Variant report

Variant	esv3459461
Chromosome Location	chr2:10076525-10077928
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:10077034..10079332-chr2:10081722..10084624,2	MCF-7	breast:
2	chr2:10077387..10079466-chr2:10182113..10184414,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TAF1B-2	chr2:10076489-10079719	ENSG00000269973.1

Variant related genes	Relation type
ENSG00000172059	chromatin interactions

Extended variants
information (count: 56 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:56 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs12474277	chr2:10076531-10076532	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
2	rs192390814	chr2:10076590-10076591	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
3	rs549179464	chr2:10076613-10076614	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
4	rs35679946	chr2:10076625-10076626	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
5	rs569142828	chr2:10076628-10076629	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
6	rs538027105	chr2:10076630-10076631	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
7	rs558275983	chr2:10076651-10076652	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
8	rs578025059	chr2:10076659-10076660	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
9	rs534206811	chr2:10076666-10076667	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
10	rs74653712	chr2:10076704-10076705	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
11	rs554423699	chr2:10076721-10076722	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
12	rs59280442	chr2:10076854-10076855	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
13	rs146104012	chr2:10076857-10076858	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
14	rs184354700	chr2:10076872-10076873	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
15	rs576334616	chr2:10076923-10076924	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
16	rs138945889	chr2:10076935-10076936	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
17	rs188790586	chr2:10076968-10076969	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
18	rs374811770	chr2:10076974-10076975	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
19	rs112623310	chr2:10076983-10076984	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
20	rs4669504	chr2:10077008-10077009	Weak transcription Strong transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
21	rs576032239	chr2:10077012-10077013	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
22	rs560513185	chr2:10077108-10077109	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
23	rs368413826	chr2:10077183-10077184	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
24	rs529625413	chr2:10077217-10077218	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
25	rs541895946	chr2:10077277-10077278	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
26	rs750872	chr2:10077293-10077294	Weak transcription Strong transcription	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs112229280	chr2:10077300-10077301	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
28	rs538470175	chr2:10077342-10077343	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
29	rs76866041	chr2:10077346-10077347	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
30	rs147458248	chr2:10077348-10077349	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
31	rs138385557	chr2:10077354-10077355	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
32	rs181582139	chr2:10077370-10077371	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
33	rs540083742	chr2:10077382-10077383	Weak transcription Strong transcription	lncRNA	n/a	Overlapped CNVs	n/a
34	rs149597503	chr2:10077427-10077428	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
35	rs73913924	chr2:10077453-10077454	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs556547015	chr2:10077540-10077541	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
37	rs576395181	chr2:10077573-10077574	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
38	rs545199084	chr2:10077621-10077622	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
39	rs564885843	chr2:10077627-10077628	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
40	rs184749987	chr2:10077636-10077637	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
41	rs540802809	chr2:10077674-10077675	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
42	rs560628123	chr2:10077675-10077676	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
43	rs529687841	chr2:10077686-10077687	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
44	rs543001557	chr2:10077703-10077704	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
45	rs533070848	chr2:10077736-10077737	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
46	rs370362347	chr2:10077737-10077738	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
47	rs560383735	chr2:10077754-10077755	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
48	rs532265012	chr2:10077768-10077769	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
49	rs545079535	chr2:10077781-10077782	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
50	rs199560283	chr2:10077790-10077791	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:61)

Disease	PMID	Source
Breast cancer	17133270	CNVD
Mental retardation	17847001	CNVD
Glioblastoma multiforme	21080181	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Cancer	20164920	CNVD
Neuroblastoma	21508638	CNVD
Breast cancer	17603634	CNVD
Cancer	16751803	CNVD
Neuroblastoma	16790693	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	17393978	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Ewing''s sarcoma	21437220	CNVD
Ependymoma	16718352	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	18458336	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Bladder cancer	21909424	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Breast cancer	21364760	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Breast cancer	21804112	CNVD
Myelofibrosis	22110671	CNVD
Glioblastoma multiforme	22286061	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Glioma	17123091	CNVD
Breast cancer	20409316	CNVD
Multiple myeloma	16616336	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Pancreatic cancer	17952125	CNVD
early-passage human iPS cells	21368824	CNVD
Ependymoma	18628472	CNVD
Leukemia	18628472	CNVD

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:9993800-10079600	Weak transcription	Gastric	stomach
2	chr2:10030400-10077200	Weak transcription	Aorta	Aorta
3	chr2:10030600-10080600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:10037200-10080400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr2:10038600-10079800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:10038600-10081400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr2:10042600-10077000	Weak transcription	Colon Smooth Muscle	Colon
8	chr2:10045800-10079600	Weak transcription	Esophagus	oesophagus
9	chr2:10047200-10080000	Weak transcription	Colonic Mucosa	Colon
10	chr2:10049000-10077400	Weak transcription	Brain Anterior Caudate	brain
11	chr2:10049400-10077200	Weak transcription	Brain Angular Gyrus	brain
12	chr2:10049400-10081000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr2:10049600-10081200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:10052800-10076600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:10053200-10077800	Weak transcription	Liver	Liver
16	chr2:10054800-10079000	Weak transcription	Fetal Kidney	kidney
17	chr2:10055000-10080800	Weak transcription	Pancreas	Pancrea
18	chr2:10055000-10080800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr2:10055000-10081800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr2:10055200-10079600	Weak transcription	K562	blood
21	chr2:10055200-10080800	Weak transcription	HMEC	breast
22	chr2:10059000-10080600	Weak transcription	HSMMtube	muscle
23	chr2:10059400-10081200	Weak transcription	GM12878-XiMat	blood
24	chr2:10060600-10080200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:10060800-10077400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr2:10061000-10079600	Weak transcription	HepG2	liver
27	chr2:10061000-10080800	Weak transcription	Brain Germinal Matrix	brain
28	chr2:10061000-10080800	Weak transcription	NH-A	brain
29	chr2:10061000-10080800	Weak transcription	NHEK	skin
30	chr2:10061400-10077800	Weak transcription	Primary B cells from cord blood	blood
31	chr2:10061600-10077800	Weak transcription	Ovary	ovary
32	chr2:10062600-10080200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr2:10063000-10080800	Weak transcription	NHLF	lung
34	chr2:10064200-10079400	Weak transcription	Fetal Muscle Leg	muscle
35	chr2:10064200-10080200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:10064600-10079200	Weak transcription	Fetal Brain Female	brain
37	chr2:10064800-10077000	Weak transcription	Fetal Lung	lung
38	chr2:10065000-10080800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:10069000-10077000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:10069600-10079800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:10070800-10080800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr2:10072600-10077800	Strong transcription	Fetal Stomach	stomach
43	chr2:10073400-10077800	Weak transcription	Left Ventricle	heart
44	chr2:10073400-10078800	Weak transcription	Adipose Nuclei	Adipose
45	chr2:10073400-10081800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr2:10073400-10084400	Weak transcription	Lung	lung
47	chr2:10073600-10088800	Weak transcription	Spleen	Spleen
48	chr2:10073800-10077000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr2:10073800-10077200	Weak transcription	Brain Substantia Nigra	brain
50	chr2:10073800-10077600	Weak transcription	Right Ventricle	heart

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