Variant report

Variant	rs4456963
Chromosome Location	chr4:95724988-95724989
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11932119	0.94[CHB][hapmap];0.88[ASN][1000 genomes]
rs12508087	0.87[ASW][hapmap];0.89[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.88[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12508155	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13116658	0.87[YRI][hapmap]
rs13128703	0.82[MEX][hapmap]
rs13139748	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs17022123	0.88[LWK][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs17022276	0.82[YRI][hapmap]
rs17022377	0.87[YRI][hapmap]
rs3775007	0.81[YRI][hapmap]
rs4401458	0.87[CHB][hapmap];0.88[CHD][hapmap]
rs4425388	0.86[CHB][hapmap];0.87[ASN][1000 genomes]
rs4431232	0.88[ASN][1000 genomes]
rs4699681	0.83[ASN][1000 genomes]
rs4699683	0.93[CHB][hapmap]
rs4699690	0.86[ASN][1000 genomes]
rs62316168	0.81[AMR][1000 genomes]
rs6817189	0.92[ASN][1000 genomes]
rs6836126	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6842692	0.93[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs6844958	0.87[ASN][1000 genomes]
rs72669047	0.90[AFR][1000 genomes]
rs7668820	0.81[AMR][1000 genomes]
rs7673420	0.94[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7685389	0.88[ASN][1000 genomes]
rs7694754	0.87[CHB][hapmap];0.94[CHD][hapmap];0.85[ASN][1000 genomes]
rs7694987	0.93[CHB][hapmap];0.97[CHD][hapmap];0.85[ASN][1000 genomes]
rs9307147	0.93[CHB][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932216	chr4:95501261-96109807	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv1003860	chr4:95507683-96120619	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv869528	chr4:95537649-96368018	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1005816	chr4:95573444-95902704	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
5	nsv518579	chr4:95706337-95755544	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	nsv594906	chr4:95713679-95755544	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1007391	chr4:95713679-95763860	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1002004	chr4:95717063-95755436	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv999588	chr4:95717063-95763860	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv997960	chr4:95719585-95766067	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv537188	chr4:95719585-95766067	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4456963	ATOH1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95710400-95732400	Weak transcription	Aorta	Aorta
2	chr4:95713800-95725800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:95720400-95726200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:95723000-95732200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:95723600-95726200	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr4:95723600-95733600	Weak transcription	Ovary	ovary
7	chr4:95723800-95725600	Weak transcription	A549	lung
8	chr4:95723800-95726400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr4:95723800-95727200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr4:95724800-95727600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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