Variant report

Variant	rs589281
Chromosome Location	chr3:54747244-54747245
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:54736841..54738842-chr3:54744528..54747366,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1008187	0.81[ASW][hapmap];1.00[YRI][hapmap]
rs11130431	0.80[ASW][hapmap]
rs11707823	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11711913	0.88[ASN][1000 genomes]
rs13095178	0.85[CEU][hapmap]
rs1346407	0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.80[MEX][hapmap]
rs2360021	1.00[CHB][hapmap]
rs2360026	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs3732748	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4353779	0.82[CHB][hapmap]
rs4384925	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs495532	0.82[CHD][hapmap]
rs515920	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs517729	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs517738	0.92[ASN][1000 genomes]
rs521694	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs550210	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs578032	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs583190	0.95[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.88[MEX][hapmap]
rs587384	0.85[ASN][1000 genomes]
rs604132	1.00[CEU][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs652424	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs661201	0.85[JPT][hapmap]
rs6809466	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs838022	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs934083	0.83[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.80[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	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
2	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs589281	GNL3	cis	cerebellum	SCAN
rs589281	FLNB	cis	cerebellum	SCAN
rs589281	VPRBP	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54743800-54751400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:54745200-54750200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:54745200-54751600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr3:54746800-54751600	Weak transcription	Right Atrium	heart
5	chr3:54747000-54747800	Enhancers	Fetal Heart	heart
6	chr3:54747200-54747600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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