Variant report

Variant	esv3459540
Chromosome Location	chr2:38944736-38947192
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38890666..38892556-chr2:38947054..38950004,2	K562	blood:
2	chr2:38944533..38947216-chr2:38977421..38979282,2	K562	blood:
3	chr2:38827236..38831286-chr2:38946528..38952512,8	K562	blood:
4	chr2:38827557..38829882-chr2:38942553..38944961,2	K562	blood:
5	chr2:38805084..38807176-chr2:38944983..38947545,2	K562	blood:
6	chr2:38822529..38824278-chr2:38946523..38948124,2	K562	blood:
7	chr2:38938428..38940592-chr2:38945131..38949430,3	K562	blood:

Variant related genes	Relation type
ENSG00000152147	chromatin interactions
ENSG00000115875	chromatin interactions
ENSG00000235586	chromatin interactions
ENSG00000143889	chromatin interactions

Extended variants
information (count: 96 )
Associated
traits (count: 61 )

Variant overlapped rSNPs/rCNVs (count:96 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs183367708	chr2:38944742-38944743	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
2	rs552543415	chr2:38944744-38944745	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
3	rs142206688	chr2:38944783-38944784	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
4	rs113819692	chr2:38944819-38944820	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
5	rs187856213	chr2:38944857-38944858	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
6	rs568546007	chr2:38944888-38944889	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
7	rs528708865	chr2:38944928-38944929	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
8	rs536102877	chr2:38944930-38944931	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
9	rs554064907	chr2:38944953-38944954	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	Overlapped CNVs	n/a
10	rs572708833	chr2:38944981-38944982	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs201772463	chr2:38944988-38944989	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs75093678	chr2:38944996-38944997	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs113016544	chr2:38945034-38945035	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs546136136	chr2:38945041-38945042	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs145814275	chr2:38945167-38945168	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs373935667	chr2:38945178-38945179	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs138393858	chr2:38945199-38945200	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
18	rs115042407	chr2:38945229-38945230	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs543001313	chr2:38945250-38945251	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs529486389	chr2:38945332-38945333	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs570884236	chr2:38945338-38945339	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs3059479	chr2:38945339-38945340	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs76018168	chr2:38945352-38945353	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs13013790	chr2:38945354-38945355	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs192789949	chr2:38945383-38945384	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs541228687	chr2:38945402-38945403	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs182469019	chr2:38945411-38945412	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs1968411	chr2:38945463-38945464	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
29	rs188068900	chr2:38945469-38945470	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs569917658	chr2:38945498-38945499	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
31	rs531766161	chr2:38945523-38945524	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs550195933	chr2:38945552-38945553	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs568611886	chr2:38945560-38945561	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs535913519	chr2:38945565-38945566	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs547974271	chr2:38945569-38945570	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs566116688	chr2:38945621-38945622	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs540143001	chr2:38945634-38945635	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs558204146	chr2:38945638-38945639	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs576308943	chr2:38945656-38945657	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs1529625	chr2:38945701-38945702	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
41	rs377532964	chr2:38945760-38945761	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs536156064	chr2:38945780-38945781	Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs140942398	chr2:38945809-38945810	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs116364578	chr2:38945878-38945879	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs573402684	chr2:38945924-38945925	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
46	rs368874864	chr2:38945930-38945931	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
47	rs192484082	chr2:38945938-38945939	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
48	rs150532562	chr2:38945973-38945974	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
49	rs557656881	chr2:38945976-38945977	Enhancers Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
50	rs1529624	chr2:38946044-38946045	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	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:125 , 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	chr2:38894800-38949400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr2:38905000-38947600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:38909200-38947800	Weak transcription	Right Ventricle	heart
5	chr2:38909400-38960600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:38909600-38947800	Weak transcription	Brain Anterior Caudate	brain
7	chr2:38910000-38948000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr2:38914600-38948000	Weak transcription	Spleen	Spleen
9	chr2:38915800-38947200	Weak transcription	Ovary	ovary
10	chr2:38918000-38949400	Weak transcription	Primary B cells from cord blood	blood
11	chr2:38918600-38947600	Weak transcription	Hela-S3	cervix
12	chr2:38918600-38956800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:38920400-38947800	Weak transcription	Esophagus	oesophagus
14	chr2:38921400-38947400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr2:38927400-38947600	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:38927600-38957000	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:38928200-38947800	Weak transcription	Stomach Mucosa	stomach
18	chr2:38928800-38971600	Weak transcription	Small Intestine	intestine
19	chr2:38930000-38946800	Weak transcription	Right Atrium	heart
20	chr2:38930000-38956600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr2:38930600-38947000	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr2:38930600-38965000	Weak transcription	Gastric	stomach
23	chr2:38931200-38948600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:38932400-38947600	Weak transcription	Colon Smooth Muscle	Colon
25	chr2:38932600-38947800	Weak transcription	Pancreas	Pancrea
26	chr2:38932800-38947000	Weak transcription	Lung	lung
27	chr2:38932800-38956800	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr2:38933200-38947600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr2:38933800-38947800	Weak transcription	Primary B cells from peripheral blood	blood
30	chr2:38934800-38947600	Weak transcription	K562	blood
31	chr2:38936400-38957200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:38936400-38960600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr2:38936400-38968400	Weak transcription	Colonic Mucosa	Colon
34	chr2:38936800-38946000	Weak transcription	Thymus	Thymus
35	chr2:38937200-38956600	Weak transcription	Fetal Brain Female	brain
36	chr2:38937600-38947600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr2:38937600-38970400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr2:38937800-38947600	Weak transcription	GM12878-XiMat	blood
39	chr2:38938000-38949400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr2:38938000-38949400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr2:38938200-38947200	Weak transcription	Fetal Stomach	stomach
42	chr2:38938400-38948600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr2:38939000-38945800	Weak transcription	Fetal Thymus	thymus
44	chr2:38939000-38947000	Weak transcription	Fetal Lung	lung
45	chr2:38939000-38947800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr2:38939000-38947800	Weak transcription	Fetal Brain Male	brain
47	chr2:38939000-38956600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:38939200-38946000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr2:38939200-38947200	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr2:38939200-38948000	Weak transcription	Fetal Kidney	kidney

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links