Variant report

Variant	esv3513448
Chromosome Location	chr1:226002744-226003278
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225998808..226002827-chr1:226008223..226011228,3	MCF-7	breast:
2	chr1:225840822..225842484-chr1:226000425..226002809,2	MCF-7	breast:
3	chr1:225999526..226002981-chr1:226005681..226008708,3	MCF-7	breast:
4	chr1:225996256..225999661-chr1:226002108..226005312,5	MCF-7	breast:
5	chr1:225962862..225967352-chr1:225996084..226002774,11	MCF-7	breast:
6	chr1:225963814..225970754-chr1:225996230..226002908,14	MCF-7	breast:

Variant related genes	Relation type
ENSG00000154380	chromatin interactions
ENSG00000143819	chromatin interactions
ENSG00000143742	chromatin interactions

Extended variants
information (count: 24 )
Associated
traits (count: 91 )

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs566257892	chr1:226002912-226002913	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs56726650	chr1:226002942-226002943	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
3	rs544480405	chr1:226002956-226002957	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs528494760	chr1:226002972-226002973	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs113519327	chr1:226002974-226002975	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs540509914	chr1:226002976-226002977	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs562012395	chr1:226002978-226002979	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs529567054	chr1:226002979-226002980	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs550850851	chr1:226002982-226002983	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs569446971	chr1:226002988-226002989	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs532873895	chr1:226002991-226002992	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs71646749	chr1:226003009-226003010	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs555017628	chr1:226003027-226003028	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs142101420	chr1:226003033-226003034	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs371202736	chr1:226003113-226003114	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs5781415	chr1:226003114-226003115	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs200270890	chr1:226003120-226003121	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs397983046	chr1:226003135-226003136	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs568643248	chr1:226003146-226003147	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs71646750	chr1:226003166-226003167	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs112030016	chr1:226003171-226003172	Weak transcription Enhancers Genic enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs181987786	chr1:226003234-226003235	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs532519384	chr1:226003251-226003252	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs533803796	chr1:226003252-226003253	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	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
Acute lymphoblastic leukemia	21098271	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
Developmental delay	21147756	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
Lung adenocarcinoma	21935476	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225998400-226007800	Enhancers	Spleen	Spleen
2	chr1:225998600-226005600	Enhancers	Stomach Mucosa	stomach
3	chr1:225999000-226002800	Enhancers	Placenta	Placenta
4	chr1:225999200-226004800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:225999200-226006400	Enhancers	Lung	lung
6	chr1:225999200-226006600	Enhancers	Psoas Muscle	Psoas
7	chr1:225999400-226004600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:225999400-226004800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:225999400-226006600	Enhancers	Right Ventricle	heart
10	chr1:225999400-226007800	Enhancers	Left Ventricle	heart
11	chr1:225999600-226003600	Enhancers	Brain Angular Gyrus	brain
12	chr1:225999600-226003800	Enhancers	Pancreas	Pancrea
13	chr1:225999600-226005200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:225999600-226006400	Enhancers	Brain Cingulate Gyrus	brain
15	chr1:225999800-226002800	Genic enhancers	Fetal Intestine Small	intestine
16	chr1:225999800-226004400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr1:225999800-226006400	Enhancers	Brain Hippocampus Middle	brain
18	chr1:226000000-226003400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr1:226000000-226003400	Genic enhancers	Fetal Muscle Trunk	muscle
20	chr1:226000000-226005400	Weak transcription	Thymus	Thymus
21	chr1:226000000-226006600	Enhancers	Brain Substantia Nigra	brain
22	chr1:226000000-226019400	Weak transcription	Fetal Brain Female	brain
23	chr1:226000200-226006400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr1:226000400-226002800	Enhancers	Brain Inferior Temporal Lobe	brain
25	chr1:226000400-226002800	Enhancers	Small Intestine	intestine
26	chr1:226000400-226004400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:226000400-226007400	Enhancers	Brain Anterior Caudate	brain
28	chr1:226000400-226015800	Enhancers	Ovary	ovary
29	chr1:226000600-226004400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr1:226001000-226004000	Weak transcription	Fetal Brain Male	brain
31	chr1:226001000-226004400	Weak transcription	Fetal Heart	heart
32	chr1:226001400-226003600	Enhancers	Right Atrium	heart
33	chr1:226001400-226004200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr1:226001400-226005000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:226001400-226005200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr1:226001400-226005400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:226001600-226002800	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr1:226001600-226002800	Enhancers	NHDF-Ad	bronchial
39	chr1:226001600-226003000	Enhancers	Colonic Mucosa	Colon
40	chr1:226001600-226003400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr1:226001600-226003400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr1:226001600-226003800	Enhancers	K562	blood
43	chr1:226001600-226004200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr1:226001600-226004200	Enhancers	Liver	Liver
45	chr1:226001600-226004200	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr1:226001600-226004200	Weak transcription	HSMM	muscle
47	chr1:226001600-226004400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr1:226001600-226004400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr1:226001600-226004400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr1:226001600-226004400	Enhancers	Rectal Mucosa Donor 29	rectum

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