Variant report

Variant	nsv980100
Chromosome Location	chr3:98714787-98766962
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:8)
LncRNA
region (count:3)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:98544275..98546874-chr3:98717004..98718969,2	MCF-7	breast:
2	chr3:98742090..98742958-chr3:98891307..98892432,5	MCF-7	breast:
3	chr3:98612664..98615119-chr3:98737659..98739776,2	K562	blood:
4	chr3:98742229..98743324-chr3:98833134..98833747,3	MCF-7	breast:
5	chr3:98742176..98742700-chr3:99472216..99472863,2	K562	blood:
6	chr3:98536130..98536715-chr3:98716022..98716899,2	MCF-7	breast:
7	chr3:98742225..98743062-chr3:98891577..98892142,2	MCF-7	breast:
8	chr2:75887719..75888507-chr3:98736202..98737122,2	MCF-7	breast:

(count:3 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ST3GAL6-1	chr3:98736900-98736966	ENSG00000239462.1
2	lnc-ST3GAL6-1	chr3:98737275-98737406	ENSG00000239462.1
3	lnc-ST3GAL6-2	chr3:98716614-98717323	NONHSAT090836

No data

Variant related genes	Relation type
ENSG00000057019	chromatin interactions

Extended variants
information (count: 1559 )
Associated
traits (count: 62 )

Variant overlapped rSNPs/rCNVs (count:1559 , 50 per page) page: 1 2 3 4 5 6 7 ... 32

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs78808757	chr3:98714813-98714814	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs368668509	chr3:98714824-98714825	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs200563895	chr3:98714828-98714829	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs540212782	chr3:98714833-98714834	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs539653533	chr3:98714851-98714852	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs190158450	chr3:98714854-98714855	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs555475586	chr3:98714855-98714856	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs138271227	chr3:98714952-98714953	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs376467693	chr3:98714954-98714955	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs541446300	chr3:98714958-98714959	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs112777664	chr3:98715020-98715021	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs555369280	chr3:98715050-98715051	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs575028858	chr3:98715098-98715099	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs540965767	chr3:98715113-98715114	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs560633501	chr3:98715140-98715141	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs193167134	chr3:98715171-98715172	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs541379704	chr3:98715185-98715186	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs1481634	chr3:98715228-98715229	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
19	rs184367353	chr3:98715236-98715237	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs374870350	chr3:98715237-98715238	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs189542207	chr3:98715369-98715370	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs564686015	chr3:98715375-98715376	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs563423079	chr3:98715384-98715385	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs181809438	chr3:98715393-98715394	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs563099376	chr3:98715397-98715398	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs547628180	chr3:98715429-98715430	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs530726473	chr3:98715434-98715435	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs539610443	chr3:98715480-98715481	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs34200903	chr3:98715485-98715486	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs532240258	chr3:98715493-98715494	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs564222471	chr3:98715528-98715529	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs143282592	chr3:98715541-98715542	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs569746281	chr3:98715566-98715567	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs6764579	chr3:98715635-98715636	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs568174346	chr3:98715663-98715664	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs114771612	chr3:98715713-98715714	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs571968559	chr3:98715717-98715718	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs185441532	chr3:98715721-98715722	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs112345099	chr3:98715739-98715740	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs554018317	chr3:98715741-98715742	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs577134024	chr3:98715759-98715760	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs148303710	chr3:98715790-98715791	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs562767804	chr3:98715798-98715799	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs189361008	chr3:98715820-98715821	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs7633464	chr3:98715823-98715824	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs562049975	chr3:98715860-98715861	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs527637353	chr3:98715871-98715872	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs547494635	chr3:98715893-98715894	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs376929903	chr3:98715908-98715909	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs564358294	chr3:98715909-98715910	Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:62)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Renal cell carcinoma	21668985	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Hirschsprung''s Disease	21712996	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Neurodevelopmental disorder	22521361	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
microdeletion syndrome	22180640	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Myelofibrosis	22110671	CNVD
Epilepsy	21858020	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
small cell lung cancer	20016488	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	17122850	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:98705600-98716400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:98711000-98721200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:98712800-98723000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:98713200-98721000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:98713800-98716400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:98716400-98717200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:98716400-98717600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:98717200-98730600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:98717600-98729200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:98721000-98721600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:98721200-98721800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:98721600-98724200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:98721800-98726200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:98722600-98723200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr3:98723000-98723600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:98726200-98726400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr3:98726400-98726600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:98726600-98740400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:98726800-98728000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr3:98728000-98728400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr3:98728200-98729000	Enhancers	K562	blood
22	chr3:98728400-98729000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr3:98730600-98730800	Enhancers	GM12878-XiMat	blood
24	chr3:98730600-98731400	Enhancers	HSMM	muscle
25	chr3:98730600-98732000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:98730800-98731200	Enhancers	Fetal Kidney	kidney
27	chr3:98730800-98731200	Flanking Active TSS	GM12878-XiMat	blood
28	chr3:98730800-98732200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:98731000-98731400	Enhancers	Primary B cells from peripheral blood	blood
30	chr3:98731200-98731800	Enhancers	GM12878-XiMat	blood
31	chr3:98731600-98732600	Enhancers	Placenta Amnion	Placenta Amnion
32	chr3:98736000-98737200	Weak transcription	Aorta	Aorta
33	chr3:98737200-98737400	Enhancers	Aorta	Aorta
34	chr3:98740400-98741200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:98740400-98741200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr3:98742600-98743200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:98747000-98753600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:98753600-98754000	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links