Variant report

Variant	esv3406090
Chromosome Location	chr3:118909062-118912860
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:118903436..118905729-chr3:118907568..118909269,2	MCF-7	breast:
2	chr3:118904646..118906555-chr3:118909442..118912016,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114638	chromatin interactions

Extended variants
information (count: 137 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:137 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs374899484	chr3:118909065-118909066	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs201217246	chr3:118909069-118909070	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs373173020	chr3:118909078-118909079	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs145863335	chr3:118909102-118909103	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs113148509	chr3:118909118-118909119	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs138448087	chr3:118909120-118909121	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
7	rs575753359	chr3:118909121-118909122	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs542978976	chr3:118909138-118909139	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs377271538	chr3:118909150-118909151	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs202053096	chr3:118909158-118909159	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs9840317	chr3:118909159-118909160	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
12	rs148991062	chr3:118909184-118909185	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs369906603	chr3:118909192-118909193	Weak transcription Enhancers Strong transcription	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs373884676	chr3:118909205-118909206	Weak transcription Strong transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs554567999	chr3:118909301-118909302	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs527839101	chr3:118909347-118909348	Weak transcription Strong transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs143754563	chr3:118909443-118909444	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
18	rs112709875	chr3:118909523-118909524	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
19	rs148120726	chr3:118909530-118909531	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
20	rs9878996	chr3:118909538-118909539	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
21	rs556917419	chr3:118909595-118909596	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
22	rs568443807	chr3:118909601-118909602	Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs576961751	chr3:118909618-118909619	Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs529354399	chr3:118909625-118909626	Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
25	rs182016340	chr3:118909641-118909642	Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
26	rs186267347	chr3:118909647-118909648	Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
27	rs41271387	chr3:118909700-118909701	Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
28	rs539228240	chr3:118909724-118909725	Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
29	rs573361289	chr3:118909758-118909759	Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
30	rs542369803	chr3:118909763-118909764	Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
31	rs78275619	chr3:118909775-118909776	Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
32	rs376288568	chr3:118909785-118909786	Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
33	rs370224982	chr3:118909789-118909790	Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
34	rs141877262	chr3:118909792-118909793	Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
35	rs147312682	chr3:118909856-118909857	Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
36	rs78761311	chr3:118909892-118909893	Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
37	rs555087775	chr3:118909929-118909930	Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
38	rs3796356	chr3:118909962-118909963	Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
39	rs367784633	chr3:118909978-118909979	Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
40	rs3796357	chr3:118909987-118909988	Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
41	rs200531778	chr3:118909991-118909992	Weak transcription Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
42	rs73854427	chr3:118910054-118910055	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
43	rs546047673	chr3:118910133-118910134	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
44	rs563257111	chr3:118910135-118910136	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
45	rs564654512	chr3:118910136-118910137	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
46	rs530342514	chr3:118910178-118910179	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
47	rs57744978	chr3:118910180-118910181	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
48	rs3796358	chr3:118910184-118910185	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
49	rs78129661	chr3:118910203-118910204	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
50	rs370281649	chr3:118910220-118910221	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:57)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Cancer	21183584	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Bipolar disorder	20877625	CNVD
Bipolar disorder	21956041	CNVD
Bipolar disorder	22241247	CNVD
Biliary cancer	18923514	CNVD
Prostate cancer	21965145	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
microdeletion syndrome	22180640	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	16608533	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Developmental delay	22180640	CNVD
Multiple myeloma	17550852	CNVD
Basal cell lymphoma	21115979	CNVD
Ovarian cancer	22174824	CNVD
lymphocytic leukemia	21291569	CNVD
small cell lung cancer	20016488	CNVD
Cancer	20164920	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Non-syndromic sensorineural hearing loss	21987784	CNVD
Glioblastoma multiforme	22286061	CNVD
Neurodevelopmental disorder	22521361	CNVD

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118884000-118914200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:118901000-118924200	Weak transcription	Pancreas	Pancrea
3	chr3:118903400-118924200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:118904400-118910600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:118904400-118912800	Weak transcription	NH-A	brain
6	chr3:118904400-118913000	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr3:118904600-118936400	Weak transcription	Gastric	stomach
8	chr3:118904800-118910400	Weak transcription	HMEC	breast
9	chr3:118904800-118913000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:118904800-118914400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:118906800-118909400	Enhancers	A549	lung
12	chr3:118906800-118910400	Strong transcription	Placenta Amnion	Placenta Amnion
13	chr3:118907000-118910600	Weak transcription	Placenta	Placenta
14	chr3:118907600-118910600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:118908400-118910800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr3:118908400-118928200	Weak transcription	Fetal Stomach	stomach
17	chr3:118908600-118909200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:118908600-118914000	Weak transcription	Aorta	Aorta
19	chr3:118908800-118909600	Weak transcription	Fetal Heart	heart
20	chr3:118909200-118914800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:118909400-118911400	Genic enhancers	A549	lung
22	chr3:118909600-118910000	Active TSS	Brain Substantia Nigra	brain
23	chr3:118910400-118911400	Enhancers	HMEC	breast
24	chr3:118910400-118911400	Enhancers	NHEK	skin
25	chr3:118910400-118913000	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr3:118910600-118910800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:118910600-118910800	Enhancers	Placenta	Placenta
28	chr3:118910600-118910800	Bivalent Enhancer	NHDF-Ad	bronchial
29	chr3:118910600-118911000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:118910600-118911200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:118910800-118911400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:118910800-118913400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr3:118911000-118912800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:118911200-118912800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:118911400-118912800	Enhancers	A549	lung
36	chr3:118911400-118913000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr3:118911400-118913000	Weak transcription	HMEC	breast
38	chr3:118911400-118913000	Weak transcription	NHEK	skin
39	chr3:118911600-118911800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:118911800-118932600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:118912600-118915200	Enhancers	NHDF-Ad	bronchial
42	chr3:118912800-118914400	Flanking Active TSS	A549	lung
43	chr3:118912800-118915000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:118912800-118915000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:118912800-118915200	Enhancers	NH-A	brain
46	chr3:118912800-118915400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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