Variant report

Variant	esv3427970
Chromosome Location	chr1:77746994-77747339
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	CREB1	chr1:77747206-77747743	H1-hESC	embryonic stem cell:	n/a	n/a
2	CREB1	chr1:77747277-77747782	H1-hESC	embryonic stem cell:	n/a	n/a
3	CTBP2	chr1:77747283-77749011	H1-hESC	embryonic stem cell:	n/a	n/a
4	E2F6	chr1:77747175-77749220	H1-hESC	embryonic stem cell:	n/a	chr1:77748216-77748223 chr1:77748216-77748223 chr1:77747532-77747541 chr1:77748193-77748202 chr1:77747603-77747612 chr1:77747579-77747589 chr1:77747787-77747797 chr1:77748216-77748223
5	E2F6	chr1:77747217-77748911	H1-hESC	embryonic stem cell:	n/a	chr1:77748216-77748223 chr1:77748216-77748223 chr1:77747532-77747541 chr1:77748193-77748202 chr1:77747603-77747612 chr1:77747579-77747589 chr1:77747787-77747797 chr1:77748216-77748223
6	FOXP2	chr1:77747294-77748019	PFSK-1	brain:	n/a	n/a
7	GABPA	chr1:77747281-77747768	H1-hESC	embryonic stem cell:	n/a	n/a
8	JUND	chr1:77747287-77747645	H1-hESC	embryonic stem cell:	n/a	n/a
9	KAP1	chr1:77747335-77748344	HEK293	kidney:	n/a	n/a
10	MAX	chr1:77747279-77748964	H1-hESC	embryonic stem cell:	n/a	chr1:77747533-77747543
11	MAX	chr1:77747291-77748382	A549	lung:	n/a	chr1:77747533-77747543
12	MAX	chr1:77747309-77749165	H1-hESC	embryonic stem cell:	n/a	chr1:77747533-77747543
13	MAX	chr1:77747294-77748277	ECC-1	luminal epithelium:	n/a	chr1:77747533-77747543
14	MAX	chr1:77747300-77748303	ECC-1	luminal epithelium:	n/a	chr1:77747533-77747543
15	MAX	chr1:77747255-77748854	SK-N-SH	brain:	n/a	chr1:77747533-77747543
16	MAX	chr1:77747206-77749055	H1-hESC	embryonic stem cell:	n/a	chr1:77747533-77747543
17	MAX	chr1:77747218-77748787	A549	lung:	n/a	chr1:77747533-77747543
18	MAZ	chr1:77747079-77749195	IMR90	lung:	n/a	chr1:77747533-77747543
19	MXI1	chr1:77747266-77748949	IMR90	lung:	n/a	chr1:77748400-77748409
20	MXI1	chr1:77747085-77749961	SK-N-SH	brain:	n/a	chr1:77748400-77748409
21	NFIC	chr1:77747318-77747919	ECC-1	luminal epithelium:	n/a	n/a
22	POLR2A	chr1:77747149-77748486	H1-neurons	neurons:	n/a	n/a
23	POLR2A	chr1:77747191-77749083	H1-hESC	embryonic stem cell:	n/a	n/a
24	POLR2A	chr1:77747260-77747389	H1-hESC	embryonic stem cell:	n/a	n/a
25	POLR2A	chr1:77747302-77747731	H1-hESC	embryonic stem cell:	n/a	n/a
26	POLR2A	chr1:77747308-77747719	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr1:77747263-77747743	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr1:77747254-77748105	H1-neurons	neurons:	n/a	n/a
29	RAD21	chr1:77747236-77748158	H1-hESC	embryonic stem cell:	n/a	n/a
30	REST	chr1:77746941-77748101	H1-neurons	neurons:	n/a	chr1:77747667-77747680 chr1:77746990-77747008 chr1:77747814-77747824 chr1:77747609-77747622 chr1:77747641-77747651
31	SIN3A	chr1:77747219-77749389	H1-hESC	embryonic stem cell:	n/a	chr1:77748356-77748367 chr1:77747741-77747749 chr1:77747735-77747748
32	TAF1	chr1:77747266-77748932	H1-hESC	embryonic stem cell:	n/a	n/a
33	TBP	chr1:77747327-77749069	H1-hESC	embryonic stem cell:	n/a	n/a
34	TCF12	chr1:77747332-77748154	ECC-1	luminal epithelium:	n/a	chr1:77747546-77747553
35	TEAD4	chr1:77747333-77747831	H1-hESC	embryonic stem cell:	n/a	n/a
36	ZBTB7A	chr1:77747275-77748169	ECC-1	luminal epithelium:	n/a	n/a
37	ZBTB7A	chr1:77747293-77748176	ECC-1	luminal epithelium:	n/a	n/a
38	ZNF263	chr1:77747288-77748400	HEK293-T-REx	kidney:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:77684670..77686781-chr1:77746398..77749229,3	MCF-7	breast:

Variant related genes	Relation type
AK5	TF binding region
ENSG00000142892	chromatin interactions

Extended variants
information (count: 9 )
Associated
traits (count: 103 )

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs375166192	chr1:77747034-77747035	Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs554920517	chr1:77747048-77747049	Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs569017521	chr1:77747112-77747113	Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs566748327	chr1:77747167-77747168	Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs11580677	chr1:77747205-77747206	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs1851736	chr1:77747248-77747249	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs551675819	chr1:77747274-77747275	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs553129992	chr1:77747290-77747291	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs35930501	chr1:77747323-77747324	Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:103)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Colorectal cancer	16272173	CNVD
Wilms tumour	21544195	CNVD
Coronary Disease	20032323	CNVD
Prostate cancer	21965145	CNVD
Glioblastoma multiforme	21080181	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Stargardt''s disease	17277736	CNVD
Neuroblastoma	17897457	CNVD
Uveal melanoma	21693616	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-syndromic sensorineural hearing loss	22290220	CNVD
Liposarcoma	21253554	CNVD
Breast cancer	21264507	CNVD
Acute myeloid leukemia	16864856	CNVD
Astrocytoma	17387387	CNVD
Cancer	21499728	CNVD
Glioblastoma multiforme	17387387	CNVD
Oligodendroglial tumors	17285580	CNVD
Papillary thyroid carcinoma	21436994	CNVD
Neuroblastoma	17535989	CNVD
Pheochromocytoma	17535989	CNVD
Prostate cancer	16705090	CNVD
Astrocytoma	17934521	CNVD
Colorectal cancer	19359472	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Gastrointestinal stromal cancer	19259404	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Gastrointestinal stromal cancer	17535989	CNVD
Neuroblastoma	17533364	CNVD
Paraganglioma	17535989	CNVD
Pulmonary chondroma	17535989	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Non-syndromic sensorineural hearing loss	21030649	CNVD
Thoracic aortic aneurysm	21092924	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Autism	22495311	CNVD
Non-small cell lung cancer	21385341	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Chordoma	21602918	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Melanoma	18172304	CNVD
Multiple myeloma	16461302	CNVD
Melanoma	17363583	CNVD
Cancer	21129771	CNVD
Autosomal dominant nocturnal frontal lobe epilepsy	18472482	CNVD
Hirschsprung''s Disease	21712996	CNVD
Non-small cell lung cancer	20864512	CNVD
Non-syndromic sensorineural hearing loss	15273396	CNVD
Thrombocytopenia-absent radius syndrome	21933853	CNVD
Psychiatric disorder	22848183	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Hepatocellular carcinoma	16750200	CNVD
Burkitt''s lymphoma	18698080	CNVD
Breast cancer	20409316	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Lung cancer	18438408	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	17393978	CNVD
Cervical cancer	21062161	CNVD
Cancer	21183584	CNVD
Breast cancer	21785460	CNVD
Breast cancer	21364760	CNVD
Rett syndrome	21593744	CNVD
Prostate cancer	16573809	CNVD
Breast cancer	16608533	CNVD
Ovarian cancer	21720365	CNVD
Breast cancer	17133270	CNVD
Type 2 diabetes	21956041	CNVD
Uveal melanoma	20484589	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
lymphocytic leukemia	21291569	CNVD
Ewing''s sarcoma	17952124	CNVD
Myelofibrosis	22110671	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Poland''s syndrome	22110015	CNVD
Glioblastoma multiforme	22286061	CNVD
Glioblastoma multiforme	21922591	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Cancer	22429812	CNVD
Effusion lymphoma	18079361	CNVD
Non-muscle invasive bladder neoplasm	19445696	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Breast cancer	22522925	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:139 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:77737200-77747400	Weak transcription	Aorta	Aorta
2	chr1:77745200-77747200	Enhancers	Primary T cells fromperipheralblood	blood
3	chr1:77745200-77747200	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr1:77745200-77747200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr1:77745200-77747800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
6	chr1:77745400-77747000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr1:77745400-77747400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
8	chr1:77745600-77747000	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
9	chr1:77745600-77747200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:77745600-77747800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
11	chr1:77745800-77747200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
12	chr1:77745800-77747400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
13	chr1:77746000-77747200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
14	chr1:77746000-77747200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:77746000-77747200	Enhancers	Brain Hippocampus Middle	brain
16	chr1:77746200-77747000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr1:77746200-77747000	Enhancers	Brain Angular Gyrus	brain
18	chr1:77746200-77747200	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr1:77746200-77747200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:77746400-77747200	Bivalent Enhancer	Primary B cells from cord blood	blood
21	chr1:77746400-77747200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
22	chr1:77746400-77747400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr1:77746600-77747000	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
24	chr1:77746600-77747000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
25	chr1:77746600-77747000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr1:77746600-77747000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:77746600-77747200	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr1:77746600-77747200	Enhancers	Brain Anterior Caudate	brain
29	chr1:77746600-77749000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
30	chr1:77746800-77747000	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
31	chr1:77746800-77747000	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
32	chr1:77746800-77747000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr1:77746800-77747000	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr1:77746800-77747000	Enhancers	Fetal Brain Female	brain
35	chr1:77746800-77747000	Flanking Active TSS	NHDF-Ad	bronchial
36	chr1:77746800-77747200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:77746800-77747200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr1:77746800-77747200	Enhancers	Brain Cingulate Gyrus	brain
39	chr1:77746800-77747600	Bivalent/Poised TSS	Fetal Kidney	kidney
40	chr1:77746800-77748400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:77746800-77749200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
42	chr1:77746800-77749400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
43	chr1:77746800-77749600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
44	chr1:77747000-77747200	Bivalent Enhancer	Primary hematopoietic stem cells	blood
45	chr1:77747000-77747200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:77747000-77747200	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr1:77747000-77747200	Enhancers	Muscle Satellite Cultured Cells	--
48	chr1:77747000-77747200	Active TSS	Fetal Brain Female	brain
49	chr1:77747000-77747200	Active TSS	NHDF-Ad	bronchial
50	chr1:77747000-77747400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell

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