Variant report

Variant	esv3341290
Chromosome Location	chr1:228638941-228639498
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	JUN	chr1:228639464-228641509	K562	blood:	n/a	chr1:228640231-228640241 chr1:228640230-228640242 chr1:228640231-228640241 chr1:228640054-228640062 chr1:228640231-228640241 chr1:228640232-228640240
2	POLR2A	chr1:228638824-228639009	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr1:228639400-228643883	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:228589639..228603795-chr1:228638211..228648676,43	MCF-7	breast:
2	chr1:228275073..228277944-chr1:228639266..228642188,2	K562	blood:
3	chr1:228565749..228568495-chr1:228638648..228642089,3	K562	blood:
4	chr1:228520549..228522898-chr1:228637916..228639790,2	K562	blood:
5	chr1:228638761..228647671-chr1:228695176..228704605,18	K562	blood:
6	chr1:228616675..228619300-chr1:228638219..228642365,5	MCF-7	breast:
7	chr1:228526564..228529508-chr1:228637709..228639977,2	K562	blood:

Variant related genes	Relation type
ENSG00000230841	TF binding region
ENSG00000154370	chromatin interactions
ENSG00000143761	chromatin interactions
ENSG00000154358	chromatin interactions
ENSG00000162931	chromatin interactions
ENSG00000215811	chromatin interactions
ENSG00000231563	chromatin interactions

Extended variants
information (count: 30 )
Associated
traits (count: 90 )

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs200045997	chr1:228639039-228639040	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
2	rs377094664	chr1:228639041-228639042	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
3	rs57197508	chr1:228639042-228639043	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
4	rs12132024	chr1:228639045-228639046	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
5	rs79769962	chr1:228639046-228639047	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
6	rs77992241	chr1:228639048-228639049	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
7	rs12131218	chr1:228639050-228639051	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
8	rs59570146	chr1:228639054-228639055	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
9	rs60778793	chr1:228639077-228639078	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
10	rs71180796	chr1:228639079-228639080	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
11	rs200204598	chr1:228639089-228639090	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
12	rs540498122	chr1:228639111-228639112	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
13	rs560475707	chr1:228639121-228639122	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
14	rs187329826	chr1:228639141-228639142	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
15	rs7533319	chr1:228639142-228639143	Weak transcription	Chromatin interactive region	5 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
16	rs562880500	chr1:228639174-228639175	Weak transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
17	rs531808152	chr1:228639206-228639207	Weak transcription Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
18	rs113049129	chr1:228639254-228639255	Weak transcription Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
19	rs551608137	chr1:228639283-228639284	Weak transcription Strong transcription	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
20	rs376168357	chr1:228639289-228639290	Weak transcription Strong transcription	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
21	rs190982265	chr1:228639301-228639302	Weak transcription Strong transcription	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
22	rs538276781	chr1:228639302-228639303	Weak transcription Strong transcription	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
23	rs527917487	chr1:228639317-228639318	Weak transcription Strong transcription	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
24	rs183183331	chr1:228639322-228639323	Weak transcription Strong transcription	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
25	rs567663549	chr1:228639329-228639330	Weak transcription Strong transcription	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
26	rs536549742	chr1:228639332-228639333	Weak transcription Strong transcription	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
27	rs187513473	chr1:228639376-228639377	Weak transcription Strong transcription	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
28	rs557689787	chr1:228639380-228639381	Weak transcription Strong transcription	Chromatin interactive region	6 gene(s)	Overlapped CNVs	n/a
29	rs568526849	chr1:228639413-228639414	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	7 gene(s)	Overlapped CNVs	n/a
30	rs537917355	chr1:228639484-228639485	Weak transcription Strong transcription Enhancers	TF binding region Chromatin interactive region	7 gene(s)	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
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
Melanoma	17363583	CNVD

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228634000-228643200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:228634200-228641600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr1:228634200-228643000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr1:228634200-228644800	Weak transcription	Gastric	stomach
5	chr1:228634400-228641600	Weak transcription	Brain Angular Gyrus	brain
6	chr1:228634400-228644200	Weak transcription	Brain Anterior Caudate	brain
7	chr1:228634400-228644600	Weak transcription	Right Atrium	heart
8	chr1:228634400-228644600	Weak transcription	Right Ventricle	heart
9	chr1:228635000-228639800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:228635000-228640200	Weak transcription	Fetal Brain Male	brain
11	chr1:228635000-228640600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr1:228635000-228641400	Weak transcription	Brain Germinal Matrix	brain
13	chr1:228635000-228641600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr1:228635000-228642000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr1:228635200-228643000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:228635200-228644200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:228635400-228639200	Weak transcription	Fetal Intestine Small	intestine
18	chr1:228635600-228641400	Weak transcription	Fetal Brain Female	brain
19	chr1:228635800-228643000	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr1:228636600-228641200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:228637000-228641600	Weak transcription	Fetal Muscle Leg	muscle
22	chr1:228637200-228640000	Weak transcription	Placenta	Placenta
23	chr1:228637400-228643000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:228637600-228643400	Weak transcription	Brain Hippocampus Middle	brain
25	chr1:228638000-228643000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr1:228638200-228639800	Weak transcription	Spleen	Spleen
27	chr1:228638200-228643200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:228638400-228639600	Weak transcription	K562	blood
29	chr1:228638400-228643400	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr1:228638400-228644600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr1:228638600-228639600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:228638600-228640200	Weak transcription	Fetal Stomach	stomach
33	chr1:228638800-228644600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:228639000-228643200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr1:228639200-228641400	Strong transcription	Fetal Intestine Small	intestine
36	chr1:228639400-228640200	Enhancers	HSMM	muscle

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