Variant report

Variant	rs57649400
Chromosome Location	chr4:79550286-79550287
allele	A/G
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr4:79542556..79545467-chr4:79549942..79551796,4	K562	blood:
2	chr4:79549970..79552473-chr4:79560389..79564299,4	K562	blood:
3	chr4:79534010..79538453-chr4:79546769..79551125,4	K562	blood:
4	chr4:79549841..79552363-chr4:79696027..79698127,2	MCF-7	breast:
5	chr4:79547404..79551814-chr4:79694410..79698430,6	K562	blood:
6	chr4:79548752..79551333-chr4:79698595..79700948,2	K562	blood:
7	chr4:79550103..79553175-chr4:79717288..79720915,3	K562	blood:
8	chr4:79549039..79550674-chr4:79611784..79614679,2	K562	blood:
9	chr4:79534997..79539335-chr4:79548255..79551176,6	K562	blood:
10	chr4:79549184..79553600-chr4:79560172..79565329,6	K562	blood:
11	chr4:79547404..79553256-chr4:79694666..79698430,7	K562	blood:
12	chr4:79527750..79532040-chr4:79547937..79551505,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000238816	Chromatin interaction
ENSG00000260278	Chromatin interaction
ENSG00000138756	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10452151	1.00[AMR][1000 genomes]
rs55994157	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56071306	1.00[AMR][1000 genomes]
rs56098630	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57648305	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59055207	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59700988	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60681937	1.00[AMR][1000 genomes]
rs60950346	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60998921	1.00[AMR][1000 genomes]
rs61075598	1.00[AMR][1000 genomes]
rs61238857	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828029	1.00[AMR][1000 genomes]
rs73828034	1.00[AMR][1000 genomes]
rs73828038	1.00[AMR][1000 genomes]
rs73828045	1.00[AMR][1000 genomes]
rs73828046	1.00[AMR][1000 genomes]
rs73828057	1.00[AMR][1000 genomes]
rs73828059	1.00[AMR][1000 genomes]
rs73828064	1.00[AMR][1000 genomes]
rs73828065	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828067	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828069	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828070	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828071	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828073	1.00[AMR][1000 genomes]
rs73828074	1.00[AMR][1000 genomes]
rs73828075	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828078	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828079	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73828080	1.00[AMR][1000 genomes]
rs73828081	1.00[AMR][1000 genomes]
rs73828083	1.00[AMR][1000 genomes]
rs73828092	1.00[AMR][1000 genomes]
rs73828098	1.00[AMR][1000 genomes]
rs73828100	1.00[AMR][1000 genomes]
rs73828102	1.00[AMR][1000 genomes]
rs73830206	1.00[AMR][1000 genomes]
rs73830208	1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79536400-79550600	Weak transcription	Left Ventricle	heart
2	chr4:79539400-79550400	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr4:79542200-79555600	Enhancers	Fetal Intestine Small	intestine
4	chr4:79542600-79555600	Enhancers	Fetal Intestine Large	intestine
5	chr4:79544200-79550600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:79545800-79550800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr4:79546600-79553000	Enhancers	Placenta	Placenta
8	chr4:79547600-79551800	Enhancers	Stomach Mucosa	stomach
9	chr4:79547800-79550400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr4:79548000-79550400	Enhancers	NHEK	skin
11	chr4:79548000-79551800	Enhancers	HepG2	liver
12	chr4:79548000-79553200	Enhancers	Placenta Amnion	Placenta Amnion
13	chr4:79548200-79551200	Weak transcription	Colonic Mucosa	Colon
14	chr4:79548200-79552600	Enhancers	Duodenum Mucosa	Duodenum
15	chr4:79548200-79555000	Weak transcription	Osteobl	bone
16	chr4:79548600-79553600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr4:79548800-79552200	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr4:79548800-79557400	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr4:79549000-79550600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr4:79549000-79550600	Weak transcription	Brain Substantia Nigra	brain
21	chr4:79549600-79550400	Flanking Active TSS	K562	blood
22	chr4:79549600-79550600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr4:79549600-79551800	Weak transcription	Small Intestine	intestine
24	chr4:79549600-79560000	Weak transcription	HMEC	breast
25	chr4:79549800-79551600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
26	chr4:79549800-79551600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr4:79549800-79551600	Enhancers	Fetal Kidney	kidney
28	chr4:79549800-79552000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:79549800-79552000	Enhancers	Pancreatic Islets	Pancreatic Islet
30	chr4:79549800-79554200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr4:79550000-79550400	Enhancers	NHDF-Ad	bronchial
32	chr4:79550000-79551400	Enhancers	Primary B cells from cord blood	blood
33	chr4:79550000-79551600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr4:79550000-79552000	Enhancers	Hela-S3	cervix
35	chr4:79550000-79552200	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr4:79550000-79552800	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr4:79550200-79550400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr4:79550200-79550400	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr4:79550200-79550600	Flanking Active TSS	GM12878-XiMat	blood
40	chr4:79550200-79550600	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr4:79550200-79550800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:79550200-79550800	Enhancers	Gastric	stomach
43	chr4:79550200-79551200	Weak transcription	Brain Angular Gyrus	brain
44	chr4:79550200-79551200	Weak transcription	Right Atrium	heart
45	chr4:79550200-79551200	Enhancers	Dnd41	blood
46	chr4:79550200-79551400	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr4:79550200-79551400	Enhancers	Pancreas	Pancrea
48	chr4:79550200-79551400	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr4:79550200-79551600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr4:79550200-79552000	Enhancers	Brain Anterior Caudate	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links