Variant report

Variant	rs1490992
Chromosome Location	chr5:125035223-125035224
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:125033776..125036628-chr5:125040323..125041930,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10056409	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1352738	0.83[EUR][1000 genomes]
rs1490986	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17153106	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17153111	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17153165	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1873483	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2201044	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28547260	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28696180	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28703569	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35433994	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4620020	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6595624	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6878672	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7706068	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7709204	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7727138	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1030992	chr5:124708549-125391503	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv537892	chr5:124708549-125391503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv534468	chr5:124943170-125634960	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 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	chr5:125021800-125055400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:125032800-125035400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr5:125033000-125035600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:125033000-125035600	Weak transcription	Fetal Intestine Small	intestine
5	chr5:125033200-125035400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:125033200-125035600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:125033200-125035600	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr5:125033200-125035600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr5:125033200-125035600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr5:125033200-125035600	Weak transcription	Osteobl	bone
11	chr5:125033200-125035800	Weak transcription	NH-A	brain
12	chr5:125033200-125036200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:125033400-125035400	Weak transcription	HepG2	liver
14	chr5:125033400-125035600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr5:125033400-125035600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:125033400-125035600	Weak transcription	NHDF-Ad	bronchial
17	chr5:125033400-125036200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr5:125033400-125039200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:125034200-125037000	Enhancers	Fetal Kidney	kidney
20	chr5:125034600-125036000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr5:125035200-125035600	Enhancers	Pancreatic Islets	Pancreatic Islet
22	chr5:125035200-125036600	Enhancers	HSMM	muscle
23	chr5:125035200-125036800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:125035200-125037000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr5:125035200-125037000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr5:125035200-125037000	Enhancers	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links