Variant report

Variant	rs13060843
Chromosome Location	chr3:54684453-54684454
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12490327	0.81[ASN][1000 genomes]
rs12496821	0.81[ASN][1000 genomes]
rs13070126	0.81[ASN][1000 genomes]
rs13081682	0.85[ASN][1000 genomes]
rs13084347	0.80[AMR][1000 genomes]
rs13084602	0.81[ASN][1000 genomes]
rs13096365	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1520575	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17815840	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1829549	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2099019	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36061401	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6798481	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6808464	0.85[ASN][1000 genomes]
rs71301895	0.82[AMR][1000 genomes]
rs7623961	0.81[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:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54677200-54685600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:54677400-54690800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:54677800-54687800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:54679200-54685800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:54679600-54685400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:54681200-54694800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr3:54681400-54685600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:54681400-54693400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:54681600-54693400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:54681800-54693200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:54683400-54686400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr3:54683600-54686200	Weak transcription	Esophagus	oesophagus
13	chr3:54683600-54693600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:54684000-54685000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:54684000-54686400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:54684200-54685800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:54684200-54694600	Weak transcription	Stomach Smooth Muscle	stomach

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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