Variant report

Variant	rs2830419
Chromosome Location	chr21:28080135-28080136
allele	A/C
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:25)

rs_ID	r²[population]
rs120261	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs120262	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17063	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2251540	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs226261	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs226262	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs226263	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs226264	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs226287	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2830380	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2830409	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2830428	0.86[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2830429	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2830431	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2830433	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2952413	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34251764	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs461868	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs462985	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs773	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9636574	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs997333	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9974075	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9974728	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9977117	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[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	nsv459223	chr21:28070037-28092531	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv587337	chr21:28070037-28092531	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2830419	APP	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:28078400-28081400	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr21:28078600-28081600	Enhancers	Dnd41	blood
3	chr21:28079600-28080800	Enhancers	Primary hematopoietic stem cells	blood
4	chr21:28080000-28083600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr21:28080000-28083600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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