Variant report

Variant	rs12492502
Chromosome Location	chr3:53715074-53715075
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12486415	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12493744	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs1872999	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1906537	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2276836	1.00[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2680658	0.94[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2680672	1.00[CHB][hapmap];0.91[CHD][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs34078083	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3774515	0.94[CEU][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs55819057	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55948017	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62251938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6762231	0.87[CHB][hapmap];0.82[CHD][hapmap]
rs6763245	0.89[CEU][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.83[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6765728	0.80[ASN][1000 genomes]
rs6793312	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6806330	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs735652	1.00[CEU][hapmap];1.00[CHB][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7648561	0.89[AMR][1000 genomes];0.92[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	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	nsv1001128	chr3:53659570-53927842	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv1013783	chr3:53694418-53934781	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53683200-53744200	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr3:53713200-53716000	Strong transcription	Fetal Intestine Large	intestine
3	chr3:53713800-53715800	Strong transcription	Fetal Intestine Small	intestine
4	chr3:53713800-53717600	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr3:53714000-53715400	Enhancers	Brain Angular Gyrus	brain
6	chr3:53714400-53715200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:53714400-53722200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr3:53714600-53715400	Weak transcription	Psoas Muscle	Psoas
9	chr3:53714600-53715600	Weak transcription	Brain Substantia Nigra	brain
10	chr3:53714600-53716800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:53714800-53717200	Strong transcription	Fetal Lung	lung

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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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