Variant report

Variant	nsv236940
Chromosome Location	chr3:49399471-49404775
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:49399867-49400079	T-47D	breast:	n/a	n/a
2	CTCF	chr3:49401391-49401443	GM10248	blood:	n/a	n/a
3	FOS	chr3:49400859-49401059	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr3:49400791-49400945	MCF10A-Er-Src	breast:	n/a	n/a
5	FOS	chr3:49400875-49400982	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr3:49400775-49401051	MCF10A-Er-Src	breast:	n/a	n/a
7	FOSL2	chr3:49400815-49401021	SK-N-SH	brain:	n/a	n/a
8	JUND	chr3:49400700-49401263	SK-N-SH	brain:	n/a	chr3:49400895-49400906
9	JUND	chr3:49400855-49400951	HepG2	liver:	n/a	chr3:49400895-49400906
10	POLR2A	chr3:49399516-49399519	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:49403435-49403581	HepG2	liver:	n/a	n/a
12	POLR2A	chr3:49399821-49399874	K562	blood:	n/a	n/a
13	POLR2A	chr3:49403649-49403746	A549	lung:	n/a	n/a
14	POLR2A	chr3:49400607-49400686	Hela-S3	cervix:	n/a	n/a
15	POLR2A	chr3:49402472-49402790	HepG2	liver:	n/a	n/a
16	POLR2A	chr3:49403880-49404373	GM12878	blood:	n/a	n/a
17	POLR2A	chr3:49399902-49399953	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr3:49400771-49401159	HL-60	blood:	n/a	n/a
19	POLR2A	chr3:49400967-49401256	HepG2	liver:	n/a	n/a
20	POLR2A	chr3:49403854-49404055	GM12878	blood:	n/a	n/a
21	POLR2A	chr3:49402591-49402610	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr3:49401312-49401364	HepG2	liver:	n/a	n/a
23	POLR2A	chr3:49400325-49400429	HepG2	liver:	n/a	n/a
24	POLR2A	chr3:49400228-49400350	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr3:49404175-49404250	HepG2	liver:	n/a	n/a
26	POLR2A	chr3:49404158-49404164	K562	blood:	n/a	n/a
27	POLR2A	chr3:49403791-49404157	HepG2	liver:	n/a	n/a
28	POLR2A	chr3:49404024-49404153	K562	blood:	n/a	n/a
29	POLR2A	chr3:49404104-49404194	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr3:49403976-49404010	K562	blood:	n/a	n/a
31	POLR2A	chr3:49399775-49399958	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr3:49401475-49401803	HepG2	liver:	n/a	n/a
33	POLR2A	chr3:49399430-49399511	HepG2	liver:	n/a	n/a
34	POLR2A	chr3:49403009-49403243	HepG2	liver:	n/a	n/a
35	POLR2A	chr3:49404017-49404018	K562	blood:	n/a	n/a
36	SP1	chr3:49399805-49400111	H1-hESC	embryonic stem cell:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr3:49399927..49402540-chr3:49449008..49451002,2	K562	blood:
2	chr3:49388313..49390760-chr3:49397473..49400161,2	K562	blood:
3	chr3:49401040..49402958-chr3:49448886..49451002,2	K562	blood:
4	chr3:49399346..49401429-chr3:49449633..49451334,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPX1-1	chr3:49402578-49402657	ENSG00000235908.1
2	lnc-GPX1-1	chr3:49404003-49404439	ENSG00000235908.1

No data

Variant related genes	Relation type
GPX1	TF binding region
RHOA-IT1	TF binding region
ENSG00000067560	chromatin interactions
ENSG00000145022	chromatin interactions

Extended variants
information (count: 183 )
Associated
traits (count: 106 )

Variant overlapped rSNPs/rCNVs (count:183 , 50 per page) page: 1 2 3 4

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs189553905	chr3:49399498-49399499	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
2	rs578181380	chr3:49399504-49399505	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
3	rs571459854	chr3:49399506-49399507	Strong transcription Weak transcription Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
4	rs533263475	chr3:49399535-49399536	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs551877494	chr3:49399542-49399543	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs142782307	chr3:49399548-49399549	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
7	rs528557832	chr3:49399577-49399578	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
8	rs556067808	chr3:49399593-49399594	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs567963207	chr3:49399615-49399616	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs372090764	chr3:49399627-49399628	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs538397434	chr3:49399632-49399633	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs556191739	chr3:49399637-49399638	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs551883544	chr3:49399678-49399679	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs544757665	chr3:49399701-49399702	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs147283934	chr3:49399706-49399707	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs140817473	chr3:49399708-49399709	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs542216360	chr3:49399716-49399717	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs528399583	chr3:49399752-49399753	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs144648358	chr3:49399773-49399774	Strong transcription Weak transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs575921051	chr3:49399804-49399805	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
21	rs543746019	chr3:49399827-49399828	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
22	rs201420764	chr3:49399865-49399866	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
23	rs367717912	chr3:49399900-49399901	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
24	rs371460390	chr3:49399936-49399937	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
25	rs368767616	chr3:49400007-49400008	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
26	rs375581663	chr3:49400069-49400070	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
27	rs532369602	chr3:49400074-49400075	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
28	rs377047325	chr3:49400095-49400096	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
29	rs551551295	chr3:49400134-49400135	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs560592273	chr3:49400187-49400188	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs527638670	chr3:49400191-49400192	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs549408260	chr3:49400237-49400238	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
33	rs139236210	chr3:49400304-49400305	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
34	rs182246457	chr3:49400319-49400320	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
35	rs56253168	chr3:49400362-49400363	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
36	rs114622176	chr3:49400424-49400425	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
37	rs974495	chr3:49400482-49400483	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
38	rs539242268	chr3:49400589-49400590	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs201829956	chr3:49400606-49400607	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs553401384	chr3:49400679-49400680	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
41	rs571815128	chr3:49400703-49400704	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
42	rs373346530	chr3:49400709-49400710	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
43	rs554140976	chr3:49400714-49400715	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
44	rs186793487	chr3:49400720-49400721	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
45	rs553337628	chr3:49400741-49400742	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
46	rs543335558	chr3:49400775-49400776	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
47	rs565202140	chr3:49400807-49400808	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
48	rs576936194	chr3:49400827-49400828	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
49	rs571749579	chr3:49400828-49400829	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
50	rs541224556	chr3:49400843-49400844	Strong transcription Weak transcription Genic enhancers Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:106)

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
Breast cancer	20668451	CNVD
Cancer	20668451	CNVD
Lung cancer	20668451	CNVD
Ovarian cancer	20668451	CNVD
Pancreas cancer	20668451	CNVD
Prostate cancer	20668451	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD
Schizophrenia	23813976	CNVD

Chromatin state (count:298 , 50 per page) page: 1 2 3 4 5 6

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49396400-49401600	Genic enhancers	Osteobl	bone
2	chr3:49396400-49413600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:49396400-49418600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:49396600-49399800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr3:49396600-49401400	Strong transcription	Primary B cells from cord blood	blood
6	chr3:49396600-49401400	Strong transcription	Placenta Amnion	Placenta Amnion
7	chr3:49396600-49401600	Strong transcription	Colon Smooth Muscle	Colon
8	chr3:49396600-49403600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:49396600-49406200	Strong transcription	Rectal Smooth Muscle	rectum
10	chr3:49396600-49410200	Weak transcription	Psoas Muscle	Psoas
11	chr3:49396600-49413200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:49396600-49413200	Strong transcription	Fetal Muscle Trunk	muscle
13	chr3:49396600-49413800	Strong transcription	Primary B cells from peripheral blood	blood
14	chr3:49396600-49414400	Weak transcription	Fetal Brain Male	brain
15	chr3:49396800-49399800	Strong transcription	Fetal Thymus	thymus
16	chr3:49396800-49399800	Weak transcription	Gastric	stomach
17	chr3:49396800-49401800	Strong transcription	Esophagus	oesophagus
18	chr3:49396800-49401800	Strong transcription	Fetal Lung	lung
19	chr3:49396800-49404000	Strong transcription	Sigmoid Colon	Sigmoid Colon
20	chr3:49396800-49406000	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:49396800-49406000	Strong transcription	Skeletal Muscle Male	skeletal muscle
22	chr3:49396800-49406200	Strong transcription	Stomach Smooth Muscle	stomach
23	chr3:49396800-49408000	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr3:49396800-49410800	Strong transcription	Primary neutrophils fromperipheralblood	blood
25	chr3:49396800-49412800	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr3:49396800-49413200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr3:49396800-49413400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:49396800-49413400	Strong transcription	Thymus	Thymus
29	chr3:49396800-49413600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:49396800-49438800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr3:49397000-49399800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:49397000-49400200	Strong transcription	Primary T cells from cord blood	blood
33	chr3:49397000-49401600	Strong transcription	Brain Anterior Caudate	brain
34	chr3:49397000-49401600	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr3:49397000-49401800	Strong transcription	Duodenum Smooth Muscle	Duodenum
36	chr3:49397000-49402000	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:49397000-49403400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr3:49397000-49406000	Strong transcription	H1 Cell Line	embryonic stem cell
39	chr3:49397000-49406200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:49397000-49406400	Strong transcription	HUES48 Cell Line	embryonic stem cell
41	chr3:49397000-49408000	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr3:49397000-49412800	Strong transcription	Lung	lung
43	chr3:49397000-49413000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:49397000-49413200	Strong transcription	Adipose Nuclei	Adipose
45	chr3:49397000-49415200	Strong transcription	Fetal Stomach	stomach
46	chr3:49397200-49400000	Strong transcription	Brain Cingulate Gyrus	brain
47	chr3:49397200-49400400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr3:49397200-49400600	Strong transcription	Fetal Brain Female	brain
49	chr3:49397200-49401000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr3:49397200-49401000	Strong transcription	Brain Hippocampus Middle	brain

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