Variant report

Variant	rs12489455
Chromosome Location	chr3:87887489-87887490
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1021338	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10511135	0.92[EUR][1000 genomes]
rs11128008	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11916422	0.92[EUR][1000 genomes]
rs11917302	0.92[EUR][1000 genomes]
rs12485247	0.92[EUR][1000 genomes]
rs12486342	0.81[EUR][1000 genomes]
rs12486894	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12491283	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12491978	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492131	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12495772	0.81[EUR][1000 genomes]
rs12497021	0.81[EUR][1000 genomes]
rs12497212	0.94[AFR][1000 genomes]
rs12497315	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12497340	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12497845	0.86[CEU][hapmap];0.92[EUR][1000 genomes]
rs12629896	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629921	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12636145	0.84[ASN][1000 genomes]
rs12636188	0.84[ASN][1000 genomes]
rs1503427	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17025082	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17025172	0.88[EUR][1000 genomes]
rs17025178	0.88[EUR][1000 genomes]
rs17025185	0.81[EUR][1000 genomes]
rs1844434	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1847304	0.92[EUR][1000 genomes]
rs1847313	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1875716	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1910399	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1910401	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2010883	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2068948	0.81[EUR][1000 genomes]
rs2099228	0.92[EUR][1000 genomes]
rs2171819	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2343771	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2343774	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2932275	0.92[EUR][1000 genomes]
rs2932302	0.92[EUR][1000 genomes]
rs55776072	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55879630	0.92[EUR][1000 genomes]
rs57226509	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57688062	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57777775	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57850268	0.92[ASN][1000 genomes]
rs58359957	0.90[ASN][1000 genomes]
rs58460783	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58521812	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59504854	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59703125	0.92[EUR][1000 genomes]
rs60057665	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72911668	0.96[AFR][1000 genomes]
rs72911684	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72913703	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72913715	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72913722	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73845078	0.96[AFR][1000 genomes]
rs73847706	0.92[EUR][1000 genomes]
rs73847712	0.92[EUR][1000 genomes]
rs73847723	0.88[EUR][1000 genomes]
rs73847733	0.81[EUR][1000 genomes]
rs73847735	0.81[EUR][1000 genomes]
rs7638490	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv590918	chr3:87323334-87910931	Enhancers Bivalent Enhancer Strong transcription Weak 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	8 gene(s)	inside rSNPs	diseases
2	nsv834756	chr3:87763793-87938179	Bivalent/Poised TSS Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv460757	chr3:87863280-87949733	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	n/a
6	nsv590919	chr3:87863280-87949733	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12489455	VCL	trans	lymphoblastoid	seeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:87867800-87912800	Weak transcription	K562	blood
2	chr3:87882200-87907600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr3:87885400-87888400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:87886800-87888400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:87887400-87888400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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