Variant report

Variant	esv3489358
Chromosome Location	chr6:55907556-55912831
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	chr6:55904181..55905774-chr6:55908809..55911144,2	MCF-7	breast:

Extended variants
information (count: 174 )
Associated
traits (count: 80 )

Variant overlapped rSNPs/rCNVs (count:174 , 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	rs563773639	chr6:55907566-55907567	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs529306672	chr6:55907623-55907624	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs543002875	chr6:55907686-55907687	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs559772993	chr6:55907736-55907737	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs528424052	chr6:55907779-55907780	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs144668502	chr6:55907834-55907835	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs7756577	chr6:55907835-55907836	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs138257730	chr6:55907844-55907845	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs550410104	chr6:55907882-55907883	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs545212648	chr6:55907975-55907976	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs556013403	chr6:55908038-55908039	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs192558664	chr6:55908066-55908067	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs565109840	chr6:55908128-55908129	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs551716192	chr6:55908162-55908163	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs566106790	chr6:55908167-55908168	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs535016003	chr6:55908183-55908184	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs184818440	chr6:55908201-55908202	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs578124937	chr6:55908316-55908317	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs188964080	chr6:55908350-55908351	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs557182270	chr6:55908453-55908454	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs192509551	chr6:55908460-55908461	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs543139495	chr6:55908465-55908466	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs564632399	chr6:55908473-55908474	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs115885759	chr6:55908493-55908494	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs528460792	chr6:55908512-55908513	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs368727526	chr6:55908529-55908530	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs532262610	chr6:55908549-55908550	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs565141818	chr6:55908674-55908675	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs144118037	chr6:55908695-55908696	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs9475543	chr6:55908707-55908708	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs567124369	chr6:55908729-55908730	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs529765238	chr6:55908743-55908744	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs547315337	chr6:55908763-55908764	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs147312787	chr6:55908786-55908787	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs566145076	chr6:55908849-55908850	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs538216509	chr6:55908901-55908902	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs140932948	chr6:55908940-55908941	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs184283989	chr6:55908981-55908982	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs116290977	chr6:55909022-55909023	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs555709506	chr6:55909150-55909151	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs557578683	chr6:55909260-55909261	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs62406121	chr6:55909270-55909271	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs543159186	chr6:55909290-55909291	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs553477328	chr6:55909334-55909335	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs189585734	chr6:55909344-55909345	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs545347016	chr6:55909369-55909370	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs142400276	chr6:55909373-55909374	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs565127154	chr6:55909381-55909382	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs558009591	chr6:55909406-55909407	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs575544455	chr6:55909448-55909449	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:80)

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
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
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
Hodgkin''s lymphoma	17606441	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
Myelofibrosis	22110671	CNVD
Glioblastoma multiforme	22286061	CNVD
Colorectal cancer	16912164	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	21364760	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
Breast cancer	21509527	CNVD
lymphocytic leukemia	21291569	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55899200-55920400	Weak transcription	Fetal Muscle Leg	muscle
2	chr6:55905800-55911600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:55906200-55908000	Weak transcription	HSMM	muscle
4	chr6:55906200-55908400	Weak transcription	NHDF-Ad	bronchial
5	chr6:55906200-55910800	Weak transcription	HSMMtube	muscle
6	chr6:55906400-55907800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr6:55906400-55907800	Weak transcription	Osteobl	bone
8	chr6:55907400-55907600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr6:55907400-55908200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:55907600-55907800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:55907800-55908000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:55907800-55908000	Enhancers	Osteobl	bone
13	chr6:55907800-55909200	Enhancers	Muscle Satellite Cultured Cells	--
14	chr6:55907800-55909200	Enhancers	HUVEC	blood vessel
15	chr6:55908000-55908200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:55908000-55908400	Weak transcription	Osteobl	bone
17	chr6:55908000-55909400	Enhancers	HSMM	muscle
18	chr6:55908200-55909000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr6:55908200-55910400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:55908400-55908600	Enhancers	NHDF-Ad	bronchial
21	chr6:55908400-55908600	Enhancers	Osteobl	bone
22	chr6:55908600-55910800	Weak transcription	Osteobl	bone
23	chr6:55909000-55910600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:55909200-55910600	Weak transcription	HUVEC	blood vessel
25	chr6:55909200-55910800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr6:55909400-55910800	Weak transcription	HSMM	muscle
27	chr6:55910400-55910800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:55910600-55911200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:55910600-55913800	Enhancers	HUVEC	blood vessel
30	chr6:55910600-55915600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:55910600-55915800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr6:55910800-55911000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:55910800-55911000	Enhancers	HSMMtube	muscle
34	chr6:55910800-55911200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
35	chr6:55910800-55912000	Enhancers	HSMM	muscle
36	chr6:55910800-55914200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:55910800-55916000	Enhancers	Osteobl	bone
38	chr6:55910800-55916400	Enhancers	Muscle Satellite Cultured Cells	--
39	chr6:55911000-55911200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
40	chr6:55911000-55912000	Enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr6:55911000-55912200	Enhancers	Primary hematopoietic stem cells	blood
42	chr6:55911000-55912400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr6:55911200-55911400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr6:55911200-55911400	Enhancers	Monocytes-CD14+_RO01746	blood
45	chr6:55911200-55911600	Enhancers	NH-A	brain
46	chr6:55911200-55912000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr6:55911200-55912000	Enhancers	HMEC	breast
48	chr6:55911200-55912200	Enhancers	Primary monocytes fromperipheralblood	blood
49	chr6:55911400-55911800	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr6:55911400-55911800	Enhancers	Left Ventricle	heart

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