Variant report

Variant	rs28459534
Chromosome Location	chr15:54897937-54897938
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	POLR2A	chr15:54896939-54898132	GM12878	blood:	n/a	n/a
2	FOXA1	chr15:54897809-54898103	T-47D	breast:	n/a	n/a
3	GATA3	chr15:54897773-54898103	T-47D	breast:	n/a	chr15:54897906-54897915 chr15:54897909-54897918
4	STAT3	chr15:54897564-54898006	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
UNC13C	TF binding region

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11630118	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11633379	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11633594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11635719	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11638551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17237683	1.00[AFR][1000 genomes]
rs17237718	1.00[AFR][1000 genomes]
rs2018231	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2460607	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28368978	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28445947	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28497275	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28548973	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28700587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2947002	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34520840	1.00[AFR][1000 genomes]
rs57406873	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62022201	1.00[AFR][1000 genomes]
rs62022202	1.00[AFR][1000 genomes]
rs62022204	1.00[AFR][1000 genomes]
rs62022205	1.00[AFR][1000 genomes]
rs62023989	1.00[AFR][1000 genomes]
rs62023993	1.00[AFR][1000 genomes]
rs62023994	1.00[AFR][1000 genomes]
rs62023995	1.00[AFR][1000 genomes]
rs62023996	1.00[AFR][1000 genomes]
rs7169130	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7178021	0.81[AMR][1000 genomes]
rs7183323	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74014271	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8029339	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817539	chr15:54132584-55095235	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1038660	chr15:54756184-55039913	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv904236	chr15:54820897-54912439	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1039548	chr15:54856965-54914519	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv569508	chr15:54876212-54904782	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv526413	chr15:54876423-54904782	Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv904237	chr15:54888537-54927484	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
8	nsv569509	chr15:54888537-54932716	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
9	nsv457154	chr15:54892583-54904782	Weak transcription Enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv569517	chr15:54892583-54904782	Enhancers Weak transcription Strong transcription Bivalent Enhancer	TF binding region CpG island lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:54896000-54898600	Enhancers	Fetal Lung	lung
2	chr15:54896600-54898000	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr15:54896800-54898400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr15:54896800-54899800	Weak transcription	Aorta	Aorta
5	chr15:54897000-54898000	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr15:54897200-54898200	Enhancers	Placenta Amnion	Placenta Amnion
7	chr15:54897800-54898000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr15:54897800-54898200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:54897800-54899000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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