Variant report

Variant	rs2338578
Chromosome Location	chr3:180189540-180189541
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs13327745	0.81[AFR][1000 genomes]
rs1520606	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2133007	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs28595523	0.83[CEU][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4490359	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4519701	0.88[CEU][hapmap]
rs4615077	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs56406114	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs59829320	0.81[AFR][1000 genomes]
rs62291003	0.93[AMR][1000 genomes]
rs6443696	0.83[CEU][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6443700	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6771979	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6789277	0.81[AFR][1000 genomes]
rs6791597	0.81[CEU][hapmap]
rs7611683	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7613520	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7624210	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7625418	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7627008	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7633440	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7643043	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7645817	0.82[YRI][hapmap]
rs7647210	0.81[CEU][hapmap]
rs904241	0.81[AFR][1000 genomes]
rs9842781	0.81[AFR][1000 genomes]
rs9857056	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9865427	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv1012271	chr3:179806875-180234871	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1007831	chr3:180162003-180348203	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv536818	chr3:180162003-180348203	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:180187400-180205600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr3:180187600-180193800	Weak transcription	HMEC	breast
3	chr3:180187600-180198800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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