Variant report

Variant	rs8115729
Chromosome Location	chr20:25130395-25130396
allele	A/G
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	CEBPB	chr20:25130136-25130425	HepG2	liver:	n/a	chr20:25130312-25130323
2	CEBPB	chr20:25130133-25130480	HepG2	liver:	n/a	chr20:25130312-25130323

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:25125843..25128254-chr20:25129443..25131955,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230725	TF binding region
ENSG00000230725	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12479688	1.00[CHB][hapmap]
rs13039906	0.89[ASN][1000 genomes]
rs2206750	0.89[ASN][1000 genomes]
rs2223687	0.89[ASN][1000 genomes]
rs4813554	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4813558	1.00[CHB][hapmap];0.85[YRI][hapmap]
rs4815375	0.89[ASN][1000 genomes]
rs4815377	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4815384	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs4815390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4815391	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55932006	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6050360	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6107007	0.89[ASN][1000 genomes]
rs6115043	0.89[ASN][1000 genomes]
rs6115048	1.00[CHB][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs6115053	0.89[ASN][1000 genomes]
rs6115054	0.89[ASN][1000 genomes]
rs6115055	0.89[ASN][1000 genomes]
rs6115080	0.89[ASN][1000 genomes]
rs6115089	1.00[CHB][hapmap];0.85[YRI][hapmap]
rs6515589	0.89[ASN][1000 genomes]
rs6515592	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs721866	1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs7267149	1.00[CHB][hapmap];0.81[YRI][hapmap];0.89[ASN][1000 genomes]
rs73337148	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7361024	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8114415	0.89[ASN][1000 genomes]
rs8114930	1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062140	chr20:24807962-25304054	Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv544219	chr20:24807962-25304054	Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1056345	chr20:24819570-25168159	Flanking Active TSS Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1055341	chr20:24848416-25302271	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv1063494	chr20:25067286-25468557	Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv1063016	chr20:25067286-25475629	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer 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	53 gene(s)	inside rSNPs	diseases
7	nsv1065101	chr20:25068046-25466542	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv544220	chr20:25068046-25466542	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
9	nsv531480	chr20:25070067-25472684	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
10	nsv585746	chr20:25071454-25470056	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
11	nsv1062742	chr20:25071454-25475629	Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
12	nsv949389	chr20:25071454-25506582	Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
13	nsv531481	chr20:25080583-25448944	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
14	nsv949479	chr20:25096494-25467359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
15	nsv1061109	chr20:25101715-25472685	Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
16	nsv544221	chr20:25101715-25472685	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs8115729	VSX1	cis	cerebellum	SCAN
rs8115729	CST1	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25128600-25131600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr20:25128800-25131400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr20:25128800-25131800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr20:25129400-25130400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr20:25129400-25131400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
6	chr20:25129400-25131600	Enhancers	Fetal Brain Male	brain
7	chr20:25129600-25130600	Enhancers	Brain Cingulate Gyrus	brain
8	chr20:25129600-25131000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
9	chr20:25129600-25131200	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr20:25129600-25131200	Enhancers	HSMMtube	muscle
11	chr20:25129800-25130600	Weak transcription	Brain Anterior Caudate	brain
12	chr20:25129800-25131000	Weak transcription	Ovary	ovary
13	chr20:25130000-25130400	Bivalent Enhancer	Brain Germinal Matrix	brain
14	chr20:25130000-25131000	Enhancers	Fetal Brain Female	brain
15	chr20:25130200-25130400	Bivalent Enhancer	HepG2	liver

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