Variant report

Variant	nsv828986
Chromosome Location	chr2:38952948-38954514
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:38808368..38809303-chr2:38952790..38953819,4	K562	blood:
2	chr2:38829722..38830596-chr2:38953255..38953803,2	MCF-7	breast:
3	chr2:38806248..38808565-chr2:38954475..38956582,2	K562	blood:
4	chr2:38830351..38831530-chr2:38952848..38953812,3	K562	blood:
5	chr2:38824669..38828895-chr2:38950792..38955552,5	K562	blood:
6	chr2:38808750..38809492-chr2:38952829..38953803,4	MCF-7	breast:
7	chr2:38951822..38954678-chr2:38974984..38978674,3	MCF-7	breast:
8	chr2:38762932..38763779-chr2:38952852..38953820,3	K562	blood:
9	chr2:38782788..38784491-chr2:38951489..38953190,2	K562	blood:
10	chr2:38948167..38950183-chr2:38951156..38954719,3	MCF-7	breast:
11	chr2:38892250..38893779-chr2:38950404..38953319,2	MCF-7	breast:
12	chr2:38803779..38806486-chr2:38953077..38954678,2	MCF-7	breast:
13	chr2:38807567..38810136-chr2:38951744..38953285,2	MCF-7	breast:
14	chr2:38830251..38831211-chr2:38952784..38953806,3	MCF-7	breast:
15	chr2:38829435..38831561-chr2:38952602..38955088,2	MCF-7	breast:
16	chr2:38952964..38955147-chr2:38962662..38964178,2	K562	blood:
17	chr2:38824718..38826820-chr2:38951264..38953232,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000115875	chromatin interactions
ENSG00000143891	chromatin interactions
ENSG00000143889	chromatin interactions
ENSG00000271443	chromatin interactions
ENSG00000235586	chromatin interactions

Extended variants
information (count: 74 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:74 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs3112144	chr2:38953000-38953001	Weak transcription Enhancers Strong transcription	Chromatin interactive region	5 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs369191040	chr2:38953010-38953011	Weak transcription Enhancers Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
3	rs573680055	chr2:38953037-38953038	Weak transcription Enhancers Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
4	rs540874316	chr2:38953038-38953039	Weak transcription Enhancers Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
5	rs553093900	chr2:38953040-38953041	Weak transcription Enhancers Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
6	rs578011866	chr2:38953043-38953044	Weak transcription Enhancers Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
7	rs545296313	chr2:38953046-38953047	Weak transcription Enhancers Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
8	rs373380582	chr2:38953051-38953052	Weak transcription Enhancers Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
9	rs372894316	chr2:38953055-38953056	Weak transcription Enhancers Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
10	rs566854926	chr2:38953071-38953072	Weak transcription Enhancers Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
11	rs558800504	chr2:38953078-38953079	Weak transcription Enhancers Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
12	rs531774494	chr2:38953102-38953103	Weak transcription Enhancers Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
13	rs376461665	chr2:38953138-38953139	Weak transcription Enhancers Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
14	rs373148894	chr2:38953216-38953217	Weak transcription Enhancers Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
15	rs192728059	chr2:38953240-38953241	Weak transcription Enhancers Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
16	rs376159873	chr2:38953248-38953249	Weak transcription Enhancers Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
17	rs529339799	chr2:38953260-38953261	Weak transcription Enhancers Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
18	rs547682377	chr2:38953282-38953283	Weak transcription Enhancers Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
19	rs565897416	chr2:38953296-38953297	Weak transcription Enhancers Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
20	rs533465463	chr2:38953297-38953298	Weak transcription Enhancers Strong transcription	Chromatin interactive region	5 gene(s)	Overlapped CNVs	n/a
21	rs371182673	chr2:38953355-38953356	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
22	rs375560759	chr2:38953359-38953360	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
23	rs551694086	chr2:38953364-38953365	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
24	rs12712615	chr2:38953365-38953366	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
25	rs398041445	chr2:38953366-38953367	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
26	rs374170432	chr2:38953371-38953372	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
27	rs12712617	chr2:38953372-38953373	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
28	rs368564868	chr2:38953373-38953374	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
29	rs370756978	chr2:38953400-38953401	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
30	rs536696318	chr2:38953522-38953523	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
31	rs555299397	chr2:38953529-38953530	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
32	rs111394336	chr2:38953559-38953560	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
33	rs376938857	chr2:38953581-38953582	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
34	rs534682234	chr2:38953597-38953598	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
35	rs552913445	chr2:38953611-38953612	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
36	rs188232803	chr2:38953615-38953616	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
37	rs545208159	chr2:38953620-38953621	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
38	rs557332853	chr2:38953638-38953639	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
39	rs148857052	chr2:38953660-38953661	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
40	rs373645432	chr2:38953687-38953688	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
41	rs180714504	chr2:38953730-38953731	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
42	rs370719083	chr2:38953742-38953743	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
43	rs562072144	chr2:38953759-38953760	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
44	rs377019854	chr2:38953769-38953770	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
45	rs184812806	chr2:38953770-38953771	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
46	rs559396377	chr2:38953782-38953783	Weak transcription Enhancers Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
47	rs146952763	chr2:38953818-38953819	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
48	rs533391907	chr2:38953838-38953839	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
49	rs190287160	chr2:38953932-38953933	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
50	rs182195532	chr2:38954009-38954010	Weak transcription Strong transcription	Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:61)

Disease	PMID	Source
Breast cancer	17393978	CNVD
Acute lymphoblastic leukemia	21098271	CNVD
Breast cancer	17603634	CNVD
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
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Ependymoma	16718352	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
lymphocytic leukemia	21291569	CNVD
Prostate cancer	18632612	CNVD
Bladder cancer	21909424	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Intellectual disability	22102821	CNVD
Cancer	20164919	CNVD
Hodgkin''s lymphoma	18641027	CNVD
Autism	22495311	CNVD
Acute lymphoblastic leukemia	20435627	CNVD
Follicular lymphoma	20505157	CNVD
Autism	17483303	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Esophageal adenocarcinoma	18519675	CNVD
Medulloblastoma	20607354	CNVD
Leukemia	18628472	CNVD
Autism	19521722	CNVD
Autism	18522746	CNVD
Non-small cell lung cancer	18927303	CNVD
Breast cancer	21785460	CNVD
Lung cancer	18438408	CNVD
Prostate cancer	21965145	CNVD
Breast cancer	16397240	CNVD
Acute lymphoblastic leukemia	21390130	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Neuroblastoma	21508638	CNVD
Neurodevelopmental disorder	22521361	CNVD
Neurocytoma	17123091	CNVD
small cell lung cancer	20016488	CNVD
Melanoma	18172304	CNVD
Cancer	16751803	CNVD
Breast cancer	21364760	CNVD
Pancreatic ductal adenocarcinoma	19077451	CNVD
Colorectal cancer	16272173	CNVD
Breast cancer	22522925	CNVD
T-cell lymphomas	22341440	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:132 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38894400-38960600	Weak transcription	Brain Substantia Nigra	brain
2	chr2:38909400-38960600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:38918600-38956800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:38927600-38957000	Weak transcription	Brain Hippocampus Middle	brain
5	chr2:38928800-38971600	Weak transcription	Small Intestine	intestine
6	chr2:38930000-38956600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr2:38930600-38965000	Weak transcription	Gastric	stomach
8	chr2:38932800-38956800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr2:38936400-38957200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:38936400-38960600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:38936400-38968400	Weak transcription	Colonic Mucosa	Colon
12	chr2:38937200-38956600	Weak transcription	Fetal Brain Female	brain
13	chr2:38937600-38970400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr2:38939000-38956600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:38939200-38958600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr2:38943600-38956000	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr2:38943600-38958600	Weak transcription	Aorta	Aorta
18	chr2:38946400-38957000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:38947800-38953200	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr2:38948000-38953400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:38948000-38955800	Weak transcription	Fetal Intestine Large	intestine
22	chr2:38948000-38958600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr2:38948200-38956600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr2:38948200-38956600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:38948200-38956600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr2:38948200-38957000	Weak transcription	Spleen	Spleen
27	chr2:38948200-38958600	Weak transcription	Esophagus	oesophagus
28	chr2:38948200-38968200	Weak transcription	Stomach Mucosa	stomach
29	chr2:38948400-38956600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:38948400-38958600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:38948400-38958800	Weak transcription	Colon Smooth Muscle	Colon
32	chr2:38948400-38964400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:38948400-38964600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr2:38948400-38970600	Weak transcription	NHEK	skin
35	chr2:38948600-38956600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:38948600-38956800	Weak transcription	Brain Anterior Caudate	brain
37	chr2:38948600-38957000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:38948600-38959600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr2:38948600-38970200	Weak transcription	NHDF-Ad	bronchial
40	chr2:38948600-38971200	Weak transcription	Fetal Kidney	kidney
41	chr2:38948800-38956600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:38948800-38956600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:38948800-38956800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr2:38948800-38957000	Weak transcription	Lung	lung
45	chr2:38948800-38960200	Weak transcription	Hela-S3	cervix
46	chr2:38948800-38960600	Weak transcription	Brain Angular Gyrus	brain
47	chr2:38948800-38964600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:38949000-38956800	Weak transcription	Ovary	ovary
49	chr2:38949000-38958600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr2:38949000-38965000	Weak transcription	Right Ventricle	heart

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