Variant report

Variant	esv3343395
Chromosome Location	chr3:50415498-50418296
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50372057..50375135-chr3:50415126..50417223,3	K562	blood:
2	chr3:50415673..50418244-chr3:50436482..50438433,2	K562	blood:
3	chr3:50406050..50408278-chr3:50414386..50416245,2	MCF-7	breast:
4	chr3:50335932..50338448-chr3:50416398..50418130,2	K562	blood:
5	chr3:50402721..50404447-chr3:50416465..50418534,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186792	chromatin interactions
ENSG00000243477	chromatin interactions
ENSG00000271858	chromatin interactions
ENSG00000068028	chromatin interactions
ENSG00000007402	chromatin interactions

Extended variants
information (count: 115 )
Associated
traits (count: 97 )

Variant overlapped rSNPs/rCNVs (count:115 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs377399843	chr3:50415518-50415519	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs201985877	chr3:50415526-50415527	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs200790128	chr3:50415537-50415538	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs587629057	chr3:50415550-50415551	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs144676126	chr3:50415572-50415573	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs184175973	chr3:50415575-50415576	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs148518110	chr3:50415579-50415580	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs587650541	chr3:50415593-50415594	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs587727641	chr3:50415631-50415632	Enhancers Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs12485286	chr3:50415642-50415643	Enhancers Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
11	rs140504242	chr3:50415664-50415665	Enhancers Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs587731602	chr3:50415686-50415687	Enhancers Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs587609031	chr3:50415697-50415698	Enhancers Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs151272438	chr3:50415781-50415782	Enhancers Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs587747581	chr3:50415808-50415809	Enhancers Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
16	rs587614821	chr3:50415860-50415861	Enhancers Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
17	rs587679485	chr3:50415874-50415875	Enhancers Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs80142410	chr3:50415981-50415982	Enhancers Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs587626450	chr3:50416002-50416003	Enhancers Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs587683492	chr3:50416047-50416048	Enhancers Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
21	rs587762068	chr3:50416070-50416071	Enhancers Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs140472079	chr3:50416088-50416089	Enhancers Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs587691377	chr3:50416115-50416116	Enhancers Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs374920567	chr3:50416127-50416128	Enhancers Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs587751221	chr3:50416128-50416129	Enhancers Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs144423512	chr3:50416153-50416154	Enhancers Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs75017764	chr3:50416181-50416182	Enhancers Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs188556110	chr3:50416239-50416240	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs180915606	chr3:50416265-50416266	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs117760698	chr3:50416287-50416288	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs587607131	chr3:50416289-50416290	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs587668162	chr3:50416293-50416294	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs202140446	chr3:50416332-50416333	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs587596090	chr3:50416333-50416334	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs375988858	chr3:50416336-50416337	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs35677804	chr3:50416346-50416347	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs370345961	chr3:50416382-50416383	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs587671504	chr3:50416383-50416384	Enhancers Weak transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
39	rs150534078	chr3:50416404-50416405	Enhancers Weak transcription Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
40	rs201386438	chr3:50416419-50416420	Enhancers Weak transcription Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
41	rs201656322	chr3:50416429-50416430	Enhancers Weak transcription Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
42	rs376124541	chr3:50416438-50416439	Enhancers Weak transcription Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
43	rs371624739	chr3:50416462-50416463	Enhancers Weak transcription Genic enhancers Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
44	rs5030977	chr3:50416501-50416502	Enhancers Weak transcription Genic enhancers Strong transcription	Chromatin interactive region	5 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
45	rs587741526	chr3:50416503-50416504	Enhancers Weak transcription Genic enhancers Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
46	rs587611382	chr3:50416508-50416509	Enhancers Weak transcription Genic enhancers Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
47	rs587694555	chr3:50416509-50416510	Enhancers Weak transcription Genic enhancers Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
48	rs150031515	chr3:50416556-50416557	Enhancers Weak transcription Genic enhancers Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
49	rs587639951	chr3:50416559-50416560	Enhancers Weak transcription Genic enhancers Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
50	rs142559701	chr3:50416594-50416595	Enhancers Weak transcription Genic enhancers Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	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
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
Developmental delay	21147756	CNVD
Urothelial carcinoma	21177765	CNVD
Pancreatic endocrine tumor	17639061	CNVD
Cancer	20164919	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50403200-50417200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:50405000-50416400	Weak transcription	Gastric	stomach
3	chr3:50408800-50423800	Weak transcription	Fetal Brain Female	brain
4	chr3:50409000-50419600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:50409200-50420200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:50410200-50415800	Weak transcription	Spleen	Spleen
7	chr3:50411400-50419200	Weak transcription	Fetal Kidney	kidney
8	chr3:50411400-50422600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:50411400-50430000	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:50411600-50416400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:50412800-50417200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr3:50412800-50428000	Weak transcription	Right Ventricle	heart
13	chr3:50413000-50417600	Weak transcription	Fetal Muscle Leg	muscle
14	chr3:50413000-50418800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:50413200-50419200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:50413200-50421000	Weak transcription	Lung	lung
17	chr3:50414000-50415600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:50414000-50420600	Weak transcription	Fetal Intestine Small	intestine
19	chr3:50414800-50416800	Weak transcription	Brain Germinal Matrix	brain
20	chr3:50415000-50419600	Weak transcription	Ovary	ovary
21	chr3:50415200-50417000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:50415200-50428400	Weak transcription	Brain Anterior Caudate	brain
23	chr3:50415400-50415600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr3:50415400-50417000	Enhancers	H1 Cell Line	embryonic stem cell
25	chr3:50415600-50416000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:50415600-50416200	Bivalent Enhancer	HepG2	liver
27	chr3:50415800-50416000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:50415800-50416000	Enhancers	Spleen	Spleen
29	chr3:50416000-50416400	Weak transcription	Spleen	Spleen
30	chr3:50416000-50421200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr3:50416400-50416800	Enhancers	Spleen	Spleen
32	chr3:50416400-50417000	Strong transcription	Gastric	stomach
33	chr3:50416400-50417400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
34	chr3:50416600-50416800	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:50416800-50417000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:50416800-50417000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr3:50416800-50419600	Weak transcription	Fetal Stomach	stomach
38	chr3:50416800-50420200	Weak transcription	Spleen	Spleen
39	chr3:50416800-50420600	Enhancers	Brain Germinal Matrix	brain
40	chr3:50417000-50417400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr3:50417000-50418400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr3:50417000-50428000	Weak transcription	Gastric	stomach
43	chr3:50417400-50420400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:50417600-50418200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
45	chr3:50417600-50421400	Enhancers	Fetal Muscle Leg	muscle
46	chr3:50417800-50418000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr3:50418000-50418400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
48	chr3:50418000-50418800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:50418200-50420000	Enhancers	Fetal Thymus	thymus
50	chr3:50418200-50421600	Enhancers	Fetal Muscle Trunk	muscle

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