Variant report

Variant	esv3403309
Chromosome Location	chr3:119892062-119896360
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119809943..119817218-chr3:119893934..119905581,30	MCF-7	breast:
2	chr3:119888337..119890858-chr3:119891647..119894832,5	MCF-7	breast:
3	chr3:119810057..119817149-chr3:119894256..119903865,22	MCF-7	breast:
4	chr3:119877444..119878944-chr3:119896183..119899107,2	MCF-7	breast:
5	chr3:119896267..119897823-chr3:119902121..119903746,2	MCF-7	breast:
6	chr3:119887283..119893170-chr3:119894592..119900399,7	MCF-7	breast:
7	chr3:119887283..119893170-chr3:119894592..119900399,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000082701	chromatin interactions
ENSG00000242622	chromatin interactions

Extended variants
information (count: 133 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:133 , 50 per page) page: 1 2 3

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs183816015	chr3:119892082-119892083	Weak transcription Enhancers Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
2	rs147227010	chr3:119892096-119892097	Weak transcription Enhancers Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
3	rs188976459	chr3:119892105-119892106	Weak transcription Enhancers Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
4	rs201161551	chr3:119892114-119892115	Weak transcription Enhancers Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
5	rs376630204	chr3:119892115-119892116	Weak transcription Enhancers Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
6	rs13064815	chr3:119892121-119892122	Weak transcription Enhancers Strong transcription ZNF genes & repeats	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
7	rs201936267	chr3:119892145-119892146	Weak transcription Enhancers Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
8	rs561396784	chr3:119892182-119892183	Weak transcription Enhancers Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
9	rs377694599	chr3:119892193-119892194	Weak transcription Enhancers Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
10	rs530427940	chr3:119892198-119892199	Weak transcription Enhancers Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
11	rs562535511	chr3:119892199-119892200	Weak transcription Enhancers Strong transcription ZNF genes & repeats	n/a	n/a	Overlapped CNVs	n/a
12	rs141895234	chr3:119892212-119892213	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs150638525	chr3:119892215-119892216	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs139943256	chr3:119892232-119892233	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs111236071	chr3:119892242-119892243	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs143351042	chr3:119892243-119892244	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs199542673	chr3:119892255-119892256	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs57059149	chr3:119892272-119892273	Weak transcription Enhancers Strong transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
19	rs528168471	chr3:119892289-119892290	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs200413838	chr3:119892320-119892321	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs551086411	chr3:119892333-119892334	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs531495176	chr3:119892337-119892338	Weak transcription Enhancers Strong transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs77362550	chr3:119892429-119892430	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs536815659	chr3:119892478-119892479	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs150770159	chr3:119892513-119892514	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs371910116	chr3:119892520-119892521	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
27	rs536590460	chr3:119892614-119892615	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs546079702	chr3:119892699-119892700	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs553090871	chr3:119892764-119892765	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs9289142	chr3:119892779-119892780	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs77809478	chr3:119892899-119892900	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs375710790	chr3:119892910-119892911	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs575832247	chr3:119893000-119893001	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs9857123	chr3:119893063-119893064	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs111696566	chr3:119893245-119893246	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs1488762	chr3:119893257-119893258	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs540966153	chr3:119893266-119893267	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs559062394	chr3:119893315-119893316	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs528106416	chr3:119893332-119893333	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs139093471	chr3:119893375-119893376	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs79507761	chr3:119893412-119893413	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs530522333	chr3:119893421-119893422	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs78210167	chr3:119893447-119893448	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs567501397	chr3:119893473-119893474	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs557471607	chr3:119893476-119893477	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs73177937	chr3:119893485-119893486	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs1488761	chr3:119893503-119893504	Enhancers Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
48	rs539008909	chr3:119893549-119893550	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs187409544	chr3:119893553-119893554	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs575770489	chr3:119893595-119893596	Enhancers Weak transcription	n/a	n/a	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
Glioblastoma multiforme	22286061	CNVD
Neurodevelopmental disorder	22521361	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD

Chromatin state (count:174 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119875200-119896000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:119883200-119895800	Weak transcription	Fetal Intestine Small	intestine
3	chr3:119884800-119895600	Weak transcription	Brain Germinal Matrix	brain
4	chr3:119885000-119895800	Weak transcription	Fetal Lung	lung
5	chr3:119886200-119892400	Strong transcription	Fetal Brain Female	brain
6	chr3:119887200-119895800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:119888400-119892600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr3:119888400-119895800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:119888400-119895800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:119888400-119896200	Enhancers	NHDF-Ad	bronchial
11	chr3:119888600-119892200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:119888600-119892600	Enhancers	Osteobl	bone
13	chr3:119888600-119893200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:119888600-119896000	Enhancers	Muscle Satellite Cultured Cells	--
15	chr3:119889400-119893600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:119890000-119893000	Weak transcription	A549	lung
17	chr3:119890000-119895800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:119890200-119892200	Strong transcription	Fetal Stomach	stomach
19	chr3:119890400-119893600	Weak transcription	Placenta	Placenta
20	chr3:119890400-119895400	Weak transcription	Psoas Muscle	Psoas
21	chr3:119890400-119895800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr3:119890400-119895800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr3:119890600-119892200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:119890600-119893600	Weak transcription	Hela-S3	cervix
25	chr3:119890600-119895600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr3:119890600-119895800	Weak transcription	Rectal Smooth Muscle	rectum
27	chr3:119890800-119895600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:119890800-119896000	Weak transcription	Right Atrium	heart
29	chr3:119891000-119895800	Weak transcription	Colon Smooth Muscle	Colon
30	chr3:119891200-119893200	Weak transcription	HMEC	breast
31	chr3:119891200-119895600	Weak transcription	Adipose Nuclei	Adipose
32	chr3:119891200-119895600	Weak transcription	Fetal Muscle Leg	muscle
33	chr3:119891400-119895200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:119891400-119895200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:119891400-119895600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:119891400-119895600	Weak transcription	NHLF	lung
37	chr3:119891400-119896200	Weak transcription	Lung	lung
38	chr3:119891600-119892200	ZNF genes & repeats	NHEK	skin
39	chr3:119892000-119892200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:119892000-119892200	Enhancers	HSMMtube	muscle
41	chr3:119892000-119892800	Enhancers	HSMM	muscle
42	chr3:119892000-119895800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr3:119892200-119892600	Weak transcription	HSMMtube	muscle
44	chr3:119892200-119893400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr3:119892200-119893600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr3:119892200-119895600	Weak transcription	NHEK	skin
47	chr3:119892200-119895800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:119892200-119896000	Weak transcription	Fetal Stomach	stomach
49	chr3:119892400-119914200	Weak transcription	Fetal Brain Female	brain
50	chr3:119892600-119892800	Enhancers	HSMMtube	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links