Variant report

Variant	rs12493980
Chromosome Location	chr3:56258725-56258726
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11715314	0.96[EUR][1000 genomes]
rs13091032	0.96[EUR][1000 genomes]
rs1349616	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1352011	0.96[EUR][1000 genomes]
rs1452205	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1452211	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1452219	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1466177	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1519032	1.00[CEU][hapmap]
rs1564906	0.87[EUR][1000 genomes]
rs1564908	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2046450	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs2046452	1.00[EUR][1000 genomes]
rs2053956	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2101321	0.96[EUR][1000 genomes]
rs2167620	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2316479	0.96[EUR][1000 genomes]
rs2316483	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2873169	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4393875	0.96[EUR][1000 genomes]
rs4585163	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4591474	0.85[AMR][1000 genomes]
rs4974117	1.00[CEU][hapmap]
rs4974125	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4974177	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6445767	0.96[EUR][1000 genomes]
rs6445781	0.85[AMR][1000 genomes]
rs6766369	0.96[EUR][1000 genomes]
rs6776414	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6786348	0.96[EUR][1000 genomes]
rs6787350	0.85[AMR][1000 genomes]
rs6800915	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6801004	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6802107	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7634869	0.96[EUR][1000 genomes]
rs935900	0.85[AMR][1000 genomes]
rs9812767	0.96[EUR][1000 genomes]
rs9822225	0.85[AMR][1000 genomes]
rs9823389	0.96[EUR][1000 genomes]
rs9824530	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs982860	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9839130	1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009709	chr3:56000827-56294945	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56252000-56272200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:56254800-56280600	Weak transcription	H9 Cell Line	embryonic stem cell

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