Variant report

Variant	nsv963300
Chromosome Location	chr3:19981798-19984730
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:19984240-19984316	HepG2	liver:	n/a	n/a
2	CTCF	chr3:19984233-19984436	K562	blood:	n/a	n/a
3	CTCF	chr3:19984240-19984390	MCF-7	breast:	n/a	n/a
4	CTCF	chr3:19984231-19984317	Hela-S3	cervix:	n/a	n/a
5	CTCF	chr3:19984256-19984345	MCF-7	breast:	n/a	n/a
6	CTCF	chr3:19984540-19984690	HFF-Myc	foreskin:	n/a	n/a
7	IRF1	chr3:19984032-19984046	K562	blood:	n/a	n/a
8	POLR2A	chr3:19984487-19984541	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr3:19981977-19982138	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr3:19984622-19984752	MCF10A-Er-Src	breast:	n/a	n/a
11	REST	chr3:19982164-19982485	MCF-7	breast:	n/a	n/a
12	REST	chr3:19982162-19982508	ECC-1	luminal epithelium:	n/a	n/a
13	REST	chr3:19982124-19982530	MCF-7	breast:	n/a	n/a
14	TBL1XR1	chr3:19982586-19982594	K562	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:19976162..19983592-chr3:19985528..19991017,8	MCF-7	breast:
2	chr3:19979250..19980946-chr3:19981520..19983771,2	K562	blood:
3	chr3:19979101..19981901-chr3:20077826..20080437,2	K562	blood:
4	chr3:19980872..19982514-chr3:19987046..19988631,2	MCF-7	breast:

No data

Variant related genes	Relation type
RAB5A	TF binding region
ENSG00000163576	chromatin interactions
ENSG00000144566	chromatin interactions

Extended variants
information (count: 111 )
Associated
traits (count: 75 )

Variant overlapped rSNPs/rCNVs (count:111 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs571004789	chr3:19981820-19981821	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs538357517	chr3:19981918-19981919	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs553307273	chr3:19981941-19981942	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs150299636	chr3:19981957-19981958	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs536122733	chr3:19981989-19981990	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs368656325	chr3:19982040-19982041	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs536520649	chr3:19982044-19982045	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs576287370	chr3:19982075-19982076	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs181554021	chr3:19982106-19982107	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs558826523	chr3:19982110-19982111	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs34675401	chr3:19982126-19982127	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs73819072	chr3:19982134-19982135	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs2170342	chr3:19982135-19982136	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
14	rs9838931	chr3:19982225-19982226	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs368565126	chr3:19982243-19982244	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs137855010	chr3:19982250-19982251	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs34659699	chr3:19982267-19982268	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs370488139	chr3:19982268-19982269	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs541889510	chr3:19982278-19982279	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs187152390	chr3:19982334-19982335	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs531155148	chr3:19982406-19982407	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs72545855	chr3:19982493-19982494	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs191790407	chr3:19982518-19982519	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs532051061	chr3:19982521-19982522	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs547106133	chr3:19982585-19982586	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs565675721	chr3:19982600-19982601	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs140727735	chr3:19982612-19982613	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs554316649	chr3:19982651-19982652	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs377656776	chr3:19982678-19982679	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs577649749	chr3:19982687-19982688	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs539861420	chr3:19982696-19982697	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs536953768	chr3:19982751-19982752	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs558736484	chr3:19982793-19982794	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs138440874	chr3:19982797-19982798	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs184095174	chr3:19982814-19982815	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs553487701	chr3:19982848-19982849	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs574863665	chr3:19982879-19982880	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs185825365	chr3:19982903-19982904	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs376006378	chr3:19982917-19982918	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs563572045	chr3:19982925-19982926	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs531189568	chr3:19982941-19982942	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs4241540	chr3:19982972-19982973	Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
43	rs142955819	chr3:19983000-19983001	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs528646797	chr3:19983058-19983059	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs546821049	chr3:19983074-19983075	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs542902594	chr3:19983075-19983076	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs565766082	chr3:19983081-19983082	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs532792114	chr3:19983124-19983125	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs529793550	chr3:19983177-19983178	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs372193597	chr3:19983194-19983195	Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:75)

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	22495311	CNVD
Autism	20531469	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Ovarian cancer	21781307	CNVD

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19973600-19987200	Weak transcription	Primary B cells from peripheral blood	blood
2	chr3:19975600-19987400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:19976000-19987400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:19979600-19987600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:19979600-19987800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:19980000-19986600	Weak transcription	K562	blood
7	chr3:19982200-19987200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:19983200-19987400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr3:19983800-19987600	Weak transcription	Aorta	Aorta
10	chr3:19984200-19984800	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr3:19984400-19984600	ZNF genes & repeats	Brain Germinal Matrix	brain
12	chr3:19984600-19987400	Weak transcription	Brain Germinal Matrix	brain

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