Variant report

Variant	rs12875956
Chromosome Location	chr13:48746463-48746464
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12100135	0.81[CHB][hapmap]
rs12870184	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12875750	0.81[CHB][hapmap]
rs1573601	0.81[CHB][hapmap]
rs2010173	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809328	0.81[CHB][hapmap]
rs520342	0.81[CHB][hapmap]
rs6561441	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6561443	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7320402	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7333467	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9316369	0.81[CHB][hapmap]
rs9526462	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534971	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9534973	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534974	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534976	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534980	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534982	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534985	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534987	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9534998	0.81[CHB][hapmap]
rs9535006	0.81[CHB][hapmap]
rs9535009	0.81[CHB][hapmap]
rs9562809	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9562811	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568024	0.81[ASN][1000 genomes]
rs9568035	0.87[CHB][hapmap]
rs9634814	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv541766	chr13:48703229-48857639	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1047140	chr13:48703732-48765860	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv541767	chr13:48703732-48765860	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3327569	chr13:48743550-48798094	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12875956	ITM2B	Cis_1M	lymphoblastoid	RTeQTL
rs12875956	SERP2	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:48746000-48746600	Enhancers	Primary neutrophils fromperipheralblood	blood
2	chr13:48746000-48746600	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr13:48746200-48746800	Enhancers	Primary monocytes fromperipheralblood	blood

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