Variant report

Variant	rs4928004
Chromosome Location	chr3:54202214-54202215
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12630117	0.95[CEU][hapmap];0.91[EUR][1000 genomes]
rs1449336	1.00[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4076708	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs4927998	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs4928001	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs4928006	0.89[JPT][hapmap];0.81[YRI][hapmap];0.93[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6445630	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6765381	0.95[CEU][hapmap]
rs6790642	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs6809942	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs73085955	0.82[ASN][1000 genomes]
rs7643707	0.80[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs7649990	0.80[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs9880752	0.80[CHB][hapmap];0.84[JPT][hapmap];0.82[ASN][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	nsv1006990	chr3:53849510-54285212	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	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
4	nsv1014157	chr3:54168755-54332321	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54192600-54202400	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr3:54198000-54202800	Weak transcription	Lung	lung
3	chr3:54199000-54202600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:54200400-54205400	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr3:54200400-54214800	Weak transcription	Psoas Muscle	Psoas
6	chr3:54201400-54202800	Enhancers	Skeletal Muscle Female	skeletal muscle
7	chr3:54202000-54203000	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr3:54202000-54203000	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr3:54202200-54203000	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr3:54202200-54203200	Enhancers	H9 Cell Line	embryonic stem cell
11	chr3:54202200-54203200	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr3:54202200-54203200	Enhancers	iPS-20b Cell Line	embryonic stem cell

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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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