Variant report

Variant	esv3339173
Chromosome Location	chr3:48292529-48302277
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:48296580-48296730	WERI-Rb-1	eye:	n/a	n/a
2	CTCF	chr3:48296723-48296782	GM12891	blood:	n/a	n/a
3	CTCF	chr3:48296698-48296771	H1-hESC	embryonic stem cell:	n/a	n/a
4	GATA3	chr3:48295927-48296143	SH-SY5Y	brain:	n/a	n/a
5	GATA3	chr3:48299386-48299649	SH-SY5Y	brain:	n/a	n/a
6	IRF1	chr3:48299278-48299383	K562	blood:	n/a	n/a
7	JUN	chr3:48300033-48300040	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr3:48301191-48301248	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr3:48297674-48297734	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr3:48300583-48300709	MCF-7	breast:	n/a	n/a
11	POLR2A	chr3:48301597-48301813	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr3:48301484-48301489	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr3:48298242-48298329	HUVEC	blood vessel:	n/a	n/a
14	POLR2A	chr3:48297521-48297830	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr3:48297660-48297662	MCF-7	breast:	n/a	n/a
16	POLR2A	chr3:48301657-48301719	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr3:48298019-48298178	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr3:48297561-48297673	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:48300493-48300752	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr3:48297677-48297753	MCF-7	breast:	n/a	n/a
21	POLR2A	chr3:48300604-48300695	MCF-7	breast:	n/a	n/a
22	POLR2A	chr3:48298332-48298351	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr3:48298041-48298485	H1-hESC	embryonic stem cell:	n/a	n/a
24	SETDB1	chr3:48295998-48296584	U2OS	brain:	n/a	n/a
25	STAT3	chr3:48299613-48299884	MCF10A-Er-Src	breast:	n/a	n/a
26	YY1	chr3:48298271-48298538	H1-hESC	embryonic stem cell:	n/a	chr3:48298420-48298432
27	YY1	chr3:48298192-48298481	GM12892	blood:	n/a	chr3:48298420-48298432
28	YY1	chr3:48298220-48298558	H1-hESC	embryonic stem cell:	n/a	chr3:48298420-48298432

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48301212..48303241-chr3:48468487..48470721,2	MCF-7	breast:
2	chr3:48298868..48300972-chr3:48308573..48310773,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CAMP-1	chr3:48298077-48298512	NONHSAT089547
2	lnc-CAMP-1	chr3:48299419-48299451	NONHSAT089547

No data

Variant related genes	Relation type
ZNF589	TF binding region
MRPS18AP1	TF binding region

Extended variants
information (count: 324 )
Associated
traits (count: 100 )

Variant overlapped rSNPs/rCNVs (count:324 , 50 per page) page: 1 2 3 4 5 6 7

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs548419819	chr3:48292530-48292531	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs190937450	chr3:48292537-48292538	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs530649655	chr3:48292552-48292553	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs371763958	chr3:48292592-48292593	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs570390885	chr3:48292601-48292602	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs534606196	chr3:48292659-48292660	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs546229870	chr3:48292664-48292665	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs568744280	chr3:48292682-48292683	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs115602435	chr3:48292752-48292753	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs543825091	chr3:48292757-48292758	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs182831944	chr3:48292758-48292759	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs188879486	chr3:48292779-48292780	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs558223072	chr3:48292799-48292800	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs555938809	chr3:48292877-48292878	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs368652747	chr3:48292881-48292882	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs528880295	chr3:48292886-48292887	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs113298003	chr3:48292887-48292888	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs192421975	chr3:48292914-48292915	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs9311420	chr3:48292916-48292917	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs574804978	chr3:48292920-48292921	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs542122029	chr3:48292923-48292924	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs563507996	chr3:48292964-48292965	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs530715775	chr3:48293011-48293012	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs78599317	chr3:48293049-48293050	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs372193777	chr3:48293060-48293061	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs74341440	chr3:48293064-48293065	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs74498868	chr3:48293065-48293066	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs9311421	chr3:48293078-48293079	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
29	rs564209268	chr3:48293094-48293095	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
30	rs546811599	chr3:48293106-48293107	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs112656033	chr3:48293115-48293116	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs528131342	chr3:48293266-48293267	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs373907660	chr3:48293278-48293279	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs375512022	chr3:48293312-48293313	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs144457544	chr3:48293330-48293331	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs111906950	chr3:48293349-48293350	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs187285215	chr3:48293410-48293411	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs191703663	chr3:48293425-48293426	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs560100189	chr3:48293464-48293465	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs544070651	chr3:48293473-48293474	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs114227128	chr3:48293483-48293484	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs111414640	chr3:48293514-48293515	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs545806766	chr3:48293522-48293523	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs35414021	chr3:48293524-48293525	Weak transcription Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
45	rs375451412	chr3:48293529-48293530	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs189815531	chr3:48293582-48293583	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs79116108	chr3:48293585-48293586	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs199706178	chr3:48293675-48293676	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs9878281	chr3:48293689-48293690	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs112143686	chr3:48293692-48293693	Weak transcription Strong transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:100)

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
Chronic lymphocytic leukemia	20421269	CNVD
Melanoma	17363583	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Medullary thyroid carcinoma	18765511	CNVD
abnormal development	18461090	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Ovarian cancer	21781307	CNVD
Pancreatic cancer	17952125	CNVD
Developmental delay	21147756	CNVD

Chromatin state (count:347 , 50 per page) page: 1 2 3 4 5 6 7

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48283200-48309800	Weak transcription	Fetal Lung	lung
2	chr3:48283400-48295200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:48283400-48297600	Weak transcription	Right Ventricle	heart
4	chr3:48283400-48300400	Weak transcription	Gastric	stomach
5	chr3:48283400-48310000	Weak transcription	NH-A	brain
6	chr3:48283400-48315200	Weak transcription	Ovary	ovary
7	chr3:48283600-48297800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr3:48283600-48300200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr3:48283600-48300800	Weak transcription	Colon Smooth Muscle	Colon
10	chr3:48283600-48309600	Weak transcription	Fetal Intestine Large	intestine
11	chr3:48283800-48297600	Weak transcription	Esophagus	oesophagus
12	chr3:48283800-48307600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr3:48283800-48309400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:48283800-48310400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr3:48284000-48292600	Weak transcription	Colonic Mucosa	Colon
16	chr3:48284200-48297600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:48284200-48302800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr3:48285200-48297600	Weak transcription	Lung	lung
19	chr3:48285400-48303000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr3:48285600-48293800	Weak transcription	HSMM	muscle
21	chr3:48285600-48295600	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:48285600-48297200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:48285600-48308200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:48285600-48312400	Weak transcription	Psoas Muscle	Psoas
25	chr3:48285800-48297600	Weak transcription	Aorta	Aorta
26	chr3:48285800-48300200	Weak transcription	Fetal Muscle Leg	muscle
27	chr3:48285800-48307600	Weak transcription	Pancreas	Pancrea
28	chr3:48285800-48310200	Weak transcription	Fetal Brain Male	brain
29	chr3:48285800-48311000	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr3:48286200-48295800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr3:48286400-48309400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:48287000-48297000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr3:48288400-48292600	Strong transcription	Primary T cells from cord blood	blood
34	chr3:48288400-48298200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:48288600-48295000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:48288600-48312800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
37	chr3:48288800-48293000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr3:48288800-48293600	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr3:48288800-48295600	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr3:48289000-48293600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
41	chr3:48289200-48293600	Strong transcription	Cortex derived primary cultured neurospheres	brain
42	chr3:48289200-48297400	Weak transcription	Brain Angular Gyrus	brain
43	chr3:48289200-48297800	Weak transcription	Primary B cells from cord blood	blood
44	chr3:48289200-48312000	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr3:48289200-48312600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr3:48289400-48292800	Strong transcription	Brain Germinal Matrix	brain
47	chr3:48289400-48293600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr3:48289600-48292600	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr3:48289600-48293400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:48289600-48293400	Strong transcription	Dnd41	blood

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