Variant report

Variant	rs4653880
Chromosome Location	chr1:228071109-228071110
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	chr1:228070687..228073614-chr1:228077834..228079933,2	MCF-7	breast:
2	chr1:228070680..228073922-chr1:228077566..228080384,3	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10799454	0.89[EUR][1000 genomes]
rs10799456	0.93[EUR][1000 genomes]
rs10799457	0.93[EUR][1000 genomes]
rs10916235	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11484724	0.86[EUR][1000 genomes]
rs12074411	0.89[EUR][1000 genomes]
rs12078365	0.89[EUR][1000 genomes]
rs1573058	0.89[EUR][1000 genomes]
rs1573059	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs20488	0.86[JPT][hapmap]
rs28376917	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28445597	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4653525	0.93[EUR][1000 genomes]
rs4653526	0.93[EUR][1000 genomes]
rs4653878	0.83[EUR][1000 genomes]
rs4653882	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4653883	0.92[EUR][1000 genomes]
rs4653885	0.93[EUR][1000 genomes]
rs4653886	0.93[EUR][1000 genomes]
rs6657894	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67645046	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72752172	0.89[EUR][1000 genomes]
rs72752178	0.89[EUR][1000 genomes]
rs72752179	0.89[EUR][1000 genomes]
rs72752184	0.84[EUR][1000 genomes]
rs72752190	0.93[EUR][1000 genomes]
rs7528139	0.92[EUR][1000 genomes]
rs870305	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv873249	chr1:227920061-228121548	Weak transcription Bivalent Enhancer Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv1005852	chr1:227957099-228148363	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
7	nsv535319	chr1:227957099-228148363	Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
8	nsv516409	chr1:228035131-228296745	Enhancers Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats 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	38 gene(s)	inside rSNPs	diseases
9	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
10	nsv873250	chr1:228051234-228121548	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv873251	chr1:228051234-228160911	Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228060800-228071400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr1:228060800-228071600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr1:228068400-228073200	Weak transcription	Gastric	stomach
4	chr1:228070600-228071600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr1:228070600-228072600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr1:228070600-228073200	Enhancers	Primary T cells fromperipheralblood	blood
7	chr1:228070600-228073200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:228070800-228072200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:228070800-228072400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
10	chr1:228070800-228073000	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr1:228070800-228073000	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr1:228070800-228074200	Enhancers	Esophagus	oesophagus
13	chr1:228071000-228072200	Enhancers	Placenta Amnion	Placenta Amnion
14	chr1:228071000-228072400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr1:228071000-228072400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr1:228071000-228072800	Weak transcription	HMEC	breast
17	chr1:228071000-228073000	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr1:228071000-228074000	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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