Variant report

Variant	esv3693290
Chromosome Location	chr2:54693204-54707562
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:57916060..57918497-chr2:54698560..54700070,2	MCF-7	breast:
2	chr2:54341619..54344136-chr2:54698378..54700154,2	MCF-7	breast:
3	chr2:54698509..54700460-chr2:54784442..54786453,2	MCF-7	breast:
4	chr2:54699717..54702089-chr2:54703143..54705442,2	K562	blood:
5	chr2:54699717..54702089-chr2:54703143..54705442,2	K562	blood:

Variant related genes	Relation type
ENSG00000115306	chromatin interactions
ENSG00000170634	chromatin interactions

Extended variants
information (count: 653 )
Associated
traits (count: 65 )

Variant overlapped rSNPs/rCNVs (count:653 , 50 per page) page: 1 2 3 4 5 6 7 ... 14

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs4671938	chr2:54693204-54693205	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
2	rs541588344	chr2:54693237-54693238	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
3	rs147570385	chr2:54693272-54693273	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
4	rs375606022	chr2:54693286-54693287	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
5	rs187642520	chr2:54693314-54693315	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
6	rs368604289	chr2:54693331-54693332	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
7	rs542345291	chr2:54693347-54693348	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
8	rs550700656	chr2:54693386-54693387	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
9	rs559452436	chr2:54693461-54693462	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
10	rs6755780	chr2:54693490-54693491	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
11	rs75631271	chr2:54693495-54693496	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
12	rs192778414	chr2:54693498-54693499	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
13	rs200048862	chr2:54693630-54693631	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
14	rs10169422	chr2:54693754-54693755	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
15	rs370618601	chr2:54693828-54693829	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
16	rs184215863	chr2:54693868-54693869	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
17	rs115486808	chr2:54693871-54693872	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
18	rs116067119	chr2:54693878-54693879	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
19	rs375646105	chr2:54693894-54693895	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
20	rs190809366	chr2:54693902-54693903	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
21	rs569479525	chr2:54693929-54693930	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
22	rs565991754	chr2:54693949-54693950	Weak transcription Enhancers Flanking Active TSS Active TSS	n/a	n/a	Overlapped CNVs	n/a
23	rs529815361	chr2:54694022-54694023	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
24	rs114403761	chr2:54694027-54694028	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
25	rs578034084	chr2:54694069-54694070	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
26	rs7573223	chr2:54694130-54694131	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
27	rs193026152	chr2:54694141-54694142	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
28	rs553763543	chr2:54694143-54694144	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
29	rs4233950	chr2:54694151-54694152	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs541752791	chr2:54694199-54694200	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
31	rs374996620	chr2:54694210-54694211	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
32	rs561731972	chr2:54694250-54694251	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
33	rs575438741	chr2:54694262-54694263	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
34	rs145631837	chr2:54694310-54694311	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
35	rs537085163	chr2:54694342-54694343	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
36	rs56039013	chr2:54694357-54694358	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
37	rs544513664	chr2:54694375-54694376	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
38	rs533081425	chr2:54694386-54694387	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
39	rs548374995	chr2:54694387-54694388	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
40	rs184554803	chr2:54694389-54694390	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers	n/a	n/a	Overlapped CNVs	n/a
41	rs560226102	chr2:54694420-54694421	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
42	rs529608152	chr2:54694487-54694488	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
43	rs112189307	chr2:54694492-54694493	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
44	rs375746310	chr2:54694540-54694541	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
45	rs116615338	chr2:54694555-54694556	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
46	rs538386924	chr2:54694586-54694587	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
47	rs111927637	chr2:54694593-54694594	Weak transcription Enhancers Active TSS Flanking Active TSS	n/a	n/a	Overlapped CNVs	n/a
48	rs547185450	chr2:54694601-54694602	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a
49	rs7573805	chr2:54694645-54694646	Weak transcription Enhancers	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
50	rs541316692	chr2:54694650-54694651	Weak transcription Enhancers	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:65)

Disease	PMID	Source
Medulloblastoma	21979893	CNVD
Lynch syndrome	18415027	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Diffuse large b-cell lymphoma	18287131	CNVD
Ovarian neoplasms	16753589	CNVD
Glioblastoma multiforme	17387387	CNVD
Neuroblastoma	17533364	CNVD
Neuroblastoma	18923191	CNVD
Endometrial cancer	22040021	CNVD
Adrenal tumor	17535989	CNVD
Breast cancer	21264507	CNVD
Basal cell lymphoma	17053054	CNVD
Medulloblastoma	17522785	CNVD
Cancer	23418310	CNVD
Breast cancer	17603634	CNVD
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	22495311	CNVD
Autism	18522746	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Colorectal cancer	16272173	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Williams Syndrome	20824207	CNVD
Breast cancer	16272173	CNVD
Endometrioid adenocarcinoma	16974079	CNVD
Ovarian cancer	21720365	CNVD
abnormal development	18461090	CNVD
Lung adenocarcinoma	17086460	CNVD
Retinoblastoma	22278416	CNVD
Cancer	21183584	CNVD
Breast cancer	16397240	CNVD
Lung cancer	17086460	CNVD
Chronic lymphocytic leukemia	17053054	CNVD
Hereditary non-polyposis colorectal cancer	19566914	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
small cell lung cancer	20016488	CNVD
Myelofibrosis	22110671	CNVD
Developmental delay	21147756	CNVD
Breast cancer	22522925	CNVD
Pancreatic cancer	17952125	CNVD
Non-syndromic sensorineural hearing loss	18451855	CNVD

Chromatin state (count:677 , 50 per page) page: 1 2 3 4 5 6 7 ... 14

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54685200-54694600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:54685200-54696600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:54685400-54696600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:54686400-54694000	Weak transcription	Fetal Stomach	stomach
5	chr2:54686400-54695600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr2:54686400-54697800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:54686600-54694000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:54686600-54694000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:54686600-54695000	Enhancers	Fetal Heart	heart
10	chr2:54686600-54696200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:54686600-54696600	Weak transcription	Lung	lung
12	chr2:54686600-54696800	Weak transcription	NH-A	brain
13	chr2:54686600-54697000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr2:54686600-54698600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr2:54687000-54700800	Weak transcription	Brain Germinal Matrix	brain
16	chr2:54687600-54696800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr2:54688400-54694600	Enhancers	Colon Smooth Muscle	Colon
18	chr2:54688600-54696200	Weak transcription	Right Ventricle	heart
19	chr2:54689400-54693800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:54689400-54694000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr2:54689400-54694000	Weak transcription	NHLF	lung
22	chr2:54689600-54693800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:54690200-54694200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:54690400-54693800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr2:54690400-54694000	Weak transcription	HSMMtube	muscle
26	chr2:54690600-54693800	Weak transcription	Brain Angular Gyrus	brain
27	chr2:54690600-54694200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr2:54690600-54695200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr2:54690600-54696600	Weak transcription	Spleen	Spleen
30	chr2:54690800-54694000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr2:54690800-54694000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr2:54690800-54694000	Weak transcription	Fetal Muscle Leg	muscle
33	chr2:54690800-54694000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr2:54690800-54694400	Weak transcription	Fetal Muscle Trunk	muscle
35	chr2:54690800-54695600	Weak transcription	Fetal Brain Male	brain
36	chr2:54690800-54696200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr2:54690800-54697600	Weak transcription	Fetal Brain Female	brain
38	chr2:54691600-54696000	Weak transcription	HepG2	liver
39	chr2:54692000-54693400	Enhancers	Stomach Smooth Muscle	stomach
40	chr2:54692200-54693400	Enhancers	Placenta Amnion	Placenta Amnion
41	chr2:54692200-54694000	Enhancers	Fetal Lung	lung
42	chr2:54692200-54696600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr2:54692600-54694000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr2:54692600-54694000	Weak transcription	Adipose Nuclei	Adipose
45	chr2:54692600-54694000	Weak transcription	Brain Substantia Nigra	brain
46	chr2:54692600-54694000	Weak transcription	Left Ventricle	heart
47	chr2:54692600-54694000	Weak transcription	Ovary	ovary
48	chr2:54692600-54694000	Weak transcription	Psoas Muscle	Psoas
49	chr2:54692600-54694000	Weak transcription	Right Atrium	heart
50	chr2:54692600-54694600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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