Variant report

Variant	nsv237162
Chromosome Location	chr3:49444917-49446470
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr3:49444565-49445007	MCF10A-Er-Src	breast:	n/a	n/a
2	PAX5	chr3:49446103-49446378	GM12878	blood:	n/a	n/a
3	PAX5	chr3:49446158-49446329	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:49445347-49445503	HepG2	liver:	n/a	n/a
5	SETDB1	chr3:49445703-49446390	U2OS	brain:	n/a	n/a
6	USF1	chr3:49445850-49446040	SK-N-SH_RA	brain:	n/a	n/a
7	USF1	chr3:49445823-49445977	HepG2	liver:	n/a	n/a
8	USF2	chr3:49445846-49446018	Hela-S3	cervix:	n/a	chr3:49445941-49445952
9	USF2	chr3:49445880-49445989	GM12878	blood:	n/a	chr3:49445941-49445952
10	ZNF384	chr3:49446176-49446387	K562	blood:	n/a	n/a
11	ZNF384	chr3:49446210-49446221	GM12878	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:49375789..49379333-chr3:49446166..49450939,13	K562	blood:
2	chr3:49443013..49445153-chr3:49447014..49449649,3	MCF-7	breast:
3	chr3:49441534..49443566-chr3:49445020..49447765,2	K562	blood:
4	chr3:49441705..49446563-chr3:49447849..49450189,5	MCF-7	breast:
5	chr3:49375112..49379681-chr3:49446166..49452291,17	K562	blood:
6	chr3:49438129..49440566-chr3:49446328..49448559,2	K562	blood:
7	chr3:49433997..49436498-chr3:49444708..49446631,2	K562	blood:
8	chr3:49208493..49210199-chr3:49443469..49445452,2	MCF-7	breast:

No data

Variant related genes	Relation type
TCTA	TF binding region
ENSG00000067560	chromatin interactions
ENSG00000145022	chromatin interactions
ENSG00000114316	chromatin interactions
ENSG00000185909	chromatin interactions

Extended variants
information (count: 79 )
Associated
traits (count: 97 )

Variant overlapped rSNPs/rCNVs (count:79 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs386660839	chr3:49444917-49444918	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
2	rs62261211	chr3:49444918-49444919	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
3	rs62261212	chr3:49444920-49444921	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
4	rs68181721	chr3:49444921-49444922	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
5	rs190716817	chr3:49444929-49444930	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
6	rs575726516	chr3:49445040-49445041	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
7	rs199976643	chr3:49445059-49445060	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
8	rs142442466	chr3:49445069-49445070	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
9	rs539486470	chr3:49445100-49445101	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
10	rs558409405	chr3:49445126-49445127	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
11	rs573505804	chr3:49445161-49445162	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
12	rs113911822	chr3:49445248-49445249	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
13	rs561955849	chr3:49445256-49445257	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
14	rs113188621	chr3:49445280-49445281	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
15	rs369289782	chr3:49445291-49445292	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
16	rs573372673	chr3:49445357-49445358	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
17	rs200963379	chr3:49445362-49445363	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
18	rs543917482	chr3:49445366-49445367	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
19	rs557183919	chr3:49445390-49445391	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
20	rs532919674	chr3:49445399-49445400	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
21	rs568876936	chr3:49445429-49445430	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
22	rs79050907	chr3:49445484-49445485	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
23	rs560383531	chr3:49445488-49445489	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
24	rs536268798	chr3:49445493-49445494	Enhancers Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
25	rs527598341	chr3:49445515-49445516	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs549150313	chr3:49445540-49445541	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs567492682	chr3:49445548-49445549	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs529374760	chr3:49445573-49445574	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
29	rs576873636	chr3:49445577-49445578	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs373571514	chr3:49445596-49445597	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs544283857	chr3:49445599-49445600	Enhancers Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs6446267	chr3:49445610-49445611	Weak transcription Active TSS Flanking Active TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	mRNA abundance
33	rs201276082	chr3:49445611-49445612	Weak transcription Active TSS Flanking Active TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs190587395	chr3:49445612-49445613	Weak transcription Active TSS Flanking Active TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs569283562	chr3:49445642-49445643	Weak transcription Active TSS Flanking Active TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs539817438	chr3:49445645-49445646	Weak transcription Active TSS Flanking Active TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs201052777	chr3:49445663-49445664	Weak transcription Active TSS Flanking Active TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs557907145	chr3:49445673-49445674	Weak transcription Active TSS Flanking Active TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs193031651	chr3:49445676-49445677	Weak transcription Active TSS Flanking Active TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs7610067	chr3:49445682-49445683	Weak transcription Active TSS Flanking Active TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs534226717	chr3:49445683-49445684	Weak transcription Active TSS Flanking Active TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs149077972	chr3:49445688-49445689	Weak transcription Active TSS Flanking Active TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs6446268	chr3:49445695-49445696	Weak transcription Active TSS Flanking Active TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs201554707	chr3:49445698-49445699	Weak transcription Active TSS Flanking Active TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs201969071	chr3:49445702-49445703	Weak transcription Active TSS Flanking Active TSS Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs374230785	chr3:49445703-49445704	Weak transcription Active TSS Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
47	rs201245476	chr3:49445704-49445705	Weak transcription Active TSS Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
48	rs544430606	chr3:49445710-49445711	Weak transcription Active TSS Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
49	rs555836358	chr3:49445732-49445733	Weak transcription Active TSS Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
50	rs6446269	chr3:49445736-49445737	Weak transcription Active TSS Flanking Active TSS Enhancers	TF binding region Chromatin interactive region	3 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a

Variant related diseases (count:97)

Disease	PMID	Source
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
Glioblastoma multiforme	21080181	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
Medulloblastoma	21979893	CNVD
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Retinoblastoma	21504564	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Renal cell carcinoma	21668985	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Thoracic aortic aneurysm	21092924	CNVD
small cell lung cancer	20016488	CNVD
Lung cancer	18438408	CNVD
Intellectual disability	22102821	CNVD
Breast cancer	17603634	CNVD
Esophageal cancer	20955586	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Breast cancer	17133270	CNVD
Uveal melanoma	20484589	CNVD
Autism	22495311	CNVD
Melanoma	20688739	CNVD
Acute myeloid leukemia	21251322	CNVD
Hepatocellular carcinoma	16750200	CNVD
Cancer	21183584	CNVD
Kartagener syndrome	16639409	CNVD
Biliary cancer	19435499	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Malignant peripheral nerve sheath tumor	18522746	CNVD
Malignant mesothelioma	18160781	CNVD
Pleural malignant mesothelioma	18160781	CNVD
Prostate cancer	18632612	CNVD
Breast cancer	16397240	CNVD
Breast cancer	22032731	CNVD
Non-small cell lung cancer	20864512	CNVD
Colorectal cancer	16912164	CNVD
Non-small cell lung cancer	19010865	CNVD
Colorectal cancer	16272173	CNVD
Non-muscle invasive bladder neoplasm	19445696	CNVD
Acute myeloid leukemia	17268525	CNVD
Salivary gland tumor	18059337	CNVD
Gastric cancer	16891809	CNVD
Night blindness	17160897	CNVD
Cancer	17160897	CNVD
Breast cancer	20409316	CNVD
Lung cancer	17297452	CNVD
Multiple myeloma	16616336	CNVD
Effusion lymphoma	18079361	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Neuroblastoma	20406844	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	21045282	CNVD
Urothelial cell carcinoma	18451213	CNVD
Neuroblastoma	17327916	CNVD
Melanoma	17363583	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medullary thyroid carcinoma	18765511	CNVD
abnormal development	18461090	CNVD
Developmental delay	21147756	CNVD
Urothelial carcinoma	21177765	CNVD

Chromatin state (count:221 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49399000-49448000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:49406000-49445200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:49413200-49447400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:49427000-49448400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:49429000-49447200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:49431200-49447200	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr3:49433800-49447200	Weak transcription	Colonic Mucosa	Colon
8	chr3:49435400-49445600	Weak transcription	Fetal Brain Male	brain
9	chr3:49435400-49447000	Weak transcription	HSMMtube	muscle
10	chr3:49435400-49447800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:49435800-49446800	Weak transcription	Brain Angular Gyrus	brain
12	chr3:49438200-49446800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:49439000-49447200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr3:49439600-49447200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr3:49439800-49447000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr3:49440200-49447000	Weak transcription	Fetal Lung	lung
17	chr3:49441400-49447000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr3:49441400-49447000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:49441400-49447200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:49441600-49446000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:49441600-49447000	Weak transcription	Fetal Brain Female	brain
22	chr3:49441600-49447200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:49441600-49447600	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr3:49441800-49445000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr3:49441800-49445200	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr3:49441800-49447000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:49441800-49447200	Weak transcription	Fetal Intestine Large	intestine
28	chr3:49442800-49445200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:49442800-49445200	Enhancers	Adipose Nuclei	Adipose
30	chr3:49442800-49446400	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr3:49442800-49447000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:49442800-49447000	Enhancers	Primary T helper cells PMA-I stimulated	--
33	chr3:49442800-49447000	Enhancers	Fetal Muscle Leg	muscle
34	chr3:49442800-49447200	Enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr3:49442800-49447200	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr3:49442800-49447400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:49443000-49445400	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr3:49443000-49445600	Enhancers	Muscle Satellite Cultured Cells	--
39	chr3:49443000-49445600	Enhancers	Left Ventricle	heart
40	chr3:49443000-49445600	Enhancers	Right Atrium	heart
41	chr3:49443000-49446200	Enhancers	Duodenum Mucosa	Duodenum
42	chr3:49443000-49446400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:49443000-49447200	Enhancers	Primary T killer memory cells from peripheral blood	blood
44	chr3:49443000-49447200	Enhancers	Liver	Liver
45	chr3:49443200-49445400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr3:49443200-49446000	Enhancers	Breast Myoepithelial Primary Cells	Breast
47	chr3:49443200-49446000	Enhancers	Stomach Mucosa	stomach
48	chr3:49443200-49446400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr3:49443200-49446600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr3:49443200-49447000	Enhancers	Primary T cells fromperipheralblood	blood

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