Variant report

Variant	esv3404238
Chromosome Location	chr1:220251379-220252477
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr1:220251438-220251554	HepG2	liver:	n/a	chr1:220251494-220251505
2	POLR2A	chr1:220251384-220251461	A549	lung:	n/a	n/a
3	POLR2A	chr1:220251373-220251380	A549	lung:	n/a	n/a
4	TCF7L2	chr1:220252152-220252271	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:220250499..220254001-chr1:220255278..220257878,3	K562	blood:
2	chr1:220236160..220238551-chr1:220252332..220254009,2	K562	blood:

Variant related genes	Relation type
BPNT1	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 97 )

Variant overlapped rSNPs/rCNVs (count:47 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs564741372	chr1:220251380-220251381	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs530616703	chr1:220251386-220251387	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs566997509	chr1:220251420-220251421	Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs550643368	chr1:220251424-220251425	Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs147996736	chr1:220251452-220251453	Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs535465231	chr1:220251456-220251457	Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs529687227	chr1:220251461-220251462	Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
8	rs546600054	chr1:220251546-220251547	Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs201312727	chr1:220251548-220251549	Weak transcription Strong transcription Genic enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs566444446	chr1:220251598-220251599	Weak transcription Strong transcription Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs372484353	chr1:220251645-220251646	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs202023986	chr1:220251656-220251657	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs116121256	chr1:220251660-220251661	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs35600968	chr1:220251666-220251667	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs558679502	chr1:220251729-220251730	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs571907868	chr1:220251730-220251731	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs181658496	chr1:220251737-220251738	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs9430910	chr1:220251763-220251764	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs9430911	chr1:220251764-220251765	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs186239691	chr1:220251787-220251788	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs58834658	chr1:220251821-220251822	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs66897228	chr1:220251822-220251823	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs35619743	chr1:220251829-220251830	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs397687983	chr1:220251830-220251831	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs373842943	chr1:220251843-220251844	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs574296427	chr1:220251852-220251853	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs199679040	chr1:220251856-220251857	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs191012875	chr1:220251890-220251891	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs377329229	chr1:220251899-220251900	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs182548890	chr1:220251901-220251902	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs370403113	chr1:220251904-220251905	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs185783284	chr1:220251949-220251950	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs553341364	chr1:220251952-220251953	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs572854770	chr1:220252010-220252011	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs12145672	chr1:220252056-220252057	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs540474793	chr1:220252098-220252099	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs369838148	chr1:220252202-220252203	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs191035252	chr1:220252216-220252217	Weak transcription Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs61484867	chr1:220252226-220252227	Weak transcription Strong transcription	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs544374458	chr1:220252272-220252273	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs537818189	chr1:220252290-220252291	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs150554546	chr1:220252343-220252344	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs116076592	chr1:220252386-220252387	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs566480764	chr1:220252389-220252390	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs532132846	chr1:220252409-220252410	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs552333760	chr1:220252426-220252427	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs568949058	chr1:220252443-220252444	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:97)

Disease	PMID	Source
Breast cancer	17603634	CNVD
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
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
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
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
Acute lymphoblastic leukemia	22237106	CNVD
Urothelial carcinoma	21177765	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Chordoma	18071362	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
Hepatocellular carcinoma	18803288	CNVD
Urothelial tumor	18831757	CNVD
Lung cancer	18438408	CNVD
Ovarian cancer	21720365	CNVD
small cell lung cancer	20016488	CNVD
Ovarian clear cell carcinoma	19293255	CNVD
Medulloblastoma	16783165	CNVD
Basal cell lymphoma	17170743	CNVD
Hirschsprung''s Disease	21712996	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Holoprosencephaly	19184110	CNVD
Breast cancer	21069454	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Mental retardation	19951919	CNVD
Non-syndromic sensorineural hearing loss	17873649	CNVD
Acute myeloid leukemia	17268525	CNVD
Lung cancer	16740712	CNVD
Renal cell carcinoma	18765545	CNVD
Basal cell lymphoma	17053054	CNVD
Developmental delay	21147756	CNVD
Pleomorphic liposarcoma	18784837	CNVD
Autism	14699429	CNVD
Breast cancer	21364760	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Pancreatic cancer	17952125	CNVD
Tetralogy of Fallot	22912587	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD

Chromatin state (count:129 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220220400-220257600	Weak transcription	Stomach Mucosa	stomach
2	chr1:220220600-220262400	Weak transcription	Pancreas	Pancrea
3	chr1:220220600-220262400	Weak transcription	NHLF	lung
4	chr1:220220800-220261600	Weak transcription	Fetal Brain Male	brain
5	chr1:220234400-220253600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:220236400-220262800	Weak transcription	Esophagus	oesophagus
7	chr1:220238000-220262800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:220238000-220267400	Weak transcription	Spleen	Spleen
9	chr1:220238200-220262800	Weak transcription	Gastric	stomach
10	chr1:220239400-220262000	Weak transcription	Brain Germinal Matrix	brain
11	chr1:220239600-220255200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:220239600-220261600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr1:220239600-220262400	Weak transcription	Right Ventricle	heart
14	chr1:220241200-220256800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:220241200-220258200	Weak transcription	Hela-S3	cervix
16	chr1:220241200-220261800	Weak transcription	A549	lung
17	chr1:220241200-220262000	Weak transcription	HMEC	breast
18	chr1:220241200-220262400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr1:220241200-220262400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr1:220241400-220262400	Weak transcription	NHEK	skin
21	chr1:220241600-220253000	Strong transcription	Fetal Intestine Small	intestine
22	chr1:220242600-220262800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:220243800-220262400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:220245800-220251800	Strong transcription	Fetal Lung	lung
25	chr1:220246200-220262000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr1:220246400-220251400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:220246400-220255000	Weak transcription	Brain Angular Gyrus	brain
28	chr1:220246400-220255000	Weak transcription	HSMMtube	muscle
29	chr1:220246400-220256000	Weak transcription	Fetal Kidney	kidney
30	chr1:220246400-220261600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr1:220246400-220261800	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr1:220246400-220262000	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:220246400-220262400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr1:220246400-220262400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr1:220246400-220262400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr1:220246400-220262400	Weak transcription	Brain Anterior Caudate	brain
37	chr1:220246400-220262400	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr1:220246400-220262400	Weak transcription	Brain Substantia Nigra	brain
39	chr1:220246400-220262400	Weak transcription	Fetal Brain Female	brain
40	chr1:220246600-220253600	Weak transcription	Primary B cells from cord blood	blood
41	chr1:220246600-220262400	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr1:220246600-220262400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr1:220246600-220262400	Weak transcription	Colonic Mucosa	Colon
44	chr1:220246800-220262400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr1:220246800-220262400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr1:220246800-220262400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr1:220246800-220262400	Weak transcription	Fetal Heart	heart
48	chr1:220246800-220262400	Weak transcription	Thymus	Thymus
49	chr1:220247000-220256800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr1:220247000-220257600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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