Variant report

Variant	rs71628821
Chromosome Location	chr3:88665810-88665811
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10446361	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs13060621	0.85[AMR][1000 genomes]
rs13063905	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13067884	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13068692	0.92[AMR][1000 genomes]
rs13073423	0.92[AMR][1000 genomes]
rs13074030	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13075366	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs13081387	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13082178	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13082894	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13083673	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13085293	0.92[AMR][1000 genomes]
rs13088227	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13089927	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13090780	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13090965	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13100049	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs13100970	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17025980	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35129035	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs36031826	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6551352	0.80[AMR][1000 genomes]
rs6768591	0.80[AMR][1000 genomes]
rs955291	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9820989	0.92[AMR][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	nsv916330	chr3:88083580-88884125	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv1014703	chr3:88623532-88733631	Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv19521	chr3:88664755-88665910	Enhancers	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88664600-88667800	Enhancers	Fetal Brain Female	brain
2	chr3:88665000-88666000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr3:88665000-88666600	Enhancers	Fetal Brain Male	brain
4	chr3:88665400-88667600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:88665600-88666000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:88665600-88666200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:88665600-88666200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr3:88665600-88666400	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr3:88665600-88666400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:88665800-88666000	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr3:88665800-88666200	Enhancers	Brain Germinal Matrix	brain

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