Variant report

Variant	esv3397939
Chromosome Location	chr1:228757647-228760264
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	BCL3	chr1:228757842-228758009	GM12878	blood:	n/a	n/a
2	BCL3	chr1:228757836-228758031	GM12878	blood:	n/a	n/a
3	CBX3	chr1:228759936-228766629	K562	blood:	n/a	n/a
4	CBX3	chr1:228756716-228760610	K562	blood:	n/a	n/a
5	CBX3	chr1:228756779-228759666	K562	blood:	n/a	n/a
6	CEBPB	chr1:228757789-228758242	GM12878	blood:	n/a	n/a
7	CEBPB	chr1:228760026-228760632	GM12878	blood:	n/a	n/a
8	CEBPB	chr1:228759206-228759599	K562	blood:	n/a	n/a
9	CEBPD	chr1:228759235-228759657	K562	blood:	n/a	n/a
10	CEBPD	chr1:228757823-228758348	K562	blood:	n/a	n/a
11	CTCF	chr1:228759359-228760804	K562	blood:	n/a	chr1:228760087-228760096 chr1:228760084-228760097 chr1:228760677-228760690
12	CTCF	chr1:228757994-228758420	K562	blood:	n/a	n/a
13	CTCF	chr1:228757848-228758573	K562	blood:	n/a	chr1:228758435-228758448 chr1:228757867-228757876 chr1:228757864-228757877
14	CTCF	chr1:228758159-228758196	LNCaP	prostate:	n/a	n/a
15	CTCF	chr1:228758836-228759127	K562	blood:	n/a	n/a
16	CTCF	chr1:228758026-228758427	K562	blood:	n/a	n/a
17	CTCF	chr1:228760241-228760669	K562	blood:	n/a	n/a
18	CTCF	chr1:228758155-228758222	GM10248	blood:	n/a	n/a
19	CTCF	chr1:228758160-228758231	Spleen_OC	spleen:	n/a	n/a
20	FOSL2	chr1:228758822-228759034	HepG2	liver:	n/a	chr1:228758886-228758895
21	FOSL2	chr1:228758055-228758374	HepG2	liver:	n/a	n/a
22	FOXA2	chr1:228759210-228759822	A549	lung:	n/a	n/a
23	FOXA2	chr1:228743895-228782766	A549	lung:	n/a	n/a
24	FOXM1	chr1:228759232-228759666	GM12878	blood:	n/a	n/a
25	FOXP2	chr1:228759414-228759659	PFSK-1	brain:	n/a	n/a
26	FOXP2	chr1:228759330-228759681	SK-N-MC	brain:	n/a	n/a
27	FOXP2	chr1:228757454-228757695	PFSK-1	brain:	n/a	n/a
28	FOXP2	chr1:228757816-228758427	PFSK-1	brain:	n/a	n/a
29	FOXP2	chr1:228759944-228760263	PFSK-1	brain:	n/a	n/a
30	GABPA	chr1:228758131-228758317	Hela-S3	cervix:	n/a	n/a
31	GABPA	chr1:228758853-228758963	Hela-S3	cervix:	n/a	n/a
32	GATA2	chr1:228758053-228758307	K562	blood:	n/a	n/a
33	HEY1	chr1:228758812-228759008	HepG2	liver:	n/a	chr1:228758865-228758880 chr1:228758971-228758986 chr1:228758974-228758989
34	HEY1	chr1:228758051-228758399	HepG2	liver:	n/a	n/a
35	HEY1	chr1:228758829-228759014	K562	blood:	n/a	chr1:228758865-228758880 chr1:228758971-228758986 chr1:228758974-228758989
36	HEY1	chr1:228758056-228758234	K562	blood:	n/a	n/a
37	HEY1	chr1:228758068-228758315	K562	blood:	n/a	n/a
38	JUND	chr1:228759199-228759669	A549	lung:	n/a	n/a
39	JUND	chr1:228758850-228758966	HepG2	liver:	n/a	chr1:228758886-228758895
40	JUND	chr1:228744099-228759006	A549	lung:	n/a	chr1:228748791-228748805 chr1:228747728-228747737 chr1:228753273-228753287 chr1:228744309-228744323 chr1:228746550-228746564 chr1:228745487-228745496 chr1:228755514-228755528 chr1:228751032-228751046 chr1:228758886-228758895 chr1:228749969-228749978 chr1:228752210-228752219 chr1:228754451-228754460 chr1:228757729-228757743
41	JUND	chr1:228759031-228765239	A549	lung:	n/a	chr1:228759949-228759963 chr1:228764430-228764444 chr1:228762191-228762205 chr1:228761128-228761137 chr1:228763367-228763376
42	MYBL2	chr1:228759036-228759828	HepG2	liver:	n/a	n/a
43	MYBL2	chr1:228760003-228760669	HepG2	liver:	n/a	n/a
44	MYBL2	chr1:228759927-228760773	HepG2	liver:	n/a	n/a
45	MYBL2	chr1:228756565-228759813	HepG2	liver:	n/a	n/a
46	NFIC	chr1:228757787-228758156	GM12878	blood:	n/a	n/a
47	NR2F2	chr1:228757758-228758493	K562	blood:	n/a	n/a
48	NR2F2	chr1:228759271-228759659	K562	blood:	n/a	n/a
49	NR2F2	chr1:228759065-228759582	K562	blood:	n/a	n/a
50	PAX5	chr1:228758239-228758373	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
RNA5S6	TF binding region
RNA5S7	TF binding region
RNA5S5	TF binding region
RNA5S4	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 90 )

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs552151310	chr1:228757925-228757926	Bivalent/Poised TSS Active TSS Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
2	rs559449286	chr1:228757926-228757927	Bivalent/Poised TSS Active TSS Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
3	rs200234224	chr1:228757935-228757936	Bivalent/Poised TSS Active TSS Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
4	rs61825676	chr1:228757936-228757937	Bivalent/Poised TSS Active TSS Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
5	rs548519035	chr1:228757938-228757939	Bivalent/Poised TSS Active TSS Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
6	rs79154558	chr1:228757942-228757943	Bivalent/Poised TSS Active TSS Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
7	rs568592811	chr1:228757947-228757948	Bivalent/Poised TSS Active TSS Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
8	rs74748147	chr1:228757948-228757949	Bivalent/Poised TSS Active TSS Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
9	rs551296850	chr1:228757984-228757985	Bivalent/Poised TSS Active TSS Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
10	rs61825677	chr1:228758016-228758017	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
11	rs61825678	chr1:228758027-228758028	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
12	rs190428826	chr1:228758044-228758045	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
13	rs11484728	chr1:228758055-228758056	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
14	rs11484729	chr1:228758060-228758061	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
15	rs11484730	chr1:228758124-228758125	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
16	rs11487481	chr1:228758138-228758139	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
17	rs11484731	chr1:228758140-228758141	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
18	rs374779647	chr1:228758164-228758165	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
19	rs1925725	chr1:228758170-228758171	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
20	rs11484732	chr1:228758186-228758187	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
21	rs558568148	chr1:228758188-228758189	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
22	rs565793485	chr1:228758198-228758199	Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
23	rs534690233	chr1:228758338-228758339	Weak transcription	TF binding region	2 gene(s)	Overlapped CNVs	n/a
24	rs112693194	chr1:228758473-228758474	Weak transcription	TF binding region	2 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:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228756800-228757800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:228757000-228771000	Weak transcription	Right Atrium	heart
3	chr1:228757800-228758000	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr1:228757800-228758200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
5	chr1:228757800-228758200	Active TSS	Adipose Nuclei	Adipose
6	chr1:228757800-228758200	Active TSS	Fetal Stomach	stomach
7	chr1:228757800-228758200	Active TSS	Dnd41	blood
8	chr1:228757800-228758200	Active TSS	HSMM	muscle
9	chr1:228758000-228758200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links