fetal Muscle Leg	muscle
48	chr12:4386600-4406800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
49	chr12:4386800-4389000	Genic enhancers	HUES48 Cell Line	embryonic stem cell
50	chr12:4386800-4391800	Genic enhancers	Primary T cells from cord blood	blood

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