Variant report

Variant	rs55993822
Chromosome Location	chr10:116657863-116657864
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr10:116657805-116658145	HepG2	liver:	n/a	n/a
2	FOXA1	chr10:116657793-116658082	HepG2	liver:	n/a	n/a
3	FOXA1	chr10:116657811-116658083	HepG2	liver:	n/a	n/a
4	FOXA1	chr10:116657754-116658092	HepG2	liver:	n/a	n/a
5	FOXA2	chr10:116657848-116658046	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
ENSG00000226428	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1007847	1.00[EUR][1000 genomes]
rs10885652	1.00[EUR][1000 genomes]
rs11196974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11197025	1.00[EUR][1000 genomes]
rs11197057	1.00[EUR][1000 genomes]
rs11197058	1.00[EUR][1000 genomes]
rs11197060	1.00[EUR][1000 genomes]
rs11197061	1.00[EUR][1000 genomes]
rs11197067	1.00[EUR][1000 genomes]
rs11197070	1.00[EUR][1000 genomes]
rs12245856	1.00[EUR][1000 genomes]
rs12252344	1.00[EUR][1000 genomes]
rs12255157	1.00[EUR][1000 genomes]
rs12264153	1.00[EUR][1000 genomes]
rs12267097	1.00[EUR][1000 genomes]
rs5023856	1.00[EUR][1000 genomes]
rs55954958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56044402	1.00[EUR][1000 genomes]
rs56866557	1.00[EUR][1000 genomes]
rs57000201	1.00[EUR][1000 genomes]
rs57423028	1.00[EUR][1000 genomes]
rs57707843	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58042685	1.00[EUR][1000 genomes]
rs58836644	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59741104	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60460075	1.00[EUR][1000 genomes]
rs60791428	1.00[EUR][1000 genomes]
rs62641708	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7069069	1.00[EUR][1000 genomes]
rs7070487	1.00[EUR][1000 genomes]
rs7074608	1.00[EUR][1000 genomes]
rs7077957	1.00[EUR][1000 genomes]
rs7078359	1.00[EUR][1000 genomes]
rs7082007	1.00[EUR][1000 genomes]
rs7082100	1.00[EUR][1000 genomes]
rs7084277	1.00[EUR][1000 genomes]
rs74158064	1.00[EUR][1000 genomes]
rs74158066	1.00[EUR][1000 genomes]
rs74158068	1.00[EUR][1000 genomes]
rs74158070	1.00[EUR][1000 genomes]
rs74158071	1.00[EUR][1000 genomes]
rs74158072	1.00[EUR][1000 genomes]
rs74158073	1.00[EUR][1000 genomes]
rs74158075	1.00[EUR][1000 genomes]
rs74158076	1.00[EUR][1000 genomes]
rs74158079	1.00[EUR][1000 genomes]
rs74158081	1.00[EUR][1000 genomes]
rs74158090	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74159814	1.00[EUR][1000 genomes]
rs74159822	1.00[EUR][1000 genomes]
rs74159823	1.00[EUR][1000 genomes]
rs74159827	1.00[EUR][1000 genomes]
rs7894976	1.00[EUR][1000 genomes]
rs7899382	1.00[EUR][1000 genomes]
rs7900110	1.00[EUR][1000 genomes]
rs7920152	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv831996	chr10:116601552-116772968	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv1039002	chr10:116643095-116879483	Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv2761634	chr10:116643095-116879495	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv1045654	chr10:116654574-116879483	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv1043242	chr10:116655057-116883386	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116656600-116660400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr10:116657800-116658000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links