Variant report

Variant	esv3340892
Chromosome Location	chr1:209393979-209395377
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:209388184..209391480-chr1:209391851..209395269,3	MCF-7	breast:
2	chr1:209393308..209395102-chr1:209556912..209559448,2	MCF-7	breast:
3	chr1:209383099..209385008-chr1:209391993..209394631,2	MCF-7	breast:
4	chr1:209389552..209391283-chr1:209392821..209394961,2	MCF-7	breast:
5	chr1:209393306..209397796-chr1:209399926..209403415,4	MCF-7	breast:

Extended variants
information (count: 50 )
Associated
traits (count: 90 )

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs530306086	chr1:209393997-209393998	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	n/a	n/a	Overlapped CNVs	n/a
2	rs76781130	chr1:209394012-209394013	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs190418138	chr1:209394036-209394037	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs534088996	chr1:209394066-209394067	Enhancers Flanking Active TSS Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs546296116	chr1:209394271-209394272	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
6	rs571316865	chr1:209394290-209394291	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
7	rs538296692	chr1:209394305-209394306	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
8	rs34937339	chr1:209394317-209394318	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
9	rs201121248	chr1:209394324-209394325	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
10	rs397861135	chr1:209394331-209394332	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
11	rs556901696	chr1:209394338-209394339	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
12	rs12239583	chr1:209394340-209394341	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
13	rs2970562	chr1:209394342-209394343	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs200670382	chr1:209394351-209394352	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
15	rs114653837	chr1:209394381-209394382	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs573076490	chr1:209394407-209394408	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs546398832	chr1:209394428-209394429	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs59200517	chr1:209394429-209394430	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs2996684	chr1:209394431-209394432	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs113556316	chr1:209394433-209394434	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs71157304	chr1:209394449-209394450	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs187626207	chr1:209394496-209394497	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs565273676	chr1:209394525-209394526	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs372267621	chr1:209394550-209394551	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs528822284	chr1:209394552-209394553	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs56898497	chr1:209394573-209394574	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs2996685	chr1:209394575-209394576	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs61470014	chr1:209394581-209394582	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs367720316	chr1:209394583-209394584	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs28372623	chr1:209394585-209394586	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs191966805	chr1:209394597-209394598	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs564691392	chr1:209394598-209394599	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs565607534	chr1:209394599-209394600	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs59953800	chr1:209394612-209394613	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs576628431	chr1:209394653-209394654	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs71157307	chr1:209394654-209394655	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs544108002	chr1:209394711-209394712	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs372078342	chr1:209394712-209394713	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs577250444	chr1:209394716-209394717	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs544305853	chr1:209394744-209394745	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs182635464	chr1:209394831-209394832	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs140014029	chr1:209394895-209394896	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs548483798	chr1:209394970-209394971	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
44	rs560369811	chr1:209395006-209395007	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
45	rs372478597	chr1:209395016-209395017	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
46	rs552728325	chr1:209395104-209395105	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
47	rs556098208	chr1:209395139-209395140	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
48	rs74995062	chr1:209395191-209395192	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs187566147	chr1:209395248-209395249	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs550377624	chr1:209395272-209395273	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:90)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Autism	22495311	CNVD
Liposarcoma	21253554	CNVD
Burkitt''s lymphoma	18698080	CNVD
Melanoma	18172304	CNVD
Rett syndrome	21593744	CNVD
Medulloblastoma	21979893	CNVD
Cancer	20164919	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Non-small cell lung cancer	21044232	CNVD
Cervical cancer	21063398	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	20632083	CNVD
Endometrial cancer	22040021	CNVD
Ewing''s sarcoma	21437220	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Glioblastoma multiforme	19960244	CNVD
Glioblastoma multiforme	21080181	CNVD
Hepatocellular carcinoma	22174799	CNVD
Medulloblastoma	21292688	CNVD
Phyllodes tumor	17334353	CNVD
Breast cancer	21264507	CNVD
Multiple myeloma	21628407	CNVD
Cancer	16751803	CNVD
Prostate cancer	16705090	CNVD
Neuroblastoma	19435921	CNVD
Breast cancer	17850661	CNVD
Breast cancer	16461572	CNVD
Intracranial tumor	16823260	CNVD
Medulloblastoma	18056178	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Primary mediastinal b-cell lymphoma	17728785	CNVD
Colorectal cancer	16272173	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Neuroblastoma	21899760	CNVD
Glioblastoma multiforme	17002787	CNVD
Breast cancer	21858162	CNVD
Non-small cell lung cancer	21385341	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	16608533	CNVD
Ewing''s sarcoma	22429812	CNVD
Acute promyelocytic leukemia	19109227	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Acute myeloid leukemia	21251322	CNVD
Multiple myeloma	17550852	CNVD
Prostate cancer	18632612	CNVD
Acute myeloid leukemia	20729466	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Testicular germ cell tumor	18059402	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Neuroblastoma	18923191	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Breast cancer	21509527	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	21611746	CNVD
Breast cancer	17393978	CNVD
Hepatocellular carcinoma	16750200	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Trisomy 5 syndrome	21098271	CNVD
Urothelial carcinoma	21177765	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Chordoma	18071362	CNVD
Macular degeneration	22558131	CNVD
Alzheimer''s disease	21403675	CNVD
Multiple myeloma	16461302	CNVD
van der Woude syndrome	22470819	CNVD
van der Woude syndrome	20818247	CNVD
T-cell lymphomas	19863542	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Cancer	17060936	CNVD
Atypical hemolytic uremic syndrome	19861685	CNVD
Hepatocellular carcinoma	18803288	CNVD
Urothelial tumor	18831757	CNVD
Lung cancer	18438408	CNVD
Ovarian cancer	21720365	CNVD
Breast cancer	21364760	CNVD
Myelofibrosis	22110671	CNVD
Neuroblastoma	20406844	CNVD
small cell lung cancer	20016488	CNVD

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209391400-209394400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:209392000-209394200	Enhancers	HMEC	breast
3	chr1:209392200-209394000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:209392200-209394400	Enhancers	Fetal Brain Male	brain
5	chr1:209392800-209394200	Enhancers	Fetal Thymus	thymus
6	chr1:209392800-209394400	Flanking Active TSS	Dnd41	blood
7	chr1:209393200-209394000	Enhancers	Primary hematopoietic stem cells	blood
8	chr1:209393200-209394000	Active TSS	Brain Anterior Caudate	brain
9	chr1:209393200-209394000	Active TSS	Brain Hippocampus Middle	brain
10	chr1:209393200-209394000	Active TSS	Brain Substantia Nigra	brain
11	chr1:209393200-209394200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr1:209393200-209394200	Enhancers	Fetal Stomach	stomach
13	chr1:209393200-209394200	Enhancers	Thymus	Thymus
14	chr1:209393400-209394000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:209393400-209394000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:209393400-209394000	Active TSS	Brain Cingulate Gyrus	brain
17	chr1:209393400-209394000	Active TSS	Brain Inferior Temporal Lobe	brain
18	chr1:209393400-209394000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:209393400-209394000	Enhancers	Placenta	Placenta
20	chr1:209393400-209394000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
21	chr1:209393400-209394000	Active TSS	Stomach Smooth Muscle	stomach
22	chr1:209393600-209394000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:209393600-209394000	Enhancers	Placenta Amnion	Placenta Amnion
24	chr1:209393600-209394000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr1:209393600-209394000	Flanking Active TSS	HSMM	muscle
26	chr1:209393600-209394400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr1:209393800-209394000	Active TSS	Muscle Satellite Cultured Cells	--
28	chr1:209393800-209394000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:209393800-209394000	Flanking Active TSS	Brain Angular Gyrus	brain
30	chr1:209393800-209394000	Enhancers	Brain Germinal Matrix	brain
31	chr1:209393800-209394000	Flanking Active TSS	Fetal Lung	lung
32	chr1:209393800-209394000	Active TSS	HSMMtube	muscle
33	chr1:209393800-209394000	Enhancers	NHEK	skin
34	chr1:209393800-209394000	Flanking Bivalent TSS/Enh	Osteobl	bone
35	chr1:209393800-209394200	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr1:209393800-209394400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:209394000-209394200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr1:209394000-209394200	Flanking Active TSS	Brain Cingulate Gyrus	brain
39	chr1:209394000-209394200	Enhancers	Brain Hippocampus Middle	brain
40	chr1:209394000-209394200	Enhancers	Brain Substantia Nigra	brain
41	chr1:209394000-209394600	Weak transcription	Fetal Brain Female	brain
42	chr1:209394000-209395800	Enhancers	Fetal Lung	lung
43	chr1:209394000-209397600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr1:209394000-209397600	Weak transcription	NHEK	skin
45	chr1:209394400-209396000	Weak transcription	Fetal Brain Male	brain
46	chr1:209394400-209396600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr1:209394400-209396800	Enhancers	Dnd41	blood
48	chr1:209395200-209395600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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