Variant report

Variant	rs12494990
Chromosome Location	chr3:59467599-59467600
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10510812	0.81[EUR][1000 genomes]
rs11130713	0.81[EUR][1000 genomes]
rs11925209	0.80[EUR][1000 genomes]
rs11925279	0.80[EUR][1000 genomes]
rs12486826	0.94[CHB][hapmap]
rs12493195	0.94[CHB][hapmap]
rs17273249	0.82[EUR][1000 genomes]
rs56963895	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6773085	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73095774	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[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	nsv1011181	chr3:58665373-59542339	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv536574	chr3:58665373-59542339	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv534257	chr3:58855959-59606464	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59465600-59468200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr3:59465600-59468600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:59465600-59468800	Enhancers	HMEC	breast
4	chr3:59466000-59468400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:59466200-59467800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr3:59466400-59468400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr3:59466600-59467800	Weak transcription	HSMM	muscle
8	chr3:59466600-59468200	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr3:59466600-59468600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:59466800-59467800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:59466800-59468000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr3:59466800-59468000	Weak transcription	NH-A	brain
13	chr3:59466800-59468200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:59466800-59468200	Weak transcription	HSMMtube	muscle
15	chr3:59466800-59468200	Enhancers	Osteobl	bone
16	chr3:59466800-59469000	Weak transcription	NHDF-Ad	bronchial
17	chr3:59466800-59469200	Enhancers	NHEK	skin
18	chr3:59467200-59468400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:59467200-59468400	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr3:59467400-59468600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:59467400-59468600	Enhancers	Muscle Satellite Cultured Cells	--

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