Variant report

Variant	rs28407648
Chromosome Location	chr2:49020754-49020755
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:49013902..49015709-chr2:49018982..49021031,2	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs12986921	0.86[EUR][1000 genomes]
rs12988380	0.86[EUR][1000 genomes]
rs12988554	0.86[EUR][1000 genomes]
rs12991639	0.86[EUR][1000 genomes]
rs12991812	0.86[EUR][1000 genomes]
rs12993350	0.86[EUR][1000 genomes]
rs12998973	0.86[EUR][1000 genomes]
rs12999088	0.86[EUR][1000 genomes]
rs13000493	0.86[EUR][1000 genomes]
rs13003416	0.86[EUR][1000 genomes]
rs13006849	0.86[EUR][1000 genomes]
rs13012154	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13013520	0.86[EUR][1000 genomes]
rs13026368	0.86[EUR][1000 genomes]
rs13026374	0.86[EUR][1000 genomes]
rs13033968	0.86[EUR][1000 genomes]
rs17555938	0.84[EUR][1000 genomes]
rs17556008	0.84[EUR][1000 genomes]
rs34096435	0.86[EUR][1000 genomes]
rs34139125	0.86[EUR][1000 genomes]
rs34177801	0.84[EUR][1000 genomes]
rs34246643	0.86[EUR][1000 genomes]
rs34316068	0.86[EUR][1000 genomes]
rs34493890	0.86[EUR][1000 genomes]
rs34519361	0.86[EUR][1000 genomes]
rs34583302	0.86[EUR][1000 genomes]
rs34679037	0.84[EUR][1000 genomes]
rs34747271	0.86[EUR][1000 genomes]
rs34790546	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34851917	0.86[EUR][1000 genomes]
rs34912705	0.86[EUR][1000 genomes]
rs35093053	0.86[EUR][1000 genomes]
rs35130245	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35323371	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35344527	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs35625756	0.86[EUR][1000 genomes]
rs35775057	0.86[EUR][1000 genomes]
rs35935449	0.86[EUR][1000 genomes]
rs35975792	0.86[EUR][1000 genomes]
rs35988365	0.86[EUR][1000 genomes]
rs36028906	0.84[EUR][1000 genomes]
rs36139546	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59605770	0.86[EUR][1000 genomes]
rs61037123	0.80[EUR][1000 genomes]
rs66479668	0.84[EUR][1000 genomes]
rs66523169	1.00[EUR][1000 genomes]
rs66524960	0.86[EUR][1000 genomes]
rs66593338	0.86[EUR][1000 genomes]
rs66709862	0.86[EUR][1000 genomes]
rs66713554	0.86[EUR][1000 genomes]
rs66898134	0.82[EUR][1000 genomes]
rs67198598	0.86[EUR][1000 genomes]
rs67386139	0.86[EUR][1000 genomes]
rs67412822	0.86[EUR][1000 genomes]
rs67476091	0.86[EUR][1000 genomes]
rs71407521	0.86[EUR][1000 genomes]
rs71407527	0.86[EUR][1000 genomes]
rs71407528	0.86[EUR][1000 genomes]
rs71407529	0.86[EUR][1000 genomes]
rs71407530	0.86[EUR][1000 genomes]
rs71407531	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72811839	0.86[EUR][1000 genomes]
rs72811841	0.86[EUR][1000 genomes]
rs72811843	0.86[EUR][1000 genomes]
rs72811844	0.86[EUR][1000 genomes]
rs72811874	0.86[EUR][1000 genomes]
rs72811886	0.86[EUR][1000 genomes]
rs72823291	0.84[EUR][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	nsv1010494	chr2:48767055-49027310	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1002793	chr2:48771220-49466550	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1004965	chr2:48796170-49443587	Bivalent Enhancer Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv535684	chr2:48796170-49443587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv498119	chr2:48808834-49422647	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv998864	chr2:49015878-49230000	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1014434	chr2:49016279-49053699	Enhancers Weak transcription Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48994600-49080200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr2:49017800-49020800	Enhancers	HUES48 Cell Line	embryonic stem cell
3	chr2:49017800-49020800	Enhancers	HUES64 Cell Line	embryonic stem cell
4	chr2:49018200-49027000	Weak transcription	Right Atrium	heart
5	chr2:49020200-49020800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr2:49020600-49020800	Enhancers	H1 Cell Line	embryonic stem cell

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