Variant report

Variant	rs12406553
Chromosome Location	chr1:46912276-46912277
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12402011	0.93[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12407445	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12407648	0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs17102209	1.00[AMR][1000 genomes]
rs2274422	0.91[ASN][1000 genomes]
rs3737742	0.91[ASN][1000 genomes]
rs3737743	0.93[AMR][1000 genomes]
rs3818506	0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3818507	0.93[AMR][1000 genomes]
rs74072346	0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic 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 target site	72 gene(s)	inside rSNPs	diseases
3	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv1000562	chr1:46832451-47027044	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv534951	chr1:46910546-46948727	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1015045	chr1:46910546-47067492	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv534952	chr1:46910546-47067492	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46908800-46912800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr1:46908800-46913400	Weak transcription	Spleen	Spleen
3	chr1:46909000-46912400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:46909000-46912600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:46909000-46913400	Weak transcription	Gastric	stomach
6	chr1:46909000-46913600	Weak transcription	Pancreas	Pancrea
7	chr1:46909000-46913800	Weak transcription	Right Atrium	heart
8	chr1:46911600-46912400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
9	chr1:46911800-46912800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
10	chr1:46911800-46912800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
11	chr1:46911800-46912800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:46911800-46913000	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
13	chr1:46911800-46913000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:46911800-46913800	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
15	chr1:46912000-46912400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
16	chr1:46912000-46912400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
17	chr1:46912000-46913400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
18	chr1:46912000-46913400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr1:46912200-46913200	Enhancers	K562	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
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