Variant report

Variant	rs2099664
Chromosome Location	chr5:152460036-152460037
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10515683	1.00[AMR][1000 genomes]
rs10515684	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11952806	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1371062	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17096206	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17113961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17113985	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17114003	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17114007	1.00[AMR][1000 genomes]
rs17114009	1.00[AMR][1000 genomes]
rs17114011	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17114019	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17114034	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17114042	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17114053	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17114059	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2083257	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34347387	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023676	chr5:151979253-152925064	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv537927	chr5:151979253-152925064	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv600089	chr5:152200109-152488891	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1017812	chr5:152220845-152467431	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv537928	chr5:152220845-152467431	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv883050	chr5:152277537-152540026	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv949596	chr5:152343943-152548821	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:152458600-152461000	Enhancers	Placenta Amnion	Placenta Amnion
2	chr5:152459200-152463800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr5:152459400-152460600	Weak transcription	HMEC	breast
4	chr5:152459400-152460600	Weak transcription	NHEK	skin
5	chr5:152459400-152461000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:152460000-152461200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:152460000-152462800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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