Variant report

Variant	esv3359559
Chromosome Location	chr1:227953029-227957427
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:227948805..227951027-chr1:227953567..227955861,2	MCF-7	breast:
2	chr1:227953908..227955707-chr1:227958879..227960406,2	K562	blood:
3	chr1:227946182..227953403-chr1:228132950..228136592,12	MCF-7	breast:
4	chr1:227951099..227952899-chr1:227953091..227955822,2	K562	blood:
5	chr1:227955528..227959696-chr1:228132593..228135770,4	MCF-7	breast:
6	chr1:227954027..227955528-chr1:228133802..228136651,2	MCF-7	breast:
7	chr1:227955493..227956067-chr1:228129746..228130568,2	MCF-7	breast:
8	chr1:227948352..227950485-chr1:227952945..227955700,2	MCF-7	breast:
9	chr1:227951444..227953989-chr1:228132939..228135911,4	MCF-7	breast:
10	chr1:227943509..227946452-chr1:227956014..227958936,2	K562	blood:
11	chr1:227922298..227924299-chr1:227956346..227958728,2	MCF-7	breast:
12	chr1:227913567..227919162-chr1:227947935..227954215,6	MCF-7	breast:
13	chr1:227952215..227955097-chr1:227966264..227970414,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143740	chromatin interactions
ENSG00000081692	chromatin interactions
ENSG00000143816	chromatin interactions

Extended variants
information (count: 210 )
Associated
traits (count: 90 )

Variant overlapped rSNPs/rCNVs (count:210 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs546876448	chr1:227953053-227953054	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs568359331	chr1:227953055-227953056	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs188973559	chr1:227953103-227953104	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs77051694	chr1:227953113-227953114	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	mRNA abundance
5	rs569217856	chr1:227953121-227953122	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs571771309	chr1:227953124-227953125	Weak transcription Strong transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs539843511	chr1:227953235-227953236	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs77469088	chr1:227953247-227953248	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs142588977	chr1:227953281-227953282	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs12073225	chr1:227953387-227953388	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
11	rs567236211	chr1:227953447-227953448	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs555699602	chr1:227953448-227953449	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs536390151	chr1:227953455-227953456	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs573913077	chr1:227953476-227953477	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs544406561	chr1:227953496-227953497	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs556241541	chr1:227953512-227953513	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs191883168	chr1:227953514-227953515	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs76573686	chr1:227953540-227953541	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs146005924	chr1:227953556-227953557	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs184017621	chr1:227953590-227953591	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs540552609	chr1:227953607-227953608	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs562028959	chr1:227953612-227953613	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs73093354	chr1:227953697-227953698	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs550865260	chr1:227953735-227953736	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs188363610	chr1:227953740-227953741	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs575590724	chr1:227953741-227953742	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs139900459	chr1:227953767-227953768	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs113409612	chr1:227953815-227953816	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs180707543	chr1:227953817-227953818	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs534166007	chr1:227953825-227953826	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs149800732	chr1:227953858-227953859	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs567535295	chr1:227953942-227953943	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs538063304	chr1:227953944-227953945	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs730684	chr1:227953955-227953956	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
35	rs563857579	chr1:227953987-227953988	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs116614060	chr1:227953996-227953997	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs544820492	chr1:227954006-227954007	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs553806807	chr1:227954016-227954017	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs186055609	chr1:227954017-227954018	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs67502955	chr1:227954020-227954021	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs578207423	chr1:227954098-227954099	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs117233105	chr1:227954217-227954218	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs529499042	chr1:227954305-227954306	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs544801116	chr1:227954330-227954331	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs562980982	chr1:227954352-227954353	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs558689807	chr1:227954387-227954388	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs190583663	chr1:227954399-227954400	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs116385708	chr1:227954429-227954430	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs144707017	chr1:227954437-227954438	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs112950014	chr1:227954449-227954450	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS	Chromatin interactive region	1 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
Non-syndromic sensorineural hearing loss	17122850	CNVD

Chromatin state (count:374 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227924200-227955000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:227945800-227954800	Weak transcription	Fetal Kidney	kidney
3	chr1:227946000-227960400	Strong transcription	Fetal Brain Female	brain
4	chr1:227947600-227954800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr1:227947800-227955400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:227948000-227953600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr1:227948200-227954600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:227948400-227955400	Weak transcription	Psoas Muscle	Psoas
9	chr1:227948400-227956000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr1:227948600-227955600	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr1:227949000-227953400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:227949200-227954400	Enhancers	Primary T killer memory cells from peripheral blood	blood
13	chr1:227949200-227954800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr1:227949200-227956000	Genic enhancers	Fetal Thymus	thymus
15	chr1:227949400-227954200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr1:227949400-227954400	Enhancers	Placenta Amnion	Placenta Amnion
17	chr1:227949400-227954600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr1:227949600-227953400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr1:227949600-227954400	Weak transcription	Brain Substantia Nigra	brain
20	chr1:227949600-227955400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:227949600-227955600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr1:227949800-227954600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:227950000-227953600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:227950000-227954000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr1:227950000-227954200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:227950000-227954600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr1:227950200-227953600	Enhancers	Primary T cells fromperipheralblood	blood
28	chr1:227950200-227954600	Weak transcription	HepG2	liver
29	chr1:227950200-227955000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr1:227950200-227955200	Weak transcription	Ovary	ovary
31	chr1:227950400-227953200	Genic enhancers	NHLF	lung
32	chr1:227950600-227953200	Weak transcription	Stomach Mucosa	stomach
33	chr1:227950600-227953400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr1:227950600-227953400	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr1:227950600-227953400	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr1:227950600-227953600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr1:227950600-227953600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:227950600-227953600	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr1:227950600-227954000	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr1:227950600-227954200	Enhancers	Primary T cells from cord blood	blood
41	chr1:227950600-227954600	Weak transcription	Primary B cells from cord blood	blood
42	chr1:227950600-227954600	Weak transcription	Fetal Brain Male	brain
43	chr1:227950800-227953200	Strong transcription	Fetal Intestine Large	intestine
44	chr1:227950800-227953800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr1:227950800-227953800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr1:227950800-227954800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:227950800-227963000	Strong transcription	Brain Germinal Matrix	brain
48	chr1:227950800-227974200	Weak transcription	Small Intestine	intestine
49	chr1:227951000-227953600	Weak transcription	Primary B cells from peripheral blood	blood
50	chr1:227951000-227954600	Strong transcription	Liver	Liver

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