Variant report

Variant	rs6439542
Chromosome Location	chr3:134706449-134706450
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]
rs11720684	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11926107	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs253877	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35231710	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35659794	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36057	0.86[ASN][1000 genomes]
rs36058	0.86[ASN][1000 genomes]
rs4082244	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55836007	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67294685	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs718130	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7613213	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7648187	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811839	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[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	nsv1009634	chr3:134543259-134820208	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv536720	chr3:134543259-134820208	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1000277	chr3:134546080-134970837	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv877516	chr3:134689420-134918522	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers 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

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134693800-134707400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr3:134694000-134707000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:134694200-134709800	Weak transcription	Brain Germinal Matrix	brain
4	chr3:134697800-134709600	Weak transcription	GM12878-XiMat	blood
5	chr3:134702600-134707800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:134705000-134707400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:134705200-134709600	Weak transcription	Fetal Brain Female	brain
8	chr3:134705800-134708000	Weak transcription	Fetal Brain Male	brain
9	chr3:134706400-134707200	Strong transcription	Breast Myoepithelial Primary Cells	Breast

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

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