Variant report

Variant	rs7616533
Chromosome Location	chr3:54339365-54339366
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs4072628	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6414572	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6769054	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6781279	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6793026	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6799791	0.83[AMR][1000 genomes]
rs7619571	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7619590	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7626750	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7640765	0.82[AMR][1000 genomes]
rs7643501	0.83[AMR][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	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised 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	31 gene(s)	inside rSNPs	diseases
2	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv817328	chr3:54250314-54380438	Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv965169	chr3:54338938-54339534	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54332200-54343600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:54334000-54343200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:54336800-54340600	Weak transcription	Aorta	Aorta
4	chr3:54337600-54339800	Enhancers	Fetal Stomach	stomach
5	chr3:54338000-54339800	Enhancers	Liver	Liver
6	chr3:54338000-54339800	Enhancers	Duodenum Smooth Muscle	Duodenum
7	chr3:54338400-54343200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:54338400-54345400	Weak transcription	Fetal Lung	lung
9	chr3:54338600-54339600	Enhancers	Rectal Smooth Muscle	rectum
10	chr3:54338800-54340600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr3:54338800-54341400	Weak transcription	Fetal Muscle Leg	muscle
12	chr3:54339000-54339400	Weak transcription	Brain Germinal Matrix	brain
13	chr3:54339000-54339800	Enhancers	Colon Smooth Muscle	Colon

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

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