Variant report

Variant	esv2640294
Chromosome Location	chr1:228571449-228573091
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	CEBPD	chr1:228572641-228573447	K562	blood:	n/a	n/a
2	CUX1	chr1:228571601-228572021	K562	blood:	n/a	n/a
3	GATA3	chr1:228572683-228573621	SH-SY5Y	brain:	n/a	chr1:228572838-228572850 chr1:228572839-228572848 chr1:228572839-228572849 chr1:228572841-228572848

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:228326695..228329093-chr1:228572036..228574543,2	K562	blood:
2	chr1:228461884..228463852-chr1:228571777..228574496,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM11-1	chr1:228572490-228572717	ENSG00000270104.1
2	lnc-TRIM11-1	chr1:228571815-228572160	ENSG00000270104.1

Variant related genes	Relation type
ENSG00000270104	TF binding region
ENSG00000269934	chromatin interactions
ENSG00000143774	chromatin interactions
ENSG00000269890	chromatin interactions

Extended variants
information (count: 46 )
Associated
traits (count: 91 )

Variant overlapped rSNPs/rCNVs (count:46 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs372729537	chr1:228571500-228571501	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs548040196	chr1:228571550-228571551	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs112254640	chr1:228571583-228571584	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs12082349	chr1:228571585-228571586	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
5	rs77670487	chr1:228571604-228571605	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs556741891	chr1:228571639-228571640	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs200572110	chr1:228571658-228571659	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs201332538	chr1:228571664-228571665	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs77801773	chr1:228571665-228571666	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs71769070	chr1:228571666-228571667	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs181340800	chr1:228571676-228571677	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs200170756	chr1:228571703-228571704	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs558443944	chr1:228571704-228571705	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs545718383	chr1:228571773-228571774	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs563905212	chr1:228571783-228571784	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs562209683	chr1:228571796-228571797	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs371712078	chr1:228571826-228571827	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
18	rs138980673	chr1:228571851-228571852	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
19	rs142118185	chr1:228571869-228571870	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
20	rs150126083	chr1:228571901-228571902	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
21	rs112668565	chr1:228571906-228571907	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
22	rs548875971	chr1:228571946-228571947	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
23	rs562718734	chr1:228571967-228571968	Weak transcription	Chromatin interactive region lncRNA	2 gene(s)	Overlapped CNVs	n/a
24	rs531488827	chr1:228572048-228572049	Weak transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
25	rs551680146	chr1:228572148-228572149	Weak transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
26	rs199593599	chr1:228572176-228572177	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
27	rs200879002	chr1:228572177-228572178	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
28	rs201672422	chr1:228572483-228572484	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
29	rs186123426	chr1:228572486-228572487	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
30	rs4344327	chr1:228572489-228572490	Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
31	rs571302578	chr1:228572541-228572542	Weak transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
32	rs533893787	chr1:228572544-228572545	Weak transcription	Chromatin interactive region lncRNA	3 gene(s)	Overlapped CNVs	n/a
33	rs367879600	chr1:228572721-228572722	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
34	rs547393207	chr1:228572726-228572727	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
35	rs138438631	chr1:228572736-228572737	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
36	rs536770131	chr1:228572740-228572741	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
37	rs77859583	chr1:228572773-228572774	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
38	rs190880652	chr1:228572848-228572849	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
39	rs183909944	chr1:228572864-228572865	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
40	rs149259953	chr1:228572900-228572901	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
41	rs538961477	chr1:228572911-228572912	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
42	rs559334899	chr1:228572974-228572975	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
43	rs572785027	chr1:228572987-228572988	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
44	rs115793003	chr1:228572998-228572999	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
45	rs560211787	chr1:228573012-228573013	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
46	rs375124115	chr1:228573083-228573084	Weak transcription	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:91)

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
Melanoma	17363583	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228566800-228583200	Weak transcription	HSMMtube	muscle
2	chr1:228567000-228579800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr1:228567000-228592800	Weak transcription	Fetal Kidney	kidney
4	chr1:228567200-228579000	Weak transcription	Gastric	stomach
5	chr1:228567200-228579400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:228567200-228581600	Weak transcription	Right Ventricle	heart
7	chr1:228567400-228575200	Weak transcription	Left Ventricle	heart
8	chr1:228567400-228579400	Weak transcription	Lung	lung
9	chr1:228567400-228579400	Weak transcription	Pancreas	Pancrea
10	chr1:228567400-228579600	Weak transcription	K562	blood
11	chr1:228567400-228579800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr1:228567400-228582200	Weak transcription	Brain Substantia Nigra	brain
13	chr1:228567600-228582600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr1:228567800-228579600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:228568200-228579400	Weak transcription	Fetal Intestine Small	intestine
16	chr1:228568200-228582800	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:228569000-228575200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:228569200-228582000	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr1:228569600-228579400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:228569800-228585600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:228571000-228591600	Weak transcription	Fetal Brain Male	brain
22	chr1:228571200-228571600	Enhancers	Duodenum Mucosa	Duodenum
23	chr1:228571200-228571600	Enhancers	Spleen	Spleen
24	chr1:228571400-228571600	Enhancers	Small Intestine	intestine
25	chr1:228571600-228579200	Weak transcription	Spleen	Spleen
26	chr1:228571600-228579400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr1:228571600-228582600	Weak transcription	Small Intestine	intestine

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