Variant report

Variant	esv2582384
Chromosome Location	chr2:39623773-39625293
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr2:39624942-39625194	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:39625232..39628414-chr2:39637317..39639794,4	K562	blood:
2	chr2:39624807..39627071-chr2:39638065..39639781,2	MCF-7	breast:
3	chr2:39623495..39626216-chr2:39663954..39666245,2	MCF-7	breast:
4	chr2:39621678..39625449-chr2:39627882..39630825,3	MCF-7	breast:

Variant related genes	Relation type
RNU6-1185P	TF binding region
ENSG00000231312	chromatin interactions
ENSG00000011566	chromatin interactions

Extended variants
information (count: 58 )
Associated
traits (count: 57 )

Variant overlapped rSNPs/rCNVs (count:58 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs540741211	chr2:39623776-39623777	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
2	rs565186348	chr2:39623788-39623789	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
3	rs185085453	chr2:39623833-39623834	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
4	rs544237586	chr2:39623856-39623857	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
5	rs138988085	chr2:39623857-39623858	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
6	rs11677611	chr2:39623860-39623861	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
7	rs11688728	chr2:39623892-39623893	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
8	rs567078786	chr2:39623898-39623899	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
9	rs528662558	chr2:39623905-39623906	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
10	rs527836893	chr2:39623956-39623957	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
11	rs552260333	chr2:39623971-39623972	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
12	rs572687524	chr2:39623989-39623990	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
13	rs368751608	chr2:39623992-39623993	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
14	rs570495966	chr2:39623998-39623999	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
15	rs537937528	chr2:39624037-39624038	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
16	rs527833693	chr2:39624039-39624040	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
17	rs72929194	chr2:39624056-39624057	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
18	rs568047984	chr2:39624084-39624085	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
19	rs371639145	chr2:39624093-39624094	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
20	rs535763541	chr2:39624135-39624136	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
21	rs553754785	chr2:39624144-39624145	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
22	rs572207246	chr2:39624153-39624154	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
23	rs545637059	chr2:39624208-39624209	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
24	rs540481258	chr2:39624297-39624298	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
25	rs557923332	chr2:39624313-39624314	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
26	rs576968006	chr2:39624377-39624378	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
27	rs562083872	chr2:39624413-39624414	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
28	rs2373535	chr2:39624443-39624444	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	mRNA abundance
29	rs550332615	chr2:39624486-39624487	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
30	rs7591563	chr2:39624504-39624505	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
31	rs545058351	chr2:39624528-39624529	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
32	rs530012094	chr2:39624545-39624546	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
33	rs542122796	chr2:39624569-39624570	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
34	rs560584870	chr2:39624597-39624598	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
35	rs527978328	chr2:39624619-39624620	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
36	rs552543531	chr2:39624639-39624640	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
37	rs571003491	chr2:39624640-39624641	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
38	rs531469867	chr2:39624675-39624676	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
39	rs372162735	chr2:39624680-39624681	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
40	rs568084748	chr2:39624682-39624683	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
41	rs535392071	chr2:39624721-39624722	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
42	rs116456240	chr2:39624767-39624768	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
43	rs565874069	chr2:39624880-39624881	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
44	rs188189287	chr2:39624916-39624917	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	Overlapped CNVs	n/a
45	rs62136497	chr2:39624926-39624927	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
46	rs3887311	chr2:39624940-39624941	Weak transcription Enhancers	Chromatin interactive region	2 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
47	rs537973591	chr2:39624960-39624961	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
48	rs114551880	chr2:39625013-39625014	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
49	rs566624656	chr2:39625025-39625026	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a
50	rs574503114	chr2:39625088-39625089	Weak transcription Enhancers	TF binding region Chromatin interactive region	3 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:57)

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
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	22495311	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
Colorectal cancer	16272173	CNVD

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39588000-39630400	Weak transcription	Placenta	Placenta
2	chr2:39603200-39638400	Weak transcription	Hela-S3	cervix
3	chr2:39603400-39625000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr2:39603400-39626800	Weak transcription	Primary T cells from cord blood	blood
5	chr2:39607000-39626800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:39607400-39624800	Weak transcription	Stomach Mucosa	stomach
7	chr2:39607600-39643400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr2:39608400-39626200	Weak transcription	Brain Substantia Nigra	brain
9	chr2:39609600-39626400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr2:39610200-39626400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:39613800-39630600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr2:39614000-39628000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:39615800-39626800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr2:39616000-39626400	Weak transcription	Gastric	stomach
15	chr2:39617600-39626200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:39617600-39626400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr2:39617800-39626200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr2:39617800-39628200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr2:39617800-39628400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr2:39617800-39630600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:39618000-39633400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:39619200-39629600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:39619800-39625600	Enhancers	HepG2	liver
24	chr2:39620000-39629400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:39620200-39635600	Weak transcription	Primary hematopoietic stem cells	blood
26	chr2:39620400-39624600	Weak transcription	Fetal Lung	lung
27	chr2:39621000-39624600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr2:39621800-39624800	Weak transcription	K562	blood
29	chr2:39621800-39628600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:39622000-39624200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr2:39622000-39626000	Weak transcription	Right Atrium	heart
32	chr2:39622000-39626400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:39622000-39626400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr2:39622000-39626400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:39622000-39626400	Weak transcription	Small Intestine	intestine
36	chr2:39622000-39626600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr2:39622000-39626600	Weak transcription	Pancreas	Pancrea
38	chr2:39622000-39628200	Weak transcription	Right Ventricle	heart
39	chr2:39622000-39628600	Weak transcription	Lung	lung
40	chr2:39622000-39635400	Weak transcription	HSMM	muscle
41	chr2:39622200-39626200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr2:39622200-39626400	Weak transcription	Aorta	Aorta
43	chr2:39622400-39626400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr2:39622400-39626600	Weak transcription	NHLF	lung
45	chr2:39622600-39626200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:39622600-39626400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr2:39622600-39626400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr2:39622600-39626400	Weak transcription	HSMMtube	muscle
49	chr2:39622600-39626400	Weak transcription	Osteobl	bone
50	chr2:39622600-39626800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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