Variant report

Variant	rs4928023
Chromosome Location	chr3:54288266-54288267
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs11130406	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11130407	1.00[CEU][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs11712961	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11715179	1.00[CEU][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs12374179	1.00[CEU][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs4373099	0.92[CEU][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs4928019	0.96[YRI][hapmap]
rs4928020	0.96[YRI][hapmap]
rs4996716	0.96[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs66808006	0.96[EUR][1000 genomes]
rs67311583	0.90[EUR][1000 genomes]
rs6783285	0.96[CEU][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs6792292	0.96[CEU][hapmap];0.89[CHB][hapmap];0.98[EUR][1000 genomes]
rs6798711	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[EUR][1000 genomes]
rs6808505	0.81[ASN][1000 genomes]
rs7340744	0.84[JPT][hapmap]
rs9812090	0.97[EUR][1000 genomes]
rs9827268	0.95[EUR][1000 genomes]
rs9846140	0.96[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs9847950	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs9849863	0.97[EUR][1000 genomes]
rs9850014	0.96[CEU][hapmap];0.97[EUR][1000 genomes]
rs9869714	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs9883496	1.00[CEU][hapmap];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003621	chr3:53448934-54425322	Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1014157	chr3:54168755-54332321	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv817328	chr3:54250314-54380438	Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv876806	chr3:54256648-54330010	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv460555	chr3:54270646-54293345	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv460556	chr3:54270646-54293345	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv590359	chr3:54270646-54293345	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv470594	chr3:54270646-54296591	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4928023	WNT5A	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54277800-54290600	Weak transcription	Fetal Kidney	kidney
2	chr3:54287600-54295400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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