Variant report

Variant	rs12492115
Chromosome Location	chr3:54247972-54247973
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11130400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130403	0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12485692	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12488090	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs12492530	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12631896	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12632437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12639082	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs34152564	1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs3923437	0.98[ASN][1000 genomes]
rs4450860	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs55720439	1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs55927212	0.93[ASN][1000 genomes]
rs73087910	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73087948	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73087960	0.96[ASN][1000 genomes]
rs73087962	1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs73087966	1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	nsv518483	chr3:54212182-54259801	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1001802	chr3:54236994-54275831	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54244200-54249400	Weak transcription	Fetal Brain Male	brain
2	chr3:54245000-54248400	Weak transcription	Right Ventricle	heart
3	chr3:54247200-54248200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:54247400-54248800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr3:54247400-54248800	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr3:54247400-54249000	Enhancers	Brain Anterior Caudate	brain
7	chr3:54247400-54249000	Enhancers	Left Ventricle	heart
8	chr3:54247400-54249000	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr3:54247400-54249200	Enhancers	Right Atrium	heart
10	chr3:54247600-54249000	Enhancers	Brain Angular Gyrus	brain
11	chr3:54247800-54248000	Enhancers	Ovary	ovary
12	chr3:54247800-54249000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr3:54247800-54254600	Weak transcription	Gastric	stomach

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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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