Variant report

Variant	nsv876595
Chromosome Location	chr3:19512074-19726308
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:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:2)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:73474420..73475033-chr3:19519900..19520713,2	MCF-7	breast:
2	chr3:16317176..16319617-chr3:19576040..19578450,2	MCF-7	breast:
3	chr3:19106420..19107155-chr3:19584445..19585029,2	MCF-7	breast:
4	chr1:62901559..62902065-chr3:19594424..19594924,2	Hela-S3	cervix:
5	chr3:19679630..19681949-chr3:19683459..19685004,2	K562	blood:
6	chr3:19679630..19681949-chr3:19683459..19685004,2	K562	blood:
7	chr3:19390113..19391205-chr3:19584358..19585952,11	MCF-7	breast:
8	chr3:19525585..19527422-chr3:19576707..19579689,2	MCF-7	breast:
9	chr3:19525585..19527422-chr3:19576707..19579689,2	MCF-7	breast:
10	chr3:19489514..19491858-chr3:19516874..19519279,2	K562	blood:
11	chr3:19390558..19391094-chr3:19584541..19585367,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EFHB-1	chr3:19717560-19717598	XLOC_003064

No data

(count:2 , 50 per page) page: 1

No.	miRNA target gene	miRNA name	Chromosome Location	mirBase accession
1	KCNH8	hsa-miR-143-3p	chr3:19576050-19576073
2	KCNH8	hsa-miR-143-3p	chr3:19576066-19576072

Variant related genes	Relation type
ENSG00000270739	chromatin interactions
ENSG00000162607	chromatin interactions
ESYT1	miRNA target sites

Extended variants
information (count: 4439 )
Associated
traits (count: 76 )

Variant overlapped rSNPs/rCNVs (count:4439 , 50 per page) page: 1 2 3 4 5 6 7 ... 89

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs6800537	chr3:19512074-19512075	Enhancers Strong transcription Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs183013992	chr3:19512100-19512101	Enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs550755562	chr3:19512125-19512126	Enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs186139258	chr3:19512163-19512164	Enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs369425753	chr3:19512170-19512171	Enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs17005998	chr3:19512172-19512173	Enhancers Strong transcription Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs551735014	chr3:19512206-19512207	Enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs190857680	chr3:19512254-19512255	Enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs534199302	chr3:19512290-19512291	Enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs573191595	chr3:19512291-19512292	Enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs202105290	chr3:19512318-19512319	Enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs373585213	chr3:19512448-19512449	Enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs184153459	chr3:19512472-19512473	Enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs565133894	chr3:19512485-19512486	Enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs377405709	chr3:19512590-19512591	Enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs187487353	chr3:19512597-19512598	Enhancers Strong transcription Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs200540466	chr3:19512622-19512623	Enhancers Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs578133087	chr3:19512683-19512684	Enhancers Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs576954008	chr3:19512690-19512691	Enhancers Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs576332868	chr3:19512697-19512698	Enhancers Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs545560700	chr3:19512698-19512699	Enhancers Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs560437114	chr3:19512705-19512706	Enhancers Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs538560815	chr3:19512721-19512722	Enhancers Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
24	rs558678543	chr3:19512776-19512777	Enhancers Weak transcription Strong transcription Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
25	rs192667593	chr3:19512827-19512828	Enhancers ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs561304646	chr3:19512828-19512829	Enhancers ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs370506072	chr3:19512843-19512844	Enhancers ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs182685277	chr3:19512881-19512882	Enhancers ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs550444939	chr3:19512966-19512967	Enhancers ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs187012406	chr3:19512994-19512995	Enhancers ZNF genes & repeats Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs191845305	chr3:19513027-19513028	Enhancers Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs551566795	chr3:19513048-19513049	Enhancers Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs566781286	chr3:19513071-19513072	Enhancers Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs184196169	chr3:19513085-19513086	Enhancers Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs541488837	chr3:19513134-19513135	Enhancers Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs374891603	chr3:19513153-19513154	Enhancers Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs549293089	chr3:19513176-19513177	Enhancers Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs567590395	chr3:19513195-19513196	Enhancers Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs140258684	chr3:19513212-19513213	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs574480221	chr3:19513221-19513222	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs188949304	chr3:19513229-19513230	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs578026253	chr3:19513237-19513238	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs543450345	chr3:19513251-19513252	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs563634299	chr3:19513305-19513306	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs577844015	chr3:19513322-19513323	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs538864344	chr3:19513340-19513341	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs78163900	chr3:19513343-19513344	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs572412243	chr3:19513344-19513345	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs533811672	chr3:19513376-19513377	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs542960644	chr3:19513380-19513381	Weak transcription ZNF genes & repeats Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:76)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Esophageal squamous carcinoma	18405350	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	17603634	CNVD
Neuroblastoma	17327916	CNVD
Glioblastoma multiforme	21080181	CNVD
Neuroblastoma	18923191	CNVD
Colorectal cancer	21297112	CNVD
Lynch syndrome	18415027	CNVD
Renal cell carcinoma	18592004	CNVD
Acute myeloid leukemia	20729466	CNVD
Urothelial carcinoma	18382360	CNVD
Melanoma	18172304	CNVD
Cervical cancer	21062161	CNVD
Hirschsprung''s Disease	21712996	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Insulin resistance	16721378	CNVD
Neuroblastoma	18664255	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Ewing''s sarcoma	21437220	CNVD
Neuroblastoma	21484798	CNVD
Non-small cell lung cancer	21044232	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Oral cancer	19627613	CNVD
Renal cell carcinoma	19461508	CNVD
Epithelial cancer	22065749	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Acute myeloid leukemia	16864856	CNVD
Liposarcoma	21253554	CNVD
Basal cell lymphoma	21115979	CNVD
Endometrial cancer	22040021	CNVD
Pancreatic endocrine tumor	20981439	CNVD
Astrocytoma	17387387	CNVD
Breast cancer	21264507	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Glioblastoma multiforme	17387387	CNVD
Oral cancer	21386901	CNVD
Cutaneous squamous cell carcinomas	19131950	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
lymphocytic leukemia	21291569	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Lung cancer	20668451	CNVD
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Esophageal cancer	20955586	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Myelofibrosis	22110671	CNVD
Gastric adenocarcinoma	19115996	CNVD
Squamous cell cancer	20885788	CNVD
Esophageal squamous carcinoma	17470683	CNVD
Breast cancer	17133270	CNVD
Developmental delay	21147756	CNVD
Uveal melanoma	20484589	CNVD
Autism	20531469	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:310 , 50 per page) page: 1 2 3 4 5 6 7

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19474400-19513200	Weak transcription	Brain Germinal Matrix	brain
2	chr3:19480400-19514400	Weak transcription	Brain Hippocampus Middle	brain
3	chr3:19498600-19512600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:19502200-19512800	Weak transcription	Primary B cells from cord blood	blood
5	chr3:19509600-19513000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:19509800-19512400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:19510600-19512800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:19511200-19513000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:19511200-19515000	Weak transcription	Pancreas	Pancrea
10	chr3:19511800-19512800	Weak transcription	Primary B cells from peripheral blood	blood
11	chr3:19512000-19512600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr3:19512200-19513200	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr3:19512400-19512600	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr3:19512400-19513000	Enhancers	H1 Cell Line	embryonic stem cell
15	chr3:19512600-19512800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:19512600-19512800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
17	chr3:19512600-19513000	Enhancers	H9 Cell Line	embryonic stem cell
18	chr3:19512600-19513000	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr3:19512600-19513000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr3:19512600-19513200	Enhancers	ES-I3 Cell Line	embryonic stem cell
21	chr3:19512600-19513200	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr3:19512600-19513200	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr3:19512800-19513000	ZNF genes & repeats	Primary B cells from cord blood	blood
24	chr3:19512800-19513200	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr3:19512800-19513200	Strong transcription	Primary B cells from peripheral blood	blood
26	chr3:19512800-19513600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:19512800-19514000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr3:19512800-19515000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:19513000-19513200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:19513000-19513800	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr3:19513000-19517400	Weak transcription	Primary B cells from cord blood	blood
32	chr3:19513000-19517600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:19513000-19532400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:19513200-19513600	Strong transcription	Brain Germinal Matrix	brain
35	chr3:19513200-19513800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:19513200-19514000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
37	chr3:19513200-19515600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr3:19513600-19515000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:19513600-19517800	Weak transcription	Brain Germinal Matrix	brain
40	chr3:19513800-19514200	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:19513800-19514400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
42	chr3:19514000-19514600	Strong transcription	Primary B cells from peripheral blood	blood
43	chr3:19514000-19514800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:19514200-19515800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:19514400-19515400	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr3:19514600-19530200	Weak transcription	Primary B cells from peripheral blood	blood
47	chr3:19514800-19517200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:19514800-19518600	Enhancers	iPS-18 Cell Line	embryonic stem cell
49	chr3:19515000-19518800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:19515000-19519200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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