Variant report

Variant	rs623696
Chromosome Location	chr3:54677523-54677524
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1965072	0.91[ASN][1000 genomes]
rs1965073	0.90[ASN][1000 genomes]
rs488451	0.86[ASN][1000 genomes]
rs492885	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs510605	0.89[ASN][1000 genomes]
rs525736	0.81[ASN][1000 genomes]
rs529098	0.94[ASN][1000 genomes]
rs530868	0.93[ASN][1000 genomes]
rs533524	0.92[ASN][1000 genomes]
rs535526	0.90[ASN][1000 genomes]
rs543828	0.92[ASN][1000 genomes]
rs550728	0.80[ASN][1000 genomes]
rs562668	0.94[ASN][1000 genomes]
rs566884	0.84[ASN][1000 genomes]
rs588784	0.89[ASN][1000 genomes]
rs596992	0.82[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs599573	0.89[ASN][1000 genomes]
rs601383	0.89[ASN][1000 genomes]
rs601420	0.89[ASN][1000 genomes]
rs608142	0.81[ASN][1000 genomes]
rs622326	0.98[ASN][1000 genomes]
rs630987	0.92[ASN][1000 genomes]
rs666071	0.88[ASN][1000 genomes]
rs838017	0.92[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	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
2	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv525644	chr3:54653316-54709987	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54663600-54683800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr3:54674400-54677800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr3:54674400-54678000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:54676200-54678000	Enhancers	H1 Cell Line	embryonic stem cell
5	chr3:54676400-54677800	Enhancers	H9 Cell Line	embryonic stem cell
6	chr3:54676400-54679000	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr3:54676800-54679200	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr3:54676800-54683200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr3:54677000-54677800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:54677000-54677800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:54677200-54677800	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr3:54677200-54678000	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr3:54677200-54678200	Genic enhancers	HUES48 Cell Line	embryonic stem cell
14	chr3:54677200-54685600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:54677400-54677600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:54677400-54677600	Enhancers	Esophagus	oesophagus
17	chr3:54677400-54678200	Genic enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr3:54677400-54690800	Weak transcription	iPS-15b 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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