Variant report

Variant	rs17254079
Chromosome Location	chr4:173868291-173868292
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10520249	1.00[CEU][hapmap]
rs10520251	0.88[CEU][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.90[TSI][hapmap]
rs12641678	0.93[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12644630	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17254611	0.88[CEU][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17254681	0.88[CEU][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs17319595	0.94[CEU][hapmap]
rs2610186	0.95[EUR][1000 genomes]
rs2610188	1.00[CEU][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2610191	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2610201	0.93[CHD][hapmap]
rs2610204	0.93[CHD][hapmap]
rs2653824	0.87[CHD][hapmap]
rs2653831	0.88[CEU][hapmap]
rs2653844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28380538	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28524136	0.83[ASN][1000 genomes]
rs28582871	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28705797	0.85[ASN][1000 genomes]
rs28800549	0.85[ASN][1000 genomes]
rs28890012	0.83[ASN][1000 genomes]
rs4547777	0.87[CEU][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56110146	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62341884	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62341886	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62341887	0.85[ASN][1000 genomes]
rs6553660	1.00[CEU][hapmap]
rs68168662	0.88[ASN][1000 genomes]
rs6852770	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7678191	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7682619	0.81[EUR][1000 genomes]
rs7693329	0.83[CEU][hapmap]
rs9997573	0.81[EUR][1000 genomes];0.85[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	nsv948856	chr4:173388217-173967546	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv949126	chr4:173466221-174051451	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17254079	SPATA4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:173853800-173872400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:173867200-173880000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr4:173868200-173869000	Enhancers	Small Intestine	intestine

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