Variant report

Variant	esv3313979
Chromosome Location	chr16:31339922-31340130
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	chr16:31339430-31340482	GM12878	blood:	n/a	n/a
2	BCL3	chr16:31339512-31340343	GM12878	blood:	n/a	n/a
3	NFATC1	chr16:31339788-31340391	GM12878	blood:	n/a	n/a
4	NFATC1	chr16:31339558-31340382	GM12878	blood:	n/a	n/a
5	NR2C2	chr16:31339597-31340368	GM12878	blood:	n/a	n/a
6	PBX3	chr16:31339778-31340295	GM12878	blood:	n/a	n/a
7	SUZ12	chr16:31339602-31340438	H1-hESC	embryonic stem cell:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COX6A2-5	chr16:31338997-31340036	NONHSAT141893

Variant related genes	Relation type
ITGAM	TF binding region

Extended variants
information (count: 18 )
Associated
traits (count: 120 )

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs369898924	chr16:31339953-31339954	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
2	rs555939346	chr16:31339962-31339963	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs373726265	chr16:31339986-31339987	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
4	rs541427935	chr16:31340003-31340004	Weak transcription Enhancers Strong transcription Bivalent Enhancer	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
5	rs565334165	chr16:31340018-31340019	Weak transcription Enhancers Strong transcription Bivalent Enhancer	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs111166760	chr16:31340025-31340026	Weak transcription Enhancers Strong transcription Bivalent Enhancer	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
7	rs551568997	chr16:31340032-31340033	Weak transcription Enhancers Strong transcription Bivalent Enhancer	TF binding region lncRNA	1 gene(s)	Overlapped CNVs	n/a
8	rs563511929	chr16:31340060-31340061	Weak transcription Enhancers Strong transcription Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs530806931	chr16:31340073-31340074	Weak transcription Enhancers Strong transcription Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
10	rs549342256	chr16:31340075-31340076	Weak transcription Enhancers Strong transcription Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
11	rs114030487	chr16:31340077-31340078	Weak transcription Enhancers Strong transcription Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
12	rs60312440	chr16:31340086-31340087	Weak transcription Enhancers Strong transcription Bivalent Enhancer	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
13	rs546280781	chr16:31340087-31340088	Weak transcription Enhancers Strong transcription Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
14	rs377327136	chr16:31340092-31340093	Weak transcription Enhancers Strong transcription Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
15	rs571291408	chr16:31340093-31340094	Weak transcription Enhancers Strong transcription Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
16	rs571735420	chr16:31340099-31340100	Weak transcription Enhancers Strong transcription Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
17	rs56784976	chr16:31340101-31340102	Weak transcription Enhancers Strong transcription Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a
18	rs200805383	chr16:31340114-31340115	Weak transcription Enhancers Strong transcription Bivalent Enhancer	TF binding region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:120)

Disease	PMID	Source
Hodgkin''s lymphoma	20651079	CNVD
Metanephric adenoma	20802469	CNVD
Melanoma	18172304	CNVD
Breast cancer	16608533	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Breast cancer	17133270	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Adenoid cystic carcinoma	17372589	CNVD
Lung adenocarcinoma	17086460	CNVD
Lung cancer	17086460	CNVD
Autism	22566537	CNVD
Intellectual disability	22566537	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Endometrial cancer	22040021	CNVD
Ewing''s sarcoma	21437220	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	17603634	CNVD
Breast cancer	21264507	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	21080181	CNVD
Acute lymphoblastic leukemia	17690704	CNVD
Autism	19415332	CNVD
Medulloblastoma	21979893	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD
Schizophrenia	22958593	CNVD
Lung cancer	18438408	CNVD
Ductal carcinoma	22052326	CNVD
Breast cancer	21509527	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Autism	22495311	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Hodgkin''s lymphoma	17606441	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Breast cancer	21858162	CNVD
Hepatocellular carcinoma	16750200	CNVD
Mental retardation	19951919	CNVD
Colorectal cancer	16272173	CNVD
Bladder cancer	21909424	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	21785460	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Breast cancer	21990379	CNVD
Astrocytoma	22246337	CNVD
Myelofibrosis	22110671	CNVD
Epilepsy	22499536	CNVD
Attention deficit hyperactivity disorder	21324949	CNVD
Austim spectrum disorder	21302340	CNVD
Autism	22513405	CNVD
Autism	22958593	CNVD
Autism	18184952	CNVD
Autism	19966786	CNVD
Autism	21394203	CNVD
Autism	21969575	CNVD
Autism	22241247	CNVD
Autism	20970697	CNVD
Autism	20942916	CNVD
Epilepsy	20970697	CNVD
Intellectual disability	22045946	CNVD
Mental retardation	19966786	CNVD
Developmental delay	20808231	CNVD
Obesity	20808231	CNVD
Autism	18923514	CNVD
Obesity	21881559	CNVD
Obesity	21956041	CNVD
Autism	20659124	CNVD
Mental retardation	21062444	CNVD
Schizophrenia	20587603	CNVD
Schizophrenia	21285140	CNVD
Schizophrenia	22885689	CNVD
Schizophrenia	20553308	CNVD
Schizophrenia	20970697	CNVD
Schizophrenia	20433910	CNVD
Schizophrenia	22241247	CNVD
Autism	19242545	CNVD
Primary central nervous system lymphoma	21088137	CNVD
Intracranial ependymoma	16609018	CNVD
Schizophrenia	21399695	CNVD
Autism	21956041	CNVD
Disorders of sex development	21048976	CNVD
Autism	22067053	CNVD
Autism	18156158	CNVD
Mental retardation	20152051	CNVD
Autism	19218893	CNVD
Autism	21289514	CNVD
Schizophrenia	19855392	CNVD
neurodevelopmental Syndrome	20503337	CNVD
Benign familial neonatal-infantile seizures	21060786	CNVD
Low-grade fibromyxoid sarcoma	0	CNVD
Cancer	21183584	CNVD
Low-grade fibromyxoid sarcoma	21536545	CNVD
Breast cancer	21045282	CNVD
Neuroblastoma	20406844	CNVD
Autism	19050728	CNVD
Epilepsy	20923578	CNVD
Psychiatric disorder	19050728	CNVD
Schizophrenia	19348701	CNVD
Attention deficit hyperactivity disorder	19097825	CNVD
Autism	20964600	CNVD
Schizophrenia	19955444	CNVD
Schizophrenia	18990708	CNVD
Schizophrenia	19571808	CNVD
Breast cancer	20409316	CNVD
Severe combined immunodeficiency	19097825	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Autism	18522746	CNVD
Urothelial carcinoma	21177765	CNVD
Chronic myeloid leukemia	21384125	CNVD
Prostate cancer	18632612	CNVD
Sezary syndrome	18413736	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31323000-31344600	Strong transcription	Primary neutrophils fromperipheralblood	blood
2	chr16:31331800-31342000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr16:31332200-31342000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr16:31333600-31342400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr16:31333800-31342400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr16:31335200-31341800	Weak transcription	Primary B cells from peripheral blood	blood
7	chr16:31335800-31342000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr16:31337000-31340800	Weak transcription	Placenta	Placenta
9	chr16:31338200-31340200	Strong transcription	Primary B cells from cord blood	blood
10	chr16:31338400-31342600	Weak transcription	Gastric	stomach
11	chr16:31338800-31342000	Strong transcription	Spleen	Spleen
12	chr16:31339000-31340000	Enhancers	GM12878-XiMat	blood
13	chr16:31339000-31340200	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr16:31339000-31340200	Enhancers	Dnd41	blood
15	chr16:31339200-31340000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr16:31339200-31340000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr16:31339400-31340000	Enhancers	K562	blood
18	chr16:31339400-31340200	Enhancers	Primary hematopoietic stem cells	blood
19	chr16:31339600-31340000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
20	chr16:31339600-31340000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr16:31339600-31340800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr16:31339800-31340000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr16:31339800-31340000	Bivalent/Poised TSS	Fetal Heart	heart
24	chr16:31339800-31340000	Active TSS	Fetal Thymus	thymus
25	chr16:31339800-31340200	Bivalent Enhancer	Duodenum Mucosa	Duodenum
26	chr16:31339800-31340400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr16:31339800-31340800	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr16:31339800-31342000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr16:31339800-31342200	Weak transcription	Thymus	Thymus
30	chr16:31340000-31340200	Bivalent Enhancer	Fetal Brain Female	brain
31	chr16:31340000-31340400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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