Variant report

Variant	rs6097934
Chromosome Location	chr20:52978194-52978195
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:52886227..52888754-chr20:52977596..52979522,2	MCF-7	breast:
2	chr20:52976917..52979046-chr20:52979757..52981463,2	MCF-7	breast:
3	chr20:52970953..52973091-chr20:52976759..52978463,2	MCF-7	breast:
4	chr20:52977120..52978918-chr20:52982695..52985421,2	MCF-7	breast:
5	chr14:106873316..106874010-chr20:52978099..52978702,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253989	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1358806	0.80[ASN][1000 genomes]
rs1358807	0.80[ASN][1000 genomes]
rs1407043	0.82[CHB][hapmap];0.81[CHD][hapmap];0.81[JPT][hapmap];0.89[ASN][1000 genomes]
rs16999559	0.92[GIH][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs16999597	0.82[CHB][hapmap];0.81[CHD][hapmap];0.87[ASN][1000 genomes]
rs1841860	0.85[ASN][1000 genomes]
rs1923118	0.88[ASN][1000 genomes]
rs2126676	0.84[ASN][1000 genomes]
rs28406117	0.95[ASN][1000 genomes]
rs28429972	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2870329	0.80[ASN][1000 genomes]
rs56881371	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59924072	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6013987	0.95[ASN][1000 genomes]
rs6013989	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.81[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6013997	0.82[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs6013999	0.88[ASN][1000 genomes]
rs6014003	0.88[ASN][1000 genomes]
rs6014004	0.86[ASN][1000 genomes]
rs6014005	0.87[ASN][1000 genomes]
rs6023153	0.99[ASN][1000 genomes]
rs6023154	0.99[ASN][1000 genomes]
rs6023155	0.98[ASN][1000 genomes]
rs6023156	0.98[ASN][1000 genomes]
rs6023158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6023163	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6023164	0.94[ASN][1000 genomes]
rs6023180	0.90[ASN][1000 genomes]
rs6023183	0.81[ASN][1000 genomes]
rs6023185	0.86[ASN][1000 genomes]
rs6023189	0.88[ASN][1000 genomes]
rs6023192	0.87[ASN][1000 genomes]
rs6023193	0.87[ASN][1000 genomes]
rs6023197	0.80[ASN][1000 genomes]
rs6023203	0.88[ASN][1000 genomes]
rs6091856	0.86[ASN][1000 genomes]
rs6097938	0.97[ASN][1000 genomes]
rs6097939	0.99[ASN][1000 genomes]
rs6097940	0.96[ASN][1000 genomes]
rs6097941	0.96[ASN][1000 genomes]
rs6097945	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6097946	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6097957	0.80[ASN][1000 genomes]
rs6097963	0.82[CHB][hapmap];0.87[ASN][1000 genomes]
rs73624107	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73624108	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73624110	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793033	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv834011	chr20:52858341-53086042	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
3	nsv834012	chr20:52921007-53097177	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 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	chr20:52974000-52978200	Weak transcription	Ovary	ovary
2	chr20:52976000-52978400	Enhancers	iPS-18 Cell Line	embryonic stem cell
3	chr20:52976600-52983400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr20:52976600-52985200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr20:52977600-52978400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr20:52977600-52985200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr20:52977800-52978400	Enhancers	Fetal Brain Female	brain
8	chr20:52977800-52979200	Enhancers	Fetal Brain Male	brain
9	chr20:52977800-52985200	Weak transcription	HUES48 Cell Line	embryonic stem cell

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