Variant report

Variant	esv3333662
Chromosome Location	chr12:39075385-39079683
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	chr12:39076476-39076890	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr12:39075635-39075643	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr12:39076526-39076871	H1-neurons	neurons:	n/a	n/a
4	STAT3	chr12:39077115-39077472	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:39078731..39079461-chr2:68493058..68493608,2	MCF-7	breast:

Variant related genes	Relation type
CPNE8	TF binding region

Extended variants
information (count: 164 )
Associated
traits (count: 56 )

Variant overlapped rSNPs/rCNVs (count:164 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs7957523	chr12:39075387-39075388	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs148189014	chr12:39075431-39075432	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs571475611	chr12:39075455-39075456	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs556538833	chr12:39075458-39075459	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs553931548	chr12:39075494-39075495	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs140610392	chr12:39075533-39075534	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs577898377	chr12:39075539-39075540	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs569559013	chr12:39075544-39075545	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs574089131	chr12:39075545-39075546	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs182338797	chr12:39075571-39075572	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs556642587	chr12:39075615-39075616	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs186465939	chr12:39075634-39075635	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs191218168	chr12:39075744-39075745	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs183129954	chr12:39075784-39075785	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs77681917	chr12:39075801-39075802	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs76309916	chr12:39075850-39075851	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs560778233	chr12:39075851-39075852	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs7294397	chr12:39075926-39075927	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs140162459	chr12:39075937-39075938	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs560936715	chr12:39075968-39075969	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs188462173	chr12:39075969-39075970	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs375367854	chr12:39075974-39075975	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs531248695	chr12:39076022-39076023	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs553487458	chr12:39076038-39076039	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs139195859	chr12:39076040-39076041	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs543690954	chr12:39076052-39076053	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs562970385	chr12:39076086-39076087	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs571161312	chr12:39076111-39076112	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs565262129	chr12:39076130-39076131	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs551632907	chr12:39076131-39076132	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs571614115	chr12:39076139-39076140	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs533619341	chr12:39076140-39076141	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs193180122	chr12:39076148-39076149	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs567652315	chr12:39076228-39076229	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs185099400	chr12:39076246-39076247	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs556581458	chr12:39076304-39076305	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs188047502	chr12:39076309-39076310	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs538467697	chr12:39076324-39076325	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs192514402	chr12:39076338-39076339	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs80080423	chr12:39076344-39076345	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs540856149	chr12:39076369-39076370	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs183792576	chr12:39076395-39076396	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs188136986	chr12:39076413-39076414	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs543081188	chr12:39076448-39076449	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs74767804	chr12:39076454-39076455	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs570025627	chr12:39076459-39076460	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs112391846	chr12:39076466-39076467	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs73269146	chr12:39076525-39076526	Weak transcription Strong transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs565229730	chr12:39076548-39076549	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
50	rs528035824	chr12:39076600-39076601	Weak transcription Strong transcription ZNF genes & repeats	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:56)

Disease	PMID	Source
Chronic lymphocytic leukemia	21546498	CNVD
Seminomas	18059402	CNVD
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
Medulloblastoma	21979893	CNVD
Malaria	21533027	CNVD
Chronic lymphocytic leukemia	22228453	CNVD
Basal cell lymphoma	17053054	CNVD
Chronic lymphocytic leukemia	21670202	CNVD
Ewing''s sarcoma	17952124	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD
Neurodevelopmental disorder	22521361	CNVD
Breast cancer	21509527	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
T-cell prolymphocytic leukemia	17713554	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
Breast cancer	21364760	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	17603634	CNVD
Cancer	21183584	CNVD
Hirschsprung''s Disease	21712996	CNVD
Lissencephaly	21572526	CNVD
Lung cancer	18438408	CNVD
Acute myeloid leukemia	21251322	CNVD
small cell lung cancer	20016488	CNVD
Autism	20858243	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Breast cancer	19602461	CNVD
Breast cancer	17899364	CNVD
Cancer	20164920	CNVD

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39046000-39085400	Weak transcription	Aorta	Aorta
2	chr12:39046800-39080400	Weak transcription	Spleen	Spleen
3	chr12:39051600-39080400	Weak transcription	Lung	lung
4	chr12:39051600-39080800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr12:39055800-39100800	Weak transcription	NHEK	skin
6	chr12:39056000-39080200	Weak transcription	Ovary	ovary
7	chr12:39056000-39092200	Weak transcription	Colon Smooth Muscle	Colon
8	chr12:39056000-39114800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr12:39056000-39168600	Weak transcription	Hela-S3	cervix
10	chr12:39056200-39078400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:39056200-39078400	Weak transcription	Adipose Nuclei	Adipose
12	chr12:39056200-39079000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr12:39056200-39080200	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr12:39056800-39083000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr12:39057400-39083000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:39058000-39077600	Weak transcription	HMEC	breast
17	chr12:39058200-39079000	Weak transcription	GM12878-XiMat	blood
18	chr12:39061200-39080400	Weak transcription	A549	lung
19	chr12:39061600-39080200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:39063800-39080400	Weak transcription	Fetal Intestine Large	intestine
21	chr12:39063800-39082600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr12:39066200-39114400	Weak transcription	Pancreas	Pancrea
23	chr12:39066600-39083400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:39067000-39076600	Weak transcription	Duodenum Mucosa	Duodenum
25	chr12:39068600-39076400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr12:39069000-39079000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr12:39069000-39080400	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr12:39069400-39114600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr12:39069800-39076400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:39069800-39078600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:39069800-39083000	Weak transcription	Left Ventricle	heart
32	chr12:39071400-39077800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr12:39071600-39079200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:39071800-39075400	Weak transcription	Liver	Liver
35	chr12:39071800-39078000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr12:39071800-39078400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr12:39072200-39075800	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr12:39074400-39098800	Weak transcription	Right Ventricle	heart
39	chr12:39075200-39080000	Weak transcription	Fetal Intestine Small	intestine
40	chr12:39075400-39080400	Strong transcription	Liver	Liver
41	chr12:39075800-39081200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr12:39076400-39077000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr12:39076400-39077600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:39076600-39076800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
45	chr12:39077000-39079800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr12:39077600-39078200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr12:39077800-39080800	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr12:39078000-39079200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr12:39078200-39080400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr12:39078400-39079400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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