Variant report

Variant	nsv525856
Chromosome Location	chr20:12941696-12947126
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:7)
LncRNA
region (count:6)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:12905418..12906763-chr20:12946186..12947828,17	MCF-7	breast:
2	chr20:12906070..12908369-chr20:12946069..12948002,2	MCF-7	breast:
3	chr20:12904584..12906657-chr20:12946403..12948442,2	MCF-7	breast:
4	chr2:201161815..201162676-chr20:12942962..12943611,2	MCF-7	breast:
5	chr20:12941463..12943706-chr20:12945619..12947454,2	MCF-7	breast:
6	chr20:12941463..12943706-chr20:12945619..12947454,2	MCF-7	breast:
7	chr20:12905518..12906454-chr20:12946845..12948133,8	MCF-7	breast:

(count:6 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPTLC3-1	chr20:12946650-12946820	NONHSAT078664
2	lnc-SPTLC3-1	chr20:12946646-12946820	XLOC_013465
3	lnc-SPTLC3-1	chr20:12946581-12946820	NONHSAT078665
4	lnc-SPTLC3-1	chr20:12946729-12946820	XLOC_013465
5	lnc-SPTLC3-1	chr20:12946646-12946820	NONHSAT078674
6	lnc-SPTLC3-1	chr20:12946729-12946820	XLOC_013465

No data

Variant related genes	Relation type
ITGB2	miRNA target sites

Extended variants
information (count: 179 )
Associated
traits (count: 54 )

Variant overlapped rSNPs/rCNVs (count:179 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs6041737	chr20:12941696-12941697	Weak transcription	n/a	n/a	Overlapped CNVs	mRNA abundance
2	rs538397611	chr20:12941703-12941704	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs189644692	chr20:12941705-12941706	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs578182121	chr20:12941749-12941750	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs113478289	chr20:12941756-12941757	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs73079703	chr20:12941782-12941783	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs191447191	chr20:12941807-12941808	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs148773886	chr20:12941811-12941812	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs542619227	chr20:12941844-12941845	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs73253225	chr20:12941850-12941851	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs576174591	chr20:12941942-12941943	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs544865426	chr20:12942016-12942017	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs565122096	chr20:12942021-12942022	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs527569502	chr20:12942081-12942082	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs543400167	chr20:12942120-12942121	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs140335685	chr20:12942140-12942141	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs371963263	chr20:12942166-12942167	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs76970748	chr20:12942175-12942176	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs533317991	chr20:12942178-12942179	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs549806407	chr20:12942212-12942213	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs567511936	chr20:12942217-12942218	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs6078843	chr20:12942239-12942240	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
23	rs6078844	chr20:12942242-12942243	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs34707796	chr20:12942311-12942312	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs184759915	chr20:12942327-12942328	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs571782648	chr20:12942367-12942368	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs371854186	chr20:12942373-12942374	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs554002175	chr20:12942388-12942389	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs573995583	chr20:12942459-12942460	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs150370776	chr20:12942468-12942469	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs6041738	chr20:12942525-12942526	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
32	rs74628219	chr20:12942526-12942527	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs189524256	chr20:12942583-12942584	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs138073123	chr20:12942590-12942591	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs8183164	chr20:12942600-12942601	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs557857533	chr20:12942624-12942625	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs547156803	chr20:12942627-12942628	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs3848744	chr20:12942649-12942650	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs181509227	chr20:12942688-12942689	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs563310819	chr20:12942691-12942692	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs184640918	chr20:12942699-12942700	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
42	rs143746101	chr20:12942755-12942756	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
43	rs373463762	chr20:12942853-12942854	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs6078845	chr20:12942961-12942962	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs189506096	chr20:12942968-12942969	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs527837422	chr20:12942992-12942993	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs181559632	chr20:12943029-12943030	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs567610115	chr20:12943089-12943090	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs536581212	chr20:12943098-12943099	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs185931202	chr20:12943201-12943202	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:54)

Disease	PMID	Source
Breast cancer	16397240	CNVD
abortions and stillbirths	19751515	CNVD
Wilms tumour	21544195	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Breast cancer	16272173	CNVD
Melanoma	18172304	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Ewing''s sarcoma	21437220	CNVD
Oral cancer	19627613	CNVD
colon cancer	17210682	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Glioblastoma multiforme	21080181	CNVD
Thyroid cancer	19087340	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Cancer	16751803	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Colorectal cancer	19359472	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Human rectal carcinomas	16397240	CNVD
Olfactory neuroblastoma	18408657	CNVD
Central neurocytomas	17123091	CNVD
Colorectal cancer	16272173	CNVD
Medulloblastoma	21979893	CNVD
Gastric cancer	17908304	CNVD
Urothelial carcinoma	21177765	CNVD
Acute myeloid leukemia	20729466	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Ewing''s sarcoma	17952124	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Colorectal cancer	21645411	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Autism	22495311	CNVD
Glaucoma	21310917	CNVD
Alagille syndrome	22470819	CNVD
Lung cancer	16773561	CNVD
Renal cell carcinoma	18765545	CNVD
Alagille syndrome	17576883	CNVD
Anaplastic large cell lymphoma	18179710	CNVD
Prostate cancer	18632612	CNVD
Ewing''s sarcoma	18628472	CNVD
Glioblastoma multiforme	18628472	CNVD
Leukemia	18628472	CNVD
Myelofibrosis	22110671	CNVD
Kabuki syndrome	21720541	CNVD
Glioblastoma multiforme	22286061	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Neurocytoma	17123091	CNVD
Autism	22102821	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:12937200-12946000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr20:12942200-12942800	Enhancers	A549	lung
3	chr20:12942800-12949200	Weak transcription	A549	lung
4	chr20:12943000-12943200	Enhancers	Fetal Kidney	kidney
5	chr20:12943000-12947400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr20:12943200-12943800	Weak transcription	Fetal Kidney	kidney
7	chr20:12943600-12944200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr20:12943600-12944600	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr20:12943600-12945800	Enhancers	Thymus	Thymus
10	chr20:12943800-12944600	Enhancers	Fetal Kidney	kidney
11	chr20:12944000-12944200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr20:12944000-12944200	Enhancers	Fetal Thymus	thymus
13	chr20:12944000-12944400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr20:12944000-12944400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr20:12944200-12944600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr20:12944400-12945400	Weak transcription	Fetal Thymus	thymus
17	chr20:12944400-12946000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr20:12944600-12946200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr20:12945400-12948400	Enhancers	Fetal Thymus	thymus
20	chr20:12945600-12946600	Enhancers	Brain Hippocampus Middle	brain
21	chr20:12945600-12946800	Enhancers	Brain Anterior Caudate	brain
22	chr20:12945600-12947800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr20:12945800-12946200	Enhancers	HUVEC	blood vessel
24	chr20:12945800-12946400	Flanking Active TSS	Thymus	Thymus
25	chr20:12945800-12946600	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr20:12945800-12946800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr20:12946000-12946400	Enhancers	HSMM	muscle
28	chr20:12946000-12946600	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr20:12946000-12946800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr20:12946000-12946800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr20:12946000-12946800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr20:12946000-12946800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr20:12946000-12946800	Enhancers	Brain Cingulate Gyrus	brain
34	chr20:12946000-12947000	Enhancers	Brain Substantia Nigra	brain
35	chr20:12946000-12947200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr20:12946200-12946600	Enhancers	Brain Germinal Matrix	brain
37	chr20:12946200-12946600	Enhancers	Fetal Muscle Leg	muscle
38	chr20:12946200-12947000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr20:12946200-12947000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr20:12946200-12947200	Enhancers	Primary T cells from cord blood	blood
41	chr20:12946200-12948000	Enhancers	Fetal Brain Male	brain
42	chr20:12946400-12946800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr20:12946400-12947000	Enhancers	HepG2	liver
44	chr20:12946400-12947400	Active TSS	Thymus	Thymus
45	chr20:12946600-12946800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr20:12947000-12947400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr20:12947000-12947400	Weak transcription	HepG2	liver

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