Variant report

Variant	rs12880228
Chromosome Location	chr14:79645984-79645985
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11622061	0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap]
rs12432016	0.95[CHB][hapmap];0.89[ASN][1000 genomes]
rs12891595	0.81[CHB][hapmap]
rs2061923	0.87[CEU][hapmap]
rs2219848	0.80[CHB][hapmap]
rs2370930	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs2370934	0.94[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.86[JPT][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2370935	0.95[CHB][hapmap];0.85[JPT][hapmap]
rs4636834	0.94[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4899736	0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.81[MKK][hapmap];0.83[YRI][hapmap]
rs61992556	0.80[EUR][1000 genomes]
rs6574499	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7151711	0.95[CHB][hapmap];0.93[CHD][hapmap]
rs7156245	0.82[CHB][hapmap];0.85[JPT][hapmap]
rs72627190	0.89[ASN][1000 genomes]
rs766023	0.81[CHB][hapmap]
rs8008994	0.92[CEU][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs8011958	0.88[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8015611	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs8016735	0.95[CHB][hapmap];0.93[CHD][hapmap];0.80[JPT][hapmap];0.90[ASN][1000 genomes]
rs8017399	0.90[ASN][1000 genomes]
rs8019231	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931412	chr14:79420297-79928269	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1040837	chr14:79583862-79711565	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	nsv902110	chr14:79624492-79998294	Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12880228	ANGEL1	cis	cerebellum	SCAN
rs12880228	VASH1	cis	cerebellum	SCAN

Chromatin state (count:0 , 50 per page) page:

No data

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