Variant report

Variant	esv3471827
Chromosome Location	chr6:53928362-53935164
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	chr6:53857425..53857943-chr6:53933277..53933955,2	MCF-7	breast:

Extended variants
information (count: 177 )
Associated
traits (count: 76 )

Variant overlapped rSNPs/rCNVs (count:177 , 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	rs534960071	chr6:53928393-53928394	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
2	rs565599962	chr6:53928397-53928398	Flanking Active TSS Enhancers Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
3	rs183032949	chr6:53928456-53928457	Flanking Active TSS Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs187528640	chr6:53928473-53928474	Flanking Active TSS Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs375336602	chr6:53928492-53928493	Flanking Active TSS Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs34601337	chr6:53928493-53928494	Flanking Active TSS Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs66621861	chr6:53928494-53928495	Flanking Active TSS Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs368630379	chr6:53928519-53928520	Flanking Active TSS Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs71713622	chr6:53928520-53928521	Flanking Active TSS Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs73741422	chr6:53928521-53928522	Flanking Active TSS Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs550903884	chr6:53928527-53928528	Flanking Active TSS Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs34102850	chr6:53928529-53928530	Flanking Active TSS Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs567889736	chr6:53928555-53928556	Flanking Active TSS Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs193215132	chr6:53928612-53928613	Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs537627177	chr6:53928628-53928629	Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs546702626	chr6:53928631-53928632	Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs566114760	chr6:53928638-53928639	Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs538261462	chr6:53928704-53928705	Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs376261477	chr6:53928710-53928711	Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs557728409	chr6:53928734-53928735	Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs568812908	chr6:53928793-53928794	Active TSS Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs183956343	chr6:53928836-53928837	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs147486679	chr6:53928902-53928903	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs574606217	chr6:53928925-53928926	Weak transcription Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs542740869	chr6:53929105-53929106	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
26	rs376396929	chr6:53929147-53929148	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
27	rs992155	chr6:53929225-53929226	Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
28	rs13191653	chr6:53929284-53929285	Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs545424904	chr6:53929300-53929301	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
30	rs376303712	chr6:53929320-53929321	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
31	rs531102291	chr6:53929331-53929332	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
32	rs73741423	chr6:53929342-53929343	Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
33	rs561301825	chr6:53929406-53929407	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
34	rs73741424	chr6:53929470-53929471	Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs12523824	chr6:53929484-53929485	Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs566249227	chr6:53929545-53929546	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
37	rs115464184	chr6:53929579-53929580	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
38	rs115586798	chr6:53929591-53929592	Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
39	rs374686716	chr6:53929797-53929798	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs537730382	chr6:53929948-53929949	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs192244123	chr6:53930042-53930043	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs183658844	chr6:53930043-53930044	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs149989712	chr6:53930046-53930047	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs576551136	chr6:53930051-53930052	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs188373041	chr6:53930070-53930071	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs191874750	chr6:53930093-53930094	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs558990341	chr6:53930205-53930206	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs116323549	chr6:53930272-53930273	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs79023834	chr6:53930288-53930289	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
50	rs532034500	chr6:53930293-53930294	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:76)

Disease	PMID	Source
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Leukemia	21518781	CNVD
Cancer	21637783	CNVD
Facial dysmorphism	22105932	CNVD
Medulloblastoma	21979893	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Endometrial cancer	22040021	CNVD
Acute myeloid leukemia	16864856	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Bladder cancer	19088036	CNVD
Wilms tumour	21544195	CNVD
Uveal melanoma	21693616	CNVD
Biliary cancer	19435499	CNVD
Malaria	21533027	CNVD
Retinoblastoma	19183342	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	21858162	CNVD
Ewing''s sarcoma	17952124	CNVD
Autism	21448237	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Autism	22495311	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Urothelial carcinoma	18382360	CNVD
Cancer	21183584	CNVD
Hodgkin''s lymphoma	17606441	CNVD
small cell lung cancer	20016488	CNVD
Gastric cancer	17908304	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Neuroblastoma	16790693	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Osteosarcoma	16790693	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Lung cancer	18438408	CNVD
Neuroblastoma	18923191	CNVD
Breast cancer	17603634	CNVD
Neurocytoma	17123091	CNVD
Systemic lupus erythematosus	17503323	CNVD
Gastrointestinal stromal cancer	20818650	CNVD
Breast cancer	16608533	CNVD
Melanoma	18172304	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Neuroblastoma	19686582	CNVD
Neuroblastoma	17289879	CNVD
Breast cancer	17899364	CNVD
Breast cancer	17133270	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Chronic lymphocytic leukemia	20421269	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma multiforme	22286061	CNVD
Colorectal cancer	16912164	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	21364760	CNVD

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53919600-53928400	Weak transcription	Duodenum Mucosa	Duodenum
2	chr6:53919600-53928400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr6:53921600-53936600	Weak transcription	Right Ventricle	heart
4	chr6:53924000-53935200	Weak transcription	Psoas Muscle	Psoas
5	chr6:53925400-53928400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:53925400-53928400	Weak transcription	Fetal Lung	lung
7	chr6:53925400-53928400	Weak transcription	Right Atrium	heart
8	chr6:53926400-53934800	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr6:53927200-53934800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr6:53927800-53929000	Active TSS	Liver	Liver
11	chr6:53927800-53930000	Weak transcription	Stomach Mucosa	stomach
12	chr6:53928000-53928400	Enhancers	Adipose Nuclei	Adipose
13	chr6:53928000-53928600	Enhancers	Fetal Heart	heart
14	chr6:53928000-53939000	Weak transcription	Left Ventricle	heart
15	chr6:53928200-53928400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:53928200-53928400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:53928200-53928400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr6:53928200-53928400	Flanking Active TSS	Osteobl	bone
19	chr6:53928200-53928600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:53928200-53928600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:53928200-53928600	Active TSS	Colon Smooth Muscle	Colon
22	chr6:53928200-53928600	Active TSS	Rectal Mucosa Donor 31	rectum
23	chr6:53928200-53928800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr6:53928200-53928800	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr6:53928200-53928800	Active TSS	Stomach Smooth Muscle	stomach
26	chr6:53928400-53928600	Flanking Active TSS	Fetal Lung	lung
27	chr6:53928400-53928800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr6:53928400-53928800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr6:53928400-53928800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:53928400-53928800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:53928400-53928800	Active TSS	Adipose Nuclei	Adipose
32	chr6:53928400-53928800	Active TSS	Aorta	Aorta
33	chr6:53928400-53928800	Active TSS	Duodenum Mucosa	Duodenum
34	chr6:53928400-53928800	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr6:53928400-53928800	Active TSS	Fetal Muscle Leg	muscle
36	chr6:53928400-53928800	Active TSS	Ovary	ovary
37	chr6:53928400-53928800	Enhancers	Rectal Mucosa Donor 29	rectum
38	chr6:53928400-53928800	Active TSS	Right Atrium	heart
39	chr6:53928400-53928800	Active TSS	NHEK	skin
40	chr6:53928400-53928800	Active TSS	Osteobl	bone
41	chr6:53928600-53928800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:53928600-53928800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:53928600-53928800	Active TSS	Fetal Lung	lung
44	chr6:53928600-53934600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr6:53928600-53939000	Weak transcription	Fetal Heart	heart
46	chr6:53928800-53934600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:53928800-53934600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr6:53928800-53934600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr6:53928800-53934800	Weak transcription	Pancreatic Islets	Pancreatic Islet
50	chr6:53928800-53934800	Weak transcription	Fetal Lung	lung

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