Variant report

Variant	rs898411
Chromosome Location	chr3:53716912-53716913
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11130377	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11711045	0.87[EUR][1000 genomes]
rs11711142	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11715072	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11720002	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs11925053	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1460118	0.82[YRI][hapmap]
rs17238364	0.95[CEU][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1870564	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3774491	0.84[CHB][hapmap]
rs58086880	0.85[EUR][1000 genomes]
rs60529666	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6780648	1.00[CEU][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6803827	1.00[CHB][hapmap]
rs6809164	0.95[CEU][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.88[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs898411	RNF123	cis	cerebellum	SCAN

Chromatin state (count:10 , 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	chr3:53713800-53717600	Enhancers	Skeletal Muscle Female	skeletal muscle
3	chr3:53714400-53722200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr3:53714800-53717200	Strong transcription	Fetal Lung	lung
5	chr3:53715600-53739600	Weak transcription	Brain Anterior Caudate	brain
6	chr3:53716000-53717200	Weak transcription	Psoas Muscle	Psoas
7	chr3:53716400-53717400	Enhancers	Fetal Intestine Small	intestine
8	chr3:53716600-53717400	Enhancers	HepG2	liver
9	chr3:53716800-53717000	Active TSS	Skeletal Muscle Male	skeletal muscle
10	chr3:53716800-53717200	Enhancers	Fetal Intestine Large	intestine

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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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