Variant report

Variant	nsv961023
Chromosome Location	chr2:30968718-30969805
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:30961063..30963636-chr2:30966785..30969337,2	K562	blood:
2	chr2:30967775..30969478-chr2:30977702..30980114,2	MCF-7	breast:
3	chr2:30962359..30964293-chr2:30967251..30969409,2	MCF-7	breast:
4	chr2:30969086..30972253-chr2:30973250..30976554,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GALNT14-1	chr2:30969310-30969567	NONHSAT069919

Variant related genes	Relation type
ENSG00000162949	chromatin interactions

Extended variants
information (count: 56 )
Associated
traits (count: 63 )

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	rs145578840	chr2:30968739-30968740	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs548224555	chr2:30968742-30968743	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs376315761	chr2:30968743-30968744	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs538136903	chr2:30968761-30968762	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs568075039	chr2:30968771-30968772	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs57880021	chr2:30968781-30968782	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs560524729	chr2:30968784-30968785	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs537043686	chr2:30968797-30968798	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs4245770	chr2:30968848-30968849	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
10	rs576705765	chr2:30968852-30968853	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs545776079	chr2:30968853-30968854	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs568181865	chr2:30968868-30968869	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs528995703	chr2:30968907-30968908	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs561956	chr2:30968929-30968930	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs552865885	chr2:30968953-30968954	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs57038400	chr2:30968965-30968966	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs541667237	chr2:30968985-30968986	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs188607889	chr2:30968992-30968993	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs575696491	chr2:30969042-30969043	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs181641239	chr2:30969052-30969053	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs564505524	chr2:30969064-30969065	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs546834003	chr2:30969112-30969113	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs533379053	chr2:30969125-30969126	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs535805689	chr2:30969135-30969136	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs144699636	chr2:30969256-30969257	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs148533173	chr2:30969292-30969293	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs549353370	chr2:30969299-30969300	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs369271089	chr2:30969305-30969306	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs141892858	chr2:30969322-30969323	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
30	rs186779076	chr2:30969330-30969331	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
31	rs540142212	chr2:30969343-30969344	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
32	rs536777620	chr2:30969381-30969382	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
33	rs550147637	chr2:30969384-30969385	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
34	rs2253243	chr2:30969385-30969386	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs539048201	chr2:30969391-30969392	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
36	rs529412449	chr2:30969398-30969399	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
37	rs114072036	chr2:30969399-30969400	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
38	rs569152671	chr2:30969411-30969412	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
39	rs535633112	chr2:30969428-30969429	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
40	rs555300624	chr2:30969455-30969456	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
41	rs2280402	chr2:30969462-30969463	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
42	rs479103	chr2:30969468-30969469	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
43	rs60866454	chr2:30969469-30969470	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
44	rs566837739	chr2:30969484-30969485	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
45	rs578037421	chr2:30969528-30969529	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
46	rs534097323	chr2:30969560-30969561	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
47	rs540641083	chr2:30969563-30969564	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
48	rs560758171	chr2:30969579-30969580	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
49	rs373541536	chr2:30969582-30969583	Weak transcription Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs150656168	chr2:30969671-30969672	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:63)

Disease	PMID	Source
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
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	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
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Autism	22495311	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Medulloblastoma	16968546	CNVD
Leukemia	18628472	CNVD
Autism	19521722	CNVD
Autism	18522746	CNVD
Breast cancer	21364760	CNVD
Wilms tumour	21544195	CNVD
Myxofibrosarcoma	16751306	CNVD
Non-small cell lung cancer	18927303	CNVD
Hepatocellular carcinoma	16750200	CNVD
Lung cancer	16740712	CNVD
Hereditary gingival fibromatosis	19633868	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Breast cancer	21785460	CNVD
Breast cancer	21509527	CNVD
Tetralogy of Fallot	22912587	CNVD
Myelofibrosis	22110671	CNVD
Barrett''s adenocarcinoma	18663352	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:30940600-30969600	Weak transcription	Stomach Mucosa	stomach
2	chr2:30957000-30969800	Weak transcription	Fetal Intestine Large	intestine
3	chr2:30960400-30980000	Weak transcription	Brain Hippocampus Middle	brain
4	chr2:30961600-30978400	Weak transcription	Pancreas	Pancrea
5	chr2:30962000-30970200	Weak transcription	Brain Substantia Nigra	brain
6	chr2:30963600-30969600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:30964000-30970600	Strong transcription	Gastric	stomach
8	chr2:30964400-30969000	Strong transcription	Fetal Intestine Small	intestine
9	chr2:30964400-30978600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr2:30965400-30968800	Strong transcription	Rectal Mucosa Donor 31	rectum
11	chr2:30965800-30999400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr2:30966000-30970000	Weak transcription	Colonic Mucosa	Colon
13	chr2:30966000-30970200	Weak transcription	Esophagus	oesophagus
14	chr2:30967400-30968800	Strong transcription	Duodenum Mucosa	Duodenum
15	chr2:30967400-30978800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:30968200-30985600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:30968600-30970400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr2:30968600-30975000	Weak transcription	Fetal Stomach	stomach
19	chr2:30968800-30969800	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr2:30968800-30970000	Weak transcription	Duodenum Mucosa	Duodenum
21	chr2:30968800-30970800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr2:30969000-30969800	Weak transcription	Fetal Intestine Small	intestine
23	chr2:30969600-30970800	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr2:30969600-30971000	Enhancers	Stomach Mucosa	stomach
25	chr2:30969800-30970200	Enhancers	Fetal Intestine Small	intestine
26	chr2:30969800-30970600	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr2:30969800-30970800	Enhancers	Fetal Intestine Large	intestine

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