Variant report

Variant	rs6458449
Chromosome Location	chr6:45571305-45571306
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12528502	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12661124	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12663210	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12665637	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1491142	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs16873543	0.81[ASW][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.89[MEX][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16873554	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2020084	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56083876	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs57939401	0.85[ASN][1000 genomes]
rs58939587	0.85[ASN][1000 genomes]
rs59074904	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60540355	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6458450	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6458453	0.80[ASN][1000 genomes]
rs6458454	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6458455	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6899443	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6930188	0.82[ASN][1000 genomes]
rs6936365	0.80[ASN][1000 genomes]
rs6938489	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6938758	0.95[YRI][hapmap];0.95[AFR][1000 genomes]
rs713270	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73738526	0.80[ASN][1000 genomes]
rs7742335	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7752183	0.85[ASN][1000 genomes]
rs7752200	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7758915	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7759415	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7766534	0.85[ASN][1000 genomes]
rs7768962	0.85[ASN][1000 genomes]
rs9296462	0.90[CHB][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9296463	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9463108	0.90[CHB][hapmap];0.90[JPT][hapmap];0.89[MEX][hapmap];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9472518	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9472521	0.85[ASN][1000 genomes]
rs9472524	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9472525	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9472530	0.85[ASN][1000 genomes]
rs9472531	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs997445	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv427755	chr6:45474631-45627025	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv532024	chr6:45475088-45982640	Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6458449	CLIC5	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45559800-45574800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:45563800-45586200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:45564200-45579200	Weak transcription	Fetal Kidney	kidney
4	chr6:45567800-45574800	Weak transcription	Esophagus	oesophagus
5	chr6:45571200-45575400	Weak transcription	Muscle Satellite Cultured Cells	--

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