Variant report

Variant	rs4533688
Chromosome Location	chr3:54296216-54296217
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs4432683	1.00[YRI][hapmap]
rs4532166	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55951932	0.89[EUR][1000 genomes]
rs9810762	0.94[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9828312	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs9828485	1.00[CEU][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs9838622	0.81[CEU][hapmap];0.94[EUR][1000 genomes]
rs9875569	0.90[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4533688	WNT5A	cis	cerebellum	SCAN
rs4533688	WDR82	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54292600-54301000	Weak transcription	Fetal Kidney	kidney
2	chr3:54292800-54297800	Enhancers	Fetal Muscle Leg	muscle
3	chr3:54294800-54298000	Weak transcription	Fetal Brain Male	brain
4	chr3:54295000-54308800	Weak transcription	Psoas Muscle	Psoas
5	chr3:54295600-54297800	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr3:54295800-54296800	Enhancers	Primary hematopoietic stem cells	blood
7	chr3:54295800-54297600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:54295800-54297600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:54296000-54296400	Enhancers	Brain Germinal Matrix	brain
10	chr3:54296200-54296400	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr3:54296200-54298400	Enhancers	Primary monocytes fromperipheralblood	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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