Variant report

Variant	esv2282019
Chromosome Location	chr15:45569842-45570398
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:70683116..70683960-chr15:45569736..45570428,2	MCF-7	breast:
2	chr15:45491756..45494677-chr15:45570318..45572091,2	MCF-7	breast:
3	chr15:45454944..45455772-chr15:45568916..45570015,4	MCF-7	breast:
4	chr15:45464381..45467214-chr15:45569783..45571800,2	MCF-7	breast:
5	chr15:45458064..45460777-chr15:45570184..45573179,2	MCF-7	breast:
6	chr15:45547330..45549104-chr15:45570394..45573078,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259539	chromatin interactions
ENSG00000260035	chromatin interactions
ENSG00000259520	chromatin interactions
ENSG00000138606	chromatin interactions

Extended variants
information (count: 27 )
Associated
traits (count: 65 )

Variant overlapped rSNPs/rCNVs (count:27 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs72709069	chr15:45569866-45569867	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
2	rs189112208	chr15:45569871-45569872	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
3	rs369516127	chr15:45569922-45569923	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
4	rs564090042	chr15:45569928-45569929	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
5	rs62026703	chr15:45569929-45569930	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
6	rs58415206	chr15:45569955-45569956	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs569409389	chr15:45569994-45569995	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
8	rs142611698	chr15:45570052-45570053	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
9	rs67828563	chr15:45570057-45570058	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
10	rs528996190	chr15:45570138-45570139	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
11	rs377463587	chr15:45570159-45570160	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
12	rs112273478	chr15:45570163-45570164	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
13	rs377082399	chr15:45570175-45570176	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
14	rs369982489	chr15:45570183-45570184	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
15	rs548556280	chr15:45570186-45570187	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs565699333	chr15:45570209-45570210	Enhancers Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs534200120	chr15:45570223-45570224	Enhancers Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs554464837	chr15:45570224-45570225	Enhancers Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs7171312	chr15:45570225-45570226	Enhancers Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
20	rs540044536	chr15:45570232-45570233	Enhancers Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs2461705	chr15:45570241-45570242	Enhancers Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
22	rs576586519	chr15:45570242-45570243	Enhancers Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs542368853	chr15:45570250-45570251	Enhancers Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs12440623	chr15:45570255-45570256	Enhancers Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs555445680	chr15:45570345-45570346	Enhancers Active TSS Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
26	rs192845051	chr15:45570362-45570363	Enhancers Active TSS Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
27	rs139381726	chr15:45570387-45570388	Enhancers Active TSS Weak transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:65)

Disease	PMID	Source
Ewing''s sarcoma	21437220	CNVD
Schizophrenia	19415332	CNVD
Breast cancer	22522925	CNVD
Autism	22495311	CNVD
Wilms tumour	21544195	CNVD
Testicular germ cell tumor	18059402	CNVD
cataract	16735990	CNVD
Cancer	21637783	CNVD
Colorectal cancer	20709793	CNVD
Medulloblastoma	21979893	CNVD
spastic paraplegia with thinning of corpus callosum	19105190	CNVD
Schizophrenia	21324950	CNVD
Astrocytoma	17387387	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Disease	21824424	CNVD
Melanoma	18172304	CNVD
Colorectal cancer	16774939	CNVD
Gastric cancer	17167181	CNVD
Neuroblastoma	19435921	CNVD
Colorectal cancer	19359472	CNVD
Monoclonal gammopathy of undetermined significance	17077331	CNVD
Multiple myeloma	17077331	CNVD
Colorectal cancer	16272173	CNVD
Gastrointestinal stromal cancer	20470368	CNVD
Multiple myeloma	17550852	CNVD
Intellectual disability	22102821	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute myeloid leukemia	20729466	CNVD
Prostate cancer	16573809	CNVD
Basal cell lymphoma	16317097	CNVD
Diffuse large b-cell lymphoma	16317097	CNVD
Multiple myeloma	20724749	CNVD
Lung cancer	18438408	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
Breast cancer	21785460	CNVD
Gastrointestinal stromal cancer	16982739	CNVD
Ovarian cancer	22174824	CNVD
Prostate cancer	18632612	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Basal cell lymphoma	17053054	CNVD
Cancer	21129771	CNVD
Papillary thyroid carcinoma	22161024	CNVD
Splenic marginal zone lymphoma	21957467	CNVD
Breast cancer	21045282	CNVD
Breast cancer	22032731	CNVD
low-grade B-cell lymphoma tumor	18367492	CNVD
Gastrointestinal stromal cancer	20877625	CNVD
Oral squamous cell carcinoma	17134496	CNVD
Basal cell lymphoma	17170743	CNVD
Follicular lymphoma	17170743	CNVD
Myelofibrosis	22110671	CNVD
Hirschsprung''s Disease	21712996	CNVD
Myeloproliferative neoplasm	20015882	CNVD
Breast cancer	16272173	CNVD
Hepatocellular carcinoma	16750200	CNVD
Abnormal phenotypes	18644119	CNVD
Cancer	16751803	CNVD
Melanoma	17363583	CNVD
Acute myeloid leukemia	19651601	CNVD
Marfan syndrome	17492313	CNVD
Esophageal adenocarcinoma	18820669	CNVD
Non-syndromic sensorineural hearing loss	22037309	CNVD

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45550200-45570600	Weak transcription	Stomach Mucosa	stomach
2	chr15:45552600-45570600	Weak transcription	Pancreas	Pancrea
3	chr15:45558000-45570400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr15:45560600-45570400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr15:45560600-45570600	Weak transcription	Fetal Stomach	stomach
6	chr15:45563000-45570400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr15:45564800-45570400	Weak transcription	Fetal Brain Female	brain
8	chr15:45566000-45570400	Weak transcription	Brain Anterior Caudate	brain
9	chr15:45567200-45570400	Weak transcription	A549	lung
10	chr15:45567800-45570400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr15:45568800-45570400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:45568800-45570400	Enhancers	HepG2	liver
13	chr15:45569000-45570400	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr15:45569000-45570400	Enhancers	Fetal Intestine Small	intestine
15	chr15:45569000-45570600	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr15:45569000-45570600	Enhancers	Brain Angular Gyrus	brain
17	chr15:45569200-45570200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr15:45569200-45570200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr15:45569200-45570200	Weak transcription	Colon Smooth Muscle	Colon
20	chr15:45569200-45570200	Weak transcription	Fetal Intestine Large	intestine
21	chr15:45569200-45570400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:45569200-45570400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr15:45569200-45570400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr15:45569200-45570400	Weak transcription	Brain Germinal Matrix	brain
25	chr15:45569400-45570200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr15:45569400-45570400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr15:45569400-45570400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr15:45569400-45570400	Weak transcription	Brain Hippocampus Middle	brain
29	chr15:45569400-45570400	Weak transcription	Brain Substantia Nigra	brain
30	chr15:45569600-45570000	Enhancers	Fetal Kidney	kidney
31	chr15:45569600-45570400	Enhancers	HMEC	breast
32	chr15:45569800-45570200	Weak transcription	Liver	Liver
33	chr15:45570000-45570400	Weak transcription	Fetal Kidney	kidney
34	chr15:45570200-45570400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:45570200-45570400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr15:45570200-45570400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr15:45570200-45570400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr15:45570200-45570400	Enhancers	Adipose Nuclei	Adipose
39	chr15:45570200-45570400	Enhancers	Colon Smooth Muscle	Colon
40	chr15:45570200-45570400	Active TSS	Duodenum Smooth Muscle	Duodenum
41	chr15:45570200-45570400	Enhancers	NHLF	lung
42	chr15:45570200-45570600	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr15:45570200-45570600	Enhancers	Liver	Liver
44	chr15:45570200-45570600	Enhancers	Fetal Intestine Large	intestine
45	chr15:45570200-45570600	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr15:45570200-45570800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr15:45570200-45572000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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