Variant report

Variant	rs6860887
Chromosome Location	chr5:59674192-59674193
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1115372	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12189147	0.87[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13159422	0.86[CEU][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs1363862	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1423246	0.91[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1423247	0.85[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1477352	0.92[ASN][1000 genomes]
rs17839379	0.86[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2042315	0.87[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2910629	0.86[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs364917	0.90[JPT][hapmap]
rs371424	0.82[CEU][hapmap];0.90[JPT][hapmap]
rs37684	0.85[JPT][hapmap]
rs37691	0.90[JPT][hapmap]
rs37702	0.81[JPT][hapmap]
rs401207	0.89[JPT][hapmap]
rs404202	0.90[JPT][hapmap]
rs411255	0.89[JPT][hapmap]
rs446883	0.90[JPT][hapmap]
rs4580739	0.86[CEU][hapmap];0.82[CHB][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6860277	0.83[YRI][hapmap]
rs6878055	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6897671	0.83[EUR][1000 genomes]
rs7714394	0.87[CEU][hapmap]
rs7737905	0.86[CEU][hapmap];0.82[CHB][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs789389	0.90[JPT][hapmap]
rs789395	0.85[JPT][hapmap]
rs789396	0.90[JPT][hapmap]
rs789615	0.90[JPT][hapmap]
rs918590	0.82[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs918591	0.91[AFR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs918592	0.82[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1025856	chr5:59188419-59928852	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv830316	chr5:59480269-59689829	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv598288	chr5:59627555-60003460	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:59647200-59694200	Weak transcription	Primary B cells from cord blood	blood
2	chr5:59650400-59674800	Weak transcription	Aorta	Aorta
3	chr5:59662600-59680200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr5:59673200-59674200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr5:59673200-59675000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:59674000-59674800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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