Variant report

Variant	nsv237797
Chromosome Location	chr3:49811452-49817742
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:20)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:20 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr3:49816557-49816694	K562	blood:	n/a	n/a
2	MXI1	chr3:49812574-49813553	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr3:49812795-49812983	K562	blood:	n/a	n/a
4	POLR2A	chr3:49814002-49814021	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:49817688-49817969	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:49817676-49817683	HepG2	liver:	n/a	n/a
7	POLR2A	chr3:49812736-49812928	GM12878	blood:	n/a	n/a
8	POLR2A	chr3:49817700-49817753	HUVEC	blood vessel:	n/a	n/a
9	POLR2A	chr3:49811343-49811653	HepG2	liver:	n/a	n/a
10	POLR2A	chr3:49816267-49816307	MCF-7	breast:	n/a	n/a
11	POLR2A	chr3:49816133-49816344	HepG2	liver:	n/a	n/a
12	POLR2A	chr3:49813679-49813782	HepG2	liver:	n/a	n/a
13	POLR2A	chr3:49813814-49813905	HepG2	liver:	n/a	n/a
14	POLR2A	chr3:49814751-49814951	HepG2	liver:	n/a	n/a
15	POLR2A	chr3:49816803-49816808	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr3:49815948-49816310	K562	blood:	n/a	n/a
17	POLR2A	chr3:49816006-49816041	K562	blood:	n/a	n/a
18	POLR2A	chr3:49812806-49812832	K562	blood:	n/a	n/a
19	RCOR1	chr3:49816856-49816945	GM12878	blood:	n/a	n/a
20	USF1	chr3:49814342-49814457	GM12878	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49810586..49813373-chr3:49816346..49818932,2	K562	blood:
2	chr3:49816078..49819977-chr3:49822757..49825335,4	MCF-7	breast:
3	chr3:49816876..49821411-chr3:49821519..49825209,5	K562	blood:
4	chr3:49812806..49814691-chr3:49816470..49819799,3	K562	blood:
5	chr3:49811337..49813407-chr3:49816815..49819575,2	MCF-7	breast:
6	chr3:49816042..49818807-chr3:49821641..49823960,2	MCF-7	breast:
7	chr3:49812806..49814691-chr3:49816470..49819799,3	K562	blood:
8	chr3:49816140..49820070-chr3:49823380..49825359,3	K562	blood:
9	chr3:49790800..49792535-chr3:49809148..49811974,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM212A-1	chr3:49812718-49813047	NONHSAT089750

No data

Variant related genes	Relation type
ENSG00000244730	TF binding region
ENSG00000176095	chromatin interactions
ENSG00000244730	chromatin interactions

Extended variants
information (count: 222 )
Associated
traits (count: 99 )

Variant overlapped rSNPs/rCNVs (count:222 , 50 per page) page: 1 2 3 4 5

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs62260660	chr3:49811452-49811453	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
2	rs535585398	chr3:49811519-49811520	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
3	rs374324466	chr3:49811560-49811561	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
4	rs569246949	chr3:49811561-49811562	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
5	rs539881060	chr3:49811599-49811600	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
6	rs558164488	chr3:49811601-49811602	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
7	rs6801718	chr3:49811614-49811615	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
8	rs74713168	chr3:49811616-49811617	Weak transcription Strong transcription Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
9	rs540903978	chr3:49811661-49811662	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs180724140	chr3:49811685-49811686	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs574139085	chr3:49811697-49811698	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs112247868	chr3:49811701-49811702	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs145501770	chr3:49811733-49811734	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs537419879	chr3:49811734-49811735	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs532855147	chr3:49811804-49811805	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs375246940	chr3:49811841-49811842	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs544639188	chr3:49811859-49811860	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs139772399	chr3:49811862-49811863	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs535839751	chr3:49811863-49811864	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs570976616	chr3:49811956-49811957	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs191959267	chr3:49811965-49811966	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs527596621	chr3:49811968-49811969	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs538288763	chr3:49812156-49812157	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs549219232	chr3:49812232-49812233	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs147171683	chr3:49812282-49812283	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs531580435	chr3:49812296-49812297	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs34791912	chr3:49812311-49812312	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs78992774	chr3:49812312-49812313	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs56061204	chr3:49812318-49812319	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs140362704	chr3:49812320-49812321	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs397727064	chr3:49812322-49812323	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs541851312	chr3:49812348-49812349	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs569406811	chr3:49812406-49812407	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs149676010	chr3:49812408-49812409	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs558202969	chr3:49812424-49812425	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs1128315	chr3:49812450-49812451	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
37	rs566840456	chr3:49812500-49812501	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs534508831	chr3:49812559-49812560	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs182097415	chr3:49812594-49812595	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs35210174	chr3:49812606-49812607	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
41	rs145450485	chr3:49812609-49812610	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
42	rs556465821	chr3:49812632-49812633	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
43	rs112543459	chr3:49812639-49812640	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
44	rs577346759	chr3:49812641-49812642	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
45	rs148915892	chr3:49812642-49812643	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
46	rs544676083	chr3:49812697-49812698	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
47	rs185806914	chr3:49812714-49812715	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
48	rs371736313	chr3:49812767-49812768	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
49	rs190366772	chr3:49812821-49812822	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	lncRNA	n/a	Overlapped CNVs	n/a
50	rs7613603	chr3:49812866-49812867	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	lncRNA	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance

Variant related diseases (count:99)

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
Neuroblastoma	20406844	CNVD
Breast cancer	21785460	CNVD
Myelofibrosis	22110671	CNVD
Breast cancer	21045282	CNVD
Urothelial cell carcinoma	18451213	CNVD
Neuroblastoma	17327916	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medullary thyroid carcinoma	18765511	CNVD
abnormal development	18461090	CNVD
Developmental delay	21147756	CNVD
Urothelial carcinoma	21177765	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Adrenocortical carcinoma	18281524	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:367 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49775600-49817000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr3:49775800-49823000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr3:49776400-49812000	Weak transcription	HSMM	muscle
4	chr3:49776400-49812200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:49776400-49812600	Weak transcription	Gastric	stomach
6	chr3:49776400-49818000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:49776400-49818000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:49776400-49818200	Weak transcription	Fetal Kidney	kidney
9	chr3:49776600-49812000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr3:49782600-49814000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:49785600-49822400	Weak transcription	HSMMtube	muscle
12	chr3:49785600-49822600	Weak transcription	Esophagus	oesophagus
13	chr3:49785800-49812400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:49785800-49818000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr3:49786000-49812400	Weak transcription	NHEK	skin
16	chr3:49786000-49812600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:49786000-49812800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:49786000-49814400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr3:49786000-49823000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:49786200-49812000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:49786200-49812600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:49786200-49812600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr3:49786200-49822400	Weak transcription	HMEC	breast
24	chr3:49786400-49817800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr3:49786600-49812800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:49786600-49817800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr3:49787800-49812600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr3:49787800-49812600	Weak transcription	Thymus	Thymus
29	chr3:49791400-49812000	Weak transcription	Colon Smooth Muscle	Colon
30	chr3:49791800-49812400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:49792400-49812600	Weak transcription	Pancreas	Pancrea
32	chr3:49793800-49817600	Weak transcription	Spleen	Spleen
33	chr3:49795000-49818000	Weak transcription	Psoas Muscle	Psoas
34	chr3:49795000-49819000	Weak transcription	Right Ventricle	heart
35	chr3:49795000-49821000	Weak transcription	K562	blood
36	chr3:49795400-49822400	Weak transcription	Stomach Mucosa	stomach
37	chr3:49797200-49812600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:49797400-49812000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr3:49802400-49818000	Weak transcription	Right Atrium	heart
40	chr3:49804000-49812800	Weak transcription	Liver	Liver
41	chr3:49804000-49822600	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr3:49804200-49816000	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr3:49805400-49812600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr3:49806200-49818800	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr3:49806600-49819000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr3:49807400-49813000	Weak transcription	Primary B cells from cord blood	blood
47	chr3:49807600-49812000	Weak transcription	Brain Hippocampus Middle	brain
48	chr3:49807600-49812600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr3:49807600-49812600	Weak transcription	HUVEC	blood vessel
50	chr3:49807600-49817800	Weak transcription	Small Intestine	intestine

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