Variant report

Variant	rs1404579
Chromosome Location	chr3:134846810-134846811
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11706256	0.80[CHD][hapmap];0.86[JPT][hapmap]
rs12492126	0.80[JPT][hapmap]
rs13074164	0.87[CEU][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13096641	1.00[CEU][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13096735	0.87[CEU][hapmap];0.93[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1553282	0.81[CHD][hapmap];0.80[JPT][hapmap];0.82[MKK][hapmap]
rs17765685	0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs2140766	0.93[CHD][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs940638	0.93[CHB][hapmap];0.96[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs9864760	1.00[CEU][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv829731	chr3:134711713-134885064	Strong transcription Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:134809200-134855200	Weak transcription	GM12878-XiMat	blood
2	chr3:134823000-134880000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:134842000-134847000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr3:134842200-134853200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr3:134845400-134847400	Enhancers	Brain Germinal Matrix	brain
6	chr3:134845800-134847400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:134846000-134847600	Enhancers	Fetal Brain Male	brain
8	chr3:134846400-134847400	Enhancers	Fetal Brain Female	brain
9	chr3:134846600-134847400	Enhancers	Brain Anterior Caudate	brain
10	chr3:134846800-134847200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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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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