Variant report

Variant	rs2060563
Chromosome Location	chr3:25211667-25211668
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1347560	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1347561	1.00[AFR][1000 genomes]
rs1347562	1.00[AFR][1000 genomes]
rs1436253	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1436254	1.00[AFR][1000 genomes]
rs1436255	1.00[AFR][1000 genomes]
rs17015892	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015894	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17015918	0.87[AFR][1000 genomes]
rs2060564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2117971	1.00[AFR][1000 genomes]
rs58763127	1.00[EUR][1000 genomes]
rs6550955	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73050349	1.00[ASN][1000 genomes]
rs7625082	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	nsv1013446	chr3:25176609-25221334	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv876631	chr3:25185448-25231571	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv949035	chr3:25194301-26084890	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases
4	nsv508213	chr3:25206150-25326196	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:25194000-25211800	Weak transcription	Aorta	Aorta
2	chr3:25200600-25214600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:25206600-25211800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:25208000-25215200	Weak transcription	Fetal Lung	lung
5	chr3:25211200-25212000	Enhancers	Fetal Stomach	stomach
6	chr3:25211200-25212600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:25211600-25211800	Enhancers	H1 Cell Line	embryonic stem cell
8	chr3:25211600-25211800	Enhancers	H9 Cell Line	embryonic stem cell
9	chr3:25211600-25213800	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr3:25211600-25213800	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr3:25211600-25214000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links