Variant report

Variant	esv3361395
Chromosome Location	chr12:41223760-41226008
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:41222882..41225557-chr7:143112465..143114503,2	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 59 )

Variant overlapped rSNPs/rCNVs (count:72 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs145571228	chr12:41223775-41223776	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
2	rs573890074	chr12:41223791-41223792	Enhancers Weak transcription Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs556617989	chr12:41223880-41223881	Enhancers Active TSS Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
4	rs190818097	chr12:41223984-41223985	Enhancers Active TSS Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
5	rs181727382	chr12:41223996-41223997	Enhancers Active TSS Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs10735960	chr12:41223999-41224000	Enhancers Active TSS Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs186353468	chr12:41224016-41224017	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs148891269	chr12:41224078-41224079	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs10735961	chr12:41224130-41224131	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs542689445	chr12:41224169-41224170	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs561314317	chr12:41224184-41224185	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs55996026	chr12:41224223-41224224	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs528838895	chr12:41224227-41224228	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs202183801	chr12:41224229-41224230	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs571926703	chr12:41224255-41224256	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs573146963	chr12:41224284-41224285	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs191028389	chr12:41224483-41224484	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs182815055	chr12:41224505-41224506	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs7961659	chr12:41224534-41224535	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs537137921	chr12:41224539-41224540	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs371419139	chr12:41224554-41224555	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs188565625	chr12:41224557-41224558	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs200211189	chr12:41224590-41224591	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs2772477	chr12:41224595-41224596	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs58265279	chr12:41224632-41224633	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs56027388	chr12:41224634-41224635	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs10592423	chr12:41224636-41224637	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs72055130	chr12:41224729-41224730	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs199816332	chr12:41224731-41224732	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs11178653	chr12:41224732-41224733	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs372935965	chr12:41224739-41224740	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs376423420	chr12:41224746-41224747	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs200206905	chr12:41224748-41224749	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs10592424	chr12:41224754-41224755	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs534288235	chr12:41224762-41224763	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs12310400	chr12:41224764-41224765	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs369185829	chr12:41224781-41224782	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs552859097	chr12:41224783-41224784	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs534163976	chr12:41224814-41224815	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs12309009	chr12:41224816-41224817	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs538470610	chr12:41224837-41224838	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs557102647	chr12:41224845-41224846	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs575676387	chr12:41224898-41224899	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs543104024	chr12:41224926-41224927	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs561163404	chr12:41225060-41225061	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs573281471	chr12:41225075-41225076	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs540584752	chr12:41225173-41225174	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs192415257	chr12:41225174-41225175	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs532823072	chr12:41225180-41225181	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs143615847	chr12:41225201-41225202	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:59)

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
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
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
Colorectal cancer	16272173	CNVD
Breast cancer	21364760	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41221400-41224000	Active TSS	Brain Cingulate Gyrus	brain
2	chr12:41221400-41224000	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr12:41221400-41224000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:41221600-41224000	Enhancers	HMEC	breast
5	chr12:41221800-41224600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:41222400-41224000	Active TSS	Brain Hippocampus Middle	brain
7	chr12:41222400-41224000	Active TSS	Fetal Brain Female	brain
8	chr12:41222600-41223800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr12:41222600-41224200	Enhancers	Pancreatic Islets	Pancreatic Islet
10	chr12:41222800-41223800	Weak transcription	Brain Anterior Caudate	brain
11	chr12:41222800-41228000	Weak transcription	Fetal Brain Male	brain
12	chr12:41223200-41223800	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr12:41223200-41224200	Enhancers	NHEK	skin
14	chr12:41223400-41224000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr12:41223400-41224000	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr12:41223400-41224000	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr12:41223400-41224000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:41223400-41224000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:41223400-41224200	Flanking Active TSS	A549	lung
20	chr12:41223600-41224000	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr12:41223600-41224000	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr12:41223800-41224000	Enhancers	Brain Anterior Caudate	brain
23	chr12:41223800-41224200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:41224000-41224200	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr12:41224000-41225200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr12:41224000-41225200	Weak transcription	HMEC	breast
27	chr12:41224000-41225600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr12:41224000-41226600	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr12:41224000-41228200	Weak transcription	Fetal Brain Female	brain
30	chr12:41224200-41225200	Weak transcription	A549	lung
31	chr12:41224200-41225200	Weak transcription	NHEK	skin
32	chr12:41224600-41225000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr12:41225000-41226800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr12:41225200-41225800	Enhancers	A549	lung
35	chr12:41225200-41226800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:41225200-41226800	Enhancers	HMEC	breast
37	chr12:41225200-41226800	Enhancers	NHEK	skin
38	chr12:41225600-41226800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr12:41225800-41227200	Weak transcription	A549	lung

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