Variant report

Variant	rs17660338
Chromosome Location	chr21:28464539-28464540
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1041423	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1041424	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10482980	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17600993	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17659214	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs233588	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2830664	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2830676	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2830685	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2830690	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28463781	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28549866	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs404112	0.88[AMR][1000 genomes]
rs7279282	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73187872	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs73187879	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73187887	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73187889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73187890	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73187892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73187893	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73187894	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73187895	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73187898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73189810	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9284446	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9975373	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9976558	0.83[AMR][1000 genomes]
rs9977974	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9984557	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067475	chr21:28238746-29046707	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv2758532	chr21:28380230-28540443	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	esv2758817	chr21:28380230-28540443	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
4	nsv1062808	chr21:28443252-28537209	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
5	nsv544414	chr21:28443252-28537209	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
6	nsv964540	chr21:28463562-28467460	Enhancers Flanking Active TSS Weak transcription Active TSS	lncRNA	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17660338	FRMD4A	trans	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:28447400-28467200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr21:28458800-28477600	Weak transcription	Fetal Kidney	kidney
3	chr21:28462400-28466800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr21:28463000-28466600	Weak transcription	Adipose Nuclei	Adipose

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