Variant report

Variant	esv3364500
Chromosome Location	chr1:224646269-224646622
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:224633064..224636103-chr1:224643208..224646617,3	K562	blood:
2	chr1:224644893..224646924-chr1:224647544..224649417,2	K562	blood:
3	chr1:224644724..224648422-chr1:224649777..224653927,3	K562	blood:
4	chr1:224615678..224629188-chr1:224635437..224647951,56	MCF-7	breast:
5	chr1:224300561..224302914-chr1:224645145..224647028,2	MCF-7	breast:
6	chr1:224619496..224626224-chr1:224640836..224649586,12	K562	blood:
7	chr1:224645408..224648550-chr1:224650858..224654034,4	K562	blood:
8	chr1:224645897..224648212-chr1:224688548..224690344,2	K562	blood:
9	chr1:224629495..224631561-chr1:224643787..224646406,3	K562	blood:
10	chr1:224617260..224625232-chr1:224640385..224647515,27	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNIH3-2	chr1:224645272-224646480	NONHSAT009806
2	lnc-CNIH3-2	chr1:224645508-224646893	NONHSAT009808

No data

Variant related genes	Relation type
ENSG00000162923	chromatin interactions
ENSG00000143786	chromatin interactions
ENSG00000143756	chromatin interactions

Extended variants
information (count: 17 )
Associated
traits (count: 102 )

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs541664321	chr1:224646282-224646283	Strong transcription Weak transcription Enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
2	rs6663522	chr1:224646328-224646329	Strong transcription Weak transcription Enhancers	Chromatin interactive region lncRNA	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
3	rs530307068	chr1:224646333-224646334	Strong transcription Weak transcription Enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
4	rs548429228	chr1:224646358-224646359	Strong transcription Weak transcription Enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
5	rs139583894	chr1:224646370-224646371	Strong transcription Weak transcription Enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
6	rs181645821	chr1:224646423-224646424	Strong transcription Weak transcription Enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
7	rs552613158	chr1:224646435-224646436	Strong transcription Weak transcription Enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
8	rs34820123	chr1:224646451-224646452	Strong transcription Weak transcription Enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
9	rs368965294	chr1:224646459-224646460	Strong transcription Weak transcription Enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
10	rs570812551	chr1:224646479-224646480	Strong transcription Weak transcription Enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
11	rs532346701	chr1:224646522-224646523	Strong transcription Weak transcription Enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
12	rs185976155	chr1:224646527-224646528	Strong transcription Weak transcription Enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
13	rs112295267	chr1:224646538-224646539	Strong transcription Weak transcription Enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
14	rs558642397	chr1:224646559-224646560	Strong transcription Weak transcription Enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
15	rs565769312	chr1:224646563-224646564	Strong transcription Weak transcription Enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
16	rs191136982	chr1:224646568-224646569	Strong transcription Weak transcription Enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
17	rs536427209	chr1:224646586-224646587	Strong transcription Weak transcription Enhancers	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:102)

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
Acute lymphoblastic leukemia	21098271	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
Congenital diaphragmatic hernia	21085971	CNVD
Mental retardation	19951919	CNVD
Non-syndromic sensorineural hearing loss	17873649	CNVD
Basal cell lymphoma	17053054	CNVD
Developmental delay	21147756	CNVD
Autism	14699429	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Autism	20808228	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
Myelofibrosis	22110671	CNVD
Liver carcinoma	19366792	CNVD
Leukoplakia	24403051	CNVD
Congenital diaphragmatic hernia	21525063	CNVD
Glioblastoma multiforme	21138945	CNVD
Ovarian clear cell carcinoma	21343371	CNVD
Cancer	20164920	CNVD
Cancer	17060936	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Breast cancer	22522925	CNVD
early-passage human iPS cells	21368824	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224624000-224646800	Weak transcription	Primary B cells from peripheral blood	blood
2	chr1:224628400-224648800	Weak transcription	Fetal Brain Female	brain
3	chr1:224628600-224653600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr1:224639000-224648400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:224642000-224646400	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr1:224643400-224649000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr1:224643600-224646600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:224644200-224647800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:224644400-224647200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:224644400-224647400	Enhancers	Brain Anterior Caudate	brain
11	chr1:224644400-224648000	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr1:224644600-224647800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:224644800-224646600	Weak transcription	Spleen	Spleen
14	chr1:224644800-224647800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr1:224644800-224647800	Enhancers	Fetal Intestine Small	intestine
16	chr1:224644800-224648200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:224644800-224651200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:224645000-224646400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr1:224645000-224647200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:224645000-224647400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr1:224645000-224647600	Weak transcription	Lung	lung
22	chr1:224645000-224649200	Weak transcription	Esophagus	oesophagus
23	chr1:224645000-224649200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr1:224645200-224646600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr1:224645200-224647400	Weak transcription	Left Ventricle	heart
26	chr1:224645200-224647400	Weak transcription	Right Atrium	heart
27	chr1:224645200-224647600	Enhancers	Brain Angular Gyrus	brain
28	chr1:224645200-224647800	Enhancers	Adipose Nuclei	Adipose
29	chr1:224645400-224646400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:224645400-224646400	Weak transcription	Primary monocytes fromperipheralblood	blood
31	chr1:224645400-224646400	Weak transcription	Fetal Intestine Large	intestine
32	chr1:224645400-224646400	Weak transcription	HUVEC	blood vessel
33	chr1:224645400-224646400	Weak transcription	K562	blood
34	chr1:224645400-224646400	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr1:224645400-224646600	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr1:224645400-224646600	Weak transcription	Brain Substantia Nigra	brain
37	chr1:224645400-224646600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr1:224645400-224646600	Weak transcription	Fetal Lung	lung
39	chr1:224645400-224646600	Weak transcription	Fetal Thymus	thymus
40	chr1:224645400-224646600	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr1:224645400-224646600	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr1:224645400-224646600	Weak transcription	NHLF	lung
43	chr1:224645400-224646800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr1:224645400-224646800	Weak transcription	Duodenum Mucosa	Duodenum
45	chr1:224645400-224646800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr1:224645400-224647000	Weak transcription	Fetal Brain Male	brain
47	chr1:224645400-224647000	Weak transcription	Fetal Heart	heart
48	chr1:224645400-224647400	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr1:224645400-224647600	Weak transcription	Liver	Liver
50	chr1:224645400-224647600	Enhancers	Colon Smooth Muscle	Colon

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