Variant report

Variant	rs16913257
Chromosome Location	chr10:52813733-52813734
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10508935	0.87[EUR][1000 genomes]
rs10740111	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10740130	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10761738	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10761807	0.85[EUR][1000 genomes]
rs10761831	0.87[EUR][1000 genomes]
rs10822188	0.84[EUR][1000 genomes]
rs10822189	0.90[EUR][1000 genomes]
rs10822194	0.90[EUR][1000 genomes]
rs10822198	0.89[EUR][1000 genomes]
rs10822210	0.88[EUR][1000 genomes]
rs10822211	0.88[EUR][1000 genomes]
rs10822229	0.85[EUR][1000 genomes]
rs10995458	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10995473	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10995526	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10995620	0.88[EUR][1000 genomes]
rs10995651	0.87[CEU][hapmap];0.88[JPT][hapmap];0.88[EUR][1000 genomes]
rs10995655	0.87[EUR][1000 genomes]
rs12218335	0.91[EUR][1000 genomes]
rs12220644	0.88[EUR][1000 genomes]
rs12221226	0.88[EUR][1000 genomes]
rs12415785	0.87[EUR][1000 genomes]
rs12767015	0.86[EUR][1000 genomes]
rs16913956	0.87[EUR][1000 genomes]
rs1983222	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2339675	0.90[EUR][1000 genomes]
rs2660202	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2666543	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3964605	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4622210	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55767509	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7074892	0.89[EUR][1000 genomes]
rs7084128	0.91[EUR][1000 genomes]
rs7084767	0.87[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7097311	0.91[EUR][1000 genomes]
rs7912628	0.91[EUR][1000 genomes]
rs9299457	0.89[EUR][1000 genomes]
rs9414806	0.94[CEU][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes]
rs9414808	0.90[EUR][1000 genomes]
rs9414810	0.91[EUR][1000 genomes]
rs9415709	0.91[EUR][1000 genomes]
rs9415710	0.91[EUR][1000 genomes]
rs9415711	0.91[EUR][1000 genomes]
rs9633564	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv831872	chr10:52663328-52818537	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv831873	chr10:52710610-52899540	Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv895394	chr10:52793177-52866503	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1036645	chr10:52804961-53159076	Enhancers Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16913257	NCOA4	cis	parietal	SCAN
rs16913257	SGMS1	cis	lymphoblastoid	seeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:52807600-52821000	Weak transcription	Aorta	Aorta
2	chr10:52808400-52814000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr10:52813200-52814400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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