Variant report

Variant	rs57828617
Chromosome Location	chr3:160533956-160533957
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:160532424..160534589-chr3:160584064..160586211,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1455870	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1455871	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831442	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16831457	0.88[EUR][1000 genomes]
rs16831471	0.94[EUR][1000 genomes]
rs16831473	0.94[EUR][1000 genomes]
rs16831516	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16831520	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17236620	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17236641	0.85[EUR][1000 genomes]
rs17236648	0.94[EUR][1000 genomes]
rs17236655	0.94[EUR][1000 genomes]
rs17236662	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17826352	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17826358	0.88[EUR][1000 genomes]
rs17826364	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17826370	0.94[EUR][1000 genomes]
rs17826376	0.94[EUR][1000 genomes]
rs2068817	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34035435	0.85[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3907061	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4549318	0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4627794	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55891037	0.95[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55905728	0.95[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55923270	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55997050	0.95[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56083575	0.94[EUR][1000 genomes]
rs56141155	0.95[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56157815	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56180903	0.94[EUR][1000 genomes]
rs56331465	0.95[AFR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58891820	0.94[EUR][1000 genomes]
rs6771910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779461	0.94[EUR][1000 genomes]
rs73877952	0.94[EUR][1000 genomes]
rs73877966	0.94[EUR][1000 genomes]
rs7618082	0.94[EUR][1000 genomes]
rs7618596	0.94[EUR][1000 genomes]
rs7629154	0.94[EUR][1000 genomes]
rs7633401	0.94[EUR][1000 genomes];0.91[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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1009249	chr3:160496237-160627378	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv536780	chr3:160496237-160627378	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160528200-160537600	Weak transcription	Hela-S3	cervix
2	chr3:160529000-160534400	Weak transcription	Aorta	Aorta
3	chr3:160530600-160536000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr3:160530600-160537800	Weak transcription	Gastric	stomach
5	chr3:160530800-160540800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:160530800-160543200	Weak transcription	Psoas Muscle	Psoas
7	chr3:160532800-160534000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:160533000-160534000	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr3:160533000-160534200	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr3:160533600-160534000	Enhancers	Colon Smooth Muscle	Colon
11	chr3:160533800-160534000	Enhancers	Brain Germinal Matrix	brain
12	chr3:160533800-160534200	Enhancers	Rectal Smooth Muscle	rectum

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