Variant report

Variant	rs4290069
Chromosome Location	chr1:221966781-221966782
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10746414	1.00[CHB][hapmap]
rs10863657	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11118883	1.00[CHB][hapmap]
rs11577023	1.00[CHB][hapmap]
rs11582814	1.00[CHB][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12083393	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12089785	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12090948	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12095068	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12125690	1.00[CHB][hapmap]
rs4581289	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56010022	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57222604	0.81[EUR][1000 genomes]
rs61696703	0.81[EUR][1000 genomes]
rs6668784	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66698149	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs66916558	0.81[EUR][1000 genomes]
rs67087803	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67220535	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469786	chr1:221855871-222040335	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv482867	chr1:221855871-222040335	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv873201	chr1:221956626-222007535	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	1 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	chr1:221960400-221970000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:221960800-221966800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:221963800-221967200	Weak transcription	HMEC	breast
4	chr1:221964600-221969200	Enhancers	Primary B cells from peripheral blood	blood
5	chr1:221965200-221967200	Enhancers	Primary B cells from cord blood	blood
6	chr1:221966400-221967000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:221966400-221967000	Enhancers	Pancreas	Pancrea
8	chr1:221966400-221967000	Enhancers	Spleen	Spleen
9	chr1:221966400-221967800	Enhancers	Primary T cells fromperipheralblood	blood
10	chr1:221966400-221968200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr1:221966600-221967400	Enhancers	Fetal Thymus	thymus
12	chr1:221966600-221967600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr1:221966600-221967600	Flanking Active TSS	GM12878-XiMat	blood
14	chr1:221966600-221967800	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr1:221966600-221967800	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr1:221966600-221967800	Enhancers	NH-A	brain
17	chr1:221966600-221967800	Enhancers	Osteobl	bone
18	chr1:221966600-221968200	Enhancers	Primary T helper cells PMA-I stimulated	--

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dbSNP/dbVar ID: rs12345 /nsv7879
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