Variant report

Variant	rs28599772
Chromosome Location	chr4:88250719-88250720
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:88242496..88244669-chr4:88248333..88250976,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170509	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10003964	0.90[EUR][1000 genomes]
rs10004027	0.85[AFR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10012256	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10028111	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10028441	0.88[ASN][1000 genomes]
rs10050247	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11732896	0.86[ASN][1000 genomes]
rs12649727	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13118664	0.93[ASN][1000 genomes]
rs13119654	0.93[ASN][1000 genomes]
rs28433555	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28445336	0.94[AFR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28514476	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28636836	0.80[ASN][1000 genomes]
rs28830804	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57041248	0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57154655	0.91[AFR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58073039	0.88[ASN][1000 genomes]
rs59107493	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6531981	0.88[ASN][1000 genomes]
rs66837437	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7685308	0.86[ASN][1000 genomes]
rs7691791	0.88[ASN][1000 genomes]
rs9992651	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997750	chr4:87933945-88264127	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv870296	chr4:88173534-88295927	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1004518	chr4:88218473-88354403	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv4412	chr4:88237813-88283368	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
5	nsv1002789	chr4:88239340-88606485	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:88238600-88253400	Weak transcription	HepG2	liver
2	chr4:88239400-88255400	Weak transcription	A549	lung
3	chr4:88250600-88259400	Weak transcription	Fetal Heart	heart

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