Variant report

Variant	rs559247
Chromosome Location	chr1:86434431-86434432
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10732722	0.93[CHB][hapmap]
rs10782561	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10873730	0.91[CEU][hapmap]
rs10873731	0.96[CEU][hapmap];0.85[TSI][hapmap]
rs1112326	1.00[CHB][hapmap]
rs1112327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1112328	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11161693	0.96[CEU][hapmap]
rs11161695	0.96[CEU][hapmap];0.85[TSI][hapmap]
rs11161710	1.00[CHB][hapmap];0.83[GIH][hapmap]
rs11161711	1.00[CHB][hapmap];0.83[GIH][hapmap]
rs12029238	0.96[CEU][hapmap]
rs12144570	0.93[CHB][hapmap]
rs12740695	0.88[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1354245	1.00[CHB][hapmap];0.83[GIH][hapmap]
rs1359421	1.00[CHB][hapmap]
rs1481201	1.00[CHB][hapmap];0.85[GIH][hapmap]
rs1502657	1.00[CHB][hapmap]
rs1698733	0.83[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17411495	0.96[CEU][hapmap];0.85[TSI][hapmap]
rs313701	0.85[CEU][hapmap]
rs313702	0.85[CEU][hapmap]
rs313705	0.85[CEU][hapmap]
rs313709	0.88[CEU][hapmap]
rs313769	0.96[CEU][hapmap];0.85[TSI][hapmap]
rs313770	0.96[CEU][hapmap]
rs313771	0.96[CEU][hapmap]
rs313775	0.96[CEU][hapmap];0.85[TSI][hapmap]
rs4303095	1.00[CHB][hapmap]
rs4486475	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs482789	0.85[CEU][hapmap]
rs483498	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs486726	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs489141	0.93[CHB][hapmap]
rs499518	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs524192	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs532186	0.93[CHB][hapmap]
rs537408	0.85[CEU][hapmap]
rs560876	1.00[CHB][hapmap]
rs571691	0.87[CHB][hapmap]
rs573444	0.81[CEU][hapmap]
rs578615	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs589698	1.00[CHB][hapmap]
rs593146	0.81[CEU][hapmap]
rs597330	0.94[CHB][hapmap];0.83[GIH][hapmap]
rs603297	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs605060	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.90[MEX][hapmap];0.90[MKK][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs606432	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs647977	1.00[CHB][hapmap]
rs6673508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6699709	1.00[CHB][hapmap]
rs6702912	1.00[CHB][hapmap]
rs682964	0.93[CHB][hapmap]
rs693436	0.81[CEU][hapmap]
rs7512039	0.91[CEU][hapmap]
rs7512890	0.94[CHB][hapmap]
rs7526013	0.88[CEU][hapmap]
rs7536101	0.96[CEU][hapmap];0.85[TSI][hapmap]
rs7541806	1.00[CHB][hapmap]
rs861933	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][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	nsv817212	chr1:86127851-86658426	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv462395	chr1:86379514-86457334	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv546726	chr1:86379514-86457334	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv462406	chr1:86412177-86509996	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv546757	chr1:86412177-86509996	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86421400-86441400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:86422800-86442400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr1:86425800-86441200	Weak transcription	Fetal Lung	lung
4	chr1:86431600-86437200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:86432200-86437000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:86433200-86438400	Weak transcription	GM12878-XiMat	blood
7	chr1:86434200-86440800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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