Variant report

Variant	rs11959781
Chromosome Location	chr5:90100353-90100354
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	chr5:90098765..90101168-chr5:90678671..90680272,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000113369	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10514338	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11950292	0.85[AMR][1000 genomes]
rs11950742	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11956622	0.85[AFR][1000 genomes]
rs11959536	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs16869139	0.85[AFR][1000 genomes]
rs16869140	0.85[AFR][1000 genomes]
rs16869154	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2438354	1.00[EUR][1000 genomes]
rs2438358	1.00[EUR][1000 genomes]
rs2443062	1.00[EUR][1000 genomes]
rs2443070	1.00[EUR][1000 genomes]
rs2460168	1.00[EUR][1000 genomes]
rs2460170	1.00[EUR][1000 genomes]
rs2460172	1.00[EUR][1000 genomes]
rs28757668	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3113635	1.00[EUR][1000 genomes]
rs62000408	0.85[AMR][1000 genomes]
rs6860302	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6872705	1.00[EUR][1000 genomes]
rs6880683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7717221	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7729495	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7732226	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432750	chr5:89410113-90137144	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv529544	chr5:89523963-90412409	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv531965	chr5:89886550-90145002	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
4	nsv882367	chr5:89956991-90209824	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv934323	chr5:89968158-90111853	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv1015449	chr5:89968626-90219398	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv517049	chr5:90003131-90262475	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:90051800-90105000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr5:90090800-90101200	Weak transcription	K562	blood
3	chr5:90090800-90104400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr5:90092000-90106400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr5:90092400-90103400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr5:90092400-90122200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:90096600-90103400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr5:90097200-90105400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr5:90098000-90103600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:90098000-90111400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr5:90098600-90103200	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr5:90098800-90111400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:90099000-90101600	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr5:90099000-90112200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr5:90100200-90105000	Weak transcription	Fetal Heart	heart

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