Variant report

Variant	esv3412312
Chromosome Location	chr3:48895048-48897746
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EGR1	chr3:48896182-48896416	K562	blood:	n/a	n/a
2	EP300	chr3:48896246-48896446	K562	blood:	n/a	n/a
3	GATA2	chr3:48896197-48896427	K562	blood:	n/a	chr3:48896308-48896324 chr3:48896308-48896324 chr3:48896305-48896326
4	JUND	chr3:48896271-48896392	K562	blood:	n/a	n/a
5	MYC	chr3:48896302-48896352	K562	blood:	n/a	n/a
6	RCOR1	chr3:48896253-48896461	K562	blood:	n/a	n/a
7	STAT5A	chr3:48896131-48896503	K562	blood:	n/a	chr3:48896288-48896300
8	STAT5A	chr3:48896211-48896533	K562	blood:	n/a	chr3:48896288-48896300
9	TAL1	chr3:48896169-48896479	K562	blood:	n/a	n/a
10	TBL1XR1	chr3:48896323-48896328	K562	blood:	n/a	n/a
11	TEAD4	chr3:48896152-48896473	K562	blood:	n/a	n/a

Variant related genes	Relation type
SLC25A20	TF binding region

Extended variants
information (count: 87 )
Associated
traits (count: 101 )

Variant overlapped rSNPs/rCNVs (count:87 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs536363178	chr3:48895133-48895134	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
2	rs147062924	chr3:48895157-48895158	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs147955193	chr3:48895235-48895236	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs377391344	chr3:48895236-48895237	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs375410820	chr3:48895239-48895240	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs192977054	chr3:48895244-48895245	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs372380084	chr3:48895401-48895402	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs559104251	chr3:48895504-48895505	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs577495175	chr3:48895508-48895509	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs541692354	chr3:48895589-48895590	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
11	rs368720000	chr3:48895590-48895591	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs559099646	chr3:48895636-48895637	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs530840756	chr3:48895637-48895638	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs112518736	chr3:48895670-48895671	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs140570398	chr3:48895730-48895731	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs7433475	chr3:48895738-48895739	Weak transcription Strong transcription Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs185260211	chr3:48895818-48895819	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
18	rs563333763	chr3:48895825-48895826	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs117092176	chr3:48895900-48895901	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
20	rs188696087	chr3:48895920-48895921	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs141742666	chr3:48895940-48895941	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs376342597	chr3:48895959-48895960	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs35989076	chr3:48896010-48896011	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
24	rs370168469	chr3:48896022-48896023	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs142417191	chr3:48896063-48896064	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs374544337	chr3:48896082-48896083	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs368663060	chr3:48896083-48896084	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs371990344	chr3:48896107-48896108	Weak transcription Strong transcription Genic enhancers Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs113719437	chr3:48896160-48896161	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
30	rs536199901	chr3:48896184-48896185	Weak transcription Strong transcription Genic enhancers Enhancers	TF binding region	1 gene(s)	Overlapped CNVs	n/a
31	rs145315871	chr3:48896251-48896252	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
32	rs569860923	chr3:48896280-48896281	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
33	rs185084537	chr3:48896291-48896292	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
34	rs550035816	chr3:48896310-48896311	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3'	TF binding region	1 gene(s)	Overlapped CNVs	n/a
35	rs373555651	chr3:48896449-48896450	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
36	rs558919571	chr3:48896480-48896481	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
37	rs374211034	chr3:48896496-48896497	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
38	rs374847484	chr3:48896497-48896498	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
39	rs143961330	chr3:48896528-48896529	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
40	rs28934589	chr3:48896530-48896531	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region	1 gene(s)	Overlapped CNVs	n/a
41	rs577331691	chr3:48896552-48896553	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs374770429	chr3:48896575-48896576	Weak transcription Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs200418177	chr3:48896611-48896612	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
44	rs553582613	chr3:48896612-48896613	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs149062915	chr3:48896629-48896630	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs367871622	chr3:48896680-48896681	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs79815571	chr3:48896701-48896702	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs529006434	chr3:48896707-48896708	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
49	rs563272819	chr3:48896716-48896717	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
50	rs575441673	chr3:48896722-48896723	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:101)

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
Developmental delay	21147756	CNVD
Urothelial carcinoma	21177765	CNVD
Non-syndromic sensorineural hearing loss	21293372	CNVD
Pancreatic cancer	17952125	CNVD
Breast cancer	22522925	CNVD

Chromatin state (count:220 , 50 per page) page: 1 2 3 4 5

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48885600-48915000	Weak transcription	Small Intestine	intestine
2	chr3:48885800-48896400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr3:48885800-48896400	Weak transcription	Ovary	ovary
4	chr3:48885800-48899600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:48885800-48900600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr3:48885800-48906600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:48885800-48913600	Weak transcription	Fetal Lung	lung
8	chr3:48886000-48895600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:48886000-48895600	Weak transcription	Placenta	Placenta
10	chr3:48886000-48895800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr3:48886000-48896000	Weak transcription	Stomach Mucosa	stomach
12	chr3:48886000-48897800	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:48886000-48899000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:48886000-48899600	Weak transcription	NHEK	skin
15	chr3:48886000-48899800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr3:48886200-48895600	Weak transcription	Esophagus	oesophagus
17	chr3:48886200-48895800	Weak transcription	Rectal Smooth Muscle	rectum
18	chr3:48886200-48895800	Weak transcription	HSMMtube	muscle
19	chr3:48886200-48896000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr3:48886200-48900000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr3:48886200-48900400	Weak transcription	NHLF	lung
22	chr3:48886200-48900800	Weak transcription	NHDF-Ad	bronchial
23	chr3:48886400-48895800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr3:48886400-48896000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr3:48886400-48896400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:48886400-48897800	Weak transcription	Osteobl	bone
27	chr3:48886400-48899800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr3:48886600-48896200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr3:48886600-48896400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr3:48886600-48901800	Weak transcription	Fetal Heart	heart
31	chr3:48889200-48902000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:48889400-48901200	Weak transcription	Fetal Brain Male	brain
33	chr3:48889600-48935400	Weak transcription	Brain Germinal Matrix	brain
34	chr3:48889800-48916800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:48890200-48896600	Weak transcription	GM12878-XiMat	blood
36	chr3:48891600-48904600	Weak transcription	HSMM	muscle
37	chr3:48892600-48896600	Strong transcription	Monocytes-CD14+_RO01746	blood
38	chr3:48892600-48897000	Strong transcription	Duodenum Smooth Muscle	Duodenum
39	chr3:48892600-48897200	Strong transcription	Adipose Nuclei	Adipose
40	chr3:48892600-48897600	Strong transcription	Liver	Liver
41	chr3:48893200-48896400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr3:48893200-48896400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
43	chr3:48893200-48896600	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr3:48893200-48897000	Strong transcription	Right Ventricle	heart
45	chr3:48893200-48897200	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr3:48893200-48897200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr3:48893200-48897200	Strong transcription	Left Ventricle	heart
48	chr3:48893200-48897200	Strong transcription	Thymus	Thymus
49	chr3:48893200-48897200	Strong transcription	Spleen	Spleen
50	chr3:48893200-48900400	Strong transcription	Primary T cells fromperipheralblood	blood

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