Variant report

Variant	rs55879630
Chromosome Location	chr3:87985050-87985051
allele	G/T
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]
rs1021338	0.92[EUR][1000 genomes]
rs10511135	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11128008	0.82[EUR][1000 genomes]
rs11916422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11917302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12485247	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12486342	0.86[EUR][1000 genomes]
rs12486894	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12489455	0.92[EUR][1000 genomes]
rs12491283	0.92[EUR][1000 genomes]
rs12491978	0.92[EUR][1000 genomes]
rs12492131	0.92[EUR][1000 genomes]
rs12495772	0.86[EUR][1000 genomes]
rs12497021	0.86[EUR][1000 genomes]
rs12497315	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12497340	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12497845	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12629896	0.90[EUR][1000 genomes]
rs12629921	0.92[EUR][1000 genomes]
rs1503427	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17025082	0.92[EUR][1000 genomes]
rs17025172	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17025178	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17025185	0.86[EUR][1000 genomes]
rs1844434	0.92[EUR][1000 genomes]
rs1847304	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1847313	0.92[EUR][1000 genomes]
rs1875716	0.92[EUR][1000 genomes]
rs1910399	0.92[EUR][1000 genomes]
rs1910401	0.92[EUR][1000 genomes]
rs2010883	0.85[EUR][1000 genomes]
rs2068948	0.86[EUR][1000 genomes]
rs2099228	0.92[EUR][1000 genomes]
rs2171819	0.92[EUR][1000 genomes]
rs2343771	0.92[EUR][1000 genomes]
rs2343774	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2932275	0.92[EUR][1000 genomes]
rs2932302	0.92[EUR][1000 genomes]
rs55776072	0.92[EUR][1000 genomes]
rs57226509	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57688062	0.92[EUR][1000 genomes]
rs57777775	0.90[EUR][1000 genomes]
rs58046740	0.88[EUR][1000 genomes]
rs58460783	0.92[EUR][1000 genomes]
rs58496925	0.88[EUR][1000 genomes]
rs58521812	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58824845	0.88[EUR][1000 genomes]
rs59504854	0.92[EUR][1000 genomes]
rs59703125	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60057665	0.92[EUR][1000 genomes]
rs72911684	0.92[EUR][1000 genomes]
rs72913703	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72913715	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72913722	0.96[EUR][1000 genomes]
rs73847706	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73847712	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73847723	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73847733	0.86[EUR][1000 genomes]
rs73847735	0.86[EUR][1000 genomes]
rs7638490	0.92[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	nsv1009981	chr3:87821573-88003956	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv536634	chr3:87821573-88003956	Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv834758	chr3:87867363-88014975	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1007981	chr3:87949316-88004036	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv527929	chr3:87949733-88003812	ZNF genes & repeats Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv877146	chr3:87983962-88159835	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:87982800-87991400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr3:87983000-87986400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr3:87984600-87989200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:87985000-87986600	Strong transcription	Primary hematopoietic stem cells	blood

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