Variant report

Variant	rs3886109
Chromosome Location	chr12:39189243-39189244
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10506129	0.81[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs10875979	0.81[EUR][1000 genomes]
rs10875991	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10876086	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168985	0.84[AMR][1000 genomes]
rs11169031	0.87[AMR][1000 genomes]
rs11169169	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11169301	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169387	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169508	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169511	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169547	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169666	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11514111	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11523606	0.81[AMR][1000 genomes]
rs11523607	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11610376	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11612004	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1486357	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1554550	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1601579	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17523988	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1843639	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34254519	0.84[AMR][1000 genomes]
rs36035670	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs55828987	0.87[AMR][1000 genomes]
rs6580755	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7301104	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973992	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv676	chr12:39184359-39215822	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Active TSS	lncRNA	n/a	inside rSNPs	diseases
2	nsv1047623	chr12:39187817-39539939	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39182600-39202800	Weak transcription	Liver	Liver
2	chr12:39184200-39205800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:39185600-39190600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr12:39188200-39193400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:39188600-39189400	ZNF genes & repeats	Primary hematopoietic stem cells	blood

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