Variant report

Variant	esv3459572
Chromosome Location	chr2:54513069-54517863
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54501772..54502741-chr2:54515554..54516142,2	MCF-7	breast:
2	chr2:54516670..54519099-chr2:54522119..54523673,2	MCF-7	breast:
3	chr2:54511470..54513165-chr2:54513322..54515700,2	K562	blood:
4	chr2:54511470..54513165-chr2:54513322..54515700,2	K562	blood:

Extended variants
information (count: 186 )
Associated
traits (count: 62 )

Variant overlapped rSNPs/rCNVs (count:186 , 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	rs1682102	chr2:54513079-54513080	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs577768188	chr2:54513097-54513098	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs569864560	chr2:54513132-54513133	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs538791816	chr2:54513144-54513145	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs540446918	chr2:54513161-54513162	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs76257345	chr2:54513164-54513165	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs573781192	chr2:54513169-54513170	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs543136690	chr2:54513185-54513186	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs562738121	chr2:54513191-54513192	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs531773149	chr2:54513197-54513198	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs544140163	chr2:54513204-54513205	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs563958925	chr2:54513215-54513216	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs6723759	chr2:54513275-54513276	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
14	rs533135461	chr2:54513279-54513280	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs546835775	chr2:54513291-54513292	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs566699225	chr2:54513349-54513350	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs528975277	chr2:54513380-54513381	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs549100555	chr2:54513400-54513401	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs568717467	chr2:54513405-54513406	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs529112189	chr2:54513417-54513418	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs187858218	chr2:54513454-54513455	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs548868297	chr2:54513455-54513456	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs558001083	chr2:54513458-54513459	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs150214642	chr2:54513497-54513498	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs138768236	chr2:54513503-54513504	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs566007587	chr2:54513522-54513523	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs553926384	chr2:54513538-54513539	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs149382742	chr2:54513598-54513599	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs79963690	chr2:54513602-54513603	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs191052015	chr2:54513611-54513612	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs535043285	chr2:54513626-54513627	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs372384859	chr2:54513654-54513655	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs545409156	chr2:54513668-54513669	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs139881539	chr2:54513680-54513681	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs373430999	chr2:54513709-54513710	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs554647011	chr2:54513723-54513724	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs560376592	chr2:54513740-54513741	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs529092896	chr2:54513741-54513742	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs843726	chr2:54513742-54513743	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
40	rs182401240	chr2:54513764-54513765	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs186629047	chr2:54513772-54513773	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs531173289	chr2:54513800-54513801	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs192696777	chr2:54513839-54513840	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs570939072	chr2:54513864-54513865	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs537342110	chr2:54513881-54513882	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs184626219	chr2:54513951-54513952	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs547725833	chr2:54513993-54513994	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs144084345	chr2:54514079-54514080	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs187490134	chr2:54514124-54514125	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs113916145	chr2:54514139-54514140	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:62)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Williams Syndrome	20824207	CNVD
Breast cancer	16272173	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Lung adenocarcinoma	17086460	CNVD
Retinoblastoma	22278416	CNVD
Cancer	21183584	CNVD
Breast cancer	16397240	CNVD
Lung cancer	17086460	CNVD
Chronic lymphocytic leukemia	17053054	CNVD
Hereditary non-polyposis colorectal cancer	19566914	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Developmental delay	21147756	CNVD

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54449800-54535200	Weak transcription	Primary T cells from cord blood	blood
2	chr2:54483400-54521200	Weak transcription	Pancreas	Pancrea
3	chr2:54488200-54514600	Weak transcription	Aorta	Aorta
4	chr2:54500200-54517800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr2:54501600-54537600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:54502600-54514600	Weak transcription	HSMMtube	muscle
7	chr2:54506800-54514600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr2:54507600-54514800	Weak transcription	Brain Angular Gyrus	brain
9	chr2:54510400-54514600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr2:54511600-54514200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:54512600-54513600	Enhancers	Brain Substantia Nigra	brain
12	chr2:54513000-54516400	Weak transcription	Primary B cells from cord blood	blood
13	chr2:54513200-54513400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:54513200-54513600	Enhancers	HepG2	liver
15	chr2:54513400-54514400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:54513600-54514600	Weak transcription	Brain Substantia Nigra	brain
17	chr2:54513600-54515800	Weak transcription	HepG2	liver
18	chr2:54514200-54515000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:54514200-54515200	Enhancers	Adipose Nuclei	Adipose
20	chr2:54514200-54515200	Enhancers	Psoas Muscle	Psoas
21	chr2:54514200-54516000	Enhancers	Fetal Muscle Leg	muscle
22	chr2:54514200-54516000	Enhancers	Rectal Smooth Muscle	rectum
23	chr2:54514200-54516000	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr2:54514400-54515400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:54514600-54514800	Enhancers	Aorta	Aorta
26	chr2:54514600-54515000	Enhancers	Placenta Amnion	Placenta Amnion
27	chr2:54514600-54515200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr2:54514600-54515200	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr2:54514600-54515200	Enhancers	Brain Substantia Nigra	brain
30	chr2:54514600-54515200	Enhancers	Left Ventricle	heart
31	chr2:54514600-54515200	Enhancers	Right Atrium	heart
32	chr2:54514600-54515400	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr2:54514600-54515400	Enhancers	HSMMtube	muscle
34	chr2:54514800-54515200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
35	chr2:54514800-54515200	Enhancers	Brain Angular Gyrus	brain
36	chr2:54514800-54515200	Enhancers	Brain Anterior Caudate	brain
37	chr2:54514800-54516800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
38	chr2:54514800-54517200	Weak transcription	Aorta	Aorta
39	chr2:54515000-54516800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
40	chr2:54515000-54516800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
41	chr2:54515200-54515400	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
42	chr2:54515200-54515600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
43	chr2:54515200-54516800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
44	chr2:54515200-54517000	Weak transcription	Brain Angular Gyrus	brain
45	chr2:54515200-54517000	Weak transcription	Brain Anterior Caudate	brain
46	chr2:54515200-54517000	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr2:54515200-54517200	Weak transcription	Left Ventricle	heart
48	chr2:54515200-54518200	Weak transcription	Right Atrium	heart
49	chr2:54515200-54522600	Weak transcription	Psoas Muscle	Psoas
50	chr2:54515200-54526200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links