Variant report

Variant	rs356407
Chromosome Location	chr2:180616609-180616610
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1139	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12052744	0.88[ASN][1000 genomes]
rs12052765	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12053119	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12465379	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs12472888	0.95[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs12473571	0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1385972	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs1533384	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs16866963	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs16866968	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16866978	0.93[ASN][1000 genomes]
rs16866986	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs16866987	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16866989	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs16866991	0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap]
rs16866992	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs356413	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs357699	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs55728092	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57390308	0.87[ASN][1000 genomes]
rs58217303	0.93[ASN][1000 genomes]
rs7574345	0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7592797	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs7607561	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs881737	0.82[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002305	chr2:180568558-180812846	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs356407	ITGA4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180610800-180621200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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