Variant report

Variant	esv2230348
Chromosome Location	chr1:171456967-171457399
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	FOS	chr1:171457351-171457697	MCF10A-Er-Src	breast:	n/a	n/a
2	FOS	chr1:171457299-171457655	MCF10A-Er-Src	breast:	n/a	n/a
3	GATA3	chr1:171457331-171458139	T-47D	breast:	n/a	chr1:171457894-171457906 chr1:171457895-171457903
4	RFX5	chr1:171457386-171457466	Hela-S3	cervix:	n/a	n/a
5	STAT3	chr1:171457321-171457617	MCF10A-Er-Src	breast:	n/a	chr1:171457556-171457564
6	STAT3	chr1:171457285-171457579	MCF10A-Er-Src	breast:	n/a	chr1:171457556-171457564
7	STAT3	chr1:171457253-171457608	MCF10A-Er-Src	breast:	n/a	chr1:171457556-171457564

No.	Distal block	Cell Line	Cell type
1	chr1:171452969..171454844-chr1:171456792..171458676,3	K562	blood:
2	chr1:171453426..171457241-chr1:171461305..171463614,3	MCF-7	breast:
3	chr1:171454832..171457416-chr1:171532662..171535516,2	MCF-7	breast:
4	chr1:171454829..171458429-chr1:171468344..171472224,4	MCF-7	breast:
5	chr1:169861616..169864007-chr1:171455760..171457373,2	MCF-7	breast:
6	chr1:171455198..171457522-chr1:171482757..171484309,2	MCF-7	breast:

Variant related genes	Relation type
RN7SL425P	TF binding region
ENSG00000000457	chromatin interactions
ENSG00000117523	chromatin interactions
ENSG00000239373	chromatin interactions

Extended variants
information (count: 14 )
Associated
traits (count: 92 )

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs554989912	chr1:171457048-171457049	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
2	rs545251362	chr1:171457089-171457090	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
3	rs11275127	chr1:171457158-171457159	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
4	rs201142042	chr1:171457159-171457160	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
5	rs199565367	chr1:171457160-171457161	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
6	rs200636956	chr1:171457161-171457162	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
7	rs199506871	chr1:171457198-171457199	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs200658025	chr1:171457199-171457200	Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs368396787	chr1:171457200-171457201	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs560374215	chr1:171457240-171457241	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs541639572	chr1:171457274-171457275	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs528605065	chr1:171457285-171457286	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
13	rs535366491	chr1:171457313-171457314	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs6702990	chr1:171457392-171457393	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance

Variant related diseases (count:92)

Disease	PMID	Source
Breast cancer	17603634	CNVD
Esophageal squamous carcinoma	21637470	CNVD
HIV/AIDS	22032296	CNVD
Schizophrenia	19415332	CNVD
Autism	22495311	CNVD
Hepatocellular carcinoma	16750200	CNVD
Liposarcoma	21253554	CNVD
Burkitt''s lymphoma	18698080	CNVD
Melanoma	18172304	CNVD
Cancer	21183584	CNVD
Multiple myeloma	16461302	CNVD
Rett syndrome	21593744	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Medulloblastoma	21979893	CNVD
Acute lymphoblastic leukemia	17443227	CNVD
Wilms tumour	21544195	CNVD
Breast cancer	17133270	CNVD
Non-small cell lung cancer	21829676	CNVD
Carcinoma ex pleomorphic adenoma	18828159	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
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
Acute lymphoblastic leukemia	21098271	CNVD
Neuroblastoma	21899760	CNVD
Bladder cancer	19088036	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17002787	CNVD
Breast cancer	21858162	CNVD
Retinoblastoma	19183342	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
Chordoma	18071362	CNVD
Hepatocellular carcinoma	18803288	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17001317	CNVD
Urothelial carcinoma	21177765	CNVD
Burkitt''s lymphoma	19759907	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
Trisomy 5 syndrome	21098271	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD
Breast cancer	21611746	CNVD
Neuroblastoma	18923191	CNVD
Soft tissue tumor	16732325	CNVD
Cancer	17060936	CNVD
Lung cancer	16740712	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Ewing''s sarcoma	17952124	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Acute lymphoblastic leukemia	19100363	CNVD
Williams-beuren syndrome	16971481	CNVD
Developmental delay	21147756	CNVD
Burkitt''s lymphoma	20823134	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Breast cancer	20409316	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Pancreatic cancer	17952125	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	21509527	CNVD

Chromatin state (count:157 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:171453600-171457400	Active TSS	GM12878-XiMat	blood
2	chr1:171453600-171458200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr1:171453800-171457600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr1:171454000-171457000	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr1:171454000-171457800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:171455400-171457600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:171455600-171457000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:171455600-171457000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr1:171455600-171457000	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr1:171455600-171458000	Flanking Active TSS	HUVEC	blood vessel
11	chr1:171455600-171458200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr1:171455600-171461600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:171455800-171457600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:171455800-171457600	Weak transcription	Esophagus	oesophagus
15	chr1:171455800-171459000	Enhancers	Stomach Mucosa	stomach
16	chr1:171455800-171461600	Weak transcription	Gastric	stomach
17	chr1:171455800-171465400	Weak transcription	Lung	lung
18	chr1:171455800-171467800	Weak transcription	Spleen	Spleen
19	chr1:171456000-171457000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:171456000-171457200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr1:171456000-171457400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr1:171456000-171457400	Flanking Active TSS	NHEK	skin
23	chr1:171456000-171457600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
24	chr1:171456000-171459000	Weak transcription	Pancreas	Pancrea
25	chr1:171456000-171481800	Weak transcription	Placenta	Placenta
26	chr1:171456200-171457000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:171456200-171457000	Enhancers	Primary B cells from peripheral blood	blood
28	chr1:171456200-171457000	Weak transcription	Small Intestine	intestine
29	chr1:171456200-171457200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:171456200-171457400	Transcr. at gene 5' and 3'	Dnd41	blood
31	chr1:171456200-171457600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr1:171456200-171457800	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr1:171456200-171457800	Enhancers	Rectal Smooth Muscle	rectum
34	chr1:171456200-171458000	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:171456200-171458000	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr1:171456200-171458000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr1:171456200-171458000	Enhancers	Placenta Amnion	Placenta Amnion
38	chr1:171456200-171459800	Enhancers	Fetal Heart	heart
39	chr1:171456200-171461600	Weak transcription	Left Ventricle	heart
40	chr1:171456200-171467800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr1:171456200-171475000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:171456400-171457000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr1:171456400-171457000	Enhancers	Fetal Kidney	kidney
44	chr1:171456400-171457000	Enhancers	NH-A	brain
45	chr1:171456400-171457200	Active TSS	HUES64 Cell Line	embryonic stem cell
46	chr1:171456400-171457400	Enhancers	Primary hematopoietic stem cells	blood
47	chr1:171456400-171457400	Weak transcription	Aorta	Aorta
48	chr1:171456400-171457400	Weak transcription	Ovary	ovary
49	chr1:171456400-171457400	Weak transcription	Right Atrium	heart
50	chr1:171456400-171457400	Active TSS	HMEC	breast

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