Variant report

Variant	rs728497
Chromosome Location	chr14:72433151-72433152
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1009017	0.87[CHB][hapmap];0.89[CHD][hapmap]
rs11158920	1.00[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11158921	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11158927	1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.90[MEX][hapmap]
rs11620690	1.00[CEU][hapmap];0.93[CHB][hapmap]
rs11623492	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.89[MEX][hapmap]
rs11623535	0.93[CHB][hapmap];0.89[CHD][hapmap];0.85[MEX][hapmap]
rs11625937	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap]
rs11627768	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap]
rs11628133	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[MEX][hapmap]
rs11628574	1.00[CEU][hapmap]
rs12148043	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.84[MEX][hapmap]
rs12433721	1.00[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12437172	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12897929	0.93[JPT][hapmap];0.84[ASN][1000 genomes]
rs17093750	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17104493	0.86[EUR][1000 genomes]
rs17105346	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.84[MEX][hapmap]
rs17105566	1.00[CEU][hapmap];0.93[CHB][hapmap]
rs17105606	1.00[CEU][hapmap];0.87[CHB][hapmap]
rs17105690	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs2067856	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2159457	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2238277	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2238280	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2877771	0.80[ASN][1000 genomes]
rs34729701	0.80[ASN][1000 genomes]
rs35051666	0.80[ASN][1000 genomes]
rs35858041	0.80[ASN][1000 genomes]
rs3784055	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3784056	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3784058	1.00[CEU][hapmap];0.93[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4243640	0.93[CHB][hapmap];0.89[CHD][hapmap];0.81[MEX][hapmap]
rs4350510	0.93[CHB][hapmap]
rs4354860	0.93[CHB][hapmap];0.89[CHD][hapmap];0.85[MEX][hapmap]
rs4899409	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4899412	0.93[CHB][hapmap];0.89[CHD][hapmap];0.83[MEX][hapmap]
rs4902958	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4902966	0.93[CHB][hapmap]
rs56067914	0.84[ASN][1000 genomes]
rs56743778	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72734102	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72735921	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72735923	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7493353	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7494103	1.00[CEU][hapmap]
rs8013467	0.93[CHB][hapmap];0.89[CHD][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	nsv530794	chr14:72113818-73034008	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs728497	PCNX	cis	cerebellum	SCAN
rs728497	ADAM20	cis	cerebellum	SCAN
rs728497	ACOT4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72426800-72437200	Weak transcription	Left Ventricle	heart
2	chr14:72430400-72435800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr14:72431200-72435400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr14:72431800-72434000	Enhancers	GM12878-XiMat	blood
5	chr14:72432400-72434400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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