Variant report

Variant	esv3372733
Chromosome Location	chr3:120030562-120034960
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	chr3:120032416..120034924-chr3:120037587..120040555,3	MCF-7	breast:

Extended variants
information (count: 186 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:186 , 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	rs552488085	chr3:120030565-120030566	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
2	rs552445767	chr3:120030568-120030569	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs569076138	chr3:120030569-120030570	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
4	rs538096378	chr3:120030599-120030600	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
5	rs554861248	chr3:120030631-120030632	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs787186	chr3:120030650-120030651	ZNF genes & repeats Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs115513286	chr3:120030659-120030660	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs787187	chr3:120030677-120030678	ZNF genes & repeats Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
9	rs553957947	chr3:120030689-120030690	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs576966179	chr3:120030723-120030724	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs137936075	chr3:120030740-120030741	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs149454147	chr3:120030760-120030761	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs576241716	chr3:120030799-120030800	ZNF genes & repeats Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs542084062	chr3:120030800-120030801	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
15	rs143416245	chr3:120030824-120030825	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
16	rs184886228	chr3:120030825-120030826	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
17	rs787188	chr3:120030876-120030877	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs559986589	chr3:120030889-120030890	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
19	rs787189	chr3:120030906-120030907	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
20	rs386665154	chr3:120030913-120030914	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
21	rs112980579	chr3:120030914-120030915	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
22	rs111480904	chr3:120030915-120030916	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
23	rs538057430	chr3:120030927-120030928	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs386665155	chr3:120030938-120030939	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs113136273	chr3:120030939-120030940	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs2638592	chr3:120030940-120030941	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs533933281	chr3:120030954-120030955	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs188476592	chr3:120030958-120030959	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs570518608	chr3:120030974-120030975	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
30	rs73856465	chr3:120030979-120030980	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs202070012	chr3:120030987-120030988	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs148376373	chr3:120030997-120030998	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs576201640	chr3:120031000-120031001	ZNF genes & repeats Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs73856468	chr3:120031010-120031011	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
35	rs787190	chr3:120031011-120031012	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
36	rs191351667	chr3:120031034-120031035	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs541362508	chr3:120031045-120031046	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs560149458	chr3:120031059-120031060	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs113558159	chr3:120031070-120031071	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs147499907	chr3:120031088-120031089	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs527575622	chr3:120031090-120031091	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs562596285	chr3:120031105-120031106	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs184286016	chr3:120031111-120031112	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs548404057	chr3:120031125-120031126	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs568263213	chr3:120031131-120031132	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs561246907	chr3:120031139-120031140	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs189635089	chr3:120031164-120031165	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs181168570	chr3:120031202-120031203	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs530160963	chr3:120031207-120031208	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs185175436	chr3:120031225-120031226	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:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120024400-120032600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:120024400-120049200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:120024600-120032600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:120025400-120040600	Weak transcription	Fetal Lung	lung
5	chr3:120026600-120030600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:120026600-120042400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:120026600-120060800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:120026800-120030600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:120026800-120032400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:120026800-120032600	Weak transcription	Pancreas	Pancrea
11	chr3:120026800-120049200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr3:120026800-120067200	Weak transcription	Aorta	Aorta
13	chr3:120027800-120030800	Weak transcription	Fetal Stomach	stomach
14	chr3:120028200-120031400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr3:120029600-120032600	Weak transcription	Primary T cells from cord blood	blood
16	chr3:120030000-120042600	Weak transcription	HMEC	breast
17	chr3:120030400-120032600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr3:120030600-120031000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr3:120030600-120034200	Weak transcription	Adipose Nuclei	Adipose
20	chr3:120030800-120031000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr3:120030800-120031000	ZNF genes & repeats	Fetal Stomach	stomach
22	chr3:120031000-120041200	Weak transcription	Fetal Stomach	stomach
23	chr3:120031000-120042400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr3:120031000-120055600	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr3:120031200-120033800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr3:120031400-120031800	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr3:120031400-120032000	Enhancers	GM12878-XiMat	blood
28	chr3:120031400-120040600	Weak transcription	Ovary	ovary
29	chr3:120031400-120042400	Weak transcription	A549	lung
30	chr3:120031600-120032600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr3:120031600-120034600	Weak transcription	Fetal Muscle Leg	muscle
32	chr3:120031800-120033800	Weak transcription	Esophagus	oesophagus
33	chr3:120031800-120034400	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr3:120032200-120034200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr3:120032400-120033200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr3:120032400-120047600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:120032600-120032800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr3:120032600-120032800	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:120032600-120032800	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr3:120032600-120032800	ZNF genes & repeats	Rectal Smooth Muscle	rectum
41	chr3:120032600-120033000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr3:120032600-120033000	Enhancers	Brain Hippocampus Middle	brain
43	chr3:120032600-120033200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr3:120032600-120033200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr3:120032600-120033200	Strong transcription	Primary T cells from cord blood	blood
46	chr3:120032600-120033200	Enhancers	Gastric	stomach
47	chr3:120032600-120033200	Genic enhancers	Pancreas	Pancrea
48	chr3:120032600-120033200	ZNF genes & repeats	Spleen	Spleen
49	chr3:120032600-120033200	ZNF genes & repeats	Dnd41	blood
50	chr3:120032600-120033600	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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