Variant report

Variant	esv3521777
Chromosome Location	chr1:228361750-228362301
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	BHLHE40	chr1:228362247-228362422	K562	blood:	n/a	n/a
2	CBX3	chr1:228362119-228362489	K562	blood:	n/a	n/a
3	CCNT2	chr1:228361622-228362663	K562	blood:	n/a	n/a
4	CREB1	chr1:228361626-228361893	A549	lung:	n/a	n/a
5	CREB1	chr1:228362102-228362403	A549	lung:	n/a	n/a
6	CTCF	chr1:228362135-228362426	K562	blood:	n/a	chr1:228362249-228362262
7	CTCF	chr1:228362180-228362330	HCT-116	colon:	n/a	chr1:228362249-228362262
8	CTCF	chr1:228362220-228362370	K562	blood:	n/a	chr1:228362249-228362262
9	CTCF	chr1:228362260-228362410	HRE	kidney:	n/a	n/a
10	CTCF	chr1:228362200-228362350	NHEK	skin:	n/a	chr1:228362249-228362262
11	CTCF	chr1:228362192-228362353	H1-hESC	embryonic stem cell:	n/a	chr1:228362249-228362262
12	CTCF	chr1:228362140-228362290	GM12869	blood:	n/a	chr1:228362249-228362262
13	CTCF	chr1:228362220-228362370	HEK293	kidney:	n/a	chr1:228362249-228362262
14	CTCFL	chr1:228362163-228362352	K562	blood:	n/a	n/a
15	EGR1	chr1:228362133-228362317	K562	blood:	n/a	n/a
16	ELF1	chr1:228361609-228361892	K562	blood:	n/a	n/a
17	ETS1	chr1:228362171-228362359	K562	blood:	n/a	n/a
18	FOXA1	chr1:228362142-228362358	T-47D	breast:	n/a	n/a
19	FOXA1	chr1:228361463-228361825	T-47D	breast:	n/a	n/a
20	GABPA	chr1:228362297-228362673	K562	blood:	n/a	n/a
21	GABPA	chr1:228362163-228362792	K562	blood:	n/a	n/a
22	GTF2F1	chr1:228361611-228361772	K562	blood:	n/a	n/a
23	HCFC1	chr1:228362156-228362568	K562	blood:	n/a	n/a
24	HEY1	chr1:228362180-228362479	K562	blood:	n/a	n/a
25	HMGN3	chr1:228361404-228362692	K562	blood:	n/a	n/a
26	IRF1	chr1:228361595-228362487	K562	blood:	n/a	n/a
27	JUND	chr1:228362202-228362417	K562	blood:	n/a	n/a
28	MAX	chr1:228361238-228361892	MCF-7	breast:	n/a	n/a
29	MAX	chr1:228361587-228361877	K562	blood:	n/a	n/a
30	MAX	chr1:228362121-228362635	ECC-1	luminal epithelium:	n/a	chr1:228362364-228362373 chr1:228362371-228362381
31	MAX	chr1:228361502-228361881	ECC-1	luminal epithelium:	n/a	n/a
32	MAX	chr1:228361667-228361827	K562	blood:	n/a	n/a
33	MAX	chr1:228362080-228362391	K562	blood:	n/a	chr1:228362364-228362373 chr1:228362371-228362381
34	MAX	chr1:228361707-228361848	K562	blood:	n/a	n/a
35	MAX	chr1:228362143-228362378	K562	blood:	n/a	chr1:228362364-228362373
36	MAX	chr1:228362125-228362642	K562	blood:	n/a	chr1:228362364-228362373 chr1:228362371-228362381
37	MAZ	chr1:228361788-228361827	K562	blood:	n/a	n/a
38	MAZ	chr1:228362115-228362522	K562	blood:	n/a	chr1:228362364-228362373 chr1:228362371-228362381
39	MYC	chr1:228361762-228362500	K562	blood:	n/a	chr1:228362364-228362373 chr1:228362371-228362381
40	MYC	chr1:228361774-228361841	MCF10A-Er-Src	breast:	n/a	n/a
41	MYC	chr1:228362207-228362225	MCF10A-Er-Src	breast:	n/a	n/a
42	MYC	chr1:228361751-228361831	K562	blood:	n/a	n/a
43	MYC	chr1:228361526-228361867	MCF-7	breast:	n/a	n/a
44	MYC	chr1:228362132-228362458	K562	blood:	n/a	chr1:228362364-228362373 chr1:228362371-228362381
45	NR2F2	chr1:228362075-228362604	K562	blood:	n/a	n/a
46	POLR2A	chr1:228362177-228362391	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr1:228362116-228362482	K562	blood:	n/a	n/a
48	POLR2A	chr1:228362127-228362542	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr1:228362168-228362468	MCF-7	breast:	n/a	n/a
50	POLR2A	chr1:228362165-228362380	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:228362275..228366557-chr1:228367502..228371326,4	MCF-7	breast:
2	chr1:228361423..228364297-chr1:228644461..228646940,2	K562	blood:
3	chr1:228295318..228298683-chr1:228360322..228363984,4	K562	blood:
4	chr1:228269154..228271874-chr1:228360119..228363775,3	K562	blood:
5	chr1:228360767..228363057-chr1:228399837..228402220,2	MCF-7	breast:
6	chr1:228350414..228357594-chr1:228359448..228365919,31	MCF-7	breast:
7	chr1:228296791..228299072-chr1:228362296..228364108,2	MCF-7	breast:
8	chr1:228331165..228333412-chr1:228361433..228363518,2	MCF-7	breast:

Variant related genes	Relation type
IBA57	TF binding region
ENSG00000162913	chromatin interactions
ENSG00000203684	chromatin interactions
ENSG00000143774	chromatin interactions
ENSG00000162910	chromatin interactions
ENSG00000196890	chromatin interactions
ENSG00000181218	chromatin interactions
ENSG00000181873	chromatin interactions
ENSG00000143761	chromatin interactions

Extended variants
information (count: 15 )
Associated
traits (count: 93 )

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs555231396	chr1:228361750-228361751	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
2	rs539177304	chr1:228361809-228361810	Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Strong transcription	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
3	rs150130570	chr1:228361812-228361813	Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Strong transcription	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
4	rs572958593	chr1:228361817-228361818	Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Strong transcription	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
5	rs542070190	chr1:228361832-228361833	Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Strong transcription	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
6	rs367817788	chr1:228361833-228361834	Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Strong transcription	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
7	rs561825896	chr1:228361845-228361846	Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Strong transcription	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
8	rs138850962	chr1:228361848-228361849	Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Strong transcription	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
9	rs544597549	chr1:228361877-228361878	Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Strong transcription	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
10	rs564486760	chr1:228361919-228361920	Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Strong transcription	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
11	rs71180782	chr1:228362025-228362026	Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Strong transcription	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
12	rs12141488	chr1:228362213-228362214	Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription	TF binding region Chromatin interactive region	9 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs560696083	chr1:228362217-228362218	Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
14	rs375346184	chr1:228362224-228362225	Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a
15	rs78028873	chr1:228362238-228362239	Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription	TF binding region Chromatin interactive region	9 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:93)

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
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Lung adenocarcinoma	21935476	CNVD
early-passage human iPS cells	21368824	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228354400-228362600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:228354400-228384600	Weak transcription	Aorta	Aorta
3	chr1:228354600-228362200	Weak transcription	Brain Germinal Matrix	brain
4	chr1:228354600-228362200	Weak transcription	Fetal Thymus	thymus
5	chr1:228354600-228362400	Weak transcription	Psoas Muscle	Psoas
6	chr1:228354600-228363600	Weak transcription	Primary B cells from cord blood	blood
7	chr1:228354600-228370400	Weak transcription	Right Atrium	heart
8	chr1:228354600-228382200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:228354600-228385200	Weak transcription	Left Ventricle	heart
10	chr1:228354800-228362200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr1:228354800-228362200	Weak transcription	NHLF	lung
12	chr1:228354800-228362400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr1:228354800-228362400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr1:228354800-228362400	Weak transcription	Adipose Nuclei	Adipose
15	chr1:228354800-228362400	Weak transcription	Brain Anterior Caudate	brain
16	chr1:228354800-228362400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr1:228354800-228362400	Weak transcription	Fetal Brain Male	brain
18	chr1:228354800-228362600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:228354800-228362600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr1:228354800-228362600	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr1:228354800-228362600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr1:228354800-228362800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:228354800-228362800	Weak transcription	Brain Angular Gyrus	brain
24	chr1:228354800-228362800	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr1:228354800-228362800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr1:228354800-228363400	Weak transcription	Colon Smooth Muscle	Colon
27	chr1:228354800-228364400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:228354800-228364400	Weak transcription	Brain Substantia Nigra	brain
29	chr1:228354800-228364600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr1:228354800-228365200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:228354800-228366400	Weak transcription	Liver	Liver
32	chr1:228354800-228367000	Weak transcription	Osteobl	bone
33	chr1:228354800-228370800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:228354800-228371200	Weak transcription	HSMMtube	muscle
35	chr1:228354800-228373200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:228355000-228362200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr1:228355000-228362400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr1:228355000-228362400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:228355000-228362400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr1:228355000-228362400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr1:228355000-228362600	Weak transcription	Primary B cells from peripheral blood	blood
42	chr1:228355000-228362600	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr1:228355000-228362600	Weak transcription	Primary T helper cells fromperipheralblood	blood
44	chr1:228355000-228362600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr1:228355000-228362800	Weak transcription	Brain Hippocampus Middle	brain
46	chr1:228355000-228364600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:228355000-228364800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr1:228355000-228364800	Weak transcription	Primary hematopoietic stem cells	blood
49	chr1:228355000-228370600	Weak transcription	HepG2	liver
50	chr1:228355000-228372400	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links