Variant report

Variant	rs56897578
Chromosome Location	chr3:119797914-119797915
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:119794849..119798718-chr3:119811485..119814707,3	K562	blood:
2	chr3:119796620..119798718-chr3:119813207..119814938,2	K562	blood:
3	chr3:119797695..119800113-chr3:119802432..119804591,2	K562	blood:

Variant related genes	Relation type
ENSG00000082701	Chromatin interaction
ENSG00000242622	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs55849075	1.00[AFR][1000 genomes]
rs56181436	1.00[AFR][1000 genomes]
rs57028282	0.92[AFR][1000 genomes]
rs59890455	0.83[AFR][1000 genomes]
rs61091679	0.92[AFR][1000 genomes]
rs73854732	0.83[AFR][1000 genomes]
rs73854734	0.92[AFR][1000 genomes]
rs73854742	0.92[AFR][1000 genomes]
rs73854743	0.92[AFR][1000 genomes]
rs73854748	0.92[AFR][1000 genomes]
rs73854754	1.00[AFR][1000 genomes]
rs73854756	0.92[AFR][1000 genomes]
rs73854758	0.92[AFR][1000 genomes]
rs73854759	1.00[AFR][1000 genomes]
rs73854760	1.00[AFR][1000 genomes]
rs73854763	0.88[AFR][1000 genomes]
rs73854768	1.00[AFR][1000 genomes]
rs73854771	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949589	chr3:119560606-120175917	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1001476	chr3:119575386-120075417	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv536704	chr3:119575386-120075417	Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
4	nsv3964	chr3:119786623-119831698	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:119760200-119805400	Weak transcription	HMEC	breast
2	chr3:119764600-119812000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:119769200-119804400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:119771400-119809400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr3:119771800-119805400	Weak transcription	NHEK	skin
6	chr3:119773200-119807600	Weak transcription	Right Ventricle	heart
7	chr3:119779400-119804200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr3:119779400-119807400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:119779600-119800200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:119779600-119807800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:119780600-119807800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr3:119788400-119805400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:119788400-119808600	Weak transcription	Primary B cells from cord blood	blood
14	chr3:119789400-119809200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:119789800-119807800	Weak transcription	Primary B cells from peripheral blood	blood
16	chr3:119790000-119807600	Weak transcription	Liver	Liver
17	chr3:119790200-119805000	Weak transcription	HepG2	liver
18	chr3:119790400-119800000	Weak transcription	Spleen	Spleen
19	chr3:119790400-119800600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:119790400-119805200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr3:119790600-119807400	Weak transcription	Brain Substantia Nigra	brain
22	chr3:119790600-119807800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:119790600-119809200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:119790800-119808000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:119790800-119809200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr3:119790800-119809400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:119791000-119809600	Weak transcription	Fetal Muscle Leg	muscle
28	chr3:119791400-119798800	Weak transcription	Fetal Intestine Small	intestine
29	chr3:119792400-119798200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr3:119793000-119807400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr3:119793200-119799400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:119793200-119805400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr3:119795000-119799400	Weak transcription	Small Intestine	intestine
34	chr3:119795200-119798600	Weak transcription	Colon Smooth Muscle	Colon
35	chr3:119795200-119805200	Weak transcription	Hela-S3	cervix
36	chr3:119796000-119798000	Enhancers	NHDF-Ad	bronchial
37	chr3:119796000-119801000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr3:119796200-119799000	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr3:119796400-119798200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:119796400-119798800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:119796400-119799800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr3:119796400-119800600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr3:119796400-119802400	Weak transcription	Fetal Heart	heart
44	chr3:119796400-119804800	Weak transcription	Stomach Mucosa	stomach
45	chr3:119796600-119799800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:119796600-119802400	Weak transcription	Adipose Nuclei	Adipose
47	chr3:119796600-119804600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr3:119796800-119806000	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr3:119797000-119807400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:119797000-119807800	Weak transcription	Pancreatic Islets	Pancreatic Islet

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