Variant report

Variant	esv3496696
Chromosome Location	chr1:228254279-228260727
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:228186754..228188818-chr1:228253056..228255508,2	MCF-7	breast:
2	chr1:228248925..228252171-chr1:228258918..228261969,3	MCF-7	breast:
3	chr1:228259486..228261831-chr1:228263458..228267215,4	MCF-7	breast:
4	chr1:228249900..228252116-chr1:228255479..228257281,2	MCF-7	breast:
5	chr1:228191984..228194843-chr1:228260469..228263373,2	MCF-7	breast:
6	chr1:228196561..228199539-chr1:228260175..228262293,2	MCF-7	breast:
7	chr1:228256397..228258359-chr1:228260087..228261703,2	MCF-7	breast:
8	chr1:228249620..228252604-chr1:228254168..228256020,2	MCF-7	breast:
9	chr1:228191350..228193786-chr1:228257693..228259549,2	MCF-7	breast:
10	chr1:228252404..228256168-chr1:228256803..228260253,5	MCF-7	breast:
11	chr1:228187251..228191319-chr1:228259829..228263819,5	MCF-7	breast:
12	chr1:228252404..228256168-chr1:228256803..228260253,5	MCF-7	breast:
13	chr1:228186931..228189875-chr1:228260382..228263090,3	MCF-7	breast:
14	chr1:228245943..228247915-chr1:228251913..228254649,3	K562	blood:
15	chr1:228252333..228254896-chr1:228269798..228271614,2	MCF-7	breast:
16	chr1:228257466..228261450-chr1:228360954..228363878,3	K562	blood:
17	chr1:228256397..228258359-chr1:228260087..228261703,2	MCF-7	breast:
18	chr1:228230050..228232873-chr1:228260583..228263014,2	MCF-7	breast:
19	chr1:228255167..228256688-chr5:676745..679087,2	K562	blood:
20	chr1:228193335..228195504-chr1:228260630..228262645,2	MCF-7	breast:
21	chr1:228230109..228232010-chr1:228259554..228261382,2	MCF-7	breast:
22	chr1:228246811..228249127-chr1:228257869..228259965,2	MCF-7	breast:
23	chr1:228189312..228191341-chr1:228252791..228255165,2	MCF-7	breast:
24	chr1:228251281..228254071-chr1:228258113..228259786,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000154342	chromatin interactions
ENSG00000143761	chromatin interactions
ENSG00000181873	chromatin interactions

Extended variants
information (count: 242 )
Associated
traits (count: 91 )

Variant overlapped rSNPs/rCNVs (count:242 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs539535380	chr1:228254399-228254400	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs150333362	chr1:228254456-228254457	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs531409509	chr1:228254457-228254458	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs549616540	chr1:228254459-228254460	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs561506261	chr1:228254462-228254463	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs58793961	chr1:228254475-228254476	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs557776042	chr1:228254476-228254477	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs370046013	chr1:228254486-228254487	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs566531215	chr1:228254509-228254510	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs141222143	chr1:228254529-228254530	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs555648399	chr1:228254637-228254638	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs562206604	chr1:228254644-228254645	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs145363132	chr1:228254647-228254648	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs74143667	chr1:228254651-228254652	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs556379538	chr1:228254716-228254717	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs529331329	chr1:228254735-228254736	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs142354222	chr1:228254736-228254737	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs560243882	chr1:228254746-228254747	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs12161517	chr1:228254753-228254754	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs542225136	chr1:228254773-228254774	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs562428043	chr1:228254810-228254811	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs529544103	chr1:228254817-228254818	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs550802155	chr1:228254918-228254919	Bivalent Enhancer Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs78627368	chr1:228254934-228254935	Bivalent Enhancer Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs369277211	chr1:228254935-228254936	Bivalent Enhancer Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs533303156	chr1:228254943-228254944	Bivalent Enhancer Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs376212746	chr1:228254960-228254961	Bivalent Enhancer Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs376820501	chr1:228254972-228254973	Bivalent Enhancer Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs537675997	chr1:228254979-228254980	Bivalent Enhancer Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs551466256	chr1:228254989-228254990	Bivalent Enhancer Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs145925726	chr1:228255019-228255020	Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs139656496	chr1:228255034-228255035	Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs555451995	chr1:228255039-228255040	Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs73092912	chr1:228255063-228255064	Bivalent Enhancer Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs537742633	chr1:228255080-228255081	Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs556446711	chr1:228255159-228255160	Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs577918826	chr1:228255176-228255177	Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs538797797	chr1:228255238-228255239	Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs185018056	chr1:228255269-228255270	Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs144564170	chr1:228255271-228255272	Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs148451965	chr1:228255325-228255326	Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs560711504	chr1:228255341-228255342	Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs371249076	chr1:228255356-228255357	Bivalent Enhancer Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs544506262	chr1:228255428-228255429	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs10916263	chr1:228255433-228255434	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs113062093	chr1:228255504-228255505	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs533361433	chr1:228255554-228255555	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs145202405	chr1:228255567-228255568	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs375727594	chr1:228255576-228255577	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs375609730	chr1:228255610-228255611	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:91)

Disease	PMID	Source
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Autism	22495311	CNVD
Melanoma	18172304	CNVD
Rett syndrome	21593744	CNVD
Medulloblastoma	21979893	CNVD
Cancer	20164919	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
Liposarcoma	21253554	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
Breast cancer	17603634	CNVD
Neuroblastoma	21899760	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
Urothelial carcinoma	21177765	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Chordoma	18071362	CNVD
T-cell lymphomas	19863542	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Hepatocellular carcinoma	18803288	CNVD
Urothelial tumor	18831757	CNVD
Lung cancer	18438408	CNVD
Medulloblastoma	16783165	CNVD
Basal cell lymphoma	17170743	CNVD
Mental retardation	19951919	CNVD
Non-syndromic sensorineural hearing loss	17873649	CNVD
Basal cell lymphoma	17053054	CNVD
Autism	14699429	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Fumarase deficiency	21572526	CNVD
Autism	17483303	CNVD
Kartagener syndrome	16639409	CNVD
Congenital abnormalities	21549014	CNVD
Developmental delay	21549014	CNVD
Mental retardation	21549014	CNVD
small cell lung cancer	20016488	CNVD
Glioblastoma multiforme	21138945	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Cancer	20164920	CNVD
Cancer	17060936	CNVD
Myelofibrosis	22110671	CNVD
abnormal development	18461090	CNVD
Breast cancer	21364760	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228248200-228269000	Weak transcription	Right Atrium	heart
2	chr1:228254000-228254600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:228254000-228255000	Enhancers	Placenta	Placenta
4	chr1:228254000-228255000	Bivalent Enhancer	Fetal Stomach	stomach
5	chr1:228254400-228254600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr1:228254600-228254800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
7	chr1:228254600-228254800	Bivalent Enhancer	Stomach Mucosa	stomach
8	chr1:228254600-228255400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr1:228255200-228255400	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:228255200-228255400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr1:228256400-228256600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:228256400-228257000	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:228258400-228258600	Bivalent Enhancer	Brain Germinal Matrix	brain
14	chr1:228258400-228258600	Enhancers	Esophagus	oesophagus
15	chr1:228258600-228269000	Weak transcription	Esophagus	oesophagus
16	chr1:228259600-228262000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr1:228260000-228260200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr1:228260000-228260200	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr1:228260000-228260200	Enhancers	Spleen	Spleen
20	chr1:228260000-228260800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:228260200-228260600	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr1:228260200-228261800	Weak transcription	Spleen	Spleen
23	chr1:228260200-228268000	Weak transcription	Gastric	stomach
24	chr1:228260200-228269000	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:228260400-228260600	Enhancers	Liver	Liver
26	chr1:228260400-228261200	Enhancers	Ovary	ovary
27	chr1:228260600-228261000	Enhancers	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links