Variant report

Variant	esv3405731
Chromosome Location	chr1:227288729-227293227
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	E2F4	chr1:227291312-227291526	MCF10A-Er-Src	breast:	n/a	n/a
2	GATA3	chr1:227289751-227289756	SH-SY5Y	brain:	n/a	n/a
3	GATA3	chr1:227290207-227290231	SH-SY5Y	brain:	n/a	n/a
4	KAP1	chr1:227290836-227291036	K562	blood:	n/a	n/a
5	MAZ	chr1:227291855-227291871	HepG2	liver:	n/a	n/a
6	POLR2A	chr1:227291330-227291359	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr1:227292533-227292565	K562	blood:	n/a	n/a
8	POLR2A	chr1:227291658-227291692	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr1:227291011-227291038	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr1:227293148-227293178	K562	blood:	n/a	n/a
11	STAT3	chr1:227288533-227288802	MCF10A-Er-Src	breast:	n/a	n/a
12	STAT3	chr1:227289162-227289423	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
CDC42BPA	TF binding region

Extended variants
information (count: 147 )
Associated
traits (count: 90 )

Variant overlapped rSNPs/rCNVs (count:147 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs538118229	chr1:227288749-227288750	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs373530803	chr1:227288810-227288811	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs201979872	chr1:227288843-227288844	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs142697103	chr1:227288850-227288851	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs201126700	chr1:227288876-227288877	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs140818561	chr1:227288904-227288905	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs200326381	chr1:227288917-227288918	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs553446047	chr1:227288984-227288985	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs573410013	chr1:227288999-227289000	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs369357087	chr1:227289002-227289003	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs534113329	chr1:227289015-227289016	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs555894768	chr1:227289046-227289047	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs576393298	chr1:227289056-227289057	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs544871167	chr1:227289070-227289071	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs497291	chr1:227289078-227289079	Weak transcription Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs532813542	chr1:227289082-227289083	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs578068058	chr1:227289101-227289102	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs79766410	chr1:227289103-227289104	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs111910235	chr1:227289114-227289115	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs189712702	chr1:227289186-227289187	Weak transcription Enhancers Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
21	rs535028152	chr1:227289259-227289260	Weak transcription Enhancers Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
22	rs548930723	chr1:227289323-227289324	Weak transcription Enhancers Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
23	rs181741287	chr1:227289423-227289424	Weak transcription Enhancers Strong transcription	TF binding region	1 gene(s)	Overlapped CNVs	n/a
24	rs368551355	chr1:227289432-227289433	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs549657190	chr1:227289487-227289488	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs570955374	chr1:227289534-227289535	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs538222535	chr1:227289550-227289551	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs150549048	chr1:227289580-227289581	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs568561130	chr1:227289588-227289589	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs565653811	chr1:227289626-227289627	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs536316646	chr1:227289653-227289654	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs372078794	chr1:227289708-227289709	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs529430	chr1:227289734-227289735	Weak transcription Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
34	rs117759115	chr1:227289846-227289847	Weak transcription Active TSS Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs538586002	chr1:227289862-227289863	Weak transcription Active TSS Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs186316265	chr1:227289868-227289869	Weak transcription Active TSS Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs191462467	chr1:227289869-227289870	Weak transcription Active TSS Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs12125514	chr1:227289879-227289880	Weak transcription Active TSS Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs531137	chr1:227289889-227289890	Weak transcription Active TSS Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
40	rs554110946	chr1:227289912-227289913	Weak transcription Active TSS Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs647702	chr1:227289913-227289914	Weak transcription Active TSS Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs534991596	chr1:227289938-227289939	Weak transcription Active TSS Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs77349570	chr1:227289967-227289968	Weak transcription Active TSS Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs183808682	chr1:227289976-227289977	Weak transcription Active TSS Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs114169091	chr1:227290059-227290060	Weak transcription Flanking Active TSS Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs531397991	chr1:227290114-227290115	Weak transcription Flanking Active TSS Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs543338326	chr1:227290124-227290125	Weak transcription Flanking Active TSS Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs533134	chr1:227290139-227290140	Weak transcription Flanking Active TSS Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
49	rs532237122	chr1:227290175-227290176	Weak transcription Flanking Active TSS Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs573173071	chr1:227290196-227290197	Weak transcription Flanking Active TSS Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:90)

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
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

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227154400-227294200	Weak transcription	Hela-S3	cervix
2	chr1:227209200-227301600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:227214800-227329200	Weak transcription	Right Ventricle	heart
4	chr1:227247400-227299800	Weak transcription	HMEC	breast
5	chr1:227251000-227300000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:227257800-227312200	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr1:227259400-227349000	Weak transcription	Colonic Mucosa	Colon
8	chr1:227271800-227299600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:227272600-227294400	Weak transcription	Fetal Heart	heart
10	chr1:227272800-227295000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:227272800-227295000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr1:227272800-227331000	Weak transcription	Lung	lung
13	chr1:227273000-227312400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr1:227275800-227302600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr1:227277200-227302600	Weak transcription	Brain Substantia Nigra	brain
16	chr1:227279800-227299000	Weak transcription	Placenta	Placenta
17	chr1:227280800-227298800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:227281800-227294400	Weak transcription	Fetal Kidney	kidney
19	chr1:227282600-227318000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:227284000-227288800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:227285200-227289000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:227285400-227288800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr1:227285600-227288800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:227285600-227297600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:227285600-227308600	Weak transcription	Pancreas	Pancrea
26	chr1:227285600-227313800	Weak transcription	Gastric	stomach
27	chr1:227286000-227288800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:227286000-227288800	Strong transcription	Adipose Nuclei	Adipose
29	chr1:227286200-227288800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:227286200-227290200	Strong transcription	HUVEC	blood vessel
31	chr1:227286400-227288800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:227286400-227288800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr1:227286400-227289000	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr1:227286400-227289800	Strong transcription	HSMM	muscle
35	chr1:227286400-227328200	Weak transcription	Brain Germinal Matrix	brain
36	chr1:227286600-227288800	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr1:227286600-227289000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr1:227286800-227288800	Strong transcription	NHDF-Ad	bronchial
39	chr1:227287000-227289000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr1:227287200-227288800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr1:227287200-227288800	Enhancers	Pancreatic Islets	Pancreatic Islet
42	chr1:227287400-227360800	Weak transcription	Psoas Muscle	Psoas
43	chr1:227287600-227288800	Strong transcription	Liver	Liver
44	chr1:227287800-227288800	Strong transcription	NHEK	skin
45	chr1:227288000-227288800	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr1:227288000-227294000	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr1:227288000-227326400	Weak transcription	A549	lung
48	chr1:227288200-227294600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr1:227288200-227296400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:227288200-227332400	Weak transcription	Sigmoid Colon	Sigmoid Colon

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