Variant report

Variant	esv3422138
Chromosome Location	chr1:228657329-228659402
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228641579..228650592-chr1:228655272..228662014,16	MCF-7	breast:
2	chr1:228528294..228529171-chr1:228659243..228660230,3	K562	blood:
3	chr1:228658472..228661206-chr1:228701587..228703125,2	K562	blood:
4	chr1:228656675..228659120-chr1:228668301..228670452,2	MCF-7	breast:
5	chr1:228652493..228655065-chr1:228656279..228659196,2	MCF-7	breast:
6	chr1:228645786..228648558-chr1:228657300..228663044,6	MCF-7	breast:
7	chr1:228658600..228660249-chr1:228674820..228676448,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181218	chromatin interactions
ENSG00000196890	chromatin interactions
ENSG00000168159	chromatin interactions
ENSG00000266174	chromatin interactions

Extended variants
information (count: 48 )
Associated
traits (count: 91 )

Variant overlapped rSNPs/rCNVs (count:48 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs377361938	chr1:228657371-228657372	Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
2	rs369853074	chr1:228657382-228657383	Bivalent/Poised TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
3	rs550129487	chr1:228657416-228657417	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
4	rs375231225	chr1:228657448-228657449	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
5	rs543184693	chr1:228657453-228657454	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
6	rs386640022	chr1:228657456-228657457	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
7	rs6692594	chr1:228657457-228657458	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs546714630	chr1:228657493-228657494	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs566544307	chr1:228657509-228657510	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs535590442	chr1:228657521-228657522	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs143997255	chr1:228657561-228657562	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs569139482	chr1:228657582-228657583	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
13	rs114430885	chr1:228657636-228657637	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs368158312	chr1:228657644-228657645	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
15	rs78771405	chr1:228657669-228657670	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs571652498	chr1:228657732-228657733	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
17	rs193107012	chr1:228657765-228657766	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
18	rs534027929	chr1:228657792-228657793	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
19	rs373307333	chr1:228657861-228657862	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
20	rs542972312	chr1:228657869-228657870	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
21	rs117772911	chr1:228657894-228657895	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
22	rs558870548	chr1:228657940-228657941	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
23	rs370652446	chr1:228657986-228657987	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
24	rs556358689	chr1:228657990-228657991	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
25	rs576304644	chr1:228657991-228657992	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
26	rs545328716	chr1:228658031-228658032	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
27	rs563917368	chr1:228658103-228658104	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
28	rs375731331	chr1:228658110-228658111	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
29	rs12746910	chr1:228658133-228658134	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs539849215	chr1:228658187-228658188	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
31	rs375191725	chr1:228658421-228658422	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
32	rs560154040	chr1:228658488-228658489	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
33	rs528994860	chr1:228658684-228658685	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
34	rs76644309	chr1:228658714-228658715	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
35	rs569102832	chr1:228658716-228658717	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
36	rs531624780	chr1:228658726-228658727	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
37	rs551742834	chr1:228658773-228658774	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
38	rs11810222	chr1:228658864-228658865	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
39	rs372457256	chr1:228658925-228658926	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
40	rs571550310	chr1:228658932-228658933	Bivalent Enhancer Enhancers Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
41	rs534153893	chr1:228659053-228659054	Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
42	rs6699055	chr1:228659126-228659127	Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription	Chromatin interactive region	4 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
43	rs185541874	chr1:228659152-228659153	Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
44	rs115324153	chr1:228659284-228659285	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
45	rs556322138	chr1:228659316-228659317	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
46	rs376595211	chr1:228659382-228659383	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
47	rs190063911	chr1:228659386-228659387	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
48	rs370706252	chr1:228659391-228659392	Enhancers Bivalent Enhancer Weak transcription	Chromatin interactive region	4 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
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
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228653800-228660600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:228656800-228659800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:228657000-228657400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:228657200-228657400	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
5	chr1:228657200-228657400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:228657200-228657600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr1:228657200-228657600	Bivalent Enhancer	Right Ventricle	heart
8	chr1:228657200-228657800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:228657200-228658000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
10	chr1:228657200-228658400	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr1:228657400-228657600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
12	chr1:228657400-228657600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr1:228657400-228657600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:228657400-228657600	Bivalent Enhancer	Brain Germinal Matrix	brain
15	chr1:228657400-228657600	Flanking Bivalent TSS/Enh	Fetal Brain Female	brain
16	chr1:228657400-228657600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr1:228657400-228657600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
18	chr1:228657400-228657800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr1:228657400-228657800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr1:228657400-228657800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:228657400-228657800	Enhancers	Esophagus	oesophagus
22	chr1:228657400-228658000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
23	chr1:228657600-228657800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
24	chr1:228657600-228657800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
25	chr1:228657600-228657800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:228657600-228657800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:228657600-228657800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:228657600-228657800	Bivalent/Poised TSS	Brain Germinal Matrix	brain
29	chr1:228657600-228657800	Bivalent Enhancer	Fetal Brain Female	brain
30	chr1:228657600-228657800	Bivalent Enhancer	HMEC	breast
31	chr1:228657600-228658000	Enhancers	HUES64 Cell Line	embryonic stem cell
32	chr1:228657800-228658000	Bivalent/Poised TSS	Fetal Brain Female	brain
33	chr1:228657800-228659800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:228658000-228659200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
35	chr1:228658400-228658600	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
36	chr1:228658400-228658600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
37	chr1:228659000-228659200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr1:228659000-228659200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr1:228659000-228659200	Bivalent Enhancer	Esophagus	oesophagus
40	chr1:228659200-228659400	Bivalent Enhancer	Fetal Intestine Large	intestine
41	chr1:228659200-228659600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr1:228659200-228659600	Bivalent Enhancer	Placenta	Placenta
43	chr1:228659200-228660200	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr1:228659200-228661200	Enhancers	K562	blood
45	chr1:228659200-228661800	Enhancers	Primary hematopoietic stem cells short term culture	blood
46	chr1:228659400-228659600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
47	chr1:228659400-228659600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr1:228659400-228659800	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
49	chr1:228659400-228660000	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr1:228659400-228660400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell

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