Variant report

Variant	rs12066872
Chromosome Location	chr1:239888533-239888534
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1030591	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10925968	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10925969	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1135	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12059584	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12062155	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12062192	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12093210	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12354162	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13376649	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16838631	0.83[EUR][1000 genomes]
rs16838669	0.83[EUR][1000 genomes]
rs16838681	0.83[EUR][1000 genomes]
rs16838689	0.83[EUR][1000 genomes]
rs16838720	0.89[EUR][1000 genomes]
rs16838848	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16838871	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16838874	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16838878	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28448804	0.83[EUR][1000 genomes]
rs61834785	0.83[EUR][1000 genomes]
rs61834786	0.83[EUR][1000 genomes]
rs61834816	0.83[EUR][1000 genomes]
rs61834817	0.83[EUR][1000 genomes]
rs61834822	0.89[EUR][1000 genomes]
rs61834823	0.89[EUR][1000 genomes]
rs61834825	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61834826	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61834828	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61834837	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834838	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834839	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834840	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834842	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61834844	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61834845	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61834846	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61834847	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61836669	0.94[EUR][1000 genomes]
rs6661636	0.89[EUR][1000 genomes]
rs7516378	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7527723	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv549435	chr1:239375010-239974006	Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	esv3377526	chr1:239623743-240111639	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv873351	chr1:239636613-240324200	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	esv2757778	chr1:239766094-240389504	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	esv2759009	chr1:239766094-240389504	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	esv3363446	chr1:239887329-239890727	Enhancers Weak transcription Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:239875400-239890800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:239878200-239891000	Weak transcription	Fetal Intestine Small	intestine
3	chr1:239885000-239894000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:239885400-239888600	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr1:239885600-239905600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr1:239885800-239888600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr1:239885800-239888600	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr1:239886200-239888800	Enhancers	Primary T cells from cord blood	blood
9	chr1:239886800-239908200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:239887200-239888600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:239887400-239888600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr1:239887400-239888800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:239887600-239888800	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr1:239888200-239889000	Enhancers	Fetal Kidney	kidney
15	chr1:239888200-239889000	Enhancers	Pancreas	Pancrea

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