Variant report

Variant	rs17026637
Chromosome Location	chr3:89097483-89097484
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CGGBP1-2	chr3:89096592-89097584	NONHSAT090710

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

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12494816	0.80[CEU][hapmap];0.86[CHB][hapmap]
rs13077331	0.80[CEU][hapmap];0.88[CHB][hapmap]
rs1496502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2173038	0.90[EUR][1000 genomes]
rs60574043	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6551398	0.80[CEU][hapmap];0.87[CHB][hapmap]
rs6767230	0.80[CEU][hapmap];0.88[CHB][hapmap]
rs6779710	0.80[CEU][hapmap];0.88[CHB][hapmap]
rs6790662	0.80[CEU][hapmap];0.88[CHB][hapmap]
rs6793981	0.80[CEU][hapmap];0.88[CHB][hapmap]
rs6800287	0.87[CHB][hapmap]
rs6804377	0.80[CEU][hapmap];0.88[CHB][hapmap]
rs6807840	0.80[CEU][hapmap];0.88[CHB][hapmap]
rs72917842	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7426466	0.80[CEU][hapmap];0.88[CHB][hapmap]
rs7426527	0.89[CEU][hapmap];0.86[CHB][hapmap]
rs7427745	0.86[CHB][hapmap]
rs7622368	0.80[CEU][hapmap];0.81[CHB][hapmap]
rs7651124	0.80[CEU][hapmap]
rs9810701	0.80[CEU][hapmap];0.88[CHB][hapmap]
rs9811026	0.88[CHB][hapmap]
rs9814718	0.80[CEU][hapmap];0.88[CHB][hapmap]
rs9815137	0.80[CEU][hapmap];0.88[CHB][hapmap]
rs9828822	0.80[CEU][hapmap];0.88[CHB][hapmap]
rs9859735	0.80[CEU][hapmap];0.88[CHB][hapmap]
rs9860030	0.80[CEU][hapmap];0.82[CHB][hapmap]
rs9861649	0.80[CEU][hapmap];0.88[CHB][hapmap]
rs9868041	0.80[CEU][hapmap];0.87[CHB][hapmap]

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	nsv834759	chr3:88901229-89105366	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv877158	chr3:89018866-89103302	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv877159	chr3:89018866-89207222	Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv877160	chr3:89051475-89135125	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv998460	chr3:89064073-89188335	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv536638	chr3:89064073-89188335	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv834760	chr3:89085529-89299398	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	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	chr3:89094600-89098200	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr3:89095200-89098000	Weak transcription	HUES64 Cell Line	embryonic stem cell

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