Variant report

Variant	rs6661636
Chromosome Location	chr1:239852389-239852390
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs1030591	0.89[EUR][1000 genomes]
rs10925968	1.00[ASN][1000 genomes]
rs10925969	1.00[ASN][1000 genomes]
rs1135	1.00[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12059584	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12062155	1.00[ASN][1000 genomes]
rs12062192	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066872	0.89[EUR][1000 genomes]
rs12093210	0.89[EUR][1000 genomes]
rs12354162	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13376649	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16832149	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16838584	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16838623	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16838631	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16838669	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16838681	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16838689	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16838720	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16838848	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16838871	1.00[ASN][1000 genomes]
rs16838874	1.00[ASN][1000 genomes]
rs16838878	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28448804	0.94[EUR][1000 genomes]
rs4145784	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61834772	1.00[ASN][1000 genomes]
rs61834776	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834781	1.00[ASN][1000 genomes]
rs61834783	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834785	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834786	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834816	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834817	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834820	0.84[AMR][1000 genomes]
rs61834821	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61834822	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834823	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834825	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834826	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834828	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834837	0.89[EUR][1000 genomes]
rs61834838	0.89[EUR][1000 genomes]
rs61834839	0.89[EUR][1000 genomes]
rs61834840	0.89[EUR][1000 genomes]
rs61834842	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834844	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61834845	1.00[ASN][1000 genomes]
rs61834846	1.00[ASN][1000 genomes]
rs61834847	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61836595	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61836669	0.83[EUR][1000 genomes]
rs62634805	0.93[AMR][1000 genomes]
rs6694025	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73124687	0.84[EUR][1000 genomes]
rs7516378	1.00[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7523711	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7527723	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	esv3440138	chr1:239850754-239853302	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3349682	chr1:239850929-239853177	Weak transcription Active TSS Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv3322953	chr1:239851229-239852677	Weak transcription Enhancers Active TSS	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	chr1:239836600-239856200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr1:239840000-239853200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:239841000-239854000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr1:239845000-239855200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr1:239845000-239879800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr1:239849800-239856600	Weak transcription	Fetal Intestine Small	intestine

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