Variant report

Variant	rs2553356
Chromosome Location	chr4:124580200-124580201
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11726784	0.96[EUR][1000 genomes]
rs11735849	0.90[EUR][1000 genomes]
rs11736421	0.81[EUR][1000 genomes]
rs12500929	0.84[EUR][1000 genomes]
rs13113892	0.96[EUR][1000 genomes]
rs1364875	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1425414	0.92[EUR][1000 genomes]
rs2042627	0.83[EUR][1000 genomes]
rs2042628	0.84[EUR][1000 genomes]
rs2553366	0.85[EUR][1000 genomes]
rs2553370	0.90[EUR][1000 genomes]
rs2589838	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2589845	0.90[EUR][1000 genomes]
rs2589854	0.88[EUR][1000 genomes]
rs2589856	0.91[EUR][1000 genomes]
rs34182893	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35748127	0.90[EUR][1000 genomes]
rs62319743	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7657498	0.84[EUR][1000 genomes]
rs890181	0.83[EUR][1000 genomes]
rs890182	0.91[EUR][1000 genomes]
rs890183	0.91[EUR][1000 genomes]
rs9307531	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34581	chr4:124271321-125247395	Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv469710	chr4:124474286-124623722	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv482747	chr4:124474286-124623722	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv830047	chr4:124504051-124699142	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv879873	chr4:124528452-124590869	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv879874	chr4:124550693-124607201	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:124573000-124581200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:124573000-124586400	Weak transcription	Pancreas	Pancrea
3	chr4:124573000-124598200	Weak transcription	Right Atrium	heart
4	chr4:124573200-124580400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr4:124573200-124580400	Weak transcription	Stomach Mucosa	stomach
6	chr4:124573200-124585000	Weak transcription	Psoas Muscle	Psoas
7	chr4:124573400-124592400	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr4:124573600-124581200	Weak transcription	Adipose Nuclei	Adipose
9	chr4:124573600-124582200	Weak transcription	Fetal Kidney	kidney
10	chr4:124573800-124595200	Weak transcription	Rectal Smooth Muscle	rectum
11	chr4:124577800-124594000	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr4:124578200-124580200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr4:124578200-124580400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr4:124578200-124580800	Strong transcription	Fetal Muscle Trunk	muscle
15	chr4:124578200-124584000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr4:124578200-124593000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr4:124578200-124596600	Weak transcription	Aorta	Aorta
18	chr4:124578800-124582000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr4:124579200-124581400	Strong transcription	Fetal Muscle Leg	muscle
20	chr4:124579800-124580800	Enhancers	HepG2	liver
21	chr4:124580000-124580600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:124580000-124580800	Enhancers	Fetal Intestine Large	intestine
23	chr4:124580000-124582400	Enhancers	Fetal Intestine Small	intestine
24	chr4:124580200-124580600	Enhancers	Duodenum Mucosa	Duodenum
25	chr4:124580200-124580600	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr4:124580200-124580800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links