Variant report

Variant	esv3449002
Chromosome Location	chr2:233570231-233570723
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:233565665..233568503-chr2:233570268..233573165,3	MCF-7	breast:
2	chr2:233560777..233562416-chr2:233568775..233570422,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GIGYF2-1	chr2:233570143-233570657	NONHSAT077441

Variant related genes	Relation type
ENSG00000204120	chromatin interactions

Extended variants
information (count: 24 )
Associated
traits (count: 62 )

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs113614962	chr2:233570264-233570265	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
2	rs541833659	chr2:233570265-233570266	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
3	rs539316373	chr2:233570274-233570275	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
4	rs561796699	chr2:233570295-233570296	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
5	rs200906994	chr2:233570300-233570301	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
6	rs527380246	chr2:233570374-233570375	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
7	rs559781691	chr2:233570381-233570382	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
8	rs547654338	chr2:233570395-233570396	Weak transcription Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
9	rs372460444	chr2:233570404-233570405	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
10	rs190341567	chr2:233570405-233570406	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
11	rs182078032	chr2:233570435-233570436	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
12	rs376952686	chr2:233570443-233570444	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
13	rs375441237	chr2:233570470-233570471	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
14	rs10185281	chr2:233570476-233570477	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	LD-proxies of rSNP Overlapped rCNV	n/a
15	rs555319273	chr2:233570517-233570518	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
16	rs565880970	chr2:233570556-233570557	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
17	rs138533263	chr2:233570582-233570583	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
18	rs557937706	chr2:233570601-233570602	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
19	rs578074407	chr2:233570615-233570616	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
20	rs528291880	chr2:233570621-233570622	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
21	rs557406821	chr2:233570625-233570626	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	Overlapped CNVs	n/a
22	rs185222294	chr2:233570664-233570665	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
23	rs541895256	chr2:233570686-233570687	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a
24	rs561659167	chr2:233570716-233570717	Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	Overlapped CNVs	n/a

Variant related diseases (count:62)

Disease	PMID	Source
Ewing''s sarcoma	21437220	CNVD
Glioblastoma multiforme	21080181	CNVD
Medulloblastoma	21979893	CNVD
Ependymoma	16718352	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Acute lymphoblastic leukemia	20067559	CNVD
Acute lymphoblastic leukemia	21980252	CNVD
Breast cancer	17603634	CNVD
Breast cancer	16272173	CNVD
Ewing''s sarcoma	17952124	CNVD
Cancer	21637783	CNVD
Non-syndromic sensorineural hearing loss	18471307	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Embryonal rhabdomyosarcoma	16790082	CNVD
Autism	16446308	CNVD
Autism	19401682	CNVD
Colorectal cancer	16272173	CNVD
Lung cancer	18438408	CNVD
Acute myeloid leukemia	20729466	CNVD
small cell lung cancer	20016488	CNVD
Biliary cancer	20360734	CNVD
Breast cancer	20360734	CNVD
Coronary artery disease	20360734	CNVD
Crohn''s disease	20360734	CNVD
Hypertension	20360734	CNVD
Rheumatoid arthritis	20360734	CNVD
Type 1 diabetes	20360734	CNVD
Type 2 diabetes	20360734	CNVD
Urothelial carcinoma	21177765	CNVD
Hodgkin''s lymphoma	17606441	CNVD
Cervical cancer	21062161	CNVD
Adenoid cystic carcinoma	18698036	CNVD
Myofibroblastic sarcoma	19369631	CNVD
Chordoma	18071362	CNVD
Developmental delay	21147756	CNVD
Acute lymphoblastic leukemia	22237106	CNVD
Cancer	22429812	CNVD
Bladder cancer	21909424	CNVD
Renal cell carcinoma	21668985	CNVD
Breast cancer	21785460	CNVD
Prostate cancer	18632612	CNVD
Malignant fibrous histiocytomas	21085701	CNVD
Wilms tumour	21544195	CNVD
Esophageal adenocarcinoma	18519675	CNVD
prenatal diagnosis	22389664	CNVD
Myelofibrosis	22110671	CNVD
Invasive pancreatic ductal carcinoma	16982739	CNVD
Mental retardation	20152051	CNVD
Cancer	21183584	CNVD
Albright''s disease	22277900	CNVD
Brachydactyly-Mental Retardation Syndrome	22470819	CNVD
T-cell acute lymphoblastic leukemia	18185524	CNVD
Colorectal cancer	19359472	CNVD
Autism	18414403	CNVD
Congenital anomalies of the kidney and urinary tract	20605837	CNVD
Breast cancer	22522925	CNVD
Cancer	20164919	CNVD
Pancreatic cancer	17952125	CNVD

Chromatin state (count:139 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:233563200-233572400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:233563800-233582600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr2:233564000-233570600	Weak transcription	Fetal Kidney	kidney
4	chr2:233564000-233570800	Weak transcription	HSMMtube	muscle
5	chr2:233564000-233579600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:233564000-233589000	Weak transcription	NH-A	brain
7	chr2:233564200-233570400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:233564200-233571000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:233564200-233596400	Weak transcription	NHLF	lung
10	chr2:233564200-233613000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:233564800-233592800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr2:233565000-233612200	Weak transcription	Fetal Brain Male	brain
13	chr2:233565200-233573800	Weak transcription	NHEK	skin
14	chr2:233565200-233589800	Weak transcription	HMEC	breast
15	chr2:233565200-233602000	Weak transcription	HUVEC	blood vessel
16	chr2:233565200-233606400	Weak transcription	Stomach Mucosa	stomach
17	chr2:233565400-233580200	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr2:233565400-233589800	Weak transcription	Hela-S3	cervix
19	chr2:233565400-233590000	Weak transcription	Colon Smooth Muscle	Colon
20	chr2:233565600-233641000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr2:233566000-233570400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:233566000-233576000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:233566000-233576000	Strong transcription	Fetal Stomach	stomach
24	chr2:233566000-233577000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr2:233566000-233578400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:233566000-233584600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr2:233566200-233574200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:233566200-233576000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr2:233566400-233572000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:233566600-233570600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr2:233566800-233571000	Weak transcription	Ovary	ovary
32	chr2:233566800-233571000	Weak transcription	Right Ventricle	heart
33	chr2:233566800-233612800	Weak transcription	Small Intestine	intestine
34	chr2:233567200-233574200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:233567200-233574200	Strong transcription	Fetal Thymus	thymus
36	chr2:233567400-233572200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:233567400-233576800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:233567600-233572200	Strong transcription	Duodenum Mucosa	Duodenum
39	chr2:233567600-233572400	Strong transcription	GM12878-XiMat	blood
40	chr2:233567600-233577800	Strong transcription	Fetal Muscle Trunk	muscle
41	chr2:233567800-233571400	Strong transcription	Left Ventricle	heart
42	chr2:233567800-233573800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr2:233567800-233574000	Strong transcription	Primary B cells from peripheral blood	blood
44	chr2:233567800-233575800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr2:233568000-233572600	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr2:233568000-233573400	Strong transcription	Dnd41	blood
47	chr2:233568000-233604400	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr2:233568200-233571000	Strong transcription	Fetal Brain Female	brain
49	chr2:233568200-233571200	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:233568200-233572600	Strong transcription	Primary T cells fromperipheralblood	blood

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